#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_NTotCov	i_NVarCov	i_NVarRat	i_ORegAnno_bin	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_dbSNPPopFreq	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
KLHL17	339451	hgsc.bcm.edu	37	1	898748	898748	+	Missense_Mutation	SNP	G	G	A			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr1:898748G>A	ENST00000338591.3	+	8	1326	c.1219G>A	c.(1219-1221)Gag>Aag	p.E407K		NM_198317.2	NP_938073.1	Q6TDP4	KLH17_HUMAN	kelch-like family member 17	407	Interaction with F-actin. {ECO:0000250}.				actin cytoskeleton organization (GO:0030036)|brain development (GO:0007420)|protein ubiquitination (GO:0016567)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|dendrite cytoplasm (GO:0032839)|extracellular space (GO:0005615)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	protein complex scaffold (GO:0032947)			central_nervous_system(1)|kidney(2)|lung(3)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	10	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00459)|Epithelial(90;1.52e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.59e-23)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|BRCA - Breast invasive adenocarcinoma(365;0.000469)|Kidney(185;0.00227)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)		GGCTACCGTGGAGTCCTACGA	0.622																																					p.E407K		Atlas-SNP	.											.	KLHL17	31	.	0			c.G1219A						PASS	.						90.0	75.0	80.0					1																	898748		2202	4300	6502	SO:0001583	missense	339451	exon8			ACCGTGGAGTCCT	AY423763	CCDS30550.1	1p36	2013-01-30	2013-01-30		ENSG00000187961	ENSG00000187961		"""Kelch-like"", ""BTB/POZ domain containing"""	24023	protein-coding gene	gene with protein product	"""actinfilin"""		"""kelch-like 17 (Drosophila)"""			12063253	Standard	NM_198317		Approved		uc001aca.2	Q6TDP4	OTTHUMG00000040721	ENST00000338591.3:c.1219G>A	chr1.hg19:g.898748G>A	ENSP00000343930:p.Glu407Lys	166.0	1.0	.		177.0	124.0	.	NM_198317	Q5SV94	Missense_Mutation	SNP	ENST00000338591.3	hg19	CCDS30550.1	.	.	.	.	.	.	.	.	.	.	G	36	5.935264	0.97122	.	.	ENSG00000187961	ENST00000338591;ENST00000455747;ENST00000540863	D	0.84516	-1.86	5.37	5.37	0.77165	Galactose oxidase, beta-propeller (1);	0.000000	0.85682	D	0.000000	D	0.95452	0.8523	H	0.98965	4.385	0.80722	D	1	D	0.57571	0.98	P	0.60012	0.867	D	0.97376	0.9979	10	0.87932	D	0	.	19.0966	0.93255	0.0:0.0:1.0:0.0	.	407	Q6TDP4	KLH17_HUMAN	K	407;283;130	ENSP00000343930:E407K	ENSP00000343930:E407K	E	+	1	0	KLHL17	888611	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	9.708000	0.98727	2.532000	0.85374	0.448000	0.29417	GAG	.	.	.	none		0.622	KLHL17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097875.3	NM_198317	
CD1C	911	hgsc.bcm.edu	37	1	158261919	158261919	+	Missense_Mutation	SNP	G	G	A			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr1:158261919G>A	ENST00000368170.3	+	3	653	c.374G>A	c.(373-375)gGa>gAa	p.G125E		NM_001765.2	NP_001756.2	P29017	CD1C_HUMAN	CD1c molecule	125					antigen processing and presentation (GO:0019882)|T cell activation involved in immune response (GO:0002286)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	endogenous lipid antigen binding (GO:0030883)|exogenous lipid antigen binding (GO:0030884)|glycolipid binding (GO:0051861)|lipopeptide binding (GO:0071723)			NS(1)|endometrium(3)|large_intestine(4)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	39	all_hematologic(112;0.0378)					CTGCATTCTGGAAAGAGCCCA	0.448																																					p.G125E		Atlas-SNP	.											.	CD1C	100	.	0			c.G374A						PASS	.						91.0	98.0	95.0					1																	158261919		2203	4300	6503	SO:0001583	missense	911	exon3			ATTCTGGAAAGAG	M28827	CCDS1175.1	1q23.1	2014-01-14	2006-03-28		ENSG00000158481	ENSG00000158481		"""CD molecules"", ""Immunoglobulin superfamily / C1-set domain containing"""	1636	protein-coding gene	gene with protein product		188340	"""CD1C antigen, c polypeptide"", ""CD1c antigen"""	CD1		2447586	Standard	NM_001765		Approved		uc001fru.3	P29017	OTTHUMG00000017514	ENST00000368170.3:c.374G>A	chr1.hg19:g.158261919G>A	ENSP00000357152:p.Gly125Glu	154.0	0.0	.		192.0	89.0	.	NM_001765	Q5TDJ7|Q6IAS4|Q9UMM0|Q9UN96	Missense_Mutation	SNP	ENST00000368170.3	hg19	CCDS1175.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	-|-	13.26|13.26	2.185038|2.185038	0.38609|0.38609	.|.	.|.	ENSG00000158481|ENSG00000158481	ENST00000368169;ENST00000368170|ENST00000443761	T|.	0.06294|.	3.32|.	3.92|3.92	-0.561|-0.561	0.11785|0.11785	MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);|.	2.458490|.	0.01726|.	N|.	0.028603|.	T|.	0.19805|.	0.0476|.	M|M	0.64997|0.64997	1.995|1.995	0.09310|0.09310	N|N	1|1	P|.	0.52577|.	0.954|.	B|.	0.44278|.	0.445|.	T|.	0.33803|.	-0.9854|.	10|.	0.87932|.	D|.	0|.	.|.	1.0278|1.0278	0.01531|0.01531	0.1994:0.1834:0.4297:0.1875|0.1994:0.1834:0.4297:0.1875	.|.	125|.	P29017|.	CD1C_HUMAN|.	E|X	125|59	ENSP00000357152:G125E|.	ENSP00000357151:G125E|.	G|W	+|+	2|3	0|0	CD1C|CD1C	156528543|156528543	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.020000|0.020000	0.10135|0.10135	-0.226000|-0.226000	0.09139|0.09139	0.093000|0.093000	0.17368|0.17368	0.644000|0.644000	0.83932|0.83932	GGA|TGG	.	.	.	none		0.448	CD1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046351.2	NM_001765	
SHCBP1L	81626	hgsc.bcm.edu	37	1	182898789	182898789	+	Missense_Mutation	SNP	G	G	T			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr1:182898789G>T	ENST00000367547.3	-	6	1411	c.1175C>A	c.(1174-1176)aCt>aAt	p.T392N	SHCBP1L_ENST00000488956.1_5'UTR|SHCBP1L_ENST00000423786.1_Missense_Mutation_p.T273N	NM_030933.2	NP_112195.2	Q9BZQ2	SHP1L_HUMAN	SHC SH2-domain binding protein 1-like	464										breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(2)|pancreas(1)|prostate(1)|skin(2)	15						TACCATTTCAGTAGTCATCAT	0.343																																					p.T392N		Atlas-SNP	.											.	SHCBP1L	64	.	0			c.C1175A						PASS	.						97.0	94.0	95.0					1																	182898789		2202	4297	6499	SO:0001583	missense	81626	exon6			ATTTCAGTAGTCA	AF288397	CCDS30955.1	1q25	2011-01-24	2011-01-24	2011-01-24	ENSG00000157060	ENSG00000157060			16788	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 14"""	C1orf14		11318611	Standard	NM_030933		Approved		uc001gpu.3	Q9BZQ2	OTTHUMG00000035419	ENST00000367547.3:c.1175C>A	chr1.hg19:g.182898789G>T	ENSP00000356518:p.Thr392Asn	21.0	0.0	.		38.0	16.0	.	NM_030933	Q4G195|Q9BZQ3|Q9H2B6	Missense_Mutation	SNP	ENST00000367547.3	hg19	CCDS30955.1	.	.	.	.	.	.	.	.	.	.	G	14.22	2.470487	0.43942	.	.	ENSG00000157060	ENST00000367547;ENST00000287709;ENST00000423786	T;T	0.47869	0.83;0.84	5.88	4.94	0.65067	Carbohydrate-binding/sugar hydrolysis domain (1);	0.212652	0.33092	N	0.005289	T	0.43277	0.1240	L	0.43152	1.355	0.25433	N	0.988169	B;B;B	0.26258	0.09;0.078;0.145	B;B;B	0.29785	0.024;0.034;0.107	T	0.38520	-0.9657	10	0.42905	T	0.14	-11.1083	14.1389	0.65306	0.0:0.1504:0.8496:0.0	.	464;273;392	Q9BZQ2;Q9BZQ2-2;Q9BZQ2-3	SHP1L_HUMAN;.;.	N	392;461;273	ENSP00000356518:T392N;ENSP00000397308:T273N	ENSP00000287709:T461N	T	-	2	0	SHCBP1L	181165412	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.607000	0.67648	1.463000	0.47967	0.644000	0.83932	ACT	.	.	.	none		0.343	SHCBP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085956.1	NM_030933	
SMC6	79677	hgsc.bcm.edu	37	2	17847696	17847696	+	Missense_Mutation	SNP	T	T	G			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr2:17847696T>G	ENST00000448223.2	-	27	3421	c.3152A>C	c.(3151-3153)cAa>cCa	p.Q1051P	SMC6_ENST00000351948.4_Missense_Mutation_p.Q1051P|SMC6_ENST00000381272.4_Missense_Mutation_p.Q1077P|SMC6_ENST00000402989.1_Missense_Mutation_p.Q1051P	NM_001142286.1	NP_001135758.1	Q96SB8	SMC6_HUMAN	structural maintenance of chromosomes 6	1051					cellular senescence (GO:0090398)|double-strand break repair via homologous recombination (GO:0000724)|telomere maintenance via recombination (GO:0000722)	chromosome, telomeric region (GO:0000781)|intracellular (GO:0005622)|nucleolus (GO:0005730)|nucleus (GO:0005634)|PML body (GO:0016605)|Smc5-Smc6 complex (GO:0030915)	ATP binding (GO:0005524)			NS(1)|biliary_tract(1)|breast(6)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(3)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	43	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					CCTCATGCTTTGAGGTGTGAG	0.308																																					p.Q1051P		Atlas-SNP	.											.	SMC6	102	.	0			c.A3152C						PASS	.						76.0	72.0	74.0					2																	17847696		2203	4300	6503	SO:0001583	missense	79677	exon27			ATGCTTTGAGGTG	AJ310551	CCDS1690.1	2p24.3	2008-02-05	2006-07-06	2006-07-06	ENSG00000163029	ENSG00000163029		"""Structural maintenance of chromosomes proteins"""	20466	protein-coding gene	gene with protein product		609387	"""SMC6 structural maintenance of chromosomes 6-like 1 (yeast)"""	SMC6L1		11230166	Standard	NM_024624		Approved	FLJ22116	uc002rcn.3	Q96SB8	OTTHUMG00000090675	ENST00000448223.2:c.3152A>C	chr2.hg19:g.17847696T>G	ENSP00000404092:p.Gln1051Pro	33.0	0.0	.		43.0	22.0	.	NM_001142286	A8K8Q6|D6W518|Q05BV4|Q9H0X3|Q9H6M0	Missense_Mutation	SNP	ENST00000448223.2	hg19	CCDS1690.1	.	.	.	.	.	.	.	.	.	.	T	19.23	3.786888	0.70337	.	.	ENSG00000163029	ENST00000448223;ENST00000351948;ENST00000381272;ENST00000402989	T;T;T;T	0.68181	-0.31;-0.31;2.02;-0.31	6.08	6.08	0.98989	RecF/RecN/SMC (1);	0.054551	0.85682	D	0.000000	T	0.79516	0.4459	M	0.66939	2.045	0.80722	D	1	D	0.89917	1.0	D	0.77557	0.99	T	0.81291	-0.0999	10	0.72032	D	0.01	.	12.8158	0.57665	0.1222:0.0:0.0:0.8778	.	1051	Q96SB8	SMC6_HUMAN	P	1051;1051;1077;1051	ENSP00000404092:Q1051P;ENSP00000323439:Q1051P;ENSP00000370672:Q1077P;ENSP00000384539:Q1051P	ENSP00000323439:Q1051P	Q	-	2	0	SMC6	17711177	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	3.920000	0.56446	2.333000	0.79357	0.482000	0.46254	CAA	.	.	.	none		0.308	SMC6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207359.1	NM_024624	
TTN	7273	hgsc.bcm.edu	37	2	179547441	179547441	+	Missense_Mutation	SNP	T	T	G			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr2:179547441T>G	ENST00000591111.1	-	133	32350	c.32126A>C	c.(32125-32127)cAt>cCt	p.H10709P	TTN_ENST00000460472.2_Intron|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000359218.5_Intron|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.H9782P|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.H11026P|TTN-AS1_ENST00000431752.1_RNA			Q8WZ42	TITIN_HUMAN	titin	0	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)			GTATTCTTCATGCTCTTCATA	0.338																																					p.H11026P		Atlas-SNP	.											.	TTN	18412	.	0			c.A33077C						PASS	.						257.0	246.0	249.0					2																	179547441		1899	4119	6018	SO:0001583	missense	7273	exon135			TCTTCATGCTCTT	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.32126A>C	chr2.hg19:g.179547441T>G	ENSP00000465570:p.His10709Pro	82.0	0.0	.		107.0	55.0	.	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	hg19		.	.	.	.	.	.	.	.	.	.	T	3.299	-0.143379	0.06669	.	.	ENSG00000155657	ENST00000342992;ENST00000414766	T;T	0.68331	-0.32;-0.1	4.98	2.59	0.31030	Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);	.	.	.	.	T	0.46889	0.1416	N	0.19112	0.55	0.58432	D	0.999996	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.35674	-0.9779	9	0.87932	D	0	.	5.0483	0.14496	0.0:0.1647:0.1536:0.6817	.	10709;10445	Q8WZ42;Q8WZ42-5	TITIN_HUMAN;.	P	9782;640	ENSP00000343764:H9782P;ENSP00000401501:H640P	ENSP00000343764:H9782P	H	-	2	0	TTN	179255686	0.000000	0.05858	0.989000	0.46669	0.230000	0.25150	-0.913000	0.04042	0.338000	0.23692	-0.256000	0.11100	CAT	.	.	.	none		0.338	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
FSIP2	401024	hgsc.bcm.edu	37	2	186671593	186671593	+	Nonsense_Mutation	SNP	C	C	T			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr2:186671593C>T	ENST00000424728.1	+	17	17560	c.17560C>T	c.(17560-17562)Cag>Tag	p.Q5854*	FSIP2_ENST00000343098.5_Nonsense_Mutation_p.Q5943*			Q5CZC0	FSIP2_HUMAN	fibrous sheath interacting protein 2	5854										NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(11)|lung(46)|pancreas(1)|urinary_tract(2)	69						TAAGGGAAATCAGTTCCCTGG	0.408																																					p.Q5943X		Atlas-SNP	.											.	FSIP2	251	.	0			c.C17827T						PASS	.						87.0	79.0	82.0					2																	186671593		1841	4085	5926	SO:0001587	stop_gained	401024	exon17			GGAAATCAGTTCC	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.17560C>T	chr2.hg19:g.186671593C>T	ENSP00000401306:p.Gln5854*	65.0	0.0	.		90.0	23.0	.	NM_173651	Q53TL3|Q53TN5|Q5HYH2|Q6ZTZ5|Q6ZU14|Q6ZU21	Nonsense_Mutation	SNP	ENST00000424728.1	hg19		.	.	.	.	.	.	.	.	.	.	C	55	24.779395	0.99962	.	.	ENSG00000188738	ENST00000343098;ENST00000424728	.	.	.	4.87	1.8	0.24995	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.15066	T	0.55	.	6.7948	0.23719	0.3174:0.4362:0.2464:0.0	.	.	.	.	X	5943;5854	.	ENSP00000344403:Q5943X	Q	+	1	0	FSIP2	186379838	0.000000	0.05858	0.002000	0.10522	0.014000	0.08584	-0.056000	0.11787	0.131000	0.18576	0.591000	0.81541	CAG	.	.	.	none		0.408	FSIP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000332778.3	NM_173651	
TNP1	7141	hgsc.bcm.edu	37	2	217724631	217724631	+	Missense_Mutation	SNP	G	G	A	rs561435538		TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr2:217724631G>A	ENST00000236979.2	-	1	156	c.127C>T	c.(127-129)Cgg>Tgg	p.R43W	AC007563.5_ENST00000607591.1_RNA|AC007563.5_ENST00000447289.1_RNA	NM_003284.3	NP_003275.1	P09430	STP1_HUMAN	transition protein 1 (during histone to protamine replacement)	43					chromatin remodeling (GO:0006338)|chromatin silencing (GO:0006342)|fertilization, exchange of chromosomal proteins (GO:0035042)|multicellular organismal development (GO:0007275)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome disassembly (GO:0006337)|sexual reproduction (GO:0019953)|single strand break repair (GO:0000012)|sperm motility (GO:0030317)|spermatid development (GO:0007286)|spermatid nucleus differentiation (GO:0007289)|spermatid nucleus elongation (GO:0007290)	male germ cell nucleus (GO:0001673)|nucleosome (GO:0000786)	DNA binding (GO:0003677)			large_intestine(1)|lung(1)|stomach(1)	3		Renal(207;0.0822)		Epithelial(149;8.97e-07)|all cancers(144;2.46e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TCATCGCCCCGTTTCCTACTT	0.552													G|||	1	0.000199681	0.0	0.0	5008	,	,		20388	0.001		0.0	False		,,,				2504	0.0				p.R43W		Atlas-SNP	.											TNP1,NS,carcinoma,0,1	TNP1	10	.	0			c.C127T						PASS	.						217.0	195.0	203.0					2																	217724631		2203	4300	6503	SO:0001583	missense	7141	exon1			CGCCCCGTTTCCT		CCDS2406.1	2q35-q36	2008-06-03			ENSG00000118245	ENSG00000118245			11951	protein-coding gene	gene with protein product		190231				2249851	Standard	NM_003284		Approved		uc002vgk.3	P09430	OTTHUMG00000133057	ENST00000236979.2:c.127C>T	chr2.hg19:g.217724631G>A	ENSP00000236979:p.Arg43Trp	126.0	0.0	.		156.0	74.0	.	NM_003284		Missense_Mutation	SNP	ENST00000236979.2	hg19	CCDS2406.1	.	.	.	.	.	.	.	.	.	.	G	12.50	1.957505	0.34565	.	.	ENSG00000118245	ENST00000236979	.	.	.	5.55	-1.5	0.08691	.	0.000000	0.52532	D	0.000080	T	0.64918	0.2642	.	.	.	0.21105	N	0.99979	D	0.89917	1.0	D	0.76071	0.987	T	0.64807	-0.6320	8	0.87932	D	0	-0.9614	15.5104	0.75776	0.0:0.0:0.2376:0.7624	.	43	P09430	STP1_HUMAN	W	43	.	ENSP00000236979:R43W	R	-	1	2	TNP1	217432876	0.771000	0.28555	0.434000	0.26772	0.816000	0.46133	0.173000	0.16724	-0.090000	0.12462	-0.182000	0.12963	CGG	.	.	.	none		0.552	TNP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256673.1	NM_003284	
AGFG1	3267	hgsc.bcm.edu	37	2	228399580	228399580	+	Silent	SNP	C	C	G			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr2:228399580C>G	ENST00000310078.8	+	8	1304	c.1044C>G	c.(1042-1044)ggC>ggG	p.G348G	AGFG1_ENST00000409315.1_Intron|AGFG1_ENST00000373671.3_Silent_p.G308G|AGFG1_ENST00000409979.2_Silent_p.G372G|AGFG1_ENST00000409171.1_Silent_p.G348G	NM_001135188.1|NM_001135189.1|NM_004504.4	NP_001128660.1|NP_001128661.1|NP_004495.2	P52594	AGFG1_HUMAN	ArfGAP with FG repeats 1	348					cell differentiation (GO:0030154)|mRNA export from nucleus (GO:0006406)|multicellular organismal development (GO:0007275)|regulation of ARF GTPase activity (GO:0032312)|spermatogenesis (GO:0007283)	cytoplasmic vesicle (GO:0031410)|intracellular membrane-bounded organelle (GO:0043231)|nuclear pore (GO:0005643)	ARF GTPase activator activity (GO:0008060)|DNA binding (GO:0003677)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|large_intestine(5)|liver(2)|lung(2)|ovary(1)|prostate(1)|skin(4)|stomach(1)	18						AGGGAAGTGGCTTTGGGACCA	0.433																																					p.G372G		Atlas-SNP	.											.	AGFG1	80	.	0			c.C1116G						PASS	.						154.0	145.0	148.0					2																	228399580		2203	4300	6503	SO:0001819	synonymous_variant	3267	exon9			AAGTGGCTTTGGG		CCDS2467.1, CCDS46533.1, CCDS46534.1, CCDS46535.1	2q36	2009-11-30	2008-09-22	2008-09-22	ENSG00000173744	ENSG00000173744		"""ADP-ribosylation factor GTPase activating proteins"""	5175	protein-coding gene	gene with protein product		600862	"""HIV-1 Rev binding protein"""	HRB		7637788	Standard	NM_004504		Approved	RIP, RAB	uc002vpd.2	P52594	OTTHUMG00000133186	ENST00000310078.8:c.1044C>G	chr2.hg19:g.228399580C>G		186.0	1.0	.		218.0	130.0	.	NM_001135187	B3KUL1|E9PHX7|Q15277|Q4VAS0|Q4VAS1|Q4VAS3|Q53QT8|Q53R11	Silent	SNP	ENST00000310078.8	hg19	CCDS2467.1																																																																																			.	.	.	none		0.433	AGFG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256895.2	NM_004504	
SH3BP4	23677	hgsc.bcm.edu	37	2	235943690	235943690	+	Missense_Mutation	SNP	C	C	T			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr2:235943690C>T	ENST00000409212.1	+	3	551	c.44C>T	c.(43-45)cCt>cTt	p.P15L	SH3BP4_ENST00000392011.2_Missense_Mutation_p.P15L|SH3BP4_ENST00000344528.4_Missense_Mutation_p.P15L			Q9P0V3	SH3B4_HUMAN	SH3-domain binding protein 4	15					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)		AATGGCCTCCCTCGCTGCAAG	0.547																																					p.P15L		Atlas-SNP	.											.	SH3BP4	109	.	0			c.C44T						PASS	.						51.0	53.0	52.0					2																	235943690		2203	4300	6503	SO:0001583	missense	23677	exon3			GCCTCCCTCGCTG	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.44C>T	chr2.hg19:g.235943690C>T	ENSP00000386862:p.Pro15Leu	76.0	0.0	.		80.0	30.0	.	NM_014521	O95082|Q309A3|Q53QD0|Q53TD1	Missense_Mutation	SNP	ENST00000409212.1	hg19	CCDS2513.1	.	.	.	.	.	.	.	.	.	.	C	14.31	2.496478	0.44352	.	.	ENSG00000130147	ENST00000392011;ENST00000420127;ENST00000416021;ENST00000409212;ENST00000344528;ENST00000444916;ENST00000446904;ENST00000454947	T;T;T;T;T	0.38560	2.49;1.18;2.49;2.49;1.13	4.91	4.03	0.46877	.	0.000000	0.85682	D	0.000000	T	0.32315	0.0825	L	0.34521	1.04	0.80722	D	1	B;B	0.13594	0.008;0.005	B;B	0.10450	0.005;0.005	T	0.11348	-1.0591	10	0.59425	D	0.04	-11.6851	11.1019	0.48179	0.0:0.9093:0.0:0.0907	.	15;15	A8K594;Q9P0V3	.;SH3B4_HUMAN	L	15	ENSP00000375867:P15L;ENSP00000403251:P15L;ENSP00000386862:P15L;ENSP00000340237:P15L;ENSP00000415391:P15L	ENSP00000340237:P15L	P	+	2	0	SH3BP4	235608429	0.999000	0.42202	0.870000	0.34147	0.360000	0.29518	4.311000	0.59147	1.064000	0.40671	0.655000	0.94253	CCT	.	.	.	none		0.547	SH3BP4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329763.1		
