#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
ALPL	249	hgsc.bcm.edu	37	1	21889674	21889674	+	Silent	SNP	C	C	A	rs201342272		TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr1:21889674C>A	ENST00000374840.3	+	5	619	c.369C>A	c.(367-369)gcC>gcA	p.A123A	ALPL_ENST00000539907.1_Silent_p.A46A|ALPL_ENST00000468526.1_3'UTR|ALPL_ENST00000540617.1_Silent_p.A68A|ALPL_ENST00000425315.2_Silent_p.A123A|ALPL_ENST00000374832.1_Silent_p.A123A	NM_000478.4	NP_000469.3	P05186	PPBT_HUMAN	alkaline phosphatase, liver/bone/kidney	123					cellular response to organic cyclic compound (GO:0071407)|cementum mineralization (GO:0071529)|developmental process involved in reproduction (GO:0003006)|endochondral ossification (GO:0001958)|osteoblast differentiation (GO:0001649)|response to antibiotic (GO:0046677)|response to glucocorticoid (GO:0051384)|response to lipopolysaccharide (GO:0032496)|response to vitamin D (GO:0033280)|skeletal system development (GO:0001501)	anchored component of membrane (GO:0031225)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	alkaline phosphatase activity (GO:0004035)|metal ion binding (GO:0046872)|pyrophosphatase activity (GO:0016462)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(1)|lung(11)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	26		all_lung(284;2.19e-05)|Lung NSC(340;2.22e-05)|Colorectal(325;3.46e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0192)|OV - Ovarian serous cystadenocarcinoma(117;8.7e-28)|COAD - Colon adenocarcinoma(152;1.57e-05)|GBM - Glioblastoma multiforme(114;2.66e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000177)|STAD - Stomach adenocarcinoma(196;0.00645)|KIRC - Kidney renal clear cell carcinoma(1967;0.00856)|READ - Rectum adenocarcinoma(331;0.0623)|Lung(427;0.146)	Amifostine(DB01143)|Fospropofol(DB06716)	GGGTGAAGGCCAATGAGGGCA	0.652													C|||	1	0.000199681	0.0	0.0	5008	,	,		17698	0.0		0.0	False		,,,				2504	0.001				p.A123A		Atlas-SNP	.											.	ALPL	50	.	0			c.C369A						PASS	.						84.0	75.0	78.0					1																	21889674		2203	4300	6503	SO:0001819	synonymous_variant	249	exon5			GAAGGCCAATGAG	BC021289	CCDS217.1, CCDS53274.1, CCDS53275.1	1p36.12	2008-02-05			ENSG00000162551	ENSG00000162551	3.1.3.1		438	protein-coding gene	gene with protein product		171760		HOPS		3532105, 3446011	Standard	NM_001127501		Approved	TNSALP	uc001bet.3	P05186	OTTHUMG00000002949	ENST00000374840.3:c.369C>A	chr1.hg19:g.21889674C>A		263.0	0.0	.		179.0	71.0	.	NM_000478	A1A4E7|B2RMP8|B7Z387|B7Z4Y6|O75090|Q2TAI7|Q59EJ7|Q5BKZ5|Q5VTG5|Q6NZI8|Q8WU32|Q9UBK0	Silent	SNP	ENST00000374840.3	hg19	CCDS217.1																																																																																			.	C|0.999;A|0.001	0.001	weak		0.652	ALPL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000008202.1	NM_000478	
FAM46B	115572	hgsc.bcm.edu	37	1	27333078	27333078	+	Missense_Mutation	SNP	A	A	T			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr1:27333078A>T	ENST00000289166.5	-	2	800	c.635T>A	c.(634-636)tTt>tAt	p.F212Y		NM_052943.3	NP_443175.2	Q96A09	FA46B_HUMAN	family with sequence similarity 46, member B	212										breast(1)|central_nervous_system(1)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(1)	10		all_cancers(24;1.29e-21)|all_epithelial(13;2.35e-19)|Colorectal(325;0.000147)|all_lung(284;0.00122)|Lung NSC(340;0.00128)|Breast(348;0.00131)|Renal(390;0.00211)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;7.71e-51)|OV - Ovarian serous cystadenocarcinoma(117;1.11e-29)|Colorectal(126;5.31e-09)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000272)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|STAD - Stomach adenocarcinoma(196;0.00114)|READ - Rectum adenocarcinoma(331;0.0419)		GCTGAATTCAAACTGGCGTCT	0.552																																					p.F212Y		Atlas-SNP	.											FAM46B,NS,carcinoma,0,1	FAM46B	44	.	0			c.T635A						PASS	.						108.0	110.0	110.0					1																	27333078		2203	4300	6503	SO:0001583	missense	115572	exon2			AATTCAAACTGGC	AK122816	CCDS294.2	1p35.3	2008-02-05			ENSG00000158246	ENSG00000158246			28273	protein-coding gene	gene with protein product						12477932	Standard	NM_052943		Approved	MGC16491	uc010ofj.2	Q96A09	OTTHUMG00000004278	ENST00000289166.5:c.635T>A	chr1.hg19:g.27333078A>T	ENSP00000289166:p.Phe212Tyr	96.0	0.0	.		53.0	16.0	.	NM_052943		Missense_Mutation	SNP	ENST00000289166.5	hg19	CCDS294.2	.	.	.	.	.	.	.	.	.	.	A	24.2	4.507004	0.85282	.	.	ENSG00000158246	ENST00000289166	T	0.28454	1.61	5.2	5.2	0.72013	Domain of unknown function DUF1693 (1);	0.045170	0.85682	D	0.000000	T	0.57066	0.2028	M	0.79614	2.46	0.80722	D	1	D	0.76494	0.999	D	0.91635	0.999	T	0.61133	-0.7124	10	0.56958	D	0.05	-1.9476	15.2153	0.73261	1.0:0.0:0.0:0.0	.	212	Q96A09	FA46B_HUMAN	Y	212	ENSP00000289166:F212Y	ENSP00000289166:F212Y	F	-	2	0	FAM46B	27205665	1.000000	0.71417	0.999000	0.59377	0.970000	0.65996	9.135000	0.94478	2.178000	0.69098	0.459000	0.35465	TTT	.	.	.	none		0.552	FAM46B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012347.2	NM_052943	
C1orf94	84970	hgsc.bcm.edu	37	1	34643683	34643683	+	Missense_Mutation	SNP	G	G	C			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr1:34643683G>C	ENST00000488417.1	+	1	413	c.293G>C	c.(292-294)aGa>aCa	p.R98T	AC115286.1_ENST00000408126.1_RNA|C1orf94_ENST00000373374.3_Intron	NM_001134734.1	NP_001128206.1	Q6P1W5	CA094_HUMAN	chromosome 1 open reading frame 94	98										central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(15)|skin(4)|upper_aerodigestive_tract(2)	32		Myeloproliferative disorder(586;0.0393)				GGAACTCTAAGAGGCAATGAG	0.537																																					p.R98T		Atlas-SNP	.											.	C1orf94	156	.	0			c.G293C						PASS	.						73.0	69.0	70.0					1																	34643683		692	1591	2283	SO:0001583	missense	84970	exon1			CTCTAAGAGGCAA	AK123355	CCDS381.1, CCDS44108.1	1p34.3	2012-06-26			ENSG00000142698	ENSG00000142698			28250	protein-coding gene	gene with protein product						12477932	Standard	NM_001134734		Approved	MGC15882	uc001bxt.3	Q6P1W5	OTTHUMG00000004012	ENST00000488417.1:c.293G>C	chr1.hg19:g.34643683G>C	ENSP00000435634:p.Arg98Thr	133.0	0.0	.		77.0	24.0	.	NM_001134734	B3KVT1|D3DPR3|E9PJ76|Q96IC8	Missense_Mutation	SNP	ENST00000488417.1	hg19	CCDS44108.1	.	.	.	.	.	.	.	.	.	.	G	0.083	-1.180380	0.01633	.	.	ENSG00000142698	ENST00000488417	T	0.44881	0.91	4.99	2.08	0.27032	.	.	.	.	.	T	0.26666	0.0652	N	0.22421	0.69	0.09310	N	1	B	0.12013	0.005	B	0.10450	0.005	T	0.23261	-1.0193	9	0.66056	D	0.02	.	5.0027	0.14273	0.1877:0.173:0.6393:0.0	.	98	Q6P1W5	CA094_HUMAN	T	98	ENSP00000435634:R98T	ENSP00000435634:R98T	R	+	2	0	C1orf94	34416270	0.867000	0.29959	0.005000	0.12908	0.004000	0.04260	1.134000	0.31442	0.277000	0.22141	0.655000	0.94253	AGA	.	.	.	none		0.537	C1orf94-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036845.2	NM_032884	
ZCCHC11	23318	hgsc.bcm.edu	37	1	52897102	52897102	+	Missense_Mutation	SNP	G	G	T			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr1:52897102G>T	ENST00000371544.3	-	28	4553	c.4291C>A	c.(4291-4293)Cag>Aag	p.Q1431K	ZCCHC11_ENST00000257177.4_Missense_Mutation_p.Q1432K	NM_001009881.2|NM_015269.2	NP_001009881.1|NP_056084.1	Q5TAX3	TUT4_HUMAN	zinc finger, CCHC domain containing 11	1431	Gln-rich.|Pro-rich.				cytokine production (GO:0001816)|miRNA catabolic process (GO:0010587)|miRNA metabolic process (GO:0010586)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|pre-miRNA processing (GO:0031054)|regulation of lipopolysaccharide-mediated signaling pathway (GO:0031664)|RNA 3'-end processing (GO:0031123)|stem cell maintenance (GO:0019827)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|RNA uridylyltransferase activity (GO:0050265)|zinc ion binding (GO:0008270)			NS(2)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(17)|ovary(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	58						GGAAATGGCTGAGGCTGAGGA	0.393																																					p.Q1432K		Atlas-SNP	.											.	ZCCHC11	151	.	0			c.C4294A						PASS	.						32.0	29.0	30.0					1																	52897102		2203	4298	6501	SO:0001583	missense	23318	exon28			ATGGCTGAGGCTG	D83776	CCDS30715.1, CCDS30716.1	1p32.3	2014-03-05			ENSG00000134744	ENSG00000134744		"""Zinc fingers, CCHC domain containing"""	28981	protein-coding gene	gene with protein product	"""TUTase4"""	613692				8724849, 12239557	Standard	NM_015269		Approved	KIAA0191, PAPD3, TUT4	uc001cty.2	Q5TAX3	OTTHUMG00000008200	ENST00000371544.3:c.4291C>A	chr1.hg19:g.52897102G>T	ENSP00000360599:p.Gln1431Lys	88.0	0.0	.		60.0	19.0	.	NM_001009881	A2RRP0|B7Z8J5|D3DQ35|Q12764|Q5TAX2|Q5TAX4|Q86XZ3	Missense_Mutation	SNP	ENST00000371544.3	hg19	CCDS30716.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.48|15.48	2.847224|2.847224	0.51164|0.51164	.|.	.|.	ENSG00000134744|ENSG00000134744	ENST00000257177;ENST00000371544;ENST00000531722|ENST00000474453	T;T|.	0.46451|.	0.87;0.88|.	5.27|5.27	5.27|5.27	0.74061|0.74061	.|.	0.248184|.	0.35466|.	N|.	0.003196|.	T|.	0.55433|.	0.1920|.	N|N	0.24115|0.24115	0.695|0.695	0.80722|0.80722	D|D	1|1	P|.	0.40144|.	0.704|.	B|.	0.32022|.	0.139|.	T|.	0.50668|.	-0.8801|.	10|.	0.40728|.	T|.	0.16|.	.|.	18.8838|18.8838	0.92367|0.92367	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	1431|.	Q5TAX3|.	TUT4_HUMAN|.	K|X	1432;1431;269|276	ENSP00000257177:Q1432K;ENSP00000360599:Q1431K|.	ENSP00000257177:Q1432K|.	Q|S	-|-	1|2	0|0	ZCCHC11|ZCCHC11	52669690|52669690	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.981000|0.981000	0.71138|0.71138	5.423000|5.423000	0.66458|0.66458	2.459000|2.459000	0.83118|0.83118	0.557000|0.557000	0.71058|0.71058	CAG|TCA	.	.	.	none		0.393	ZCCHC11-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000022462.1	XM_038288	
RABIF	5877	hgsc.bcm.edu	37	1	202850297	202850297	+	Missense_Mutation	SNP	C	C	T			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr1:202850297C>T	ENST00000367262.3	-	2	217	c.181G>A	c.(181-183)Gac>Aac	p.D61N		NM_002871.4	NP_002862.2	P47224	MSS4_HUMAN	RAB interacting factor	61					membrane fusion (GO:0061025)|positive regulation of GTPase activity (GO:0043547)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)		guanyl-nucleotide exchange factor activity (GO:0005085)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(2)|ovary(1)	4			BRCA - Breast invasive adenocarcinoma(75;0.166)			AGATCGCCGTCAGGATTGCTG	0.507																																					p.D61N		Atlas-SNP	.											.	RABIF	11	.	0			c.G181A						PASS	.						68.0	64.0	65.0					1																	202850297		2203	4300	6503	SO:0001583	missense	5877	exon2			CGCCGTCAGGATT	S78873	CCDS1428.1	1q32.1	2008-05-14			ENSG00000183155	ENSG00000183155			9797	protein-coding gene	gene with protein product		603417		RASGRF3		9441742, 7619808	Standard	NM_002871		Approved	mss4	uc001gyl.3	P47224	OTTHUMG00000041400	ENST00000367262.3:c.181G>A	chr1.hg19:g.202850297C>T	ENSP00000356231:p.Asp61Asn	63.0	0.0	.		48.0	18.0	.	NM_002871	B2R4P4|Q92992	Missense_Mutation	SNP	ENST00000367262.3	hg19	CCDS1428.1	.	.	.	.	.	.	.	.	.	.	C	10.55	1.382058	0.24944	.	.	ENSG00000183155	ENST00000367262	.	.	.	5.75	4.84	0.62591	Mss4-like (1);Mss4/translationally controlled tumour-associated TCTP (1);	0.332353	0.37136	N	0.002226	T	0.55955	0.1953	L	0.40543	1.245	0.80722	D	1	B	0.25809	0.135	B	0.29176	0.099	T	0.55528	-0.8127	9	0.51188	T	0.08	-57.0511	14.6684	0.68926	0.0:0.9296:0.0:0.0704	.	61	P47224	MSS4_HUMAN	N	61	.	ENSP00000356231:D61N	D	-	1	0	RABIF	201116920	1.000000	0.71417	0.009000	0.14445	0.008000	0.06430	5.492000	0.66893	1.447000	0.47661	-0.254000	0.11334	GAC	.	.	.	none		0.507	RABIF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099183.1		
CENPF	1063	hgsc.bcm.edu	37	1	214826247	214826247	+	Missense_Mutation	SNP	T	T	C			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr1:214826247T>C	ENST00000366955.3	+	16	8405	c.8237T>C	c.(8236-8238)aTa>aCa	p.I2746T	CENPF_ENST00000467765.1_3'UTR	NM_016343.3	NP_057427.3	P49454	CENPF_HUMAN	centromere protein F, 350/400kDa	2842	Sufficient for centromere localization.|Sufficient for self-association.				cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|DNA replication (GO:0006260)|G2/M transition of mitotic cell cycle (GO:0000086)|kinetochore assembly (GO:0051382)|metaphase plate congression (GO:0051310)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|muscle organ development (GO:0007517)|negative regulation of transcription, DNA-templated (GO:0045892)|protein transport (GO:0015031)|regulation of cell cycle (GO:0051726)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of striated muscle tissue development (GO:0016202)|response to drug (GO:0042493)	chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|midbody (GO:0030496)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|pronucleus (GO:0045120)|spindle (GO:0005819)|spindle pole (GO:0000922)	chromatin binding (GO:0003682)|dynein binding (GO:0045502)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|transcription factor binding (GO:0008134)			NS(2)|breast(2)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(37)|lung(47)|ovary(7)|prostate(3)|skin(6)|stomach(1)|urinary_tract(1)	126				all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833)		AAGCTGGAGATAGACCTTTTA	0.328																																					p.I2746T	Colon(80;575 1284 11000 14801 43496)	Atlas-SNP	.											.	CENPF	321	.	0			c.T8237C						PASS	.						91.0	94.0	93.0					1																	214826247		2203	4300	6503	SO:0001583	missense	1063	exon16			TGGAGATAGACCT	U30872	CCDS31023.1	1q41	2013-11-05	2013-01-17		ENSG00000117724	ENSG00000117724			1857	protein-coding gene	gene with protein product	"""mitosin"""	600236	"""centromere protein F, 350/400kDa (mitosin)"""			7904902, 7851898	Standard	NM_016343		Approved	hcp-1	uc001hkm.3	P49454	OTTHUMG00000036955	ENST00000366955.3:c.8237T>C	chr1.hg19:g.214826247T>C	ENSP00000355922:p.Ile2746Thr	101.0	0.0	.		120.0	25.0	.	NM_016343	Q13171|Q13246|Q5VVM7	Missense_Mutation	SNP	ENST00000366955.3	hg19	CCDS31023.1	.	.	.	.	.	.	.	.	.	.	T	11.84	1.757432	0.31137	.	.	ENSG00000117724	ENST00000366955;ENST00000391896	T	0.04234	3.67	3.93	3.93	0.45458	.	.	.	.	.	T	0.05410	0.0143	L	0.47716	1.5	0.20489	N	0.999898	B	0.33694	0.421	B	0.22152	0.038	T	0.28106	-1.0054	9	0.42905	T	0.14	.	11.9872	0.53155	0.0:0.0:0.0:1.0	.	2842	P49454	CENPF_HUMAN	T	2746;145	ENSP00000355922:I2746T	ENSP00000355922:I2746T	I	+	2	0	CENPF	212892870	0.990000	0.36364	0.042000	0.18584	0.923000	0.55619	3.757000	0.55212	1.429000	0.47314	0.418000	0.28097	ATA	.	.	.	none		0.328	CENPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089749.1	NM_016343	
OBSCN	84033	hgsc.bcm.edu	37	1	228511117	228511117	+	Missense_Mutation	SNP	G	G	A			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr1:228511117G>A	ENST00000422127.1	+	56	15506	c.15462G>A	c.(15460-15462)atG>atA	p.M5154I	OBSCN_ENST00000366707.4_Missense_Mutation_p.M2788I|OBSCN_ENST00000284548.11_Missense_Mutation_p.M5154I|OBSCN_ENST00000570156.2_Missense_Mutation_p.M6111I|OBSCN_ENST00000366709.4_Missense_Mutation_p.M2273I	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	5154	Ig-like 49.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				GTCAGCCCATGCCCAGTGTGC	0.522																																					p.M6111I		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G18333A						PASS	.						92.0	94.0	93.0					1																	228511117		2155	4253	6408	SO:0001583	missense	84033	exon67			GCCCATGCCCAGT	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.15462G>A	chr1.hg19:g.228511117G>A	ENSP00000409493:p.Met5154Ile	112.0	0.0	.		102.0	23.0	.	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	hg19	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	G	10.73	1.431705	0.25813	.	.	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709	T;T;T;T	0.66638	-0.22;-0.22;-0.22;-0.22	5.07	5.07	0.68467	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.660669	0.14435	N	0.319744	T	0.46034	0.1372	N	0.04959	-0.14	0.27969	N	0.936468	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.13629	-1.0502	10	0.16896	T	0.51	.	15.681	0.77367	0.0:0.2016:0.7984:0.0	.	5154;5154	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	I	5154;5154;2788;2273	ENSP00000284548:M5154I;ENSP00000409493:M5154I;ENSP00000355668:M2788I;ENSP00000355670:M2273I	ENSP00000284548:M5154I	M	+	3	0	OBSCN	226577740	1.000000	0.71417	0.991000	0.47740	0.034000	0.12701	1.113000	0.31184	2.629000	0.89072	0.655000	0.94253	ATG	.	.	.	none		0.522	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
OR2W3	343171	hgsc.bcm.edu	37	1	248059782	248059782	+	Silent	SNP	G	G	A			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr1:248059782G>A	ENST00000360358.3	+	1	894	c.894G>A	c.(892-894)aaG>aaA	p.K298K	OR2W3_ENST00000537741.1_Silent_p.K298K	NM_001001957.2	NP_001001957.2	Q7Z3T1	OR2W3_HUMAN	olfactory receptor, family 2, subfamily W, member 3	298						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|kidney(2)|large_intestine(2)|lung(33)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)	49	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0319)			GAGAGGTGAAGGGGGCACTGG	0.537																																					p.K298K		Atlas-SNP	.											.	OR2W3	113	.	0			c.G894A						PASS	.						39.0	40.0	40.0					1																	248059782		2203	4300	6503	SO:0001819	synonymous_variant	343171	exon1			GGTGAAGGGGGCA	N75737	CCDS31099.1	1q44	2012-08-09		2004-03-10	ENSG00000238243	ENSG00000238243		"""GPCR / Class A : Olfactory receptors"""	15021	protein-coding gene	gene with protein product				OR2W8P, OR2W3P		14983052	Standard	NM_001001957		Approved	OST718	uc010pzb.2	Q7Z3T1	OTTHUMG00000040204	ENST00000360358.3:c.894G>A	chr1.hg19:g.248059782G>A		111.0	0.0	.		80.0	5.0	.	NM_001001957	Q6IF06|Q8NG86	Silent	SNP	ENST00000360358.3	hg19	CCDS31099.1																																																																																			.	.	.	none		0.537	OR2W3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096861.1	NM_001001957	
LRPPRC	10128	hgsc.bcm.edu	37	2	44116985	44116986	+	Missense_Mutation	DNP	GC	GC	AG			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr2:44116985_44116986GC>AG	ENST00000260665.7	-	37	4072_4073	c.4015_4016GC>CT	c.(4015-4017)GCa>CTa	p.A1339L	RNU6-1048P_ENST00000364054.1_RNA	NM_133259.3	NP_573566.2	P42704	LPPRC_HUMAN	leucine-rich pentatricopeptide repeat containing	1339	RNA-binding.				mitochondrion transport along microtubule (GO:0047497)|mRNA transport (GO:0051028)|negative regulation of mitochondrial RNA catabolic process (GO:0000961)|regulation of mitochondrial translation (GO:0070129)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	condensed nuclear chromosome (GO:0000794)|cytoskeleton (GO:0005856)|membrane (GO:0016020)|microtubule (GO:0005874)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|ribonucleoprotein complex (GO:0030529)	beta-tubulin binding (GO:0048487)|microtubule binding (GO:0008017)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)			breast(3)|endometrium(3)|kidney(5)|large_intestine(9)|lung(15)|ovary(2)|prostate(2)|skin(2)	41		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)				TTCATACAGTGCTTTAGCAGAT	0.366																																					p.A1339V|p.A1339P		Atlas-SNP	.											.	LRPPRC	105	.	0			c.C4016T|c.G4015C						PASS	.																																			SO:0001583	missense	10128	exon37			TACAGTGCTTTAG|ACAGTGCTTTAGC	M92439	CCDS33189.1	2p21	2012-02-24	2012-02-24		ENSG00000138095	ENSG00000138095			15714	protein-coding gene	gene with protein product		607544	"""Leigh syndrome, French-Canadian type (cytochrome oxidase deficiency)"""	LSFC		8012652, 8619474, 22045337	Standard	NM_133259		Approved	GP130, LRP130	uc002rtr.2	P42704	OTTHUMG00000152782	ENST00000260665.7:c.4015_4016delinsAG	chr2.hg19:g.44116985_44116986delinsAG	ENSP00000260665:p.Ala1339Leu	243.0|244.0	0.0	.		219.0|217.0	48.0	.	NM_133259	A0PJE3|A8K1V1|Q53PC0|Q53QN7|Q6ZUD8|Q7Z7A6|Q96D84	Missense_Mutation	SNP	ENST00000260665.7	hg19	CCDS33189.1																																																																																			.	.	.	none		0.366	LRPPRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327823.1	NM_133259	
