#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
PRDM16	63976	hgsc.bcm.edu	37	1	3334463	3334463	+	Silent	SNP	C	C	G			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr1:3334463C>G	ENST00000270722.5	+	11	2812	c.2763C>G	c.(2761-2763)tcC>tcG	p.S921S	PRDM16_ENST00000512462.1_3'UTR|PRDM16_ENST00000378398.3_Silent_p.S921S|PRDM16_ENST00000378391.2_Silent_p.S921S|PRDM16_ENST00000442529.2_Silent_p.S920S|PRDM16_ENST00000511072.1_Silent_p.S922S|PRDM16_ENST00000514189.1_Silent_p.S921S|PRDM16_ENST00000441472.2_Silent_p.S920S			Q9HAZ2	PRD16_HUMAN	PR domain containing 16	921	Interaction with CTBP1 and CTBP2. {ECO:0000250}.|Mediates interaction with SKI and regulation of TGF-beta signaling.				brown fat cell differentiation (GO:0050873)|negative regulation of granulocyte differentiation (GO:0030853)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neurogenesis (GO:0022008)|palate development (GO:0060021)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cellular respiration (GO:0043457)|somatic stem cell maintenance (GO:0035019)|tongue development (GO:0043586)|transcription, DNA-templated (GO:0006351)|white fat cell differentiation (GO:0050872)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)			breast(4)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(7)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(3)	59	all_cancers(77;0.00208)|all_epithelial(69;0.000732)|Ovarian(185;0.0634)|Lung NSC(156;0.109)|all_lung(157;0.111)	all_epithelial(116;2.03e-21)|all_lung(118;7.55e-09)|Lung NSC(185;1.28e-06)|Breast(487;0.000792)|Renal(390;0.00137)|Hepatocellular(190;0.00515)|Myeloproliferative disorder(586;0.0267)|Ovarian(437;0.0365)|Lung SC(97;0.114)|Medulloblastoma(700;0.134)		Epithelial(90;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(86;1.99e-20)|GBM - Glioblastoma multiforme(42;3.72e-11)|Colorectal(212;0.000425)|BRCA - Breast invasive adenocarcinoma(365;0.000946)|COAD - Colon adenocarcinoma(227;0.000968)|Kidney(185;0.00155)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0175)|Lung(427;0.137)		CGGGCAGCTCCCTGCAGCCCC	0.602			T	EVI1	"""MDS, AML"""																																p.S921S		Atlas-SNP	.		Dom	yes		1	1p36.23-p33	63976	PR domain containing 16		L	.	PRDM16	147	.	0			c.C2763G						PASS	.						79.0	89.0	86.0					1																	3334463		2010	4175	6185	SO:0001819	synonymous_variant	63976	exon11			CAGCTCCCTGCAG	AF294278	CCDS41236.1, CCDS44048.1, CCDS41236.2, CCDS44048.2	1p36.23-p33	2013-01-08			ENSG00000142611	ENSG00000142611		"""Zinc fingers, C2H2-type"""	14000	protein-coding gene	gene with protein product	"""MDS1/EVI1-like"", ""PR-domain zinc finger protein 16"", ""transcription factor MEL1"""	605557				11050005	Standard	NM_199454		Approved	MEL1, PFM13, KIAA1675, MGC166915	uc001akf.3	Q9HAZ2	OTTHUMG00000000581	ENST00000270722.5:c.2763C>G	chr1.hg19:g.3334463C>G		395.0	0.0	.		315.0	109.0	.	NM_022114	A6NHQ8|B1AJP7|B1AJP8|B1AJP9|B1WB48|Q8WYJ9|Q9C0I8	Silent	SNP	ENST00000270722.5	hg19	CCDS41236.2																																																																																			.	.	.	none		0.602	PRDM16-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000001382.3	NM_022114	
ZMYM6	9204	hgsc.bcm.edu	37	1	35452999	35452999	+	Silent	SNP	G	G	A	rs61744849		TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr1:35452999G>A	ENST00000357182.4	-	16	3911	c.3684C>T	c.(3682-3684)acC>acT	p.T1228T	ZMYM6_ENST00000373340.2_Intron|ZMYM6_ENST00000487874.1_Intron|RP11-244H3.1_ENST00000417456.1_RNA|ZMYM6NB_ENST00000373337.3_5'Flank|ZMYM6_ENST00000493328.1_5'UTR	NM_007167.3	NP_009098.3	O95789	ZMYM6_HUMAN	zinc finger, MYM-type 6	1228					cytoskeleton organization (GO:0007010)|multicellular organismal development (GO:0007275)|regulation of cell morphogenesis (GO:0022604)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(10)|ovary(4)|pancreas(1)|prostate(1)|skin(1)	44		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.13)				CTTCGAAGTCGGTGAGATTAT	0.358																																					p.T1228T		Atlas-SNP	.											.	ZMYM6	110	.	0			c.C3684T						PASS	.						86.0	85.0	85.0					1																	35452999		1822	4084	5906	SO:0001819	synonymous_variant	9204	exon16			GAAGTCGGTGAGA	AF055470	CCDS387.2	1p34.2	2014-05-12	2005-09-12	2005-09-12	ENSG00000163867	ENSG00000163867		"""Zinc fingers, MYM type"", ""Zinc fingers, BED-type"""	13050	protein-coding gene	gene with protein product	"""zinc finger, BED-type containing 7"""	613567	"""zinc finger protein 258"", ""zinc finger, MYM-type containing 6"""	ZNF258		10486218, 23533661	Standard	NM_007167		Approved	ZNF198L4, MYM, Buster2, ZBED7	uc001byh.3	O95789	OTTHUMG00000004163	ENST00000357182.4:c.3684C>T	chr1.hg19:g.35452999G>A		98.0	0.0	.		90.0	4.0	.	NM_007167	B4DRJ6|Q32Q23|Q4G108|Q5SVZ9|Q5SW00|Q69YL4|Q96IY0|Q9NWF1|Q9P2J4	Silent	SNP	ENST00000357182.4	hg19	CCDS387.2																																																																																			.	G|0.986;A|0.014	0.014	weak		0.358	ZMYM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011999.1	NM_007167	
FLAD1	80308	hgsc.bcm.edu	37	1	154956520	154956520	+	Missense_Mutation	SNP	T	T	G			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr1:154956520T>G	ENST00000292180.3	+	1	672	c.350T>G	c.(349-351)aTt>aGt	p.I117S	FLAD1_ENST00000315144.10_Missense_Mutation_p.I20S|FLAD1_ENST00000368433.1_Missense_Mutation_p.I117S|FLAD1_ENST00000487371.1_3'UTR|FLAD1_ENST00000368431.3_De_novo_Start_InFrame|FLAD1_ENST00000368432.1_Missense_Mutation_p.I20S	NM_025207.4	NP_079483.3	Q8NFF5	FAD1_HUMAN	flavin adenine dinucleotide synthetase 1	117	Molybdenum cofactor biosynthesis protein- like.				FAD biosynthetic process (GO:0006747)|Mo-molybdopterin cofactor biosynthetic process (GO:0006777)|riboflavin metabolic process (GO:0006771)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|FMN adenylyltransferase activity (GO:0003919)			endometrium(3)|kidney(4)|large_intestine(2)|lung(7)|ovary(3)|skin(3)	22	all_epithelial(22;2.77e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			GGCATCATCATTGTTGGAGAT	0.587																																					p.I117S		Atlas-SNP	.											.	FLAD1	52	.	0			c.T350G						PASS	.						25.0	23.0	23.0					1																	154956520		2203	4300	6503	SO:0001583	missense	80308	exon1			TCATCATTGTTGG		CCDS1078.1, CCDS1079.1, CCDS53371.1, CCDS53372.1	1q22	2013-03-05	2013-03-05		ENSG00000160688	ENSG00000160688	2.7.7.2		24671	protein-coding gene	gene with protein product		610595	"""Fad1, flavin adenine dinucleotide synthetase, homolog (yeast)"", ""FAD1 flavin adenine dinucleotide synthetase homolog (S. cerevisiae)"", ""flavin adenine dinucleotide synthetase"""				Standard	NM_001184891		Approved	PP591, FAD1	uc001fgf.2	Q8NFF5	OTTHUMG00000037416	ENST00000292180.3:c.350T>G	chr1.hg19:g.154956520T>G	ENSP00000292180:p.Ile117Ser	41.0	0.0	.		54.0	28.0	.	NM_025207	Q8N5J1|Q8N686|Q8WU93|Q8WUJ4|Q96CR8|Q99764|Q9HBN6	Missense_Mutation	SNP	ENST00000292180.3	hg19	CCDS1078.1	.	.	.	.	.	.	.	.	.	.	T	32	5.175833	0.94807	.	.	ENSG00000160688	ENST00000368433;ENST00000315144;ENST00000368432;ENST00000292180	T;T;T;T	0.75477	-0.94;-0.94;-0.94;-0.94	5.45	5.45	0.79879	Molybdopterin binding (4);	0.000000	0.85682	D	0.000000	T	0.72211	0.3432	L	0.49126	1.545	0.80722	D	1	P	0.43287	0.802	P	0.52343	0.696	T	0.76528	-0.2926	10	0.62326	D	0.03	-10.5785	13.7506	0.62906	0.0:0.0:0.0:1.0	.	117	Q8NFF5	FAD1_HUMAN	S	117;20;20;117	ENSP00000357418:I117S;ENSP00000317296:I20S;ENSP00000357417:I20S;ENSP00000292180:I117S	ENSP00000292180:I117S	I	+	2	0	FLAD1	153223144	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.610000	0.74178	2.065000	0.61736	0.454000	0.30748	ATT	.	.	.	none		0.587	FLAD1-001	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000091089.1	NM_025207	
INSRR	3645	hgsc.bcm.edu	37	1	156823981	156823981	+	Missense_Mutation	SNP	T	T	C			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr1:156823981T>C	ENST00000368195.3	-	2	596	c.200A>G	c.(199-201)gAc>gGc	p.D67G	NTRK1_ENST00000392302.2_Intron	NM_014215.2	NP_055030.1	P14616	INSRR_HUMAN	insulin receptor-related receptor	67					actin cytoskeleton reorganization (GO:0031532)|cellular response to alkaline pH (GO:0071469)|male sex determination (GO:0030238)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(13)|ovary(7)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	42	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					GCCGCGGAAGTCCTCCCCGGT	0.627																																					p.D67G		Atlas-SNP	.											.	INSRR	309	.	0			c.A200G						PASS	.						70.0	69.0	69.0					1																	156823981		2203	4300	6503	SO:0001583	missense	3645	exon2			CGGAAGTCCTCCC	J05046	CCDS1160.1	1q21-q23	2013-02-11			ENSG00000027644	ENSG00000027644		"""Fibronectin type III domain containing"""	6093	protein-coding gene	gene with protein product		147671				2768234, 2249481	Standard	NM_014215		Approved	IRR	uc010pht.2	P14616	OTTHUMG00000041291	ENST00000368195.3:c.200A>G	chr1.hg19:g.156823981T>C	ENSP00000357178:p.Asp67Gly	49.0	0.0	.		63.0	22.0	.	NM_014215	O60724|Q5VZS3	Missense_Mutation	SNP	ENST00000368195.3	hg19	CCDS1160.1	.	.	.	.	.	.	.	.	.	.	T	19.23	3.787541	0.70337	.	.	ENSG00000027644	ENST00000368195	T	0.79749	-1.3	5.06	5.06	0.68205	EGF receptor, L domain (1);	0.000000	0.50627	D	0.000108	T	0.77025	0.4070	.	.	.	0.41280	D	0.986901	P	0.48640	0.913	P	0.48901	0.594	T	0.80919	-0.1167	9	0.62326	D	0.03	.	12.7616	0.57367	0.0:0.0:0.0:1.0	.	67	P14616	INSRR_HUMAN	G	67	ENSP00000357178:D67G	ENSP00000357178:D67G	D	-	2	0	INSRR	155090605	1.000000	0.71417	1.000000	0.80357	0.891000	0.51852	3.428000	0.52792	1.918000	0.55548	0.455000	0.32223	GAC	.	.	.	none		0.627	INSRR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098929.1	NM_014215	
KIAA1804	84451	hgsc.bcm.edu	37	1	233518353	233518353	+	Missense_Mutation	SNP	G	G	T			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr1:233518353G>T	ENST00000366624.3	+	10	3268	c.3007G>T	c.(3007-3009)Gac>Tac	p.D1003Y	MLK4_ENST00000366622.1_Missense_Mutation_p.D449Y	NM_032435.2	NP_115811.2																					ACTGGATGCTGACGTGGAAGG	0.522																																					p.D1003Y		Atlas-SNP	.											.	KIAA1804	129	.	0			c.G3007T						PASS	.						109.0	92.0	98.0					1																	233518353		2203	4300	6503	SO:0001583	missense	0	exon10			GATGCTGACGTGG																												ENST00000366624.3:c.3007G>T	chr1.hg19:g.233518353G>T	ENSP00000355583:p.Asp1003Tyr	49.0	0.0	.		91.0	33.0	.	NM_032435		Missense_Mutation	SNP	ENST00000366624.3	hg19	CCDS1598.1	.	.	.	.	.	.	.	.	.	.	G	18.64	3.667893	0.67814	.	.	ENSG00000143674	ENST00000366624;ENST00000366622	T;T	0.80214	-1.35;2.71	4.77	2.47	0.30058	.	0.256767	0.28901	N	0.013763	T	0.81621	0.4861	L	0.41492	1.28	0.09310	N	0.999995	D;D	0.89917	1.0;0.966	D;P	0.69479	0.964;0.603	T	0.70590	-0.4830	10	0.87932	D	0	.	6.1916	0.20528	0.1283:0.1738:0.6979:0.0	.	450;1003	Q5TCX8-3;Q5TCX8	.;M3KL4_HUMAN	Y	1003;449	ENSP00000355583:D1003Y;ENSP00000355581:D449Y	ENSP00000355581:D449Y	D	+	1	0	RP5-862P8.2	231584976	0.988000	0.35896	0.000000	0.03702	0.340000	0.28889	3.723000	0.54955	0.379000	0.24794	0.563000	0.77884	GAC	.	.	.	none		0.522	MLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092495.1		
GLS	2744	hgsc.bcm.edu	37	2	191769861	191769861	+	Missense_Mutation	SNP	T	T	C			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr2:191769861T>C	ENST00000320717.3	+	6	1205	c.947T>C	c.(946-948)cTa>cCa	p.L316P	GLS_ENST00000338435.4_Missense_Mutation_p.L316P	NM_014905.4	NP_055720.3	O94925	GLSK_HUMAN	glutaminase	316					cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|glutamate biosynthetic process (GO:0006537)|glutamate secretion (GO:0014047)|glutamine catabolic process (GO:0006543)|neurotransmitter secretion (GO:0007269)|protein homotetramerization (GO:0051289)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|small molecule metabolic process (GO:0044281)|suckling behavior (GO:0001967)|synaptic transmission (GO:0007268)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	glutaminase activity (GO:0004359)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|lung(9)|ovary(1)|skin(1)|urinary_tract(1)	16			OV - Ovarian serous cystadenocarcinoma(117;0.00625)|Epithelial(96;0.0744)|all cancers(119;0.181)		L-Glutamine(DB00130)	CCGAGTGGACTAAGATTCAAC	0.328																																					p.L316P		Atlas-SNP	.											.	GLS	47	.	0			c.T947C						PASS	.						106.0	106.0	106.0					2																	191769861		2203	4300	6503	SO:0001583	missense	2744	exon6			GTGGACTAAGATT	AB020645	CCDS2308.1, CCDS58744.1	2q32-q34	2013-01-10			ENSG00000115419	ENSG00000115419	3.5.1.2	"""Ankyrin repeat domain containing"""	4331	protein-coding gene	gene with protein product		138280				10048485	Standard	NM_014905		Approved	KIAA0838, GLS1	uc002usf.3	O94925	OTTHUMG00000132701	ENST00000320717.3:c.947T>C	chr2.hg19:g.191769861T>C	ENSP00000317379:p.Leu316Pro	85.0	0.0	.		75.0	4.0	.	NM_014905	Q9UL05|Q9UL06|Q9UL07|Q9UN40	Missense_Mutation	SNP	ENST00000320717.3	hg19	CCDS2308.1	.	.	.	.	.	.	.	.	.	.	T	18.98	3.737804	0.69304	.	.	ENSG00000115419	ENST00000320717;ENST00000338435	T;T	0.44083	0.93;0.93	5.74	5.74	0.90152	Beta-lactamase/transpeptidase-like (1);	0.000000	0.64402	D	0.000001	T	0.59905	0.2228	M	0.84511	2.7	0.80722	D	1	D;D	0.59767	0.978;0.986	P;P	0.52454	0.683;0.699	T	0.62932	-0.6749	10	0.32370	T	0.25	-11.2118	16.3785	0.83418	0.0:0.0:0.0:1.0	.	316;316	O94925;O94925-3	GLSK_HUMAN;.	P	316	ENSP00000317379:L316P;ENSP00000340689:L316P	ENSP00000317379:L316P	L	+	2	0	GLS	191478106	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.997000	0.88414	2.323000	0.78572	0.529000	0.55759	CTA	.	.	.	none		0.328	GLS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255999.2		
DOCK10	55619	hgsc.bcm.edu	37	2	225688357	225688357	+	Missense_Mutation	SNP	C	C	T	rs375357151		TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr2:225688357C>T	ENST00000258390.7	-	28	3111	c.3044G>A	c.(3043-3045)cGg>cAg	p.R1015Q	DOCK10_ENST00000409592.3_Missense_Mutation_p.R1009Q	NM_014689.2	NP_055504.2	Q96BY6	DOC10_HUMAN	dedicator of cytokinesis 10	1015					regulation of cell migration (GO:0030334)|small GTPase mediated signal transduction (GO:0007264)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(10)|large_intestine(16)|lung(40)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	87		Renal(207;0.0113)|all_lung(227;0.0486)|Lung NSC(271;0.0653)|all_hematologic(139;0.14)		Epithelial(121;2.37e-10)|all cancers(144;2.26e-07)|Lung(261;0.0143)|LUSC - Lung squamous cell carcinoma(224;0.0178)		TCTCTGAGGCCGGGGAAGCTA	0.368																																					p.R1015Q		Atlas-SNP	.											.	DOCK10	308	.	0			c.G3044A						PASS	.	C	GLN/ARG	1,3805		0,1,1902	100.0	96.0	98.0		3044	5.9	0.7	2		98	0,8240		0,0,4120	no	missense	DOCK10	NM_014689.2	43	0,1,6022	TT,TC,CC		0.0,0.0263,0.0083	probably-damaging	1015/2187	225688357	1,12045	1903	4120	6023	SO:0001583	missense	55619	exon28			TGAGGCCGGGGAA	AB014594	CCDS46528.1, CCDS74661.1	2q36.3	2013-01-10			ENSG00000135905	ENSG00000135905		"""Pleckstrin homology (PH) domain containing"""	23479	protein-coding gene	gene with protein product	"""zizimin3"""	611518				12432077	Standard	NM_014689		Approved	ZIZ3, KIAA0694	uc010fwz.1	Q96BY6	OTTHUMG00000153428	ENST00000258390.7:c.3044G>A	chr2.hg19:g.225688357C>T	ENSP00000258390:p.Arg1015Gln	27.0	0.0	.		42.0	20.0	.	NM_014689	B3FL70|O75178|Q9NW06|Q9NXI8	Missense_Mutation	SNP	ENST00000258390.7	hg19	CCDS46528.1	.	.	.	.	.	.	.	.	.	.	C	32	5.175160	0.94807	2.63E-4	0.0	ENSG00000135905	ENST00000409592;ENST00000258390	T;T	0.03635	3.86;3.86	5.9	5.9	0.94986	.	0.050922	0.85682	D	0.000000	T	0.26011	0.0634	M	0.88775	2.98	0.43287	D	0.995263	D;D	0.89917	1.0;1.0	D;D	0.85130	0.996;0.997	T	0.01280	-1.1397	10	0.87932	D	0	.	20.2799	0.98512	0.0:1.0:0.0:0.0	.	1015;1009	Q96BY6;B3FL70	DOC10_HUMAN;.	Q	1009;1015	ENSP00000386694:R1009Q;ENSP00000258390:R1015Q	ENSP00000258390:R1015Q	R	-	2	0	DOCK10	225396601	1.000000	0.71417	0.705000	0.30386	0.991000	0.79684	6.501000	0.73691	2.800000	0.96347	0.643000	0.83706	CGG	.	.	.	weak		0.368	DOCK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331246.1		
RAB17	64284	hgsc.bcm.edu	37	2	238494751	238494751	+	Missense_Mutation	SNP	T	T	A			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr2:238494751T>A	ENST00000264601.3	-	2	676	c.47A>T	c.(46-48)cAg>cTg	p.Q16L	RAB17_ENST00000409822.1_Intron|RAB17_ENST00000409576.1_Intron|RAB17_ENST00000416106.1_5'UTR|RAB17_ENST00000538644.1_5'UTR	NM_022449.3	NP_071894.1	Q9H0T7	RAB17_HUMAN	RAB17, member RAS oncogene family	16					cilium assembly (GO:0042384)|endocytic recycling (GO:0032456)|establishment of melanosome localization (GO:0032401)|filopodium assembly (GO:0046847)|GTP catabolic process (GO:0006184)|immunoglobulin transcytosis in epithelial cells mediated by polymeric immunoglobulin receptor (GO:0002415)|melanosome transport (GO:0032402)|protein transport (GO:0015031)|regulation of dendrite development (GO:0050773)|regulation of filopodium assembly (GO:0051489)|regulation of synapse assembly (GO:0051963)|small GTPase mediated signal transduction (GO:0007264)|transcytosis (GO:0045056)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|dendrite (GO:0030425)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|melanosome (GO:0042470)|neuronal cell body (GO:0043025)|recycling endosome (GO:0055037)|recycling endosome membrane (GO:0055038)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)|lung(1)	4		Renal(207;0.00272)|Breast(86;0.00297)|all_hematologic(139;0.182)|Ovarian(221;0.221)		Epithelial(121;9.36e-23)|OV - Ovarian serous cystadenocarcinoma(60;1.26e-10)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000354)|Lung(119;0.011)|LUSC - Lung squamous cell carcinoma(224;0.026)		CACACGGGGCTGGCTGGGGGC	0.587																																					p.Q16L	Colon(56;987 1029 6466 13943 27336)	Atlas-SNP	.											.	RAB17	17	.	0			c.A47T						PASS	.						47.0	51.0	49.0					2																	238494751		2203	4300	6503	SO:0001583	missense	64284	exon2			CGGGGCTGGCTGG	AK022600	CCDS2520.1	2q37.3	2008-05-23			ENSG00000124839	ENSG00000124839		"""RAB, member RAS oncogene"""	16523	protein-coding gene	gene with protein product		602206				9624171	Standard	NM_022449		Approved		uc002vwz.2	Q9H0T7	OTTHUMG00000133299	ENST00000264601.3:c.47A>T	chr2.hg19:g.238494751T>A	ENSP00000264601:p.Gln16Leu	103.0	0.0	.		95.0	29.0	.	NM_022449	Q53QV6|Q6IA73|Q6PJZ0|Q9BVU1|Q9H9U9	Missense_Mutation	SNP	ENST00000264601.3	hg19	CCDS2520.1	.	.	.	.	.	.	.	.	.	.	T	15.36	2.811895	0.50527	.	.	ENSG00000124839	ENST00000264601;ENST00000411462	T;T	0.79940	-1.32;-1.32	4.47	0.593	0.17478	.	0.379404	0.19708	N	0.107863	T	0.55816	0.1944	N	0.11000	0.08	0.80722	D	1	P	0.38922	0.651	B	0.32677	0.15	T	0.44636	-0.9315	10	0.44086	T	0.13	-11.2708	5.8348	0.18601	0.0:0.0935:0.347:0.5595	.	16	Q9H0T7	RAB17_HUMAN	L	16	ENSP00000264601:Q16L;ENSP00000400240:Q16L	ENSP00000264601:Q16L	Q	-	2	0	RAB17	238159490	1.000000	0.71417	0.067000	0.19924	0.045000	0.14185	2.158000	0.42329	-0.134000	0.11516	0.482000	0.46254	CAG	.	.	.	none		0.587	RAB17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257084.2		