GPR87	53836	hgsc.bcm.edu	37	3	151012432	151012432	+	Missense_Mutation	SNP	A	A	T			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr3:151012432A>T	ENST00000260843.4	-	3	1066	c.602T>A	c.(601-603)gTc>gAc	p.V201D	MED12L_ENST00000273432.4_Intron|MED12L_ENST00000474524.1_Intron|MED12L_ENST00000491549.1_Intron	NM_023915.3	NP_076404.3	Q9BY21	GPR87_HUMAN	G protein-coupled receptor 87	201					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)			ATGCCATTTGACCCCCAAAGG	0.453																																					p.V201D		Atlas-SNP	.											.	GPR87	52	.	0			c.T602A						PASS	.						119.0	114.0	116.0					3																	151012432		2203	4300	6503	SO:0001583	missense	53836	exon3			CATTTGACCCCCA	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.602T>A	chr3.hg19:g.151012432A>T	ENSP00000260843:p.Val201Asp	125.0	0.0	.		178.0	36.0	.	NM_023915	Q5KU35|Q96JZ8|Q9BXC2	Missense_Mutation	SNP	ENST00000260843.4	hg19	CCDS3157.1	.	.	.	.	.	.	.	.	.	.	A	11.72	1.721769	0.30503	.	.	ENSG00000138271	ENST00000260843	T	0.36699	1.24	5.45	1.74	0.24563	GPCR, rhodopsin-like superfamily (1);	0.457951	0.21222	N	0.078134	T	0.25082	0.0609	L	0.29908	0.895	0.20821	N	0.999843	B	0.31274	0.317	B	0.38842	0.283	T	0.29027	-1.0025	10	0.10902	T	0.67	-6.9007	8.0205	0.30406	0.6554:0.0:0.3446:0.0	.	201	Q9BY21	GPR87_HUMAN	D	201	ENSP00000260843:V201D	ENSP00000260843:V201D	V	-	2	0	GPR87	152495122	0.000000	0.05858	0.009000	0.14445	0.543000	0.35085	1.208000	0.32345	0.120000	0.18254	-0.408000	0.06270	GTC	.	.	.	none		0.453	GPR87-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357788.1		
BOD1L1	259282	hgsc.bcm.edu	37	4	13602646	13602646	+	Missense_Mutation	SNP	T	T	G			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr4:13602646T>G	ENST00000040738.5	-	10	6013	c.5878A>C	c.(5878-5880)Agt>Cgt	p.S1960R		NM_148894.2	NP_683692.2	Q8NFC6	BD1L1_HUMAN	biorientation of chromosomes in cell division 1-like 1	1960						nucleus (GO:0005634)	DNA binding (GO:0003677)										GAGACTGCACTGGTCACACTG	0.448																																					p.S1960R		Atlas-SNP	.											.	.	.	.	0			c.A5878C						PASS	.						140.0	135.0	136.0					4																	13602646		2203	4300	6503	SO:0001583	missense	259282	exon10			CTGCACTGGTCAC	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.5878A>C	chr4.hg19:g.13602646T>G	ENSP00000040738:p.Ser1960Arg	114.0	0.0	.		152.0	14.0	.	NM_148894	Q6P0M8|Q96AL1|Q9H6G0|Q9NTD6|Q9P2L9	Missense_Mutation	SNP	ENST00000040738.5	hg19	CCDS3411.2	.	.	.	.	.	.	.	.	.	.	T	17.39	3.376793	0.61735	.	.	ENSG00000038219	ENST00000040738	T	0.17691	2.26	5.55	4.35	0.52113	.	0.000000	0.64402	D	0.000002	T	0.13970	0.0338	L	0.34521	1.04	0.39358	D	0.96587	P	0.41673	0.759	B	0.38327	0.271	T	0.03315	-1.1049	10	0.72032	D	0.01	-6.7552	11.456	0.50183	0.0:0.0:0.1507:0.8493	.	1960	Q8NFC6	BOD1L_HUMAN	R	1960	ENSP00000040738:S1960R	ENSP00000040738:S1960R	S	-	1	0	BOD1L	13211744	1.000000	0.71417	1.000000	0.80357	0.715000	0.41141	4.808000	0.62583	0.904000	0.36572	0.459000	0.35465	AGT	.	.	.	none		0.448	BOD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207321.1	NM_148894	
SLC10A4	201780	hgsc.bcm.edu	37	4	48485850	48485850	+	Missense_Mutation	SNP	C	C	G			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr4:48485850C>G	ENST00000273861.4	+	1	491	c.272C>G	c.(271-273)cCc>cGc	p.P91R		NM_152679.3	NP_689892.1	Q96EP9	NTCP4_HUMAN	solute carrier family 10, member 4	91						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bile acid:sodium symporter activity (GO:0008508)			central_nervous_system(1)|large_intestine(1)|lung(1)|ovary(1)|prostate(1)|urinary_tract(1)	6						CCCTGGGCGCCCCACGCGCTC	0.756																																					p.P91R		Atlas-SNP	.											.	SLC10A4	23	.	0			c.C272G						PASS	.																																			SO:0001583	missense	201780	exon1			GGGCGCCCCACGC	BC012048	CCDS3482.1	4p12	2013-07-18	2013-07-18		ENSG00000145248	ENSG00000145248		"""Solute carriers"""	22980	protein-coding gene	gene with protein product							Standard	NM_152679		Approved	MGC29802	uc003gyc.2	Q96EP9	OTTHUMG00000102092	ENST00000273861.4:c.272C>G	chr4.hg19:g.48485850C>G	ENSP00000273861:p.Pro91Arg	2.0	0.0	.		34.0	10.0	.	NM_152679	Q8WUZ2	Missense_Mutation	SNP	ENST00000273861.4	hg19	CCDS3482.1	.	.	.	.	.	.	.	.	.	.	c	14.82	2.648971	0.47362	.	.	ENSG00000145248	ENST00000273861	T	0.09255	3.0	4.58	3.74	0.42951	.	0.434744	0.26692	N	0.022981	T	0.08802	0.0218	L	0.40543	1.245	0.19575	N	0.999969	B	0.09022	0.002	B	0.06405	0.002	T	0.21690	-1.0238	10	0.45353	T	0.12	-26.3851	6.3555	0.21398	0.0:0.6733:0.1543:0.1724	.	91	Q96EP9	NTCP4_HUMAN	R	91	ENSP00000273861:P91R	ENSP00000273861:P91R	P	+	2	0	SLC10A4	48180607	0.004000	0.15560	0.599000	0.28851	0.923000	0.55619	1.782000	0.38654	1.159000	0.42565	-0.348000	0.07805	CCC	.	.	.	none		0.756	SLC10A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219926.3	NM_152679	
KIAA1109	84162	hgsc.bcm.edu	37	4	123260393	123260393	+	Missense_Mutation	SNP	T	T	A			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr4:123260393T>A	ENST00000264501.4	+	72	12555	c.12182T>A	c.(12181-12183)gTa>gAa	p.V4061E	KIAA1109_ENST00000388738.3_Missense_Mutation_p.V4061E			Q2LD37	K1109_HUMAN	KIAA1109	4061					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						TGTTTACCAGTATCAAGAGTA	0.368																																					p.V4061E		Atlas-SNP	.											.	KIAA1109	424	.	0			c.T12182A						PASS	.						134.0	120.0	124.0					4																	123260393		1830	4088	5918	SO:0001583	missense	84162	exon70			TACCAGTATCAAG	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.12182T>A	chr4.hg19:g.123260393T>A	ENSP00000264501:p.Val4061Glu	115.0	0.0	.		121.0	66.0	.	NM_015312	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Missense_Mutation	SNP	ENST00000264501.4	hg19	CCDS43267.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	T|T|T	28.3|28.3|28.3	4.907716|4.907716|4.907716	0.92107|0.92107|0.92107	.|.|.	.|.|.	ENSG00000138688|ENSG00000138688|ENSG00000138688	ENST00000442707|ENST00000264501;ENST00000388738;ENST00000438707|ENST00000306802	.|T;T;T|.	.|0.35789|.	.|2.31;2.31;1.29|.	5.81|5.81|5.81	5.81|5.81|5.81	0.92471|0.92471|0.92471	.|.|.	.|0.067355|.	.|0.64402|.	.|D|.	.|0.000010|.	T|T|T	0.68540|0.68540|0.68540	0.3012|0.3012|0.3012	L|L|L	0.49126|0.49126|0.49126	1.545|1.545|1.545	0.80722|0.80722|0.80722	D|D|D	1|1|1	.|P;P|.	.|0.49961|.	.|0.899;0.93|.	.|P;P|.	.|0.45232|.	.|0.474;0.462|.	T|T|T	0.65853|0.65853|0.65853	-0.6067|-0.6067|-0.6067	5|10|5	.|0.66056|.	.|D|.	.|0.02|.	.|.|.	16.1637|16.1637|16.1637	0.81739|0.81739|0.81739	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.|.	.|4060;4061|.	.|Q2LD37-4;Q2LD37|.	.|.;K1109_HUMAN|.	R|E|N	6|4061;4061;730|437	.|ENSP00000264501:V4061E;ENSP00000373390:V4061E;ENSP00000410874:V730E|.	.|ENSP00000264501:V4061E|.	S|V|Y	+|+|+	3|2|1	2|0|0	KIAA1109|KIAA1109|KIAA1109	123479843|123479843|123479843	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	0.997000|0.997000|0.997000	0.53966|0.53966|0.53966	0.999000|0.999000|0.999000	0.98932|0.98932|0.98932	7.963000|7.963000|7.963000	0.87922|0.87922|0.87922	2.216000|2.216000|2.216000	0.71823|0.71823|0.71823	0.533000|0.533000|0.533000	0.62120|0.62120|0.62120	AGT|GTA|TAT	.	.	.	none		0.368	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797	
TENM3	55714	hgsc.bcm.edu	37	4	183713663	183713663	+	Silent	SNP	C	C	T			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr4:183713663C>T	ENST00000511685.1	+	26	5961	c.5838C>T	c.(5836-5838)gtC>gtT	p.V1946V	TENM3_ENST00000406950.2_Silent_p.V1946V			Q9P273	TEN3_HUMAN	teneurin transmembrane protein 3	1946					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)										GTCGGAGGGTCTTATTCAAAT	0.448																																					p.V1946V		Atlas-SNP	.											.	.	.	.	0			c.C5838T						PASS	.						63.0	63.0	63.0					4																	183713663		1880	4104	5984	SO:0001819	synonymous_variant	55714	exon25			GAGGGTCTTATTC	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.5838C>T	chr4.hg19:g.183713663C>T		149.0	0.0	.		206.0	69.0	.	NM_001080477	Q5XUL9|Q96SY2|Q9NV77|Q9NVW1|Q9NZJ2	Silent	SNP	ENST00000511685.1	hg19	CCDS47165.1																																																																																			.	.	.	none		0.448	TENM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361734.1		
NKD2	85409	hgsc.bcm.edu	37	5	1033498	1033498	+	Missense_Mutation	SNP	G	G	A	rs144426465		TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr5:1033498G>A	ENST00000296849.5	+	5	443	c.214G>A	c.(214-216)Gct>Act	p.A72T	NKD2_ENST00000537972.1_Missense_Mutation_p.A72T|NKD2_ENST00000274150.4_Missense_Mutation_p.A72T	NM_033120.3	NP_149111.1	Q969F2	NKD2_HUMAN	naked cuticle homolog 2 (Drosophila)	72	Targeting to the basolateral cell membrane.				exocytosis (GO:0006887)|Golgi vesicle fusion to target membrane (GO:0048210)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein processing (GO:0010954)|protein targeting to plasma membrane (GO:0072661)|Wnt signaling pathway (GO:0016055)	basolateral plasma membrane (GO:0016323)|cell periphery (GO:0071944)|cytoplasmic vesicle (GO:0031410)	calcium ion binding (GO:0005509)|growth factor binding (GO:0019838)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|central_nervous_system(3)|large_intestine(1)|lung(8)|pancreas(1)	14	Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;3.28e-09)		Epithelial(17;0.00093)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00417)|Lung(60;0.165)			GGCACTCCCCGCTGAGAAAGC	0.692																																					p.A72T		Atlas-SNP	.											.	NKD2	39	.	0			c.G214A						PASS	.	C	THR/ALA	0,4370		0,0,2185	18.0	22.0	20.0		214	-0.3	0.0	5	dbSNP_134	20	6,8568		0,6,4281	yes	missense	NKD2	NM_033120.2	58	0,6,6466	AA,AG,GG		0.07,0.0,0.0464	benign	72/452	1033498	6,12938	2185	4287	6472	SO:0001583	missense	85409	exon5			CTCCCCGCTGAGA	AF358137	CCDS3859.1, CCDS59486.1	5p15.3	2013-01-10			ENSG00000145506	ENSG00000145506		"""EF-hand domain containing"""	17046	protein-coding gene	gene with protein product	"""naked cuticle-2"", ""Dvl-binding protein NKD2"""	607852				11356022, 11604995	Standard	NM_033120		Approved	Naked2	uc003jbt.2	Q969F2	OTTHUMG00000090348	ENST00000296849.5:c.214G>A	chr5.hg19:g.1033498G>A	ENSP00000296849:p.Ala72Thr	90.0	0.0	.		226.0	51.0	.	NM_001271082	Q96EK8|Q9BSN0	Missense_Mutation	SNP	ENST00000296849.5	hg19	CCDS3859.1	.	.	.	.	.	.	.	.	.	.	N	10.61	1.399838	0.25291	0.0	7.0E-4	ENSG00000145506	ENST00000296849;ENST00000274150;ENST00000537972	T;T;T	0.00535	6.73;6.73;6.73	3.69	-0.271	0.12922	.	0.159534	0.41396	N	0.000898	T	0.00328	0.0010	N	0.22421	0.69	0.80722	D	1	B;B	0.33022	0.002;0.394	B;B	0.25506	0.002;0.061	T	0.72721	-0.4208	10	0.66056	D	0.02	-8.4045	2.08	0.03633	0.1396:0.4077:0.273:0.1798	.	72;72	Q969F2-2;Q969F2	.;NKD2_HUMAN	T	72	ENSP00000296849:A72T;ENSP00000274150:A72T;ENSP00000440925:A72T	ENSP00000274150:A72T	A	+	1	0	NKD2	1086498	0.000000	0.05858	0.002000	0.10522	0.001000	0.01503	-0.116000	0.10724	-0.934000	0.03733	-5.484000	0.00000	GCT	.	G|1.000;A|0.000	0.000	weak		0.692	NKD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206720.2	NM_033120	
DEPDC1B	55789	hgsc.bcm.edu	37	5	59893587	59893587	+	Missense_Mutation	SNP	C	C	T			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr5:59893587C>T	ENST00000265036.5	-	11	1650	c.1583G>A	c.(1582-1584)cGa>cAa	p.R528Q	DEPDC1B_ENST00000453022.2_Missense_Mutation_p.R466Q|DEPDC1B_ENST00000545085.1_Missense_Mutation_p.R439Q	NM_018369.2	NP_060839.2	Q8WUY9	DEP1B_HUMAN	DEP domain containing 1B	528					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(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(6)|ovary(1)|pancreas(2)|skin(2)	17		Lung NSC(810;0.000214)|Prostate(74;0.0147)|Breast(144;0.0991)|Ovarian(174;0.17)				TTATTACATTCGAAAACTTCT	0.418																																					p.R528Q		Atlas-SNP	.											DEPDC1B,NS,carcinoma,-1,1	DEPDC1B	56	.	0			c.G1583A						PASS	.						174.0	167.0	170.0					5																	59893587		2203	4300	6503	SO:0001583	missense	55789	exon11			TACATTCGAAAAC	AF303178	CCDS3977.1, CCDS47214.1	5q12	2008-02-05			ENSG00000035499	ENSG00000035499			24902	protein-coding gene	gene with protein product	"""breast cancer cell 3"""					12477932	Standard	NM_001145208		Approved	XTP1, BRCC3	uc003jsh.3	Q8WUY9	OTTHUMG00000097083	ENST00000265036.5:c.1583G>A	chr5.hg19:g.59893587C>T	ENSP00000265036:p.Arg528Gln	71.0	0.0	.		77.0	21.0	.	NM_018369	A8K3R9|B4DUT4|Q86WJ3|Q8IZY6|Q9NUN3|Q9NW57	Missense_Mutation	SNP	ENST00000265036.5	hg19	CCDS3977.1	.	.	.	.	.	.	.	.	.	.	C	34	5.383654	0.95967	.	.	ENSG00000035499	ENST00000265036;ENST00000453022;ENST00000545085	T;T;T	0.49432	1.96;1.18;0.78	5.46	5.46	0.80206	.	0.000000	0.85682	D	0.000000	T	0.67767	0.2928	M	0.68593	2.085	0.53688	D	0.999979	D;D	0.89917	0.997;1.0	D;D	0.70227	0.968;0.941	T	0.64850	-0.6310	9	.	.	.	-9.0991	19.4868	0.95032	0.0:1.0:0.0:0.0	.	466;528	B4DUT4;Q8WUY9	.;DEP1B_HUMAN	Q	528;466;439	ENSP00000265036:R528Q;ENSP00000389101:R466Q;ENSP00000438320:R439Q	.	R	-	2	0	DEPDC1B	59929344	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	6.694000	0.74587	2.838000	0.97847	0.591000	0.81541	CGA	.	.	.	none		0.418	DEPDC1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214207.1	NM_018369	
AP3B1	8546	hgsc.bcm.edu	37	5	77521385	77521385	+	Missense_Mutation	SNP	A	A	C			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr5:77521385A>C	ENST00000255194.6	-	6	759	c.584T>G	c.(583-585)cTt>cGt	p.L195R	AP3B1_ENST00000519295.1_Missense_Mutation_p.L146R	NM_001271769.1	NP_001258698.1	O00203	AP3B1_HUMAN	adaptor-related protein complex 3, beta 1 subunit	195					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)		ATCTTTCAGAAGTTTTTCAAT	0.239									Hermansky-Pudlak syndrome																												p.L195R		Atlas-SNP	.											.	AP3B1	94	.	0			c.T584G						PASS	.						55.0	55.0	55.0					5																	77521385		2193	4276	6469	SO:0001583	missense	8546	exon6	Familial Cancer Database	HPS, HPS1-8	TTCAGAAGTTTTT	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.584T>G	chr5.hg19:g.77521385A>C	ENSP00000255194:p.Leu195Arg	46.0	0.0	.		88.0	54.0	.	NM_003664	E5RJ68|O00580|Q7Z393|Q9HD66	Missense_Mutation	SNP	ENST00000255194.6	hg19	CCDS4041.1	.	.	.	.	.	.	.	.	.	.	A	18.69	3.678934	0.68042	.	.	ENSG00000132842	ENST00000255194;ENST00000519295;ENST00000535760;ENST00000535667	T;T	0.18502	2.21;2.21	5.59	4.44	0.53790	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.54431	0.1858	H	0.97023	3.925	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.67023	-0.5775	10	0.87932	D	0	-1.7217	11.3981	0.49854	0.9293:0.0:0.0707:0.0	.	195	O00203	AP3B1_HUMAN	R	195;146;195;99	ENSP00000255194:L195R;ENSP00000430597:L146R	ENSP00000255194:L195R	L	-	2	0	AP3B1	77557141	1.000000	0.71417	0.998000	0.56505	0.992000	0.81027	9.245000	0.95431	0.959000	0.37980	-0.361000	0.07541	CTT	.	.	.	none		0.239	AP3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000225548.2		
IK	3550	hgsc.bcm.edu	37	5	140037217	140037217	+	Missense_Mutation	SNP	C	C	T			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr5:140037217C>T	ENST00000417647.2	+	10	1019	c.880C>T	c.(880-882)Cgt>Tgt	p.R294C		NM_006083.3	NP_006074.2	Q13123	RED_HUMAN	IK cytokine, down-regulator of HLA II	294					cell-cell signaling (GO:0007267)|immune response (GO:0006955)	extracellular space (GO:0005615)|nucleus (GO:0005634)	identical protein binding (GO:0042802)			large_intestine(1)	1		all_hematologic(541;4.8e-07)|all_lung(500;0.000434)|Lung NSC(810;0.00161)|Breast(839;0.128)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCAGGGAACCCGTAACAAGAA	0.473																																					p.R294C		Atlas-SNP	.											.	IK	46	.	0			c.C880T						PASS	.						129.0	116.0	120.0					5																	140037217		1910	4122	6032	SO:0001583	missense	3550	exon10			GGAACCCGTAACA	BC051295	CCDS47280.1	5q31.3	2008-08-07			ENSG00000113141	ENSG00000113141			5958	protein-coding gene	gene with protein product		600549				7970704	Standard	NM_006083		Approved		uc003lgq.3	Q13123	OTTHUMG00000163374	ENST00000417647.2:c.880C>T	chr5.hg19:g.140037217C>T	ENSP00000396301:p.Arg294Cys	203.0	0.0	.		269.0	59.0	.	NM_006083	Q6IPD8	Missense_Mutation	SNP	ENST00000417647.2	hg19	CCDS47280.1	.	.	.	.	.	.	.	.	.	.	C	24.9	4.584507	0.86748	.	.	ENSG00000113141	ENST00000417647	.	.	.	5.48	5.48	0.80851	RED-like, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.80722	0.4677	M	0.85373	2.75	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.83092	-0.0132	9	0.72032	D	0.01	.	14.198	0.65684	0.1496:0.8504:0.0:0.0	.	294;294	Q9UK43;Q13123	.;RED_HUMAN	C	294	.	ENSP00000396301:R294C	R	+	1	0	IK	140017401	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	3.692000	0.54727	2.730000	0.93505	0.655000	0.94253	CGT	.	.	.	none		0.473	IK-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372897.1	NM_006083	
FAM65B	9750	hgsc.bcm.edu	37	6	24836059	24836059	+	Missense_Mutation	SNP	C	C	T			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr6:24836059C>T	ENST00000259698.4	-	16	2318	c.2143G>A	c.(2143-2145)Gaa>Aaa	p.E715K	FAM65B_ENST00000538035.1_Missense_Mutation_p.E694K	NM_014722.2	NP_055537.2	Q9Y4F9	FA65B_HUMAN	family with sequence similarity 65, member B	715					cell differentiation (GO:0030154)|muscle organ development (GO:0007517)	cell projection (GO:0042995)|cytoskeleton (GO:0005856)|mitochondrion (GO:0005739)				breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	25						GTGAGCGCTTCACTGAGATGC	0.527																																					p.E715K		Atlas-SNP	.											.	FAM65B	134	.	0			c.G2143A						PASS	.						105.0	90.0	94.0					6																	24836059		692	1591	2283	SO:0001583	missense	9750	exon16			GCGCTTCACTGAG	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.2143G>A	chr6.hg19:g.24836059C>T	ENSP00000259698:p.Glu715Lys	170.0	0.0	.		252.0	75.0	.	NM_014722	A6NHP2|Q13529|Q5VV37|Q5VV38|Q9BQ28	Missense_Mutation	SNP	ENST00000259698.4	hg19	CCDS47383.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.966222	0.74131	.	.	ENSG00000111913	ENST00000259698;ENST00000538035	T;T	0.35789	1.29;1.29	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	T	0.24084	0.0583	L	0.43152	1.355	0.80722	D	1	B;B	0.31548	0.264;0.328	B;B	0.30495	0.085;0.116	T	0.09640	-1.0665	10	0.66056	D	0.02	-10.1386	19.1916	0.93669	0.0:1.0:0.0:0.0	.	694;715	F5GX51;Q9Y4F9	.;FA65B_HUMAN	K	715;694	ENSP00000259698:E715K;ENSP00000441138:E694K	ENSP00000259698:E715K	E	-	1	0	FAM65B	24944038	1.000000	0.71417	0.595000	0.28798	0.748000	0.42578	7.452000	0.80683	2.541000	0.85698	0.655000	0.94253	GAA	.	.	.	none		0.527	FAM65B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040024.2		