ROBO2	6092	hgsc.bcm.edu	37	3	77671536	77671536	+	Missense_Mutation	SNP	A	A	T			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr3:77671536A>T	ENST00000461745.1	+	23	4613	c.3713A>T	c.(3712-3714)gAc>gTc	p.D1238V	ROBO2_ENST00000487694.3_Missense_Mutation_p.D1254V|ROBO2_ENST00000332191.8_Missense_Mutation_p.D1238V	NM_002942.4	NP_002933.1	Q9HCK4	ROBO2_HUMAN	roundabout, axon guidance receptor, homolog 2 (Drosophila)	1238					apoptotic process involved in luteolysis (GO:0061364)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|brain development (GO:0007420)|cellular response to hormone stimulus (GO:0032870)|central nervous system development (GO:0007417)|homophilic cell adhesion (GO:0007156)|metanephros development (GO:0001656)|negative regulation of negative chemotaxis (GO:0050925)|negative regulation of synapse assembly (GO:0051964)|olfactory bulb interneuron development (GO:0021891)|positive regulation of axonogenesis (GO:0050772)|retinal ganglion cell axon guidance (GO:0031290)|ureteric bud development (GO:0001657)	axolemma (GO:0030673)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)			NS(1)|biliary_tract(5)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(23)|liver(1)|lung(52)|ovary(2)|pancreas(2)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	117				Epithelial(33;0.00199)|LUSC - Lung squamous cell carcinoma(21;0.008)|BRCA - Breast invasive adenocarcinoma(55;0.00884)|Lung(72;0.0183)|KIRC - Kidney renal clear cell carcinoma(39;0.0832)|Kidney(39;0.103)		AGAGCACTGGACCAGACTCCT	0.463																																					p.D1238V		Atlas-SNP	.											.	ROBO2	527	.	0			c.A3713T						PASS	.						74.0	77.0	76.0					3																	77671536		1902	4120	6022	SO:0001583	missense	6092	exon23			CACTGGACCAGAC	AF040991	CCDS43109.1, CCDS54609.1	3p12.3	2013-02-11	2001-11-28		ENSG00000185008	ENSG00000185008		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	10250	protein-coding gene	gene with protein product		602431	"""roundabout (axon guidance receptor, Drosophila) homolog 2"""			9458045	Standard	NM_002942		Approved	KIAA1568	uc003dpy.4	Q9HCK4	OTTHUMG00000158935	ENST00000461745.1:c.3713A>T	chr3.hg19:g.77671536A>T	ENSP00000417164:p.Asp1238Val	70.0	0.0	.		48.0	19.0	.	NM_002942	O43608|Q19AB4|Q19AB5	Missense_Mutation	SNP	ENST00000461745.1	hg19	CCDS43109.1	.	.	.	.	.	.	.	.	.	.	A	15.72	2.917020	0.52546	.	.	ENSG00000185008	ENST00000487694;ENST00000403211;ENST00000461745;ENST00000332191	T;T;T	0.61510	0.1;0.14;0.12	5.56	5.56	0.83823	.	0.299670	0.23303	N	0.049659	T	0.43897	0.1268	N	0.08118	0	0.30052	N	0.811715	B;B;B	0.26512	0.151;0.096;0.151	B;B;B	0.34093	0.086;0.175;0.086	T	0.56667	-0.7941	9	0.56958	D	0.05	.	15.6959	0.77499	1.0:0.0:0.0:0.0	.	1254;1238;1238	Q19AB5;F8W703;Q9HCK4	.;.;ROBO2_HUMAN	V	1254;1254;1238;1238	ENSP00000417335:D1254V;ENSP00000417164:D1238V;ENSP00000327536:D1238V	ENSP00000327536:D1238V	D	+	2	0	ROBO2	77754226	1.000000	0.71417	1.000000	0.80357	0.826000	0.46750	8.962000	0.93254	2.110000	0.64415	0.528000	0.53228	GAC	.	.	.	none		0.463	ROBO2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352600.2	XM_031246	
ATP6V1A	523	hgsc.bcm.edu	37	3	113505224	113505224	+	Missense_Mutation	SNP	T	T	C			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr3:113505224T>C	ENST00000273398.3	+	6	818	c.710T>C	c.(709-711)cTt>cCt	p.L237P	ATP6V1A_ENST00000538620.1_Missense_Mutation_p.L204P	NM_001690.3	NP_001681.2	P38606	VATA_HUMAN	ATPase, H+ transporting, lysosomal 70kDa, V1 subunit A	237					ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|microvillus (GO:0005902)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|proton-transporting two-sector ATPase complex (GO:0016469)|proton-transporting V-type ATPase, V1 domain (GO:0033180)	ATP binding (GO:0005524)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(17)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34					Alendronate(DB00630)|Etidronic acid(DB01077)|Tiludronate(DB01133)	CTTGATGCCCTTTTTCCGTAA	0.423																																					p.L237P		Atlas-SNP	.											ATP6V1A,NS,malignant_melanoma,0,1	ATP6V1A	71	.	0			c.T710C						PASS	.						219.0	201.0	207.0					3																	113505224		2203	4300	6503	SO:0001583	missense	523	exon6			ATGCCCTTTTTCC	L09235	CCDS2976.1	3q13.31	2010-04-21	2002-08-29	2003-04-25	ENSG00000114573	ENSG00000114573	3.6.3.14	"""ATPases / V-type"""	851	protein-coding gene	gene with protein product		607027	"""ATPase, H+ transporting, lysosomal (vacuolar proton pump), alpha polypeptide, 70kD, isoform 1"""	VPP2, ATP6A1, ATP6V1A1		8463241	Standard	NM_001690		Approved	Vma1, VA68	uc003eao.3	P38606	OTTHUMG00000159295	ENST00000273398.3:c.710T>C	chr3.hg19:g.113505224T>C	ENSP00000273398:p.Leu237Pro	102.0	0.0	.		88.0	4.0	.	NM_001690	B2RBR8|B7Z1R5|D3DN75|Q53YD9|Q96DY6|Q9UHY3	Missense_Mutation	SNP	ENST00000273398.3	hg19	CCDS2976.1	.	.	.	.	.	.	.	.	.	.	T	20.3	3.972517	0.74246	.	.	ENSG00000114573	ENST00000273398;ENST00000538620	D;D	0.84223	-1.82;-1.82	5.33	4.17	0.49024	ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.94062	0.8097	H	0.96208	3.785	0.80722	D	1	D	0.71674	0.998	D	0.73708	0.981	D	0.94260	0.7501	10	0.87932	D	0	-16.1423	10.9912	0.47551	0.0:0.0737:0.0:0.9263	.	237	P38606	VATA_HUMAN	P	237;204	ENSP00000273398:L237P;ENSP00000439874:L204P	ENSP00000273398:L237P	L	+	2	0	ATP6V1A	114987914	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	7.484000	0.81180	0.873000	0.35799	-0.353000	0.07706	CTT	.	.	.	none		0.423	ATP6V1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354457.1	NM_001690	
AMOTL2	51421	hgsc.bcm.edu	37	3	134078995	134078995	+	Missense_Mutation	SNP	A	A	C			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr3:134078995A>C	ENST00000422605.2	-	7	2002	c.1836T>G	c.(1834-1836)aaT>aaG	p.N612K	AMOTL2_ENST00000513145.1_Missense_Mutation_p.N610K|AMOTL2_ENST00000514516.1_Missense_Mutation_p.N670K|AMOTL2_ENST00000249883.5_Missense_Mutation_p.N612K			Q9Y2J4	AMOL2_HUMAN	angiomotin like 2	612					hippo signaling (GO:0035329)|Wnt signaling pathway (GO:0016055)	apical plasma membrane (GO:0016324)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endosome (GO:0005768)|tight junction (GO:0005923)				endometrium(8)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	19						GCAGACCCTCATTGAAGCTGC	0.622																																					p.N612K		Atlas-SNP	.											.	AMOTL2	52	.	0			c.T1836G						PASS	.						57.0	50.0	52.0					3																	134078995		2203	4300	6503	SO:0001583	missense	51421	exon7			ACCCTCATTGAAG	AF175966	CCDS33860.1, CCDS63783.1, CCDS63784.1	3q21-q22	2008-07-18			ENSG00000114019	ENSG00000114019			17812	protein-coding gene	gene with protein product	"""Leman coiled-coil protein"", ""angiomotin-like protein 2"""	614658					Standard	NM_016201		Approved	LCCP	uc003eqg.1	Q9Y2J4	OTTHUMG00000159777	ENST00000422605.2:c.1836T>G	chr3.hg19:g.134078995A>C	ENSP00000409999:p.Asn612Lys	78.0	0.0	.		62.0	19.0	.	NM_016201	A8K6F1|B7Z5Q1|E9PHW3|Q53EP1|Q96F99|Q9UKB4	Missense_Mutation	SNP	ENST00000422605.2	hg19		.	.	.	.	.	.	.	.	.	.	A	16.66	3.183876	0.57800	.	.	ENSG00000114019	ENST00000249883;ENST00000422605;ENST00000514516;ENST00000513145	T;T;T;T	0.17370	2.29;2.29;2.28;2.29	5.23	-0.975	0.10289	.	0.000000	0.85682	D	0.000000	T	0.26810	0.0656	L	0.57536	1.79	0.58432	D	0.999996	D;D;D	0.64830	0.992;0.992;0.994	P;P;D	0.63793	0.866;0.866;0.918	T	0.14727	-1.0462	10	0.11794	T	0.64	-26.2587	11.2577	0.49063	0.5554:0.0:0.4446:0.0	.	610;612;670	Q9Y2J4-3;Q9Y2J4-2;E9PHW3	.;.;.	K	612;612;670;610	ENSP00000249883:N612K;ENSP00000409999:N612K;ENSP00000424765:N670K;ENSP00000425475:N610K	ENSP00000249883:N612K	N	-	3	2	AMOTL2	135561685	0.461000	0.25783	0.993000	0.49108	0.925000	0.55904	-0.316000	0.08071	-0.263000	0.09378	-0.441000	0.05720	AAT	.	.	.	none		0.622	AMOTL2-014	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000358149.1	NM_016201	
SLC25A36	55186	hgsc.bcm.edu	37	3	140675502	140675502	+	Missense_Mutation	SNP	G	G	A			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr3:140675502G>A	ENST00000324194.6	+	2	343	c.175G>A	c.(175-177)Gta>Ata	p.V59I	SLC25A36_ENST00000453248.2_Missense_Mutation_p.V59I|SLC25A36_ENST00000446041.2_Missense_Mutation_p.V59I|SLC25A36_ENST00000393015.4_3'UTR|SLC25A36_ENST00000507429.1_Missense_Mutation_p.V59I			Q96CQ1	S2536_HUMAN	solute carrier family 25 (pyrimidine nucleotide carrier ), member 36	59					response to estradiol (GO:0032355)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				endometrium(2)|large_intestine(2)|lung(1)|upper_aerodigestive_tract(1)	6						TGTCAACCGAGTAGTGTCTCC	0.433																																					p.V59I		Atlas-SNP	.											.	SLC25A36	24	.	0			c.G175A						PASS	.						140.0	135.0	137.0					3																	140675502		2203	4300	6503	SO:0001583	missense	55186	exon2			AACCGAGTAGTGT	AK001480	CCDS3114.1, CCDS46927.1	3q23	2013-05-22	2012-03-29		ENSG00000114120	ENSG00000114120		"""Solute carriers"""	25554	protein-coding gene	gene with protein product			"""solute carrier family 25, member 36"""				Standard	NM_001104647		Approved	FLJ10618, PNC2	uc003etr.2	Q96CQ1	OTTHUMG00000160260	ENST00000324194.6:c.175G>A	chr3.hg19:g.140675502G>A	ENSP00000320688:p.Val59Ile	85.0	0.0	.		73.0	24.0	.	NM_018155	A8MYF7|Q05CY1|Q9H0G8|Q9NVN5	Missense_Mutation	SNP	ENST00000324194.6	hg19	CCDS46927.1	.	.	.	.	.	.	.	.	.	.	G	11.53	1.666084	0.29604	.	.	ENSG00000114120	ENST00000446041;ENST00000507429;ENST00000324194;ENST00000453248;ENST00000513887	T;T;T;T	0.78924	-1.22;-1.22;-1.22;-1.17	5.29	-0.772	0.10998	Mitochondrial carrier domain (2);	0.517046	0.21808	N	0.068811	T	0.62551	0.2437	L	0.31578	0.945	0.09310	N	0.999996	B;B;B;B	0.13594	0.0;0.001;0.008;0.0	B;B;B;B	0.13407	0.005;0.003;0.009;0.005	T	0.43130	-0.9410	10	0.23302	T	0.38	-6.1006	11.8956	0.52654	0.3779:0.0:0.6221:0.0	.	59;59;59;59	B4DL01;Q96CQ1-3;Q96CQ1;F6SDC8	.;.;S2536_HUMAN;.	I	59;59;59;59;9	ENSP00000401938:V59I;ENSP00000421470:V59I;ENSP00000320688:V59I;ENSP00000391521:V59I	ENSP00000320688:V59I	V	+	1	0	SLC25A36	142158192	0.994000	0.37717	0.770000	0.31555	0.903000	0.53119	1.349000	0.33998	-0.689000	0.05149	-0.813000	0.03139	GTA	.	.	.	none		0.433	SLC25A36-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359929.1	NM_018155	
MED12L	116931	hgsc.bcm.edu	37	3	151107816	151107816	+	Missense_Mutation	SNP	T	T	G			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr3:151107816T>G	ENST00000474524.1	+	36	5434	c.5396T>G	c.(5395-5397)aTc>aGc	p.I1799S	MED12L_ENST00000273432.4_Missense_Mutation_p.I1659S	NM_053002.4	NP_443728.3	Q86YW9	MD12L_HUMAN	mediator complex subunit 12-like	1799						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			NS(1)|breast(3)|central_nervous_system(3)|cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(27)|lung(50)|ovary(6)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	128			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			TACTCGCCTATCTCCTCCCAA	0.468																																					p.I1799S		Atlas-SNP	.											.	MED12L	271	.	0			c.T5396G						PASS	.						175.0	171.0	172.0					3																	151107816		2203	4300	6503	SO:0001583	missense	116931	exon36			CGCCTATCTCCTC	AB046855, AF388364	CCDS33876.1	3q25.1	2007-07-30	2007-07-30		ENSG00000144893	ENSG00000144893			16050	protein-coding gene	gene with protein product		611318	"""mediator of RNA polymerase II transcription, subunit 12 homolog (S. cerevisiae)-like"""			11524702	Standard	XM_006713487		Approved	KIAA1635, TNRC11L, TRALPUSH, TRALP	uc003eyp.3	Q86YW9	OTTHUMG00000159844	ENST00000474524.1:c.5396T>G	chr3.hg19:g.151107816T>G	ENSP00000417235:p.Ile1799Ser	101.0	0.0	.		88.0	37.0	.	NM_053002	Q96PC7|Q96PC8|Q9H9M5|Q9HCD7|Q9UI69	Missense_Mutation	SNP	ENST00000474524.1	hg19	CCDS33876.1	.	.	.	.	.	.	.	.	.	.	T	14.12	2.440148	0.43326	.	.	ENSG00000144893	ENST00000474524;ENST00000273432	T;T	0.60171	0.43;0.21	5.73	5.73	0.89815	.	0.222920	0.46442	D	0.000300	T	0.39682	0.1087	N	0.08118	0	0.32093	N	0.591569	B;B	0.23058	0.005;0.079	B;B	0.19666	0.002;0.026	T	0.52132	-0.8616	10	0.87932	D	0	-5.497	14.2508	0.66019	0.0:0.0:0.0:1.0	.	1659;1799	F8WAE6;Q86YW9	.;MD12L_HUMAN	S	1799;1659	ENSP00000417235:I1799S;ENSP00000273432:I1659S	ENSP00000273432:I1659S	I	+	2	0	MED12L	152590506	0.493000	0.26035	0.865000	0.33974	0.987000	0.75469	3.781000	0.55394	2.186000	0.69663	0.459000	0.35465	ATC	.	.	.	none		0.468	MED12L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357707.2	NM_053002	
MUC4	4585	hgsc.bcm.edu	37	3	195516343	195516343	+	Missense_Mutation	SNP	C	C	A			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr3:195516343C>A	ENST00000463781.3	-	2	2567	c.2108G>T	c.(2107-2109)gGt>gTt	p.G703V	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.G703V|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	708					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GGTTGTGTGACCATCCCCGGT	0.612																																					p.G703V		Atlas-SNP	.											.	MUC4	1505	.	0			c.G2108T						PASS	.						90.0	101.0	97.0					3																	195516343		2126	4247	6373	SO:0001583	missense	4585	exon2			GTGTGACCATCCC	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.2108G>T	chr3.hg19:g.195516343C>A	ENSP00000417498:p.Gly703Val	115.0	0.0	.		84.0	19.0	.	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	hg19	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	-	3.634	-0.074901	0.07184	.	.	ENSG00000145113	ENST00000463781;ENST00000475231;ENST00000392409	T;T	0.59364	0.27;0.3	3.16	0.13	0.14746	.	1.957170	0.02848	N	0.128792	T	0.33673	0.0871	N	0.22421	0.69	0.09310	N	1	P;B	0.43477	0.808;0.316	B;B	0.33568	0.166;0.067	T	0.20174	-1.0283	10	0.13108	T	0.6	0.0732	1.7414	0.02953	0.2123:0.457:0.2069:0.1238	.	703;708	E7ESK3;Q99102	.;MUC4_HUMAN	V	703;703;677	ENSP00000417498:G703V;ENSP00000420243:G703V	ENSP00000376209:G677V	G	-	2	0	MUC4	197000738	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.726000	0.04936	0.016000	0.14998	-0.166000	0.13349	GGT	.	.	.	none		0.612	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
TLR10	81793	hgsc.bcm.edu	37	4	38776735	38776735	+	Missense_Mutation	SNP	G	G	T			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr4:38776735G>T	ENST00000308973.4	-	4	1082	c.477C>A	c.(475-477)ttC>ttA	p.F159L	TLR10_ENST00000506111.1_Missense_Mutation_p.F159L|TLR10_ENST00000361424.2_Missense_Mutation_p.F159L|TLR10_ENST00000507953.1_5'Flank|TLR10_ENST00000508334.1_Missense_Mutation_p.F159L	NM_001017388.2|NM_001195107.1|NM_030956.3	NP_001017388.1|NP_001182036.1|NP_112218.2	Q9BXR5	TLR10_HUMAN	toll-like receptor 10	159					immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of inflammatory response (GO:0050729)|regulation of cytokine secretion (GO:0050707)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor signaling pathway (GO:0002224)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(11)|prostate(1)|urinary_tract(2)	25						CAATTTTCTGGAAATCTGATT	0.398																																					p.F159L		Atlas-SNP	.											.	TLR10	87	.	0			c.C477A						PASS	.						57.0	61.0	59.0					4																	38776735		2202	4299	6501	SO:0001583	missense	81793	exon2			TTTCTGGAAATCT	AF296673	CCDS3445.1	4p14	2009-11-23			ENSG00000174123	ENSG00000174123		"""CD molecules"""	15634	protein-coding gene	gene with protein product		606270				11267672	Standard	NM_030956		Approved	CD290	uc003gtk.3	Q9BXR5	OTTHUMG00000128578	ENST00000308973.4:c.477C>A	chr4.hg19:g.38776735G>T	ENSP00000308925:p.Phe159Leu	41.0	0.0	.		43.0	9.0	.	NM_001017388	A8K7L1|B3Y668|D1CS21|D1CS22|Q32MI7|Q32MI8|Q5FWG4|Q6UXL3	Missense_Mutation	SNP	ENST00000308973.4	hg19	CCDS3445.1	.	.	.	.	.	.	.	.	.	.	G	1.875	-0.459352	0.04508	.	.	ENSG00000174123	ENST00000308973;ENST00000506111;ENST00000361424;ENST00000508334	T;T;T;T	0.18338	2.22;2.22;2.22;2.22	5.23	2.42	0.29668	.	0.111310	0.38272	N	0.001753	T	0.07503	0.0189	N	0.17082	0.46	0.41978	D	0.990781	B	0.09022	0.002	B	0.10450	0.005	T	0.20107	-1.0285	10	0.10636	T	0.68	.	4.4622	0.11671	0.1433:0.1228:0.6077:0.1263	.	159	Q9BXR5	TLR10_HUMAN	L	159	ENSP00000308925:F159L;ENSP00000421483:F159L;ENSP00000354459:F159L;ENSP00000424923:F159L	ENSP00000308925:F159L	F	-	3	2	TLR10	38453130	0.010000	0.17322	1.000000	0.80357	0.982000	0.71751	-0.202000	0.09451	1.211000	0.43351	0.655000	0.94253	TTC	.	.	.	none		0.398	TLR10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250430.1		
SYNPO2	171024	hgsc.bcm.edu	37	4	119952865	119952865	+	Missense_Mutation	SNP	T	T	A			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr4:119952865T>A	ENST00000429713.2	+	4	3117	c.2935T>A	c.(2935-2937)Ttc>Atc	p.F979I	SYNPO2_ENST00000448416.2_Intron|SYNPO2_ENST00000434046.2_Missense_Mutation_p.F979I|SYNPO2_ENST00000307142.4_Missense_Mutation_p.F979I	NM_001128933.1	NP_001122405.1	Q9UMS6	SYNP2_HUMAN	synaptopodin 2	979						actin cytoskeleton (GO:0015629)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|Z disc (GO:0030018)	14-3-3 protein binding (GO:0071889)|muscle alpha-actinin binding (GO:0051371)			breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(20)|lung(18)|ovary(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	64						CTTGTTTACTTTCCAACCTCC	0.498																																					p.F979I		Atlas-SNP	.											.	SYNPO2	353	.	0			c.T2935A						PASS	.						96.0	78.0	84.0					4																	119952865		2203	4300	6503	SO:0001583	missense	171024	exon4			TTTACTTTCCAAC	AJ010482	CCDS34054.1, CCDS47128.1, CCDS47129.1, CCDS75185.1, CCDS75186.1	4q26	2008-08-29			ENSG00000172403	ENSG00000172403			17732	protein-coding gene	gene with protein product						11673475, 17828378	Standard	NM_133477		Approved	MYOPODIN	uc010inb.3	Q9UMS6	OTTHUMG00000161165	ENST00000429713.2:c.2935T>A	chr4.hg19:g.119952865T>A	ENSP00000395143:p.Phe979Ile	129.0	0.0	.		140.0	28.0	.	NM_001128934	B2RWP6|B2Y8J9|Q9UK89|S5XAM4	Missense_Mutation	SNP	ENST00000429713.2	hg19	CCDS47129.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	23.5|23.5	4.425277|4.425277	0.83667|0.83667	.|.	.|.	ENSG00000172403|ENSG00000172403	ENST00000307142;ENST00000429713;ENST00000434046|ENST00000504178	T;T;T|.	0.16324|.	2.35;2.39;2.37|.	5.3|5.3	5.3|5.3	0.74995|0.74995	.|.	0.000000|0.000000	0.64402|0.64402	D|D	0.000004|0.000004	T|T	0.75398|0.75398	0.3844|0.3844	M|M	0.77103|0.77103	2.36|2.36	0.80722|0.80722	D|D	1|1	D;D;D;D|.	0.89917|.	0.999;1.0;0.999;0.991|.	D;D;D;D|.	0.80764|.	0.994;0.992;0.991;0.955|.	T|T	0.76713|0.76713	-0.2858|-0.2858	9|6	.|.	.|.	.|.	-21.6986|-21.6986	15.246|15.246	0.73507|0.73507	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	979;979;979;979|.	B9EG60;Q9UMS6-2;E9PEM2;Q9UMS6|.	.;.;.;SYNP2_HUMAN|.	I|Y	979|930	ENSP00000306015:F979I;ENSP00000395143:F979I;ENSP00000390965:F979I|.	.|.	F|F	+|+	1|2	0|0	SYNPO2|SYNPO2	120172313|120172313	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.992000|0.992000	0.81027|0.81027	7.841000|7.841000	0.86834|0.86834	2.013000|2.013000	0.59113|0.59113	0.533000|0.533000	0.62120|0.62120	TTC|TTT	.	.	.	none		0.498	SYNPO2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364020.1		