KIF1A	547	hgsc.bcm.edu	37	2	241696846	241696846	+	Intron	SNP	C	C	A			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr2:241696846C>A	ENST00000320389.7	-	25	2714				KIF1A_ENST00000498729.2_Missense_Mutation_p.E916D	NM_004321.6	NP_004312.2	Q12756	KIF1A_HUMAN	kinesin family member 1A						anterograde axon cargo transport (GO:0008089)|ATP catabolic process (GO:0006200)|cell death (GO:0008219)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|motor activity (GO:0003774)|plus-end-directed microtubule motor activity (GO:0008574)			NS(1)|central_nervous_system(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(25)|ovary(1)|prostate(5)|skin(2)|urinary_tract(1)	66		all_epithelial(40;1.35e-15)|Breast(86;2.14e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0295)|all_neural(83;0.0459)|Lung NSC(271;0.0942)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;6.12e-30)|all cancers(36;3.46e-27)|OV - Ovarian serous cystadenocarcinoma(60;1.38e-14)|Kidney(56;5e-09)|KIRC - Kidney renal clear cell carcinoma(57;5e-08)|BRCA - Breast invasive adenocarcinoma(100;5.87e-06)|Lung(119;0.00209)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Colorectal(34;0.0282)|COAD - Colon adenocarcinoma(134;0.176)		cctcatcctcctcctcctcct	0.687																																					p.E916D		Atlas-SNP	.											.	KIF1A	152	.	0			c.G2748T						PASS	.																																			SO:0001627	intron_variant	547	exon27			ATCCTCCTCCTCC	AF004425	CCDS46561.1, CCDS58757.1	2q37.2	2014-09-17	2004-01-09	2004-01-14	ENSG00000130294	ENSG00000130294		"""Kinesins"", ""Pleckstrin homology (PH) domain containing"""	888	protein-coding gene	gene with protein product		601255	"""axonal transport of synaptic vesicles"", ""chromosome 2 open reading frame 20"", ""spastic paraplegia 30 (autosomal recessive)"""	ATSV, C2orf20, SPG30		7539720, 10323250, 22258533	Standard	NM_001244008		Approved	UNC104	uc010fzk.3	Q12756	OTTHUMG00000151940	ENST00000320389.7:c.2555+930G>T	chr2.hg19:g.241696846C>A		119.0	0.0	.		137.0	16.0	.	NM_001244008	B0I1S5|F5H045|O95068|Q13355|Q14752|Q2NKJ6|Q4LE42|Q53T78|Q59GH1|Q63Z40|Q6P1R9|Q7KZ57	Missense_Mutation	SNP	ENST00000320389.7	hg19	CCDS46561.1	.	.	.	.	.	.	.	.	.	.	C	11.67	1.707384	0.30322	.	.	ENSG00000130294	ENST00000498729;ENST00000373308;ENST00000404283	T;T	0.73047	-0.63;-0.71	4.04	3.1	0.35709	.	.	.	.	.	T	0.49830	0.1580	.	.	.	0.26677	N	0.971617	B;B	0.06786	0.001;0.0	B;B	0.06405	0.002;0.002	T	0.24835	-1.0149	8	0.11794	T	0.64	.	10.7257	0.46066	0.3406:0.6594:0.0:0.0	.	916;916	F5H045;Q12756-2	.;.	D	916	ENSP00000438388:E916D;ENSP00000384231:E916D	ENSP00000362405:E916D	E	-	3	2	KIF1A	241345519	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	3.037000	0.49775	1.793000	0.52555	0.462000	0.41574	GAG	.	.	.	none		0.687	KIF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324536.3	NM_138483	
CACNA1D	776	hgsc.bcm.edu	37	3	53845336	53845336	+	Missense_Mutation	SNP	T	T	C			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr3:53845336T>C	ENST00000350061.5	+	48	6900	c.6389T>C	c.(6388-6390)cTa>cCa	p.L2130P	CACNA1D_ENST00000288139.4_Missense_Mutation_p.L2150P|CACNA1D_ENST00000422281.2_Missense_Mutation_p.L2106P	NM_001128840.1	NP_001122312.1	Q01668	CAC1D_HUMAN	calcium channel, voltage-dependent, L type, alpha 1D subunit	2130					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|energy reserve metabolic process (GO:0006112)|membrane depolarization during action potential (GO:0086010)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|membrane repolarization during SA node cell action potential (GO:0086052)|positive regulation of calcium ion transport (GO:0051928)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of insulin secretion (GO:0050796)|regulation of potassium ion transmembrane transport (GO:1901379)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|ankyrin binding (GO:0030506)|high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)|voltage-gated calcium channel activity involved in cardiac muscle cell action potential (GO:0086007)|voltage-gated calcium channel activity involved SA node cell action potential (GO:0086059)			breast(3)|central_nervous_system(9)|cervix(2)|endometrium(11)|kidney(7)|large_intestine(13)|liver(1)|lung(29)|ovary(6)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	90				BRCA - Breast invasive adenocarcinoma(193;0.00029)|KIRC - Kidney renal clear cell carcinoma(284;0.0145)|Kidney(284;0.0175)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)	Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	GACTATGAGCTACAGGACTTT	0.602																																					p.L2150P		Atlas-SNP	.											.	CACNA1D	324	.	0			c.T6449C						PASS	.						68.0	63.0	65.0					3																	53845336		2203	4300	6503	SO:0001583	missense	776	exon49			ATGAGCTACAGGA	AB209171	CCDS2872.1, CCDS46848.1, CCDS46849.1	3p14.3	2012-03-07			ENSG00000157388	ENSG00000157388		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1391	protein-coding gene	gene with protein product		114206		CCHL1A2, CACNL1A2		1664412	Standard	NM_000720		Approved	Cav1.3, CACH3, CACN4	uc003dgu.5	Q01668	OTTHUMG00000158278	ENST00000350061.5:c.6389T>C	chr3.hg19:g.53845336T>C	ENSP00000288133:p.Leu2130Pro	64.0	0.0	.		85.0	29.0	.	NM_000720	B0FYA3|Q13916|Q13931|Q71UT1|Q9UDC3	Missense_Mutation	SNP	ENST00000350061.5	hg19	CCDS46848.1	.	.	.	.	.	.	.	.	.	.	T	17.42	3.384600	0.61845	.	.	ENSG00000157388	ENST00000350061;ENST00000288139;ENST00000422281;ENST00000481478	D;D;D;D	0.96265	-3.93;-3.96;-3.95;-3.95	5.56	4.37	0.52481	.	0.786356	0.11452	N	0.562709	D	0.97455	0.9167	M	0.73962	2.25	0.80722	D	1	P;D;D;D	0.65815	0.836;0.994;0.966;0.995	P;P;P;D	0.63957	0.572;0.878;0.642;0.92	D	0.94470	0.7684	10	0.33940	T	0.23	.	12.0173	0.53321	0.1296:0.0:0.0:0.8703	.	2106;1823;2130;2150	B0FYA3;Q59GD8;Q01668;Q01668-2	.;.;CAC1D_HUMAN;.	P	2130;2150;2106;1823	ENSP00000288133:L2130P;ENSP00000288139:L2150P;ENSP00000409174:L2106P;ENSP00000418014:L1823P	ENSP00000288139:L2150P	L	+	2	0	CACNA1D	53820376	1.000000	0.71417	0.997000	0.53966	0.974000	0.67602	7.466000	0.80914	1.010000	0.39314	0.533000	0.62120	CTA	.	.	.	none		0.602	CACNA1D-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350557.1	NM_000720	
SHQ1	55164	hgsc.bcm.edu	37	3	72842103	72842103	+	Missense_Mutation	SNP	T	T	C			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr3:72842103T>C	ENST00000325599.8	-	10	1284	c.1145A>G	c.(1144-1146)tAc>tGc	p.Y382C	SHQ1_ENST00000463369.1_Missense_Mutation_p.Y354C|SHQ1_ENST00000468371.1_5'UTR	NM_018130.2	NP_060600.2	Q6PI26	SHQ1_HUMAN	SHQ1, H/ACA ribonucleoprotein assembly factor	382					negative regulation of rRNA processing (GO:2000233)|positive regulation of apoptotic process (GO:0043065)|ribonucleoprotein complex assembly (GO:0022618)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				NS(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	27		Prostate(10;0.00482)|Lung NSC(201;0.0339)|Myeloproliferative disorder(1037;0.204)		BRCA - Breast invasive adenocarcinoma(55;9.68e-05)|Epithelial(33;0.000563)|LUSC - Lung squamous cell carcinoma(21;0.00229)|Lung(16;0.00688)|KIRC - Kidney renal clear cell carcinoma(39;0.018)|Kidney(39;0.0213)		GTCTGAGATGTAGAGATCATT	0.333																																					p.Y382C		Atlas-SNP	.											.	SHQ1	60	.	0			c.A1145G						PASS	.						85.0	83.0	83.0					3																	72842103		2203	4299	6502	SO:0001583	missense	55164	exon10			GAGATGTAGAGAT	BC025270	CCDS33788.1	3p13	2013-01-08	2013-01-08		ENSG00000144736	ENSG00000144736			25543	protein-coding gene	gene with protein product		613663	"""SHQ1 homolog (S. cerevisiae)"""			12477932	Standard	NM_018130		Approved	FLJ10539, Shq1p	uc003dpf.3	Q6PI26	OTTHUMG00000158814	ENST00000325599.8:c.1145A>G	chr3.hg19:g.72842103T>C	ENSP00000315182:p.Tyr382Cys	51.0	0.0	.		54.0	17.0	.	NM_018130	B4DL05|Q6MZJ4|Q7Z748|Q9H7E5|Q9NVS8	Missense_Mutation	SNP	ENST00000325599.8	hg19	CCDS33788.1	.	.	.	.	.	.	.	.	.	.	T	19.89	3.911519	0.72983	.	.	ENSG00000144736	ENST00000325599;ENST00000463369	T;T	0.42900	0.99;0.96	5.85	5.85	0.93711	SHQ1 protein (1);	0.129663	0.53938	D	0.000048	T	0.67618	0.2912	M	0.86651	2.83	0.80722	D	1	D	0.89917	1.0	D	0.77557	0.99	T	0.73603	-0.3930	10	0.87932	D	0	-9.0575	11.9499	0.52948	0.1373:0.0:0.0:0.8627	.	382	Q6PI26	SHQ1_HUMAN	C	382;354	ENSP00000315182:Y382C;ENSP00000417452:Y354C	ENSP00000315182:Y382C	Y	-	2	0	SHQ1	72924793	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.194000	0.72082	2.237000	0.73441	0.528000	0.53228	TAC	.	.	.	none		0.333	SHQ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352310.1	NM_018130	
PIK3CB	5291	hgsc.bcm.edu	37	3	138478176	138478176	+	Missense_Mutation	SNP	T	T	C			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr3:138478176T>C	ENST00000477593.1	-	2	83	c.10A>G	c.(10-12)Agt>Ggt	p.S4G	PIK3CB_ENST00000289153.2_Missense_Mutation_p.S4G			P42338	PK3CB_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit beta	4					activation of MAPK activity (GO:0000187)|autophagy (GO:0006914)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|cellular calcium ion homeostasis (GO:0006874)|chemotaxis (GO:0006935)|embryonic cleavage (GO:0040016)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|positive regulation of autophagy (GO:0010508)|regulation of cell-matrix adhesion (GO:0001952)|regulation of clathrin-mediated endocytosis (GO:2000369)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytosol (GO:0005829)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)			NS(1)|breast(3)|endometrium(5)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(4)	41					Caffeine(DB00201)	ATTATGAAACTGAAGCACATT	0.423																																					p.S4G		Atlas-SNP	.											PIK3CB,NS,carcinoma,0,1	PIK3CB	103	.	0			c.A10G						PASS	.						82.0	79.0	80.0					3																	138478176		2203	4300	6503	SO:0001583	missense	5291	exon1			TGAAACTGAAGCA		CCDS3104.1	3q22.3	2013-09-19	2012-07-13		ENSG00000051382	ENSG00000051382	2.7.1.153		8976	protein-coding gene	gene with protein product		602925	"""phosphoinositide-3-kinase, catalytic, beta polypeptide"""	PIK3C1		8246984	Standard	NM_006219		Approved		uc011bmq.3	P42338	OTTHUMG00000159893	ENST00000477593.1:c.10A>G	chr3.hg19:g.138478176T>C	ENSP00000418143:p.Ser4Gly	222.0	0.0	.		239.0	81.0	.	NM_006219	D3DNF0|Q24JU2	Missense_Mutation	SNP	ENST00000477593.1	hg19	CCDS3104.1	.	.	.	.	.	.	.	.	.	.	T	10.66	1.411956	0.25465	.	.	ENSG00000051382	ENST00000477593;ENST00000289153;ENST00000483968;ENST00000461451;ENST00000465581	T;T;T;T	0.72725	-0.39;-0.39;-0.67;-0.68	5.84	0.546	0.17196	.	0.811304	0.11165	N	0.592607	T	0.41604	0.1166	N	0.08118	0	0.18873	N	0.999989	B	0.15141	0.012	B	0.12156	0.007	T	0.21109	-1.0255	10	0.11794	T	0.64	0.1673	2.9379	0.05820	0.2173:0.0698:0.3812:0.3317	.	4	P42338	PK3CB_HUMAN	G	4	ENSP00000418143:S4G;ENSP00000289153:S4G;ENSP00000419857:S4G;ENSP00000420399:S4G	ENSP00000289153:S4G	S	-	1	0	PIK3CB	139960866	0.002000	0.14202	0.079000	0.20413	0.996000	0.88848	-0.054000	0.11826	-0.128000	0.11641	0.533000	0.62120	AGT	.	.	.	none		0.423	PIK3CB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358019.1		
EIF4G1	1981	hgsc.bcm.edu	37	3	184052524	184052524	+	Missense_Mutation	SNP	G	G	A			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr3:184052524G>A	ENST00000346169.2	+	33	4899	c.4628G>A	c.(4627-4629)cGg>cAg	p.R1543Q	FAM131A_ENST00000418281.1_5'Flank|EIF4G1_ENST00000352767.3_Missense_Mutation_p.R1550Q|EIF4G1_ENST00000424196.1_Missense_Mutation_p.R1550Q|EIF4G1_ENST00000392537.2_Missense_Mutation_p.R1456Q|EIF4G1_ENST00000342981.4_Missense_Mutation_p.R1544Q|FAM131A_ENST00000340957.5_5'Flank|EIF4G1_ENST00000441154.1_Missense_Mutation_p.R1380Q|EIF2B5_ENST00000444495.1_Intron|FAM131A_ENST00000383847.2_5'Flank|EIF4G1_ENST00000350481.5_Missense_Mutation_p.R1379Q|EIF4G1_ENST00000414031.1_Missense_Mutation_p.R1503Q|EIF4G1_ENST00000319274.6_Missense_Mutation_p.R1543Q|FAM131A_ENST00000450976.1_5'Flank|EIF4G1_ENST00000435046.2_Missense_Mutation_p.R1347Q|EIF4G1_ENST00000427845.1_Missense_Mutation_p.R1457Q|EIF4G1_ENST00000382330.3_Missense_Mutation_p.R1550Q|EIF4G1_ENST00000434061.2_Missense_Mutation_p.R1348Q|EIF4G1_ENST00000411531.1_Missense_Mutation_p.R1504Q	NM_198241.2	NP_937884	Q04637	IF4G1_HUMAN	eukaryotic translation initiation factor 4 gamma, 1	1543	EIF4A-binding.|W2. {ECO:0000255|PROSITE- ProRule:PRU00695}.				cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|insulin receptor signaling pathway (GO:0008286)|lung development (GO:0030324)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of translational initiation (GO:0006446)|response to ethanol (GO:0045471)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)|viral process (GO:0016032)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			central_nervous_system(1)|cervix(2)|endometrium(3)|kidney(5)|large_intestine(14)|lung(41)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	75	all_cancers(143;1.06e-10)|Ovarian(172;0.0339)		Epithelial(37;1.53e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			GACCTGCTGCGGATGTTCTTT	0.597																																					p.R1550Q		Atlas-SNP	.											.	EIF4G1	151	.	0			c.G4649A						PASS	.						103.0	87.0	92.0					3																	184052524		2203	4300	6503	SO:0001583	missense	1981	exon34			TGCTGCGGATGTT	D12686	CCDS3259.1, CCDS3260.1, CCDS3261.1, CCDS46970.1, CCDS46970.2, CCDS54687.1, CCDS54688.1	3q27.1	2013-09-19			ENSG00000114867	ENSG00000114867		"""Parkinson disease"""	3296	protein-coding gene	gene with protein product		600495		EIF4G, EIF4F		1429670, 9372926, 21907011	Standard	NM_182917		Approved	p220, PARK18	uc010hxy.3	Q04637	OTTHUMG00000156784	ENST00000346169.2:c.4628G>A	chr3.hg19:g.184052524G>A	ENSP00000316879:p.Arg1543Gln	68.0	0.0	.		54.0	19.0	.	NM_001194946	D3DNT2|D3DNT4|D3DNT5|E9PFM1|G5E9S1|O43177|O95066|Q5HYG0|Q6ZN21|Q8N102	Missense_Mutation	SNP	ENST00000346169.2	hg19	CCDS3259.1	.	.	.	.	.	.	.	.	.	.	G	11.33	1.605908	0.28623	.	.	ENSG00000114867	ENST00000346169;ENST00000414031;ENST00000392537;ENST00000382330;ENST00000350481;ENST00000352767;ENST00000427845;ENST00000342981;ENST00000319274;ENST00000424196;ENST00000411531;ENST00000441154;ENST00000434061;ENST00000435046	D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.81739	-1.53;-1.53;-1.53;-1.53;-1.53;-1.53;-1.53;-1.53;-1.53;-1.53;-1.53;-1.53;-1.53;-1.53	4.24	0.0401	0.14207	eIF4-gamma/eIF5/eIF2-epsilon (3);Armadillo-type fold (1);MIF4-like, type 1/2/3 (1);	0.139826	0.48767	D	0.000171	T	0.72399	0.3455	L	0.42581	1.335	0.52099	D	0.999947	D;D;D	0.55605	0.972;0.972;0.972	P;B;B	0.45639	0.488;0.384;0.384	T	0.66118	-0.6003	10	0.27785	T	0.31	0.0016	10.3514	0.43939	0.0:0.4071:0.453:0.1399	.	1550;1544;1543	E9PFM1;D3DNT2;Q04637	.;.;IF4G1_HUMAN	Q	1543;1503;1456;1550;1379;1550;1457;1544;1543;1550;1504;1380;1348;1347	ENSP00000316879:R1543Q;ENSP00000391935:R1503Q;ENSP00000376320:R1456Q;ENSP00000371767:R1550Q;ENSP00000317600:R1379Q;ENSP00000338020:R1550Q;ENSP00000407682:R1457Q;ENSP00000343450:R1544Q;ENSP00000323737:R1543Q;ENSP00000416255:R1550Q;ENSP00000395974:R1504Q;ENSP00000399858:R1380Q;ENSP00000411826:R1348Q;ENSP00000404754:R1347Q	ENSP00000323737:R1543Q	R	+	2	0	EIF4G1	185535218	1.000000	0.71417	0.541000	0.28102	0.051000	0.14879	7.719000	0.84751	-0.196000	0.10366	0.555000	0.69702	CGG	.	.	.	none		0.597	EIF4G1-007	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000345733.1	NM_182917	
ARAP2	116984	hgsc.bcm.edu	37	4	36179487	36179487	+	Missense_Mutation	SNP	A	A	C			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr4:36179487A>C	ENST00000303965.4	-	9	2308	c.1819T>G	c.(1819-1821)Tta>Gta	p.L607V		NM_015230.3	NP_056045.2	Q8WZ64	ARAP2_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 2	607	PH 2. {ECO:0000255|PROSITE- ProRule:PRU00145}.				regulation of ARF GTPase activity (GO:0032312)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|liver(1)|lung(32)|ovary(2)|pancreas(1)|prostate(3)|skin(7)|urinary_tract(1)	82						TTTCCACTTAACACAGTAAAA	0.368																																					p.L607V		Atlas-SNP	.											.	ARAP2	210	.	0			c.T1819G						PASS	.						150.0	148.0	149.0					4																	36179487		2203	4300	6503	SO:0001583	missense	116984	exon9			CACTTAACACAGT	AF411982	CCDS3441.1	4p15.1	2013-01-11	2008-09-22	2008-09-22	ENSG00000047365	ENSG00000047365		"""ADP-ribosylation factor GTPase activating proteins"", ""Sterile alpha motif (SAM) domain containing"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	16924	protein-coding gene	gene with protein product		606645	"""centaurin, delta 1"""	CENTD1			Standard	NM_015230		Approved	PARX	uc003gsq.2	Q8WZ64	OTTHUMG00000097811	ENST00000303965.4:c.1819T>G	chr4.hg19:g.36179487A>C	ENSP00000302895:p.Leu607Val	46.0	0.0	.		54.0	20.0	.	NM_015230	Q4W5D2|Q7Z2L5|Q96L70|Q96P49|Q9Y4E4	Missense_Mutation	SNP	ENST00000303965.4	hg19	CCDS3441.1	.	.	.	.	.	.	.	.	.	.	A	14.67	2.605214	0.46423	.	.	ENSG00000047365	ENST00000303965	D	0.91686	-2.89	5.34	4.12	0.48240	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.51477	D	0.000090	D	0.91707	0.7378	L	0.37800	1.135	0.32339	N	0.560068	P;D	0.89917	0.699;1.0	P;D	0.87578	0.759;0.998	D	0.89237	0.3581	10	0.34782	T	0.22	.	4.7854	0.13222	0.7056:0.0:0.1545:0.1399	.	537;607	A7E2A5;Q8WZ64	.;ARAP2_HUMAN	V	607	ENSP00000302895:L607V	ENSP00000302895:L607V	L	-	1	2	ARAP2	35855882	0.971000	0.33674	0.999000	0.59377	0.995000	0.86356	1.567000	0.36407	0.838000	0.34948	0.402000	0.26972	TTA	.	.	.	none		0.368	ARAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215074.2	NM_015230	
SLC4A9	83697	hgsc.bcm.edu	37	5	139747021	139747021	+	Missense_Mutation	SNP	G	G	A			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr5:139747021G>A	ENST00000230993.6	+	15	2137	c.2102G>A	c.(2101-2103)cGt>cAt	p.R701H	SLC4A9_ENST00000507527.1_Missense_Mutation_p.R701H|SLC4A9_ENST00000506757.2_Missense_Mutation_p.R677H|SLC4A9_ENST00000506545.1_Missense_Mutation_p.R614H|SLC4A9_ENST00000432095.2_Missense_Mutation_p.R663H	NM_001258428.1	NP_001245357.1	Q96Q91	B3A4_HUMAN	solute carrier family 4, sodium bicarbonate cotransporter, member 9	701	Membrane (anion exchange).				bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)			endometrium(4)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)	14			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTCCCTGGGCGTGGCTGGCTG	0.587																																					p.R701H		Atlas-SNP	.											.	SLC4A9	125	.	0			c.G2102A						PASS	.						27.0	30.0	29.0					5																	139747021		2069	4197	6266	SO:0001583	missense	83697	exon15			CTGGGCGTGGCTG	AF313465	CCDS47278.1, CCDS58973.1, CCDS58974.1, CCDS58975.1	5q31.3	2013-05-22			ENSG00000113073	ENSG00000113073		"""Solute carriers"""	11035	protein-coding gene	gene with protein product		610207				11305939	Standard	NM_031467		Approved	AE4	uc003lfk.2	Q96Q91	OTTHUMG00000163352	ENST00000230993.6:c.2102G>A	chr5.hg19:g.139747021G>A	ENSP00000230993:p.Arg701His	18.0	0.0	.		24.0	20.0	.	NM_001258428	B7ZL63|D3DQD4|D3DQD5|D3DQD6|E9PDK1|Q96RM5|Q9BXF2|Q9BXN3	Missense_Mutation	SNP	ENST00000230993.6	hg19	CCDS58973.1	.	.	.	.	.	.	.	.	.	.	G	27.2	4.813602	0.90790	.	.	ENSG00000113073	ENST00000230993;ENST00000506757;ENST00000432095;ENST00000506545;ENST00000507527	D;D;D;D;D	0.86562	-2.14;-2.14;-2.14;-2.14;-2.14	5.21	4.34	0.51931	Bicarbonate transporter, C-terminal (1);	0.000000	0.64402	D	0.000002	D	0.95095	0.8411	M	0.94142	3.5	0.58432	D	0.999999	P;D;D;D	0.89917	0.681;1.0;1.0;1.0	B;D;D;D	0.91635	0.168;0.999;0.999;0.999	D	0.96394	0.9291	10	0.87932	D	0	.	14.6165	0.68552	0.0705:0.0:0.9295:0.0	.	614;701;663;677	E9PDK1;Q96Q91;Q96Q91-2;Q96Q91-3	.;B3A4_HUMAN;.;.	H	701;677;663;614;701	ENSP00000230993:R701H;ENSP00000424424:R677H;ENSP00000410056:R663H;ENSP00000422855:R614H;ENSP00000427661:R701H	ENSP00000230993:R701H	R	+	2	0	SLC4A9	139727205	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.786000	0.85741	1.569000	0.49696	0.655000	0.94253	CGT	.	.	.	none		0.587	SLC4A9-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000372823.1	NM_031467	