HIST1H1C	3006	hgsc.bcm.edu	37	6	26056096	26056096	+	Silent	SNP	T	T	C			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr6:26056096T>C	ENST00000343677.2	-	1	603	c.561A>G	c.(559-561)aaA>aaG	p.K187K		NM_005319.3	NP_005310.1	P16403	H12_HUMAN	histone cluster 1, H1c	187					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						TAGCAGCACTTTTGGCAGCTT	0.547																																					p.K187K		Atlas-SNP	.											.	HIST1H1C	80	.	0			c.A561G						PASS	.						89.0	96.0	93.0					6																	26056096		2203	4300	6503	SO:0001819	synonymous_variant	3006	exon1			AGCACTTTTGGCA	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.561A>G	chr6.hg19:g.26056096T>C		95.0	0.0	.		143.0	12.0	.	NM_005319	A8K4I2	Silent	SNP	ENST00000343677.2	hg19	CCDS4577.1																																																																																			.	.	.	none		0.547	HIST1H1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043372.1	NM_005319	
SLC26A5	375611	hgsc.bcm.edu	37	7	103050896	103050896	+	Missense_Mutation	SNP	G	G	C			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr7:103050896G>C	ENST00000306312.3	-	7	932	c.671C>G	c.(670-672)tCc>tGc	p.S224C	SLC26A5_ENST00000393729.1_Missense_Mutation_p.S187C|SLC26A5_ENST00000393735.2_Missense_Mutation_p.S224C|SLC26A5_ENST00000432958.2_Missense_Mutation_p.S224C|SLC26A5_ENST00000339444.6_Missense_Mutation_p.S224C|SLC26A5_ENST00000393723.1_Missense_Mutation_p.S224C|SLC26A5_ENST00000393727.1_Missense_Mutation_p.S224C|SLC26A5_ENST00000356767.4_Missense_Mutation_p.S224C|SLC26A5_ENST00000393730.1_Missense_Mutation_p.S224C|SLC26A5_ENST00000354356.4_5'UTR	NM_198999.2	NP_945350.1	P58743	S26A5_HUMAN	solute carrier family 26 (anion exchanger), member 5	224					regulation of cell shape (GO:0008360)|regulation of membrane potential (GO:0042391)|sensory perception of sound (GO:0007605)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)	secondary active sulfate transmembrane transporter activity (GO:0008271)			endometrium(5)|kidney(2)|large_intestine(9)|lung(15)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(5)	43						TTTTAACATGGAGGTGAAGAC	0.443																																					p.S224C		Atlas-SNP	.											.	SLC26A5	231	.	0			c.C671G						PASS	.						73.0	71.0	71.0					7																	103050896		2203	4300	6503	SO:0001583	missense	375611	exon7			AACATGGAGGTGA	AC005064	CCDS5733.1, CCDS43630.1, CCDS55150.1, CCDS5732.1, CCDS43629.1	7q22	2013-07-18	2013-07-18	2005-09-13	ENSG00000170615	ENSG00000170615		"""Solute carriers"""	9359	protein-coding gene	gene with protein product	"""deafness, neurosensory, autosomal recessive, 61"""	604943	"""prestin (motor protein)"""	PRES		10821263	Standard	NM_206883		Approved	DFNB61	uc003vbz.3	P58743	OTTHUMG00000149911	ENST00000306312.3:c.671C>G	chr7.hg19:g.103050896G>C	ENSP00000304783:p.Ser224Cys	86.0	0.0	.		83.0	26.0	.	NM_206883	Q496J2|Q7Z7F3|Q86UF8|Q86UF9|Q86UG0	Missense_Mutation	SNP	ENST00000306312.3	hg19	CCDS5733.1	.	.	.	.	.	.	.	.	.	.	G	27.3	4.816614	0.90790	.	.	ENSG00000170615	ENST00000339444;ENST00000356767;ENST00000393735;ENST00000306312;ENST00000393730;ENST00000432958;ENST00000393729;ENST00000393727;ENST00000393723	D;D;D;D;D;D;D;D;D	0.93859	-3.3;-3.3;-3.3;-3.3;-3.3;-3.3;-3.3;-3.3;-3.3	5.72	5.72	0.89469	Sulphate transporter (1);	0.000000	0.85682	D	0.000000	D	0.97898	0.9309	H	0.95365	3.66	0.80722	D	1	D;D;D;D;D	0.76494	0.997;0.998;0.999;0.997;0.999	D;D;D;D;D	0.73380	0.98;0.974;0.967;0.931;0.956	D	0.98561	1.0641	10	0.87932	D	0	.	19.885	0.96909	0.0:0.0:1.0:0.0	.	224;224;224;224;224	P58743;Q496J2;P58743-4;P58743-3;P58743-2	S26A5_HUMAN;.;.;.;.	C	224;224;224;224;224;224;187;224;224	ENSP00000342396:S224C;ENSP00000349210:S224C;ENSP00000377336:S224C;ENSP00000304783:S224C;ENSP00000377331:S224C;ENSP00000389733:S224C;ENSP00000377330:S187C;ENSP00000377328:S224C;ENSP00000377324:S224C	ENSP00000304783:S224C	S	-	2	0	SLC26A5	102838132	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.330000	0.96422	2.708000	0.92522	0.591000	0.81541	TCC	.	.	.	none		0.443	SLC26A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313860.1	NM_198999	
STAU2	27067	hgsc.bcm.edu	37	8	74464271	74464271	+	Silent	SNP	A	A	G			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr8:74464271A>G	ENST00000521451.1	-	8	1222	c.846T>C	c.(844-846)taT>taC	p.Y282Y	STAU2_ENST00000517542.1_Silent_p.Y464Y|STAU2_ENST00000523558.1_Silent_p.Y330Y|STAU2_ENST00000521210.1_Silent_p.Y398Y|STAU2_ENST00000524300.1_Silent_p.Y502Y|STAU2_ENST00000522695.1_Silent_p.Y470Y|STAU2_ENST00000519961.1_Silent_p.Y502Y|STAU2_ENST00000355780.5_Silent_p.Y470Y|STAU2_ENST00000521727.1_Silent_p.Y482Y|STAU2_ENST00000522509.1_Silent_p.Y470Y			Q9NUL3	STAU2_HUMAN	staufen double-stranded RNA binding protein 2	502					transport (GO:0006810)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|microtubule (GO:0005874)|nucleus (GO:0005634)	double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|liver(1)|lung(6)|ovary(1)	19	Breast(64;0.0138)		Epithelial(68;0.026)|BRCA - Breast invasive adenocarcinoma(89;0.0483)|all cancers(69;0.0972)			TCCTTGCTAAATATTCCAGTT	0.363																																					p.Y502Y		Atlas-SNP	.											.	STAU2	148	.	0			c.T1506C						PASS	.						56.0	61.0	59.0					8																	74464271		2203	4297	6500	SO:0001819	synonymous_variant	27067	exon13			TGCTAAATATTCC	Y19062	CCDS6214.1, CCDS55244.1, CCDS55245.1, CCDS55246.1, CCDS55247.1, CCDS55248.1	8q21.11	2013-06-05	2013-06-05		ENSG00000040341	ENSG00000040341			11371	protein-coding gene	gene with protein product		605920	"""staufen (Drosophila, RNA-binding protein) homolog 2"", ""staufen, RNA binding protein, homolog 2 (Drosophila)"""			10585778	Standard	NM_014393		Approved	39K2	uc003xzm.3	Q9NUL3	OTTHUMG00000164499	ENST00000521451.1:c.846T>C	chr8.hg19:g.74464271A>G		152.0	0.0	.		143.0	61.0	.	NM_001164380	B7Z1I6|B7Z292|B7Z8B4|E7ER74|E9PEI3|E9PF26|E9PF50|Q6AHY7|Q96HM0|Q96HM1|Q9NVI5|Q9UGG6	Silent	SNP	ENST00000521451.1	hg19																																																																																				.	.	.	none		0.363	STAU2-006	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000379006.4	NM_001164380	
OR13F1	138805	hgsc.bcm.edu	37	9	107267461	107267461	+	Missense_Mutation	SNP	T	T	G			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr9:107267461T>G	ENST00000334726.2	+	1	1007	c.918T>G	c.(916-918)atT>atG	p.I306M		NM_001004485.1	NP_001004485.1	Q8NGS4	O13F1_HUMAN	olfactory receptor, family 13, subfamily F, member 1	306						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(6)|lung(17)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	31						AATTGCTGATTAGAAATCATT	0.353																																					p.I306M		Atlas-SNP	.											.	OR13F1	75	.	0			c.T918G						PASS	.						39.0	42.0	41.0					9																	107267461		2203	4300	6503	SO:0001583	missense	138805	exon1			GCTGATTAGAAAT		CCDS35087.1	9q31.1	2013-09-24			ENSG00000186881	ENSG00000186881		"""GPCR / Class A : Olfactory receptors"""	14723	protein-coding gene	gene with protein product							Standard	NM_001004485		Approved		uc011lvm.2	Q8NGS4	OTTHUMG00000020404	ENST00000334726.2:c.918T>G	chr9.hg19:g.107267461T>G	ENSP00000334452:p.Ile306Met	69.0	0.0	.		44.0	18.0	.	NM_001004485	Q6IF50	Missense_Mutation	SNP	ENST00000334726.2	hg19	CCDS35087.1	.	.	.	.	.	.	.	.	.	.	T	2.865	-0.235310	0.05983	.	.	ENSG00000186881	ENST00000334726	T	0.37411	1.2	4.3	-3.06	0.05379	.	0.941008	0.08732	N	0.901923	T	0.15262	0.0368	N	0.10972	0.075	0.09310	N	1	B	0.16166	0.016	B	0.10450	0.005	T	0.20207	-1.0282	10	0.33141	T	0.24	.	3.0534	0.06176	0.1435:0.0881:0.443:0.3254	.	306	Q8NGS4	O13F1_HUMAN	M	306	ENSP00000334452:I306M	ENSP00000334452:I306M	I	+	3	3	OR13F1	106307282	0.000000	0.05858	0.004000	0.12327	0.446000	0.32137	-0.563000	0.05943	-0.521000	0.06426	-0.290000	0.09829	ATT	.	.	.	none		0.353	OR13F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053475.1		
SPTAN1	6709	hgsc.bcm.edu	37	9	131379924	131379924	+	Missense_Mutation	SNP	A	A	G			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr9:131379924A>G	ENST00000372731.4	+	41	5458	c.5348A>G	c.(5347-5349)aAg>aGg	p.K1783R	SPTAN1_ENST00000372739.3_Missense_Mutation_p.K1788R|SPTAN1_ENST00000358161.5_Missense_Mutation_p.K1788R	NM_001195532.1|NM_003127.3	NP_001182461.1|NP_003118.2	Q13813	SPTN1_HUMAN	spectrin, alpha, non-erythrocytic 1	1783					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						TTCAGGGAGAAGAAGCTGCTG	0.567																																					p.K1788R	NSCLC(120;833 1744 2558 35612 37579)	Atlas-SNP	.											.	SPTAN1	266	.	0			c.A5363G						PASS	.						53.0	54.0	54.0					9																	131379924		2203	4300	6503	SO:0001583	missense	6709	exon42			GGGAGAAGAAGCT	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.5348A>G	chr9.hg19:g.131379924A>G	ENSP00000361816:p.Lys1783Arg	118.0	0.0	.		143.0	50.0	.	NM_001130438	Q13186|Q15324|Q16606|Q59EF1|Q5VXV5|Q5VXV6|Q7Z6M5|Q9P0V0	Missense_Mutation	SNP	ENST00000372731.4	hg19	CCDS6905.1	.	.	.	.	.	.	.	.	.	.	A	25.3	4.628279	0.87560	.	.	ENSG00000197694	ENST00000358161;ENST00000372731;ENST00000372739;ENST00000372719;ENST00000372721	T;T;T	0.56444	0.46;0.46;0.46	5.46	5.46	0.80206	.	0.000000	0.85682	D	0.000000	T	0.68622	0.3021	L	0.55103	1.725	0.80722	D	1	D;D;D	0.89917	1.0;0.999;0.999	D;D;D	0.97110	1.0;0.996;0.998	T	0.71101	-0.4690	10	0.66056	D	0.02	.	15.8191	0.78626	1.0:0.0:0.0:0.0	.	1763;1788;1783	Q13813-3;Q13813-2;Q13813	.;.;SPTA2_HUMAN	R	1788;1783;1788;1763;32	ENSP00000350882:K1788R;ENSP00000361816:K1783R;ENSP00000361824:K1788R	ENSP00000350882:K1788R	K	+	2	0	SPTAN1	130419745	1.000000	0.71417	1.000000	0.80357	0.685000	0.39939	8.824000	0.92023	2.202000	0.70862	0.379000	0.24179	AAG	.	.	.	none		0.567	SPTAN1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054472.1	NM_003127	
EHMT1	79813	hgsc.bcm.edu	37	9	140710514	140710514	+	Splice_Site	SNP	G	G	A			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr9:140710514G>A	ENST00000460843.1	+	23	3401	c.3374G>A	c.(3373-3375)aGg>aAg	p.R1125K		NM_024757.4	NP_079033.4	Q9H9B1	EHMT1_HUMAN	euchromatic histone-lysine N-methyltransferase 1	1125					chromatin modification (GO:0016568)|DNA methylation (GO:0006306)|embryo development (GO:0009790)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-lysine dimethylation (GO:0018027)|peptidyl-lysine monomethylation (GO:0018026)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	histone methyltransferase activity (H3-K27 specific) (GO:0046976)|histone methyltransferase activity (H3-K9 specific) (GO:0046974)|histone-lysine N-methyltransferase activity (GO:0018024)|methyltransferase activity (GO:0008168)|p53 binding (GO:0002039)|protein-lysine N-methyltransferase activity (GO:0016279)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(16)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	41	all_cancers(76;0.164)			OV - Ovarian serous cystadenocarcinoma(145;0.000183)|Epithelial(140;0.000728)		AATGGTCTCAGGTGAGAGGCA	0.552																																					p.R1125K		Atlas-SNP	.											.	EHMT1	196	.	0			c.G3374A						PASS	.						52.0	45.0	48.0					9																	140710514		2203	4300	6503	SO:0001630	splice_region_variant	79813	exon23			GTCTCAGGTGAGA	AY083210	CCDS7050.1, CCDS7050.2, CCDS56595.1	9q34.3	2013-09-20			ENSG00000181090	ENSG00000181090	2.1.1.43	"""Chromatin-modifying enzymes / K-methyltransferases"", ""Ankyrin repeat domain containing"""	24650	protein-coding gene	gene with protein product		607001	"""euchromatic histone methyltransferase 1"""			11347906, 12004135	Standard	NM_024757		Approved	Eu-HMTase1, FLJ12879, KIAA1876, bA188C12.1, KMT1D	uc011mfc.2	Q9H9B1	OTTHUMG00000020995	ENST00000460843.1:c.3374+1G>A	chr9.hg19:g.140710514G>A		57.0	0.0	.		67.0	35.0	.	NM_024757	B1AQ58|B1AQ59|Q86X08|Q8TCN7|Q96F53|Q96JF1|Q96KH4	Missense_Mutation	SNP	ENST00000460843.1	hg19	CCDS7050.2	.	.	.	.	.	.	.	.	.	.	G	10.78	1.447711	0.26074	.	.	ENSG00000181090	ENST00000371400;ENST00000460843	D	0.88741	-2.42	5.11	5.11	0.69529	SET domain (1);	0.042517	0.85682	D	0.000000	T	0.73048	0.3537	N	0.04805	-0.155	0.80722	D	1	B	0.12013	0.005	B	0.08055	0.003	T	0.68379	-0.5424	10	0.02654	T	1	.	11.9694	0.53055	0.0798:0.0:0.9202:0.0	.	1125	Q9H9B1	EHMT1_HUMAN	K	1094;1125	ENSP00000417980:R1125K	ENSP00000360453:R1094K	R	+	2	0	EHMT1	139830335	1.000000	0.71417	1.000000	0.80357	0.809000	0.45718	7.876000	0.87215	2.357000	0.79964	0.591000	0.81541	AGG	.	.	.	none		0.552	EHMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055371.2	NM_024757	Missense_Mutation
CUBN	8029	hgsc.bcm.edu	37	10	17169853	17169853	+	Missense_Mutation	SNP	C	C	A	rs543983858		TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr10:17169853C>A	ENST00000377833.4	-	3	388	c.323G>T	c.(322-324)aGt>aTt	p.S108I	CUBN_ENST00000377823.1_Missense_Mutation_p.S108I	NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	108					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)	ATAGATTTGACTAGATATATT	0.338																																					p.S108I		Atlas-SNP	.											.	CUBN	515	.	0			c.G323T						PASS	.						202.0	199.0	200.0					10																	17169853		2202	4300	6502	SO:0001583	missense	8029	exon3			ATTTGACTAGATA	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.323G>T	chr10.hg19:g.17169853C>A	ENSP00000367064:p.Ser108Ile	58.0	0.0	.		39.0	19.0	.	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Missense_Mutation	SNP	ENST00000377833.4	hg19	CCDS7113.1	.	.	.	.	.	.	.	.	.	.	C	14.20	2.465566	0.43839	.	.	ENSG00000107611	ENST00000377833;ENST00000377823	T;D	0.89939	-1.04;-2.59	5.39	-1.65	0.08291	.	0.658141	0.14204	N	0.334504	T	0.77103	0.4081	N	0.19112	0.55	0.24501	N	0.994254	P	0.41265	0.744	B	0.36030	0.216	T	0.66991	-0.5783	10	0.33940	T	0.23	.	11.3077	0.49345	0.0:0.445:0.0:0.555	.	108	O60494	CUBN_HUMAN	I	108	ENSP00000367064:S108I;ENSP00000367054:S108I	ENSP00000367054:S108I	S	-	2	0	CUBN	17209859	0.964000	0.33143	0.979000	0.43373	0.946000	0.59487	-0.127000	0.10547	-0.237000	0.09739	0.650000	0.86243	AGT	.	.	.	none		0.338	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081	
SLC25A28	81894	hgsc.bcm.edu	37	10	101370968	101370968	+	Missense_Mutation	SNP	T	T	A			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr10:101370968T>A	ENST00000370495.4	-	4	761	c.733A>T	c.(733-735)Acc>Tcc	p.T245S	SLC25A28_ENST00000496035.1_5'UTR	NM_031212.3	NP_112489.3	Q96A46	MFRN2_HUMAN	solute carrier family 25 (mitochondrial iron transporter), member 28	245					ion transport (GO:0006811)|iron ion homeostasis (GO:0055072)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				endometrium(1)|kidney(2)|large_intestine(4)|liver(1)|lung(2)|stomach(1)	11		Colorectal(252;0.234)		Epithelial(162;2.57e-10)|all cancers(201;2.01e-08)		AATTCATAGGTCATGAAGTGA	0.567																																					p.T245S		Atlas-SNP	.											.	SLC25A28	34	.	0			c.A733T						PASS	.						66.0	69.0	68.0					10																	101370968		2005	4172	6177	SO:0001583	missense	81894	exon4			CATAGGTCATGAA	AF327402	CCDS41559.1	10q24.2	2013-05-22	2012-03-29		ENSG00000155287	ENSG00000155287		"""Solute carriers"""	23472	protein-coding gene	gene with protein product	"""mitoferrin 2"""	609767	"""solute carrier family 25, member 28"""			11297739	Standard	NM_031212		Approved	MRS3/4, MRS4L	uc001kpx.2	Q96A46	OTTHUMG00000018886	ENST00000370495.4:c.733A>T	chr10.hg19:g.101370968T>A	ENSP00000359526:p.Thr245Ser	185.0	0.0	.		137.0	44.0	.	NM_031212	Q4VBZ0|Q5T777|Q86VX5|Q969G8|Q9H2J3	Missense_Mutation	SNP	ENST00000370495.4	hg19	CCDS41559.1	.	.	.	.	.	.	.	.	.	.	T	18.84	3.710038	0.68730	.	.	ENSG00000155287	ENST00000434701;ENST00000370495	T;T	0.80123	-1.34;-1.34	5.41	5.41	0.78517	Mitochondrial carrier domain (2);	0.000000	0.85682	D	0.000000	T	0.76681	0.4021	L	0.49126	1.545	0.58432	D	0.999999	P	0.42456	0.78	B	0.42138	0.377	T	0.78175	-0.2306	10	0.52906	T	0.07	-32.8904	10.7365	0.46128	0.0:0.0735:0.0:0.9265	.	245	Q96A46	MFRN2_HUMAN	S	106;245	ENSP00000399102:T106S;ENSP00000359526:T245S	ENSP00000359526:T245S	T	-	1	0	SLC25A28	101360958	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.678000	0.61641	2.271000	0.75665	0.459000	0.35465	ACC	.	.	.	none		0.567	SLC25A28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049801.1	NM_031212	
VAX1	11023	hgsc.bcm.edu	37	10	118893699	118893699	+	Silent	SNP	C	C	T			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr10:118893699C>T	ENST00000369206.5	-	3	824	c.825G>A	c.(823-825)ctG>ctA	p.L275L	VAX1_ENST00000277905.2_Intron	NM_001112704.1	NP_001106175.1	Q5SQQ9	VAX1_HUMAN	ventral anterior homeobox 1	275					axon guidance (GO:0007411)|brain development (GO:0007420)|camera-type eye development (GO:0043010)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|palate development (GO:0060021)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|large_intestine(1)|lung(8)|ovary(2)	12				all cancers(201;0.0108)		AGGGCACCGGCAGGCTGAAGA	0.736																																					p.L275L		Atlas-SNP	.											.	VAX1	50	.	0			c.G825A						PASS	.						18.0	20.0	19.0					10																	118893699		692	1591	2283	SO:0001819	synonymous_variant	11023	exon3			CACCGGCAGGCTG	AK127095	CCDS7597.1, CCDS44483.1	10q26.11	2011-06-20			ENSG00000148704	ENSG00000148704		"""Homeoboxes / ANTP class : NKL subclass"""	12660	protein-coding gene	gene with protein product		604294				9636075, 10485894	Standard	NM_199131		Approved		uc009xyx.3	Q5SQQ9	OTTHUMG00000019117	ENST00000369206.5:c.825G>A	chr10.hg19:g.118893699C>T		7.0	0.0	.		15.0	8.0	.	NM_001112704	B1AVW5|Q6ZSX0	Silent	SNP	ENST00000369206.5	hg19	CCDS44483.1																																																																																			.	.	.	none		0.736	VAX1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050559.3	XM_301242	
KCNQ1	3784	hgsc.bcm.edu	37	11	2798240	2798240	+	Silent	SNP	C	C	G			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr11:2798240C>G	ENST00000155840.5	+	14	1818	c.1710C>G	c.(1708-1710)ccC>ccG	p.P570P	KCNQ1_ENST00000335475.5_Silent_p.P443P	NM_000218.2	NP_000209.2	P51787	KCNQ1_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 1	570					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)	TTGGGAAGCCCTCACTGTTCA	0.602																																					p.P570P		Atlas-SNP	.											.	KCNQ1	60	.	0			c.C1710G	GRCh37	CD057258	KCNQ1	D		PASS	.						249.0	175.0	200.0					11																	2798240		2202	4299	6501	SO:0001819	synonymous_variant	3784	exon14			GAAGCCCTCACTG	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.1710C>G	chr11.hg19:g.2798240C>G		142.0	0.0	.		185.0	53.0	.	NM_000218	O00347|O60607|O94787|Q14D14|Q7Z6G9|Q92960|Q9UMN8|Q9UMN9	Silent	SNP	ENST00000155840.5	hg19	CCDS7736.1																																																																																			.	.	.	none		0.602	KCNQ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027382.2	NM_000218	