TENM3	55714	hgsc.bcm.edu	37	4	183245385	183245385	+	Missense_Mutation	SNP	C	C	A			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr4:183245385C>A	ENST00000511685.1	+	2	335	c.212C>A	c.(211-213)gCa>gAa	p.A71E	TENM3_ENST00000406950.2_Missense_Mutation_p.A71E			Q9P273	TEN3_HUMAN	teneurin transmembrane protein 3	71	Teneurin N-terminal. {ECO:0000255|PROSITE-ProRule:PRU00694}.				camera-type eye morphogenesis (GO:0048593)|homophilic cell adhesion (GO:0007156)|positive regulation of neuron projection development (GO:0010976)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)										CACAGAGAAGCAGACGAGTTC	0.458																																					p.A71E		Atlas-SNP	.											.	.	.	.	0			c.C212A						PASS	.						98.0	97.0	98.0					4																	183245385		1955	4146	6101	SO:0001583	missense	55714	exon1			GAGAAGCAGACGA	AF195420	CCDS47165.1	4q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000218336	ENSG00000218336			29944	protein-coding gene	gene with protein product		610083	"""odz, odd Oz/ten-m homolog 3 (Drosophila)"""	ODZ3		10331952, 10625539	Standard	NM_001080477		Approved	Ten-M3, KIAA1455	uc003ivd.1	Q9P273	OTTHUMG00000160682	ENST00000511685.1:c.212C>A	chr4.hg19:g.183245385C>A	ENSP00000424226:p.Ala71Glu	58.0	0.0	.		66.0	9.0	.	NM_001080477	Q5XUL9|Q96SY2|Q9NV77|Q9NVW1|Q9NZJ2	Missense_Mutation	SNP	ENST00000511685.1	hg19	CCDS47165.1	.	.	.	.	.	.	.	.	.	.	C	16.66	3.184679	0.57909	.	.	ENSG00000218336	ENST00000512480;ENST00000511685;ENST00000406950	T;T;T	0.31769	1.48;1.48;1.48	5.65	5.65	0.86999	Teneurin intracellular, N-terminal (2);	.	.	.	.	T	0.52256	0.1723	L	0.60455	1.87	0.30938	N	0.726181	D;P	0.62365	0.991;0.77	P;B	0.61132	0.884;0.255	T	0.51934	-0.8642	9	0.72032	D	0.01	.	19.9142	0.97043	0.0:1.0:0.0:0.0	.	71;71	D6RGC5;Q9P273	.;TEN3_HUMAN	E	71	ENSP00000421320:A71E;ENSP00000424226:A71E;ENSP00000385276:A71E	ENSP00000385276:A71E	A	+	2	0	ODZ3	183482379	0.995000	0.38212	0.986000	0.45419	0.986000	0.74619	3.658000	0.54482	2.941000	0.99782	0.655000	0.94253	GCA	.	.	.	none		0.458	TENM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361734.1		
FAT1	2195	hgsc.bcm.edu	37	4	187517964	187517964	+	Missense_Mutation	SNP	C	C	G			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr4:187517964C>G	ENST00000441802.2	-	25	12939	c.12730G>C	c.(12730-12732)Gac>Cac	p.D4244H	FAT1_ENST00000512347.1_5'Flank	NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	4244					actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						GGTGGTATGTCTGAGTAAATG	0.478										HNSCC(5;0.00058)																											p.D4244H	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.G12730C						PASS	.						70.0	69.0	69.0					4																	187517964		1861	4100	5961	SO:0001583	missense	2195	exon25			GTATGTCTGAGTA	X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"""Cadherins / Cadherin-related"""	3595	protein-coding gene	gene with protein product	"""cadherin-related family member 8"""	600976	"""FAT tumor suppressor (Drosophila) homolog"", ""FAT tumor suppressor homolog 1 (Drosophila)"""	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.12730G>C	chr4.hg19:g.187517964C>G	ENSP00000406229:p.Asp4244His	90.0	0.0	.		97.0	26.0	.	NM_005245		Missense_Mutation	SNP	ENST00000441802.2	hg19	CCDS47177.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	23.7|23.7	4.443680|4.443680	0.83993|0.83993	.|.	.|.	ENSG00000083857|ENSG00000083857	ENST00000441802;ENST00000260147|ENST00000512772	T|.	0.70869|.	-0.52|.	5.39|5.39	5.39|5.39	0.77823|0.77823	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.72961|0.72961	0.3526|0.3526	L|L	0.60455|0.60455	1.87|1.87	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.91635|.	0.999|.	T|T	0.69304|0.69304	-0.5180|-0.5180	10|5	0.66056|.	D|.	0.02|.	.|.	19.3359|19.3359	0.94319|0.94319	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	4244|.	Q14517|.	FAT1_HUMAN|.	H|T	4244;4246|11	ENSP00000406229:D4244H|.	ENSP00000260147:D4246H|.	D|R	-|-	1|2	0|0	FAT1|FAT1	187754958|187754958	1.000000|1.000000	0.71417|0.71417	0.831000|0.831000	0.32960|0.32960	0.737000|0.737000	0.42083|0.42083	7.651000|7.651000	0.83577|0.83577	2.809000|2.809000	0.96659|0.96659	0.555000|0.555000	0.69702|0.69702	GAC|AGA	.	.	.	none		0.478	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245	
TRIP13	9319	hgsc.bcm.edu	37	5	908120	908120	+	Silent	SNP	C	C	T			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr5:908120C>T	ENST00000166345.3	+	8	1046	c.690C>T	c.(688-690)acC>acT	p.T230T		NM_004237.3	NP_004228.1	Q15645	PCH2_HUMAN	thyroid hormone receptor interactor 13	230					double-strand break repair (GO:0006302)|female meiosis I (GO:0007144)|male meiosis I (GO:0007141)|oocyte maturation (GO:0001556)|oogenesis (GO:0048477)|reciprocal meiotic recombination (GO:0007131)|regulation of RNA biosynthetic process (GO:2001141)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)|transcription from RNA polymerase II promoter (GO:0006366)	male germ cell nucleus (GO:0001673)|nucleus (GO:0005634)	ATP binding (GO:0005524)|transcription cofactor activity (GO:0003712)			breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(1)|skin(1)	18			Epithelial(17;0.00147)|OV - Ovarian serous cystadenocarcinoma(19;0.00271)|all cancers(22;0.00622)|Lung(60;0.165)			AGCTGGTAACCAAGATGTTTC	0.498																																					p.T230T		Atlas-SNP	.											.	TRIP13	41	.	0			c.C690T						PASS	.						169.0	149.0	155.0					5																	908120		2203	4300	6503	SO:0001819	synonymous_variant	9319	exon8			GGTAACCAAGATG	L40384	CCDS3858.1	5p15	2010-04-21			ENSG00000071539	ENSG00000071539		"""ATPases / AAA-type"""	12307	protein-coding gene	gene with protein product	"""thyroid receptor interacting protein 13"""	604507				7776974	Standard	NM_004237		Approved	16E1BP	uc003jbr.3	Q15645	OTTHUMG00000090349	ENST00000166345.3:c.690C>T	chr5.hg19:g.908120C>T		96.0	0.0	.		123.0	38.0	.	NM_004237	C9K0T3|D3DTC0|O15324	Silent	SNP	ENST00000166345.3	hg19	CCDS3858.1	.	.	.	.	.	.	.	.	.	.	.	8.882	0.951814	0.18431	.	.	ENSG00000071539	ENST00000513435	.	.	.	5.62	-11.2	0.00127	.	.	.	.	.	T	0.41259	0.1151	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.49214	-0.8963	4	.	.	.	-32.367	5.2498	0.15515	0.143:0.5019:0.2154:0.1397	.	.	.	.	L	226	.	.	P	+	2	0	TRIP13	961120	0.006000	0.16342	0.087000	0.20705	0.969000	0.65631	-1.282000	0.02799	-2.592000	0.00456	-0.345000	0.07892	CCA	.	.	.	none		0.498	TRIP13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206721.2	NM_004237	
CDH12	1010	hgsc.bcm.edu	37	5	21752166	21752166	+	Missense_Mutation	SNP	T	T	C			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr5:21752166T>C	ENST00000382254.1	-	15	3151	c.2065A>G	c.(2065-2067)Att>Gtt	p.I689V	RP11-804N13.1_ENST00000522350.1_RNA|CDH12_ENST00000504376.2_Missense_Mutation_p.I689V|CDH12_ENST00000522262.1_Missense_Mutation_p.I649V|CDH12_ENST00000521384.1_5'UTR	NM_004061.3	NP_004052.2	P55289	CAD12_HUMAN	cadherin 12, type 2 (N-cadherin 2)	689					adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(2)|breast(2)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(19)|lung(75)|ovary(2)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	120						TCCCTGCGAATTTTGTTCTCC	0.458										HNSCC(59;0.17)																											p.I689V		Atlas-SNP	.											.	CDH12	238	.	0			c.A2065G						PASS	.						188.0	161.0	171.0					5																	21752166		2203	4300	6503	SO:0001583	missense	1010	exon15			TGCGAATTTTGTT	L33477	CCDS3890.1	5p14.3	2010-01-26			ENSG00000154162	ENSG00000154162		"""Cadherins / Major cadherins"""	1751	protein-coding gene	gene with protein product		600562				7731968	Standard	NM_004061		Approved	Br-cadherin, CDHB	uc003jgk.2	P55289	OTTHUMG00000090591	ENST00000382254.1:c.2065A>G	chr5.hg19:g.21752166T>C	ENSP00000371689:p.Ile689Val	203.0	0.0	.		221.0	60.0	.	NM_004061	B2RBT1|B7Z2U6|Q86UD2	Missense_Mutation	SNP	ENST00000382254.1	hg19	CCDS3890.1	.	.	.	.	.	.	.	.	.	.	T	5.372	0.253855	0.10185	.	.	ENSG00000154162	ENST00000504376;ENST00000382254;ENST00000522262	T;T;T	0.76186	-1.0;-1.0;-1.0	5.12	3.92	0.45320	Cadherin, cytoplasmic domain (1);	0.479938	0.25538	N	0.029988	T	0.51958	0.1705	N	0.14661	0.345	0.31334	N	0.684456	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.0	T	0.46938	-0.9155	10	0.17369	T	0.5	.	6.6994	0.23217	0.0:0.0776:0.1551:0.7673	.	649;689	B7Z2U6;P55289	.;CAD12_HUMAN	V	689;689;649	ENSP00000423577:I689V;ENSP00000371689:I689V;ENSP00000428786:I649V	ENSP00000371689:I689V	I	-	1	0	CDH12	21787923	1.000000	0.71417	1.000000	0.80357	0.886000	0.51366	1.798000	0.38814	0.765000	0.33221	0.383000	0.25322	ATT	.	.	.	none		0.458	CDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207139.1	NM_004061	
DST	667	hgsc.bcm.edu	37	6	56504731	56504731	+	Missense_Mutation	SNP	C	C	T			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr6:56504731C>T	ENST00000361203.3	-	15	1989	c.1982G>A	c.(1981-1983)aGt>aAt	p.S661N	DST_ENST00000370769.4_Missense_Mutation_p.S661N|DST_ENST00000312431.6_Missense_Mutation_p.S661N|DST_ENST00000421834.2_Missense_Mutation_p.S661N|DST_ENST00000446842.2_Missense_Mutation_p.S335N|DST_ENST00000518935.1_Missense_Mutation_p.S335N|DST_ENST00000244364.6_Missense_Mutation_p.S335N|DST_ENST00000370788.2_Missense_Mutation_p.S661N|DST_ENST00000370754.5_Missense_Mutation_p.S839N|DST_ENST00000370765.6_Missense_Mutation_p.S335N			Q03001	DYST_HUMAN	dystonin	661					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)			ACATACCTCACTGATTTTAGC	0.284																																					p.S335N		Atlas-SNP	.											.	DST	1427	.	0			c.G1004A						PASS	.						47.0	51.0	50.0					6																	56504731		2203	4299	6502	SO:0001583	missense	667	exon5			ACCTCACTGATTT	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.1982G>A	chr6.hg19:g.56504731C>T	ENSP00000354508:p.Ser661Asn	98.0	0.0	.		81.0	30.0	.	NM_001723	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Missense_Mutation	SNP	ENST00000361203.3	hg19		.	.	.	.	.	.	.	.	.	.	C	17.97	3.519255	0.64634	.	.	ENSG00000151914	ENST00000244364;ENST00000370754;ENST00000370769;ENST00000421834;ENST00000446842;ENST00000312431;ENST00000370788;ENST00000361203;ENST00000439203;ENST00000520645;ENST00000370765;ENST00000518935	T;T;T;T;T;D;T;T;T;D;T;T	0.83992	1.18;0.02;0.02;0.17;0.96;-1.53;0.13;-0.0;-0.3;-1.79;-0.69;-0.14	5.45	4.58	0.56647	.	0.000000	0.64402	D	0.000017	T	0.80486	0.4632	L	0.44542	1.39	0.29528	N	0.852973	P;B;P;B;D;B;B;P;B;B	0.55385	0.899;0.235;0.944;0.354;0.971;0.016;0.115;0.917;0.235;0.277	B;B;D;B;P;B;B;P;B;B	0.63597	0.401;0.149;0.916;0.149;0.73;0.02;0.134;0.897;0.149;0.329	T	0.78265	-0.2271	9	0.17832	T	0.49	.	14.2099	0.65756	0.0:0.9287:0.0:0.0713	.	690;661;661;839;777;335;335;335;661;335	B4DGY0;Q5TBT1;E7ERU2;E9PEB9;Q03001-13;Q6P0N6;Q03001-3;Q03001-9;Q03001;Q03001-8	.;.;.;.;.;.;.;.;DYST_HUMAN;.	N	335;839;661;661;335;661;661;661;335;701;335;335	ENSP00000244364:S335N;ENSP00000359790:S839N;ENSP00000359805:S661N;ENSP00000400883:S661N;ENSP00000393645:S335N;ENSP00000307959:S661N;ENSP00000359824:S661N;ENSP00000354508:S661N;ENSP00000404924:S335N;ENSP00000431030:S701N;ENSP00000359801:S335N;ENSP00000431003:S335N	ENSP00000244364:S335N	S	-	2	0	DST	56612690	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	3.897000	0.56273	1.525000	0.49052	0.655000	0.94253	AGT	.	.	.	none		0.284	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723	
RIMS1	22999	hgsc.bcm.edu	37	6	72960096	72960096	+	Missense_Mutation	SNP	C	C	G			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr6:72960096C>G	ENST00000521978.1	+	13	2305	c.2305C>G	c.(2305-2307)Cta>Gta	p.L769V	RIMS1_ENST00000520567.1_Missense_Mutation_p.L769V|RIMS1_ENST00000522291.1_Missense_Mutation_p.L769V|RIMS1_ENST00000517827.1_Missense_Mutation_p.L228V|RIMS1_ENST00000264839.7_Missense_Mutation_p.L769V|RIMS1_ENST00000538414.1_5'Flank|RIMS1_ENST00000425662.2_Missense_Mutation_p.L162V|RIMS1_ENST00000348717.5_Missense_Mutation_p.L769V|RIMS1_ENST00000517960.1_Missense_Mutation_p.L769V|RIMS1_ENST00000401910.3_Missense_Mutation_p.L243V|RIMS1_ENST00000523963.1_Missense_Mutation_p.L243V|RIMS1_ENST00000518273.1_Missense_Mutation_p.L769V|RIMS1_ENST00000491071.2_Missense_Mutation_p.L769V	NM_014989.5	NP_055804.2	Q86UR5	RIMS1_HUMAN	regulating synaptic membrane exocytosis 1	769	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|glutamate secretion (GO:0014047)|intracellular protein transport (GO:0006886)|membrane fusion (GO:0061025)|neurotransmitter secretion (GO:0007269)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of gene expression (GO:0010628)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|protein complex assembly (GO:0006461)|regulated secretory pathway (GO:0045055)|regulation of catalytic activity (GO:0050790)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of neurotransmitter secretion (GO:0046928)|response to stimulus (GO:0050896)|secretion (GO:0046903)|synaptic transmission (GO:0007268)|synaptic vesicle exocytosis (GO:0016079)|visual perception (GO:0007601)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|Rab GTPase binding (GO:0017137)|small GTPase regulator activity (GO:0005083)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(25)|liver(4)|lung(35)|ovary(9)|pancreas(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	102		all_epithelial(107;0.179)|all_hematologic(105;0.212)				AGCAACAGATCTACCTGCTAG	0.348																																					p.L769V		Atlas-SNP	.											.	RIMS1	278	.	0			c.C2305G						PASS	.						89.0	83.0	84.0					6																	72960096		1846	4102	5948	SO:0001583	missense	22999	exon13			ACAGATCTACCTG	AB002338	CCDS47449.1, CCDS55029.1, CCDS55030.1, CCDS55031.1, CCDS55032.1, CCDS55033.1	6q12-q13	2008-10-16	2002-06-12	2002-06-14	ENSG00000079841	ENSG00000079841			17282	protein-coding gene	gene with protein product	"""Rab3-interacting molecule"""	606629	"""RAB3 interacting protein 2"""	RAB3IP2, CORD7		9205841, 11438518	Standard	NM_001168407		Approved	RIM, KIAA0340, RIM1	uc003pga.4	Q86UR5	OTTHUMG00000015009	ENST00000521978.1:c.2305C>G	chr6.hg19:g.72960096C>G	ENSP00000428417:p.Leu769Val	71.0	0.0	.		90.0	14.0	.	NM_014989	A7MBN6|B7Z2M0|B7Z2Q9|B7Z3S3|B7Z6S2|E7EX08|E9PCB7|E9PCZ1|E9PF48|E9PHF5|E9PHR1|O15048|Q5JY21|Q5JY25|Q5SZK1|Q8TDY9|Q8TDZ5|Q9HBA1|Q9HBA2|Q9HBA3|Q9HBA4|Q9HBA5|Q9HBA6	Missense_Mutation	SNP	ENST00000521978.1	hg19	CCDS47449.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.83|18.83	3.706633|3.706633	0.68615|0.68615	.|.	.|.	ENSG00000079841|ENSG00000079841	ENST00000491071;ENST00000350827;ENST00000352008;ENST00000348717;ENST00000349908;ENST00000346609;ENST00000264839;ENST00000517960;ENST00000518273;ENST00000520567;ENST00000522291;ENST00000521978;ENST00000401910;ENST00000523963;ENST00000425662;ENST00000453976;ENST00000517827|ENST00000517433	D;D;D;D;D;D;D;D;D;D;D;D;D|.	0.82344|.	-1.6;-1.6;-1.6;-1.6;-1.6;-1.6;-1.6;-1.6;-1.6;-1.6;-1.6;-1.6;-1.6|.	5.28|5.28	4.38|4.38	0.52667|0.52667	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);|.	0.000000|.	0.52532|.	D|.	0.000072|.	T|T	0.69663|0.69663	0.3136|0.3136	M|M	0.87971|0.87971	2.92|2.92	0.80722|0.80722	D|D	1|1	D;D;D;D;D;D;D|.	0.76494|.	0.999;0.962;0.99;0.99;0.998;0.994;0.99|.	D;D;D;D;D;D;D|.	0.97110|.	1.0;0.983;0.996;0.996;0.999;0.996;0.996|.	T|T	0.74475|0.74475	-0.3653|-0.3653	10|5	0.87932|.	D|.	0|.	-12.8523|-12.8523	10.4795|10.4795	0.44684|0.44684	0.0:0.8222:0.0:0.1778|0.0:0.8222:0.0:0.1778	.|.	228;243;769;228;243;769;769|.	B7Z3S3;E9PHF5;E9PHR1;B7Z9Z3;E9PF48;C9JNW6;Q86UR5|.	.;.;.;.;.;.;RIMS1_HUMAN|.	V|C	769;769;769;769;769;769;769;769;769;769;769;769;243;243;162;162;228|342	ENSP00000430101:L769V;ENSP00000275037:L769V;ENSP00000264839:L769V;ENSP00000429959:L769V;ENSP00000430408:L769V;ENSP00000430502:L769V;ENSP00000430932:L769V;ENSP00000428417:L769V;ENSP00000385649:L243V;ENSP00000428328:L243V;ENSP00000411235:L162V;ENSP00000389503:L162V;ENSP00000428367:L228V|.	ENSP00000264839:L769V|.	L|S	+|+	1|2	2|0	RIMS1|RIMS1	73016817|73016817	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.838000|0.838000	0.47535|0.47535	4.060000|4.060000	0.57477|0.57477	1.279000|1.279000	0.44446|0.44446	0.585000|0.585000	0.79938|0.79938	CTA|TCT	.	.	.	none		0.348	RIMS1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374968.1		
VGLL2	245806	hgsc.bcm.edu	37	6	117591730	117591730	+	Missense_Mutation	SNP	G	G	T			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr6:117591730G>T	ENST00000326274.5	+	3	606	c.416G>T	c.(415-417)cGc>cTc	p.R139L	VGLL2_ENST00000352536.3_Intron	NM_182645.3	NP_872586.1	Q8N8G2	VGLL2_HUMAN	vestigial-like family member 2	139					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal muscle tissue development (GO:0007519)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)			central_nervous_system(1)|kidney(1)|lung(3)	5				GBM - Glioblastoma multiforme(226;0.0254)|all cancers(137;0.0676)|OV - Ovarian serous cystadenocarcinoma(136;0.0757)		ATGAGCCAGCGCAGCTTCCCC	0.697																																					p.R139L		Atlas-SNP	.											.	VGLL2	18	.	0			c.G416T						PASS	.						13.0	15.0	14.0					6																	117591730		2195	4285	6480	SO:0001583	missense	245806	exon3			GCCAGCGCAGCTT	AY056583	CCDS5114.1, CCDS5115.1	6q22.31	2014-03-03	2014-03-03		ENSG00000170162	ENSG00000170162			20232	protein-coding gene	gene with protein product		609979	"""vestigial like 2 (Drosophila)"""			12376544	Standard	NM_153453		Approved		uc003pxn.3	Q8N8G2	OTTHUMG00000015451	ENST00000326274.5:c.416G>T	chr6.hg19:g.117591730G>T	ENSP00000320957:p.Arg139Leu	72.0	0.0	.		53.0	4.0	.	NM_182645	Q8WWX1	Missense_Mutation	SNP	ENST00000326274.5	hg19	CCDS5115.1	.	.	.	.	.	.	.	.	.	.	G	34	5.331271	0.95733	.	.	ENSG00000170162	ENST00000326274	T	0.54866	0.55	4.86	4.86	0.63082	.	0.056880	0.64402	D	0.000003	T	0.68393	0.2996	M	0.73962	2.25	0.80722	D	1	D	0.76494	0.999	D	0.81914	0.995	T	0.72360	-0.4317	10	0.72032	D	0.01	-24.0493	18.1693	0.89740	0.0:0.0:1.0:0.0	.	139	Q8N8G2	VGLL2_HUMAN	L	139	ENSP00000320957:R139L	ENSP00000320957:R139L	R	+	2	0	VGLL2	117698423	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.078000	0.94023	2.528000	0.85240	0.549000	0.68633	CGC	.	.	.	none		0.697	VGLL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041975.2	NM_153453	
TBC1D32	221322	hgsc.bcm.edu	37	6	121433801	121433801	+	Nonsense_Mutation	SNP	G	G	T			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr6:121433801G>T	ENST00000398212.2	-	29	3223	c.3174C>A	c.(3172-3174)tgC>tgA	p.C1058*	TBC1D32_ENST00000398197.2_5'UTR|TBC1D32_ENST00000275159.6_Nonsense_Mutation_p.C1099*	NM_152730.4	NP_689943.4	Q96NH3	BROMI_HUMAN	TBC1 domain family, member 32	1058					cilium morphogenesis (GO:0060271)|embryonic digit morphogenesis (GO:0042733)|lens development in camera-type eye (GO:0002088)|protein localization to cilium (GO:0061512)|retinal pigment epithelium development (GO:0003406)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	cilium (GO:0005929)|cytoplasm (GO:0005737)	Rab GTPase activator activity (GO:0005097)										TCCCTTGCAGGCAGACTGAAA	0.274																																					p.C1058X		Atlas-SNP	.											.	C6orf170	146	.	0			c.C3174A						PASS	.						54.0	49.0	50.0					6																	121433801		1803	4070	5873	SO:0001587	stop_gained	221322	exon29			TTGCAGGCAGACT	AK055461	CCDS43501.1	6q22.31	2014-02-20	2013-07-10	2013-07-10	ENSG00000146350	ENSG00000146350			21485	protein-coding gene	gene with protein product	"""broad-minded homolog"""	615867	"""chromosome 6 open reading frame 171"", ""chromosome 6 open reading frame 170"""	C6orf171, C6orf170		20159594, 24285566	Standard	NM_152730		Approved	FLJ30899, dJ310J6.1, FLJ34235, bA57L9.1, BROMI	uc003pyo.1	Q96NH3	OTTHUMG00000015474	ENST00000398212.2:c.3174C>A	chr6.hg19:g.121433801G>T	ENSP00000381270:p.Cys1058*	54.0	0.0	.		67.0	4.0	.	NM_152730	Q5SZD6|Q5SZM6|Q6ZMY4|Q6ZUR7|Q8NB47	Nonsense_Mutation	SNP	ENST00000398212.2	hg19	CCDS43501.1	.	.	.	.	.	.	.	.	.	.	G	33	5.220888	0.95139	.	.	ENSG00000146350	ENST00000275159;ENST00000398212	.	.	.	5.41	3.63	0.41609	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.3109	0.32071	0.3125:0.0:0.6875:0.0	.	.	.	.	X	1099;1058	.	ENSP00000275159:C1099X	C	-	3	2	C6orf170	121475500	1.000000	0.71417	0.998000	0.56505	0.007000	0.05969	2.668000	0.46816	0.674000	0.31244	0.585000	0.79938	TGC	.	.	.	none		0.274	TBC1D32-005	PUTATIVE	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380937.2	NM_152730	