TINAG	27283	hgsc.bcm.edu	37	6	54214540	54214540	+	Missense_Mutation	SNP	T	T	C			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr6:54214540T>C	ENST00000259782.4	+	7	1022	c.926T>C	c.(925-927)cTt>cCt	p.L309P		NM_014464.3	NP_055279.3	Q9UJW2	TINAG_HUMAN	tubulointerstitial nephritis antigen	309					cell adhesion (GO:0007155)|immune response (GO:0006955)	basement membrane (GO:0005604)	cysteine-type endopeptidase activity (GO:0004197)|nucleotide binding (GO:0000166)|polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(11)|ovary(4)|skin(1)	34	Lung NSC(77;0.0518)		LUSC - Lung squamous cell carcinoma(124;0.246)			TGCTACCCACTTTTCAAAGAC	0.423																																					p.L309P		Atlas-SNP	.											.	TINAG	102	.	0			c.T926C						PASS	.						145.0	135.0	138.0					6																	54214540		2203	4300	6503	SO:0001583	missense	27283	exon7			ACCCACTTTTCAA	AB022277	CCDS4955.1	6p12.1	2008-05-15			ENSG00000137251	ENSG00000137251			14599	protein-coding gene	gene with protein product		606749				10652240	Standard	NM_014464		Approved		uc003pcj.2	Q9UJW2	OTTHUMG00000014893	ENST00000259782.4:c.926T>C	chr6.hg19:g.54214540T>C	ENSP00000259782:p.Leu309Pro	81.0	0.0	.		87.0	43.0	.	NM_014464	Q5T467|Q9UJW1|Q9ULZ4	Missense_Mutation	SNP	ENST00000259782.4	hg19	CCDS4955.1	.	.	.	.	.	.	.	.	.	.	T	19.03	3.748832	0.69533	.	.	ENSG00000137251	ENST00000339741;ENST00000259782	D	0.87179	-2.22	5.87	5.87	0.94306	Peptidase C1A, papain C-terminal (2);	0.129015	0.40064	N	0.001200	D	0.88366	0.6417	L	0.43152	1.355	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	D	0.90038	0.4140	10	0.66056	D	0.02	.	12.6692	0.56858	0.0:0.0:0.0:1.0	.	309	Q9UJW2	TINAG_HUMAN	P	168;309	ENSP00000259782:L309P	ENSP00000259782:L309P	L	+	2	0	TINAG	54322499	1.000000	0.71417	1.000000	0.80357	0.841000	0.47740	3.982000	0.56909	2.247000	0.74100	0.482000	0.46254	CTT	.	.	.	none		0.423	TINAG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040984.1	NM_014464	
DST	667	hgsc.bcm.edu	37	6	56494230	56494230	+	Silent	SNP	A	A	G			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr6:56494230A>G	ENST00000361203.3	-	28	3667	c.3660T>C	c.(3658-3660)tcT>tcC	p.S1220S	DST_ENST00000370769.4_Silent_p.S1220S|DST_ENST00000421834.2_Silent_p.S1220S|DST_ENST00000446842.2_Silent_p.S894S|DST_ENST00000518935.1_Silent_p.S894S|DST_ENST00000370788.2_Silent_p.S1220S|DST_ENST00000370765.6_Silent_p.S894S|DST_ENST00000244364.6_Silent_p.S894S|DST_ENST00000312431.6_Silent_p.S1220S|DST_ENST00000370754.5_Silent_p.S1398S			Q03001	DYST_HUMAN	dystonin	1220					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)			NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			CATCTACTTCAGATCTCCATT	0.308																																					p.S894S		Atlas-SNP	.											.	DST	1427	.	0			c.T2682C						PASS	.						92.0	88.0	89.0					6																	56494230		2203	4300	6503	SO:0001819	synonymous_variant	667	exon18			TACTTCAGATCTC	M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"""EF-hand domain containing"""	1090	protein-coding gene	gene with protein product		113810	"""bullous pemphigoid antigen 1, 230/240kDa"""	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000361203.3:c.3660T>C	chr6.hg19:g.56494230A>G		45.0	0.0	.		64.0	26.0	.	NM_001723	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Silent	SNP	ENST00000361203.3	hg19																																																																																				.	.	.	none		0.308	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723	
LAMA4	3910	hgsc.bcm.edu	37	6	112430643	112430644	+	Missense_Mutation	DNP	GG	GG	AT			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr6:112430643_112430644GG>AT	ENST00000230538.7	-	39	5865_5866	c.5468_5469CC>AT	c.(5467-5469)gCC>gAT	p.A1823D	LAMA4_ENST00000389463.4_Missense_Mutation_p.A1816D|LAMA4_ENST00000424408.2_Missense_Mutation_p.A1816D|LAMA4_ENST00000522006.1_Missense_Mutation_p.A1816D	NM_001105206.2	NP_001098676.2	Q16363	LAMA4_HUMAN	laminin, alpha 4	1823					blood vessel development (GO:0001568)|brown fat cell differentiation (GO:0050873)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)	extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(42)|ovary(4)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(8)	100		all_cancers(87;0.000196)|all_hematologic(75;0.000114)|all_epithelial(87;0.00542)|Colorectal(196;0.0209)		all cancers(137;0.0335)|OV - Ovarian serous cystadenocarcinoma(136;0.0578)|Epithelial(106;0.0748)|BRCA - Breast invasive adenocarcinoma(108;0.242)		TGTCATGTCAGGCTGCTGGACA	0.52																																					p.A1823A|p.A1823D		Atlas-SNP	.											.	LAMA4	227	.	0			c.C5469T|c.C5468A						PASS	.																																			SO:0001583	missense	3910	exon39			ATGTCAGGCTGCT|TGTCAGGCTGCTG		CCDS34514.1, CCDS43491.1, CCDS43492.1	6q21	2014-09-17			ENSG00000112769	ENSG00000112769		"""Laminins"""	6484	protein-coding gene	gene with protein product		600133				7959779	Standard	NM_001105206		Approved	LAMA3	uc003pvu.3	Q16363	OTTHUMG00000015386	ENST00000230538.7:c.5468_5469delinsAT	chr6.hg19:g.112430643_112430644delinsAT	ENSP00000230538:p.Ala1823Asp	56.0	0.0	.		48.0|49.0	25.0	.	NM_001105206	Q14731|Q14735|Q15335|Q4LE44|Q5SZG8|Q9BTB8|Q9UE18|Q9UJN9	Silent|Missense_Mutation	SNP	ENST00000230538.7	hg19	CCDS43491.1																																																																																			.	.	.	none		0.520	LAMA4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041876.2	NM_001105206	
RAPGEF5	9771	hgsc.bcm.edu	37	7	22200190	22200190	+	Missense_Mutation	SNP	A	A	G			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr7:22200190A>G	ENST00000401957.2	-	4	810	c.563T>C	c.(562-564)aTa>aCa	p.I188T	RAPGEF5_ENST00000344041.6_Missense_Mutation_p.I338T			Q92565	RPGF5_HUMAN	Rap guanine nucleotide exchange factor (GEF) 5	188	N-terminal Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00135}.				nervous system development (GO:0007399)|positive regulation of Rap GTPase activity (GO:0032854)|positive regulation of Ras GTPase activity (GO:0032320)|small GTPase mediated signal transduction (GO:0007264)	nucleus (GO:0005634)	GTP-dependent protein binding (GO:0030742)|Rap guanyl-nucleotide exchange factor activity (GO:0017034)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(2)|ovary(1)	6						TTTTTCAAGTATTGGATATTC	0.323																																					p.I338T		Atlas-SNP	.											.	RAPGEF5	96	.	0			c.T1013C						PASS	.						45.0	42.0	43.0					7																	22200190		1788	3990	5778	SO:0001583	missense	9771	exon14			TCAAGTATTGGAT	D87467	CCDS55093.1	7p15.3	2004-03-01			ENSG00000136237	ENSG00000136237			16862	protein-coding gene	gene with protein product	"""M-Ras-regulated GEF"""	609527				9039502, 10486569	Standard	NM_012294		Approved	KIAA0277, GFR, MR-GEF	uc003svg.3	Q92565	OTTHUMG00000152525	ENST00000401957.2:c.563T>C	chr7.hg19:g.22200190A>G	ENSP00000384044:p.Ile188Thr	29.0	0.0	.		41.0	19.0	.	NM_012294	A4D140|Q8IXU5	Missense_Mutation	SNP	ENST00000401957.2	hg19		.	.	.	.	.	.	.	.	.	.	A	10.32	1.317657	0.23994	.	.	ENSG00000136237	ENST00000344041;ENST00000425852;ENST00000258735;ENST00000401957;ENST00000458533	T;T;T	0.28666	1.6;1.6;1.6	6.03	6.03	0.97812	Ras guanine nucleotide exchange factor, domain (1);Ras-like guanine nucleotide exchange factor, N-terminal (2);	0.495212	0.24470	N	0.038242	T	0.23210	0.0561	N	0.19112	0.55	0.29386	N	0.862978	B;B	0.09022	0.0;0.002	B;B	0.08055	0.003;0.002	T	0.08269	-1.0730	10	0.32370	T	0.25	.	16.5594	0.84535	1.0:0.0:0.0:0.0	.	188;338	Q92565;A8MQ07	RPGF5_HUMAN;.	T	338;188;188;188;76	ENSP00000343656:I338T;ENSP00000384044:I188T;ENSP00000415664:I76T	ENSP00000258735:I188T	I	-	2	0	RAPGEF5	22166715	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.076000	0.64413	2.313000	0.78055	0.519000	0.50382	ATA	.	.	.	none		0.323	RAPGEF5-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000326590.2	NM_012294	
VPS41	27072	hgsc.bcm.edu	37	7	38902201	38902201	+	Missense_Mutation	SNP	A	A	T			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr7:38902201A>T	ENST00000310301.4	-	4	244	c.190T>A	c.(190-192)Tat>Aat	p.Y64N	VPS41_ENST00000395969.2_Missense_Mutation_p.Y64N	NM_014396.3	NP_055211.2	P49754	VPS41_HUMAN	vacuolar protein sorting 41 homolog (S. cerevisiae)	64					Golgi vesicle transport (GO:0048193)|intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	cytosol (GO:0005829)|early endosome (GO:0005769)|Golgi-associated vesicle (GO:0005798)|HOPS complex (GO:0030897)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)	zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(5)|lung(17)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)	44						ACCTTGCCATAATGTGTGCCC	0.308																																					p.Y64N		Atlas-SNP	.											.	VPS41	102	.	0			c.T190A						PASS	.						83.0	84.0	83.0					7																	38902201		2203	4300	6503	SO:0001583	missense	27072	exon4			TGCCATAATGTGT	U87309	CCDS5457.1, CCDS5458.2	7p14.1-p13	2009-05-08	2006-12-19		ENSG00000006715	ENSG00000006715			12713	protein-coding gene	gene with protein product		605485	"""vacuolar protein sorting 41 (yeast homolog)"", ""vacuolar protein sorting 41 (yeast)"""			9159129	Standard	NM_080631		Approved	HVSP41	uc003tgy.3	P49754	OTTHUMG00000023629	ENST00000310301.4:c.190T>A	chr7.hg19:g.38902201A>T	ENSP00000309457:p.Tyr64Asn	53.0	0.0	.		101.0	35.0	.	NM_080631	E9PF36|Q86TP8|Q99851|Q99852	Missense_Mutation	SNP	ENST00000310301.4	hg19	CCDS5457.1	.	.	.	.	.	.	.	.	.	.	A	12.72	2.023444	0.35701	.	.	ENSG00000006715	ENST00000310301;ENST00000395969;ENST00000414632;ENST00000418457;ENST00000457055	T;T;T;T;T	0.51817	2.5;2.48;3.47;0.69;2.45	5.62	5.62	0.85841	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.168014	0.53938	D	0.000041	T	0.15132	0.0365	N	0.01424	-0.875	0.43994	D	0.99669	P;P;P	0.37864	0.61;0.61;0.61	B;B;B	0.24541	0.054;0.054;0.054	T	0.28267	-1.0049	10	0.09843	T	0.71	-19.4277	10.9878	0.47532	0.8608:0.0:0.0:0.1392	.	64;64;64	B2RB94;E9PF36;P49754	.;.;VPS41_HUMAN	N	64;64;51;14;14	ENSP00000309457:Y64N;ENSP00000379297:Y64N;ENSP00000411919:Y51N;ENSP00000407835:Y14N;ENSP00000398584:Y14N	ENSP00000265745:Y64N	Y	-	1	0	VPS41	38868726	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	6.754000	0.74909	2.133000	0.65898	0.477000	0.44152	TAT	.	.	.	none		0.308	VPS41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226986.3		
PHF20L1	51105	hgsc.bcm.edu	37	8	133823301	133823301	+	Silent	SNP	A	A	G			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr8:133823301A>G	ENST00000395386.2	+	9	1157	c.858A>G	c.(856-858)gcA>gcG	p.A286A	PHF20L1_ENST00000395390.2_Silent_p.A261A|PHF20L1_ENST00000395379.1_Silent_p.A286A|PHF20L1_ENST00000395376.1_Silent_p.A291A|PHF20L1_ENST00000220847.7_5'UTR|PHF20L1_ENST00000337920.4_Silent_p.A260A	NM_016018.4	NP_057102.4	A8MW92	P20L1_HUMAN	PHD finger protein 20-like 1	286							zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|large_intestine(1)|lung(10)|ovary(2)	15	all_neural(3;2.72e-06)|Medulloblastoma(3;7.08e-05)|Ovarian(258;0.00438)|Esophageal squamous(12;0.00507)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;4.46e-05)			GTTTGTTGGCATCCAAAGCTG	0.338																																					p.A286A		Atlas-SNP	.											.	PHF20L1	129	.	0			c.A858G						PASS	.						142.0	152.0	148.0					8																	133823301		2203	4300	6503	SO:0001819	synonymous_variant	51105	exon9			GTTGGCATCCAAA	AF230666	CCDS6367.2, CCDS6368.1, CCDS75791.1	8q24.22	2014-03-24			ENSG00000129292	ENSG00000129292		"""Tudor domain containing"", ""Zinc fingers, PHD-type"""	24280	protein-coding gene	gene with protein product	"""tudor domain containing 20B"""					10810093, 24492612	Standard	NM_016018		Approved	CGI-72, FLJ13649, MGC64923, FLJ21615, TDRD20B	uc003ytt.3	A8MW92	OTTHUMG00000148656	ENST00000395386.2:c.858A>G	chr8.hg19:g.133823301A>G		69.0	0.0	.		84.0	51.0	.	NM_016018	A8MZC9|Q86U89|Q86W43|Q96BT0|Q9H702|Q9HBK3|Q9NYR3|Q9Y381	Silent	SNP	ENST00000395386.2	hg19	CCDS6367.2																																																																																			.	.	.	none		0.338	PHF20L1-008	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308949.3	NM_016018	
LRRC14	9684	hgsc.bcm.edu	37	8	145741535	145741535	+	5'Flank	SNP	C	C	T			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr8:145741535C>T	ENST00000292524.1	+	0	0				RECQL4_ENST00000428558.2_Missense_Mutation_p.S323N|CTD-2517M22.17_ENST00000580385.1_RNA|LRRC14_ENST00000529022.1_5'Flank|RECQL4_ENST00000532237.1_5'UTR	NM_001272036.1|NM_014665.2	NP_001258965.1|NP_055480.1	Q15048	LRC14_HUMAN	leucine rich repeat containing 14											endometrium(1)|lung(3)|prostate(1)	5	all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055)			ACTGGAGGGGCTGAGTCCGTG	0.647																																					p.S323N		Atlas-SNP	.											.	RECQL4	75	.	0			c.G968A						PASS	.						74.0	92.0	86.0					8																	145741535		2086	4208	6294	SO:0001631	upstream_gene_variant	9401	exon5			GAGGGGCTGAGTC	BC011377	CCDS6432.1	8q24.3	2012-08-20			ENSG00000160959	ENSG00000160959			20419	protein-coding gene	gene with protein product						7584026	Standard	NM_001272036		Approved	KIAA0014, LRRC14A	uc003zdk.3	Q15048	OTTHUMG00000165179		chr8.hg19:g.145741535C>T	Exception_encountered	84.0	0.0	.		61.0	37.0	.	NM_004260	A8K0A8|D3DWM8	Missense_Mutation	SNP	ENST00000292524.1	hg19	CCDS6432.1																																																																																			.	.	.	none		0.647	LRRC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382494.1	NM_014665	
TSTD2	158427	hgsc.bcm.edu	37	9	100389788	100389788	+	Missense_Mutation	SNP	T	T	G			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr9:100389788T>G	ENST00000341170.4	-	2	439	c.57A>C	c.(55-57)agA>agC	p.R19S	TSTD2_ENST00000354801.2_5'UTR	NM_139246.4	NP_640339.4	Q5T7W7	TSTD2_HUMAN	thiosulfate sulfurtransferase (rhodanese)-like domain containing 2	19										large_intestine(3)|lung(6)|ovary(2)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	15						GGTCAGAAAATCTTAAAATGC	0.383																																					p.R19S		Atlas-SNP	.											.	TSTD2	42	.	0			c.A57C						PASS	.						131.0	134.0	133.0					9																	100389788		2203	4300	6503	SO:0001583	missense	158427	exon2			AGAAAATCTTAAA	AF258575	CCDS6727.2	9q22.33	2013-09-20	2009-08-12	2009-08-12	ENSG00000136925	ENSG00000136925			30087	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 97"""	C9orf97		12477932	Standard	NM_139246		Approved	PP4189	uc004axn.3	Q5T7W7	OTTHUMG00000020328	ENST00000341170.4:c.57A>C	chr9.hg19:g.100389788T>G	ENSP00000342499:p.Arg19Ser	74.0	0.0	.		69.0	21.0	.	NM_139246	A6NMJ4|A8K584|Q6ZQZ6|Q8IYM3|Q8WY73|Q96ML6|Q96MU1	Missense_Mutation	SNP	ENST00000341170.4	hg19	CCDS6727.2	.	.	.	.	.	.	.	.	.	.	T	15.64	2.893135	0.52121	.	.	ENSG00000136925	ENST00000341170	T	0.32753	1.44	5.38	0.147	0.14838	.	0.161832	0.42420	D	0.000719	T	0.23846	0.0577	L	0.54323	1.7	0.80722	D	1	B	0.24483	0.104	B	0.22386	0.039	T	0.05818	-1.0862	10	0.72032	D	0.01	-3.0007	5.2921	0.15733	0.0:0.2549:0.1411:0.604	.	19	Q5T7W7	TSTD2_HUMAN	S	19	ENSP00000342499:R19S	ENSP00000342499:R19S	R	-	3	2	TSTD2	99429609	1.000000	0.71417	0.722000	0.30670	0.975000	0.68041	1.016000	0.29976	0.064000	0.16427	0.533000	0.62120	AGA	.	.	.	none		0.383	TSTD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053325.4	NM_139246	
GATA3	2625	hgsc.bcm.edu	37	10	8111467	8111467	+	Missense_Mutation	SNP	C	C	A			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr10:8111467C>A	ENST00000346208.3	+	5	1408	c.953C>A	c.(952-954)gCg>gAg	p.A318E	GATA3_ENST00000379328.3_Missense_Mutation_p.A319E|GATA3_ENST00000461472.1_3'UTR			P23771	GATA3_HUMAN	GATA binding protein 3	318					anatomical structure formation involved in morphogenesis (GO:0048646)|anatomical structure morphogenesis (GO:0009653)|aortic valve morphogenesis (GO:0003180)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|canonical Wnt signaling pathway involved in metanephric kidney development (GO:0061290)|cardiac right ventricle morphogenesis (GO:0003215)|cell fate determination (GO:0001709)|cell maturation (GO:0048469)|cellular response to BMP stimulus (GO:0071773)|cellular response to interferon-alpha (GO:0035457)|cellular response to interleukin-4 (GO:0071353)|cellular response to tumor necrosis factor (GO:0071356)|defense response (GO:0006952)|developmental growth (GO:0048589)|ear development (GO:0043583)|embryonic hemopoiesis (GO:0035162)|erythrocyte differentiation (GO:0030218)|humoral immune response (GO:0006959)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear morphogenesis (GO:0042472)|interferon-gamma secretion (GO:0072643)|interleukin-4 secretion (GO:0072602)|kidney development (GO:0001822)|lens development in camera-type eye (GO:0002088)|lymphocyte migration (GO:0072676)|male gonad development (GO:0008584)|mast cell differentiation (GO:0060374)|mesenchymal to epithelial transition (GO:0060231)|mesonephros development (GO:0001823)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell motility (GO:2000146)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell proliferation involved in mesonephros development (GO:2000607)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of fibroblast growth factor receptor signaling pathway involved in ureteric bud formation (GO:2000703)|negative regulation of glial cell-derived neurotrophic factor receptor signaling pathway involved in ureteric bud formation (GO:2000734)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|negative regulation of transcription, DNA-templated (GO:0045892)|nephric duct formation (GO:0072179)|nephric duct morphogenesis (GO:0072178)|neuron migration (GO:0001764)|norepinephrine biosynthetic process (GO:0042421)|otic vesicle development (GO:0071599)|parathyroid gland development (GO:0060017)|parathyroid hormone secretion (GO:0035898)|pharyngeal system development (GO:0060037)|phosphatidylinositol 3-kinase signaling (GO:0014065)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of interleukin-13 production (GO:0032736)|positive regulation of interleukin-13 secretion (GO:2000667)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of interleukin-5 production (GO:0032754)|positive regulation of interleukin-5 secretion (GO:2000664)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of signal transduction (GO:0009967)|positive regulation of T cell differentiation (GO:0045582)|positive regulation of thyroid hormone generation (GO:2000611)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription regulatory region DNA binding (GO:2000679)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ureteric bud formation (GO:0072107)|post-embryonic development (GO:0009791)|pro-T cell differentiation (GO:0002572)|regulation of CD4-positive, alpha-beta T cell differentiation (GO:0043370)|regulation of cellular response to X-ray (GO:2000683)|regulation of cytokine biosynthetic process (GO:0042035)|regulation of establishment of cell polarity (GO:2000114)|regulation of histone H3-K27 methylation (GO:0061085)|regulation of histone H3-K4 methylation (GO:0051569)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of neuron apoptotic process (GO:0043523)|regulation of neuron projection development (GO:0010975)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to ethanol (GO:0045471)|response to gamma radiation (GO:0010332)|response to virus (GO:0009615)|signal transduction (GO:0007165)|sympathetic nervous system development (GO:0048485)|T cell receptor signaling pathway (GO:0050852)|T-helper 2 cell differentiation (GO:0045064)|thymic T cell selection (GO:0045061)|thymus development (GO:0048538)|TOR signaling (GO:0031929)|transcription from RNA polymerase II promoter (GO:0006366)|type IV hypersensitivity (GO:0001806)|ureter maturation (GO:0035799)|ureteric bud formation (GO:0060676)|uterus development (GO:0060065)|ventricular septum development (GO:0003281)	nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	core promoter proximal region sequence-specific DNA binding (GO:0000987)|core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|E-box binding (GO:0070888)|enhancer sequence-specific DNA binding (GO:0001158)|HMG box domain binding (GO:0071837)|nucleic acid binding transcription factor activity (GO:0001071)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)|zinc ion binding (GO:0008270)			NS(1)|breast(44)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(24)|ovary(3)|skin(2)	87						ACGTCCTGTGCGAACTGTCAG	0.502			"""F, N, S"""		breast		"""HDR syndrome (HYPOPARATHYROIDISM, SENSORINEURAL DEAFNESS, AND RENAL DISEASE)"""																														p.A319E		Atlas-SNP	.		