KCNA4	3739	hgsc.bcm.edu	37	11	30032894	30032894	+	Silent	SNP	T	T	C			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr11:30032894T>C	ENST00000328224.6	-	2	2565	c.1332A>G	c.(1330-1332)agA>agG	p.R444R	KCNA4_ENST00000526518.1_5'Flank	NM_002233.3	NP_002224.1	P22459	KCNA4_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 4	444					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	potassium ion binding (GO:0030955)|voltage-gated potassium channel activity (GO:0005249)			central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(17)|lung(39)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	78					Dalfampridine(DB06637)	GACGAATGATTCTGAGGATGG	0.572																																					p.R444R		Atlas-SNP	.											.	KCNA4	158	.	0			c.A1332G						PASS	.						70.0	68.0	69.0					11																	30032894		2059	4216	6275	SO:0001819	synonymous_variant	3739	exon2			AATGATTCTGAGG	M55514	CCDS41629.1	11p14	2012-07-05	2002-07-10			ENSG00000182255		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6222	protein-coding gene	gene with protein product		176266	"""potassium voltage-gated channel, shaker-related subfamily, member 4-like"""	KCNA4L		2263489, 16382104	Standard	NM_002233		Approved	Kv1.4, HK1, HPCN2	uc001msk.3	P22459		ENST00000328224.6:c.1332A>G	chr11.hg19:g.30032894T>C		71.0	0.0	.		104.0	30.0	.	NM_002233		Silent	SNP	ENST00000328224.6	hg19	CCDS41629.1																																																																																			.	.	.	none		0.572	KCNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388074.2	NM_002233	
SPX	80763	hgsc.bcm.edu	37	12	21680692	21680692	+	Silent	SNP	G	G	C			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr12:21680692G>C	ENST00000256969.2	+	4	343	c.177G>C	c.(175-177)cgG>cgC	p.R59R		NM_030572.2	NP_085049.1	Q9BT56	SPXN_HUMAN		59					long-chain fatty acid import (GO:0044539)|negative regulation of appetite (GO:0032099)|negative regulation of heart rate (GO:0010459)|negative regulation of renal sodium excretion (GO:0035814)|positive regulation of systemic arterial blood pressure (GO:0003084)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of sensory perception of pain (GO:0051930)	cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)	neuropeptide hormone activity (GO:0005184)|type 2 galanin receptor binding (GO:0031765)|type 3 galanin receptor binding (GO:0031766)			endometrium(3)|large_intestine(1)|lung(2)|urinary_tract(1)	7						ACCAGAGCCGGAGAAAGGACC	0.647																																					p.R59R		Atlas-SNP	.											.	C12orf39	18	.	0			c.G177C						PASS	.						20.0	21.0	21.0					12																	21680692		2195	4272	6467	SO:0001819	synonymous_variant	80763	exon4			GAGCCGGAGAAAG																												ENST00000256969.2:c.177G>C	chr12.hg19:g.21680692G>C		203.0	1.0	.		215.0	158.0	.	NM_030572	B3KND6	Silent	SNP	ENST00000256969.2	hg19	CCDS31757.1																																																																																			.	.	.	none		0.647	C12orf39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402389.1		
KMT2D	8085	hgsc.bcm.edu	37	12	49436945	49436945	+	Missense_Mutation	SNP	G	G	A			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr12:49436945G>A	ENST00000301067.7	-	25	5557	c.5558C>T	c.(5557-5559)gCa>gTa	p.A1853V		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	1853					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)										CACTGGGGATGCCTTCACGCC	0.587																																					p.A1853V		Atlas-SNP	.											.	MLL2	1173	.	0			c.C5558T						PASS	.						69.0	71.0	71.0					12																	49436945		2031	4183	6214	SO:0001583	missense	8085	exon25			GGGGATGCCTTCA	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.5558C>T	chr12.hg19:g.49436945G>A	ENSP00000301067:p.Ala1853Val	96.0	0.0	.		104.0	8.0	.	NM_003482	O14687	Missense_Mutation	SNP	ENST00000301067.7	hg19	CCDS44873.1	.	.	.	.	.	.	.	.	.	.	G	12.58	1.980996	0.34942	.	.	ENSG00000167548	ENST00000301067	T	0.79554	-1.28	5.61	4.72	0.59763	.	0.000000	0.36303	N	0.002670	T	0.69504	0.3118	L	0.29908	0.895	0.30174	N	0.801069	B	0.26363	0.147	B	0.19391	0.025	T	0.69472	-0.5136	10	0.87932	D	0	.	10.4356	0.44433	0.0892:0.0:0.9108:0.0	.	1853	O14686	MLL2_HUMAN	V	1853	ENSP00000301067:A1853V	ENSP00000301067:A1853V	A	-	2	0	MLL2	47723212	1.000000	0.71417	1.000000	0.80357	0.889000	0.51656	2.943000	0.49026	1.371000	0.46172	0.655000	0.94253	GCA	.	.	.	none		0.587	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2		
PABPC3	5042	hgsc.bcm.edu	37	13	25671122	25671122	+	Silent	SNP	C	C	T	rs79072440		TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr13:25671122C>T	ENST00000281589.3	+	1	823	c.786C>T	c.(784-786)taC>taT	p.Y262Y		NM_030979.2	NP_112241.2	Q9H361	PABP3_HUMAN	poly(A) binding protein, cytoplasmic 3	262	RRM 3. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA metabolic process (GO:0016071)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)			breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(21)|ovary(4)|pancreas(1)|skin(3)	47		Lung SC(185;0.0225)|Breast(139;0.0602)		all cancers(112;0.0071)|Epithelial(112;0.0398)|OV - Ovarian serous cystadenocarcinoma(117;0.151)|GBM - Glioblastoma multiforme(144;0.222)|Lung(94;0.241)		AACAAATTTACGTTGGTCGAG	0.408																																					p.Y262Y		Atlas-SNP	.											.	PABPC3	129	.	0			c.C786T						PASS	.																																			SO:0001819	synonymous_variant	5042	exon1			AATTTACGTTGGT	AF132026	CCDS9311.1	13q12-q13	2013-02-12	2001-11-28		ENSG00000151846	ENSG00000151846		"""RNA binding motif (RRM) containing"""	8556	protein-coding gene	gene with protein product	"""testis PABP"""	604680	"""poly(A)-binding protein, cytoplasmic 3"""	PABPL3		8432538, 10543404	Standard	NM_030979		Approved	PABP3, tPABP	uc001upy.3	Q9H361	OTTHUMG00000016601	ENST00000281589.3:c.786C>T	chr13.hg19:g.25671122C>T		134.0	0.0	.		196.0	12.0	.	NM_030979	Q8NHV0|Q9H086	Silent	SNP	ENST00000281589.3	hg19	CCDS9311.1																																																																																			.	C|0.500;T|0.500	0.500	weak		0.408	PABPC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044220.2	NM_030979	
MYH7	4625	hgsc.bcm.edu	37	14	23886422	23886422	+	Missense_Mutation	SNP	C	C	T			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr14:23886422C>T	ENST00000355349.3	-	32	4621	c.4459G>A	c.(4459-4461)Gcc>Acc	p.A1487T	CTD-2201G16.1_ENST00000557368.1_RNA|MIR208B_ENST00000401172.1_RNA	NM_000257.2	NP_000248.2	P12883	MYH7_HUMAN	myosin, heavy chain 7, cardiac muscle, beta	1487					adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)			NS(3)|breast(4)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(19)|lung(57)|ovary(5)|prostate(9)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	137	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00725)		TCCTCATAGGCGTTCTTGAGT	0.597																																					p.A1487T		Atlas-SNP	.											.	MYH7	349	.	0			c.G4459A						PASS	.						118.0	124.0	122.0					14																	23886422		2203	4300	6503	SO:0001583	missense	4625	exon32			CATAGGCGTTCTT	M58018	CCDS9601.1	14q11.2-q13	2014-09-17	2006-09-29		ENSG00000092054	ENSG00000092054		"""Myosins / Myosin superfamily : Class II"""	7577	protein-coding gene	gene with protein product		160760	"""myopathy, distal 1"", ""myosin, heavy polypeptide 7, cardiac muscle, beta"""	CMH1, MPD1		2494889, 8483915, 15322983	Standard	XM_005267696		Approved	CMD1S	uc001wjx.3	P12883	OTTHUMG00000028755	ENST00000355349.3:c.4459G>A	chr14.hg19:g.23886422C>T	ENSP00000347507:p.Ala1487Thr	97.0	0.0	.		83.0	34.0	.	NM_000257	A2TDB6|B6D424|Q14836|Q14837|Q14904|Q16579|Q2M1Y6|Q92679|Q9H1D5|Q9UDA2|Q9UMM8	Missense_Mutation	SNP	ENST00000355349.3	hg19	CCDS9601.1	.	.	.	.	.	.	.	.	.	.	C	23.1	4.374149	0.82573	.	.	ENSG00000092054	ENST00000355349;ENST00000544444	T	0.78364	-1.17	5.27	5.27	0.74061	Myosin tail (1);	.	.	.	.	D	0.84000	0.5376	M	0.81942	2.565	0.39473	D	0.967754	P	0.43662	0.814	P	0.50440	0.641	D	0.86199	0.1617	9	0.59425	D	0.04	.	13.987	0.64341	0.1513:0.8487:0.0:0.0	.	1487	P12883	MYH7_HUMAN	T	1487;1492	ENSP00000347507:A1487T	ENSP00000347507:A1487T	A	-	1	0	MYH7	22956262	0.987000	0.35691	0.998000	0.56505	0.982000	0.71751	2.764000	0.47613	2.746000	0.94184	0.591000	0.81541	GCC	.	.	.	none		0.597	MYH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071798.3	NM_000257	
ABHD12B	145447	hgsc.bcm.edu	37	14	51368558	51368558	+	Silent	SNP	C	C	T			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr14:51368558C>T	ENST00000337334.2	+	10	807	c.792C>T	c.(790-792)aaC>aaT	p.N264N	ABHD12B_ENST00000353130.1_Silent_p.N187N|ABHD12B_ENST00000395752.1_Silent_p.N157N|PYGL_ENST00000532462.1_Intron	NM_001206673.1	NP_001193602.1	Q7Z5M8	AB12B_HUMAN	abhydrolase domain containing 12B	264							hydrolase activity (GO:0016787)			breast(2)|endometrium(1)|large_intestine(2)|lung(5)	10	all_epithelial(31;0.00481)|Breast(41;0.148)					TTTACCGGAACATTCCAGGAT	0.308																																					p.N264N		Atlas-SNP	.											.	ABHD12B	53	.	0			c.C792T						PASS	.						58.0	54.0	55.0					14																	51368558		2202	4297	6499	SO:0001819	synonymous_variant	145447	exon10			CCGGAACATTCCA	BG698443	CCDS9702.1, CCDS55916.1	14q21.3	2009-10-09	2007-04-03	2007-04-03	ENSG00000131969	ENSG00000131969		"""Abhydrolase domain containing"""	19837	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 29"""	C14orf29			Standard	NM_181814		Approved	BEM46L3	uc001wys.3	Q7Z5M8	OTTHUMG00000140286	ENST00000337334.2:c.792C>T	chr14.hg19:g.51368558C>T		108.0	0.0	.		68.0	45.0	.	NM_001206673	Q3KNR9|Q3KNS0|Q7Z5M6|Q7Z5M7|Q8N4D2	Silent	SNP	ENST00000337334.2	hg19	CCDS55916.1																																																																																			.	.	.	none		0.308	ABHD12B-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000411030.1		
MPP5	64398	hgsc.bcm.edu	37	14	67787027	67787027	+	Silent	SNP	T	T	C			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr14:67787027T>C	ENST00000261681.4	+	12	2111	c.1450T>C	c.(1450-1452)Ttg>Ctg	p.L484L	MPP5_ENST00000555925.1_Silent_p.L450L|ATP6V1D_ENST00000553974.1_Intron	NM_022474.3	NP_071919.2	Q8N3R9	MPP5_HUMAN	membrane protein, palmitoylated 5 (MAGUK p55 subfamily member 5)	484	Guanylate kinase-like. {ECO:0000255|PROSITE-ProRule:PRU00100}.				cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|establishment of protein localization to plasma membrane (GO:0090002)|morphogenesis of an epithelial sheet (GO:0002011)|myelin assembly (GO:0032288)|peripheral nervous system myelin maintenance (GO:0032287)|protein localization to myelin sheath abaxonal region (GO:0035750)|tight junction assembly (GO:0070830)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|lateral loop (GO:0043219)|myelin sheath adaxonal region (GO:0035749)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|Schmidt-Lanterman incisure (GO:0043220)|tight junction (GO:0005923)	protein domain specific binding (GO:0019904)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(8)|ovary(1)|skin(1)	18				all cancers(60;0.000388)|OV - Ovarian serous cystadenocarcinoma(108;0.00762)|BRCA - Breast invasive adenocarcinoma(234;0.0106)		ACCTATCATCTTGATTGGTCC	0.408																																					p.L484L		Atlas-SNP	.											.	MPP5	46	.	0			c.T1450C						PASS	.						111.0	104.0	107.0					14																	67787027		2203	4300	6503	SO:0001819	synonymous_variant	64398	exon12			ATCATCTTGATTG	AK022677	CCDS9779.1, CCDS58325.1	14q23.3	2008-08-11				ENSG00000072415			18669	protein-coding gene	gene with protein product	"""stardust"""	606958				11927608	Standard	NM_022474		Approved	PALS1, FLJ12615	uc001xjc.4	Q8N3R9		ENST00000261681.4:c.1450T>C	chr14.hg19:g.67787027T>C		47.0	0.0	.		40.0	30.0	.	NM_022474	A1L380|Q7Z631|Q86T98|Q8N7I5|Q9H9Q0	Silent	SNP	ENST00000261681.4	hg19	CCDS9779.1																																																																																			.	.	.	none		0.408	MPP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412498.1	NM_022474	
YLPM1	56252	hgsc.bcm.edu	37	14	75248111	75248111	+	Nonsense_Mutation	SNP	G	G	A			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr14:75248111G>A	ENST00000552421.1	+	4	1489	c.1365G>A	c.(1363-1365)tgG>tgA	p.W455*	YLPM1_ENST00000238571.3_Intron|YLPM1_ENST00000325680.7_Nonsense_Mutation_p.W455*			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)		ACCAAGAATGGGAGCGAGAGT	0.423																																					p.W455X		Atlas-SNP	.											.	YLPM1	298	.	0			c.G1365A						PASS	.						40.0	37.0	38.0					14																	75248111		1917	4135	6052	SO:0001587	stop_gained	56252	exon4			AGAATGGGAGCGA	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.1365G>A	chr14.hg19:g.75248111G>A	ENSP00000447921:p.Trp455*	197.0	0.0	.		166.0	124.0	.	NM_019589	P49752|Q96I64|Q9P1V7	Nonsense_Mutation	SNP	ENST00000552421.1	hg19		.	.	.	.	.	.	.	.	.	.	G	35	5.452918	0.96223	.	.	ENSG00000119596	ENST00000552421;ENST00000325680;ENST00000423680	.	.	.	5.81	5.81	0.92471	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	20.0557	0.97650	0.0:0.0:1.0:0.0	.	.	.	.	X	455;455;168	.	ENSP00000324463:W455X	W	+	3	0	YLPM1	74317864	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.471000	0.97696	2.732000	0.93576	0.591000	0.81541	TGG	.	.	.	none		0.423	YLPM1-008	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000404450.1	NM_019589	
CATSPERB	79820	hgsc.bcm.edu	37	14	92195753	92195753	+	Missense_Mutation	SNP	T	T	C			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr14:92195753T>C	ENST00000256343.3	-	2	227	c.71A>G	c.(70-72)tAt>tGt	p.Y24C		NM_024764.2	NP_079040.2	Q9H7T0	CTSRB_HUMAN	catsper channel auxiliary subunit beta	24					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)				ACCTTTATTATATACTATTCC	0.279																																					p.Y24C		Atlas-SNP	.											.	CATSPERB	114	.	0			c.A71G						PASS	.						32.0	36.0	35.0					14																	92195753		2194	4276	6470	SO:0001583	missense	79820	exon2			TTATTATATACTA	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.71A>G	chr14.hg19:g.92195753T>C	ENSP00000256343:p.Tyr24Cys	173.0	0.0	.		152.0	68.0	.	NM_024764	A0AV51	Missense_Mutation	SNP	ENST00000256343.3	hg19	CCDS32142.1	.	.	.	.	.	.	.	.	.	.	T	13.15	2.150476	0.37923	.	.	ENSG00000133962	ENST00000256343;ENST00000553329;ENST00000554560;ENST00000556661;ENST00000553676	T	0.56941	0.43	5.22	4.05	0.47172	.	0.528936	0.15705	N	0.248736	T	0.58935	0.2157	L	0.47716	1.5	0.26423	N	0.976068	D	0.65815	0.995	P	0.58873	0.847	T	0.50550	-0.8815	10	0.66056	D	0.02	-4.0069	8.4676	0.32966	0.1734:0.0:0.0:0.8266	.	24	Q9H7T0	CTSRB_HUMAN	C	24	ENSP00000256343:Y24C	ENSP00000256343:Y24C	Y	-	2	0	CATSPERB	91265506	0.928000	0.31464	0.216000	0.23742	0.648000	0.38561	2.017000	0.40981	0.893000	0.36288	0.397000	0.26171	TAT	.	.	.	none		0.279	CATSPERB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411769.1	NM_024764	
CASC5	57082	hgsc.bcm.edu	37	15	40913801	40913801	+	Nonsense_Mutation	SNP	A	A	T			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr15:40913801A>T	ENST00000346991.5	+	11	1807	c.1417A>T	c.(1417-1419)Aga>Tga	p.R473*	CASC5_ENST00000399668.2_Nonsense_Mutation_p.R447*|CASC5_ENST00000527044.1_3'UTR			Q8NG31	CASC5_HUMAN	cancer susceptibility candidate 5	473	Interaction with BUB1 and BUB1B.				acrosome assembly (GO:0001675)|attachment of spindle microtubules to kinetochore (GO:0008608)|CENP-A containing nucleosome assembly (GO:0034080)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of phosphatase activity (GO:0010923)|nucleosome assembly (GO:0006334)|protein localization to kinetochore (GO:0034501)|spindle assembly checkpoint (GO:0071173)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				NS(1)|breast(7)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(13)|lung(16)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	57		all_cancers(109;2.03e-18)|all_epithelial(112;4.26e-15)|Lung NSC(122;1.12e-10)|all_lung(180;2.59e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;4.99e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0861)|COAD - Colon adenocarcinoma(120;0.211)		CTCAAATATGAGAGAGGAGAA	0.328																																					p.R473X		Atlas-SNP	.											.	CASC5	269	.	0			c.A1417T						PASS	.						67.0	65.0	65.0					15																	40913801		1822	4080	5902	SO:0001587	stop_gained	57082	exon11			AATATGAGAGAGG	AF173994	CCDS42023.1, CCDS42024.1	15q14	2013-07-03			ENSG00000137812	ENSG00000137812		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	24054	protein-coding gene	gene with protein product	"""cancer/testis antigen 29"", ""kinetochore null 1 homolog (C. elegans)"", ""blinkin, bub-linking kinetochore protein"", ""protein phosphatase 1, regulatory subunit 55"""	609173				10980622, 10780384, 18045986	Standard	NM_170589		Approved	D40, AF15Q14, CT29, hKNL-1, KNL1, hSpc105, PPP1R55, Spc7	uc010bbt.1	Q8NG31	OTTHUMG00000166532	ENST00000346991.5:c.1417A>T	chr15.hg19:g.40913801A>T	ENSP00000335463:p.Arg473*	184.0	0.0	.		146.0	57.0	.	NM_170589	Q8NHE1|Q8WXA6|Q9HCK2|Q9NR92	Nonsense_Mutation	SNP	ENST00000346991.5	hg19	CCDS42023.1	.	.	.	.	.	.	.	.	.	.	A	38	7.205877	0.98136	.	.	ENSG00000137812	ENST00000346991;ENST00000260369;ENST00000399668	.	.	.	5.94	2.3	0.28687	.	1.023320	0.07757	N	0.949536	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	5.4785	0.16710	0.5262:0.2673:0.2064:0.0	.	.	.	.	X	473;447;447	.	ENSP00000260369:R447X	R	+	1	2	CASC5	38701093	0.001000	0.12720	0.969000	0.41365	0.966000	0.64601	0.013000	0.13310	0.490000	0.27771	0.455000	0.32223	AGA	.	.	.	none		0.328	CASC5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390224.2	NM_144508	
RNF111	54778	hgsc.bcm.edu	37	15	59344604	59344604	+	Missense_Mutation	SNP	G	G	T	rs137923008	byFrequency	TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr15:59344604G>T	ENST00000557998.1	+	3	1268	c.981G>T	c.(979-981)gaG>gaT	p.E327D	RNF111_ENST00000559209.1_Missense_Mutation_p.E327D|RNF111_ENST00000434298.1_Missense_Mutation_p.E327D|RNF111_ENST00000348370.4_Missense_Mutation_p.E327D|RNF111_ENST00000561186.1_Missense_Mutation_p.E327D	NM_001270530.1	NP_001257459.1	Q6ZNA4	RN111_HUMAN	ring finger protein 111	327	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)		GTGAAGTGGAGATTGTAACAG	0.333																																					p.E327D	NSCLC(72;983 1365 10746 34387 47081)	Atlas-SNP	.											.	RNF111	179	.	0			c.G981T						PASS	.						119.0	108.0	112.0					15																	59344604		2192	4291	6483	SO:0001583	missense	54778	exon3			AGTGGAGATTGTA	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.981G>T	chr15.hg19:g.59344604G>T	ENSP00000452732:p.Glu327Asp	74.0	0.0	.		61.0	23.0	.	NM_017610	C9JUS4|H0YN55|Q6P9A4|Q6ZMU2|Q7L428|Q7Z346|Q8N1P9|Q8WUA3|Q9NSR1	Missense_Mutation	SNP	ENST00000557998.1	hg19	CCDS58366.1	.	.	.	.	.	.	.	.	.	.	G	12.55	1.972394	0.34848	.	.	ENSG00000157450	ENST00000348370;ENST00000434298	T;T	0.39997	1.05;1.06	5.6	1.64	0.23874	.	0.000000	0.85682	D	0.000000	T	0.36082	0.0954	L	0.59436	1.845	0.51012	D	0.9999	B;B;B	0.27732	0.187;0.117;0.187	B;B;B	0.29267	0.1;0.046;0.1	T	0.15607	-1.0431	10	0.87932	D	0	-5.7934	6.825	0.23878	0.1993:0.0:0.6759:0.1248	.	327;327;327	Q6ZNA4-3;Q6ZNA4;Q6ZNA4-2	.;RN111_HUMAN;.	D	327	ENSP00000288199:E327D;ENSP00000393641:E327D	ENSP00000288199:E327D	E	+	3	2	RNF111	57131896	1.000000	0.71417	0.997000	0.53966	0.284000	0.27059	4.092000	0.57707	0.051000	0.15978	-0.241000	0.12123	GAG	.	G|0.998;A|0.002	.	alt		0.333	RNF111-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000416012.1	NM_017610	