EGFR	1956	hgsc.bcm.edu	37	7	55272975	55272975	+	Missense_Mutation	SNP	A	A	G			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr7:55272975A>G	ENST00000275493.2	+	28	3475	c.3298A>G	c.(3298-3300)Agg>Ggg	p.R1100G	EGFR_ENST00000442591.1_Intron|EGFR_ENST00000454757.2_Missense_Mutation_p.R1047G	NM_005228.3	NP_005219.2	P00533	EGFR_HUMAN	epidermal growth factor receptor	1100					activation of phospholipase A2 activity by calcium-mediated signaling (GO:0043006)|activation of phospholipase C activity (GO:0007202)|alkanesulfonate metabolic process (GO:0019694)|astrocyte activation (GO:0048143)|axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cellular response to amino acid stimulus (GO:0071230)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to drug (GO:0035690)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to estradiol stimulus (GO:0071392)|cellular response to mechanical stimulus (GO:0071260)|cerebral cortex cell migration (GO:0021795)|circadian rhythm (GO:0007623)|digestive tract morphogenesis (GO:0048546)|diterpenoid metabolic process (GO:0016101)|embryonic placenta development (GO:0001892)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hair follicle development (GO:0001942)|hydrogen peroxide metabolic process (GO:0042743)|innate immune response (GO:0045087)|learning or memory (GO:0007611)|liver development (GO:0001889)|lung development (GO:0030324)|magnesium ion homeostasis (GO:0010960)|MAPK cascade (GO:0000165)|morphogenesis of an epithelial fold (GO:0060571)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein catabolic process (GO:0042177)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification (GO:0001503)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|polysaccharide metabolic process (GO:0005976)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of DNA repair (GO:0045739)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of inflammatory response (GO:0050729)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vasoconstriction (GO:0045907)|positive regulation of vasodilation (GO:0045909)|protein autophosphorylation (GO:0046777)|protein insertion into membrane (GO:0051205)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to calcium ion (GO:0051592)|response to cobalamin (GO:0033590)|response to hydroxyisoflavone (GO:0033594)|response to osmotic stress (GO:0006970)|response to oxidative stress (GO:0006979)|response to stress (GO:0006950)|response to UV-A (GO:0070141)|salivary gland morphogenesis (GO:0007435)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|tongue development (GO:0043586)|translation (GO:0006412)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|Shc-EGFR complex (GO:0070435)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|epidermal growth factor-activated receptor activity (GO:0005006)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)|ubiquitin protein ligase binding (GO:0031625)			NS(2)|adrenal_gland(5)|biliary_tract(8)|bone(3)|breast(18)|central_nervous_system(106)|endometrium(26)|eye(3)|haematopoietic_and_lymphoid_tissue(9)|kidney(11)|large_intestine(85)|liver(2)|lung(13575)|oesophagus(21)|ovary(38)|pancreas(3)|peritoneum(11)|pleura(2)|prostate(35)|salivary_gland(11)|skin(9)|small_intestine(1)|soft_tissue(4)|stomach(41)|thymus(2)|thyroid(14)|upper_aerodigestive_tract(59)|urinary_tract(6)	14110	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Afatinib(DB08916)|Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)|Vandetanib(DB05294)	CGTTCCCAAAAGGCCCGCTGG	0.532		8	"""A, O, Mis"""		"""glioma, NSCLC"""	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)																											p.R1100G		Atlas-SNP	.	yes	Dom	yes	Familial lung cancer	7	7p12.3-p12.1	1956	"""epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian)"""		"""E, O"""	.	EGFR	20426	.	0			c.A3298G						PASS	.						64.0	62.0	62.0					7																	55272975		2203	4300	6503	SO:0001583	missense	1956	exon28	Familial Cancer Database	incl. Hereditary Lung cancer, Hereditary Non-Small Cell Lung cancer	CCCAAAAGGCCCG		CCDS5514.1, CCDS5515.1, CCDS5516.1, CCDS47587.1	7p12	2014-09-17	2010-06-25		ENSG00000146648	ENSG00000146648			3236	protein-coding gene	gene with protein product	"""erythroblastic leukemia viral (v-erb-b) oncogene homolog (avian)"""	131550	"""epidermal growth factor receptor (avian erythroblastic leukemia viral (v-erb-b) oncogene homolog)"""	ERBB		1505215	Standard	NM_201282		Approved	ERBB1	uc003tqk.3	P00533	OTTHUMG00000023661	ENST00000275493.2:c.3298A>G	chr7.hg19:g.55272975A>G	ENSP00000275493:p.Arg1100Gly	112.0	0.0	.		103.0	5.0	.	NM_005228	O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	Missense_Mutation	SNP	ENST00000275493.2	hg19	CCDS5514.1	.	.	.	.	.	.	.	.	.	.	A	14.14	2.447696	0.43429	.	.	ENSG00000146648	ENST00000395504;ENST00000275493;ENST00000454757	T;T	0.77489	-1.1;-1.09	5.2	4.01	0.46588	.	0.344819	0.30519	N	0.009445	T	0.75324	0.3834	M	0.76328	2.33	0.23865	N	0.996623	B	0.20459	0.045	B	0.18263	0.021	T	0.66720	-0.5852	10	0.49607	T	0.09	.	10.3302	0.43818	0.6825:0.3175:0.0:0.0	.	1100	P00533	EGFR_HUMAN	G	970;1100;1047	ENSP00000275493:R1100G;ENSP00000395243:R1047G	ENSP00000275493:R1100G	R	+	1	2	EGFR	55240469	0.901000	0.30685	1.000000	0.80357	0.979000	0.70002	1.436000	0.34980	0.876000	0.35872	0.456000	0.33151	AGG	.	.	.	none		0.532	EGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251456.2	NM_005228	
MUC12	10071	hgsc.bcm.edu	37	7	100646199	100646199	+	Missense_Mutation	SNP	T	T	C	rs181671450	byFrequency	TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr7:100646199T>C	ENST00000379442.3	+	5	12784	c.12784T>C	c.(12784-12786)Ttt>Ctt	p.F4262L	MUC12_ENST00000536621.1_Missense_Mutation_p.F4119L			Q9UKN1	MUC12_HUMAN	mucin 12, cell surface associated	4262	28 X 19 AA approximate tandem repeats of E-E-S-X-X-X-H-X-X-P-X-X-T-X-T-X-X-X-P.|Ser-rich.				cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|regulation of cell growth (GO:0001558)	Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)				breast(6)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|prostate(1)|stomach(13)	25						AACAACACACTTTTCTGCCAG	0.552													T|||	1164	0.232428	0.2829	0.1571	5008	,	,		41858	0.2063		0.2624	False		,,,				2504	0.2137				p.F4119L		Atlas-SNP	.											MUC12,NS,carcinoma,0,1	MUC12	140	.	0			c.T12355C						PASS	.						8.0	10.0	9.0					7																	100646199		491	1071	1562	SO:0001583	missense	10071	exon2			ACACACTTTTCTG	AF147790, AF147791	CCDS55139.1	7q22	2007-01-17	2006-03-14		ENSG00000205277	ENSG00000205277		"""Mucins"""	7510	protein-coding gene	gene with protein product		604609	"""mucin 11"""	MUC11		10463611	Standard	NM_001164462		Approved		uc003uxo.3	Q9UKN1	OTTHUMG00000157042	ENST00000379442.3:c.12784T>C	chr7.hg19:g.100646199T>C	ENSP00000368755:p.Phe4262Leu	2.0	0.0	.		2.0	2.0	.	NM_001164462	A6ND38|F5GWV9|Q9UKN0	Missense_Mutation	SNP	ENST00000379442.3	hg19		.	.	.	.	.	.	.	.	.	.	T	4.831	0.154453	0.09236	.	.	ENSG00000205277	ENST00000379442;ENST00000536621	T;T	0.11712	2.75;2.75	0.53	0.53	0.17102	.	.	.	.	.	T	0.04679	0.0127	N	0.08118	0	0.80722	P	0.0	.	.	.	.	.	.	T	0.41645	-0.9497	6	0.20519	T	0.43	.	5.2833	0.15688	0.0:1.0E-4:0.0:0.9999	.	.	.	.	L	4262;4119	ENSP00000368755:F4262L;ENSP00000441929:F4119L	ENSP00000368755:F4262L	F	+	1	0	MUC12	100432919	0.000000	0.05858	0.002000	0.10522	0.001000	0.01503	-0.028000	0.12350	0.435000	0.26365	0.164000	0.16699	TTT	.	C|1.000;|0.000	1.000	weak		0.552	MUC12-001	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000347234.1	XM_379904	
TMEM67	91147	hgsc.bcm.edu	37	8	94805453	94805453	+	Missense_Mutation	SNP	G	G	C			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr8:94805453G>C	ENST00000453321.3	+	16	1661	c.1603G>C	c.(1603-1605)Gct>Cct	p.A535P	TMEM67_ENST00000409623.3_Missense_Mutation_p.A454P	NM_153704.5	NP_714915.3	Q5HYA8	MKS3_HUMAN	transmembrane protein 67	535					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|negative regulation of centrosome duplication (GO:0010826)	centrosome (GO:0005813)|ciliary membrane (GO:0060170)|cytoplasmic vesicle membrane (GO:0030659)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|TCTN-B9D complex (GO:0036038)	filamin binding (GO:0031005)|unfolded protein binding (GO:0051082)			breast(3)|endometrium(8)|kidney(5)|large_intestine(4)|liver(2)|lung(15)|ovary(2)|skin(1)|urinary_tract(1)	41	Breast(36;4.14e-07)		BRCA - Breast invasive adenocarcinoma(8;0.00896)			GGGTGGGCTAGCTGTTTTAGC	0.368																																					p.A535P		Atlas-SNP	.											.	TMEM67	187	.	0			c.G1603C						PASS	.						157.0	153.0	154.0					8																	94805453		2203	4300	6503	SO:0001583	missense	91147	exon16			GGGCTAGCTGTTT	BX648768	CCDS6258.2, CCDS47893.1	8q22.1	2014-09-17			ENSG00000164953	ENSG00000164953			28396	protein-coding gene	gene with protein product	"""Meckelin"""	609884	"""Meckel syndrome, type 3"""	MKS3		12384791, 16415887, 19508969	Standard	NM_153704		Approved	MGC26979, JBTS6, NPHP11	uc011lgk.2	Q5HYA8	OTTHUMG00000153119	ENST00000453321.3:c.1603G>C	chr8.hg19:g.94805453G>C	ENSP00000389998:p.Ala535Pro	101.0	0.0	.		116.0	31.0	.	NM_153704	B3KRU5|B3KT47|G5E9H2|Q3ZCX3|Q7Z5T8|Q8IZ06	Missense_Mutation	SNP	ENST00000453321.3	hg19	CCDS6258.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	26.1|26.1	4.706160|4.706160	0.89018|0.89018	.|.	.|.	ENSG00000164953|ENSG00000164953	ENST00000453321;ENST00000409623|ENST00000520680	D;D|.	0.97256|.	-4.31;-4.31|.	5.6|5.6	5.6|5.6	0.85130|0.85130	.|.	0.111849|.	0.64402|.	D|.	0.000016|.	T|T	0.78317|0.78317	0.4264|0.4264	M|M	0.77103|0.77103	2.36|2.36	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.83275|.	0.993;0.996;0.992|.	T|T	0.77584|0.77584	-0.2533|-0.2533	10|5	0.66056|.	D|.	0.02|.	-17.8669|-17.8669	19.6017|19.6017	0.95566|0.95566	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	535;454;454|.	Q5HYA8;B3KRU5;G5E9H2|.	MKS3_HUMAN;.;.|.	P|T	535;454|183	ENSP00000389998:A535P;ENSP00000386966:A454P|.	ENSP00000314488:A525P|.	A|S	+|+	1|2	0|0	TMEM67|TMEM67	94874629|94874629	1.000000|1.000000	0.71417|0.71417	0.993000|0.993000	0.49108|0.49108	0.997000|0.997000	0.91878|0.91878	6.318000|6.318000	0.72866|0.72866	2.622000|2.622000	0.88805|0.88805	0.655000|0.655000	0.94253|0.94253	GCT|AGC	.	.	.	none		0.368	TMEM67-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329641.2	NM_153704	
RECK	8434	hgsc.bcm.edu	37	9	36091304	36091304	+	Missense_Mutation	SNP	G	G	T			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr9:36091304G>T	ENST00000377966.3	+	10	1615	c.1049G>T	c.(1048-1050)tGt>tTt	p.C350F		NM_021111.2	NP_066934.1	O95980	RECK_HUMAN	reversion-inducing-cysteine-rich protein with kazal motifs	350					blood vessel maturation (GO:0001955)|embryo implantation (GO:0007566)|extracellular matrix organization (GO:0030198)|negative regulation of endopeptidase activity (GO:0010951)	anchored component of membrane (GO:0031225)|membrane (GO:0016020)|plasma membrane (GO:0005886)	endopeptidase inhibitor activity (GO:0004866)|metalloendopeptidase inhibitor activity (GO:0008191)|serine-type endopeptidase inhibitor activity (GO:0004867)			cervix(1)|endometrium(7)|kidney(3)|large_intestine(6)|lung(10)|ovary(1)|pancreas(1)|skin(2)|stomach(1)	32			LUSC - Lung squamous cell carcinoma(32;0.112)|STAD - Stomach adenocarcinoma(86;0.228)			CAGTTGGGCTGTAGAAACCTT	0.353																																					p.C350F		Atlas-SNP	.											.	RECK	73	.	0			c.G1049T						PASS	.						119.0	109.0	112.0					9																	36091304		2203	4300	6503	SO:0001583	missense	8434	exon10			TGGGCTGTAGAAA	E13833	CCDS6597.1	9p13.3	2008-05-15			ENSG00000122707	ENSG00000122707			11345	protein-coding gene	gene with protein product		605227		ST15		9789069	Standard	NM_021111		Approved	hRECK	uc003zyv.3	O95980	OTTHUMG00000019898	ENST00000377966.3:c.1049G>T	chr9.hg19:g.36091304G>T	ENSP00000367202:p.Cys350Phe	137.0	0.0	.		100.0	4.0	.	NM_021111	B2RNS1|Q5W0K6|Q8WX37	Missense_Mutation	SNP	ENST00000377966.3	hg19	CCDS6597.1	.	.	.	.	.	.	.	.	.	.	G	24.7	4.556454	0.86231	.	.	ENSG00000122707	ENST00000377966	T	0.73575	-0.76	6.03	6.03	0.97812	.	0.000000	0.85682	D	0.000000	D	0.85999	0.5828	M	0.74467	2.265	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	D	0.86690	0.1922	10	0.87932	D	0	-10.6063	16.0667	0.80887	0.0:0.0:1.0:0.0	.	350;350	A8K9D8;O95980	.;RECK_HUMAN	F	350	ENSP00000367202:C350F	ENSP00000367202:C350F	C	+	2	0	RECK	36081304	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.869000	0.99810	2.854000	0.98071	0.655000	0.94253	TGT	.	.	.	none		0.353	RECK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052409.1		
DNAJC25	548645	hgsc.bcm.edu	37	9	114412019	114412019	+	Missense_Mutation	SNP	A	A	G			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr9:114412019A>G	ENST00000313525.3	+	3	832	c.776A>G	c.(775-777)tAt>tGt	p.Y259C	DNAJC25_ENST00000556107.1_Intron|DNAJC25-GNG10_ENST00000374294.3_Intron	NM_001015882.2	NP_001015882.2	Q9H1X3	DJC25_HUMAN	DnaJ (Hsp40) homolog, subfamily C , member 25	259						integral component of membrane (GO:0016021)				kidney(1)|large_intestine(2)|lung(1)|skin(4)	8						CTATGCTCATATATAGTTTGG	0.328																																					p.Y259C		Atlas-SNP	.											.	DNAJC25	20	.	0			c.A776G						PASS	.						48.0	50.0	49.0					9																	114412019		1817	4067	5884	SO:0001583	missense	548645	exon3			GCTCATATATAGT		CCDS43862.1	9q31.3	2011-09-02			ENSG00000059769	ENSG00000059769		"""Heat shock proteins / DNAJ (HSP40)"""	34187	protein-coding gene	gene with protein product							Standard	NM_001015882		Approved	bA16L21.2.1	uc004bfl.3	Q9H1X3	OTTHUMG00000020491	ENST00000313525.3:c.776A>G	chr9.hg19:g.114412019A>G	ENSP00000320650:p.Tyr259Cys	138.0	0.0	.		178.0	41.0	.	NM_001015882	Q5QTD8|Q96BN9	Missense_Mutation	SNP	ENST00000313525.3	hg19	CCDS43862.1	.	.	.	.	.	.	.	.	.	.	A	16.14	3.039309	0.55003	.	.	ENSG00000059769	ENST00000313525	T	0.52057	0.68	6.17	5.03	0.67393	.	0.000000	0.85682	D	0.000000	T	0.49729	0.1574	M	0.79475	2.455	0.80722	D	1	B	0.20887	0.049	B	0.19666	0.026	T	0.49244	-0.8960	10	0.56958	D	0.05	-6.1843	11.1739	0.48588	0.9308:0.0:0.0692:0.0	.	259	Q9H1X3	DJC25_HUMAN	C	259	ENSP00000320650:Y259C	ENSP00000320650:Y259C	Y	+	2	0	DNAJC25	113451840	1.000000	0.71417	0.055000	0.19348	0.793000	0.44817	6.943000	0.75934	1.144000	0.42321	0.533000	0.62120	TAT	.	.	.	none		0.328	DNAJC25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000156218.3	NM_001015882	
MLLT10	8028	hgsc.bcm.edu	37	10	21970293	21970293	+	Missense_Mutation	SNP	T	T	A			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr10:21970293T>A	ENST00000307729.7	+	12	1832	c.1654T>A	c.(1654-1656)Tgc>Agc	p.C552S	MLLT10_ENST00000377072.3_Missense_Mutation_p.C552S|MLLT10_ENST00000446906.2_Missense_Mutation_p.C552S|MLLT10_ENST00000377059.3_Missense_Mutation_p.C552S			P55197	AF10_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 10	552	DNA-binding.				positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			NS(1)|large_intestine(2)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	6						TGATGGAGcttgcccaacaac	0.428			T	"""MLL, PICALM, CDK6"""	AL																																p.C552S		Atlas-SNP	.		Dom	yes		10	10p12	8028	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 10 (AF10)"""		L	.	MLLT10	183	.	0			c.T1654A						PASS	.						118.0	114.0	115.0					10																	21970293		2203	4300	6503	SO:0001583	missense	8028	exon11			GGAGCTTGCCCAA	U13948	CCDS7135.1, CCDS55706.1, CCDS55707.1, CCDS55708.1	10p12	2013-01-28	2001-11-28		ENSG00000078403	ENSG00000078403		"""Zinc fingers, PHD-type"""	16063	protein-coding gene	gene with protein product		602409	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 10"""			7888665	Standard	NM_004641		Approved	AF10	uc021pny.1	P55197	OTTHUMG00000017799	ENST00000307729.7:c.1654T>A	chr10.hg19:g.21970293T>A	ENSP00000307411:p.Cys552Ser	88.0	0.0	.		97.0	29.0	.	NM_001195626	B1ANA8|Q5JT37|Q5VX90|Q66K63	Missense_Mutation	SNP	ENST00000307729.7	hg19	CCDS55708.1	.	.	.	.	.	.	.	.	.	.	T	10.13	1.266891	0.23136	.	.	ENSG00000078403	ENST00000377072;ENST00000446906;ENST00000307729;ENST00000396529;ENST00000377059;ENST00000438473;ENST00000538639	T;T;T;T	0.14766	2.5;2.48;2.48;2.48	4.67	4.67	0.58626	.	0.392955	0.33309	N	0.005051	T	0.08670	0.0215	L	0.38175	1.15	0.48135	D	0.999596	B;B;B;B	0.33694	0.008;0.001;0.421;0.0	B;B;B;B	0.21360	0.004;0.0;0.034;0.001	T	0.22034	-1.0228	10	0.13470	T	0.59	.	10.6549	0.45669	0.0:0.0:0.0:1.0	.	247;552;552;552	Q5HYC6;E9PBP4;Q5VX90;P55197	.;.;.;AF10_HUMAN	S	552;552;552;398;552;195;194	ENSP00000366272:C552S;ENSP00000401406:C552S;ENSP00000307411:C552S;ENSP00000366258:C552S	ENSP00000307411:C552S	C	+	1	0	MLLT10	22010299	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	2.116000	0.41930	2.095000	0.63458	0.477000	0.44152	TGC	.	.	.	none		0.428	MLLT10-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047136.1		
ENKUR	219670	hgsc.bcm.edu	37	10	25288439	25288439	+	Missense_Mutation	SNP	G	G	T			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr10:25288439G>T	ENST00000331161.4	-	2	333	c.114C>A	c.(112-114)gaC>gaA	p.D38E	ENKUR_ENST00000376363.1_Missense_Mutation_p.D38E	NM_145010.3	NP_659447.1	Q8TC29	ENKUR_HUMAN	enkurin, TRPC channel interacting protein	38						motile cilium (GO:0031514)				endometrium(2)|large_intestine(4)|lung(3)|skin(1)	10						CTTTTTGCATGTCATCTTTTA	0.299																																					p.D38E		Atlas-SNP	.											ENKUR,NS,carcinoma,-2,1	ENKUR	30	.	0			c.C114A						PASS	.						107.0	95.0	99.0					10																	25288439		2201	4297	6498	SO:0001583	missense	219670	exon2			TTGCATGTCATCT	AK095021	CCDS7146.1, CCDS73075.1	10p12.31	2014-08-13	2009-04-28	2009-04-28	ENSG00000151023	ENSG00000151023			28388	protein-coding gene	gene with protein product		611025	"""chromosome 10 open reading frame 63"""	C10orf63		17217053, 15385169	Standard	NM_145010		Approved	MGC26778, enkurin, CFAP106	uc001isg.2	Q8TC29	OTTHUMG00000017827	ENST00000331161.4:c.114C>A	chr10.hg19:g.25288439G>T	ENSP00000331044:p.Asp38Glu	72.0	0.0	.		86.0	19.0	.	NM_145010	A8K8Y0|D3DRV2	Missense_Mutation	SNP	ENST00000331161.4	hg19	CCDS7146.1	.	.	.	.	.	.	.	.	.	.	G	2.150	-0.394650	0.04899	.	.	ENSG00000151023	ENST00000331161;ENST00000376363	.	.	.	5.98	0.497	0.16902	.	0.090535	0.85682	D	0.000000	T	0.07413	0.0187	N	0.02539	-0.55	0.09310	N	0.999997	B	0.06786	0.001	B	0.01281	0.0	T	0.32079	-0.9920	9	0.02654	T	1	-22.9569	2.4844	0.04595	0.1405:0.2598:0.3993:0.2004	.	38	Q8TC29	ENKUR_HUMAN	E	38	.	ENSP00000331044:D38E	D	-	3	2	ENKUR	25328445	0.018000	0.18449	0.721000	0.30653	0.930000	0.56654	-0.003000	0.12901	0.428000	0.26173	0.591000	0.81541	GAC	.	.	.	none		0.299	ENKUR-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047239.2	NM_145010	