Rec	yes		10	10p15	2625	GATA binding protein 3	yes	E	.	GATA3	182	.	0			c.C956A						PASS	.						156.0	117.0	130.0					10																	8111467		2203	4300	6503	SO:0001583	missense	2625	exon5			CCTGTGCGAACTG	X55122	CCDS7083.1, CCDS31143.1	10p15	2013-01-25	2001-11-28		ENSG00000107485	ENSG00000107485		"""GATA zinc finger domain containing"""	4172	protein-coding gene	gene with protein product		131320	"""GATA-binding protein 3"""			2050118, 15087456	Standard	NM_002051		Approved	HDR	uc001ijz.3	P23771	OTTHUMG00000017640	ENST00000346208.3:c.953C>A	chr10.hg19:g.8111467C>A	ENSP00000341619:p.Ala318Glu	68.0	0.0	.		60.0	21.0	.	NM_001002295	Q5VWG7|Q5VWG8|Q96J16	Missense_Mutation	SNP	ENST00000346208.3	hg19	CCDS7083.1	.	.	.	.	.	.	.	.	.	.	C	33	5.264336	0.95399	.	.	ENSG00000107485	ENST00000379328;ENST00000346208	D;D	0.99436	-5.9;-5.9	5.21	5.21	0.72293	Zinc finger, NHR/GATA-type (1);Zinc finger, GATA-type (4);	0.000000	0.85682	D	0.000000	D	0.99563	0.9843	M	0.84948	2.725	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.995	D	0.98364	1.0550	10	0.87932	D	0	-22.289	19.1275	0.93391	0.0:1.0:0.0:0.0	.	318;319	P23771;P23771-2	GATA3_HUMAN;.	E	319;318	ENSP00000368632:A319E;ENSP00000341619:A318E	ENSP00000341619:A318E	A	+	2	0	GATA3	8151473	1.000000	0.71417	0.987000	0.45799	0.958000	0.62258	7.776000	0.85560	2.590000	0.87494	0.561000	0.74099	GCG	.	.	.	none		0.502	GATA3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000046719.1	NM_001002295	
ZNF438	220929	hgsc.bcm.edu	37	10	31138190	31138190	+	Missense_Mutation	SNP	T	T	C			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr10:31138190T>C	ENST00000361310.3	-	6	1473	c.1144A>G	c.(1144-1146)Aga>Gga	p.R382G	ZNF438_ENST00000436087.2_Missense_Mutation_p.R382G|ZNF438_ENST00000413025.1_Missense_Mutation_p.R382G|ZNF438_ENST00000452305.1_Missense_Mutation_p.R372G|ZNF438_ENST00000444692.2_Missense_Mutation_p.R372G|ZNF438_ENST00000442986.1_Missense_Mutation_p.R382G|ZNF438_ENST00000538351.2_Missense_Mutation_p.R333G|ZNF438_ENST00000375311.1_5'UTR|ZNF438_ENST00000331737.6_Missense_Mutation_p.R372G			Q7Z4V0	ZN438_HUMAN	zinc finger protein 438	382					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(15)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35		Prostate(175;0.0587)				CTTCCTTTTCTCTTTGCTGCT	0.398																																					p.R382G		Atlas-SNP	.											.	ZNF438	90	.	0			c.A1144G						PASS	.						112.0	107.0	109.0					10																	31138190		2203	4300	6503	SO:0001583	missense	220929	exon7			CTTTTCTCTTTGC	AK057323	CCDS7168.1, CCDS44369.1, CCDS53504.1	10p11.23	2006-02-15			ENSG00000183621	ENSG00000183621		"""Zinc fingers, C2H2-type"""	21029	protein-coding gene	gene with protein product							Standard	NM_182755		Approved	bA330O11.1	uc010qeb.2	Q7Z4V0	OTTHUMG00000017904	ENST00000361310.3:c.1144A>G	chr10.hg19:g.31138190T>C	ENSP00000354663:p.Arg382Gly	65.0	0.0	.		51.0	22.0	.	NM_182755	A2A3J4|A8K9L5|Q5T426|Q658Q4|Q6ZN65	Missense_Mutation	SNP	ENST00000361310.3	hg19	CCDS7168.1	.	.	.	.	.	.	.	.	.	.	T	17.20	3.327742	0.60743	.	.	ENSG00000183621	ENST00000331737;ENST00000361310;ENST00000436087;ENST00000442986;ENST00000413025;ENST00000452305;ENST00000444692;ENST00000538351;ENST00000430896	T;T;T;T;T;T;T;T	0.12879	2.64;2.64;2.64;2.64;2.64;2.64;2.64;2.64	5.73	5.73	0.89815	.	0.090652	0.85682	D	0.000000	T	0.34629	0.0904	M	0.73598	2.24	0.49051	D	0.999748	D;D	0.63046	0.986;0.992	P;P	0.59357	0.722;0.856	T	0.09684	-1.0663	10	0.87932	D	0	-28.0386	15.1883	0.73023	0.0:0.0:0.0:1.0	.	382;372	Q7Z4V0;Q7Z4V0-2	ZN438_HUMAN;.	G	372;382;382;382;382;372;372;333;101	ENSP00000333571:R372G;ENSP00000354663:R382G;ENSP00000406934:R382G;ENSP00000412363:R382G;ENSP00000387546:R382G;ENSP00000413060:R372G;ENSP00000410898:R372G;ENSP00000445461:R333G	ENSP00000333571:R372G	R	-	1	2	ZNF438	31178196	1.000000	0.71417	0.642000	0.29436	0.135000	0.20990	7.162000	0.77515	2.186000	0.69663	0.528000	0.53228	AGA	.	.	.	none		0.398	ZNF438-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277006.1	NM_182755	
PCDH15	65217	hgsc.bcm.edu	37	10	56423964	56423964	+	Missense_Mutation	SNP	A	A	T			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr10:56423964A>T	ENST00000320301.6	-	2	453	c.59T>A	c.(58-60)cTc>cAc	p.L20H	PCDH15_ENST00000409834.1_5'UTR|PCDH15_ENST00000373957.3_Missense_Mutation_p.L20H|PCDH15_ENST00000437009.1_Missense_Mutation_p.L20H|PCDH15_ENST00000395433.1_Missense_Mutation_p.L20H|PCDH15_ENST00000395432.2_Missense_Mutation_p.L20H|PCDH15_ENST00000395446.1_Missense_Mutation_p.L20H|PCDH15_ENST00000395440.1_Missense_Mutation_p.L20H|PCDH15_ENST00000395430.1_Missense_Mutation_p.L20H|PCDH15_ENST00000373965.2_Missense_Mutation_p.L20H|PCDH15_ENST00000395438.1_Missense_Mutation_p.L20H|PCDH15_ENST00000373955.1_Missense_Mutation_p.L20H|PCDH15_ENST00000395442.1_Missense_Mutation_p.L20H|PCDH15_ENST00000361849.3_Missense_Mutation_p.L20H|PCDH15_ENST00000395445.1_Missense_Mutation_p.L20H|PCDH15_ENST00000414778.1_Missense_Mutation_p.L20H	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	20					equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)			NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				GATTTCAAAGAGAGAGCCCAG	0.383										HNSCC(58;0.16)																											p.L20H		Atlas-SNP	.											.	PCDH15	1715	.	0			c.T59A						PASS	.						80.0	73.0	75.0					10																	56423964		2203	4300	6503	SO:0001583	missense	65217	exon2			TCAAAGAGAGAGC	AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275		"""Cadherins / Cadherin-related"""	14674	protein-coding gene	gene with protein product	"""cadherin-related family member 15"""	605514	"""deafness, autosomal recessive 23"", ""protocadherin 15"""	USH1F, DFNB23		11398101, 14570705	Standard	NM_033056		Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000320301.6:c.59T>A	chr10.hg19:g.56423964A>T	ENSP00000322604:p.Leu20His	36.0	0.0	.		76.0	27.0	.	NM_001142763	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Missense_Mutation	SNP	ENST00000320301.6	hg19	CCDS7248.1	.	.	.	.	.	.	.	.	.	.	A	13.70	2.314590	0.40996	.	.	ENSG00000150275	ENST00000373965;ENST00000414778;ENST00000455746;ENST00000395438;ENST00000395445;ENST00000395446;ENST00000395442;ENST00000395440;ENST00000395432;ENST00000361849;ENST00000395433;ENST00000373957;ENST00000320301;ENST00000395430;ENST00000417177;ENST00000437009;ENST00000373955;ENST00000458638	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.68765	0.34;0.34;0.26;0.27;0.25;0.46;0.36;0.19;0.23;-0.35;-0.35;0.24;0.24;0.26;0.39;0.55	5.8	5.8	0.92144	.	.	.	.	.	T	0.72407	0.3456	L	0.40543	1.245	0.19300	N	0.999976	D;D;D;D;D;D;D;D;D;D;D;P;P;D;D	0.67145	0.986;0.986;0.986;0.986;0.992;0.986;0.986;0.981;0.996;0.996;0.996;0.81;0.931;0.975;0.986	P;P;P;P;P;P;P;P;P;P;P;B;P;P;P	0.58873	0.789;0.832;0.832;0.832;0.765;0.832;0.789;0.695;0.847;0.784;0.789;0.378;0.678;0.789;0.832	T	0.66555	-0.5894	9	0.87932	D	0	.	13.6644	0.62387	1.0:0.0:0.0:0.0	.	20;20;20;20;20;20;20;20;20;20;20;20;20;20;20	A2A3E8;E7EMG4;A2A3E7;C9JIG1;E7EM53;E7EMG0;A2A3E6;A2A3E3;C6ZEF5;A2A3E2;C6ZEF7;C9J4F3;Q96QU1-3;A2A3D8;Q96QU1	.;.;.;.;.;.;.;.;.;.;.;.;.;.;PCD15_HUMAN	H	20	ENSP00000363076:L20H;ENSP00000410304:L20H;ENSP00000378826:L20H;ENSP00000378832:L20H;ENSP00000378833:L20H;ENSP00000378829:L20H;ENSP00000378827:L20H;ENSP00000378820:L20H;ENSP00000354950:L20H;ENSP00000378821:L20H;ENSP00000363068:L20H;ENSP00000322604:L20H;ENSP00000378818:L20H;ENSP00000412628:L20H;ENSP00000363066:L20H;ENSP00000394465:L20H	ENSP00000322604:L20H	L	-	2	0	PCDH15	56093970	0.993000	0.37304	0.031000	0.17742	0.006000	0.05464	5.603000	0.67619	2.216000	0.71823	0.402000	0.26972	CTC	.	.	.	none		0.383	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2	NM_033056	
MKI67	4288	hgsc.bcm.edu	37	10	129910660	129910660	+	Missense_Mutation	SNP	A	A	G			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr10:129910660A>G	ENST00000368654.3	-	9	2081	c.1706T>C	c.(1705-1707)gTg>gCg	p.V569A	MKI67_ENST00000484853.1_5'UTR|MKI67_ENST00000368653.3_Missense_Mutation_p.V209A	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	569					cell proliferation (GO:0008283)|cellular response to heat (GO:0034605)|DNA metabolic process (GO:0006259)|hyaluronan metabolic process (GO:0030212)|meiotic nuclear division (GO:0007126)|organ regeneration (GO:0031100)|response to organic cyclic compound (GO:0014070)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(30)|lung(64)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|soft_tissue(1)|stomach(10)|upper_aerodigestive_tract(4)|urinary_tract(4)	159		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)				CTTCACTTCCACATGGATTTC	0.458																																					p.V569A		Atlas-SNP	.											.	MKI67	363	.	0			c.T1706C						PASS	.						133.0	143.0	140.0					10																	129910660		2203	4300	6503	SO:0001583	missense	4288	exon9			ACTTCCACATGGA	X65550	CCDS7659.1, CCDS53588.1	10q26.2	2014-06-12	2013-10-10		ENSG00000148773	ENSG00000148773			7107	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 105"""	176741	"""antigen identified by monoclonal antibody Ki-67"""			2571566, 16206250	Standard	NM_002417		Approved	MIB-, PPP1R105	uc001lke.3	P46013	OTTHUMG00000019255	ENST00000368654.3:c.1706T>C	chr10.hg19:g.129910660A>G	ENSP00000357643:p.Val569Ala	61.0	0.0	.		70.0	30.0	.	NM_002417	Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	hg19	CCDS7659.1	.	.	.	.	.	.	.	.	.	.	A	10.71	1.426189	0.25726	.	.	ENSG00000148773	ENST00000368654;ENST00000368653;ENST00000537609;ENST00000368652	T;T	0.01446	4.94;4.88	4.05	2.73	0.32206	.	0.976288	0.08358	N	0.958088	T	0.01222	0.0040	N	0.19112	0.55	0.09310	N	1	B;B;B	0.28636	0.218;0.218;0.139	B;B;B	0.24848	0.056;0.056;0.025	T	0.42310	-0.9459	10	0.02654	T	1	.	6.0887	0.19983	0.866:0.0:0.134:0.0	.	569;209;569	F5H4V4;P46013-2;P46013	.;.;KI67_HUMAN	A	569;209;569;144	ENSP00000357643:V569A;ENSP00000357642:V209A	ENSP00000357641:V144A	V	-	2	0	MKI67	129800650	0.000000	0.05858	0.009000	0.14445	0.003000	0.03518	-0.223000	0.09177	0.593000	0.29745	0.460000	0.39030	GTG	.	.	.	none		0.458	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417	
NLRP14	338323	hgsc.bcm.edu	37	11	7083573	7083573	+	Silent	SNP	C	C	A			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr11:7083573C>A	ENST00000299481.4	+	10	3160	c.2814C>A	c.(2812-2814)ggC>ggA	p.G938G		NM_176822.3	NP_789792.1	Q86W24	NAL14_HUMAN	NLR family, pyrin domain containing 14	938					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)		ATP binding (GO:0005524)			breast(3)|large_intestine(7)|lung(1)|ovary(3)|pancreas(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	21				Epithelial(150;4.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0871)		GATTGATGGGCTGTGTTCTCA	0.408																																					p.G938G		Atlas-SNP	.											.	NLRP14	187	.	0			c.C2814A						PASS	.						122.0	118.0	119.0					11																	7083573		2201	4296	6497	SO:0001819	synonymous_variant	338323	exon10			GATGGGCTGTGTT	BK001107	CCDS7776.1	11p15.4	2006-12-08	2006-12-08	2006-12-08		ENSG00000158077		"""Nucleotide-binding domain and leucine rich repeat containing"""	22939	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 14"""	609665	"""NACHT, leucine rich repeat and PYD containing 14"""	NALP14		12563287	Standard	NM_176822		Approved	NOD5, GC-LRR, Nalp-iota, PAN8, CLR11.2	uc001mfb.1	Q86W24		ENST00000299481.4:c.2814C>A	chr11.hg19:g.7083573C>A		75.0	0.0	.		94.0	38.0	.	NM_176822	Q7RTR6	Silent	SNP	ENST00000299481.4	hg19	CCDS7776.1																																																																																			.	.	.	none		0.408	NLRP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384551.1	NM_176822	
IL18BP	10068	hgsc.bcm.edu	37	11	71716361	71716361	+	IGR	SNP	T	T	C			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr11:71716361T>C	ENST00000393703.4	+	0	1788				NUMA1_ENST00000358965.6_Missense_Mutation_p.D1902G|NUMA1_ENST00000351960.6_Missense_Mutation_p.D780G|NUMA1_ENST00000393695.3_Missense_Mutation_p.D1916G	NM_001039660.1	NP_001034749.1	O95998	I18BP_HUMAN	interleukin 18 binding protein						cellular response to hydrogen peroxide (GO:0070301)|cellular response to tumor necrosis factor (GO:0071356)|extracellular negative regulation of signal transduction (GO:1900116)|response to lipopolysaccharide (GO:0032496)|T-helper 1 type immune response (GO:0042088)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	interleukin-18 binding (GO:0042007)|receptor antagonist activity (GO:0048019)			endometrium(2)|kidney(1)|large_intestine(3)|lung(1)	7						GCGGTTCCAGTCATCCAGCTG	0.592																																					p.D1916G		Atlas-SNP	.											.	NUMA1	142	.	0			c.A5747G						PASS	.						103.0	87.0	92.0					11																	71716361		2200	4293	6493	SO:0001628	intergenic_variant	4926	exon23			TTCCAGTCATCCA	AF110798	CCDS8206.2, CCDS44666.1	11q13	2013-01-11			ENSG00000137496	ENSG00000137496		"""Interleukins and interleukin receptors"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5987	protein-coding gene	gene with protein product	"""MC51L-53L-54L homolog gene product"""	604113				10023777	Standard	NM_001145055		Approved	IL18BPa	uc001orf.1	O95998	OTTHUMG00000133713		chr11.hg19:g.71716361T>C		41.0	0.0	.		31.0	15.0	.	NM_006185	B3KUZ0|B7WPK4|O95993|O96027|Q9NZA9|Q9UBR7	Missense_Mutation	SNP	ENST00000393703.4	hg19	CCDS8206.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	25.3|25.3	4.625967|4.625967	0.87560|0.87560	.|.	.|.	ENSG00000137497|ENSG00000137497	ENST00000351960;ENST00000358965;ENST00000393695;ENST00000359652;ENST00000536544|ENST00000541584	T;T;T|.	0.25579|.	1.79;2.22;2.22|.	4.85|4.85	4.85|4.85	0.62838|0.62838	.|.	0.000000|.	0.56097|.	D|.	0.000032|.	T|T	0.53981|0.53981	0.1830|0.1830	L|L	0.29908|0.29908	0.895|0.895	0.47819|0.47819	D|D	0.999521|0.999521	D;D;D;D|.	0.89917|.	1.0;0.998;1.0;1.0|.	D;D;D;D|.	0.91635|.	0.999;0.977;0.999;0.999|.	T|T	0.51076|0.51076	-0.8751|-0.8751	10|5	0.87932|.	D|.	0|.	.|.	14.2872|14.2872	0.66254|0.66254	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	1922;1902;1916;780|.	Q4LE64;Q14980-2;Q14980;Q9BTE9|.	.;.;NUMA1_HUMAN;.|.	G|A	780;1902;1916;1465;889|765	ENSP00000260051:D780G;ENSP00000351851:D1902G;ENSP00000377298:D1916G|.	ENSP00000260051:D780G|.	D|T	-|-	2|1	0|0	NUMA1|NUMA1	71394009|71394009	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.990000|0.990000	0.78478|0.78478	6.173000|6.173000	0.71937|0.71937	2.038000|2.038000	0.60285|0.60285	0.533000|0.533000	0.62120|0.62120	GAC|ACT	.	.	.	none		0.592	IL18BP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000258012.2	NM_173042	
MMP10	4319	hgsc.bcm.edu	37	11	102649966	102649966	+	Missense_Mutation	SNP	T	T	C			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr11:102649966T>C	ENST00000279441.4	-	3	510	c.474A>G	c.(472-474)atA>atG	p.I158M		NM_002425.2	NP_002416.1	P09238	MMP10_HUMAN	matrix metallopeptidase 10 (stromelysin 2)	158					collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)|regulation of cell migration (GO:0030334)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|liver(2)|lung(6)	22	all_epithelial(12;0.00961)	all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	Epithelial(9;0.0303)|Lung(13;0.0828)|all cancers(10;0.116)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0145)	Marimastat(DB00786)	AAGAGATCATTATATCAGCCT	0.408																																					p.I158M		Atlas-SNP	.											.	MMP10	44	.	0			c.A474G						PASS	.						150.0	151.0	151.0					11																	102649966		2203	4299	6502	SO:0001583	missense	4319	exon3			GATCATTATATCA	X07820	CCDS8321.1	11q22.3	2008-02-05	2005-08-08		ENSG00000166670	ENSG00000166670	3.4.24.22		7156	protein-coding gene	gene with protein product		185260	"""matrix metalloproteinase 10 (stromelysin 2)"""	STMY2			Standard	NM_002425		Approved		uc001phg.2	P09238	OTTHUMG00000168083	ENST00000279441.4:c.474A>G	chr11.hg19:g.102649966T>C	ENSP00000279441:p.Ile158Met	56.0	0.0	.		91.0	33.0	.	NM_002425	B2R9X9|Q53HH9	Missense_Mutation	SNP	ENST00000279441.4	hg19	CCDS8321.1	.	.	.	.	.	.	.	.	.	.	t	13.80	2.346268	0.41599	.	.	ENSG00000166670	ENST00000279441;ENST00000539681	T;T	0.36878	1.23;1.23	4.38	-1.36	0.09085	Peptidase M10, metallopeptidase (1);Peptidase, metallopeptidase (1);Metallopeptidase, catalytic domain (1);	0.000000	0.64402	D	0.000003	T	0.66906	0.2837	H	0.96111	3.77	0.53688	D	0.999972	D	0.69078	0.997	D	0.68483	0.958	T	0.76468	-0.2948	10	0.87932	D	0	.	13.7321	0.62794	0.0:0.0:0.5402:0.4598	.	158	P09238	MMP10_HUMAN	M	158	ENSP00000279441:I158M;ENSP00000441485:I158M	ENSP00000279441:I158M	I	-	3	3	MMP10	102155176	0.952000	0.32445	0.984000	0.44739	0.380000	0.30137	-0.019000	0.12546	-0.302000	0.08869	0.482000	0.46254	ATA	.	.	.	none		0.408	MMP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398014.1		