VPS13C	54832	hgsc.bcm.edu	37	15	62155703	62155703	+	Nonsense_Mutation	SNP	C	C	A			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr15:62155703C>A	ENST00000261517.5	-	82	10961	c.10888G>T	c.(10888-10890)Gag>Tag	p.E3630*	VPS13C_ENST00000249837.3_Nonsense_Mutation_p.E3587*	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						CGGTAAGTCTCTCCTTCCAAC	0.353																																					p.E3630X		Atlas-SNP	.											.	VPS13C	506	.	0			c.G10888T						PASS	.						156.0	136.0	143.0					15																	62155703		2203	4300	6503	SO:0001587	stop_gained	54832	exon82			AAGTCTCTCCTTC	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.10888G>T	chr15.hg19:g.62155703C>A	ENSP00000261517:p.Glu3630*	151.0	0.0	.		115.0	41.0	.	NM_020821		Nonsense_Mutation	SNP	ENST00000261517.5	hg19	CCDS32257.1	.	.	.	.	.	.	.	.	.	.	C	53	21.012209	0.99936	.	.	ENSG00000129003	ENST00000249837;ENST00000261517	.	.	.	5.68	5.68	0.88126	.	0.055754	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.56958	D	0.05	.	20.1554	0.98111	0.0:1.0:0.0:0.0	.	.	.	.	X	3587;3630	.	ENSP00000249837:E3587X	E	-	1	0	VPS13C	59942995	1.000000	0.71417	0.981000	0.43875	0.992000	0.81027	6.594000	0.74104	2.838000	0.97847	0.591000	0.81541	GAG	.	.	.	none		0.353	VPS13C-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415997.1	NM_017684	
PIAS1	8554	hgsc.bcm.edu	37	15	68434644	68434644	+	Missense_Mutation	SNP	A	A	G			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr15:68434644A>G	ENST00000249636.6	+	4	719	c.571A>G	c.(571-573)Aaa>Gaa	p.K191E	PIAS1_ENST00000545237.1_Missense_Mutation_p.K193E	NM_016166.1	NP_057250.1	O75925	PIAS1_HUMAN	protein inhibitor of activated STAT, 1	191	PINIT. {ECO:0000255|PROSITE- ProRule:PRU00799}.				androgen receptor signaling pathway (GO:0030521)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|JAK-STAT cascade (GO:0007259)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein sumoylation (GO:0033235)|positive regulation of smooth muscle cell differentiation (GO:0051152)|positive regulation of transcription, DNA-templated (GO:0045893)|protein sumoylation (GO:0016925)|protein-DNA complex assembly (GO:0065004)|regulation of cell proliferation (GO:0042127)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	androgen receptor binding (GO:0050681)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|SUMO ligase activity (GO:0019789)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			breast(2)|endometrium(5)|kidney(3)|large_intestine(5)|lung(8)|ovary(1)	24						TTCTGGGACCAAATGTGACTT	0.353																																					p.K191E		Atlas-SNP	.											.	PIAS1	42	.	0			c.A571G						PASS	.						55.0	51.0	53.0					15																	68434644		1818	4073	5891	SO:0001583	missense	8554	exon4			GGGACCAAATGTG	AF077951	CCDS45290.1	15q	2011-10-11	2002-04-19	2002-04-19		ENSG00000033800		"""Zinc fingers, MIZ-type"""	2752	protein-coding gene	gene with protein product	"""zinc finger, MIZ-type containing 3"""	603566	"""DEAD/H (Asp-Glu-Ala-Asp/His) box binding protein 1"""	DDXBP1		9724754, 9177271	Standard	XM_005254735		Approved	GBP, GU/RH-II, ZMIZ3	uc002aqz.3	O75925		ENST00000249636.6:c.571A>G	chr15.hg19:g.68434644A>G	ENSP00000249636:p.Lys191Glu	131.0	0.0	.		150.0	55.0	.	NM_016166	B2RB67|B3KSY9|C5J4B4|Q147X4|Q99751|Q9UN02	Missense_Mutation	SNP	ENST00000249636.6	hg19	CCDS45290.1	.	.	.	.	.	.	.	.	.	.	A	27.7	4.858688	0.91433	.	.	ENSG00000033800	ENST00000249636;ENST00000545237	T;T	0.36340	1.26;1.26	5.39	5.39	0.77823	PINIT domain (1);	0.000000	0.85682	D	0.000000	T	0.58750	0.2144	M	0.73217	2.22	0.80722	D	1	D;B	0.54047	0.964;0.107	D;P	0.65773	0.938;0.475	T	0.62793	-0.6779	10	0.72032	D	0.01	-13.0322	15.4074	0.74890	1.0:0.0:0.0:0.0	.	191;191	C5J4B4;O75925	.;PIAS1_HUMAN	E	191;193	ENSP00000249636:K191E;ENSP00000438574:K193E	ENSP00000249636:K191E	K	+	1	0	PIAS1	66221698	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.883000	0.92426	2.042000	0.60477	0.477000	0.44152	AAA	.	.	.	none		0.353	PIAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419642.2		
IL16	3603	hgsc.bcm.edu	37	15	81517938	81517938	+	Silent	SNP	A	A	G			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr15:81517938A>G	ENST00000302987.4	+	1	198	c.198A>G	c.(196-198)acA>acG	p.T66T	IL16_ENST00000394660.2_Silent_p.T66T			Q14005	IL16_HUMAN	interleukin 16	66					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						TGGCAGACACATCGGAGGCTG	0.552																																					p.T66T		Atlas-SNP	.											.	IL16	254	.	0			c.A198G						PASS	.						65.0	65.0	65.0					15																	81517938		2006	4190	6196	SO:0001819	synonymous_variant	3603	exon2			AGACACATCGGAG	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.198A>G	chr15.hg19:g.81517938A>G		127.0	0.0	.		116.0	29.0	.	NM_001172128	A6NM20|A8MU65|B5TY35|B9EGR6|H3BVH5|Q16435|Q6VVE6|Q6ZMQ7|Q9UP18	Silent	SNP	ENST00000302987.4	hg19	CCDS42069.1																																																																																			.	.	.	none		0.552	IL16-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000303952.1	NM_172217	
FANCI	55215	hgsc.bcm.edu	37	15	89856164	89856164	+	Silent	SNP	A	A	T			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr15:89856164A>T	ENST00000310775.7	+	35	3767	c.3681A>T	c.(3679-3681)ggA>ggT	p.G1227G	FANCI_ENST00000566615.1_3'UTR|FANCI_ENST00000300027.8_Silent_p.G1167G	NM_001113378.1	NP_001106849.1	Q9NVI1	FANCI_HUMAN	Fanconi anemia, complementation group I	1227					cell cycle (GO:0007049)|DNA repair (GO:0006281)|positive regulation of protein ubiquitination (GO:0031398)	membrane (GO:0016020)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|DNA polymerase binding (GO:0070182)			breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	Lung NSC(78;0.0472)|all_lung(78;0.089)					ACTATACGGGAGAGAAAAAGG	0.423								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.G1227G		Atlas-SNP	.											.	FANCI	129	.	0			c.A3681T						PASS	.						77.0	76.0	76.0					15																	89856164		2200	4299	6499	SO:0001819	synonymous_variant	55215	exon35	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	TACGGGAGAGAAA	BC004277	CCDS10349.2, CCDS45346.1	15q26.1	2014-09-17	2007-05-03	2007-05-03	ENSG00000140525	ENSG00000140525		"""Fanconi anemia, complementation groups"""	25568	protein-coding gene	gene with protein product		611360	"""KIAA1794"""	KIAA1794		14630800, 17460694, 17412408	Standard	NM_001113378		Approved	FLJ10719	uc010bnp.1	Q9NVI1	OTTHUMG00000132993	ENST00000310775.7:c.3681A>T	chr15.hg19:g.89856164A>T		61.0	0.0	.		51.0	21.0	.	NM_001113378	A4ZVE4|A5YMH4|A6NJZ0|Q96JN1|Q96ST0|Q9BT96	Silent	SNP	ENST00000310775.7	hg19	CCDS45346.1																																																																																			.	.	.	none		0.423	FANCI-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421140.1	NM_018193	
FAHD1	81889	hgsc.bcm.edu	37	16	1877593	1877593	+	Silent	SNP	G	G	T			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr16:1877593G>T	ENST00000427358.2	+	1	369	c.363G>T	c.(361-363)ctG>ctT	p.L121L	HAGH_ENST00000455446.2_5'Flank|FAHD1_ENST00000382666.4_Silent_p.L121L|HAGH_ENST00000397353.2_5'Flank|HAGH_ENST00000566709.1_5'Flank|HAGH_ENST00000397356.3_5'Flank|FAHD1_ENST00000382668.4_Silent_p.L121L	NM_031208.3	NP_112485.1	Q6P587	FAHD1_HUMAN	fumarylacetoacetate hydrolase domain containing 1	121						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						CCTGGACTCTGGCGAAGAGCT	0.642																																					p.L121L		Atlas-SNP	.											.	FAHD1	18	.	0			c.G363T						PASS	.						38.0	34.0	36.0					16																	1877593		2199	4300	6499	SO:0001819	synonymous_variant	81889	exon1			GACTCTGGCGAAG	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.363G>T	chr16.hg19:g.1877593G>T		114.0	0.0	.		273.0	39.0	.	NM_031208	B1AK40|B1AK41|Q6FIC7|Q96RY1|Q9H0N6	Silent	SNP	ENST00000427358.2	hg19	CCDS10448.1																																																																																			.	.	.	none		0.642	FAHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250550.2	NM_001018104	
CMTM4	146223	hgsc.bcm.edu	37	16	66670440	66670440	+	Silent	SNP	T	T	A			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr16:66670440T>A	ENST00000330687.4	-	2	412	c.231A>T	c.(229-231)gcA>gcT	p.A77A	CMTM4_ENST00000563952.1_Silent_p.A48A|CMTM4_ENST00000394106.2_Silent_p.A77A	NM_178818.2|NM_181521.2	NP_848933.1|NP_852662.1	Q8IZR5	CKLF4_HUMAN	CKLF-like MARVEL transmembrane domain containing 4	77	MARVEL. {ECO:0000255|PROSITE- ProRule:PRU00581}.				chemotaxis (GO:0006935)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)				cervix(1)|kidney(1)|large_intestine(3)|lung(1)|ovary(1)|pancreas(1)|stomach(1)	9		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0811)|Epithelial(162;0.214)		ACGGGGAGCATGCCATGATGG	0.443																																					p.A77A		Atlas-SNP	.											.	CMTM4	19	.	0			c.A231T						PASS	.						117.0	103.0	108.0					16																	66670440		2201	4300	6501	SO:0001819	synonymous_variant	146223	exon2			GGAGCATGCCATG	AF479814	CCDS10817.1, CCDS42170.1	16q22.1-q22.3	2008-02-05	2005-11-08	2005-11-08	ENSG00000183723	ENSG00000183723			19175	protein-coding gene	gene with protein product		607887	"""chemokine-like factor super family 4"", ""chemokine-like factor superfamily 4"""	CKLFSF4		12782130	Standard	NM_178818		Approved		uc002epz.3	Q8IZR5	OTTHUMG00000137500	ENST00000330687.4:c.231A>T	chr16.hg19:g.66670440T>A		120.0	0.0	.		95.0	5.0	.	NM_178818	Q52M40|Q8IZR4|Q8IZV1	Silent	SNP	ENST00000330687.4	hg19	CCDS10817.1																																																																																			.	.	.	none		0.443	CMTM4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268807.1		
PRDM7	11105	hgsc.bcm.edu	37	16	90127007	90127007	+	Missense_Mutation	SNP	A	A	T			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr16:90127007A>T	ENST00000449207.2	-	9	994	c.975T>A	c.(973-975)gaT>gaA	p.D325E	PRDM7_ENST00000407825.1_Intron|PRDM7_ENST00000325921.6_Intron	NM_001098173.1	NP_001091643.1	Q9NQW5	PRDM7_HUMAN	PR domain containing 7	325	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				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)		TCTGCTCTTCATCATCCCGGG	0.547																																					p.D325E		Atlas-SNP	.											.	PRDM7	53	.	0			c.T975A						PASS	.						78.0	77.0	77.0					16																	90127007		1938	4120	6058	SO:0001583	missense	11105	exon9			CTCTTCATCATCC	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.975T>A	chr16.hg19:g.90127007A>T	ENSP00000396732:p.Asp325Glu	343.0	0.0	.		210.0	119.0	.	NM_001098173	A4Q9G8|Q08EM4|Q9NQW4	Missense_Mutation	SNP	ENST00000449207.2	hg19	CCDS45557.1	.	.	.	.	.	.	.	.	.	.	.	0.006	-2.026388	0.00414	.	.	ENSG00000126856	ENST00000449207	T	0.41065	1.01	2.23	-4.45	0.03546	SET domain (2);	.	.	.	.	T	0.10594	0.0259	N	0.01297	-0.9	0.09310	N	0.999998	B	0.06786	0.001	B	0.06405	0.002	T	0.17137	-1.0379	8	.	.	.	-0.9636	1.139	0.01761	0.2061:0.3427:0.2807:0.1705	.	325	Q9NQW5	PRDM7_HUMAN	E	325	ENSP00000396732:D325E	.	D	-	3	2	PRDM7	88654508	0.000000	0.05858	0.092000	0.20876	0.342000	0.28953	-2.198000	0.01239	-1.546000	0.01717	0.397000	0.26171	GAT	.	.	.	none		0.547	PRDM7-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420560.1		
SHPK	23729	hgsc.bcm.edu	37	17	3514081	3514081	+	Silent	SNP	G	G	T			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr17:3514081G>T	ENST00000225519.3	-	7	1312	c.1210C>A	c.(1210-1212)Cga>Aga	p.R404R	SHPK_ENST00000572705.1_5'Flank	NM_013276.2	NP_037408	Q9UHJ6	SHPK_HUMAN	sedoheptulokinase	404					carbohydrate metabolic process (GO:0005975)|cellular response to interleukin-13 (GO:0035963)|cellular response to interleukin-4 (GO:0071353)|cellular response to lipopolysaccharide (GO:0071222)|pentose-phosphate shunt, non-oxidative branch (GO:0009052)|phosphorylation (GO:0016310)|regulation of inflammatory response (GO:0050727)|regulation of macrophage activation (GO:0043030)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|sedoheptulokinase activity (GO:0050277)			breast(1)|endometrium(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16				COAD - Colon adenocarcinoma(5;0.0828)		ACAATGCCTCGGCACAGAGCC	0.642																																					p.R404R		Atlas-SNP	.											.	SHPK	34	.	0			c.C1210A						PASS	.						110.0	111.0	111.0					17																	3514081		2203	4300	6503	SO:0001819	synonymous_variant	23729	exon7			TGCCTCGGCACAG	AF163573	CCDS11030.1	17p13	2008-02-08	2008-02-08	2008-02-08	ENSG00000197417	ENSG00000197417	2.7.1.14		1492	protein-coding gene	gene with protein product		605060	"""carbohydrate kinase-like"""	CARKL		10673275, 18186520	Standard	NM_013276		Approved	SHK	uc002fvz.1	Q9UHJ6	OTTHUMG00000090694	ENST00000225519.3:c.1210C>A	chr17.hg19:g.3514081G>T		126.0	0.0	.		169.0	99.0	.	NM_013276	B2R640|Q8WUH3	Silent	SNP	ENST00000225519.3	hg19	CCDS11030.1																																																																																			.	.	.	none		0.642	SHPK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207378.2		
P2RX1	5023	hgsc.bcm.edu	37	17	3808622	3808622	+	Missense_Mutation	SNP	G	G	C			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr17:3808622G>C	ENST00000225538.3	-	2	451	c.177C>G	c.(175-177)agC>agG	p.S59R		NM_002558.2	NP_002549.1	P51575	P2RX1_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 1	59					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ceramide biosynthetic process (GO:0046513)|insemination (GO:0007320)|ion transport (GO:0006811)|neuronal action potential (GO:0019228)|platelet activation (GO:0030168)|positive regulation of ion transport (GO:0043270)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|purinergic nucleotide receptor signaling pathway (GO:0035590)|regulation of blood pressure (GO:0008217)|regulation of calcium ion transport (GO:0051924)|regulation of vascular smooth muscle contraction (GO:0003056)|response to ATP (GO:0033198)|serotonin secretion by platelet (GO:0002554)|signal transduction (GO:0007165)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)|vasoconstriction (GO:0042310)	external side of cell outer membrane (GO:0031240)|integral component of nuclear inner membrane (GO:0005639)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)|drug binding (GO:0008144)|extracellular ATP-gated cation channel activity (GO:0004931)|purinergic nucleotide receptor activity (GO:0001614)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(2)	13				LUAD - Lung adenocarcinoma(2;1.9e-05)|Lung(3;0.0173)		TGATGAGGCCGCTCGAGGTCT	0.627																																					p.S59R		Atlas-SNP	.											.	P2RX1	38	.	0			c.C177G						PASS	.						56.0	60.0	59.0					17																	3808622		2203	4300	6503	SO:0001583	missense	5023	exon2			GAGGCCGCTCGAG	X83688	CCDS11040.1	17p13.3	2012-01-17				ENSG00000108405		"""Purinergic receptors"", ""Ligand-gated ion channels / Purinergic receptors, ionotropic"""	8533	protein-coding gene	gene with protein product		600845				8834001	Standard	NM_002558		Approved	P2X1	uc002fww.3	P51575		ENST00000225538.3:c.177C>G	chr17.hg19:g.3808622G>C	ENSP00000225538:p.Ser59Arg	99.0	0.0	.		117.0	31.0	.	NM_002558	Q9UK84	Missense_Mutation	SNP	ENST00000225538.3	hg19	CCDS11040.1	.	.	.	.	.	.	.	.	.	.	G	19.16	3.773763	0.69992	.	.	ENSG00000108405	ENST00000225538	T	0.04551	3.6	5.84	-11.4	0.00090	.	0.368613	0.32671	N	0.005781	T	0.05273	0.0140	L	0.43152	1.355	0.09310	N	1	P	0.37122	0.583	P	0.46299	0.511	T	0.17167	-1.0378	10	0.87932	D	0	-16.9741	10.8476	0.46751	0.5956:0.089:0.3154:0.0	.	59	P51575	P2RX1_HUMAN	R	59	ENSP00000225538:S59R	ENSP00000225538:S59R	S	-	3	2	P2RX1	3755371	0.011000	0.17503	0.000000	0.03702	0.860000	0.49131	-0.937000	0.03942	-2.012000	0.00950	-0.291000	0.09656	AGC	.	.	.	none		0.627	P2RX1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438391.1	NM_002558	
MYO15A	51168	hgsc.bcm.edu	37	17	18023902	18023902	+	Silent	SNP	G	G	C			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr17:18023902G>C	ENST00000205890.5	+	2	2126	c.1788G>C	c.(1786-1788)cgG>cgC	p.R596R		NM_016239.3	NP_057323.3	Q9UKN7	MYO15_HUMAN	myosin XVA	596					inner ear morphogenesis (GO:0042472)|locomotory behavior (GO:0007626)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|stereocilium (GO:0032420)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(5)|central_nervous_system(2)|endometrium(17)|kidney(3)|large_intestine(16)|lung(27)|ovary(3)|pancreas(1)|prostate(6)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	99	all_neural(463;0.228)					AGAAGGCCCGGGCGGGCGGCC	0.697																																					p.R596R		Atlas-SNP	.											.	MYO15A	268	.	0			c.G1788C						PASS	.						5.0	6.0	6.0					17																	18023902		1638	3647	5285	SO:0001819	synonymous_variant	51168	exon2			GGCCCGGGCGGGC	AF144094	CCDS42271.1	17p11.2	2011-09-27			ENSG00000091536	ENSG00000091536		"""Myosins / Myosin superfamily : Class XV"""	7594	protein-coding gene	gene with protein product		602666		DFNB3, MYO15		9603736	Standard	NM_016239		Approved		uc021trl.1	Q9UKN7	OTTHUMG00000059390	ENST00000205890.5:c.1788G>C	chr17.hg19:g.18023902G>C		12.0	0.0	.		88.0	4.0	.	NM_016239	B4DFC7	Silent	SNP	ENST00000205890.5	hg19	CCDS42271.1																																																																																			.	.	.	none		0.697	MYO15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132048.1	NM_016239	
TP53I13	90313	hgsc.bcm.edu	37	17	27899239	27899239	+	Missense_Mutation	SNP	C	C	G			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr17:27899239C>G	ENST00000301057.7	+	6	708	c.593C>G	c.(592-594)tCt>tGt	p.S198C	RP11-68I3.2_ENST00000581474.1_RNA|RP11-68I3.4_ENST00000579050.1_RNA	NM_138349.2	NP_612358.3	Q8NBR0	P5I13_HUMAN	tumor protein p53 inducible protein 13	198						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|kidney(1)|lung(1)|urinary_tract(1)	4				READ - Rectum adenocarcinoma(3;0.236)		AGGCAGCCCTCTTCTAGTGGT	0.657																																					p.S198C		Atlas-SNP	.											.	TP53I13	17	.	0			c.C593G						PASS	.						22.0	24.0	24.0					17																	27899239		1986	4140	6126	SO:0001583	missense	90313	exon6			AGCCCTCTTCTAG	AK075341	CCDS42289.1	17q11.2	2006-01-16				ENSG00000167543			25102	protein-coding gene	gene with protein product						14767535	Standard	NM_138349		Approved	DSCP1	uc002hee.3	Q8NBR0		ENST00000301057.7:c.593C>G	chr17.hg19:g.27899239C>G	ENSP00000301057:p.Ser198Cys	32.0	0.0	.		37.0	15.0	.	NM_138349	Q7L5U3	Missense_Mutation	SNP	ENST00000301057.7	hg19	CCDS42289.1	.	.	.	.	.	.	.	.	.	.	C	15.38	2.816310	0.50527	.	.	ENSG00000167543	ENST00000301057	.	.	.	3.94	1.89	0.25635	.	0.645758	0.14735	N	0.301505	T	0.51550	0.1681	M	0.63428	1.95	0.09310	N	1	D	0.69078	0.997	P	0.60345	0.873	T	0.36939	-0.9727	9	0.87932	D	0	-2.2609	5.6779	0.17759	0.0:0.7387:0.0:0.2613	.	198	Q8NBR0	P5I13_HUMAN	C	198	.	ENSP00000301057:S198C	S	+	2	0	TP53I13	24923365	0.000000	0.05858	0.002000	0.10522	0.018000	0.09664	-0.070000	0.11523	0.412000	0.25729	0.462000	0.41574	TCT	.	.	.	none		0.657	TP53I13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447804.2	NM_138349	