HK1	3098	hgsc.bcm.edu	37	10	71136714	71136714	+	Missense_Mutation	SNP	G	G	T			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr10:71136714G>T	ENST00000359426.6	+	8	1004	c.900G>T	c.(898-900)atG>atT	p.M300I	HK1_ENST00000448642.2_Missense_Mutation_p.M335I|HK1_ENST00000360289.2_Missense_Mutation_p.M288I|HK1_ENST00000404387.2_Missense_Mutation_p.M304I|HK1_ENST00000298649.3_Missense_Mutation_p.M299I|HK1_ENST00000494253.1_3'UTR	NM_000188.2	NP_000179.2	P19367	HXK1_HUMAN	hexokinase 1	300	Hexokinase type-2 1.|Regulatory.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|cell death (GO:0008219)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glucose transport (GO:0015758)|glycolytic process (GO:0006096)|hexose metabolic process (GO:0019318)|hexose transport (GO:0008645)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|hexokinase activity (GO:0004396)|mannokinase activity (GO:0019158)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|liver(1)|lung(14)|ovary(1)|urinary_tract(2)	35						TCAGTGGCATGTACTTGGGAG	0.567																																					p.M304I		Atlas-SNP	.											.	HK1	170	.	0			c.G912T						PASS	.						163.0	143.0	150.0					10																	71136714		2203	4300	6503	SO:0001583	missense	3098	exon11			TGGCATGTACTTG	M75126	CCDS7289.1, CCDS7290.1, CCDS7291.1, CCDS7292.1	10q22	2014-09-17			ENSG00000156515	ENSG00000156515	2.7.1.1		4922	protein-coding gene	gene with protein product		142600					Standard	NM_033496		Approved		uc001jpi.4	P19367	OTTHUMG00000018380	ENST00000359426.6:c.900G>T	chr10.hg19:g.71136714G>T	ENSP00000352398:p.Met300Ile	236.0	0.0	.		255.0	59.0	.	NM_033498	E9PCK0|O43443|O43444|O75574|Q5VTC3|Q96HC8|Q9NNZ4|Q9NNZ5	Missense_Mutation	SNP	ENST00000359426.6	hg19	CCDS7292.1	.	.	.	.	.	.	.	.	.	.	G	17.53	3.413479	0.62511	.	.	ENSG00000156515	ENST00000360289;ENST00000448642;ENST00000404387;ENST00000298649;ENST00000359426;ENST00000405407	T;T;T;T;T	0.12255	2.7;2.7;2.7;2.7;2.7	4.94	4.94	0.65067	Hexokinase, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.26011	0.0634	M	0.86573	2.825	0.80722	D	1	B;B;B;B;B;P	0.39717	0.191;0.191;0.004;0.013;0.05;0.684	B;B;B;B;B;B	0.37267	0.243;0.16;0.012;0.089;0.078;0.245	T	0.30880	-0.9963	10	0.72032	D	0.01	-26.1047	18.1516	0.89676	0.0:0.0:1.0:0.0	.	300;300;299;335;304;288	A8K7J7;P19367;P19367-2;E7ENR4;P19367-3;P19367-4	.;HXK1_HUMAN;.;.;.;.	I	288;335;304;299;300;300	ENSP00000353433:M288I;ENSP00000402103:M335I;ENSP00000384774:M304I;ENSP00000298649:M299I;ENSP00000352398:M300I	ENSP00000298649:M299I	M	+	3	0	HK1	70806720	1.000000	0.71417	1.000000	0.80357	0.561000	0.35649	7.941000	0.87700	2.293000	0.77203	0.585000	0.79938	ATG	.	.	.	none		0.567	HK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048429.2	NM_000188	
GBF1	8729	hgsc.bcm.edu	37	10	104103846	104103846	+	Missense_Mutation	SNP	T	T	G			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr10:104103846T>G	ENST00000369983.3	+	4	462	c.202T>G	c.(202-204)Ttt>Gtt	p.F68V		NM_001199378.1|NM_001199379.1|NM_004193.2	NP_001186307.1|NP_001186308.1|NP_004184.1	Q92538	GBF1_HUMAN	golgi brefeldin A resistant guanine nucleotide exchange factor 1	68					COPI coating of Golgi vesicle (GO:0048205)|membrane organization (GO:0061024)|positive regulation of GTPase activity (GO:0043547)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of ARF protein signal transduction (GO:0032012)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|vesicle-mediated transport (GO:0016192)|viral process (GO:0016032)	cis-Golgi network (GO:0005801)|endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisome (GO:0005777)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(14)|kidney(8)|large_intestine(15)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	71		Colorectal(252;0.0236)		Epithelial(162;5.16e-08)|all cancers(201;1.19e-06)		CCTTCGACCTTTTCTGGAAGT	0.428																																					p.F68V		Atlas-SNP	.											.	GBF1	142	.	0			c.T202G						PASS	.						163.0	145.0	151.0					10																	104103846		2203	4300	6503	SO:0001583	missense	8729	exon4			CGACCTTTTCTGG	D87435	CCDS7533.1	10q24	2010-02-12	2010-02-12		ENSG00000107862	ENSG00000107862			4181	protein-coding gene	gene with protein product		603698	"""golgi-specific brefeldin A resistance factor 1"""			9828135	Standard	NM_004193		Approved	KIAA0248, ARF1GEF	uc001kux.2	Q92538	OTTHUMG00000018955	ENST00000369983.3:c.202T>G	chr10.hg19:g.104103846T>G	ENSP00000359000:p.Phe68Val	82.0	0.0	.		116.0	27.0	.	NM_001199378	Q5VXX3|Q96CK6|Q96HZ3|Q9H473	Missense_Mutation	SNP	ENST00000369983.3	hg19	CCDS7533.1	.	.	.	.	.	.	.	.	.	.	T	29.0	4.967181	0.92855	.	.	ENSG00000107862	ENST00000369983	T	0.68025	-0.3	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	D	0.85741	0.5767	M	0.91663	3.23	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;0.999;1.0	D;D;D;D	0.91635	0.998;0.999;0.994;0.999	D	0.88884	0.3341	10	0.87932	D	0	-13.687	16.3736	0.83374	0.0:0.0:0.0:1.0	.	68;68;68;68	Q149P1;Q149P0;Q92538;Q504U7	.;.;GBF1_HUMAN;.	V	68	ENSP00000359000:F68V	ENSP00000359000:F68V	F	+	1	0	GBF1	104093836	1.000000	0.71417	1.000000	0.80357	0.921000	0.55340	7.922000	0.87538	2.273000	0.75805	0.482000	0.46254	TTT	.	.	.	none		0.428	GBF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050051.1		
MUC2	4583	hgsc.bcm.edu	37	11	1093271	1093271	+	Missense_Mutation	SNP	C	C	G			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr11:1093271C>G	ENST00000441003.2	+	30	5117	c.5090C>G	c.(5089-5091)aCa>aGa	p.T1697R	MUC2_ENST00000361558.6_Intron|MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000359061.5_Missense_Mutation_p.T1664R	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)		p.T1697R(2)|p.T1664R(2)		NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	cagaccccaacatcgacaccc	0.637																																					p.T1697R		Atlas-SNP	.											MUC2_ENST00000441003,NS,carcinoma,-1,4	MUC2	614	.	4	Substitution - Missense(4)	kidney(2)|skin(2)	c.C5090G						PASS	.						126.0	165.0	151.0					11																	1093271		1844	3338	5182	SO:0001583	missense	4583	exon30			CCCCAACATCGAC	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"""Mucins"""	7512	protein-coding gene	gene with protein product		158370	"""mucin 2, intestinal/tracheal"""			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.5090C>G	chr11.hg19:g.1093271C>G	ENSP00000415183:p.Thr1697Arg	82.0	0.0	.		94.0	8.0	.	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	hg19		.	.	.	.	.	.	.	.	.	.	C	5.778	0.327961	0.10956	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.13538	2.93;2.58	1.43	1.43	0.22495	.	27.718000	0.04275	U	0.342784	T	0.27027	0.0662	.	.	.	0.20307	N	0.999915	D	0.64830	0.994	D	0.67725	0.953	T	0.19647	-1.0299	9	0.30078	T	0.28	.	6.2291	0.20724	0.0:1.0:0.0:0.0	.	1697	E7EUV1	.	R	1697;1664	ENSP00000415183:T1697R;ENSP00000351956:T1664R	ENSP00000351956:T1664R	T	+	2	0	MUC2	1083271	0.001000	0.12720	0.002000	0.10522	0.003000	0.03518	0.752000	0.26362	0.796000	0.33947	0.184000	0.17185	ACA	.	.	.	none		0.637	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
OR52M1	119772	hgsc.bcm.edu	37	11	4567069	4567069	+	Missense_Mutation	SNP	A	A	T			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr11:4567069A>T	ENST00000360213.1	+	1	649	c.649A>T	c.(649-651)Att>Ttt	p.I217F		NM_001004137.1	NP_001004137.1	Q8NGK5	O52M1_HUMAN	olfactory receptor, family 52, subfamily M, member 1	217						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|large_intestine(2)|lung(9)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	18		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;8.45e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0285)|LUSC - Lung squamous cell carcinoma(625;0.19)		CTCAGTGGCTATTGCTGCATC	0.532																																					p.I217F		Atlas-SNP	.											.	OR52M1	53	.	0			c.A649T						PASS	.						267.0	251.0	257.0					11																	4567069		2201	4298	6499	SO:0001583	missense	119772	exon1			GTGGCTATTGCTG	AB065789	CCDS31353.1	11p15.4	2012-08-09	2002-11-13	2002-11-15	ENSG00000197790	ENSG00000197790		"""GPCR / Class A : Olfactory receptors"""	15225	protein-coding gene	gene with protein product			"""olfactory receptor, family 52, subfamily M, member 1 pseudogene"""	OR52M1P			Standard	NM_001004137		Approved		uc010qyf.2	Q8NGK5	OTTHUMG00000165706	ENST00000360213.1:c.649A>T	chr11.hg19:g.4567069A>T	ENSP00000353343:p.Ile217Phe	155.0	0.0	.		144.0	32.0	.	NM_001004137		Missense_Mutation	SNP	ENST00000360213.1	hg19	CCDS31353.1	.	.	.	.	.	.	.	.	.	.	A	15.46	2.838966	0.51057	.	.	ENSG00000197790	ENST00000360213	T	0.00333	8.07	5.01	3.86	0.44501	GPCR, rhodopsin-like superfamily (1);	0.000000	0.47852	D	0.000207	T	0.01092	0.0036	H	0.96916	3.905	0.09310	N	1	D	0.89917	1.0	D	0.91635	0.999	T	0.35450	-0.9788	10	0.87932	D	0	.	5.4232	0.16411	0.7442:0.0:0.0856:0.1702	.	217	Q8NGK5	O52M1_HUMAN	F	217	ENSP00000353343:I217F	ENSP00000353343:I217F	I	+	1	0	OR52M1	4523645	1.000000	0.71417	0.265000	0.24526	0.813000	0.45954	4.973000	0.63763	0.995000	0.38917	0.528000	0.53228	ATT	.	.	.	none		0.532	OR52M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385847.1	NM_001004137	
RIC3	79608	hgsc.bcm.edu	37	11	8132577	8132577	+	Missense_Mutation	SNP	C	C	T			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr11:8132577C>T	ENST00000309737.6	-	6	777	c.778G>A	c.(778-780)Gaa>Aaa	p.E260K	RIC3_ENST00000335425.7_Missense_Mutation_p.E78K|RIC3_ENST00000343202.4_Missense_Mutation_p.E259K|RIC3_ENST00000530060.1_5'UTR|RIC3_ENST00000539720.1_Missense_Mutation_p.E211K|RIC3_ENST00000396677.2_Missense_Mutation_p.E98K|RIC3_ENST00000425599.2_Missense_Mutation_p.E179K			Q7Z5B4	RIC3_HUMAN	RIC3 acetylcholine receptor chaperone	260					cellular protein complex assembly (GO:0043623)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein folding (GO:0006457)|synaptic transmission, cholinergic (GO:0007271)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|large_intestine(2)|lung(9)|ovary(2)|pancreas(1)	17				Epithelial(150;2.89e-07)|BRCA - Breast invasive adenocarcinoma(625;0.204)		TCAGCTATTTCTTCAGCAGAA	0.428																																					p.E260K		Atlas-SNP	.											.	RIC3	42	.	0			c.G778A						PASS	.						112.0	111.0	112.0					11																	8132577		2201	4296	6497	SO:0001583	missense	79608	exon6			CTATTTCTTCAGC		CCDS7788.1, CCDS44533.1, CCDS55741.1, CCDS55742.1	11p15.4	2013-08-05	2013-08-05		ENSG00000166405	ENSG00000166405			30338	protein-coding gene	gene with protein product		610509	"""resistance to inhibitors of cholinesterase 3 homolog (C. elegans)"""			12821669	Standard	NM_024557		Approved	FLJ11608, PRO1385, AYST720	uc001mgd.2	Q7Z5B4	OTTHUMG00000165694	ENST00000309737.6:c.778G>A	chr11.hg19:g.8132577C>T	ENSP00000308820:p.Glu260Lys	192.0	0.0	.		231.0	47.0	.	NM_001206671	B0B1U0|B2RD25|D3DQU5|Q6UX78|Q7Z5B3|Q86T94|Q8TBJ9|Q9HAH8	Missense_Mutation	SNP	ENST00000309737.6	hg19	CCDS55742.1	.	.	.	.	.	.	.	.	.	.	C	25.3	4.626069	0.87560	.	.	ENSG00000166405	ENST00000396677;ENST00000335425;ENST00000343202;ENST00000309737;ENST00000543346;ENST00000539720;ENST00000425599;ENST00000531450	T;T;T;T;T	0.37752	1.24;1.24;1.26;1.18;1.2	6.06	6.06	0.98353	.	0.154914	0.45606	D	0.000353	T	0.57651	0.2068	M	0.72118	2.19	0.51233	D	0.999912	D;D;D;D;D;D	0.67145	0.996;0.971;0.99;0.99;0.99;0.99	P;P;P;P;P;P	0.62560	0.904;0.651;0.817;0.857;0.857;0.766	T	0.58250	-0.7669	10	0.72032	D	0.01	.	16.0307	0.80574	0.0:0.8665:0.1335:0.0	.	288;179;78;260;259;98	B7Z1U4;B0B1U0;Q7Z5B4-3;Q7Z5B4;Q7Z5B4-5;D3DQU6	.;.;.;RIC3_HUMAN;.;.	K	98;78;259;260;288;211;179;288	ENSP00000344904:E259K;ENSP00000308820:E260K;ENSP00000443871:E211K;ENSP00000395320:E179K;ENSP00000431658:E288K	ENSP00000308820:E260K	E	-	1	0	RIC3	8089153	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.792000	0.62467	2.882000	0.98803	0.655000	0.94253	GAA	.	.	.	none		0.428	RIC3-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000385900.1	NM_024557	
LRP4	4038	hgsc.bcm.edu	37	11	46895104	46895104	+	Missense_Mutation	SNP	C	C	G			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr11:46895104C>G	ENST00000378623.1	-	29	4512	c.4270G>C	c.(4270-4272)Ggg>Cgg	p.G1424R	LRP4-AS1_ENST00000502049.2_RNA|LRP4-AS1_ENST00000531719.1_RNA	NM_002334.3	NP_002325.2	O75096	LRP4_HUMAN	low density lipoprotein receptor-related protein 4	1424					dendrite morphogenesis (GO:0048813)|dorsal/ventral pattern formation (GO:0009953)|embryonic digit morphogenesis (GO:0042733)|endocytosis (GO:0006897)|extracellular matrix organization (GO:0030198)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|limb development (GO:0060173)|negative regulation of axonogenesis (GO:0050771)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of ossification (GO:0030279)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of presynaptic membrane organization (GO:1901631)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|protein heterotetramerization (GO:0051290)|proximal/distal pattern formation (GO:0009954)|regulation of protein phosphorylation (GO:0001932)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|synapse organization (GO:0050808)|synaptic growth at neuromuscular junction (GO:0051124)|Wnt signaling pathway (GO:0016055)	cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)|synaptic membrane (GO:0097060)	calcium ion binding (GO:0005509)|receptor tyrosine kinase binding (GO:0030971)|scaffold protein binding (GO:0097110)			breast(7)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(24)|ovary(3)|pancreas(2)|prostate(5)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	70				Lung(87;0.159)		AGCCCTCGCCCGATCACTGTC	0.572																																					p.G1424R		Atlas-SNP	.											.	LRP4	160	.	0			c.G4270C						PASS	.						80.0	72.0	75.0					11																	46895104		2201	4299	6500	SO:0001583	missense	4038	exon29			CTCGCCCGATCAC	AB011540	CCDS31478.1	11p11.2	2013-05-29			ENSG00000134569	ENSG00000134569		"""Low density lipoprotein receptors"""	6696	protein-coding gene	gene with protein product		604270				9693030	Standard	NM_002334		Approved	MEGF7, CLSS, LRP-4, SOST2	uc001ndn.4	O75096	OTTHUMG00000166700	ENST00000378623.1:c.4270G>C	chr11.hg19:g.46895104C>G	ENSP00000367888:p.Gly1424Arg	78.0	0.0	.		84.0	25.0	.	NM_002334	B2RN39|Q4AC85|Q5KTZ5	Missense_Mutation	SNP	ENST00000378623.1	hg19	CCDS31478.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.347774	0.82022	.	.	ENSG00000134569	ENST00000378623	D	0.95690	-3.78	5.91	5.91	0.95273	Six-bladed beta-propeller, TolB-like (1);	0.048798	0.85682	D	0.000000	D	0.91975	0.7458	N	0.12527	0.23	0.80722	D	1	P	0.35107	0.484	B	0.41088	0.347	D	0.89603	0.3836	10	0.22706	T	0.39	.	20.2985	0.98592	0.0:1.0:0.0:0.0	.	1424	O75096	LRP4_HUMAN	R	1424	ENSP00000367888:G1424R	ENSP00000367888:G1424R	G	-	1	0	LRP4	46851680	1.000000	0.71417	1.000000	0.80357	0.892000	0.51952	5.943000	0.70211	2.793000	0.96121	0.655000	0.94253	GGG	.	.	.	none		0.572	LRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391133.1	NM_002334	
BRMS1	25855	hgsc.bcm.edu	37	11	66108763	66108763	+	Missense_Mutation	SNP	T	T	A	rs199933125	byFrequency	TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr11:66108763T>A	ENST00000359957.3	-	4	432	c.272A>T	c.(271-273)gAg>gTg	p.E91V	RP11-867G23.12_ENST00000526655.1_RNA|BRMS1_ENST00000425825.2_Missense_Mutation_p.E91V	NM_015399.3	NP_056214.1	Q9HCU9	BRMS1_HUMAN	breast cancer metastasis suppressor 1	91					apoptotic process (GO:0006915)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of anoikis (GO:2000210)|positive regulation of protein deacetylation (GO:0090312)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	NF-kappaB binding (GO:0051059)			large_intestine(1)|liver(1)|lung(1)|prostate(1)|skin(1)	5						CCCCACTTCCTCCAGCCGCAA	0.602																																					p.E91V	GBM(7;55 307 2662 20856 28942)	Atlas-SNP	.											.	BRMS1	42	.	0			c.A272T						PASS	.						32.0	36.0	35.0					11																	66108763		2200	4295	6495	SO:0001583	missense	25855	exon4			ACTTCCTCCAGCC	AF147350	CCDS8135.1, CCDS44654.1	11q13-q13.2	2008-02-05				ENSG00000174744			17262	protein-coding gene	gene with protein product		606259				10850410	Standard	XM_005273883		Approved	DKFZP564A063	uc001oho.1	Q9HCU9		ENST00000359957.3:c.272A>T	chr11.hg19:g.66108763T>A	ENSP00000353042:p.Glu91Val	80.0	0.0	.		72.0	15.0	.	NM_015399	Q6IAI2	Missense_Mutation	SNP	ENST00000359957.3	hg19	CCDS8135.1	.	.	.	.	.	.	.	.	.	.	T	18.88	3.718118	0.68844	.	.	ENSG00000174744	ENST00000425825;ENST00000359957;ENST00000530756	.	.	.	4.17	4.17	0.49024	.	0.121890	0.53938	D	0.000052	T	0.54431	0.1858	L	0.45228	1.405	0.44175	D	0.99698	B;B	0.31790	0.256;0.34	B;B	0.41135	0.348;0.343	T	0.55075	-0.8197	9	0.38643	T	0.18	-29.1846	11.4756	0.50295	0.0:0.0:0.0:1.0	.	91;91	Q9HCU9;G5E9I4	BRMS1_HUMAN;.	V	91	.	ENSP00000353042:E91V	E	-	2	0	BRMS1	65865339	0.983000	0.35010	1.000000	0.80357	0.998000	0.95712	1.690000	0.37711	1.889000	0.54706	0.460000	0.39030	GAG	.	T|0.993;C|0.007	.	alt		0.602	BRMS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392958.2	NM_015399	
TAOK3	51347	hgsc.bcm.edu	37	12	118651868	118651868	+	Missense_Mutation	SNP	A	A	T			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr12:118651868A>T	ENST00000392533.3	-	10	1181	c.691T>A	c.(691-693)Tat>Aat	p.Y231N	TAOK3_ENST00000419821.2_Missense_Mutation_p.Y231N	NM_016281.3	NP_057365.3	Q9H2K8	TAOK3_HUMAN	TAO kinase 3	231	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|MAPK cascade (GO:0000165)|mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of JNK cascade (GO:0046329)|negative regulation of protein kinase activity (GO:0006469)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase inhibitor activity (GO:0004860)|protein serine/threonine kinase activity (GO:0004674)|transferase activity (GO:0016740)			central_nervous_system(1)|lung(5)|skin(1)	7	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					GCAATGTGATATAAGGCACTC	0.413																																					p.Y231N		Atlas-SNP	.											.	TAOK3	151	.	0			c.T691A						PASS	.						153.0	148.0	150.0					12																	118651868		2203	4300	6503	SO:0001583	missense	51347	exon10			TGTGATATAAGGC	AF135158	CCDS9188.1	12q	2007-08-03				ENSG00000135090			18133	protein-coding gene	gene with protein product						10559204, 10924369	Standard	NM_016281		Approved	JIK, DPK, MAP3K18	uc001twy.4	Q9H2K8		ENST00000392533.3:c.691T>A	chr12.hg19:g.118651868A>T	ENSP00000376317:p.Tyr231Asn	58.0	0.0	.		83.0	17.0	.	NM_016281	Q658N1|Q8IUM4|Q9HC79|Q9NZM9|Q9UHG7	Missense_Mutation	SNP	ENST00000392533.3	hg19	CCDS9188.1	.	.	.	.	.	.	.	.	.	.	A	26.4	4.731562	0.89390	.	.	ENSG00000135090	ENST00000419821;ENST00000392533;ENST00000538601	D;D;D	0.85484	-1.99;-1.99;-1.99	5.24	5.24	0.73138	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.072210	0.64402	D	0.000020	D	0.89245	0.6660	L	0.45228	1.405	0.80722	D	1	D	0.71674	0.998	D	0.74348	0.983	D	0.90431	0.4424	10	0.87932	D	0	.	15.3625	0.74492	1.0:0.0:0.0:0.0	.	231	Q9H2K8	TAOK3_HUMAN	N	231;231;129	ENSP00000416374:Y231N;ENSP00000376317:Y231N;ENSP00000437389:Y129N	ENSP00000376317:Y231N	Y	-	1	0	TAOK3	117136251	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.087000	0.94110	2.210000	0.71456	0.472000	0.43445	TAT	.	.	.	none		0.413	TAOK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401456.2	NM_016281	