GRIK4	2900	hgsc.bcm.edu	37	11	120745851	120745851	+	Missense_Mutation	SNP	G	G	A			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr11:120745851G>A	ENST00000527524.2	+	11	1350	c.1063G>A	c.(1063-1065)Gaa>Aaa	p.E355K	RP11-640N11.2_ENST00000505153.2_RNA|GRIK4_ENST00000438375.2_Missense_Mutation_p.E355K	NM_001282470.1	NP_001269399.1	Q16099	GRIK4_HUMAN	glutamate receptor, ionotropic, kainate 4	355					glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|response to corticosteroid (GO:0031960)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|kainate selective glutamate receptor complex (GO:0032983)|nucleus (GO:0005634)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	extracellular-glutamate-gated ion channel activity (GO:0005234)|kainate selective glutamate receptor activity (GO:0015277)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(20)|liver(1)|lung(29)|ovary(2)|pancreas(1)|prostate(4)|skin(2)|urinary_tract(1)	69		Breast(109;0.000868)|Medulloblastoma(222;0.0453)|all_neural(223;0.116)|all_hematologic(192;0.21)		BRCA - Breast invasive adenocarcinoma(274;1.24e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.116)		TGGACAGGTAGAATTGGAAGG	0.478																																					p.E355K		Atlas-SNP	.											.	GRIK4	149	.	0			c.G1063A						PASS	.						108.0	95.0	99.0					11																	120745851		2203	4299	6502	SO:0001583	missense	2900	exon9			CAGGTAGAATTGG	S67803	CCDS8433.1	11q23.3	2012-08-29			ENSG00000149403	ENSG00000149403		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4582	protein-coding gene	gene with protein product		600282		GRIK			Standard	NM_001282470		Approved	GluK4, KA1	uc009zax.1	Q16099	OTTHUMG00000048255	ENST00000527524.2:c.1063G>A	chr11.hg19:g.120745851G>A	ENSP00000435648:p.Glu355Lys	44.0	0.0	.		62.0	20.0	.	NM_014619	A8K9L1	Missense_Mutation	SNP	ENST00000527524.2	hg19	CCDS8433.1	.	.	.	.	.	.	.	.	.	.	g	22.6	4.305970	0.81247	.	.	ENSG00000149403	ENST00000527524;ENST00000438375	T;T	0.36157	1.27;1.27	5.92	4.95	0.65309	Extracellular ligand-binding receptor (1);	0.137856	0.64402	D	0.000004	T	0.40222	0.1108	M	0.66939	2.045	0.58432	D	0.999997	B;B	0.34226	0.443;0.309	B;B	0.34346	0.18;0.18	T	0.39583	-0.9607	10	0.56958	D	0.05	.	15.9157	0.79517	0.0:0.0:0.8642:0.1358	.	355;355	A6H8K8;Q16099	.;GRIK4_HUMAN	K	355	ENSP00000435648:E355K;ENSP00000404063:E355K	ENSP00000404063:E355K	E	+	1	0	GRIK4	120251061	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.544000	0.82117	2.793000	0.96121	0.651000	0.88453	GAA	.	.	.	none		0.478	GRIK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109760.4	NM_014619	
ITFG2	55846	hgsc.bcm.edu	37	12	2929937	2929937	+	Silent	SNP	G	G	A			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr12:2929937G>A	ENST00000228799.2	+	6	733	c.594G>A	c.(592-594)ctG>ctA	p.L198L	ITFG2_ENST00000542548.1_Silent_p.L86L|ITFG2_ENST00000419778.2_Silent_p.L21L	NM_018463.3	NP_060933.3	Q969R8	ITFG2_HUMAN	integrin alpha FG-GAP repeat containing 2	198					germinal center B cell differentiation (GO:0002314)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)				central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(13)|upper_aerodigestive_tract(2)	19			OV - Ovarian serous cystadenocarcinoma(31;0.000818)			TTCCTGAACTGATGGTGTCTC	0.562																																					p.L198L		Atlas-SNP	.											.	ITFG2	38	.	0			c.G594A						PASS	.						137.0	116.0	123.0					12																	2929937		2203	4300	6503	SO:0001819	synonymous_variant	55846	exon6			TGAACTGATGGTG	AF220048	CCDS8513.1	12p13.33	2006-11-29		2006-07-25	ENSG00000111203	ENSG00000111203			30879	protein-coding gene	gene with protein product						12477932	Standard	NM_018463		Approved	MDS028	uc001qlb.2	Q969R8	OTTHUMG00000130617	ENST00000228799.2:c.594G>A	chr12.hg19:g.2929937G>A		54.0	0.0	.		61.0	22.0	.	NM_018463	A8K4Z5|D3DUQ2|Q6PKU5|Q96SX6	Silent	SNP	ENST00000228799.2	hg19	CCDS8513.1																																																																																			.	.	.	none		0.562	ITFG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253091.1	NM_018463	
KLRG1	10219	hgsc.bcm.edu	37	12	9161629	9161629	+	Missense_Mutation	SNP	C	C	G			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr12:9161629C>G	ENST00000266551.4	+	4	431	c.416C>G	c.(415-417)tCt>tGt	p.S139C	KLRG1_ENST00000356986.3_Missense_Mutation_p.S139C|KLRG1_ENST00000538029.1_3'UTR	NM_005810.3	NP_005801.3	Q96E93	KLRG1_HUMAN	killer cell lectin-like receptor subfamily G, member 1	139	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				cell surface receptor signaling pathway (GO:0007166)|cellular defense response (GO:0006968)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|regulation of immune response (GO:0050776)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			breast(1)|central_nervous_system(1)|kidney(1)|lung(3)|pancreas(1)|upper_aerodigestive_tract(1)	8						AGGAACAATTCTGGCTGGAGG	0.453																																					p.S139C		Atlas-SNP	.											.	KLRG1	16	.	0			c.C416G						PASS	.						93.0	90.0	91.0					12																	9161629		2203	4300	6503	SO:0001583	missense	10219	exon4			ACAATTCTGGCTG	AF097358	CCDS8599.1	12p13.31	2011-08-30			ENSG00000139187	ENSG00000139187		"""Killer cell lectin-like receptors"", ""C-type lectin domain containing"""	6380	protein-coding gene	gene with protein product	"""C-type lectin domain family 15, member A"""	604874				9862378, 9842918, 16461340, 16140789	Standard	NM_005810		Approved	MAFA, 2F1, MAFA-L, CLEC15A	uc001qvg.3	Q96E93		ENST00000266551.4:c.416C>G	chr12.hg19:g.9161629C>G	ENSP00000266551:p.Ser139Cys	86.0	0.0	.		106.0	46.0	.	NM_005810	B7ZAM2|O43198|O75613	Missense_Mutation	SNP	ENST00000266551.4	hg19		.	.	.	.	.	.	.	.	.	.	C	6.937	0.542572	0.13250	.	.	ENSG00000139187	ENST00000539240;ENST00000356986;ENST00000266551;ENST00000543895	T;T;T;T	0.18657	2.2;2.2;2.2;2.2	3.61	-0.812	0.10853	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	1.481950	0.04134	N	0.318442	T	0.29783	0.0744	L	0.58669	1.825	0.09310	N	1	D;P	0.63880	0.993;0.939	P;B	0.52793	0.709;0.401	T	0.18116	-1.0347	10	0.66056	D	0.02	-6.6127	3.0673	0.06219	0.4231:0.3431:0.0:0.2338	.	139;139	Q96E93;Q96E93-2	KLRG1_HUMAN;.	C	60;139;139;60	ENSP00000445627:S60C;ENSP00000349477:S139C;ENSP00000266551:S139C;ENSP00000443658:S60C	ENSP00000266551:S139C	S	+	2	0	KLRG1	9052896	0.003000	0.15002	0.000000	0.03702	0.116000	0.19942	-0.279000	0.08479	-0.173000	0.10761	0.643000	0.83706	TCT	.	.	.	none		0.453	KLRG1-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000399145.1	NM_005810	
PAN2	9924	hgsc.bcm.edu	37	12	56718077	56718077	+	Splice_Site	SNP	C	C	T			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr12:56718077C>T	ENST00000425394.2	-	12	2305		c.e12+1		PAN2_ENST00000548043.1_Splice_Site|PAN2_ENST00000440411.3_Splice_Site|PAN2_ENST00000257931.5_Splice_Site	NM_001127460.2	NP_001120932	Q9HBH5	RDH14_HUMAN	PAN2 poly(A) specific ribonuclease subunit						osteoblast differentiation (GO:0001649)	endoplasmic reticulum (GO:0005783)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	oxidoreductase activity (GO:0016491)			NS(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|liver(1)|lung(18)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	41					Vitamin A(DB00162)	TGATTTCATACCTGCCTCCAG	0.453																																					.		Atlas-SNP	.											.	PAN2	107	.	0			c.1928+1G>A						PASS	.						94.0	96.0	95.0					12																	56718077		2203	4300	6503	SO:0001630	splice_region_variant	9924	exon13			TTCATACCTGCCT	AB014610	CCDS8915.1, CCDS44922.1, CCDS53802.1	12q13.2	2014-03-27	2014-03-27	2008-01-08		ENSG00000135473		"""Ubiquitin-specific peptidases"""	20074	protein-coding gene	gene with protein product	"""PAN2 homolog, PABP1 dependent poly A specific ribonuclease subunit (S. cerevisiae)"""		"""ubiquitin specific protease 52"", ""ubiquitin specific peptidase 52"", ""PAN2 poly(A) specific ribonuclease subunit homolog (S. cerevisiae)"""	USP52		12838346, 14583602	Standard	NM_014871		Approved	KIAA0710, hPAN2	uc001skx.3	Q504Q3	OTTHUMG00000170412	ENST00000425394.2:c.1928+1G>A	chr12.hg19:g.56718077C>T		20.0	0.0	.		28.0	12.0	.	NM_014871		Splice_Site	SNP	ENST00000425394.2	hg19	CCDS44922.1	.	.	.	.	.	.	.	.	.	.	C	15.93	2.977115	0.53720	.	.	ENSG00000135473	ENST00000425394;ENST00000440411;ENST00000257931;ENST00000548043	.	.	.	5.39	4.49	0.54785	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.85	0.63489	0.0:0.8469:0.1531:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	PAN2	55004344	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	5.365000	0.66116	1.393000	0.46605	0.557000	0.71058	.	.	.	.	none		0.453	PAN2-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409024.1	NM_014871	Intron
LRP1	4035	hgsc.bcm.edu	37	12	57548344	57548344	+	Missense_Mutation	SNP	G	G	A			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr12:57548344G>A	ENST00000243077.3	+	8	1553	c.1087G>A	c.(1087-1089)Gac>Aac	p.D363N	LRP1_ENST00000554174.1_Missense_Mutation_p.D363N	NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	363					aging (GO:0007568)|aorta morphogenesis (GO:0035909)|apoptotic cell clearance (GO:0043277)|beta-amyloid clearance (GO:0097242)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of platelet-derived growth factor receptor-beta signaling pathway (GO:2000587)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of Wnt signaling pathway (GO:0030178)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of lipid transport (GO:0032370)|positive regulation of protein transport (GO:0051222)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|receptor-mediated endocytosis (GO:0006898)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cholesterol transport (GO:0032374)|regulation of phospholipase A2 activity (GO:0032429)|retinoid metabolic process (GO:0001523)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|lipoprotein particle receptor binding (GO:0070325)|lipoprotein transporter activity (GO:0042954)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|receptor activity (GO:0004872)	p.D363N(1)		NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(33)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(26)|lung(58)|ovary(10)|pancreas(2)|prostate(11)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	184				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	CAAGCTCGTCGACAGCAAGAT	0.522																																					p.D363N		Atlas-SNP	.											LRP1,NS,carcinoma,0,1	LRP1	428	.	1	Substitution - Missense(1)	endometrium(1)	c.G1087A						PASS	.						114.0	80.0	91.0					12																	57548344		2203	4300	6503	SO:0001583	missense	4035	exon8			CTCGTCGACAGCA	X13916	CCDS8932.1	12q13.3	2013-05-28	2010-01-26		ENSG00000123384	ENSG00000123384		"""CD molecules"", ""Low density lipoprotein receptors"""	6692	protein-coding gene	gene with protein product		107770	"""alpha-2-macroglobulin receptor"""	APR, A2MR		2548950	Standard	NM_002332		Approved	LRP, CD91, LRP1A, APOER	uc001snd.3	Q07954	OTTHUMG00000044412	ENST00000243077.3:c.1087G>A	chr12.hg19:g.57548344G>A	ENSP00000243077:p.Asp363Asn	81.0	1.0	.		101.0	33.0	.	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Missense_Mutation	SNP	ENST00000243077.3	hg19	CCDS8932.1	.	.	.	.	.	.	.	.	.	.	G	15.05	2.719692	0.48728	.	.	ENSG00000123384	ENST00000243077;ENST00000554174	D;D	0.96104	-3.41;-3.91	4.53	4.53	0.55603	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.64402	D	0.000001	D	0.95623	0.8577	L	0.38175	1.15	0.43835	D	0.996413	D;D	0.89917	0.999;1.0	D;D	0.72625	0.978;0.978	D	0.93779	0.7082	10	0.23891	T	0.37	.	15.1647	0.72814	0.0:0.0:1.0:0.0	.	363;363	Q07954;Q6PJ72	LRP1_HUMAN;.	N	363	ENSP00000243077:D363N;ENSP00000451737:D363N	ENSP00000243077:D363N	D	+	1	0	LRP1	55834611	1.000000	0.71417	0.977000	0.42913	0.916000	0.54674	9.657000	0.98554	2.521000	0.84997	0.650000	0.86243	GAC	.	.	.	none		0.522	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332	
GLI1	2735	hgsc.bcm.edu	37	12	57858618	57858618	+	Missense_Mutation	SNP	G	G	A			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr12:57858618G>A	ENST00000228682.2	+	4	447	c.356G>A	c.(355-357)gGc>gAc	p.G119D	GLI1_ENST00000546141.1_Missense_Mutation_p.G78D|GLI1_ENST00000543426.1_5'UTR	NM_005269.2	NP_005260.1	P08151	GLI1_HUMAN	GLI family zinc finger 1	119					cerebellar cortex morphogenesis (GO:0021696)|digestive tract morphogenesis (GO:0048546)|dorsal/ventral pattern formation (GO:0009953)|epidermal cell differentiation (GO:0009913)|lung development (GO:0030324)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|notochord regression (GO:0060032)|osteoblast differentiation (GO:0001649)|pituitary gland development (GO:0021983)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA replication (GO:0045740)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proximal/distal pattern formation (GO:0009954)|regulation of smoothened signaling pathway (GO:0008589)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation (GO:0021938)|spermatogenesis (GO:0007283)|ventral midline development (GO:0007418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|primary cilium (GO:0072372)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(8)|lung(22)|ovary(6)|pancreas(2)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	69			GBM - Glioblastoma multiforme(3;3.99e-32)			TCTCCAGGAGGCTCCTACGGT	0.587																																					p.G119D	Pancreas(157;841 1936 10503 41495 50368)	Atlas-SNP	.											.	GLI1	141	.	0			c.G356A						PASS	.						118.0	102.0	108.0					12																	57858618		2203	4300	6503	SO:0001583	missense	2735	exon4			CAGGAGGCTCCTA		CCDS8940.1, CCDS53806.1, CCDS53807.1	12q13.2-q13.3	2013-01-25	2009-03-05	2005-01-14		ENSG00000111087		"""Zinc fingers, C2H2-type"""	4317	protein-coding gene	gene with protein product		165220	"""glioma-associated oncogene homolog 1 (zinc finger protein)"", ""glioma-associated oncogene family zinc finger 1"""	GLI		2850480	Standard	NM_005269		Approved		uc001snx.3	P08151		ENST00000228682.2:c.356G>A	chr12.hg19:g.57858618G>A	ENSP00000228682:p.Gly119Asp	52.0	0.0	.		33.0	15.0	.	NM_005269	D0EUY3|E9PQQ9|F5H6H8|Q8TDN9	Missense_Mutation	SNP	ENST00000228682.2	hg19	CCDS8940.1	.	.	.	.	.	.	.	.	.	.	g	23.4	4.417691	0.83449	.	.	ENSG00000111087	ENST00000228682;ENST00000546141;ENST00000528432;ENST00000528467	T;T;T	0.18502	2.21;2.24;2.24	3.62	3.62	0.41486	.	0.000000	0.47852	D	0.000216	T	0.41143	0.1146	M	0.75085	2.285	0.52099	D	0.999942	D	0.76494	0.999	D	0.76071	0.987	T	0.45131	-0.9282	10	0.72032	D	0.01	.	14.557	0.68106	0.0:0.0:1.0:0.0	.	119	P08151	GLI1_HUMAN	D	119;78;119;78	ENSP00000228682:G119D;ENSP00000441006:G78D;ENSP00000434408:G78D	ENSP00000228682:G119D	G	+	2	0	GLI1	56144885	1.000000	0.71417	1.000000	0.80357	0.681000	0.39784	9.508000	0.98000	2.017000	0.59298	0.556000	0.70494	GGC	.	.	.	none		0.587	GLI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394197.1	NM_005269	
USP44	84101	hgsc.bcm.edu	37	12	95922715	95922716	+	Missense_Mutation	DNP	CC	CC	TA			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr12:95922715_95922716CC>TA	ENST00000258499.3	-	3	1779_1780	c.1491_1492GG>TA	c.(1489-1494)ttGGag>ttTAag	p.497_498LE>FK	USP44_ENST00000537435.2_Missense_Mutation_p.497_498LE>FK|USP44_ENST00000552440.1_Intron|USP44_ENST00000393091.2_Missense_Mutation_p.497_498LE>FK	NM_001278393.1|NM_032147.2	NP_001265322.1|NP_115523.2	Q9H0E7	UBP44_HUMAN	ubiquitin specific peptidase 44	497	USP.				mitotic nuclear division (GO:0007067)|negative regulation of mitotic anaphase-promoting complex activity (GO:0060564)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein deubiquitination (GO:0016579)|regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090266)|regulation of spindle checkpoint (GO:0090231)	nucleus (GO:0005634)	ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(5)|ovary(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	36						TCTGGAAACTCCAATGACAAGT	0.371																																					p.E498K|p.L497F		Atlas-SNP	.											.	USP44	83	.	0			c.G1492A|c.G1491T						PASS	.																																			SO:0001583	missense	84101	exon3			GAAACTCCAATGA|AAACTCCAATGAC	AK027434	CCDS9053.1	12q21.33	2005-08-08	2005-08-08			ENSG00000136014		"""Ubiquitin-specific peptidases"""	20064	protein-coding gene	gene with protein product		610993	"""ubiquitin specific protease 44"""			12838346	Standard	NM_001278393		Approved	FLJ14528	uc001teg.3	Q9H0E7		ENST00000258499.3:c.1491_1492delinsTA	chr12.hg19:g.95922715_95922716delinsTA	ENSP00000258499:p.L497_E498delinsFK	68.0|67.0	0.0	.		49.0	21.0	.	NM_032147	B2RDW3	Missense_Mutation	SNP	ENST00000258499.3	hg19	CCDS9053.1																																																																																			.	.	.	none		0.371	USP44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408312.1	NM_032147	
CKAP4	10970	hgsc.bcm.edu	37	12	106633493	106633493	+	Missense_Mutation	SNP	A	A	C			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr12:106633493A>C	ENST00000378026.4	-	2	1254	c.1118T>G	c.(1117-1119)cTg>cGg	p.L373R	CKAP4_ENST00000552828.1_5'Flank	NM_006825.3	NP_006816.2	Q07065	CKAP4_HUMAN	cytoskeleton-associated protein 4	373						cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lipid particle (GO:0005811)|membrane (GO:0016020)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)			NS(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(8)|pancreas(1)|urinary_tract(1)	20						CTCTTCCTCCAGTCTCCGGAT	0.647																																					p.L373R		Atlas-SNP	.											.	CKAP4	49	.	0			c.T1118G						PASS	.						33.0	37.0	36.0					12																	106633493		2201	4300	6501	SO:0001583	missense	10970	exon2			TCCTCCAGTCTCC	X69910	CCDS9103.1	12q23.3	2006-06-23				ENSG00000136026			16991	protein-coding gene	gene with protein product						8314870	Standard	NM_006825		Approved	P63, CLIMP-63, ERGIC-63	uc001tlk.3	Q07065		ENST00000378026.4:c.1118T>G	chr12.hg19:g.106633493A>C	ENSP00000367265:p.Leu373Arg	51.0	0.0	.		44.0	13.0	.	NM_006825	Q504S5|Q53ES6	Missense_Mutation	SNP	ENST00000378026.4	hg19	CCDS9103.1	.	.	.	.	.	.	.	.	.	.	A	21.2	4.107665	0.77096	.	.	ENSG00000136026	ENST00000378026	T	0.78816	-1.21	5.82	5.82	0.92795	.	0.216802	0.39210	N	0.001438	D	0.87180	0.6113	M	0.76328	2.33	0.52501	D	0.999951	D	0.89917	1.0	D	0.91635	0.999	D	0.85499	0.1190	10	0.28530	T	0.3	-22.5377	16.19	0.81981	1.0:0.0:0.0:0.0	.	373	Q07065	CKAP4_HUMAN	R	373	ENSP00000367265:L373R	ENSP00000367265:L373R	L	-	2	0	CKAP4	105157623	1.000000	0.71417	0.932000	0.37286	0.809000	0.45718	7.726000	0.84824	2.225000	0.72522	0.460000	0.39030	CTG	.	.	.	none		0.647	CKAP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407196.1		