ATAD5	79915	hgsc.bcm.edu	37	17	29220519	29220519	+	Nonsense_Mutation	SNP	A	A	T			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr17:29220519A>T	ENST00000321990.4	+	21	5026	c.4648A>T	c.(4648-4650)Aaa>Taa	p.K1550*		NM_024857.3	NP_079133.3	Q96QE3	ATAD5_HUMAN	ATPase family, AAA domain containing 5	1550					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)				TCTTGCTAGGAAACACTCTGA	0.358																																					p.K1550X		Atlas-SNP	.											.	ATAD5	150	.	0			c.A4648T						PASS	.						42.0	50.0	47.0					17																	29220519		2201	4297	6498	SO:0001587	stop_gained	79915	exon21			GCTAGGAAACACT		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.4648A>T	chr17.hg19:g.29220519A>T	ENSP00000313171:p.Lys1550*	70.0	0.0	.		93.0	54.0	.	NM_024857	Q05DH0|Q69YR6|Q9H9I1	Nonsense_Mutation	SNP	ENST00000321990.4	hg19	CCDS11260.1	.	.	.	.	.	.	.	.	.	.	A	42	9.739259	0.99252	.	.	ENSG00000176208	ENST00000321990	.	.	.	6.08	5.01	0.66863	.	0.805371	0.11834	N	0.524975	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	2.577	0.04808	0.6185:0.1452:0.0786:0.1577	.	.	.	.	X	1550	.	ENSP00000313171:K1550X	K	+	1	0	ATAD5	26244645	0.002000	0.14202	0.899000	0.35326	0.203000	0.24098	0.236000	0.17967	2.333000	0.79357	0.482000	0.46254	AAA	.	.	.	none		0.358	ATAD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256206.2	NM_024857	
CEP131	22994	hgsc.bcm.edu	37	17	79166615	79166615	+	Missense_Mutation	SNP	A	A	T			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr17:79166615A>T	ENST00000269392.4	-	19	2606	c.2359T>A	c.(2359-2361)Tgg>Agg	p.W787R	AZI1_ENST00000450824.2_Missense_Mutation_p.W784R|AZI1_ENST00000374782.3_Intron|AZI1_ENST00000575907.1_Intron	NM_014984.2	NP_055799.2	Q9UPN4	CP131_HUMAN		787					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)			tgcagcgcccactgctcctgc	0.736																																					p.W784R		Atlas-SNP	.											.	AZI1	145	.	0			c.T2350A						PASS	.						14.0	17.0	16.0					17																	79166615		2089	4202	6291	SO:0001583	missense	22994	exon19			GCGCCCACTGCTC																												ENST00000269392.4:c.2359T>A	chr17.hg19:g.79166615A>T	ENSP00000269392:p.Trp787Arg	3.0	0.0	.		97.0	4.0	.	NM_014984	A6NHI8|B2RN11|Q96F50	Missense_Mutation	SNP	ENST00000269392.4	hg19		.	.	.	.	.	.	.	.	.	.	A	0.069	-1.206900	0.01568	.	.	ENSG00000141577	ENST00000450824;ENST00000269392	T;T	0.12255	2.7;2.7	3.32	-0.767	0.11016	.	0.637872	0.14277	N	0.329778	T	0.02455	0.0075	N	0.00538	-1.39	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.41805	-0.9488	10	0.09338	T	0.73	-14.4324	3.6545	0.08215	0.1041:0.1576:0.5766:0.1617	.	787;784	Q9UPN4;Q9UPN4-2	AZI1_HUMAN;.	R	784;787	ENSP00000393583:W784R;ENSP00000269392:W787R	ENSP00000269392:W787R	W	-	1	0	AZI1	76781210	0.999000	0.42202	0.980000	0.43619	0.571000	0.35966	0.724000	0.25954	0.039000	0.15632	0.383000	0.25322	TGG	.	.	.	none		0.736	AZI1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000256070.1		
PIEZO2	63895	hgsc.bcm.edu	37	18	10691260	10691260	+	Nonsense_Mutation	SNP	T	T	A			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr18:10691260T>A	ENST00000503781.3	-	44	6972	c.6973A>T	c.(6973-6975)Aag>Tag	p.K2325*	PIEZO2_ENST00000302079.6_Nonsense_Mutation_p.K2325*|PIEZO2_ENST00000285141.4_Nonsense_Mutation_p.K180*|PIEZO2_ENST00000580640.1_Nonsense_Mutation_p.K2350*|PIEZO2_ENST00000538948.1_Nonsense_Mutation_p.K282*	NM_022068.2	NP_071351.2	Q9H5I5	PIEZ2_HUMAN	piezo-type mechanosensitive ion channel component 2	2325					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)										TTGTAGCTCTTGGTGAGGAAG	0.493																																					p.K2325X		Atlas-SNP	.											.	.	.	.	0			c.A6973T						PASS	.						128.0	112.0	118.0					18																	10691260		2203	4300	6503	SO:0001587	stop_gained	63895	exon44			AGCTCTTGGTGAG	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.6973A>T	chr18.hg19:g.10691260T>A	ENSP00000421377:p.Lys2325*	194.0	0.0	.		272.0	76.0	.	NM_022068	B7Z812|M4GPJ9|Q6ZS91|Q8N787|Q8NAR6|Q9H5R4	Nonsense_Mutation	SNP	ENST00000503781.3	hg19		.	.	.	.	.	.	.	.	.	.	T	43	9.868735	0.99284	.	.	ENSG00000154864	ENST00000503781;ENST00000302079;ENST00000538948;ENST00000285141	.	.	.	5.62	5.62	0.85841	.	0.142737	0.47455	D	0.000228	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	16.1189	0.81329	0.0:0.0:0.0:1.0	.	.	.	.	X	282;2325;282;180	.	ENSP00000285141:K180X	K	-	1	0	FAM38B	10681260	1.000000	0.71417	0.998000	0.56505	0.966000	0.64601	8.005000	0.88553	2.263000	0.75096	0.533000	0.62120	AAG	.	.	.	none		0.493	PIEZO2-003	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000442385.4	NM_022068	
RBBP8	5932	hgsc.bcm.edu	37	18	20606136	20606136	+	Missense_Mutation	SNP	C	C	G			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr18:20606136C>G	ENST00000399722.2	+	19	2978	c.2627C>G	c.(2626-2628)cCt>cGt	p.P876R	RBBP8_ENST00000327155.5_Missense_Mutation_p.P876R|RBBP8_ENST00000399725.2_Missense_Mutation_p.L844V|Y_RNA_ENST00000411091.1_RNA|RBBP8_ENST00000360790.5_Missense_Mutation_p.P881R|RBBP8_ENST00000581687.1_Missense_Mutation_p.P54R	NM_203291.1	NP_976036.1	Q99708	COM1_HUMAN	retinoblastoma binding protein 8	876					blastocyst hatching (GO:0001835)|cell cycle checkpoint (GO:0000075)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing involved in repair via single-strand annealing (GO:0010792)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|G1/S transition of mitotic cell cycle (GO:0000082)|G2 DNA damage checkpoint (GO:0031572)|meiotic nuclear division (GO:0007126)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	nucleolus (GO:0005730)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	damaged DNA binding (GO:0003684)|RNA polymerase II repressing transcription factor binding (GO:0001103)|RNA polymerase II transcription corepressor activity (GO:0001106)|single-stranded DNA endodeoxyribonuclease activity (GO:0000014)	p.P876L(1)|p.L844F(1)		central_nervous_system(1)|cervix(2)|endometrium(5)|large_intestine(2)|lung(9)|ovary(3)|prostate(1)|skin(1)	24	all_cancers(21;4.34e-05)|all_epithelial(16;8.3e-07)|Lung NSC(20;0.0107)|Colorectal(14;0.0202)|all_lung(20;0.0291)|Ovarian(20;0.19)		OV - Ovarian serous cystadenocarcinoma(1;0.00196)			GATCCTTGTCCTCGTCCAAAA	0.368								Homologous recombination																													p.P876R		Atlas-SNP	.											RBBP8_ENST00000399725,NS,carcinoma,0,2	RBBP8	138	.	2	Substitution - Missense(2)	prostate(2)	c.C2627G						PASS	.						128.0	114.0	119.0					18																	20606136		2203	4300	6503	SO:0001583	missense	5932	exon19			CTTGTCCTCGTCC	AF043431	CCDS11874.1, CCDS11875.1	18q11.2	2012-11-05	2001-11-28		ENSG00000101773	ENSG00000101773			9891	protein-coding gene	gene with protein product	"""CTBP-interacting protein"""	604124	"""retinoblastoma-binding protein 8"", ""Seckel syndrome 2"""	SCKL2		9721205, 17965729, 21998596	Standard	NM_002894		Approved	CtIP, RIM, COM1	uc002ktw.3	Q99708	OTTHUMG00000131769	ENST00000399722.2:c.2627C>G	chr18.hg19:g.20606136C>G	ENSP00000382628:p.Pro876Arg	232.0	0.0	.		305.0	78.0	.	NM_002894	A6NKN2|A8K8W6|E7ETY1|O75371|Q8NHQ3	Missense_Mutation	SNP	ENST00000399722.2	hg19	CCDS11875.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	11.52|11.52	1.661903|1.661903	0.29515|0.29515	.|.	.|.	ENSG00000101773|ENSG00000101773	ENST00000399725;ENST00000399721|ENST00000327155;ENST00000399722;ENST00000360790	T|T;T;T	0.35048|0.30182	1.33|1.54;1.54;1.54	5.75|5.75	5.75|5.75	0.90469|0.90469	.|.	.|0.429012	.|0.25735	.|N	.|0.028643	T|T	0.24967|0.24967	0.0606|0.0606	N|N	0.14661|0.14661	0.345|0.345	0.30511|0.30511	N|N	0.769444|0.769444	P|D;D	0.42827|0.59767	0.791|0.986;0.986	B|P;P	0.38378|0.48873	0.272|0.593;0.593	T|T	0.07481|0.07481	-1.0770|-1.0770	9|10	0.87932|0.38643	D|T	0|0.18	-7.0083|-7.0083	12.5437|12.5437	0.56186|0.56186	0.2615:0.7385:0.0:0.0|0.2615:0.7385:0.0:0.0	.|.	844|881;876	A6NKN2|E7ETY1;Q99708	.|.;COM1_HUMAN	V|R	844|876;876;881	ENSP00000382630:L844V|ENSP00000323050:P876R;ENSP00000382628:P876R;ENSP00000354024:P881R	ENSP00000382627:L844V|ENSP00000323050:P876R	L|P	+|+	1|2	0|0	RBBP8|RBBP8	18860134|18860134	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.979000|0.979000	0.70002|0.70002	1.895000|1.895000	0.39778|0.39778	2.716000|2.716000	0.92895|0.92895	0.655000|0.655000	0.94253|0.94253	CTC|CCT	.	.	.	none		0.368	RBBP8-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446387.1	NM_203291	
C19orf25	148223	hgsc.bcm.edu	37	19	1481811	1481811	+	5'Flank	SNP	G	G	A	rs377189780		TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr19:1481811G>A	ENST00000436106.2	-	0	0				C19orf25_ENST00000591027.1_5'Flank|CTB-25B13.6_ENST00000585643.1_RNA|C19orf25_ENST00000427685.2_5'Flank|C19orf25_ENST00000585675.1_5'Flank|C19orf25_ENST00000586564.1_5'Flank|C19orf25_ENST00000588849.1_5'Flank|C19orf25_ENST00000592872.1_5'Flank|C19orf25_ENST00000588871.1_5'Flank|PCSK4_ENST00000300954.5_Missense_Mutation_p.R739C|C19orf25_ENST00000588427.1_5'Flank			Q9UFG5	CS025_HUMAN	chromosome 19 open reading frame 25														Acute lymphoblastic leukemia(61;3.02e-13)|all_hematologic(61;4.32e-09)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GCCCTGGCACGGGAGAGCCAG	0.672																																					p.R739C		Atlas-SNP	.											.	PCSK4	44	.	0			c.C2215T						PASS	.						21.0	25.0	24.0					19																	1481811		2202	4296	6498	SO:0001631	upstream_gene_variant	54760	exon15			TGGCACGGGAGAG	AK075267	CCDS45898.1	19p13.3	2012-10-24			ENSG00000119559	ENSG00000119559			26711	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_152482		Approved	FLJ36666	uc010dsk.3	Q9UFG5	OTTHUMG00000180092		chr19.hg19:g.1481811G>A	Exception_encountered	75.0	0.0	.		104.0	12.0	.	NM_017573	B3KQN6|Q8N9R7|Q8WV94	Missense_Mutation	SNP	ENST00000436106.2	hg19	CCDS45898.1	.	.	.	.	.	.	.	.	.	.	g	8.277	0.814622	0.16607	.	.	ENSG00000115257	ENST00000300954	T	0.70749	-0.51	1.2	-2.4	0.06583	.	.	.	.	.	T	0.46268	0.1384	L	0.36672	1.1	0.09310	N	1	P	0.46457	0.878	B	0.26094	0.066	T	0.30880	-0.9963	9	0.52906	T	0.07	.	4.3765	0.11272	0.0:0.4776:0.2063:0.3161	.	739	Q6UW60	PCSK4_HUMAN	C	739	ENSP00000300954:R739C	ENSP00000300954:R739C	R	-	1	0	PCSK4	1432811	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-3.167000	0.00575	-2.042000	0.00914	-1.041000	0.02371	CGT	.	.	.	alt		0.672	C19orf25-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449694.1	NM_152482	
NRTN	4902	hgsc.bcm.edu	37	19	5827909	5827909	+	Missense_Mutation	SNP	G	G	A	rs375707068		TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr19:5827909G>A	ENST00000303212.2	+	2	683	c.319G>A	c.(319-321)Gag>Aag	p.E107K		NM_004558.3	NP_004549.1	Q99748	NRTN_HUMAN	neurturin	107					axon guidance (GO:0007411)|MAPK cascade (GO:0000165)|nerve development (GO:0021675)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neuron projection development (GO:0031175)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	axon (GO:0030424)|extracellular region (GO:0005576)	receptor binding (GO:0005102)			large_intestine(1)	1						CGGGCTGCGCGAGCTGGAGGT	0.806																																					p.E107K		Atlas-SNP	.											.	NRTN	4	.	0			c.G319A						PASS	.	G	LYS/GLU	0,3794		0,0,1897	5.0	5.0	5.0		319	4.3	1.0	19		5	1,7493		0,1,3746	no	missense	NRTN	NM_004558.3	56	0,1,5643	AA,AG,GG		0.0133,0.0,0.0089	possibly-damaging	107/198	5827909	1,11287	1897	3747	5644	SO:0001583	missense	4902	exon2			CTGCGCGAGCTGG	U78110	CCDS12151.1	19p13.3	2014-01-30				ENSG00000171119		"""Endogenous ligands"""	8007	protein-coding gene	gene with protein product	"""prepro-neurturin"""	602018				8945474	Standard	NM_004558		Approved	NTN	uc002mde.3	Q99748		ENST00000303212.2:c.319G>A	chr19.hg19:g.5827909G>A	ENSP00000302648:p.Glu107Lys	0.0	0.0	.		9.0	8.0	.	NM_004558	B2RPE8	Missense_Mutation	SNP	ENST00000303212.2	hg19	CCDS12151.1	.	.	.	.	.	.	.	.	.	.	G	25.6	4.650912	0.87958	0.0	1.33E-4	ENSG00000171119	ENST00000303212	D	0.84146	-1.81	4.33	4.33	0.51752	Transforming growth factor-beta, C-terminal (3);	0.128790	0.51477	D	0.000084	D	0.82513	0.5053	L	0.34521	1.04	0.39656	D	0.970533	D	0.63046	0.992	P	0.54856	0.762	T	0.81088	-0.1091	10	0.33940	T	0.23	-8.9466	8.5435	0.33406	0.1094:0.0:0.8906:0.0	.	107	Q99748	NRTN_HUMAN	K	107	ENSP00000302648:E107K	ENSP00000302648:E107K	E	+	1	0	NRTN	5778909	1.000000	0.71417	1.000000	0.80357	0.850000	0.48378	3.082000	0.50128	2.153000	0.67306	0.491000	0.48974	GAG	.	.	.	weak		0.806	NRTN-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451882.2	NM_004558	
TBCB	1155	hgsc.bcm.edu	37	19	36606539	36606539	+	Missense_Mutation	SNP	A	A	T			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr19:36606539A>T	ENST00000221855.3	+	1	652	c.77A>T	c.(76-78)aAg>aTg	p.K26M	TBCB_ENST00000589996.1_Missense_Mutation_p.K26M|TBCB_ENST00000585746.1_5'Flank|TBCB_ENST00000392178.4_3'UTR|TBCB_ENST00000586868.1_5'Flank|POLR2I_ENST00000221859.4_5'Flank	NM_001281.2	NP_001272.2	Q99426	TBCB_HUMAN	tubulin folding cofactor B	26					'de novo' posttranslational protein folding (GO:0051084)|cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|nervous system development (GO:0007399)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)				large_intestine(2)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	5	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			CGCTCCGAGAAGCGATACAGC	0.662																																					p.K26M		Atlas-SNP	.											.	TBCB	13	.	0			c.A77T						PASS	.						34.0	23.0	27.0					19																	36606539		2202	4299	6501	SO:0001583	missense	1155	exon1			CCGAGAAGCGATA	AF013488	CCDS12488.1, CCDS74344.1	19q13.11-q13.12	2008-02-05	2006-11-22	2006-11-22	ENSG00000105254	ENSG00000105254			1989	protein-coding gene	gene with protein product		601303	"""cytoskeleton-associated protein 1"", ""cytoskeleton associated protein 1"""	CKAP1		8978778	Standard	NM_001281		Approved	CG22, CKAPI	uc002odg.1	Q99426	OTTHUMG00000048143	ENST00000221855.3:c.77A>T	chr19.hg19:g.36606539A>T	ENSP00000221855:p.Lys26Met	98.0	0.0	.		159.0	72.0	.	NM_001281	O00111|O00674|O14728|Q6FGY5	Missense_Mutation	SNP	ENST00000221855.3	hg19	CCDS12488.1	.	.	.	.	.	.	.	.	.	.	A	20.6	4.024046	0.75390	.	.	ENSG00000105254	ENST00000221855;ENST00000392178	D	0.92249	-3.0	5.33	4.31	0.51392	.	0.180969	0.47852	D	0.000214	D	0.90964	0.7159	M	0.76002	2.32	0.80722	D	1	P	0.44260	0.83	B	0.42422	0.387	D	0.89084	0.3478	10	0.54805	T	0.06	-27.6416	9.2292	0.37425	0.9131:0.0:0.0869:0.0	.	26	Q99426	TBCB_HUMAN	M	26	ENSP00000221855:K26M	ENSP00000221855:K26M	K	+	2	0	TBCB	41298379	1.000000	0.71417	0.979000	0.43373	0.871000	0.50021	2.209000	0.42806	0.863000	0.35553	0.397000	0.26171	AAG	.	.	.	none		0.662	TBCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000156291.2	NM_001281	
FBL	2091	hgsc.bcm.edu	37	19	40330915	40330915	+	Silent	SNP	G	G	A			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr19:40330915G>A	ENST00000221801.3	-	4	449	c.336C>T	c.(334-336)gtC>gtT	p.V112V	FBL_ENST00000593503.1_5'Flank	NM_001436.3	NP_001427.2	P22087	FBRL_HUMAN	fibrillarin	112					histone glutamine methylation (GO:1990258)|osteoblast differentiation (GO:0001649)|rRNA processing (GO:0006364)|snoRNA metabolic process (GO:0016074)|tRNA processing (GO:0008033)	box C/D snoRNP complex (GO:0031428)|Cajal body (GO:0015030)|extracellular vesicular exosome (GO:0070062)|granular component (GO:0001652)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	histone-glutamine methyltransferase activity (GO:1990259)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(1)|kidney(1)|large_intestine(4)|lung(2)|ovary(1)	9	all_cancers(60;5.79e-06)|all_lung(34;5.2e-08)|Lung NSC(34;6.14e-08)|Ovarian(47;0.06)	Renal(1328;0.000518)|Hepatocellular(1079;0.0893)	Epithelial(26;5.74e-25)|OV - Ovarian serous cystadenocarcinoma(5;3.13e-24)|all cancers(26;8.59e-23)	GBM - Glioblastoma multiforme(1328;0.000826)|STAD - Stomach adenocarcinoma(1328;0.138)		ATTCCCCAGGGACCAGGTTCT	0.577																																					p.V112V		Atlas-SNP	.											.	FBL	37	.	0			c.C336T						PASS	.						103.0	91.0	95.0					19																	40330915		2203	4300	6503	SO:0001819	synonymous_variant	2091	exon4			CCCAGGGACCAGG	AC005393	CCDS12545.1	19q13.1	2010-02-17			ENSG00000105202	ENSG00000105202			3599	protein-coding gene	gene with protein product		134795				1846968, 2026646	Standard	NM_001436		Approved	RNU3IP1, FLRN, FIB	uc002omn.3	P22087		ENST00000221801.3:c.336C>T	chr19.hg19:g.40330915G>A		172.0	0.0	.		93.0	26.0	.	NM_001436	B5BUE8|O75259|Q6IAT5|Q9UPI6	Silent	SNP	ENST00000221801.3	hg19	CCDS12545.1																																																																																			.	.	.	none		0.577	FBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462509.4	NM_001436	
KLK5	25818	hgsc.bcm.edu	37	19	51451945	51451945	+	Missense_Mutation	SNP	T	T	G			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr19:51451945T>G	ENST00000336334.3	-	5	1029	c.677A>C	c.(676-678)gAt>gCt	p.D226A	CTB-147C22.8_ENST00000594939.1_RNA|KLK5_ENST00000391809.2_Missense_Mutation_p.D226A|KLK5_ENST00000593428.1_Missense_Mutation_p.D226A|CTB-147C22.8_ENST00000601506.1_RNA	NM_012427.4	NP_036559	Q9Y337	KLK5_HUMAN	kallikrein-related peptidase 5	226	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				epidermis development (GO:0008544)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)	epidermal lamellar body (GO:0097209)|extracellular space (GO:0005615)	peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			NS(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|urinary_tract(1)	15		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00379)|GBM - Glioblastoma multiforme(134;0.00888)		CATGGTGTCATCTATCTGTCT	0.507																																					p.D226A		Atlas-SNP	.											.	KLK5	37	.	0			c.A677C						PASS	.						170.0	133.0	146.0					19																	51451945		2203	4300	6503	SO:0001583	missense	25818	exon5			GTGTCATCTATCT	AF135028	CCDS12810.1	19q13.33	2008-02-05	2006-10-27			ENSG00000167754		"""Kallikreins"""	6366	protein-coding gene	gene with protein product		605643	"""kallikrein 5"""			10514489, 10608802, 1680072, 4, 16800723, 17012259	Standard	NM_012427		Approved	SCTE, KLK-L2	uc002puf.3	Q9Y337		ENST00000336334.3:c.677A>C	chr19.hg19:g.51451945T>G	ENSP00000337733:p.Asp226Ala	138.0	0.0	.		114.0	53.0	.	NM_012427	Q53ZR3|Q9HBG8	Missense_Mutation	SNP	ENST00000336334.3	hg19	CCDS12810.1	.	.	.	.	.	.	.	.	.	.	t	10.10	1.257295	0.22965	.	.	ENSG00000167754	ENST00000336334;ENST00000391809	D;D	0.88201	-2.35;-2.35	4.67	2.49	0.30216	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.000000	0.34386	U	0.004020	T	0.79776	0.4504	N	0.16066	0.365	0.09310	N	1	P	0.40398	0.716	B	0.41036	0.346	T	0.71111	-0.4687	10	0.51188	T	0.08	.	10.2185	0.43184	0.0:0.0:0.5204:0.4796	.	226	Q9Y337	KLK5_HUMAN	A	226	ENSP00000337733:D226A;ENSP00000375685:D226A	ENSP00000337733:D226A	D	-	2	0	KLK5	56143757	1.000000	0.71417	0.006000	0.13384	0.020000	0.10135	5.146000	0.64845	0.262000	0.21774	-0.316000	0.08728	GAT	.	.	.	none		0.507	KLK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465057.1	NM_012427	