G2E3	55632	hgsc.bcm.edu	37	14	31081505	31081505	+	Silent	SNP	G	G	A			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr14:31081505G>A	ENST00000206595.6	+	13	1747	c.1593G>A	c.(1591-1593)acG>acA	p.T531T	G2E3_ENST00000438909.2_Silent_p.T485T|G2E3_ENST00000553504.1_Silent_p.T561T	NM_017769.3	NP_060239.2	Q7L622	G2E3_HUMAN	G2/M-phase specific E3 ubiquitin protein ligase	531	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				apoptotic process (GO:0006915)|blastocyst development (GO:0001824)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|protein polyubiquitination (GO:0000209)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	23						GACTTATAACGACATTAAGTG	0.313																																					p.T531T		Atlas-SNP	.											.	G2E3	82	.	0			c.G1593A						PASS	.						100.0	103.0	102.0					14																	31081505		2203	4295	6498	SO:0001819	synonymous_variant	55632	exon13			TATAACGACATTA	AK000340	CCDS9638.1	14q12	2013-01-28	2010-09-17	2009-02-03	ENSG00000092140	ENSG00000092140		"""Zinc fingers, PHD-type"""	20338	protein-coding gene	gene with protein product	"""PHD finger protein 7B"""	611299	"""KIAA1333"""	KIAA1333		18511420, 17239372	Standard	NM_017769		Approved	FLJ20333, PHF7B	uc001wqk.2	Q7L622	OTTHUMG00000140204	ENST00000206595.6:c.1593G>A	chr14.hg19:g.31081505G>A		183.0	0.0	.		175.0	40.0	.	NM_017769	Q9BVR2|Q9H9E9|Q9NXC0|Q9P2L3	Silent	SNP	ENST00000206595.6	hg19	CCDS9638.1																																																																																			.	.	.	none		0.313	G2E3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276613.2	NM_017769	
FANCM	57697	hgsc.bcm.edu	37	14	45645152	45645152	+	Missense_Mutation	SNP	C	C	G			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr14:45645152C>G	ENST00000267430.5	+	14	3280	c.3195C>G	c.(3193-3195)tgC>tgG	p.C1065W	FANCM_ENST00000542564.2_Missense_Mutation_p.C1039W	NM_020937.2	NP_065988.1	Q8IYD8	FANCM_HUMAN	Fanconi anemia, complementation group M	1065					DNA repair (GO:0006281)|replication fork processing (GO:0031297)|resolution of meiotic recombination intermediates (GO:0000712)	FANCM-MHF complex (GO:0071821)|Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|nuclease activity (GO:0004518)			breast(4)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(18)|liver(2)|lung(31)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	85						AAAAAAGTTGCCTTTATGATA	0.299								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.C1065W		Atlas-SNP	.											.	FANCM	225	.	0			c.C3195G						PASS	.						25.0	26.0	25.0					14																	45645152		2203	4296	6499	SO:0001583	missense	57697	exon14	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	AAGTTGCCTTTAT	AK001672	CCDS32070.1	14q21.3	2014-09-17	2005-09-01	2005-09-01		ENSG00000187790		"""Fanconi anemia, complementation groups"""	23168	protein-coding gene	gene with protein product		609644	"""KIAA1596"""	KIAA1596		10997877, 16116422	Standard	NM_020937		Approved	FAAP250	uc001wwd.4	Q8IYD8		ENST00000267430.5:c.3195C>G	chr14.hg19:g.45645152C>G	ENSP00000267430:p.Cys1065Trp	87.0	0.0	.		123.0	31.0	.	NM_020937	B2RTQ9|Q3YFH9|Q8N9X6|Q9HCH6	Missense_Mutation	SNP	ENST00000267430.5	hg19	CCDS32070.1	.	.	.	.	.	.	.	.	.	.	C	6.697	0.497283	0.12762	.	.	ENSG00000187790	ENST00000267430;ENST00000542564;ENST00000556250	T;T;T	0.18657	2.79;2.79;2.2	5.23	-2.33	0.06724	.	1.440870	0.03493	N	0.216880	T	0.30885	0.0779	L	0.56769	1.78	0.09310	N	0.999999	D;D	0.58620	0.964;0.983	P;P	0.53006	0.624;0.715	T	0.38067	-0.9678	10	0.66056	D	0.02	.	5.9826	0.19415	0.0:0.3342:0.137:0.5287	.	1039;1065	B2RTQ9;Q8IYD8	.;FANCM_HUMAN	W	1065;1039;581	ENSP00000267430:C1065W;ENSP00000442493:C1039W;ENSP00000452033:C581W	ENSP00000267430:C1065W	C	+	3	2	FANCM	44714902	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.431000	0.06965	-0.270000	0.09285	-0.229000	0.12294	TGC	.	.	.	none		0.299	FANCM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410474.1	XM_048128	
DLGAP5	9787	hgsc.bcm.edu	37	14	55642723	55642723	+	Missense_Mutation	SNP	C	C	A			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr14:55642723C>A	ENST00000247191.2	-	9	1279	c.1063G>T	c.(1063-1065)Gca>Tca	p.A355S	DLGAP5_ENST00000395425.2_Missense_Mutation_p.A355S	NM_014750.4	NP_055565.3	Q15398	DLGP5_HUMAN	discs, large (Drosophila) homolog-associated protein 5	355					cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|dephosphorylation (GO:0016311)|mitotic chromosome movement towards spindle pole (GO:0007079)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)	cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)|spindle pole centrosome (GO:0031616)	phosphoprotein phosphatase activity (GO:0004721)			biliary_tract(1)|breast(2)|cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	44						TCTTTTGTTGCTTGAGACTCA	0.313																																					p.A355S		Atlas-SNP	.											.	DLGAP5	84	.	0			c.G1063T						PASS	.						131.0	125.0	127.0					14																	55642723		2203	4297	6500	SO:0001583	missense	9787	exon9			TTGTTGCTTGAGA	D13633	CCDS9723.1, CCDS53897.1	14q22.3	2008-05-30	2008-05-30	2008-05-30	ENSG00000126787	ENSG00000126787			16864	protein-coding gene	gene with protein product			"""discs, large homolog 7 (Drosophila)"""	DLG7		7584026, 7584028	Standard	NM_014750		Approved	KIAA0008, DLG1, HURP	uc001xbs.3	Q15398	OTTHUMG00000140310	ENST00000247191.2:c.1063G>T	chr14.hg19:g.55642723C>A	ENSP00000247191:p.Ala355Ser	71.0	0.0	.		73.0	10.0	.	NM_014750	A8MTM6|B4DRM8|Q86T11|Q8NG58	Missense_Mutation	SNP	ENST00000247191.2	hg19	CCDS9723.1	.	.	.	.	.	.	.	.	.	.	C	11.71	1.720936	0.30503	.	.	ENSG00000126787	ENST00000395425;ENST00000247191	T;T	0.15952	2.38;2.38	3.83	2.93	0.34026	.	1.470090	0.03875	N	0.276195	T	0.16342	0.0393	L	0.36672	1.1	0.24747	N	0.993003	B;B	0.26902	0.163;0.095	B;B	0.30105	0.111;0.078	T	0.32798	-0.9893	10	0.13108	T	0.6	.	9.5155	0.39102	0.0:0.7848:0.2152:0.0	.	355;355	A8MTM6;Q15398	.;DLGP5_HUMAN	S	355	ENSP00000378815:A355S;ENSP00000247191:A355S	ENSP00000247191:A355S	A	-	1	0	DLGAP5	54712476	0.784000	0.28713	0.566000	0.28421	0.957000	0.61999	1.018000	0.30002	1.213000	0.43380	0.650000	0.86243	GCA	.	.	.	none		0.313	DLGAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276908.2	NM_014750	
AP4E1	23431	hgsc.bcm.edu	37	15	51285700	51285700	+	Missense_Mutation	SNP	G	G	T			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr15:51285700G>T	ENST00000261842.5	+	17	2330	c.2224G>T	c.(2224-2226)Gat>Tat	p.D742Y	AP4E1_ENST00000560508.1_Missense_Mutation_p.D667Y	NM_001252127.1|NM_007347.4	NP_001239056.1|NP_031373.2	Q9UPM8	AP4E1_HUMAN	adaptor-related protein complex 4, epsilon 1 subunit	742					intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	coated pit (GO:0005905)|Golgi apparatus (GO:0005794)|membrane coat (GO:0030117)				breast(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(5)|skin(2)	27				all cancers(107;0.000893)|GBM - Glioblastoma multiforme(94;0.00364)		GGAGAATGTAGATCAAGCTAT	0.408																																					p.D742Y		Atlas-SNP	.											.	AP4E1	78	.	0			c.G2224T						PASS	.						105.0	92.0	97.0					15																	51285700		2196	4294	6490	SO:0001583	missense	23431	exon17			AATGTAGATCAAG	AB030653	CCDS32240.1, CCDS58362.1	15q21.2	2014-09-17			ENSG00000081014	ENSG00000081014			573	protein-coding gene	gene with protein product		607244				10436028, 21620353	Standard	NM_007347		Approved	AP-4-EPSILON, SPG51	uc001zyx.2	Q9UPM8	OTTHUMG00000172458	ENST00000261842.5:c.2224G>T	chr15.hg19:g.51285700G>T	ENSP00000261842:p.Asp742Tyr	59.0	0.0	.		56.0	8.0	.	NM_007347	A0AVD6|A1L4A9|A6NNX7|H0YKX4|Q68D31|Q9Y588	Missense_Mutation	SNP	ENST00000261842.5	hg19	CCDS32240.1	.	.	.	.	.	.	.	.	.	.	G	15.90	2.969624	0.53614	.	.	ENSG00000081014	ENST00000261842	T	0.19250	2.16	5.29	5.29	0.74685	.	0.278842	0.38778	N	0.001568	T	0.22898	0.0553	N	0.24115	0.695	0.35318	D	0.784497	P	0.51653	0.947	P	0.47744	0.556	T	0.19844	-1.0293	10	0.72032	D	0.01	-17.9497	17.9229	0.88973	0.0:0.0:1.0:0.0	.	742	Q9UPM8	AP4E1_HUMAN	Y	742	ENSP00000261842:D742Y	ENSP00000261842:D742Y	D	+	1	0	AP4E1	49072992	0.989000	0.36119	0.774000	0.31636	0.968000	0.65278	3.111000	0.50360	2.455000	0.83008	0.563000	0.77884	GAT	.	.	.	none		0.408	AP4E1-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418656.1		
CHD2	1106	hgsc.bcm.edu	37	15	93541851	93541851	+	Splice_Site	SNP	G	G	T			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr15:93541851G>T	ENST00000394196.4	+	31	5076	c.4008G>T	c.(4006-4008)gaG>gaT	p.E1336D	CHD2_ENST00000557381.1_Splice_Site_p.E1336D	NM_001271.3	NP_001262.3	O14647	CHD2_HUMAN	chromodomain helicase DNA binding protein 2	1336					cellular response to DNA damage stimulus (GO:0006974)|chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|hematopoietic stem cell differentiation (GO:0060218)|muscle organ development (GO:0007517)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|histone binding (GO:0042393)|poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(2)|large_intestine(10)|lung(17)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	47	Lung NSC(78;0.00976)|all_lung(78;0.016)		BRCA - Breast invasive adenocarcinoma(143;0.0282)|OV - Ovarian serous cystadenocarcinoma(32;0.0814)			GTGGGGAAGAGGTGAGTACGC	0.552																																					p.E1336D		Atlas-SNP	.											.	CHD2	280	.	0			c.G4008T						PASS	.						92.0	92.0	92.0					15																	93541851		2197	4298	6495	SO:0001630	splice_region_variant	1106	exon31			GGAAGAGGTGAGT	AF006514	CCDS10374.2, CCDS45356.1	15q26	2008-07-18			ENSG00000173575	ENSG00000173575			1917	protein-coding gene	gene with protein product		602119				9326634	Standard	NM_001042572		Approved	FLJ38614, DKFZp547I1315, DKFZp781D1727, DKFZp686E01200	uc002bsp.3	O14647	OTTHUMG00000149845	ENST00000394196.4:c.4008+1G>T	chr15.hg19:g.93541851G>T		74.0	0.0	.		74.0	4.0	.	NM_001271	C6G482|Q96IP5	Missense_Mutation	SNP	ENST00000394196.4	hg19	CCDS10374.2	.	.	.	.	.	.	.	.	.	.	G	15.00	2.702923	0.48412	.	.	ENSG00000173575	ENST00000394196;ENST00000557381	D;D	0.89939	-2.59;-2.58	5.16	5.16	0.70880	.	0.000000	0.34484	U	0.003936	D	0.92410	0.7591	L	0.59436	1.845	0.80722	D	1	D;D	0.67145	0.984;0.996	D;P	0.68192	0.956;0.789	D	0.89962	0.4087	10	0.22109	T	0.4	-32.7161	17.2006	0.86904	0.0:0.0:1.0:0.0	.	1336;1336	O14647;O14647-2	CHD2_HUMAN;.	D	1336	ENSP00000377747:E1336D;ENSP00000451366:E1336D	ENSP00000377747:E1336D	E	+	3	2	CHD2	91342855	1.000000	0.71417	1.000000	0.80357	0.415000	0.31203	8.987000	0.93497	2.578000	0.87016	0.561000	0.74099	GAG	.	.	.	none		0.552	CHD2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000313528.3	NM_001271	Missense_Mutation
CCDC64B	146439	hgsc.bcm.edu	37	16	3078701	3078701	+	Splice_Site	SNP	T	T	A			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr16:3078701T>A	ENST00000572449.1	-	8	1300	c.1238A>T	c.(1237-1239)aAg>aTg	p.K413M	CCDC64B_ENST00000389347.4_Splice_Site_p.K413M|CCDC64B_ENST00000573514.1_Splice_Site_p.K206M			A1A5D9	BICR2_HUMAN	coiled-coil domain containing 64B	413										breast(1)|endometrium(2)|large_intestine(1)	4						TGAGGCTTACTTGTTCACGGC	0.637																																					p.K413M		Atlas-SNP	.											.	CCDC64B	19	.	0			c.A1238T						PASS	.						35.0	49.0	44.0					16																	3078701		1994	4127	6121	SO:0001630	splice_region_variant	146439	exon7			GCTTACTTGTTCA	BC128602	CCDS45393.1	16p13.3	2008-07-04				ENSG00000162069			33584	protein-coding gene	gene with protein product							Standard	NM_001103175		Approved		uc002ctf.4	A1A5D9		ENST00000572449.1:c.1238+1A>T	chr16.hg19:g.3078701T>A		72.0	0.0	.		70.0	16.0	.	NM_001103175	Q658L9	Missense_Mutation	SNP	ENST00000572449.1	hg19	CCDS45393.1	.	.	.	.	.	.	.	.	.	.	T	18.59	3.656736	0.67586	.	.	ENSG00000162069	ENST00000389347	T	0.39592	1.07	4.28	4.28	0.50868	.	0.067259	0.56097	D	0.000027	T	0.57989	0.2091	M	0.72118	2.19	0.58432	D	0.999993	D	0.76494	0.999	D	0.63192	0.912	T	0.59936	-0.7360	9	.	.	.	-53.638	11.4408	0.50096	0.0:0.0:0.0:1.0	.	413	A1A5D9	BICR2_HUMAN	M	413	ENSP00000373998:K413M	.	K	-	2	0	CCDC64B	3018702	1.000000	0.71417	1.000000	0.80357	0.619000	0.37552	2.792000	0.47837	1.814000	0.52955	0.459000	0.35465	AAG	.	.	.	none		0.637	CCDC64B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436991.1		Missense_Mutation
GTF3C1	2975	hgsc.bcm.edu	37	16	27549611	27549611	+	Silent	SNP	C	C	T			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr16:27549611C>T	ENST00000356183.4	-	3	513	c.498G>A	c.(496-498)gaG>gaA	p.E166E	GTF3C1_ENST00000561623.1_Silent_p.E166E	NM_001520.3	NP_001511.2	Q12789	TF3C1_HUMAN	general transcription factor IIIC, polypeptide 1, alpha 220kDa	166					5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|rRNA transcription (GO:0009303)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)|tRNA transcription (GO:0009304)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|transcription factor TFIIIC complex (GO:0000127)	DNA binding (GO:0003677)			breast(2)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(14)|liver(3)|lung(28)|ovary(2)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	80						CGGGATCCCCCTCCTGGCCTA	0.582																																					p.E166E		Atlas-SNP	.											.	GTF3C1	210	.	0			c.G498A						PASS	.						70.0	66.0	68.0					16																	27549611		2197	4300	6497	SO:0001819	synonymous_variant	2975	exon3			ATCCCCCTCCTGG	U06485	CCDS32414.1, CCDS66988.1	16p12	2010-03-23	2002-08-29			ENSG00000077235		"""General transcription factors"""	4664	protein-coding gene	gene with protein product		603246	"""general transcription factor IIIC, polypeptide 1 (alpha subunit, 220kD )"""			8164661, 8127861	Standard	NM_001520		Approved	TFIIIC220	uc002dov.2	Q12789		ENST00000356183.4:c.498G>A	chr16.hg19:g.27549611C>T		79.0	0.0	.		74.0	20.0	.	NM_001520	B2RP21|Q12838|Q6DKN9|Q9Y4W9	Silent	SNP	ENST00000356183.4	hg19	CCDS32414.1	.	.	.	.	.	.	.	.	.	.	C	8.560	0.877594	0.17395	.	.	ENSG00000077235	ENST00000388971	.	.	.	5.5	1.98	0.26296	.	.	.	.	.	T	0.61640	0.2363	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.58036	-0.7707	5	0.38643	T	0.18	-3.8349	11.4639	0.50227	0.0:0.6864:0.0:0.3136	.	.	.	.	R	166	.	ENSP00000373623:G166R	G	-	1	0	GTF3C1	27457112	0.875000	0.30112	0.996000	0.52242	0.914000	0.54420	-0.027000	0.12371	0.389000	0.25086	-1.945000	0.00491	GGG	.	.	.	none		0.582	GTF3C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433856.1	NM_001520	
CDH1	999	hgsc.bcm.edu	37	16	68853183	68853183	+	Splice_Site	SNP	A	A	C			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr16:68853183A>C	ENST00000261769.5	+	11	1757	c.1566A>C	c.(1564-1566)acA>acC	p.T522T	RP11-354M1.2_ENST00000563916.1_RNA|CDH1_ENST00000562836.1_3'UTR|CDH1_ENST00000422392.2_Splice_Site_p.T461T	NM_004360.3	NP_004351.1	P12830	CADH1_HUMAN	cadherin 1, type 1, E-cadherin (epithelial)	522	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|calcium-dependent cell-cell adhesion (GO:0016339)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to amino acid stimulus (GO:0071230)|cellular response to indole-3-methanol (GO:0071681)|cellular response to lithium ion (GO:0071285)|cochlea development (GO:0090102)|epithelial cell morphogenesis (GO:0003382)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|homophilic cell adhesion (GO:0007156)|intestinal epithelial cell development (GO:0060576)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of epithelial cell proliferation (GO:0050680)|neuron projection development (GO:0031175)|pituitary gland development (GO:0021983)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription, DNA-templated (GO:0045893)|protein homooligomerization (GO:0051260)|protein localization to plasma membrane (GO:0072659)|protein metabolic process (GO:0019538)|regulation of branching involved in salivary gland morphogenesis (GO:0060693)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of immune response (GO:0050776)|regulation of neuron migration (GO:2001222)|regulation of protein localization to cell surface (GO:2000008)|regulation of water loss via skin (GO:0033561)|response to drug (GO:0042493)|response to toxic substance (GO:0009636)|salivary gland cavitation (GO:0060662)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)|tight junction assembly (GO:0070830)|trophectodermal cell differentiation (GO:0001829)	actin cytoskeleton (GO:0015629)|aggresome (GO:0016235)|apical junction complex (GO:0043296)|apical part of cell (GO:0045177)|axon terminus (GO:0043679)|basolateral plasma membrane (GO:0016323)|catenin complex (GO:0016342)|cell junction (GO:0030054)|cell surface (GO:0009986)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lateral loop (GO:0043219)|lateral plasma membrane (GO:0016328)|node of Ranvier (GO:0033268)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|Schmidt-Lanterman incisure (GO:0043220)|trans-Golgi network (GO:0005802)	ankyrin binding (GO:0030506)|beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|gamma-catenin binding (GO:0045295)|glycoprotein binding (GO:0001948)|GTPase activating protein binding (GO:0032794)	p.?(1)		NS(6)|biliary_tract(8)|breast(161)|central_nervous_system(4)|endometrium(9)|kidney(4)|large_intestine(13)|lung(13)|oesophagus(3)|ovary(2)|prostate(3)|soft_tissue(2)|stomach(76)|thyroid(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	311		all_neural(199;0.0189)|Ovarian(137;0.0563)		Epithelial(162;8.44e-05)|all cancers(182;0.000404)|OV - Ovarian serous cystadenocarcinoma(108;0.000426)|BRCA - Breast invasive adenocarcinoma(181;0.0261)		CCCCGTTCAGATATCGGATTT	0.493			"""Mis, N, F, S"""		"""lobular breast, gastric"""	gastric			Hereditary Diffuse Gastric Cancer																												p.T522T		Atlas-SNP	.	yes	Rec	yes	Familial gastric carcinoma	16	16q22.1	999	"""cadherin 1, type 1, E-cadherin (epithelial) (ECAD)"""		E	.	CDH1	535	.	1	Unknown(1)	breast(1)	c.A1566C						PASS	.						89.0	78.0	82.0					16																	68853183		2198	4300	6498	SO:0001630	splice_region_variant	999	exon11	Familial Cancer Database	HDGC	GTTCAGATATCGG	L08599	CCDS10869.1	16q22.1	2014-09-17			ENSG00000039068	ENSG00000039068		"""CD molecules"", ""Cadherins / Major cadherins"""	1748	protein-coding gene	gene with protein product	"""E-Cadherin"""	192090		UVO		9925936	Standard	NM_004360		Approved	uvomorulin, CD324	uc002ewg.1	P12830	OTTHUMG00000137561	ENST00000261769.5:c.1566-1A>C	chr16.hg19:g.68853183A>C		116.0	0.0	.		92.0	22.0	.	NM_004360	A8K1U7|Q13799|Q14216|Q15855|Q16194|Q4PJ14|Q9UII8	Silent	SNP	ENST00000261769.5	hg19	CCDS10869.1																																																																																			.	.	.	none		0.493	CDH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268897.2	NM_004360	Silent
CPNE7	27132	hgsc.bcm.edu	37	16	89650107	89650107	+	Silent	SNP	T	T	A			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr16:89650107T>A	ENST00000268720.5	+	5	715	c.585T>A	c.(583-585)atT>atA	p.I195I	CPNE7_ENST00000319518.8_Silent_p.I120I	NM_014427.4	NP_055242.1	Q9UBL6	CPNE7_HUMAN	copine VII	195					lipid metabolic process (GO:0006629)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)	transporter activity (GO:0005215)			breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(8)|ovary(2)	17		all_hematologic(23;0.0748)		all cancers(4;3.63e-08)|OV - Ovarian serous cystadenocarcinoma(4;1.7e-06)|BRCA - Breast invasive adenocarcinoma(80;0.0147)		ACTTACAGATTGTGGCCCAGA	0.672																																					p.I195I		Atlas-SNP	.											.	CPNE7	56	.	0			c.T585A						PASS	.						48.0	45.0	46.0					16																	89650107		2198	4300	6498	SO:0001819	synonymous_variant	27132	exon5			ACAGATTGTGGCC	AJ133798	CCDS10980.1, CCDS10981.1	16q24.3	2008-07-03			ENSG00000178773	ENSG00000178773			2320	protein-coding gene	gene with protein product		605689					Standard	NM_014427		Approved		uc002fnq.3	Q9UBL6	OTTHUMG00000138051	ENST00000268720.5:c.585T>A	chr16.hg19:g.89650107T>A		120.0	0.0	.		107.0	29.0	.	NM_014427		Silent	SNP	ENST00000268720.5	hg19	CCDS10980.1																																																																																			.	.	.	none		0.672	CPNE7-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000269929.2		