PARP4	143	hgsc.bcm.edu	37	13	25033245	25033245	+	Missense_Mutation	SNP	C	C	G			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr13:25033245C>G	ENST00000381989.3	-	20	2466	c.2361G>C	c.(2359-2361)atG>atC	p.M787I	PARP4_ENST00000480576.1_5'UTR	NM_006437.3	NP_006428.2	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4	787					cell death (GO:0008219)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|inflammatory response (GO:0006954)|protein ADP-ribosylation (GO:0006471)|response to drug (GO:0042493)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spindle microtubule (GO:0005876)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(14)|lung(18)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63		all_epithelial(30;7.67e-16)|Lung SC(185;0.0225)|Breast(139;0.052)		all cancers(112;0.000127)|Epithelial(112;0.000778)|Kidney(163;0.039)|OV - Ovarian serous cystadenocarcinoma(117;0.0578)|KIRC - Kidney renal clear cell carcinoma(186;0.135)|Lung(94;0.195)		TCTCAATAGACATAGTCAAAG	0.299																																					p.M787I		Atlas-SNP	.											.	PARP4	142	.	0			c.G2361C						PASS	.						82.0	83.0	83.0					13																	25033245		2202	4300	6502	SO:0001583	missense	143	exon20			AATAGACATAGTC	AF057160	CCDS9307.1	13q11	2010-09-29	2004-08-20	2004-08-26	ENSG00000102699	ENSG00000102699		"""Poly (ADP-ribose) polymerases"""	271	protein-coding gene	gene with protein product	"""von Willebrand factor A domain containing 5C"""	607519	"""ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1"""	ADPRTL1		10644454	Standard	NM_006437		Approved	VAULT3, p193, VPARP, VWA5C	uc001upl.3	Q9UKK3	OTTHUMG00000016582	ENST00000381989.3:c.2361G>C	chr13.hg19:g.25033245C>G	ENSP00000371419:p.Met787Ile	226.0	0.0	.		223.0	84.0	.	NM_006437	O75903|Q14682|Q5QNZ9|Q9H1M6	Missense_Mutation	SNP	ENST00000381989.3	hg19	CCDS9307.1	.	.	.	.	.	.	.	.	.	.	C	6.984	0.551711	0.13374	.	.	ENSG00000102699	ENST00000381989	T	0.01685	4.69	4.48	2.67	0.31697	.	0.232106	0.48286	D	0.000199	T	0.02533	0.0077	L	0.58669	1.825	0.40080	D	0.976127	B	0.11235	0.004	B	0.08055	0.003	T	0.43180	-0.9407	10	0.49607	T	0.09	-9.9497	9.293	0.37797	0.0:0.8127:0.0:0.1873	.	787	Q9UKK3	PARP4_HUMAN	I	787	ENSP00000371419:M787I	ENSP00000371419:M787I	M	-	3	0	PARP4	23931245	1.000000	0.71417	0.770000	0.31555	0.185000	0.23345	1.818000	0.39012	1.107000	0.41642	0.447000	0.29281	ATG	.	.	.	none		0.299	PARP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044189.1	NM_006437	
TSC22D1	8848	hgsc.bcm.edu	37	13	45148240	45148240	+	Silent	SNP	T	T	C			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr13:45148240T>C	ENST00000458659.2	-	1	2461	c.1971A>G	c.(1969-1971)gtA>gtG	p.V657V	TSC22D1_ENST00000460842.1_5'Flank|TSC22D1_ENST00000501704.2_Intron	NM_183422.3	NP_904358.2	Q15714	T22D1_HUMAN	TSC22 domain family, member 1	657	Gln-rich.				negative regulation of apoptotic process (GO:0043066)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell proliferation (GO:0008284)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		all_hematologic(4;8.74e-08)|Acute lymphoblastic leukemia(4;1.78e-07)|Lung NSC(96;2.21e-05)|Breast(139;0.000625)|Prostate(109;0.000947)|Hepatocellular(98;0.0202)|Lung SC(185;0.0262)		GBM - Glioblastoma multiforme(144;0.000522)|BRCA - Breast invasive adenocarcinoma(63;0.118)		GCTGCTGTTGTACATACTCTG	0.498																																					p.V657V		Atlas-SNP	.											.	TSC22D1	88	.	0			c.A1971G						PASS	.						95.0	91.0	92.0					13																	45148240		2203	4300	6503	SO:0001819	synonymous_variant	8848	exon1			CTGTTGTACATAC	AJ222700	CCDS9392.1, CCDS31966.1, CCDS58291.1, CCDS73565.1	13q14	2008-02-05	2005-03-01	2005-03-03	ENSG00000102804	ENSG00000102804			16826	protein-coding gene	gene with protein product		607715	"""transforming growth factor beta 1 induced transcript 4"""	TGFB1I4		8651929, 9022669	Standard	NM_183422		Approved	TSC22, MGC17597	uc001uzn.4	Q15714	OTTHUMG00000016838	ENST00000458659.2:c.1971A>G	chr13.hg19:g.45148240T>C		33.0	0.0	.		42.0	4.0	.	NM_183422	B3KRL7|B9EGI0|O00666|Q6AHX5|Q6IBU1|Q8NCN1|Q96JS5	Silent	SNP	ENST00000458659.2	hg19	CCDS31966.1																																																																																			.	.	.	none		0.498	TSC22D1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044743.2	NM_006022	
EXD2	55218	hgsc.bcm.edu	37	14	69697226	69697226	+	Missense_Mutation	SNP	C	C	A			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr14:69697226C>A	ENST00000409018.3	+	4	756	c.628C>A	c.(628-630)Ctc>Atc	p.L210I	EXD2_ENST00000409949.1_Missense_Mutation_p.L85I|EXD2_ENST00000312994.5_Missense_Mutation_p.L210I|EXD2_ENST00000409675.1_Missense_Mutation_p.L85I|EXD2_ENST00000409014.1_Missense_Mutation_p.L85I|EXD2_ENST00000449989.1_Missense_Mutation_p.L85I|EXD2_ENST00000492815.1_3'UTR|EXD2_ENST00000409242.1_Missense_Mutation_p.L85I	NM_001193361.1	NP_001180290.1	Q9NVH0	EXD2_HUMAN	exonuclease 3'-5' domain containing 2	210	3'-5' exonuclease.						3'-5' exonuclease activity (GO:0008408)|nucleic acid binding (GO:0003676)			breast(1)|endometrium(1)|large_intestine(2)|liver(1)|lung(7)|prostate(1)|urinary_tract(1)	14						CCTGAAGTCCCTCGCTGAGAC	0.433																																					p.L210I		Atlas-SNP	.											.	EXD2	43	.	0			c.C628A						PASS	.						166.0	157.0	160.0					14																	69697226		2203	4300	6503	SO:0001583	missense	55218	exon4			AAGTCCCTCGCTG	AK001600	CCDS9793.1, CCDS53902.1	14q24.1	2009-02-24	2009-02-24	2009-02-24	ENSG00000081177	ENSG00000081177			20217	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 114"", ""exonuclease 3'-5' domain-like 2"""	C14orf114, EXDL2			Standard	NM_018199		Approved	FLJ10738	uc001xkv.3	Q9NVH0	OTTHUMG00000154496	ENST00000409018.3:c.628C>A	chr14.hg19:g.69697226C>A	ENSP00000387331:p.Leu210Ile	46.0	0.0	.		58.0	19.0	.	NM_001193361	B4DIH6|G5E947|Q6AWB6|Q8N3D3	Missense_Mutation	SNP	ENST00000409018.3	hg19	CCDS53902.1	.	.	.	.	.	.	.	.	.	.	C	24.3	4.515379	0.85389	.	.	ENSG00000081177	ENST00000409018;ENST00000193422;ENST00000409014;ENST00000409675;ENST00000409949;ENST00000409242;ENST00000312994;ENST00000413191;ENST00000449989	D;D;D;D;D;D;D;D	0.84730	-1.89;-1.89;-1.89;-1.89;-1.89;-1.89;-1.89;-1.89	5.33	5.33	0.75918	-5&apos (1);Ribonuclease H-like (1); exonuclease (1);3&apos (1);	0.000000	0.85682	D	0.000000	D	0.91686	0.7372	M	0.78344	2.41	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.99;0.998	D	0.92163	0.5737	10	0.72032	D	0.01	-13.1435	13.1813	0.59655	0.0:0.9164:0.0:0.0836	.	210;85	G5E947;Q9NVH0	.;EXD2_HUMAN	I	210;210;85;85;85;85;210;85;85	ENSP00000387331:L210I;ENSP00000386915:L85I;ENSP00000386762:L85I;ENSP00000386632:L85I;ENSP00000386839:L85I;ENSP00000313140:L210I;ENSP00000409089:L85I;ENSP00000392177:L85I	ENSP00000193422:L210I	L	+	1	0	EXD2	68766979	0.998000	0.40836	0.971000	0.41717	0.854000	0.48673	3.595000	0.54016	2.637000	0.89404	0.655000	0.94253	CTC	.	.	.	none		0.433	EXD2-002	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000335504.1		
KIF26A	26153	hgsc.bcm.edu	37	14	104618786	104618786	+	Silent	SNP	G	G	A			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr14:104618786G>A	ENST00000423312.2	+	3	723	c.723G>A	c.(721-723)ccG>ccA	p.P241P	KIF26A_ENST00000315264.7_Silent_p.P102P	NM_015656.1	NP_056471.1	Q9ULI4	KI26A_HUMAN	kinesin family member 26A	241					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|blood coagulation (GO:0007596)|enteric nervous system development (GO:0048484)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|negative regulation of signal transduction (GO:0009968)|regulation of cell growth by extracellular stimulus (GO:0001560)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule binding (GO:0008017)|microtubule motor activity (GO:0003777)			autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	21		all_cancers(154;0.109)|Melanoma(154;0.0525)|all_epithelial(191;0.0767)	Epithelial(46;0.152)	Epithelial(152;0.161)		GCTTCCTCCCGCCGGCGTGCC	0.657																																					p.P241P		Atlas-SNP	.											.	KIF26A	84	.	0			c.G723A						PASS	.						6.0	6.0	6.0					14																	104618786		1915	3779	5694	SO:0001819	synonymous_variant	26153	exon3			CCTCCCGCCGGCG	AB033062	CCDS45171.1	14q32.33	2009-03-19			ENSG00000066735	ENSG00000066735		"""Kinesins"""	20226	protein-coding gene	gene with protein product		613231				10574462, 11416179	Standard	NM_015656		Approved	KIAA1236, DKFZP434N178	uc001yos.4	Q9ULI4	OTTHUMG00000154986	ENST00000423312.2:c.723G>A	chr14.hg19:g.104618786G>A		90.0	0.0	.		49.0	15.0	.	NM_015656	Q8TAZ7|Q96GK3|Q9UFL3	Silent	SNP	ENST00000423312.2	hg19	CCDS45171.1																																																																																			.	.	.	none		0.657	KIF26A-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414356.1		
PKM	5315	hgsc.bcm.edu	37	15	72502795	72502795	+	Missense_Mutation	SNP	C	C	T			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr15:72502795C>T	ENST00000335181.5	-	4	374	c.271G>A	c.(271-273)Gtg>Atg	p.V91M	PKM_ENST00000568459.1_Missense_Mutation_p.V91M|PKM_ENST00000319622.6_Missense_Mutation_p.V91M|PKM_ENST00000568883.1_Intron|PKM_ENST00000565184.1_Missense_Mutation_p.V91M|PKM_ENST00000449901.2_Missense_Mutation_p.V76M|PKM_ENST00000565154.1_Missense_Mutation_p.V91M|PKM_ENST00000389093.3_Missense_Mutation_p.V91M	NM_002654.4	NP_002645.3	P14618	KPYM_HUMAN	pyruvate kinase, muscle	91					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|programmed cell death (GO:0012501)|small molecule metabolic process (GO:0044281)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|MHC class II protein complex binding (GO:0023026)|poly(A) RNA binding (GO:0044822)|potassium ion binding (GO:0030955)|pyruvate kinase activity (GO:0004743)			endometrium(1)|lung(7)	8					Pyruvic acid(DB00119)	GCTGTGCGCACATTCTTGATG	0.552																																					p.V165M		Atlas-SNP	.											.	PKM	25	.	0			c.G493A						PASS	.						111.0	94.0	100.0					15																	72502795		2199	4297	6496	SO:0001583	missense	5315	exon5			TGCGCACATTCTT	M23725	CCDS32284.1, CCDS32285.1, CCDS55972.1, CCDS73752.1	15q23	2012-10-02		2012-05-23	ENSG00000067225	ENSG00000067225	2.7.1.40		9021	protein-coding gene	gene with protein product		179050		PKM2		2040271	Standard	NM_002654		Approved	THBP1, OIP3, PK3	uc002atr.1	P14618	OTTHUMG00000172709	ENST00000335181.5:c.271G>A	chr15.hg19:g.72502795C>T	ENSP00000334983:p.Val91Met	48.0	0.0	.		56.0	23.0	.	NM_001206796	A6NFK3|B2R5N8|B3KRY0|B4DFX8|B4DUU6|P14786|Q53GK4|Q96E76|Q9BWB5|Q9UCV6|Q9UPF2	Missense_Mutation	SNP	ENST00000335181.5	hg19	CCDS32284.1	.	.	.	.	.	.	.	.	.	.	C	23.6	4.440858	0.83993	.	.	ENSG00000067225	ENST00000319622;ENST00000335181;ENST00000389093;ENST00000449901	D;D;D;D	0.99591	-6.24;-6.24;-6.24;-6.24	5.38	5.38	0.77491	Pyruvate/Phosphoenolpyruvate kinase (2);Pyruvate kinase, barrel (1);	0.000000	0.85682	D	0.000000	D	0.99732	0.9895	M	0.92923	3.36	0.80722	D	1	D;D;D;D;D	0.89917	1.0;0.999;1.0;1.0;0.999	D;D;D;D;D	0.97110	1.0;0.994;0.992;0.992;0.986	D	0.97546	1.0089	10	0.87932	D	0	-27.492	19.4991	0.95086	0.0:1.0:0.0:0.0	.	76;91;91;91;91	B4DUU6;B4DRT3;E7EUQ8;P14618;P14618-2	.;.;.;KPYM_HUMAN;.	M	91;91;91;76	ENSP00000320171:V91M;ENSP00000334983:V91M;ENSP00000373745:V91M;ENSP00000403365:V76M	ENSP00000320171:V91M	V	-	1	0	PKM2	70289849	0.982000	0.34865	0.980000	0.43619	0.825000	0.46686	2.637000	0.46553	2.669000	0.90835	0.563000	0.77884	GTG	.	.	.	none		0.552	PKM-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420056.1		
ARIH1	25820	hgsc.bcm.edu	37	15	72855824	72855824	+	Missense_Mutation	SNP	A	A	C			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr15:72855824A>C	ENST00000379887.4	+	7	1208	c.894A>C	c.(892-894)aaA>aaC	p.K298N		NM_005744.3	NP_005735.2	Q9Y4X5	ARI1_HUMAN	ariadne RBR E3 ubiquitin protein ligase 1	298					cytokine-mediated signaling pathway (GO:0019221)|protein ubiquitination (GO:0016567)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|ubiquitin ligase complex (GO:0000151)	small conjugating protein ligase activity (GO:0019787)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(4)|large_intestine(3)|lung(4)|prostate(1)|skin(1)	14						TTCGCTGCAAATGTGGGCGCC	0.403																																					p.K298N		Atlas-SNP	.											.	ARIH1	42	.	0			c.A894C						PASS	.						111.0	103.0	105.0					15																	72855824		2198	4297	6495	SO:0001583	missense	25820	exon7			CTGCAAATGTGGG	AF072832	CCDS10244.1	15q24	2013-10-03	2013-10-03		ENSG00000166233	ENSG00000166233			689	protein-coding gene	gene with protein product	"""ariadne, Drosophila, homolog of"""	605624	"""ariadne (Drosophila) homolog, ubiquitin-conjugating enzyme E2-binding protein, 1"", ""ariadne homolog, ubiquitin-conjugating enzyme E2 binding protein, 1 (Drosophila)"""			10521492, 24058416	Standard	NM_005744		Approved	HARI, HHARI, UBCH7BP, ARI	uc002aut.4	Q9Y4X5	OTTHUMG00000133474	ENST00000379887.4:c.894A>C	chr15.hg19:g.72855824A>C	ENSP00000369217:p.Lys298Asn	96.0	0.0	.		85.0	30.0	.	NM_005744	B2R6U3|O76026|Q9H3T6|Q9UEN0|Q9UP39	Missense_Mutation	SNP	ENST00000379887.4	hg19	CCDS10244.1	.	.	.	.	.	.	.	.	.	.	A	14.32	2.500753	0.44455	.	.	ENSG00000166233	ENST00000379887;ENST00000299305	T	0.80994	-1.44	5.75	2.12	0.27331	Zinc finger, C6HC-type (2);Zinc finger, RING-type (1);	0.000000	0.85682	D	0.000000	T	0.74943	0.3783	M	0.64170	1.965	0.58432	D	0.999993	P	0.36712	0.566	B	0.36766	0.232	T	0.68224	-0.5465	10	0.42905	T	0.14	.	8.948	0.35771	0.7351:0.0:0.2649:0.0	.	298	Q9Y4X5	ARI1_HUMAN	N	298;268	ENSP00000369217:K298N	ENSP00000299305:K268N	K	+	3	2	ARIH1	70642878	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.418000	0.44662	0.108000	0.17862	0.449000	0.29647	AAA	.	.	.	none		0.403	ARIH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257350.1	NM_005744	
KIF1C	10749	hgsc.bcm.edu	37	17	4925768	4925768	+	Missense_Mutation	SNP	G	G	T			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr17:4925768G>T	ENST00000320785.5	+	22	2749	c.2392G>T	c.(2392-2394)Gct>Tct	p.A798S	AC109333.10_ENST00000438266.1_RNA	NM_006612.5	NP_006603.2	O43896	KIF1C_HUMAN	kinesin family member 1C	798					ATP catabolic process (GO:0006200)|cell death (GO:0008219)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|motor activity (GO:0003774)|plus-end-directed microtubule motor activity (GO:0008574)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(4)|endometrium(4)|kidney(2)|large_intestine(8)|lung(6)|skin(1)|urinary_tract(3)	30						CGCCTGGAGGGCTGTGGCCCG	0.697																																					p.A798S	Melanoma(96;1023 1447 10250 19259 33730)	Atlas-SNP	.											.	KIF1C	70	.	0			c.G2392T						PASS	.						29.0	30.0	30.0					17																	4925768		2200	4291	6491	SO:0001583	missense	10749	exon22			TGGAGGGCTGTGG	U91329	CCDS11065.1	17p13.2	2014-03-03			ENSG00000129250	ENSG00000129250		"""Kinesins"""	6317	protein-coding gene	gene with protein product		603060	"""spastic ataxia 2 (autosomal recessive)"""	SAX2		9685376, 24319291, 24482476	Standard	NM_006612		Approved	SPAX2, SPG58	uc002gan.2	O43896	OTTHUMG00000099451	ENST00000320785.5:c.2392G>T	chr17.hg19:g.4925768G>T	ENSP00000320821:p.Ala798Ser	90.0	0.0	.		92.0	5.0	.	NM_006612	D3DTL6|O75186|Q5U618	Missense_Mutation	SNP	ENST00000320785.5	hg19	CCDS11065.1	.	.	.	.	.	.	.	.	.	.	G	16.63	3.177065	0.57692	.	.	ENSG00000129250	ENST00000320785	T	0.73681	-0.77	4.67	4.67	0.58626	.	.	.	.	.	T	0.76681	0.4021	N	0.25890	0.77	0.49915	D	0.999834	D	0.63880	0.993	D	0.70227	0.968	T	0.73515	-0.3958	9	0.25751	T	0.34	.	15.1017	0.72284	0.0:0.0:1.0:0.0	.	798	O43896	KIF1C_HUMAN	S	798	ENSP00000320821:A798S	ENSP00000320821:A798S	A	+	1	0	KIF1C	4866492	1.000000	0.71417	0.993000	0.49108	0.886000	0.51366	9.657000	0.98554	2.436000	0.82500	0.655000	0.94253	GCT	.	.	.	none		0.697	KIF1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216916.1		
MPDU1	9526	hgsc.bcm.edu	37	17	7490749	7490749	+	Silent	SNP	C	C	T	rs371550829		TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr17:7490749C>T	ENST00000250124.6	+	7	840	c.624C>T	c.(622-624)acC>acT	p.T208T	MPDU1_ENST00000423172.2_Intron|MPDU1_ENST00000396501.4_Missense_Mutation_p.P189L	NM_004870.3	NP_004861.2	O75352	MPU1_HUMAN	mannose-P-dolichol utilization defect 1	208	PQ-loop 2.				dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|oligosaccharide biosynthetic process (GO:0009312)|protein folding (GO:0006457)|transport (GO:0006810)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrion (GO:0005739)				central_nervous_system(1)|cervix(1)|kidney(3)|large_intestine(1)|lung(1)	7						ACCAGGAAACCGGAGATCCCC	0.567																																					p.T208T		Atlas-SNP	.											.	MPDU1	14	.	0			c.C624T						PASS	.	C		1,4405	2.1+/-5.4	0,1,2202	105.0	103.0	104.0		624	-9.3	0.7	17		104	0,8600		0,0,4300	no	coding-synonymous	MPDU1	NM_004870.3		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		208/248	7490749	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	9526	exon7			GGAAACCGGAGAT	AF038961	CCDS11115.1	17p13.1-p12	2008-07-03			ENSG00000129255	ENSG00000129255			7207	protein-coding gene	gene with protein product		604041				8663248, 9653160, 11733564	Standard	NM_004870		Approved	SL15, Lec35, PQLC5, CDGIf	uc002ghw.3	O75352	OTTHUMG00000108147	ENST00000250124.6:c.624C>T	chr17.hg19:g.7490749C>T		69.0	0.0	.		53.0	19.0	.	NM_004870	B3KQP1|B4DT74|Q9BUU8	Silent	SNP	ENST00000250124.6	hg19	CCDS11115.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.40|12.40	1.925630|1.925630	0.34002|0.34002	2.27E-4|2.27E-4	0.0|0.0	ENSG00000129255|ENSG00000129255	ENST00000396501|ENST00000359822	.|.	.|.	.|.	5.24|5.24	-9.26|-9.26	0.00662|0.00662	.|.	.|1.727610	.|0.03156	.|N	.|0.168713	T|T	0.54481|0.54481	0.1861|0.1861	.|.	.|.	.|.	0.54753|0.54753	D|D	0.99998|0.99998	B|.	0.06786|.	0.001|.	B|.	0.04013|.	0.001|.	T|T	0.59611|0.59611	-0.7422|-0.7422	7|6	0.87932|0.62326	D|D	0|0.03	3.3529|3.3529	6.9724|6.9724	0.24656|0.24656	0.3396:0.4581:0.0:0.2023|0.3396:0.4581:0.0:0.2023	.|.	256|.	B4DLH7|.	.|.	L|W	208|208	.|.	ENSP00000379758:P208L|ENSP00000352876:R208W	P|R	+|+	2|1	0|2	MPDU1|MPDU1	7431473|7431473	0.002000|0.002000	0.14202|0.14202	0.713000|0.713000	0.30519|0.30519	0.941000|0.941000	0.58515|0.58515	-2.148000|-2.148000	0.01292|0.01292	-1.641000|-1.641000	0.01523|0.01523	-0.238000|-0.238000	0.12139|0.12139	CCG|CGG	.	.	.	weak		0.567	MPDU1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226950.4		
FNDC8	54752	hgsc.bcm.edu	37	17	33457438	33457438	+	Silent	SNP	C	C	T			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr17:33457438C>T	ENST00000158009.5	+	4	1075	c.960C>T	c.(958-960)taC>taT	p.Y320Y	NLE1_ENST00000586869.1_3'UTR	NM_017559.2	NP_060029.1	Q8TC99	FNDC8_HUMAN	fibronectin type III domain containing 8	320						nucleus (GO:0005634)				breast(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|skin(1)	11		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.022)		ATCTGGAATACCTATTTCCCT	0.587																																					p.Y320Y		Atlas-SNP	.											.	FNDC8	28	.	0			c.C960T						PASS	.						45.0	47.0	46.0					17																	33457438		2203	4300	6503	SO:0001819	synonymous_variant	54752	exon4			GGAATACCTATTT	BC024002	CCDS11290.1	17q12	2013-02-11			ENSG00000073598	ENSG00000073598		"""Fibronectin type III domain containing"""	25286	protein-coding gene	gene with protein product						12477932	Standard	XM_005257993		Approved	DKFZp434H2215	uc002hix.3	Q8TC99	OTTHUMG00000132932	ENST00000158009.5:c.960C>T	chr17.hg19:g.33457438C>T		39.0	0.0	.		33.0	6.0	.	NM_017559	B2R9G6|Q9UFC2	Silent	SNP	ENST00000158009.5	hg19	CCDS11290.1																																																																																			.	.	.	none		0.587	FNDC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256459.2	NM_017559	