ZNF814	730051	hgsc.bcm.edu	37	19	58385793	58385793	+	Missense_Mutation	SNP	C	C	T	rs113623532		TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr19:58385793C>T	ENST00000435989.2	-	3	1199	c.965G>A	c.(964-966)aGa>aAa	p.R322K	ZNF814_ENST00000596604.1_Intron|ZNF814_ENST00000595295.1_Intron|ZNF814_ENST00000597342.1_Intron|ZNF814_ENST00000600634.1_Intron|ZNF814_ENST00000597832.1_Intron	NM_001144989.1	NP_001138461.1	B7Z6K7	ZN814_HUMAN	zinc finger protein 814	322					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						TTCATAAGGTCTTTTCCCAGT	0.358																																					p.R322K		Atlas-SNP	.											.	ZNF814	93	.	0			c.G965A						PASS	.						15.0	12.0	13.0					19																	58385793		687	1562	2249	SO:0001583	missense	730051	exon3			TAAGGTCTTTTCC		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.965G>A	chr19.hg19:g.58385793C>T	ENSP00000410545:p.Arg322Lys	86.0	0.0	.		86.0	16.0	.	NM_001144989	A6NF35	Missense_Mutation	SNP	ENST00000435989.2	hg19	CCDS46212.1	.	.	.	.	.	.	.	.	.	.	.	0.023	-1.395361	0.01175	.	.	ENSG00000204514	ENST00000435989	T	0.12361	2.69	2.27	9.47E-4	0.14044	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.03608	0.0103	N	0.02225	-0.63	0.09310	N	0.999999	B	0.29301	0.241	B	0.28916	0.096	T	0.40534	-0.9558	9	0.02654	T	1	.	4.6969	0.12808	0.0:0.4166:0.0:0.5834	.	322	B7Z6K7	ZN814_HUMAN	K	322	ENSP00000410545:R322K	ENSP00000410545:R322K	R	-	2	0	ZNF814	63077605	0.000000	0.05858	0.024000	0.17045	0.009000	0.06853	-1.883000	0.01623	0.331000	0.23511	-1.381000	0.01174	AGA	.	C|0.500;T|0.500	0.500	weak		0.358	ZNF814-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466976.1	XM_001725708	
PCSK2	5126	hgsc.bcm.edu	37	20	17417493	17417493	+	Missense_Mutation	SNP	C	C	T			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr20:17417493C>T	ENST00000262545.2	+	8	1165	c.850C>T	c.(850-852)Ctc>Ttc	p.L284F	PCSK2_ENST00000536609.1_Missense_Mutation_p.L249F|PCSK2_ENST00000377899.1_Missense_Mutation_p.L265F	NM_002594.3	NP_002585.2	P16519	NEC2_HUMAN	proprotein convertase subtilisin/kexin type 2	284	Peptidase S8.			EL -> DV (in Ref. 1; AAA60032). {ECO:0000305}.	cellular protein metabolic process (GO:0044267)|embryo development (GO:0009790)|enkephalin processing (GO:0034230)|insulin processing (GO:0030070)|islet amyloid polypeptide processing (GO:0034231)|nervous system development (GO:0007399)|protein autoprocessing (GO:0016540)|proteolysis (GO:0006508)	dendrite (GO:0030425)|extracellular space (GO:0005615)|membrane (GO:0016020)|perikaryon (GO:0043204)|secretory granule lumen (GO:0034774)	serine-type endopeptidase activity (GO:0004252)			breast(2)|central_nervous_system(2)|endometrium(5)|kidney(5)|large_intestine(7)|lung(17)|ovary(3)|pancreas(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	53					"""""""Insulin(DB00071)|Insulin Regular(DB00030)"""	GCCCCGGGAGCTCACGCTGCA	0.642																																					p.L284F		Atlas-SNP	.											.	PCSK2	112	.	0			c.C850T						PASS	.						34.0	32.0	33.0					20																	17417493		2203	4300	6503	SO:0001583	missense	5126	exon8			CGGGAGCTCACGC	AK312341	CCDS13125.1, CCDS56179.1, CCDS56180.1	20p11.2	2008-08-01			ENSG00000125851	ENSG00000125851			8744	protein-coding gene	gene with protein product	"""neuroendocrine convertase 2"", ""KEX2-like endoprotease 2"""	162151		NEC2		1765368	Standard	NM_001201528		Approved	PC2, SPC2	uc002wpm.3	P16519	OTTHUMG00000031941	ENST00000262545.2:c.850C>T	chr20.hg19:g.17417493C>T	ENSP00000262545:p.Leu284Phe	81.0	0.0	.		174.0	65.0	.	NM_002594	B1ANH9|B4DFQ3|Q14927|Q5JYQ1|Q8IWA8|Q9NQG3|Q9NUG1|Q9UJC6	Missense_Mutation	SNP	ENST00000262545.2	hg19	CCDS13125.1	.	.	.	.	.	.	.	.	.	.	C	23.5	4.421696	0.83559	.	.	ENSG00000125851	ENST00000377899;ENST00000262545;ENST00000536609	D;D;D	0.87887	-2.31;-2.31;-2.31	5.38	5.38	0.77491	Peptidase S8/S53, subtilisin/kexin/sedolisin (3);	0.000000	0.85682	D	0.000000	D	0.92192	0.7524	M	0.79693	2.465	0.80722	D	1	B;D	0.53745	0.24;0.962	B;P	0.55391	0.146;0.775	D	0.92722	0.6192	10	0.56958	D	0.05	-19.6799	17.6879	0.88261	0.0:1.0:0.0:0.0	.	249;284	B4DFQ3;P16519	.;NEC2_HUMAN	F	265;284;249	ENSP00000367131:L265F;ENSP00000262545:L284F;ENSP00000437458:L249F	ENSP00000262545:L284F	L	+	1	0	PCSK2	17365493	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.647000	0.61418	2.519000	0.84933	0.655000	0.94253	CTC	.	.	.	none		0.642	PCSK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078120.2	NM_002594	
BPIFB1	92747	hgsc.bcm.edu	37	20	31892698	31892698	+	Splice_Site	SNP	G	G	A			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr20:31892698G>A	ENST00000253354.1	+	13	1415		c.e13+1		BPIFB1_ENST00000464032.1_Splice_Site	NM_033197.2	NP_149974.2	Q8TDL5	BPIB1_HUMAN	BPI fold containing family B, member 1						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)										CTGGTTCCAAGTAAGTGTTAA	0.532																																					.		Atlas-SNP	.											.	.	.	.	0			c.1254+1G>A						PASS	.						104.0	86.0	92.0					20																	31892698		2203	4300	6503	SO:0001630	splice_region_variant	92747	exon13			TTCCAAGTAAGTG	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.1254+1G>A	chr20.hg19:g.31892698G>A		98.0	0.0	.		201.0	73.0	.	NM_033197	A8K2H8|Q5QP43|Q6UWY1|Q6ZRU7|Q96HK6|Q9BQP8|Q9BWZ6|Q9H4V6	Splice_Site	SNP	ENST00000253354.1	hg19	CCDS13218.1	.	.	.	.	.	.	.	.	.	.	G	12.79	2.043780	0.36085	.	.	ENSG00000125999	ENST00000253354	.	.	.	5.26	5.26	0.73747	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.217	0.65800	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	BPIFB1	31356359	0.999000	0.42202	0.998000	0.56505	0.266000	0.26442	4.225000	0.58600	2.740000	0.93945	0.561000	0.74099	.	.	.	.	none		0.532	BPIFB1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106499.2	NM_033197	Intron
MYT1	4661	hgsc.bcm.edu	37	20	62859303	62859303	+	Missense_Mutation	SNP	A	A	T			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr20:62859303A>T	ENST00000328439.1	+	18	3018	c.2654A>T	c.(2653-2655)aAg>aTg	p.K885M	MYT1_ENST00000536311.1_Missense_Mutation_p.K912M|MYT1_ENST00000360149.4_Missense_Mutation_p.K564M	NM_004535.2	NP_004526.1	Q99640	PMYT1_HUMAN	myelin transcription factor 1	0					G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of phosphatase activity (GO:0010923)|regulation of cell cycle (GO:0051726)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of mitosis (GO:0007088)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(12)|liver(1)|lung(17)|ovary(5)|prostate(2)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55	all_cancers(38;1.82e-11)|all_epithelial(29;3.3e-13)|Lung NSC(23;5.21e-10)|all_lung(23;1.92e-09)					AAGGACGACAAGGAGGACCCC	0.483																																					p.K885M	GBM(59;481 1041 20555 21139 33705)	Atlas-SNP	.											.	MYT1	152	.	0			c.A2654T						PASS	.						89.0	88.0	88.0					20																	62859303		2203	4300	6503	SO:0001583	missense	4661	exon18			ACGACAAGGAGGA	M96980	CCDS13558.1	20q13.33	2014-03-24			ENSG00000196132	ENSG00000196132		"""Zinc fingers, C2HC-type containing"""	7622	protein-coding gene	gene with protein product	"""neural zinc finger transcription factor 2"""	600379		PLPB1		1280325, 9268380	Standard	NM_004535		Approved	MTF1, MYTI, ZC2HC4A, NZF2	uc002yii.3	Q01538	OTTHUMG00000149988	ENST00000328439.1:c.2654A>T	chr20.hg19:g.62859303A>T	ENSP00000327465:p.Lys885Met	141.0	0.0	.		213.0	82.0	.	NM_004535	B3KUN8|B4DXD4|D3DUA4|F8W164|I3L1V2|O14731|Q7LE24|Q8TCM9	Missense_Mutation	SNP	ENST00000328439.1	hg19	CCDS13558.1	.	.	.	.	.	.	.	.	.	.	A	17.01	3.279871	0.59758	.	.	ENSG00000196132	ENST00000360149;ENST00000328439;ENST00000536311	T;T;T	0.54071	0.59;0.65;0.61	5.67	4.58	0.56647	.	0.115126	0.64402	D	0.000018	T	0.69251	0.3090	M	0.78637	2.42	0.53688	D	0.999978	D;D;D	0.67145	0.996;0.993;0.986	D;P;P	0.64144	0.922;0.886;0.621	T	0.72272	-0.4342	10	0.72032	D	0.01	-30.9363	11.5655	0.50802	0.9301:0.0:0.0699:0.0	.	912;885;564	F5H7M8;Q01538;Q6P6D5	.;MYT1_HUMAN;.	M	564;885;912	ENSP00000353269:K564M;ENSP00000327465:K885M;ENSP00000442412:K912M	ENSP00000327465:K885M	K	+	2	0	MYT1	62329747	1.000000	0.71417	1.000000	0.80357	0.811000	0.45836	6.166000	0.71896	0.990000	0.38787	0.533000	0.62120	AAG	.	.	.	none		0.483	MYT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080297.1	NM_004535	
ZNF280A	129025	hgsc.bcm.edu	37	22	22869192	22869192	+	Missense_Mutation	SNP	T	T	C			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr22:22869192T>C	ENST00000302097.3	-	2	1015	c.763A>G	c.(763-765)Att>Gtt	p.I255V	snoU13_ENST00000459485.1_RNA	NM_080740.3	NP_542778.1	P59817	Z280A_HUMAN	zinc finger protein 280A	255					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)		AGACTTGAAATGTCTGTCATT	0.413																																					p.I255V		Atlas-SNP	.											.	ZNF280A	67	.	0			c.A763G						PASS	.						126.0	115.0	119.0					22																	22869192		2203	4300	6503	SO:0001583	missense	129025	exon2			TTGAAATGTCTGT	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.763A>G	chr22.hg19:g.22869192T>C	ENSP00000302855:p.Ile255Val	129.0	1.0	.		121.0	100.0	.	NM_080740		Missense_Mutation	SNP	ENST00000302097.3	hg19	CCDS13800.1	.	.	.	.	.	.	.	.	.	.	T	2.685	-0.274412	0.05679	.	.	ENSG00000169548	ENST00000302097	T	0.01126	5.3	3.66	1.52	0.23074	.	.	.	.	.	T	0.00695	0.0023	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.48163	-0.9059	9	0.20519	T	0.43	-0.1797	4.2473	0.10677	0.5866:0.2055:0.0:0.2079	.	255	P59817	Z280A_HUMAN	V	255	ENSP00000302855:I255V	ENSP00000302855:I255V	I	-	1	0	ZNF280A	21199192	0.001000	0.12720	0.000000	0.03702	0.003000	0.03518	0.195000	0.17155	0.264000	0.21851	-1.173000	0.01734	ATT	.	.	.	none		0.413	ZNF280A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075433.3	NM_080740	
CSF2RA	1438	hgsc.bcm.edu	37	X	1407702	1407702	+	Missense_Mutation	SNP	G	G	T			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chrX:1407702G>T	ENST00000381524.3	+	6	580	c.394G>T	c.(394-396)Gat>Tat	p.D132Y	CSF2RA_ENST00000417535.2_Missense_Mutation_p.D132Y|CSF2RA_ENST00000432318.2_Missense_Mutation_p.D132Y|CSF2RA_ENST00000381529.3_Missense_Mutation_p.D132Y|CSF2RA_ENST00000381509.3_Missense_Mutation_p.D132Y|CSF2RA_ENST00000355805.2_Missense_Mutation_p.D132Y|CSF2RA_ENST00000501036.2_5'UTR|CSF2RA_ENST00000355432.3_Missense_Mutation_p.D132Y|BX649553.3_ENST00000581137.1_RNA|CSF2RA_ENST00000494969.2_Intron|CSF2RA_ENST00000361536.3_Missense_Mutation_p.D132Y|CSF2RA_ENST00000381500.1_Missense_Mutation_p.D132Y			P15509	CSF2R_HUMAN	colony stimulating factor 2 receptor, alpha, low-affinity (granulocyte-macrophage)	132					response to ethanol (GO:0045471)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cytokine receptor activity (GO:0004896)|receptor activity (GO:0004872)			central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(6)|lung(21)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	45		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)	CTACAATGCGGATTTAATGAA	0.468																																					p.D132Y	Esophageal Squamous(131;723 1707 25334 40494 41806)	Atlas-SNP	.											.	CSF2RA	153	.	0			c.G394T						PASS	.						173.0	182.0	179.0					X																	1407702		2203	4296	6499	SO:0001583	missense	1438	exon4			AATGCGGATTTAA	M64445	CCDS35190.1, CCDS35191.1, CCDS35192.1, CCDS35193.1, CCDS55359.1, CCDS55360.1, CCDS55361.1	Xp22.32 and Yp11.3	2014-09-17			ENSG00000198223	ENSG00000198223		"""CD molecules"", ""Pseudoautosomal regions / PAR1"""	2435	protein-coding gene	gene with protein product		306250, 425000		CSF2R		1702217	Standard	NM_006140		Approved	CD116	uc010ncv.2	P15509	OTTHUMG00000012533	ENST00000381524.3:c.394G>T	chrX.hg19:g.1407702G>T	ENSP00000370935:p.Asp132Tyr	282.0	0.0	.		389.0	127.0	.	NM_172247	A7J003|A8KAM1|B4DW68|J3JS76|J3JS77|O00207|Q14429|Q14430|Q14431|Q16564	Missense_Mutation	SNP	ENST00000381524.3	hg19	CCDS35191.1	.	.	.	.	.	.	.	.	.	.	.	3.532	-0.095615	0.07010	.	.	ENSG00000198223	ENST00000381529;ENST00000432318;ENST00000361536;ENST00000381507;ENST00000381524;ENST00000412290;ENST00000419094;ENST00000381509;ENST00000355805;ENST00000355432;ENST00000417535;ENST00000381500	D;D;T;D;T;T;D;T;T;D;T	0.96104	-3.91;-3.91;0.5;-3.91;0.5;0.5;-3.91;0.5;0.5;-3.91;0.5	2.02	-0.156	0.13391	Interleukin-6 receptor alpha chain, binding (1);Fibronectin, type III (1);Immunoglobulin-like fold (1);	1.244990	0.06574	U	0.749174	D	0.95896	0.8664	.	.	.	0.18873	N	0.999989	P;P;P;D;B;P	0.57899	0.488;0.483;0.685;0.981;0.428;0.483	B;B;B;P;B;B	0.60012	0.092;0.239;0.269;0.867;0.154;0.157	D	0.86489	0.1796	9	0.66056	D	0.02	.	3.1267	0.06409	0.1944:0.2787:0.5269:0.0	.	132;132;132;132;132;132	P15509-2;A7J003;P15509-3;P15509-6;P15509-5;P15509	.;.;.;.;.;CSF2R_HUMAN	Y	132	ENSP00000370940:D132Y;ENSP00000416437:D132Y;ENSP00000354836:D132Y;ENSP00000370935:D132Y;ENSP00000410667:D132Y;ENSP00000397452:D132Y;ENSP00000370920:D132Y;ENSP00000348058:D132Y;ENSP00000347606:D132Y;ENSP00000394227:D132Y;ENSP00000370911:D132Y	ENSP00000347606:D132Y	D	+	1	0	CSF2RA	1367702	0.006000	0.16342	0.001000	0.08648	0.041000	0.13682	-0.778000	0.04664	-0.259000	0.09432	0.280000	0.19369	GAT	.	.	.	none		0.468	CSF2RA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000035013.2		
NAA10	8260	hgsc.bcm.edu	37	X	153198018	153198018	+	Missense_Mutation	SNP	C	C	T			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chrX:153198018C>T	ENST00000464845.1	-	4	517	c.199G>A	c.(199-201)Gtg>Atg	p.V67M	NAA10_ENST00000393712.3_Missense_Mutation_p.V67M|NAA10_ENST00000370009.1_Missense_Mutation_p.V67M|NAA10_ENST00000393710.3_5'UTR|NAA10_ENST00000370015.4_Missense_Mutation_p.V67M	NM_001256120.1|NM_003491.3	NP_001243049.1|NP_003482.1	P41227	NAA10_HUMAN	N(alpha)-acetyltransferase 10, NatA catalytic subunit	67	N-acetyltransferase. {ECO:0000255|PROSITE-ProRule:PRU00532}.				DNA packaging (GO:0006323)|internal protein amino acid acetylation (GO:0006475)|N-terminal protein amino acid acetylation (GO:0006474)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|membrane (GO:0016020)|NatA complex (GO:0031415)|nucleolus (GO:0005730)|nucleus (GO:0005634)	N-acetyltransferase activity (GO:0008080)|peptide alpha-N-acetyltransferase activity (GO:0004596)			breast(1)|endometrium(3)|kidney(1)|lung(3)|ovary(1)|prostate(1)	10						CCATGGGGCACATCATCTGGG	0.587																																					p.V67M	Ovarian(94;1099 1433 38814 45882 51063)	Atlas-SNP	.											.	NAA10	18	.	0			c.G199A						PASS	.						68.0	49.0	55.0					X																	153198018		2202	4297	6499	SO:0001583	missense	8260	exon4			GGGGCACATCATC	BC000308	CCDS14737.1, CCDS59179.1	Xq28	2010-05-07	2010-01-14	2010-01-14	ENSG00000102030	ENSG00000102030	2.3.1.88	"""N(alpha)-acetyltransferase subunits"""	18704	protein-coding gene	gene with protein product		300013	"""ARD1 homolog, N-acetyltransferase (S. cerevisiae)"", ""ARD1 homolog A, N-acetyltransferase (S. cerevisiae)"""	ARD1, ARD1A		7981673, 19660095	Standard	NM_003491		Approved	DXS707, TE2	uc004fjm.2	P41227	OTTHUMG00000024225	ENST00000464845.1:c.199G>A	chrX.hg19:g.153198018C>T	ENSP00000417763:p.Val67Met	51.0	0.0	.		87.0	32.0	.	NM_001256119	A6NM98	Missense_Mutation	SNP	ENST00000464845.1	hg19	CCDS14737.1	.	.	.	.	.	.	.	.	.	.	C	15.36	2.811472	0.50527	.	.	ENSG00000102030	ENST00000464845;ENST00000370015;ENST00000393712;ENST00000370009;ENST00000545734;ENST00000370011;ENST00000432089	T;T;T;T;T;T	0.30981	1.51;1.51;1.51;1.51;1.51;1.51	5.04	3.25	0.37280	GCN5-related N-acetyltransferase (GNAT) domain (2);Acyl-CoA N-acyltransferase (2);	0.000000	0.85682	D	0.000000	T	0.37892	0.1020	L	0.47016	1.485	0.54753	D	0.999981	B;P;P	0.44195	0.251;0.454;0.828	B;P;P	0.53954	0.375;0.738;0.738	T	0.08330	-1.0727	10	0.46703	T	0.11	-18.5174	9.0852	0.36577	0.0:0.8122:0.0:0.1878	.	67;67;67	B7Z9N2;A6NM98;P41227	.;.;NAA10_HUMAN	M	67;67;67;67;67;61;61	ENSP00000417763:V67M;ENSP00000359032:V67M;ENSP00000377315:V67M;ENSP00000359026:V67M;ENSP00000359028:V61M;ENSP00000413668:V61M	ENSP00000359026:V67M	V	-	1	0	NAA10	152851212	1.000000	0.71417	0.899000	0.35326	0.948000	0.59901	4.628000	0.61282	0.909000	0.36697	0.525000	0.51046	GTG	.	.	.	none		0.587	NAA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061108.2	NM_003491	
PLXNA3	55558	hgsc.bcm.edu	37	X	153700940	153700940	+	Missense_Mutation	SNP	C	C	T			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chrX:153700940C>T	ENST00000369682.3	+	33	5703	c.5528C>T	c.(5527-5529)aCg>aTg	p.T1843M		NM_017514.3	NP_059984.3	P51805	PLXA3_HUMAN	plexin A3	1843					axon guidance (GO:0007411)|branchiomotor neuron axon guidance (GO:0021785)|facial nerve structural organization (GO:0021612)|hippocampus development (GO:0021766)|multicellular organismal development (GO:0007275)|negative chemotaxis (GO:0050919)|negative regulation of axon extension involved in axon guidance (GO:0048843)|positive regulation of cytoskeleton organization (GO:0051495)|pyramidal neuron development (GO:0021860)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|trigeminal nerve structural organization (GO:0021637)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(26)|ovary(2)|prostate(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	48	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					CAGATTCTCACGGCTCTGGAC	0.607																																					p.T1843M		Atlas-SNP	.											.	PLXNA3	156	.	0			c.C5528T						PASS	.						122.0	101.0	108.0					X																	153700940		2203	4300	6503	SO:0001583	missense	55558	exon33			TTCTCACGGCTCT	X74609	CCDS14752.1	Xq28	2008-02-05			ENSG00000130827	ENSG00000130827		"""Plexins"""	9101	protein-coding gene	gene with protein product		300022		PLXN4		8248200, 8733135	Standard	NM_017514		Approved	SEX, XAP-6, 6.3, Plxn3	uc004flm.3	P51805	OTTHUMG00000033290	ENST00000369682.3:c.5528C>T	chrX.hg19:g.153700940C>T	ENSP00000358696:p.Thr1843Met	137.0	0.0	.		205.0	178.0	.	NM_017514	Q5HY36	Missense_Mutation	SNP	ENST00000369682.3	hg19	CCDS14752.1	.	.	.	.	.	.	.	.	.	.	C	12.00	1.807947	0.31961	.	.	ENSG00000130827	ENST00000369682	T	0.01015	5.44	5.32	0.143	0.14820	.	0.182827	0.46758	D	0.000265	T	0.01029	0.0034	L	0.52011	1.625	0.44295	D	0.997164	B	0.19583	0.037	B	0.14578	0.011	T	0.58880	-0.7558	10	0.46703	T	0.11	.	5.7954	0.18383	0.1253:0.3656:0.4303:0.0788	.	1843	P51805	PLXA3_HUMAN	M	1843	ENSP00000358696:T1843M	ENSP00000358696:T1843M	T	+	2	0	PLXNA3	153354134	0.000000	0.05858	0.001000	0.08648	0.032000	0.12392	0.251000	0.18257	-0.517000	0.06461	-0.191000	0.12829	ACG	.	.	.	none		0.607	PLXNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081634.1	NM_017514	