ELP5	23587	hgsc.bcm.edu	37	17	7157996	7157996	+	Missense_Mutation	SNP	T	T	C			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr17:7157996T>C	ENST00000396628.2	+	4	548	c.331T>C	c.(331-333)Tgc>Cgc	p.C111R	CTDNEP1_ENST00000572043.1_5'Flank|ELP5_ENST00000356683.2_Missense_Mutation_p.C111R|ELP5_ENST00000574255.1_Missense_Mutation_p.C111R|ELP5_ENST00000574993.1_Missense_Mutation_p.C111R|ELP5_ENST00000396627.2_Missense_Mutation_p.C111R|RP1-4G17.5_ENST00000577138.1_Intron|ELP5_ENST00000573657.1_Missense_Mutation_p.C111R|CTDNEP1_ENST00000318988.6_5'Flank|CTDNEP1_ENST00000573600.1_5'Flank|ELP5_ENST00000354429.2_Missense_Mutation_p.C111R	NM_203414.1	NP_981959.1	Q8TE02	ELP5_HUMAN	elongator acetyltransferase complex subunit 5	111					chromatin organization (GO:0006325)|positive regulation of cell migration (GO:0030335)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Elongator holoenzyme complex (GO:0033588)|nucleus (GO:0005634)											GAGAGCCATGTGCAAGAGGAC	0.562																																					p.C111R		Atlas-SNP	.											.	.	.	.	0			c.T331C						PASS	.						126.0	93.0	104.0					17																	7157996		2203	4300	6503	SO:0001583	missense	23587	exon4			GCCATGTGCAAGA	BC002762	CCDS11094.1, CCDS11095.1	17p13.1	2012-08-14	2012-08-08	2012-08-08	ENSG00000170291	ENSG00000170291		"""Elongator acetyltransferase complex subunits"""	30617	protein-coding gene	gene with protein product	"""dermal papilla derived protein 6"", ""S-phase 2 protein"""	615019	"""chromosome 17 open reading frame 81"""	C17orf81		22854966	Standard	NM_203415		Approved	DERP6	uc002gfi.1	Q8TE02	OTTHUMG00000177974	ENST00000396628.2:c.331T>C	chr17.hg19:g.7157996T>C	ENSP00000379869:p.Cys111Arg	62.0	0.0	.		71.0	19.0	.	NM_203414	A8K1M5|D3DTN9|Q659B6|Q7Z2T4|Q8TDR9|Q9BUB2|Q9Y2Q4	Missense_Mutation	SNP	ENST00000396628.2	hg19	CCDS11094.1	.	.	.	.	.	.	.	.	.	.	T	12.68	2.009540	0.35415	.	.	ENSG00000170291	ENST00000354429;ENST00000396628;ENST00000396627;ENST00000356683	T;T;T;T	0.47869	1.54;1.54;1.54;0.83	5.51	0.78	0.18556	.	0.815021	0.11405	N	0.567376	T	0.41858	0.1177	L	0.56769	1.78	0.19575	N	0.999968	B;B;B;B	0.26002	0.029;0.114;0.139;0.021	B;B;B;B	0.31290	0.025;0.053;0.127;0.025	T	0.43925	-0.9361	10	0.56958	D	0.05	-0.1605	4.5046	0.11881	0.0:0.2406:0.3505:0.4089	.	111;111;111;111	Q8TE02-2;Q8TE02-3;A8K1M5;Q8TE02	.;.;.;DERP6_HUMAN	R	111	ENSP00000346412:C111R;ENSP00000379869:C111R;ENSP00000379868:C111R;ENSP00000349111:C111R	ENSP00000346412:C111R	C	+	1	0	C17orf81	7098720	0.003000	0.15002	0.001000	0.08648	0.794000	0.44872	0.167000	0.16602	0.127000	0.18452	0.482000	0.46254	TGC	.	.	.	none		0.562	ELP5-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000440111.1	NM_015362	
ATPAF2	91647	hgsc.bcm.edu	37	17	17925092	17925092	+	Missense_Mutation	SNP	G	G	A			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr17:17925092G>A	ENST00000474627.3	-	6	737	c.583C>T	c.(583-585)Cac>Tac	p.H195Y	ATPAF2_ENST00000469327.1_5'UTR|ATPAF2_ENST00000585101.1_Intron	NM_145691.3	NP_663729.1	Q8N5M1	ATPF2_HUMAN	ATP synthase mitochondrial F1 complex assembly factor 2	195					proton-transporting ATP synthase complex assembly (GO:0043461)	mitochondrion (GO:0005739)|nuclear speck (GO:0016607)				breast(2)|endometrium(1)|kidney(2)|large_intestine(1)|lung(1)|urinary_tract(1)	8	all_neural(463;0.228)					GATGCCAGGTGGCTGACGAGC	0.547																																					p.H195Y		Atlas-SNP	.											.	ATPAF2	15	.	0			c.C583T						PASS	.						234.0	205.0	215.0					17																	17925092		2203	4300	6503	SO:0001583	missense	91647	exon6			CCAGGTGGCTGAC	AF052185	CCDS32585.1	17p11.2	2012-10-12			ENSG00000171953	ENSG00000171953		"""Mitochondrial respiratory chain complex assembly factors"""	18802	protein-coding gene	gene with protein product		608918				11410595, 11997338	Standard	NM_145691		Approved	Atp12p, ATP12, LP3663, MGC29736	uc002gse.1	Q8N5M1	OTTHUMG00000059354	ENST00000474627.3:c.583C>T	chr17.hg19:g.17925092G>A	ENSP00000417190:p.His195Tyr	126.0	0.0	.		125.0	34.0	.	NM_145691	A6NDE5|A8K2J2|Q6XYC7	Missense_Mutation	SNP	ENST00000474627.3	hg19	CCDS32585.1	.	.	.	.	.	.	.	.	.	.	G	16.89	3.247071	0.59103	.	.	ENSG00000171953	ENST00000474627;ENST00000444058	T;T	0.75821	-0.97;-0.97	5.41	5.41	0.78517	ATPase assembly, ATP12, domain (1);	0.000000	0.85682	D	0.000000	T	0.78767	0.4335	L	0.38175	1.15	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	T	0.70182	-0.4942	10	0.02654	T	1	4.9557	19.5423	0.95278	0.0:0.0:1.0:0.0	.	195	Q8N5M1	ATPF2_HUMAN	Y	195	ENSP00000417190:H195Y;ENSP00000397198:H195Y	ENSP00000434980:H195Y	H	-	1	0	ATPAF2	17865817	1.000000	0.71417	1.000000	0.80357	0.784000	0.44337	7.369000	0.79578	2.692000	0.91855	0.655000	0.94253	CAC	.	.	.	none		0.547	ATPAF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131934.3	NM_145691	
DYM	54808	hgsc.bcm.edu	37	18	46798650	46798650	+	Silent	SNP	C	C	G			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr18:46798650C>G	ENST00000269445.6	-	11	1606	c.1149G>C	c.(1147-1149)ctG>ctC	p.L383L	DYM_ENST00000442713.2_Silent_p.L193L	NM_017653.3	NP_060123.3	Q7RTS9	DYM_HUMAN	dymeclin	383					bone development (GO:0060348)|Golgi organization (GO:0007030)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)	enzyme binding (GO:0019899)			NS(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	18						CAACATGATACAGAATCTCAA	0.299																																					p.L383L		Atlas-SNP	.											DYM,NS,carcinoma,0,1	DYM	52	.	0			c.G1149C						PASS	.						77.0	72.0	74.0					18																	46798650		2203	4299	6502	SO:0001819	synonymous_variant	54808	exon11			ATGATACAGAATC	AK000078	CCDS11937.1	18q21.1	2008-03-12			ENSG00000141627	ENSG00000141627			21317	protein-coding gene	gene with protein product		607461					Standard	NM_017653		Approved	FLJ20071, DMC, SMC	uc002ldi.1	Q7RTS9	OTTHUMG00000132659	ENST00000269445.6:c.1149G>C	chr18.hg19:g.46798650C>G		151.0	1.0	.		123.0	35.0	.	NM_017653	A8K5I8|B2RCF9|B4DKI7|Q3ZTS8|Q6P2P5|Q8N2M0|Q9BVE9|Q9NPU7	Silent	SNP	ENST00000269445.6	hg19	CCDS11937.1																																																																																			.	.	.	none		0.299	DYM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255912.3	NM_017653	
HMHA1	23526	hgsc.bcm.edu	37	19	1082889	1082889	+	Silent	SNP	G	G	T			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr19:1082889G>T	ENST00000313093.2	+	20	2799	c.2568G>T	c.(2566-2568)ctG>ctT	p.L856L	HMHA1_ENST00000536472.1_Silent_p.L724L|HMHA1_ENST00000539243.2_Silent_p.L872L|HMHA1_ENST00000586866.1_Silent_p.L860L|HMHA1_ENST00000590577.1_Silent_p.L491L|HMHA1_ENST00000590214.1_Silent_p.L883L|HMHA1_ENST00000543365.1_Silent_p.L739L	NM_012292.3	NP_036424.2	Q92619	HMHA1_HUMAN	histocompatibility (minor) HA-1	856	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|lung(7)|ovary(1)|prostate(2)	16		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TCGTAGGGCTGGCCAAGGACA	0.711																																					p.L872L		Atlas-SNP	.											.	HMHA1	78	.	0			c.G2616T						PASS	.						13.0	12.0	12.0					19																	1082889		2193	4288	6481	SO:0001819	synonymous_variant	23526	exon20			AGGGCTGGCCAAG	D86976	CCDS32863.1, CCDS58637.1, CCDS74242.1, CCDS74243.1	19p13.3	2011-09-07				ENSG00000180448		"""Rho GTPase activating proteins"""	17102	protein-coding gene	gene with protein product		601155				9820596, 9039502	Standard	NM_012292		Approved	KIAA0223, HA-1, ARHGAP45	uc010xgd.2	Q92619		ENST00000313093.2:c.2568G>T	chr19.hg19:g.1082889G>T		49.0	0.0	.		49.0	19.0	.	NM_001258328	B4DTS4|F6QP70|Q6P189|Q7LE26|Q86WS1|Q8HX84|Q9GJN9|Q9GJP0|Q9GJP1|Q9MY24	Silent	SNP	ENST00000313093.2	hg19	CCDS32863.1																																																																																			.	.	.	none		0.711	HMHA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458026.1		
C19orf53	28974	hgsc.bcm.edu	37	19	13883025	13883025	+	5'Flank	SNP	A	A	T			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr19:13883025A>T	ENST00000588234.1	+	0	0				CTB-5E10.3_ENST00000586297.1_RNA|CTB-5E10.3_ENST00000591826.1_RNA|C19orf53_ENST00000593274.1_5'Flank|MRI1_ENST00000040663.6_Missense_Mutation_p.E347V|CTB-5E10.3_ENST00000586894.1_RNA|MRI1_ENST00000319545.8_Missense_Mutation_p.E300V	NM_014047.2	NP_054766.1	Q9UNZ5	L10K_HUMAN	chromosome 19 open reading frame 53											breast(1)|large_intestine(1)|lung(1)|ovary(2)|upper_aerodigestive_tract(1)	6			OV - Ovarian serous cystadenocarcinoma(19;7.7e-24)|Epithelial(5;2.53e-19)			TTTGCCCCTGAGGAGCTCCGG	0.577																																					p.E347V		Atlas-SNP	.											.	MRI1	35	.	0			c.A1040T						PASS	.						95.0	88.0	91.0					19																	13883025		2203	4300	6503	SO:0001631	upstream_gene_variant	84245	exon6			CCCCTGAGGAGCT	AF078852	CCDS12298.1	19p13.2	2011-11-24			ENSG00000104979	ENSG00000104979			24991	protein-coding gene	gene with protein product	"""leydig cell tumor 10 kDa protein homolog"""					11042152	Standard	NM_014047		Approved	HSPC023, LYDG10	uc002mxg.3	Q9UNZ5			chr19.hg19:g.13883025A>T	Exception_encountered	217.0	0.0	.		208.0	48.0	.	NM_001031727	B2R4J9	Missense_Mutation	SNP	ENST00000588234.1	hg19	CCDS12298.1	.	.	.	.	.	.	.	.	.	.	A	11.35	1.611851	0.28712	.	.	ENSG00000037757	ENST00000040663;ENST00000319545	T;T	0.31247	1.5;1.5	4.88	3.84	0.44239	.	0.235842	0.36409	N	0.002620	T	0.27900	0.0687	L	0.48986	1.54	0.32290	N	0.566403	B;B	0.29085	0.232;0.011	B;B	0.30251	0.113;0.027	T	0.29518	-1.0009	10	0.42905	T	0.14	-48.5554	10.0893	0.42436	0.8314:0.1686:0.0:0.0	.	300;347	Q9BV20-2;Q9BV20	.;MTNA_HUMAN	V	347;300	ENSP00000040663:E347V;ENSP00000314871:E300V	ENSP00000040663:E347V	E	+	2	0	MRI1	13744025	0.000000	0.05858	0.400000	0.26346	0.621000	0.37620	0.854000	0.27791	0.685000	0.31468	0.397000	0.26171	GAG	.	.	.	none		0.577	C19orf53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453621.1	NM_014047	
USHBP1	83878	hgsc.bcm.edu	37	19	17366410	17366410	+	Silent	SNP	G	G	A			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr19:17366410G>A	ENST00000252597.3	-	10	1649	c.1476C>T	c.(1474-1476)gcC>gcT	p.A492A	AC010646.3_ENST00000594059.1_5'Flank|USHBP1_ENST00000431146.2_Silent_p.A428A	NM_031941.3	NP_114147.2			Usher syndrome 1C binding protein 1											breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(10)|liver(1)|lung(12)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	44						GGTCCGCCAGGGCCTCCTGTG	0.632																																					p.A492A		Atlas-SNP	.											.	USHBP1	85	.	0			c.C1476T						PASS	.						10.0	12.0	11.0					19																	17366410		2188	4264	6452	SO:0001819	synonymous_variant	83878	exon10			CGCCAGGGCCTCC	AK096028	CCDS12353.1	19p13.11	2013-06-10			ENSG00000130307	ENSG00000130307			24058	protein-coding gene	gene with protein product		611810				11311560	Standard	XM_005260093		Approved	MCC2, AIEBP, FLJ38709	uc002nfs.1	Q8N6Y0	OTTHUMG00000182730	ENST00000252597.3:c.1476C>T	chr19.hg19:g.17366410G>A		79.0	0.0	.		79.0	14.0	.	NM_031941		Silent	SNP	ENST00000252597.3	hg19	CCDS12353.1																																																																																			.	.	.	none		0.632	USHBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463328.1	NM_031941	
DMKN	93099	hgsc.bcm.edu	37	19	36002420	36002420	+	Missense_Mutation	SNP	C	C	T	rs72334573	byFrequency	TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr19:36002420C>T	ENST00000339686.3	-	5	987	c.811G>A	c.(811-813)Ggc>Agc	p.G271S	DMKN_ENST00000492341.2_5'Flank|DMKN_ENST00000392206.2_5'Flank|DMKN_ENST00000602781.1_5'Flank|DMKN_ENST00000467637.1_5'Flank|DMKN_ENST00000488892.1_5'Flank|DMKN_ENST00000429837.1_Intron|DMKN_ENST00000419602.1_Intron|DMKN_ENST00000462126.1_5'Flank|DMKN_ENST00000424570.2_Missense_Mutation_p.G271S|DMKN_ENST00000402589.2_5'Flank|DMKN_ENST00000451297.2_Missense_Mutation_p.G271S|DMKN_ENST00000436012.1_5'Flank|DMKN_ENST00000461300.1_5'Flank|DMKN_ENST00000458071.1_5'Flank|DMKN_ENST00000474928.1_5'Flank|DMKN_ENST00000447113.2_Missense_Mutation_p.G271S|DMKN_ENST00000440396.1_Missense_Mutation_p.G271S|DMKN_ENST00000472252.2_5'Flank|DMKN_ENST00000414866.2_5'Flank|DMKN_ENST00000443640.1_5'Flank|DMKN_ENST00000418261.1_Missense_Mutation_p.G271S|DMKN_ENST00000480502.1_5'Flank	NM_033317.4	NP_201574	Q6E0U4	DMKN_HUMAN	dermokine	271	Gly-rich.			Missing (in Ref. 3; ABN11273/ABN11274). {ECO:0000305}.		extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(7)|ovary(1)|prostate(1)|skin(2)	27	all_lung(56;1.89e-08)|Lung NSC(56;2.9e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			ctgctgctgccaccactgctg	0.657																																					p.G271S		Atlas-SNP	.											DMKN,colon,carcinoma,0,1	DMKN	116	.	0			c.G811A						PASS	.						30.0	23.0	25.0					19																	36002420		2169	4246	6415	SO:0001583	missense	93099	exon5			TGCTGCCACCACT	BC035311	CCDS12463.1, CCDS42549.1, CCDS46051.1, CCDS46052.1, CCDS46053.1, CCDS46054.1, CCDS46054.2, CCDS54250.1, CCDS54251.1, CCDS54252.1	19q13.12	2008-10-27			ENSG00000161249	ENSG00000161249			25063	protein-coding gene	gene with protein product						16374476	Standard	NM_001035516		Approved	ZD52F10	uc002nzm.4	Q6E0U4	OTTHUMG00000048101	ENST00000339686.3:c.811G>A	chr19.hg19:g.36002420C>T	ENSP00000342012:p.Gly271Ser	22.0	2.0	.		26.0	3.0	.	NM_001126058	A3EZ79|A3EZ80|A3EZ81|A3EZ82|A3EZ83|C9J4P6|C9J5N8|C9JAL3|Q32W58|Q32W62|Q32W63|Q32W64|Q32W65|Q32W66|Q32W67|Q6E0U5|Q6UXC7|Q96EW8|Q9BSY6	Missense_Mutation	SNP	ENST00000339686.3	hg19	CCDS12463.1	.	.	.	.	.	.	.	.	.	.	C	0.987	-0.695138	0.03303	.	.	ENSG00000161249	ENST00000339686;ENST00000392207;ENST00000447113;ENST00000440396;ENST00000418261;ENST00000424570;ENST00000451297	T;T;T;T;T;T	0.42513	0.97;0.97;0.97;0.97;0.97;0.97	3.44	-2.87	0.05700	.	1.607200	0.03581	N	0.230096	T	0.18759	0.0450	N	0.12746	0.255	0.09310	N	1	B;B;B;B;B	0.31931	0.347;0.347;0.347;0.347;0.347	B;B;B;B;B	0.25140	0.058;0.058;0.058;0.058;0.058	T	0.16689	-1.0394	10	0.02654	T	1	.	7.7195	0.28723	0.0:0.3991:0.0:0.6009	.	271;271;271;271;271	E7EUS0;Q6E0U4-7;Q6E0U4-3;Q6E0U4-5;Q6E0U4	.;.;.;.;DMKN_HUMAN	S	271	ENSP00000342012:G271S;ENSP00000394908:G271S;ENSP00000415277:G271S;ENSP00000414743:G271S;ENSP00000388404:G271S;ENSP00000409513:G271S	ENSP00000342012:G271S	G	-	1	0	DMKN	40694260	0.001000	0.12720	0.000000	0.03702	0.004000	0.04260	0.439000	0.21575	-0.412000	0.07519	-0.418000	0.06021	GGC	.	.	.	none		0.657	DMKN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109461.2	NM_033317	
CBLC	23624	hgsc.bcm.edu	37	19	45281521	45281521	+	Missense_Mutation	SNP	C	C	G			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr19:45281521C>G	ENST00000270279.3	+	1	396	c.333C>G	c.(331-333)ttC>ttG	p.F111L	CBLC_ENST00000341505.4_Missense_Mutation_p.F111L	NM_012116.3	NP_036248.3	Q9ULV8	CBLC_HUMAN	Cbl proto-oncogene C, E3 ubiquitin protein ligase	111	4H.|Cbl-PTB. {ECO:0000255|PROSITE- ProRule:PRU00839}.				cell surface receptor signaling pathway (GO:0007166)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of epidermal growth factor-activated receptor activity (GO:0007175)|negative regulation of MAP kinase activity (GO:0043407)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|epidermal growth factor receptor binding (GO:0005154)|ligase activity (GO:0016874)|phosphotyrosine binding (GO:0001784)|SH3 domain binding (GO:0017124)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|kidney(1)|lung(6)|ovary(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	17	Lung NSC(12;0.00136)|all_lung(12;0.00371)	Ovarian(192;0.231)				ACGAGCTCTTCCGGGCGGGCT	0.657			M		AML																																p.F111L		Atlas-SNP	.		Rec	yes		19	19q13.2	23624	Cas-Br-M (murine) ecotropic retroviral transforming sequence c		L	.	CBLC	41	.	0			c.C333G						PASS	.						4.0	5.0	5.0					19																	45281521		1948	3848	5796	SO:0001583	missense	23624	exon1			GCTCTTCCGGGCG	AB028645	CCDS12643.1, CCDS46109.1	19q13.2	2013-07-09	2013-07-09		ENSG00000142273	ENSG00000142273		"""RING-type (C3HC4) zinc fingers"""	15961	protein-coding gene	gene with protein product		608453	"""Cas-Br-M (murine) ectropic retroviral transforming sequence c"", ""Cas-Br-M (murine) ecotropic retroviral transforming sequence c"""			10362357, 10571044	Standard	NM_012116		Approved	CBL-3, CBL-SL, RNF57	uc002ozs.3	Q9ULV8	OTTHUMG00000150715	ENST00000270279.3:c.333C>G	chr19.hg19:g.45281521C>G	ENSP00000270279:p.Phe111Leu	18.0	0.0	.		19.0	5.0	.	NM_001130852	Q8N1E5|Q9Y5Z2|Q9Y5Z3	Missense_Mutation	SNP	ENST00000270279.3	hg19	CCDS12643.1	.	.	.	.	.	.	.	.	.	.	.	14.98	2.697608	0.48307	.	.	ENSG00000142273	ENST00000270279;ENST00000341505	T;T	0.78924	-1.22;-1.22	3.49	3.49	0.39957	Adaptor protein Cbl, N-terminal helical (3);Adaptor protein Cbl, PTB domain (1);	0.000000	0.64402	D	0.000016	T	0.78978	0.4369	M	0.81497	2.545	0.39134	D	0.961902	P;D	0.52996	0.939;0.957	P;P	0.45310	0.476;0.469	D	0.83554	0.0103	10	0.66056	D	0.02	-25.9304	10.6934	0.45884	0.0:1.0:0.0:0.0	.	111;111	Q9ULV8-2;Q9ULV8	.;CBLC_HUMAN	L	111	ENSP00000270279:F111L;ENSP00000340250:F111L	ENSP00000270279:F111L	F	+	3	2	CBLC	49973361	1.000000	0.71417	1.000000	0.80357	0.227000	0.25037	2.404000	0.44539	1.962000	0.57031	0.556000	0.70494	TTC	.	.	.	none		0.657	CBLC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319732.2	NM_012116	
ZNF577	84765	hgsc.bcm.edu	37	19	52376955	52376955	+	Silent	SNP	A	A	G			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr19:52376955A>G	ENST00000301399.5	-	7	653	c.288T>C	c.(286-288)ttT>ttC	p.F96F	ZNF577_ENST00000412216.1_Intron|ZNF577_ENST00000485702.1_Intron|ZNF577_ENST00000420592.1_Intron|ZNF577_ENST00000451628.2_Intron	NM_032679.2	NP_116068.2	Q9BSK1	ZN577_HUMAN	zinc finger protein 577	96					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	21		all_neural(266;0.0602)		GBM - Glioblastoma multiforme(134;0.00161)|OV - Ovarian serous cystadenocarcinoma(262;0.019)		TCTGGATTACAAAACCTAAAT	0.358																																					p.F96F		Atlas-SNP	.											.	ZNF577	63	.	0			c.T288C						PASS	.						37.0	34.0	35.0					19																	52376955		2203	4299	6502	SO:0001819	synonymous_variant	84765	exon7			GATTACAAAACCT	AL832871	CCDS12842.2, CCDS46160.1	19q13.41	2013-09-20			ENSG00000161551	ENSG00000161551		"""Zinc fingers, C2H2-type"", ""-"""	28673	protein-coding gene	gene with protein product						12477932	Standard	NM_032679		Approved	MGC4400	uc010yde.2	Q9BSK1	OTTHUMG00000157045	ENST00000301399.5:c.288T>C	chr19.hg19:g.52376955A>G		41.0	0.0	.		59.0	13.0	.	NM_032679	A8K0B4|A8K6Z7|C9JFB9	Silent	SNP	ENST00000301399.5	hg19	CCDS12842.2																																																																																			.	.	.	none		0.358	ZNF577-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347243.1	NM_032679	