ASB16	92591	hgsc.bcm.edu	37	17	42254547	42254547	+	Missense_Mutation	SNP	A	A	T			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr17:42254547A>T	ENST00000293414.1	+	3	1095	c.1011A>T	c.(1009-1011)gaA>gaT	p.E337D	ASB16-AS1_ENST00000591166.1_RNA|ASB16-AS1_ENST00000585457.1_RNA|ASB16-AS1_ENST00000588785.1_RNA|ASB16-AS1_ENST00000592897.1_RNA	NM_080863.4	NP_543139.4	Q96NS5	ASB16_HUMAN	ankyrin repeat and SOCS box containing 16	337					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)					central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(2)|liver(2)|lung(2)|prostate(1)	14		Breast(137;0.00765)|Prostate(33;0.0313)		BRCA - Breast invasive adenocarcinoma(366;0.114)		GGGAGCCTGAAGTCCTTTTCG	0.701																																					p.E337D		Atlas-SNP	.											.	ASB16	34	.	0			c.A1011T						PASS	.						2.0	3.0	3.0					17																	42254547		1844	3714	5558	SO:0001583	missense	92591	exon3			GCCTGAAGTCCTT	AK054727	CCDS11478.1	17q21.31	2013-01-10	2011-01-25		ENSG00000161664	ENSG00000161664		"""Ankyrin repeat domain containing"""	19768	protein-coding gene	gene with protein product		615056	"""ankyrin repeat and SOCS box-containing 16"""			12076535	Standard	NM_080863		Approved	FLJ30165	uc002ifl.1	Q96NS5	OTTHUMG00000181809	ENST00000293414.1:c.1011A>T	chr17.hg19:g.42254547A>T	ENSP00000293414:p.Glu337Asp	67.0	0.0	.		83.0	21.0	.	NM_080863	B2RBC0|Q8WXK0	Missense_Mutation	SNP	ENST00000293414.1	hg19	CCDS11478.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	10.37|10.37	1.331654|1.331654	0.24167|0.24167	.|.	.|.	ENSG00000161664|ENSG00000168597	ENST00000293414|ENST00000303061	T|.	0.66460|.	-0.21|.	4.95|4.95	0.684|0.684	0.18003|0.18003	Ankyrin repeat-containing domain (2);|.	0.335476|.	0.34223|.	N|.	0.004160|.	T|T	0.35828|0.35828	0.0945|0.0945	M|M	0.61703|0.61703	1.905|1.905	0.33725|0.33725	D|D	0.617503|0.617503	B|P	0.06786|0.39696	0.001|0.683	B|B	0.06405|0.33295	0.002|0.161	T|T	0.47661|0.47661	-0.9100|-0.9100	10|8	0.42905|0.87932	T|D	0.14|0	-12.3109|-12.3109	2.7739|2.7739	0.05342|0.05342	0.1522:0.2645:0.4472:0.136|0.1522:0.2645:0.4472:0.136	.|.	337|25	Q96NS5|Q495Z4	ASB16_HUMAN|CQ065_HUMAN	D|H	337|25	ENSP00000293414:E337D|.	ENSP00000293414:E337D|ENSP00000366342:L25H	E|L	+|-	3|2	2|0	ASB16|C17orf65	39610073|39610073	0.839000|0.839000	0.29477|0.29477	0.954000|0.954000	0.39281|0.39281	0.094000|0.094000	0.18550|0.18550	1.047000|1.047000	0.30367|0.30367	0.021000|0.021000	0.15133|0.15133	-0.253000|-0.253000	0.11424|0.11424	GAA|CTT	.	.	.	none		0.701	ASB16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457703.1		
JMJD6	23210	hgsc.bcm.edu	37	17	74714915	74714915	+	Missense_Mutation	SNP	T	T	C			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr17:74714915T>C	ENST00000397625.4	-	6	1222	c.1108A>G	c.(1108-1110)Aca>Gca	p.T370A	JMJD6_ENST00000445478.2_Missense_Mutation_p.T370A|JMJD6_ENST00000585429.1_Silent_p.G323G	NM_015167.2	NP_055982.2	Q6NYC1	JMJD6_HUMAN	jumonji domain containing 6	370					cell surface receptor signaling pathway (GO:0007166)|erythrocyte development (GO:0048821)|heart development (GO:0007507)|histone H3-R2 demethylation (GO:0070078)|histone H4-R3 demethylation (GO:0070079)|kidney development (GO:0001822)|lung development (GO:0030324)|macrophage activation (GO:0042116)|mRNA processing (GO:0006397)|peptidyl-lysine hydroxylation to 5-hydroxy-L-lysine (GO:0018395)|recognition of apoptotic cell (GO:0043654)|regulation of mRNA splicing, via spliceosome (GO:0048024)|regulation of transcription, DNA-templated (GO:0006355)|retina development in camera-type eye (GO:0060041)|RNA splicing (GO:0008380)|sprouting angiogenesis (GO:0002040)|T cell differentiation in thymus (GO:0033077)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	histone demethylase activity (H3-R2 specific) (GO:0033746)|histone demethylase activity (H4-R3 specific) (GO:0033749)|identical protein binding (GO:0042802)|iron ion binding (GO:0005506)|peptidyl-lysine 5-dioxygenase activity (GO:0070815)|receptor activity (GO:0004872)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)			endometrium(2)|kidney(5)|large_intestine(2)|lung(3)|ovary(2)|skin(2)	16						CGGTGCACTGTCCCATCGCCC	0.567																																					p.T370A		Atlas-SNP	.											.	JMJD6	57	.	0			c.A1108G						PASS	.						85.0	90.0	89.0					17																	74714915		2130	4233	6363	SO:0001583	missense	23210	exon6			GCACTGTCCCATC	AB011157	CCDS42383.1, CCDS42384.1	17q25	2007-11-20	2007-02-16	2007-02-16	ENSG00000070495	ENSG00000070495			19355	protein-coding gene	gene with protein product		604914	"""phosphatidylserine receptor"""	PTDSR		11877474	Standard	NM_015167		Approved	PTDSR1, KIAA0585	uc002jsn.1	Q6NYC1	OTTHUMG00000169267	ENST00000397625.4:c.1108A>G	chr17.hg19:g.74714915T>C	ENSP00000380750:p.Thr370Ala	63.0	0.0	.		58.0	4.0	.	NM_001081461	B3KMN8|B4DGX1|Q86VY0|Q8IUM5|Q9Y4E2	Missense_Mutation	SNP	ENST00000397625.4	hg19	CCDS42384.1	.	.	.	.	.	.	.	.	.	.	T	11.90	1.775446	0.31411	.	.	ENSG00000070495	ENST00000445478;ENST00000397625	.	.	.	6.17	5.1	0.69264	.	0.345176	0.33959	N	0.004383	T	0.20414	0.0491	N	0.08118	0	0.27217	N	0.959752	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.17684	-1.0361	9	0.06099	T	0.92	-17.7187	12.092	0.53733	0.0:0.0663:0.0:0.9337	.	370;370	Q6NYC1;Q6NYC1-3	JMJD6_HUMAN;.	A	370	.	ENSP00000380750:T370A	T	-	1	0	JMJD6	72226510	0.585000	0.26774	0.030000	0.17652	0.900000	0.52787	2.454000	0.44979	1.160000	0.42584	0.533000	0.62120	ACA	.	.	.	none		0.567	JMJD6-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403211.1	NM_015167	
CHST9	83539	hgsc.bcm.edu	37	18	24722672	24722672	+	Missense_Mutation	SNP	C	C	A			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr18:24722672C>A	ENST00000284224.8	-	2	379	c.102G>T	c.(100-102)tgG>tgT	p.W34C	CHST9_ENST00000580774.1_Missense_Mutation_p.W34C|CHST9_ENST00000581714.1_Missense_Mutation_p.W34C|AQP4-AS1_ENST00000578701.1_RNA	NM_031422.5	NP_113610.2	Q7L1S5	CHST9_HUMAN	carbohydrate (N-acetylgalactosamine 4-0) sulfotransferase 9	34					carbohydrate biosynthetic process (GO:0016051)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|hormone biosynthetic process (GO:0042446)|proteoglycan biosynthetic process (GO:0030166)|small molecule metabolic process (GO:0044281)|sulfur compound metabolic process (GO:0006790)	extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	N-acetylgalactosamine 4-O-sulfotransferase activity (GO:0001537)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(7)|ovary(2)|pancreas(1)|skin(3)	28	all_lung(6;0.0145)|Ovarian(20;0.124)					GTTCTTCAATCCAGACTTGCA	0.348																																					p.W34C		Atlas-SNP	.											.	CHST9	114	.	0			c.G102T						PASS	.						97.0	90.0	92.0					18																	24722672		1834	4082	5916	SO:0001583	missense	83539	exon2			TTCAATCCAGACT	AF239821	CCDS42422.1, CCDS58618.1	18q11.2	2011-04-28			ENSG00000154080	ENSG00000154080		"""Sulfotransferases, membrane-bound"""	19898	protein-coding gene	gene with protein product		610191				11139592, 11445554	Standard	NM_031422		Approved	GALNAC4ST-2, GALNAC-4-ST2	uc002kwe.4	Q7L1S5		ENST00000284224.8:c.102G>T	chr18.hg19:g.24722672C>A	ENSP00000284224:p.Trp34Cys	45.0	0.0	.		30.0	16.0	.	NM_001256316	Q6UX69|Q9BXH3|Q9BXH4|Q9BZW9	Missense_Mutation	SNP	ENST00000284224.8	hg19	CCDS42422.1	.	.	.	.	.	.	.	.	.	.	C	9.223	1.033889	0.19590	.	.	ENSG00000154080	ENST00000284224	T	0.75154	-0.91	5.21	2.32	0.28847	.	0.949413	0.08796	N	0.892524	T	0.56949	0.2020	N	0.12182	0.205	0.50313	D	0.999866	B	0.02656	0.0	B	0.04013	0.001	T	0.35649	-0.9780	10	0.42905	T	0.14	1.249	8.8188	0.35011	0.3043:0.5489:0.1469:0.0	.	34	Q7L1S5	CHST9_HUMAN	C	34	ENSP00000284224:W34C	ENSP00000284224:W34C	W	-	3	0	CHST9	22976670	1.000000	0.71417	0.998000	0.56505	0.991000	0.79684	0.897000	0.28390	0.167000	0.19631	0.484000	0.47621	TGG	.	.	.	none		0.348	CHST9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446549.1	NM_031422	
ZNF567	163081	hgsc.bcm.edu	37	19	37210602	37210602	+	Missense_Mutation	SNP	G	G	T			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr19:37210602G>T	ENST00000536254.2	+	6	1198	c.976G>T	c.(976-978)Gat>Tat	p.D326Y	ZNF567_ENST00000360729.4_Missense_Mutation_p.D295Y|ZNF567_ENST00000585696.1_Missense_Mutation_p.D295Y|ZNF567_ENST00000392163.2_Missense_Mutation_p.D295Y|ZNF850_ENST00000589390.1_Intron|ZNF567_ENST00000588311.1_Missense_Mutation_p.D295Y			Q8N184	ZN567_HUMAN	zinc finger protein 567	326					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	24	Esophageal squamous(110;0.198)		COAD - Colon adenocarcinoma(19;0.0454)|Colorectal(19;0.065)			AGCCCTCACTGATCATCAGAG	0.438																																					p.D295Y		Atlas-SNP	.											.	ZNF567	61	.	0			c.G883T						PASS	.						64.0	62.0	63.0					19																	37210602		2203	4300	6503	SO:0001583	missense	163081	exon4			CTCACTGATCATC	AK093034	CCDS12495.1, CCDS74349.1	19q13.12	2013-10-08				ENSG00000189042		"""Zinc fingers, C2H2-type"", ""-"""	28696	protein-coding gene	gene with protein product						12477932	Standard	XM_006723064		Approved	MGC45586	uc002oep.4	Q8N184		ENST00000536254.2:c.976G>T	chr19.hg19:g.37210602G>T	ENSP00000441838:p.Asp326Tyr	83.0	0.0	.		93.0	21.0	.	NM_152603	B3KX49|Q6N044	Missense_Mutation	SNP	ENST00000536254.2	hg19		.	.	.	.	.	.	.	.	.	.	G	13.05	2.119936	0.37436	.	.	ENSG00000189042	ENST00000536254;ENST00000360729;ENST00000423498;ENST00000392163	T;T;T	0.16073	2.37;2.37;2.37	4.53	1.14	0.20703	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.144563	0.32134	N	0.006533	T	0.09555	0.0235	N	0.05383	-0.06	0.09310	N	0.999994	P;P	0.50710	0.938;0.924	P;P	0.48952	0.596;0.461	T	0.11518	-1.0584	10	0.46703	T	0.11	.	3.8123	0.08802	0.2795:0.1877:0.5328:0.0	.	326;295	Q8N184;F8WEL6	ZN567_HUMAN;.	Y	326;295;325;295	ENSP00000441838:D326Y;ENSP00000353957:D295Y;ENSP00000376003:D295Y	ENSP00000353957:D295Y	D	+	1	0	ZNF567	41902442	0.000000	0.05858	0.938000	0.37757	0.987000	0.75469	-0.067000	0.11579	0.608000	0.30000	0.462000	0.41574	GAT	.	.	.	none		0.438	ZNF567-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000453549.1	NM_152603	
REM1	28954	hgsc.bcm.edu	37	20	30064340	30064340	+	Missense_Mutation	SNP	G	G	A			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr20:30064340G>A	ENST00000201979.2	+	2	385	c.92G>A	c.(91-93)gGc>gAc	p.G31D	DEFB124_ENST00000481595.1_Intron	NM_014012.4	NP_054731.2	O75628	REM1_HUMAN	RAS (RAD and GEM)-like GTP-binding 1	31					GTP catabolic process (GO:0006184)|small GTPase mediated signal transduction (GO:0007264)	membrane (GO:0016020)	GTP binding (GO:0005525)			kidney(3)|large_intestine(3)|lung(14)|pancreas(2)|upper_aerodigestive_tract(1)	23	all_cancers(5;0.000119)|Lung NSC(7;1.32e-05)|all_lung(7;2.14e-05)|all_hematologic(12;0.158)|Ovarian(7;0.198)		Colorectal(19;0.00254)|COAD - Colon adenocarcinoma(19;0.0347)			CACCAGCCTGGCCGCCTGAGC	0.642																																					p.G31D		Atlas-SNP	.											.	REM1	54	.	0			c.G92A						PASS	.						76.0	87.0	84.0					20																	30064340		2203	4300	6503	SO:0001583	missense	28954	exon2			AGCCTGGCCGCCT	AF152863	CCDS13181.1	20q11.21	2014-05-09	2004-04-14	2004-04-16	ENSG00000088320	ENSG00000088320			15922	protein-coding gene	gene with protein product	"""GTPase GES"""	610388	"""RAS (RAD and GEM)-like GTP-binding"""	REM		10831614, 14623965	Standard	NM_014012		Approved	GES	uc002wwa.3	O75628	OTTHUMG00000032168	ENST00000201979.2:c.92G>A	chr20.hg19:g.30064340G>A	ENSP00000201979:p.Gly31Asp	118.0	0.0	.		102.0	37.0	.	NM_014012	E1P5L1|Q5TZR7|Q5TZR8|Q9NP57	Missense_Mutation	SNP	ENST00000201979.2	hg19	CCDS13181.1	.	.	.	.	.	.	.	.	.	.	G	13.55	2.271745	0.40194	.	.	ENSG00000088320	ENST00000201979	T	0.64991	-0.13	4.55	3.58	0.41010	.	0.709246	0.12931	N	0.427349	T	0.50939	0.1645	L	0.27053	0.805	0.43338	D	0.99538	B	0.17268	0.021	B	0.23419	0.046	T	0.45614	-0.9249	10	0.49607	T	0.09	.	12.1576	0.54085	0.0:0.174:0.826:0.0	.	31	O75628	REM1_HUMAN	D	31	ENSP00000201979:G31D	ENSP00000201979:G31D	G	+	2	0	REM1	29528001	1.000000	0.71417	0.997000	0.53966	0.943000	0.58893	3.986000	0.56937	1.088000	0.41272	0.655000	0.94253	GGC	.	.	.	none		0.642	REM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078508.2	NM_014012	
HNF1B	6928	hgsc.bcm.edu	37	17	36104669	36104680	+	In_Frame_Del	DEL	GTGGCCGTTGGT	GTGGCCGTTGGT	-			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	GTGGCCGTTGGT	GTGGCCGTTGGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr17:36104669_36104680delGTGGCCGTTGGT	ENST00000225893.4	-	1	557_568	c.196_207delACCAACGGCCAC	c.(196-207)accaacggccacdel	p.TNGH66del	HNF1B_ENST00000427275.2_In_Frame_Del_p.TNGH66del|RP11-115K3.1_ENST00000558143.1_RNA|HNF1B_ENST00000560016.1_In_Frame_Del_p.TNGH66del|HNF1B_ENST00000561193.1_In_Frame_Del_p.TNGH66del	NM_000458.2|NM_001165923.1	NP_000449.1|NP_001159395.1	P35680	HNF1B_HUMAN	HNF1 homeobox B	66					anterior/posterior pattern specification (GO:0009952)|branching morphogenesis of an epithelial tube (GO:0048754)|embryonic digestive tract morphogenesis (GO:0048557)|endocrine pancreas development (GO:0031018)|endodermal cell fate specification (GO:0001714)|epithelial cell proliferation (GO:0050673)|genitalia development (GO:0048806)|hepatoblast differentiation (GO:0061017)|hindbrain development (GO:0030902)|inner cell mass cell differentiation (GO:0001826)|insulin secretion (GO:0030073)|kidney development (GO:0001822)|mesonephric duct formation (GO:0072181)|negative regulation of mesenchymal cell apoptotic process involved in mesonephric nephron morphogenesis (GO:0061296)|negative regulation of mesenchymal cell apoptotic process involved in metanephros development (GO:1900212)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephric nephron tubule development (GO:0039020)|pronephros development (GO:0048793)|regulation of branch elongation involved in ureteric bud branching (GO:0072095)|regulation of endodermal cell fate specification (GO:0042663)|regulation of pronephros size (GO:0035565)|regulation of Wnt signaling pathway (GO:0030111)|response to glucose (GO:0009749)|ureteric bud elongation (GO:0060677)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|protein homodimerization activity (GO:0042803)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(6)|kidney(3)|large_intestine(2)|liver(1)|lung(3)|ovary(3)|prostate(1)|skin(2)	28		Breast(25;0.00765)|Ovarian(249;0.15)	STAD - Stomach adenocarcinoma(1;0.0142)			GGCCCTTGGCGTGGCCGTTGGTGAGAGTATGG	0.67																																					p.66_70del	Colon(71;102 1179 9001 27917 43397)	Atlas-Indel,Pindel	.											.	HNF1B	61	.	0			c.197_208del	GRCh37	CD024193	HNF1B	D		PASS	.																																			SO:0001651	inframe_deletion	6928	exon1			.	BC017714	CCDS11324.1, CCDS58538.1	17q12	2014-05-06	2007-08-24	2007-08-24	ENSG00000108753	ENSG00000275410		"""Homeoboxes / HNF class"""	11630	protein-coding gene	gene with protein product		189907	"""transcription factor 2, hepatic; LF-B3; variant hepatic nuclear factor"""	TCF2		1677179, 10484768	Standard	NM_000458		Approved	LFB3, VHNF1, HNF1beta, MODY5	uc002hok.4	P35680	OTTHUMG00000188478	ENST00000225893.4:c.196_207delACCAACGGCCAC	chr17.hg19:g.36104669_36104680delGTGGCCGTTGGT	ENSP00000225893:p.Thr66_His69del	96.0	0.0	0		86.0	35.0	0.406977	NM_001165923	B4DKM3|E0YMJ9	In_Frame_Del	DEL	ENST00000225893.4	hg19	CCDS11324.1																																																																																			.	.	.	none		0.670	HNF1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256807.3	NM_000458	
DMPK	1760	hgsc.bcm.edu	37	19	46273845	46273847	+	In_Frame_Del	DEL	AAC	AAC	-	rs201332435	byFrequency	TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	AAC	AAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr19:46273845_46273847delAAC	ENST00000291270.4	-	15	1914_1916	c.1789_1791delGTT	c.(1789-1791)gttdel	p.V597del	AC074212.5_ENST00000592217.2_RNA|AC074212.6_ENST00000586498.1_RNA|SIX5_ENST00000317578.6_5'Flank|AC074212.5_ENST00000559756.1_RNA|AC074212.6_ENST00000591530.1_RNA|AC074212.6_ENST00000590076.1_RNA|AC074212.6_ENST00000586251.1_RNA|DMPK_ENST00000354227.5_3'UTR|DMPK_ENST00000447742.2_In_Frame_Del_p.V592del|DMPK_ENST00000458663.2_In_Frame_Del_p.L590del|SIX5_ENST00000560168.1_5'Flank|DMPK_ENST00000343373.4_In_Frame_Del_p.V607del|DMPK_ENST00000600757.1_In_Frame_Del_p.L600del	NM_004409.3	NP_004400.4	Q09013	DMPK_HUMAN	dystrophia myotonica-protein kinase	597					cellular calcium ion homeostasis (GO:0006874)|muscle cell apoptotic process (GO:0010657)|nuclear envelope organization (GO:0006998)|protein phosphorylation (GO:0006468)|regulation of catalytic activity (GO:0050790)|regulation of excitatory postsynaptic membrane potential involved in skeletal muscle contraction (GO:0014853)|regulation of heart contraction (GO:0008016)|regulation of myotube differentiation (GO:0010830)|regulation of skeletal muscle contraction by calcium ion signaling (GO:0014722)|regulation of sodium ion transport (GO:0002028)|regulation of synapse structural plasticity (GO:0051823)	cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|integral component of mitochondrial outer membrane (GO:0031307)|nuclear membrane (GO:0031965)|plasma membrane (GO:0005886)|sarcoplasmic reticulum membrane (GO:0033017)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|myosin phosphatase regulator activity (GO:0017020)|protein serine/threonine kinase activity (GO:0004674)			endometrium(5)|kidney(1)|large_intestine(1)|lung(6)|stomach(1)|urinary_tract(2)	16		Ovarian(192;0.0308)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00616)|GBM - Glioblastoma multiforme(486;0.0825)|Epithelial(262;0.24)		CACGAGACAGAACAACGGCGAAC	0.695											OREG0025561	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.607_608del	Esophageal Squamous(35;307 869 9153 24033 28903)	Atlas-Indel,Pindel	.											.	DMPK	74	.	0			c.1820_1822del						PASS	.																																			SO:0001651	inframe_deletion	1760	exon14			.	L19268	CCDS12674.1, CCDS46117.1, CCDS46118.1, CCDS46119.1, CCDS74400.1	19q13.3	2014-02-05					2.7.11.1		2933	protein-coding gene	gene with protein product	"""dystrophia myotonica 1"", ""DM protein kinase"", ""myotonin protein kinase A"", ""myotonic dystrophy associated protein kinase"", ""thymopoietin homolog"""	605377	"""dystrophia myotonica 1 (includes dystrophia myotonia protein kinase)"""	DM1, DM		1546325, 1546326	Standard	NM_001288765		Approved	DMK, DM1PK, MDPK, MT-PK	uc002pdf.1	Q09013		ENST00000291270.4:c.1789_1791delGTT	chr19.hg19:g.46273848_46273850delAAC	ENSP00000291270:p.Val597del	335.0	0.0	0	938	210.0	68.0	0.32381	NM_001081563	E5KR08|Q16205|Q6P5Z6	In_Frame_Del	DEL	ENST00000291270.4	hg19	CCDS12674.1																																																																																			.	.	.	none		0.695	DMPK-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460572.1	NM_004409	