SSFA2	6744	hgsc.bcm.edu	37	2	182765617	182765618	+	Frame_Shift_Ins	INS	-	-	T			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr2:182765617_182765618insT	ENST00000431877.2	+	7	877_878	c.698_699insT	c.(697-702)aattatfs	p.Y234fs	SSFA2_ENST00000409001.1_Frame_Shift_Ins_p.Y234fs|SSFA2_ENST00000320370.7_Frame_Shift_Ins_p.Y234fs|SSFA2_ENST00000428267.2_Frame_Shift_Ins_p.Y81fs	NM_001130445.1	NP_001123917.1	P28290	SSFA2_HUMAN	sperm specific antigen 2	234						cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(5)|lung(18)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	38			OV - Ovarian serous cystadenocarcinoma(117;0.0856)			GAAAACCCAAATTATGCTTTAA	0.302																																					p.N233fs		Atlas-Indel,Pindel	.											.	SSFA2	130	.	0			c.698_699insT						PASS	.																																			SO:0001589	frameshift_variant	6744	exon7			.	M61199	CCDS2284.1, CCDS46467.1, CCDS74611.1	2q32.1	2012-02-01			ENSG00000138434	ENSG00000138434			11319	protein-coding gene	gene with protein product	"""cleavage signal-1 protein"", ""KRAS-induced actin-interacting protein"", ""sperm associated antigen 13"""	118990				1555770	Standard	XM_005246812		Approved	CS-1, SPAG13, KRAP, KIAA1927	uc002uoh.3	P28290	OTTHUMG00000132584	ENST00000431877.2:c.700dupT	chr2.hg19:g.182765619_182765619dupT	ENSP00000388731:p.Tyr234fs	69.0	0.0	0		84.0	19.0	0.22619	NM_001130445	A8K6T0|Q68DA6|Q7Z7L2|Q8N1L3|Q8N263|Q8N7H2|Q8NEN5|Q96E36|Q96PW1	Frame_Shift_Ins	INS	ENST00000431877.2	hg19	CCDS46467.1																																																																																			.	.	.	none		0.302	SSFA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255793.2	NM_006751	
SETD2	29072	hgsc.bcm.edu	37	3	47098859	47098859	+	Frame_Shift_Del	DEL	G	G	-			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr3:47098859delG	ENST00000409792.3	-	15	6457	c.6415delC	c.(6415-6417)caafs	p.Q2140fs		NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	2140	Low charge region.				angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)			breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		TGCATCTGTTGCTGTTGTTTC	0.478			"""N, F, S, Mis"""		clear cell renal carcinoma																																p.Q2139fs		Atlas-INDEL	.		Rec	yes		3	3p21.31	29072	SET domain containing 2		E	.	SETD2	721	.	0			c.6416delA						PASS	.						160.0	148.0	152.0					3																	47098859		2203	4300	6503	SO:0001589	frameshift_variant	29072	exon15			.	AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"""Chromatin-modifying enzymes / K-methyltransferases"""	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.6415delC	chr3.hg19:g.47098859delG	ENSP00000386759:p.Gln2140fs	164.0	0.0	0		112.0	83.0	0.741071	NM_014159	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Frame_Shift_Del	DEL	ENST00000409792.3	hg19	CCDS2749.2																																																																																			.	.	.	none		0.478	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159	
ITGA6	3655	hgsc.bcm.edu	37	2	173352476	173352476	+	Frame_Shift_Del	DEL	A	A	-			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr2:173352476delA	ENST00000264106.6	+	18	2585	c.2382delA	c.(2380-2382)ttafs	p.L794fs	ITGA6_ENST00000409080.1_Frame_Shift_Del_p.L755fs|AC093818.1_ENST00000442417.1_RNA|ITGA6_ENST00000264107.7_Frame_Shift_Del_p.L755fs|ITGA6_ENST00000409532.1_Frame_Shift_Del_p.L636fs|ITGA6_ENST00000343713.4_Frame_Shift_Del_p.L750fs|ITGA6_ENST00000375221.2_Frame_Shift_Del_p.L794fs			P23229	ITA6_HUMAN	integrin, alpha 6	794					amelogenesis (GO:0097186)|blood coagulation (GO:0007596)|brown fat cell differentiation (GO:0050873)|cell adhesion mediated by integrin (GO:0033627)|cell junction assembly (GO:0034329)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cell-substrate junction assembly (GO:0007044)|cellular response to extracellular stimulus (GO:0031668)|cellular response to organic cyclic compound (GO:0071407)|digestive tract development (GO:0048565)|ectodermal cell differentiation (GO:0010668)|extracellular matrix organization (GO:0030198)|filopodium assembly (GO:0046847)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|nail development (GO:0035878)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of phosphorylation (GO:0042327)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|renal system development (GO:0072001)|single organismal cell-cell adhesion (GO:0016337)|skin development (GO:0043588)	basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell surface (GO:0009986)|cell-cell adherens junction (GO:0005913)|external side of plasma membrane (GO:0009897)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integrin alpha6-beta4 complex (GO:0034676)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			NS(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	44			OV - Ovarian serous cystadenocarcinoma(117;0.0979)			ATTTGGTTTTAAGTACAACTG	0.333																																					p.L755X		Atlas-Indel,Pindel	.											.	ITGA6	171	.	0			c.2264delT						PASS	.						123.0	118.0	120.0					2																	173352476		2203	4300	6503	SO:0001589	frameshift_variant	3655	exon17			.		CCDS2249.1, CCDS46451.1	2q31.1	2010-09-20			ENSG00000091409	ENSG00000091409		"""CD molecules"", ""Integrins"""	6142	protein-coding gene	gene with protein product		147556					Standard	NM_001079818		Approved	CD49f	uc002uhp.1	P23229	OTTHUMG00000132277	ENST00000264106.6:c.2382delA	chr2.hg19:g.173352476delA	ENSP00000264106:p.Leu794fs	81.0	0.0	0		73.0	14.0	0.191781	NM_000210	B2RMU9|B4DG69|B4DKB8|C4AM96|G5E9H1|Q08443|Q0MRC7|Q14646|Q16508|Q53RX7|Q59HB7|Q86VL6|Q9UCT1|Q9UN03	Frame_Shift_Del	DEL	ENST00000264106.6	hg19																																																																																				.	.	.	none		0.333	ITGA6-201	KNOWN	basic	protein_coding	protein_coding			
SENP5	205564	hgsc.bcm.edu	37	3	196612951	196612952	+	Frame_Shift_Ins	INS	-	-	T	rs148425489		TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr3:196612951_196612952insT	ENST00000323460.5	+	2	1148_1149	c.899_900insT	c.(898-903)tcttgtfs	p.C301fs	SENP5_ENST00000445299.2_Frame_Shift_Ins_p.C301fs|SENP5_ENST00000419026.1_Intron	NM_152699.4	NP_689912.2	Q96HI0	SENP5_HUMAN	SUMO1/sentrin specific peptidase 5	301					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)		AAAGACCCTTCTTGTCGGCATC	0.53																																					p.S300fs	Ovarian(47;891 1095 11174 13858 51271)	Atlas-Indel,Pindel	.											.	SENP5	68	.	0			c.899_900insT						PASS	.																																			SO:0001589	frameshift_variant	205564	exon2			.	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.901dupT	chr3.hg19:g.196612953_196612953dupT	ENSP00000327197:p.Cys301fs	72.0	0.0	0		94.0	46.0	0.489362	NM_152699	B4DY82|Q96SA5	Frame_Shift_Ins	INS	ENST00000323460.5	hg19	CCDS3322.1																																																																																			.	.	.	none		0.530	SENP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340524.1	NM_152699	
PDS5A	23244	hgsc.bcm.edu	37	4	39851206	39851213	+	Frame_Shift_Del	DEL	CTTCATAA	CTTCATAA	-			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	CTTCATAA	CTTCATAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr4:39851206_39851213delCTTCATAA	ENST00000303538.8	-	27	3685_3692	c.3146_3153delTTATGAAG	c.(3145-3153)tttatgaagfs	p.FMK1049fs		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						CTGCCATCTTCTTCATAAAGGCATGGCT	0.38																																					p.1049_1052del		Atlas-INDEL	.											.	PDS5A	114	.	0			c.3147_3154del						PASS	.																																			SO:0001589	frameshift_variant	23244	exon27			.	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.3146_3153delTTATGAAG	chr4.hg19:g.39851206_39851213delCTTCATAA	ENSP00000303427:p.Phe1049fs	95.0	0.0	0		82.0	23.0	0.280488	NM_001100399		Frame_Shift_Del	DEL	ENST00000303538.8	hg19	CCDS47045.1																																																																																			.	.	.	none		0.380	PDS5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361287.1	NM_015200	
SERF1A	8293	hgsc.bcm.edu	37	5	70196698	70196698	+	Start_Codon_Del	DEL	T	T	-			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr5:70196698delT	ENST00000354833.3	+	0	185				SERF1A_ENST00000504458.1_Start_Codon_Del|SERF1A_ENST00000513436.2_Start_Codon_Del|SERF1A_ENST00000317633.9_Start_Codon_Del|SERF1A_ENST00000507348.1_5'Flank|SERF1A_ENST00000512649.1_5'Flank	NM_021967.2	NP_068802.1	O75920	SERF1_HUMAN	small EDRK-rich factor 1A (telomeric)						nervous system development (GO:0007399)								Lung NSC(167;4.15e-05)|Prostate(74;0.00996)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;3.04e-60)|Epithelial(20;7.09e-58)|all cancers(19;1.13e-53)|Lung(70;0.0174)		GTGGTCGGCATGGCCCGTGAG	0.687																																					p.M1fs		Atlas-INDEL	.											.	.	.	.	0			c.1delA						PASS	.																																			SO:0001582	initiator_codon_variant	8293	exon1			.	AF073518	CCDS47228.1, CCDS47229.1	5q13	2008-08-14			ENSG00000172058	ENSG00000172058			10755	protein-coding gene	gene with protein product	"""SMA modifier 1"", ""spinal muscular atrophy-related gene H4F5"""	603011		SERF1		9731538	Standard	NM_021967		Approved	H4F5, 4F5, FAM2A, SMAM1	uc003jyb.3	O75920	OTTHUMG00000162419		chr5.hg19:g.70196698delT		119.0	0.0	0		307.0	48.0	0.156352	NM_021967	B7ZKM2|O75919|Q52LK5	Frame_Shift_Del	DEL	ENST00000354833.3	hg19	CCDS47228.1																																																																																			.	.	.	none		0.687	SERF1A-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000368854.1	NM_021967	
TRIM44	54765	hgsc.bcm.edu	37	11	35684955	35684956	+	Frame_Shift_Ins	INS	-	-	T	rs534573468	byFrequency	TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr11:35684955_35684956insT	ENST00000299413.5	+	1	603_604	c.296_297insT	c.(295-300)agtgagfs	p.E100fs	RP1-276E15.1_ENST00000525573.2_lincRNA	NM_017583.4	NP_060053.2	Q96DX7	TRI44_HUMAN	tripartite motif containing 44	100	Glu-rich.					intracellular (GO:0005622)	zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(8)|lung(4)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	18	all_lung(20;0.0317)|Lung NSC(22;0.0661)|all_epithelial(35;0.115)	all_hematologic(20;0.107)				ggggaagagagtgagtcggagg	0.589																																					p.S99fs		Atlas-Indel,Pindel	.											.	TRIM44	29	.	0			c.296_297insT						PASS	.																																			SO:0001589	frameshift_variant	54765	exon1			.	BC024031	CCDS31461.1	11p13	2011-04-20	2011-01-25		ENSG00000166326	ENSG00000166326		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	19016	protein-coding gene	gene with protein product		612298	"""tripartite motif-containing 44"""				Standard	NM_017583		Approved	DIPB, MC7	uc001mwi.2	Q96DX7	OTTHUMG00000166312	ENST00000299413.5:c.297dupT	chr11.hg19:g.35684956_35684956dupT	ENSP00000299413:p.Glu100fs	174.0	0.0	0		253.0	66.0	0.26087	NM_017583	D3DR14|Q96QY2|Q9UGK0	Frame_Shift_Ins	INS	ENST00000299413.5	hg19	CCDS31461.1																																																																																			.	.	.	none		0.589	TRIM44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389081.1	NM_017583	
ARMC8	25852	hgsc.bcm.edu	37	3	137964017	137964040	+	Splice_Site	DEL	CGGAAGAAGGTGAGTCTGGGAGAG	CGGAAGAAGGTGAGTCTGGGAGAG	-			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	CGGAAGAAGGTGAGTCTGGGAGAG	CGGAAGAAGGTGAGTCTGGGAGAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr3:137964017_137964040delCGGAAGAAGGTGAGTCTGGGAGAG	ENST00000469044.1	+	12	1397_1405	c.1126_1134delCGGAAGAAGGTGAGTCTGGGAGAG	c.(1126-1134)cggaagaagdel	p.RKK376del	ARMC8_ENST00000461822.1_Splice_Site_p.RKK309del|ARMC8_ENST00000538260.1_Splice_Site_p.RKK345del|ARMC8_ENST00000491704.1_Splice_Site_p.RKK334del|ARMC8_ENST00000471453.1_In_Frame_Del_p.RKKVSLGE362del|ARMC8_ENST00000358441.2_In_Frame_Del_p.RKKVSLGE362del|ARMC8_ENST00000470821.1_In_Frame_Del_p.RKKVSLGE376del|ARMC8_ENST00000485396.1_Splice_Site_p.RKK303del|ARMC8_ENST00000489213.1_In_Frame_Del_p.RKKVSLGE334del|ARMC8_ENST00000393058.3_Splice_Site_p.RKK366del|ARMC8_ENST00000481646.1_Splice_Site_p.RKK362del	NM_001267041.1|NM_001267042.1	NP_001253970.1|NP_001253971.1	Q8IUR7	ARMC8_HUMAN	armadillo repeat containing 8	376										endometrium(2)|kidney(1)|large_intestine(7)|lung(5)|upper_aerodigestive_tract(1)	16						TGAAGACATCCGGAAGAAGGTGAGTCTGGGAGAGGGGCGTCCCC	0.491																																					p.361_364del		Atlas-Indel,Pindel	.											.	ARMC8	79	.	0			c.1083_1092del						PASS	.																																			SO:0001630	splice_region_variant	25852	exon13			.		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.1134+1CGGAAGAAGGTGAGTCTGGGAGAG>-	chr3.hg19:g.137964017_137964040delCGGAAGAAGGTGAGTCTGGGAGAG		147.0	0.0	0		139.0	22.0	0.158273	NM_015396	A8K0L2|B7Z441|B7Z453|D3DNE6|F5GWK4|Q6PIL2|Q96D19|Q96HZ5|Q9NV02|Q9NV94|Q9Y4R9	Frame_Shift_Del	DEL	ENST00000469044.1	hg19																																																																																				.	.	.	none		0.491	ARMC8-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000357560.1	NM_015396	In_Frame_Del
PSIP1	11168	hgsc.bcm.edu	37	9	15468982	15468982	+	Frame_Shift_Del	DEL	G	G	-			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr9:15468982delG	ENST00000380733.4	-	13	1522	c.1179delC	c.(1177-1179)cacfs	p.H393fs	PSIP1_ENST00000380738.4_Frame_Shift_Del_p.H393fs			O75475	PSIP1_HUMAN	PC4 and SFRS1 interacting protein 1	393					establishment of integrated proviral latency (GO:0075713)|mRNA 5'-splice site recognition (GO:0000395)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to heat (GO:0009408)|response to oxidative stress (GO:0006979)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear heterochromatin (GO:0005720)|nuclear periphery (GO:0034399)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptionally active chromatin (GO:0035327)	activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription coactivator activity (GO:0001105)|supercoiled DNA binding (GO:0097100)			breast(2)|endometrium(2)|kidney(1)|lung(3)|prostate(1)	9				GBM - Glioblastoma multiforme(50;2.38e-06)		TCATCTCTGTGTGTTTCTGAG	0.328																																					p.T394fs		Atlas-Indel,Pindel	.											.	PSIP1	93	.	0			c.1180delA						PASS	.						89.0	82.0	84.0					9																	15468982		2202	4300	6502	SO:0001589	frameshift_variant	11168	exon13			.	AF098482	CCDS6479.1, CCDS6480.1	9p22.2	2008-02-05	2004-02-24		ENSG00000164985	ENSG00000164985			9527	protein-coding gene	gene with protein product		603620	"""PC4 and SFRS1 interacting protein 2"""	PSIP2		9822615, 9885563	Standard	NM_033222		Approved	p52, LEDGF, p75	uc003zlw.4	O75475	OTTHUMG00000021021	ENST00000380733.4:c.1179delC	chr9.hg19:g.15468982delG	ENSP00000370109:p.His393fs	99.0	0.0	0		51.0	28.0	0.54902	NM_001128217	D3DRI9|O00256|O95368|Q6P391|Q86YB9|Q9NZI3|Q9UER6	Frame_Shift_Del	DEL	ENST00000380733.4	hg19	CCDS6479.1																																																																																			.	.	.	none		0.328	PSIP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055445.1	NM_033222	
FGGY	55277	hgsc.bcm.edu	37	1	60019871	60019884	+	Frame_Shift_Del	DEL	TCTGTGGAACGTCT	TCTGTGGAACGTCT	-	rs144977691|rs116481036|rs147926450	byFrequency	TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	TCTGTGGAACGTCT	TCTGTGGAACGTCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr1:60019871_60019884delTCTGTGGAACGTCT	ENST00000303721.7	+	8	1049_1062	c.875_888delTCTGTGGAACGTCT	c.(874-888)atctgtggaacgtctfs	p.ICGTS292fs	FGGY_ENST00000371212.1_Frame_Shift_Del_p.ICGTS204fs|FGGY_ENST00000371218.4_Frame_Shift_Del_p.ICGTS292fs|FGGY_ENST00000474476.1_3'UTR|FGGY_ENST00000371210.1_5'UTR	NM_018291.3	NP_060761.3	Q96C11	FGGY_HUMAN	FGGY carbohydrate kinase domain containing	292					carbohydrate metabolic process (GO:0005975)|cell death (GO:0008219)|neuron cellular homeostasis (GO:0070050)		kinase activity (GO:0016301)|phosphotransferase activity, alcohol group as acceptor (GO:0016773)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(13)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	22	all_cancers(7;7.36e-05)					CTGGCTGTCATCTGTGGAACGTCTTCTTGTCACA	0.561																																					p.292_296del		Pindel	.											.	FGGY	99	.	0			c.874_887del						PASS	.																																			SO:0001589	frameshift_variant	55277	exon8			.		CCDS611.2, CCDS44155.1, CCDS58003.1, CCDS60155.1	1p32.1	2008-10-23			ENSG00000172456	ENSG00000172456			25610	protein-coding gene	gene with protein product		611370				17671248	Standard	NM_018291		Approved	FLJ10986	uc009wac.3	Q96C11	OTTHUMG00000008424	ENST00000303721.7:c.875_888delTCTGTGGAACGTCT	chr1.hg19:g.60019871_60019884delTCTGTGGAACGTCT	ENSP00000305922:p.Ile292fs	236.0	0.0	.		157.0	48.0	0.306	NM_001113411	B1AK92|B1AK93|B1AK94|B2RDR8|D3DQ56|Q9HA63|Q9NV20	Frame_Shift_Del	DEL	ENST00000303721.7	hg19	CCDS611.2																																																																																			.	.	.	none		0.561	FGGY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023210.2	NM_001113411	
SETD2	29072	hgsc.bcm.edu	37	3	47098859	47098860	+	Frame_Shift_Del	DEL	GC	GC	-			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	GC	GC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr3:47098859_47098860delGC	ENST00000409792.3	-	15	6456_6457	c.6414_6415delGC	c.(6412-6417)cagcaafs	p.QQ2138fs		NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	2138	Low charge region.				angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)			breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		TGCATCTGTTGCTGTTGTTTCT	0.475			"""N, F, S, Mis"""		clear cell renal carcinoma																																p.2139_2139del		Pindel	.		Rec	yes		3	3p21.31	29072	SET domain containing 2		E	.	SETD2	721	.	0			c.6415_6416del						PASS	.																																			SO:0001589	frameshift_variant	29072	exon15			.	AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"""Chromatin-modifying enzymes / K-methyltransferases"""	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.6414_6415delGC	chr3.hg19:g.47098859_47098860delGC	ENSP00000386759:p.Gln2138fs	163.0	0.0	.		114.0	48.0	0.421	NM_014159	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Frame_Shift_Del	DEL	ENST00000409792.3	hg19	CCDS2749.2																																																																																			.	.	.	none		0.475	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159	
PDS5A	23244	hgsc.bcm.edu	37	4	39851206	39851214	+	In_Frame_Del	DEL	CTTCATAAA	CTTCATAAA	-			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	CTTCATAAA	CTTCATAAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr4:39851206_39851214delCTTCATAAA	ENST00000303538.8	-	27	3684_3692	c.3145_3153delTTTATGAAG	c.(3145-3153)tttatgaagdel	p.FMK1049del		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						CTGCCATCTTCTTCATAAAGGCATGGCTA	0.383																																					p.1049_1052del		Pindel	.											.	PDS5A	114	.	0			c.3146_3154del						PASS	.																																			SO:0001651	inframe_deletion	23244	exon27			.	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.3145_3153delTTTATGAAG	chr4.hg19:g.39851206_39851214delCTTCATAAA	ENSP00000303427:p.Phe1049_Lys1051del	93.0	0.0	.		86.0	11.0	0.128	NM_001100399		In_Frame_Del	DEL	ENST00000303538.8	hg19	CCDS47045.1																																																																																			.	.	.	none		0.383	PDS5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361287.1	NM_015200	