PSMD1	5707	hgsc.bcm.edu	37	2	232030606	232030607	+	Frame_Shift_Ins	INS	-	-	A			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr2:232030606_232030607insA	ENST00000308696.6	+	23	2752_2753	c.2590_2591insA	c.(2590-2592)gaafs	p.E864fs	PSMD1_ENST00000409643.1_Frame_Shift_Ins_p.E833fs|PSMD1_ENST00000373635.4_Frame_Shift_Ins_p.E833fs	NM_002807.3	NP_002798.2	Q99460	PSMD1_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 1	864					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of protein catabolic process (GO:0042176)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)	enzyme regulator activity (GO:0030234)			breast(1)|endometrium(2)|kidney(2)|large_intestine(10)|lung(10)|ovary(1)|prostate(1)|skin(4)	31		Ovarian(221;0.000626)|Medulloblastoma(418;0.0109)|Renal(207;0.0112)|Lung NSC(271;0.0538)|all_lung(227;0.0713)|all_hematologic(139;0.0748)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;4e-26)|LUSC - Lung squamous cell carcinoma(224;0.0138)|Lung(119;0.0168)	Bortezomib(DB00188)	GAAAAAGGAGGAAAAAGAGAAG	0.406																																					p.E864fs		Atlas-INDEL	.											.	PSMD1	77	.	0			c.2590_2591insA						PASS	.																																			SO:0001589	frameshift_variant	5707	exon23			.	D44466	CCDS2482.1, CCDS54436.1	2q37.1	2008-05-22			ENSG00000173692	ENSG00000173692		"""Proteasome (prosome, macropain) subunits"""	9554	protein-coding gene	gene with protein product						8816993	Standard	NM_002807		Approved	S1, P112, Rpn2	uc002vrn.2	Q99460	OTTHUMG00000133223	ENST00000308696.6:c.2595dupA	chr2.hg19:g.232030611_232030611dupA	ENSP00000309474:p.Glu864fs	41.0	0.0	0		36.0	13.0	0.361111	NM_002807	B8ZZH9|Q24JU0|Q53TI2|Q6GMU5|Q6P2P4|Q6PJM7|Q6PKG9|Q86VU1|Q8IV79	Frame_Shift_Ins	INS	ENST00000308696.6	hg19	CCDS2482.1																																																																																			.	.	.	none		0.406	PSMD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256958.2		
CCDC88B	283234	hgsc.bcm.edu	37	11	64110796	64110797	+	Splice_Site	INS	-	-	GGCAT	rs561918725		TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr11:64110796_64110797insGGCAT	ENST00000356786.5	+	11	1252_1253	c.1208_1209insGGCAT	c.(1207-1212)gcggag>gcGGCATggag	p.E404fs	CCDC88B_ENST00000463837.1_3'UTR|CCDC88B_ENST00000301897.4_5'Flank	NM_032251.5	NP_115627.6	A6NC98	CC88B_HUMAN	coiled-coil domain containing 88B	404						membrane (GO:0016020)				endometrium(1)|kidney(2)|large_intestine(1)|lung(12)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						GAGGCCCATGCGGTAAGGTAGC	0.639																																					p.A403fs		Atlas-Indel,Pindel	.											.	CCDC88B	89	.	0			c.1208_1209insGGCAT						PASS	.																																			SO:0001630	splice_region_variant	283234	exon11			.	AK090436	CCDS8072.2	11q13.1	2013-03-13	2007-05-31	2007-05-31	ENSG00000168071	ENSG00000168071			26757	protein-coding gene	gene with protein product	"""brain leucine zipper protein"", ""GRP78-interacting protein induced by ER stress"""	611205	"""coiled-coil domain containing 88"""	CCDC88		15882442, 21289099	Standard	NM_032251		Approved	FLJ37970, BRLZ, HkRP3, FLJ00354, GIPIE	uc001nzy.3	A6NC98	OTTHUMG00000045419	ENST00000356786.5:c.1209+1->GGCAT	chr11.hg19:g.64110796_64110797insGGCAT		76.0	0.0	0		76.0	12.0	0.157895	NM_032251	A5D8Y5|B5MDM2|Q05BL2|Q6RUV3|Q8N1Q6|Q8NF44|Q9H0H1	Frame_Shift_Ins	INS	ENST00000356786.5	hg19	CCDS8072.2																																																																																			.	.	.	none		0.639	CCDC88B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104845.1	NM_032251	Frame_Shift_Ins
ITGAX	3687	hgsc.bcm.edu	37	16	31371685	31371696	+	In_Frame_Del	DEL	CATTGTCATCAC	CATTGTCATCAC	-			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	CATTGTCATCAC	CATTGTCATCAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr16:31371685_31371696delCATTGTCATCAC	ENST00000268296.4	+	8	883_894	c.762_773delCATTGTCATCAC	c.(760-774)ctcattgtcatcact>ctt	p.IVIT255del	ITGAX_ENST00000562522.1_In_Frame_Del_p.IVIT255del	NM_000887.3	NP_000878.2	P20702	ITAX_HUMAN	integrin, alpha X (complement component 3 receptor 4 subunit)	255	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|organ morphogenesis (GO:0009887)	cell surface (GO:0009986)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(42)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	77						CCAAAATTCTCATTGTCATCACTGATGGGAAG	0.528																																					p.254_258del		Atlas-Indel,Pindel	.											.	ITGAX	198	.	0			c.761_772del						PASS	.																																			SO:0001651	inframe_deletion	3687	exon8			.	BC038237	CCDS10711.1, CCDS67014.1	16p11.2	2010-03-23	2006-02-10		ENSG00000140678	ENSG00000140678		"""CD molecules"", ""Complement system"", ""Integrins"""	6152	protein-coding gene	gene with protein product		151510	"""integrin, alpha X (antigen CD11C (p150), alpha polypeptide)"""	CD11C		3284962, 2303426	Standard	NM_001286375		Approved	CD11c	uc002ebu.1	P20702	OTTHUMG00000132465	ENST00000268296.4:c.762_773delCATTGTCATCAC	chr16.hg19:g.31371685_31371696delCATTGTCATCAC	ENSP00000268296:p.Ile255_Thr258del	49.0	0.0	0		50.0	19.0	0.38	NM_000887	Q8IVA6	In_Frame_Del	DEL	ENST00000268296.4	hg19	CCDS10711.1																																																																																			.	.	.	none		0.528	ITGAX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255628.2	NM_000887	
NHSL1	57224	hgsc.bcm.edu	37	6	138745824	138745824	+	Frame_Shift_Del	DEL	A	A	-			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr6:138745824delA	ENST00000427025.2	-	7	4855	c.4227delT	c.(4225-4227)attfs	p.I1409fs	NHSL1_ENST00000343505.5_Frame_Shift_Del_p.I1405fs	NM_020464.1	NP_065197.1	Q5SYE7	NHSL1_HUMAN	NHS-like 1	1409										breast(2)|endometrium(4)|kidney(1)	7						TGCTTCTCTGAATCGACCCCA	0.582																																					p.Q1410fs		Atlas-INDEL	.											.	NHSL1	99	.	0			c.4228delC						PASS	.						55.0	51.0	52.0					6																	138745824		692	1591	2283	SO:0001589	frameshift_variant	57224	exon7			.	AB037778	CCDS47487.1, CCDS55063.1	6q23.3	2009-02-18	2004-10-07	2004-10-07	ENSG00000135540	ENSG00000135540			21021	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 63"""	C6orf63			Standard	NM_001144060		Approved	bA43P8.1, KIAA1357	uc011edp.2	Q5SYE7	OTTHUMG00000016321	ENST00000427025.2:c.4227delT	chr6.hg19:g.138745824delA	ENSP00000394546:p.Ile1409fs	55.0	0.0	0		41.0	11.0	0.268293	NM_020464	Q3ZCS5|Q5SYE8|Q9P2J0	Frame_Shift_Del	DEL	ENST00000427025.2	hg19	CCDS55063.1																																																																																			.	.	.	none		0.582	NHSL1-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043700.2	XM_050421	
VWF	7450	hgsc.bcm.edu	37	12	6061052	6061053	+	Intron	DEL	AA	AA	-			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	AA	AA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr12:6061052_6061053delAA	ENST00000261405.5	-	50	8370					NM_000552.3	NP_000543	P04275	VWF_HUMAN	von Willebrand factor						blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|cell-substrate adhesion (GO:0031589)|extracellular matrix organization (GO:0030198)|hemostasis (GO:0007599)|liver development (GO:0001889)|placenta development (GO:0001890)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein homooligomerization (GO:0051260)|response to wounding (GO:0009611)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|proteinaceous extracellular matrix (GO:0005578)|Weibel-Palade body (GO:0033093)	chaperone binding (GO:0051087)|collagen binding (GO:0005518)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|immunoglobulin binding (GO:0019865)|integrin binding (GO:0005178)|protease binding (GO:0002020)|protein homodimerization activity (GO:0042803)|protein N-terminus binding (GO:0047485)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(41)|ovary(7)|pancreas(2)|prostate(6)|skin(15)|stomach(1)|upper_aerodigestive_tract(5)	129					Antihemophilic Factor(DB00025)	ATTTTACCCTAAGAAAACAGCA	0.46																																					.		Atlas-Indel,Pindel	.											.	VWF	338	.	0			.						PASS	.																																			SO:0001627	intron_variant	7450	.			.		CCDS8539.1	12p13.3	2014-09-17			ENSG00000110799	ENSG00000110799		"""Endogenous ligands"""	12726	protein-coding gene	gene with protein product		613160		F8VWF		2251280	Standard	NM_000552		Approved		uc001qnn.1	P04275	OTTHUMG00000168265	ENST00000261405.5:c.8116-3TT>-	chr12.hg19:g.6061052_6061053delAA		123.0	0.0	0		139.0	47.0	0.338129	.	Q8TCE8|Q99806	Splice_Site	DEL	ENST00000261405.5	hg19	CCDS8539.1																																																																																			.	.	.	none		0.460	VWF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399020.1	NM_000552	
UGT1A7	54577	hgsc.bcm.edu	37	2	234590634	234590634	+	Frame_Shift_Del	DEL	G	G	-			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr2:234590634delG	ENST00000373426.3	+	1	51	c.51delG	c.(49-51)ctgfs	p.L18fs	UGT1A1_ENST00000373450.4_Intron|UGT1A1_ENST00000609637.1_Intron|UGT1A10_ENST00000344644.5_Intron|UGT1A9_ENST00000354728.4_Intron|UGT1A10_ENST00000373445.1_Intron	NM_019077.2	NP_061950.2	Q9HAW7	UD17_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A7	18					cellular glucuronidation (GO:0052695)|coumarin metabolic process (GO:0009804)|drug metabolic process (GO:0017144)|excretion (GO:0007588)|flavone metabolic process (GO:0051552)|flavonoid glucuronidation (GO:0052696)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cellular glucuronidation (GO:2001030)|negative regulation of fatty acid metabolic process (GO:0045922)|retinoic acid metabolic process (GO:0042573)|xenobiotic glucuronidation (GO:0052697)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	drug binding (GO:0008144)|enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|glucuronosyltransferase activity (GO:0015020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)|retinoic acid binding (GO:0001972)			NS(1)|endometrium(6)|kidney(5)|large_intestine(5)|liver(1)|lung(12)|ovary(1)|prostate(1)|skin(1)	33		Breast(86;0.000765)|all_lung(227;0.00267)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0328)|Lung NSC(271;0.0457)|Lung SC(224;0.128)		Epithelial(121;8.93e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000412)|Lung(119;0.00333)|LUSC - Lung squamous cell carcinoma(224;0.00746)	Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)	TGTGTCTACTGCTGACCTGTG	0.557																																					p.L17fs		Atlas-INDEL	.											.	UGT1A7	74	.	0			c.50delT						PASS	.						133.0	125.0	127.0					2																	234590634		2203	4300	6503	SO:0001589	frameshift_variant	54577	exon1			.	U39570	CCDS2506.1	2q37	2010-03-05	2005-07-20		ENSG00000244122	ENSG00000244122		"""UDP glucuronosyltransferases"""	12539	other	complex locus constituent		606432	"""UDP glycosyltransferase 1 family, polypeptide A6"""			9295054, 11434514	Standard	NM_019077		Approved	UGT1G		Q9HAW7	OTTHUMG00000059004	ENST00000373426.3:c.51delG	chr2.hg19:g.234590634delG	ENSP00000362525:p.Leu18fs	50.0	0.0	0		55.0	22.0	0.4	NM_019077	B8K293|O00473	Frame_Shift_Del	DEL	ENST00000373426.3	hg19	CCDS2506.1																																																																																			.	.	.	none		0.557	UGT1A7-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000130614.1	NM_019077	
MAP2K3	5606	hgsc.bcm.edu	37	17	21203904	21203904	+	Frame_Shift_Del	DEL	C	C	-			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr17:21203904delC	ENST00000342679.4	+	4	462	c.213delC	c.(211-213)ggcfs	p.G71fs	MAP2K3_ENST00000316920.6_Frame_Shift_Del_p.G42fs|MAP2K3_ENST00000361818.5_Frame_Shift_Del_p.G42fs	NM_145109.2	NP_659731.1	P46734	MP2K3_HUMAN	mitogen-activated protein kinase kinase 3	71	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|cardiac muscle contraction (GO:0060048)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokine biosynthetic process (GO:0042035)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|MAP kinase kinase activity (GO:0004708)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)								COAD - Colon adenocarcinoma(3;0.0131)|Colorectal(15;0.0553)		CAGAACTGGGCCGTGGAGCCT	0.602																																					p.G71fs		Atlas-INDEL	.											.	MAP2K3	135	.	0			c.212delG						PASS	.						60.0	55.0	57.0					17																	21203904		2203	4300	6503	SO:0001589	frameshift_variant	5606	exon4			.	L36719	CCDS11217.1, CCDS11218.1	17q11.2	2011-06-09			ENSG00000034152	ENSG00000034152		"""Mitogen-activated protein kinase cascade / Kinase kinases"""	6843	protein-coding gene	gene with protein product	"""MAPK/ERK kinase 3"", ""MAP kinase kinase 3"", ""dual specificity mitogen activated protein kinase kinase 3"""	602315		PRKMK3		9465908	Standard	NM_145109		Approved	MEK3, MKK3, MAPKK3	uc002gys.3	P46734	OTTHUMG00000134322	ENST00000342679.4:c.213delC	chr17.hg19:g.21203904delC	ENSP00000345083:p.Gly71fs	98.0	0.0	0		140.0	13.0	0.0928571	NM_145109	B3KSK7|Q99441|Q9UE71|Q9UE72	Frame_Shift_Del	DEL	ENST00000342679.4	hg19	CCDS11217.1																																																																																			.	.	.	none		0.602	MAP2K3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259374.2	NM_145109	
SEC14L1	6397	hgsc.bcm.edu	37	17	75202482	75202482	+	Splice_Site	DEL	G	G	-			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr17:75202482delG	ENST00000413679.2	+	12	1644	c.1341delG	c.(1339-1341)ctg>ct	p.L447fs	SEC14L1_ENST00000443798.4_Splice_Site_p.L447fs|SEC14L1_ENST00000392476.2_Splice_Site_p.L447fs|SEC14L1_ENST00000431431.2_Splice_Site_p.L413fs|SEC14L1_ENST00000585618.1_Splice_Site_p.L447fs|SEC14L1_ENST00000591437.1_Splice_Site_p.L413fs|SEC14L1_ENST00000436233.4_Splice_Site_p.L447fs|SEC14L1_ENST00000430767.4_Splice_Site_p.L447fs	NM_001143998.1|NM_001143999.1|NM_003003.3	NP_001137470|NP_001137471|NP_002994	Q92503	S14L1_HUMAN	SEC14-like 1 (S. cerevisiae)	447	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.				transport (GO:0006810)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				NS(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(12)|ovary(3)|prostate(2)|skin(2)	31						TCTGGACGCTGGTGGGTTGAG	0.517																																					p.L447fs		Atlas-Indel,Pindel	.											.	SEC14L1	81	.	0			c.1340delT						PASS	.						60.0	56.0	57.0					17																	75202482		2203	4300	6503	SO:0001630	splice_region_variant	6397	exon12			.	D67029	CCDS11752.1, CCDS42385.1, CCDS45789.1	17q25.2	2008-02-01	2001-11-28			ENSG00000129657			10698	protein-coding gene	gene with protein product		601504	"""SEC14 (S. cerevisiae)-like 1"""	SEC14L		8697811	Standard	NM_001143998		Approved	PRELID4A	uc002jto.3	Q92503		ENST00000413679.2:c.1341+1G>-	chr17.hg19:g.75202482delG		62.0	0.0	0		93.0	29.0	0.311828	NM_001143998	A8K4E8|B4DDI5|D5G3K1|Q99780	Frame_Shift_Del	DEL	ENST00000413679.2	hg19	CCDS11752.1																																																																																			.	.	.	none		0.517	SEC14L1-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000436240.1	NM_003003	Frame_Shift_Del
KIRREL	55243	hgsc.bcm.edu	37	1	158058227	158058227	+	Frame_Shift_Del	DEL	A	A	-			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr1:158058227delA	ENST00000359209.6	+	8	1094	c.1027delA	c.(1027-1029)aaafs	p.K344fs	KIRREL_ENST00000368172.1_Frame_Shift_Del_p.K142fs|KIRREL_ENST00000368173.3_Frame_Shift_Del_p.K344fs|KIRREL_ENST00000392272.2_Frame_Shift_Del_p.K241fs|KIRREL_ENST00000416935.2_Frame_Shift_Del_p.K244fs|KIRREL_ENST00000360089.4_Frame_Shift_Del_p.K180fs			Q96J84	KIRR1_HUMAN	kin of IRRE like (Drosophila)	344	Ig-like C2-type 4.				excretion (GO:0007588)|negative regulation of protein phosphorylation (GO:0001933)|positive regulation of actin filament polymerization (GO:0030838)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|dendritic shaft (GO:0043198)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	myosin binding (GO:0017022)			NS(1)|autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(5)|lung(9)|ovary(1)|prostate(5)|skin(3)|stomach(1)	38	all_hematologic(112;0.0378)					CACCTGGACCAAAAAGGACTC	0.463																																					p.T342fs		Pindel	.											.	KIRREL	346	.	0			c.1026delC						PASS	.						101.0	100.0	100.0					1																	158058227		2203	4300	6503	SO:0001589	frameshift_variant	55243	exon8			.	AK001707	CCDS1172.2, CCDS72952.1	1q21-q25	2013-01-29			ENSG00000183853	ENSG00000183853		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15734	protein-coding gene	gene with protein product	"""nephrin-like protein 1"""	607428				12424224	Standard	NM_001286349		Approved	NEPH1	uc001frn.4	Q96J84	OTTHUMG00000022438	ENST00000359209.6:c.1027delA	chr1.hg19:g.158058227delA	ENSP00000352138:p.Lys344fs	136.0	0.0	.		121.0	28.0	0.231	NM_018240	Q5W0F8|Q5XKC6|Q7Z696|Q7Z7N8|Q8TB15|Q9H9N1|Q9NVA5	Frame_Shift_Del	DEL	ENST00000359209.6	hg19	CCDS1172.2																																																																																			.	.	.	none		0.463	KIRREL-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058342.3	NM_018240	
UGT1A7	54577	hgsc.bcm.edu	37	2	234590634	234590635	+	Frame_Shift_Del	DEL	GC	GC	-			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	GC	GC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr2:234590634_234590635delGC	ENST00000373426.3	+	1	51_52	c.51_52delGC	c.(49-54)ctgctgfs	p.LL17fs	UGT1A1_ENST00000373450.4_Intron|UGT1A1_ENST00000609637.1_Intron|UGT1A10_ENST00000344644.5_Intron|UGT1A9_ENST00000354728.4_Intron|UGT1A10_ENST00000373445.1_Intron	NM_019077.2	NP_061950.2	Q9HAW7	UD17_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A7	17					cellular glucuronidation (GO:0052695)|coumarin metabolic process (GO:0009804)|drug metabolic process (GO:0017144)|excretion (GO:0007588)|flavone metabolic process (GO:0051552)|flavonoid glucuronidation (GO:0052696)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cellular glucuronidation (GO:2001030)|negative regulation of fatty acid metabolic process (GO:0045922)|retinoic acid metabolic process (GO:0042573)|xenobiotic glucuronidation (GO:0052697)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	drug binding (GO:0008144)|enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|glucuronosyltransferase activity (GO:0015020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)|retinoic acid binding (GO:0001972)			NS(1)|endometrium(6)|kidney(5)|large_intestine(5)|liver(1)|lung(12)|ovary(1)|prostate(1)|skin(1)	33		Breast(86;0.000765)|all_lung(227;0.00267)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0328)|Lung NSC(271;0.0457)|Lung SC(224;0.128)		Epithelial(121;8.93e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000412)|Lung(119;0.00333)|LUSC - Lung squamous cell carcinoma(224;0.00746)	Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)	TGTGTCTACTGCTGACCTGTGG	0.559																																					p.17_17del		Pindel	.											.	UGT1A7	74	.	0			c.50_51del						PASS	.																																			SO:0001589	frameshift_variant	54577	exon1			.	U39570	CCDS2506.1	2q37	2010-03-05	2005-07-20		ENSG00000244122	ENSG00000244122		"""UDP glucuronosyltransferases"""	12539	other	complex locus constituent		606432	"""UDP glycosyltransferase 1 family, polypeptide A6"""			9295054, 11434514	Standard	NM_019077		Approved	UGT1G		Q9HAW7	OTTHUMG00000059004	ENST00000373426.3:c.51_52delGC	chr2.hg19:g.234590634_234590635delGC	ENSP00000362525:p.Leu17fs	51.0	0.0	.		57.0	16.0	0.281	NM_019077	B8K293|O00473	Frame_Shift_Del	DEL	ENST00000373426.3	hg19	CCDS2506.1																																																																																			.	.	.	none		0.559	UGT1A7-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000130614.1	NM_019077	