ZNF606	80095	hgsc.bcm.edu	37	19	58489700	58489700	+	Missense_Mutation	SNP	T	T	C			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr19:58489700T>C	ENST00000341164.4	-	7	2968	c.2348A>G	c.(2347-2349)cAg>cGg	p.Q783R	ZNF606_ENST00000536132.1_Missense_Mutation_p.Q693R	NM_025027.3	NP_079303.2	Q8WXB4	ZN606_HUMAN	zinc finger protein 606	783					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Colorectal(82;5.46e-05)|all_neural(62;0.0182)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0168)		GTGATTTCTCTGGTGTTGAAG	0.368																																					p.Q783R		Atlas-SNP	.											.	ZNF606	155	.	0			c.A2348G						PASS	.						91.0	84.0	86.0					19																	58489700		2203	4300	6503	SO:0001583	missense	80095	exon7			TTTCTCTGGTGTT	AB058755	CCDS12968.1	19q13.43	2013-01-08			ENSG00000166704	ENSG00000166704		"""Zinc fingers, C2H2-type"", ""-"""	25879	protein-coding gene	gene with protein product		613905		ZNF328		11347906	Standard	XM_005259276		Approved	FLJ14260, KIAA1852	uc002qqw.3	Q8WXB4	OTTHUMG00000169804	ENST00000341164.4:c.2348A>G	chr19.hg19:g.58489700T>C	ENSP00000343617:p.Gln783Arg	134.0	0.0	.		152.0	39.0	.	NM_025027	A8KAN2|Q8NE04|Q96JH5	Missense_Mutation	SNP	ENST00000341164.4	hg19	CCDS12968.1	.	.	.	.	.	.	.	.	.	.	T	9.820	1.185460	0.21870	.	.	ENSG00000166704	ENST00000341164;ENST00000536132	T;T	0.25749	1.78;1.78	4.77	2.52	0.30459	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.40302	N	0.001121	T	0.18882	0.0453	L	0.39147	1.195	0.23988	N	0.996254	B	0.11235	0.004	B	0.10450	0.005	T	0.16217	-1.0410	10	0.49607	T	0.09	.	7.2862	0.26340	0.0:0.0828:0.145:0.7722	.	783	Q8WXB4	ZN606_HUMAN	R	783;693	ENSP00000343617:Q783R;ENSP00000445624:Q693R	ENSP00000343617:Q783R	Q	-	2	0	ZNF606	63181512	0.000000	0.05858	1.000000	0.80357	0.997000	0.91878	0.272000	0.18644	0.941000	0.37499	0.528000	0.53228	CAG	.	.	.	none		0.368	ZNF606-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405961.1	NM_025027	
BPIFB6	128859	hgsc.bcm.edu	37	20	31627181	31627181	+	Missense_Mutation	SNP	C	C	A	rs370022331		TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr20:31627181C>A	ENST00000349552.1	+	10	929	c.929C>A	c.(928-930)cCc>cAc	p.P310H		NM_174897.2	NP_777557.1	Q8NFQ5	BPIB6_HUMAN	BPI fold containing family B, member 6	310						extracellular region (GO:0005576)	lipid binding (GO:0008289)										AAGTCAAAGCCCTTGACGACC	0.522																																					p.P310H		Atlas-SNP	.											.	.	.	.	0			c.C929A						PASS	.						102.0	107.0	105.0					20																	31627181		2203	4300	6503	SO:0001583	missense	128859	exon10			CAAAGCCCTTGAC	AF465767	CCDS13211.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000167104	ENSG00000167104		"""BPI fold containing"""	16504	protein-coding gene	gene with protein product		614110	"""bactericidal/permeability-increasing protein-like 3"""	BPIL3		12185532, 21787333	Standard	NM_174897		Approved	LPLUNC6	uc010zuc.2	Q8NFQ5	OTTHUMG00000032238	ENST00000349552.1:c.929C>A	chr20.hg19:g.31627181C>A	ENSP00000344929:p.Pro310His	112.0	0.0	.		88.0	33.0	.	NM_174897		Missense_Mutation	SNP	ENST00000349552.1	hg19	CCDS13211.1	.	.	.	.	.	.	.	.	.	.	C	11.65	1.703220	0.30232	.	.	ENSG00000167104	ENST00000349552	T	0.08896	3.04	4.44	3.47	0.39725	.	0.000000	0.56097	D	0.000035	T	0.25606	0.0623	M	0.81497	2.545	0.29520	N	0.853577	D	0.71674	0.998	D	0.66716	0.946	T	0.05354	-1.0890	10	0.46703	T	0.11	.	10.1046	0.42526	0.0:0.7964:0.2036:0.0	.	310	Q8NFQ5	BPIB6_HUMAN	H	310	ENSP00000344929:P310H	ENSP00000344929:P310H	P	+	2	0	BPIFB6	31090842	1.000000	0.71417	0.986000	0.45419	0.039000	0.13416	1.937000	0.40193	1.047000	0.40274	0.561000	0.74099	CCC	.	.	.	alt		0.522	BPIFB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078658.2	NM_174897	
TTPAL	79183	hgsc.bcm.edu	37	20	43108944	43108944	+	Missense_Mutation	SNP	A	A	G			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr20:43108944A>G	ENST00000372904.3	+	3	448	c.305A>G	c.(304-306)tAc>tGc	p.Y102C	TTPAL_ENST00000372906.2_Missense_Mutation_p.Y102C|TTPAL_ENST00000262605.4_Missense_Mutation_p.Y102C	NM_024331.4	NP_077307.2	Q9BTX7	TTPAL_HUMAN	tocopherol (alpha) transfer protein-like	102						intracellular (GO:0005622)|membrane (GO:0016020)	transporter activity (GO:0005215)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(2)|ovary(2)|skin(5)	18						CTCGTCAACTACCACAGCTGT	0.567																																					p.Y102C		Atlas-SNP	.											.	TTPAL	31	.	0			c.A305G						PASS	.						51.0	44.0	46.0					20																	43108944		2203	4300	6503	SO:0001583	missense	79183	exon2			TCAACTACCACAG	BC003071	CCDS13332.2	20q13.12	2008-06-23	2008-06-23	2008-06-23	ENSG00000124120	ENSG00000124120			16114	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 121"""	C20orf121			Standard	NM_024331		Approved	dJ179M20.3	uc002xmd.2	Q9BTX7	OTTHUMG00000032536	ENST00000372904.3:c.305A>G	chr20.hg19:g.43108944A>G	ENSP00000361995:p.Tyr102Cys	167.0	0.0	.		153.0	49.0	.	NM_001039199	E1P5X3|Q5QPC1|Q9H1G2|Q9NQG8	Missense_Mutation	SNP	ENST00000372904.3	hg19	CCDS13332.2	.	.	.	.	.	.	.	.	.	.	A	22.6	4.306489	0.81247	.	.	ENSG00000124120	ENST00000262605;ENST00000372904;ENST00000372906;ENST00000456317	D;D;D;D	0.86432	-2.12;-2.12;-2.12;-2.12	5.1	5.1	0.69264	Phosphatidylinositol transfer protein-like, N-terminal (1);Cellular retinaldehyde-binding/triple function, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.92886	0.7737	M	0.76328	2.33	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.93787	0.7089	10	0.87932	D	0	-22.794	14.903	0.70696	1.0:0.0:0.0:0.0	.	102	Q9BTX7	TTPAL_HUMAN	C	102	ENSP00000262605:Y102C;ENSP00000361995:Y102C;ENSP00000361997:Y102C;ENSP00000412720:Y102C	ENSP00000262605:Y102C	Y	+	2	0	TTPAL	42542358	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.317000	0.96327	1.909000	0.55274	0.533000	0.62120	TAC	.	.	.	none		0.567	TTPAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106886.2	NM_024331	
ADA	100	hgsc.bcm.edu	37	20	43251682	43251682	+	Missense_Mutation	SNP	G	G	A			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr20:43251682G>A	ENST00000372874.4	-	7	778	c.644C>T	c.(643-645)gCc>gTc	p.A215V	ADA_ENST00000537820.1_Intron|PKIG_ENST00000372882.3_Intron|PKIG_ENST00000372887.1_Intron|ADA_ENST00000464097.1_5'UTR	NM_000022.2	NP_000013.2	P00813	ADA_HUMAN	adenosine deaminase	215			A -> T (in ADASCID; dbSNP:rs114025668). {ECO:0000269|PubMed:2166947}.		adenosine catabolic process (GO:0006154)|aging (GO:0007568)|cell adhesion (GO:0007155)|dATP catabolic process (GO:0046061)|deoxyadenosine catabolic process (GO:0006157)|embryonic digestive tract development (GO:0048566)|germinal center B cell differentiation (GO:0002314)|histamine secretion (GO:0001821)|hypoxanthine salvage (GO:0043103)|inosine biosynthetic process (GO:0046103)|liver development (GO:0001889)|lung alveolus development (GO:0048286)|negative regulation of adenosine receptor signaling pathway (GO:0060169)|negative regulation of circadian sleep/wake cycle, non-REM sleep (GO:0042323)|negative regulation of inflammatory response (GO:0050728)|negative regulation of leukocyte migration (GO:0002686)|negative regulation of mature B cell apoptotic process (GO:0002906)|negative regulation of mucus secretion (GO:0070256)|negative regulation of penile erection (GO:0060407)|negative regulation of thymocyte apoptotic process (GO:0070244)|nucleobase-containing small molecule metabolic process (GO:0055086)|Peyer's patch development (GO:0048541)|placenta development (GO:0001890)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of germinal center formation (GO:0002636)|positive regulation of heart rate (GO:0010460)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of T cell differentiation in thymus (GO:0033089)|positive regulation of T cell receptor signaling pathway (GO:0050862)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide salvage (GO:0032261)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|purine-containing compound salvage (GO:0043101)|regulation of cell-cell adhesion mediated by integrin (GO:0033632)|response to drug (GO:0042493)|response to hydrogen peroxide (GO:0042542)|response to hypoxia (GO:0001666)|response to morphine (GO:0043278)|response to vitamin E (GO:0033197)|small molecule metabolic process (GO:0044281)|T cell activation (GO:0042110)|trophectodermal cell differentiation (GO:0001829)|xanthine biosynthetic process (GO:0046111)	cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite cytoplasm (GO:0032839)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|lysosome (GO:0005764)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	adenosine deaminase activity (GO:0004000)|purine nucleoside binding (GO:0001883)|zinc ion binding (GO:0008270)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|ovary(1)|pancreas(2)|prostate(3)|skin(2)|urinary_tract(1)	18		all_lung(126;1.24e-07)|Lung NSC(126;1.94e-07)|Myeloproliferative disorder(115;0.0122)	COAD - Colon adenocarcinoma(18;0.00189)		Adenosine(DB00640)|Dipyridamole(DB00975)|Edetic Acid(DB00974)|Nelarabine(DB01280)|Pentostatin(DB00552)|Theophylline(DB00277)|Vidarabine(DB00194)	CACCTCCCCGGCGTGGACAGT	0.657									Adenosine Deaminase Deficiency																												p.A215V		Atlas-SNP	.											.	ADA	42	.	0			c.C644T						PASS	.						67.0	68.0	68.0					20																	43251682		2203	4300	6503	SO:0001583	missense	100	exon7	Familial Cancer Database	Severe Combined Immunodeficiency (SCID) due to ADA-deficiency	TCCCCGGCGTGGA	X02994	CCDS13335.1	20q13.12	2014-09-17			ENSG00000196839	ENSG00000196839	3.5.4.4		186	protein-coding gene	gene with protein product		608958				6198240, 6090454	Standard	NM_000022		Approved		uc002xmj.3	P00813	OTTHUMG00000033081	ENST00000372874.4:c.644C>T	chr20.hg19:g.43251682G>A	ENSP00000361965:p.Ala215Val	112.0	0.0	.		98.0	20.0	.	NM_000022	Q53F92|Q6LA59	Missense_Mutation	SNP	ENST00000372874.4	hg19	CCDS13335.1	.	.	.	.	.	.	.	.	.	.	G	17.39	3.377508	0.61735	.	.	ENSG00000196839	ENST00000372874	D	0.97114	-4.25	4.89	3.9	0.45041	Adenosine/AMP deaminase (1);	0.048514	0.85682	D	0.000000	D	0.98466	0.9489	M	0.91196	3.185	0.80722	D	1	D	0.89917	1.0	D	0.63113	0.911	D	0.98951	1.0794	10	0.87932	D	0	-9.5965	15.4157	0.74966	0.0:0.1385:0.8615:0.0	.	215	P00813	ADA_HUMAN	V	215	ENSP00000361965:A215V	ENSP00000361965:A215V	A	-	2	0	ADA	42685096	1.000000	0.71417	0.136000	0.22124	0.136000	0.21042	6.472000	0.73567	2.549000	0.85964	0.563000	0.77884	GCC	.	.	.	none		0.657	ADA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080509.2	NM_000022	
HELZ2	85441	hgsc.bcm.edu	37	20	62201870	62201870	+	Missense_Mutation	SNP	G	G	A			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr20:62201870G>A	ENST00000467148.1	-	3	626	c.557C>T	c.(556-558)gCc>gTc	p.A186V	HELZ2_ENST00000427522.2_5'Flank|HELZ2_ENST00000479540.1_5'UTR	NM_001037335.2	NP_001032412.2	Q9BYK8	HELZ2_HUMAN	helicase with zinc finger 2, transcriptional coactivator	186					cellular lipid metabolic process (GO:0044255)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)										AGAGTGGACGGCAAACGTCCA	0.627																																					p.A186V		Atlas-SNP	.											.	.	.	.	0			c.C557T						PASS	.						82.0	71.0	75.0					20																	62201870		2202	4300	6502	SO:0001583	missense	85441	exon4			TGGACGGCAAACG	AB201715	CCDS13527.1, CCDS33508.1	20q13.33	2012-09-26			ENSG00000130589	ENSG00000130589			30021	protein-coding gene	gene with protein product	"""peroxisomal proliferator activated receptor A interacting complex 285"", ""PPARG-DBD-interacting protein 1"""	611265				11214970, 12189208, 16239304	Standard	NM_001037335		Approved	PDIP1, PRIC285, KIAA1769	uc002yfm.2	Q9BYK8	OTTHUMG00000032969	ENST00000467148.1:c.557C>T	chr20.hg19:g.62201870G>A	ENSP00000417401:p.Ala186Val	93.0	0.0	.		81.0	4.0	.	NM_001037335	Q3C2G2|Q4VXQ1|Q8TEF3|Q96ND3|Q9C094	Missense_Mutation	SNP	ENST00000467148.1	hg19	CCDS33508.1	.	.	.	.	.	.	.	.	.	.	G	11.29	1.596213	0.28445	.	.	ENSG00000130589	ENST00000467148	T	0.02421	4.3	4.28	-7.27	0.01461	.	2.233770	0.02265	N	0.067890	T	0.01835	0.0058	N	0.19112	0.55	0.09310	N	1	B;B	0.18310	0.027;0.0	B;B	0.15052	0.012;0.0	T	0.43956	-0.9359	10	0.56958	D	0.05	-1.1836	0.4194	0.00453	0.206:0.2023:0.2358:0.3559	.	186;186	Q4VXQ0;Q9BYK8	.;PR285_HUMAN	V	186	ENSP00000417401:A186V	ENSP00000417401:A186V	A	-	2	0	RP4-697K14.7	61672314	0.000000	0.05858	0.000000	0.03702	0.041000	0.13682	-2.542000	0.00935	-1.101000	0.03027	0.558000	0.71614	GCC	.	.	.	none		0.627	HELZ2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354127.1	NM_001037335	
KCNE2	9992	hgsc.bcm.edu	37	21	35743124	35743124	+	Missense_Mutation	SNP	C	C	T	rs199473367		TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr21:35743124C>T	ENST00000290310.3	+	2	487	c.347C>T	c.(346-348)gCg>gTg	p.A116V	AP000320.6_ENST00000440403.1_RNA	NM_172201.1	NP_751951.1	Q9Y6J6	KCNE2_HUMAN	potassium voltage-gated channel, Isk-related family, member 2	116					aging (GO:0007568)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cellular protein localization (GO:0034613)|cellular response to drug (GO:0035690)|membrane repolarization (GO:0086009)|membrane repolarization during action potential (GO:0086011)|positive regulation of proteasomal protein catabolic process (GO:1901800)|potassium ion export (GO:0071435)|potassium ion import (GO:0010107)|potassium ion transmembrane transport (GO:0071805)|regulation of cyclic nucleotide-gated ion channel activity (GO:1902159)|regulation of delayed rectifier potassium channel activity (GO:1902259)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of inward rectifier potassium channel activity (GO:1901979)|regulation of membrane repolarization (GO:0060306)|regulation of potassium ion transmembrane transport (GO:1901379)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|tongue development (GO:0043586)|ventricular cardiac muscle cell action potential (GO:0086005)	cell surface (GO:0009986)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|inward rectifier potassium channel activity (GO:0005242)|ion channel binding (GO:0044325)|potassium channel regulator activity (GO:0015459)|voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization (GO:1902282)			endometrium(1)|large_intestine(1)	2						AACATTGGTGCGGCTGGGTTC	0.488																																					p.A116V		Atlas-SNP	.											KCNE2,colon,carcinoma,0,1	KCNE2	13	.	0			c.C347T	GRCh37	CM003450	KCNE2	M		PASS	.						44.0	40.0	42.0					21																	35743124		2203	4300	6503	SO:0001583	missense	9992	exon2			TTGGTGCGGCTGG	AF071002	CCDS13635.1	21q22.1	2014-09-17			ENSG00000159197	ENSG00000159197		"""Potassium channels"""	6242	protein-coding gene	gene with protein product		603796				10219239	Standard	NM_172201		Approved	MiRP1, LQT6	uc002ytt.1	Q9Y6J6	OTTHUMG00000086189	ENST00000290310.3:c.347C>T	chr21.hg19:g.35743124C>T	ENSP00000290310:p.Ala116Val	97.0	0.0	.		99.0	26.0	.	NM_172201	A5H1P3|D3DSF8|Q52LJ5	Missense_Mutation	SNP	ENST00000290310.3	hg19	CCDS13635.1	.	.	.	.	.	.	.	.	.	.	C	19.32	3.805758	0.70682	.	.	ENSG00000159197	ENST00000290310	D	0.93307	-3.2	5.66	5.66	0.87406	.	0.000000	0.64402	D	0.000007	D	0.94686	0.8286	L	0.32530	0.975	0.42882	D	0.994175	D	0.89917	1.0	D	0.78314	0.991	D	0.95265	0.8372	10	0.66056	D	0.02	-27.5208	17.5309	0.87814	0.0:1.0:0.0:0.0	.	116	Q9Y6J6	KCNE2_HUMAN	V	116	ENSP00000290310:A116V	ENSP00000290310:A116V	A	+	2	0	KCNE2	34664994	0.991000	0.36638	0.150000	0.22450	0.102000	0.19082	3.221000	0.51215	2.657000	0.90304	0.655000	0.94253	GCG	.	.	.	weak		0.488	KCNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194068.2		
USP9X	8239	hgsc.bcm.edu	37	X	41043810	41043810	+	Missense_Mutation	SNP	C	C	T			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chrX:41043810C>T	ENST00000324545.8	+	23	4073	c.3440C>T	c.(3439-3441)gCc>gTc	p.A1147V	USP9X_ENST00000378308.2_Missense_Mutation_p.A1147V	NM_001039590.2|NM_001039591.2	NP_001034679.2|NP_001034680.2	Q93008	USP9X_HUMAN	ubiquitin specific peptidase 9, X-linked	1147					axon extension (GO:0048675)|BMP signaling pathway (GO:0030509)|cerebellar cortex structural organization (GO:0021698)|chromosome segregation (GO:0007059)|female gamete generation (GO:0007292)|gene expression (GO:0010467)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|post-embryonic development (GO:0009791)|protein deubiquitination (GO:0016579)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent protein catabolic process (GO:0006511)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)|membrane (GO:0016020)	co-SMAD binding (GO:0070410)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|ubiquitin thiolesterase activity (GO:0004221)			NS(3)|breast(6)|central_nervous_system(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(16)|lung(29)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	87						CGAAGGGGTGCCTACCTCAAT	0.463																																					p.A1147V	Ovarian(172;1807 2695 35459 49286)	Atlas-SNP	.											.	USP9X	385	.	0			c.C3440T						PASS	.						107.0	99.0	101.0					X																	41043810		2177	4280	6457	SO:0001583	missense	8239	exon23			GGGGTGCCTACCT	X98296	CCDS43930.1, CCDS55403.1	Xp11.4	2010-08-03	2006-02-14		ENSG00000124486	ENSG00000124486		"""Ubiquitin-specific peptidases"""	12632	protein-coding gene	gene with protein product		300072	"""ubiquitin specific protease 9, X chromosome (fat facets-like Drosophila)"", ""ubiquitin specific protease 9, X-linked (fat facets-like, Drosophila)"", ""ubiquitin specific peptidase 9, X-linked (fat facets-like, Drosophila)"""			8922996	Standard	NM_001039590		Approved	DFFRX, FAF	uc004dfb.3	Q93008	OTTHUMG00000021367	ENST00000324545.8:c.3440C>T	chrX.hg19:g.41043810C>T	ENSP00000316357:p.Ala1147Val	154.0	0.0	.		143.0	72.0	.	NM_001039591	O75550|Q8WWT3|Q8WX12	Missense_Mutation	SNP	ENST00000324545.8	hg19	CCDS43930.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.984913	0.74474	.	.	ENSG00000124486	ENST00000378308;ENST00000324545	T;T	0.11712	2.75;2.75	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	T	0.10723	0.0262	L	0.35723	1.085	0.80722	D	1	B;B	0.16802	0.019;0.019	B;B	0.17098	0.017;0.017	T	0.15321	-1.0441	10	0.09843	T	0.71	.	18.7017	0.91623	0.0:1.0:0.0:0.0	.	1147;1147	Q93008-1;Q93008	.;USP9X_HUMAN	V	1147	ENSP00000367558:A1147V;ENSP00000316357:A1147V	ENSP00000316357:A1147V	A	+	2	0	USP9X	40928754	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.729000	0.84864	2.361000	0.80049	0.513000	0.50165	GCC	.	.	.	none		0.463	USP9X-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000056250.4	NM_004652	
UPF3B	65109	hgsc.bcm.edu	37	X	118977251	118977251	+	Silent	SNP	T	T	C			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chrX:118977251T>C	ENST00000276201.2	-	5	552	c.483A>G	c.(481-483)agA>agG	p.R161R	UPF3B_ENST00000345865.2_Silent_p.R161R|UPF3B_ENST00000478840.1_5'UTR	NM_080632.2	NP_542199.1	Q9BZI7	REN3B_HUMAN	UPF3 regulator of nonsense transcripts homolog B (yeast)	161	Necessary for interaction with UPF2.|Sufficient for association with EJC core.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|mRNA splicing, via spliceosome (GO:0000398)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|positive regulation of translation (GO:0045727)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|exon-exon junction complex (GO:0035145)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleocytoplasmic transporter activity (GO:0005487)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(4)|kidney(1)|large_intestine(7)|lung(12)|ovary(2)|prostate(1)	30						CCAAAAACTTTCTATATTCTG	0.279																																					p.R161R		Atlas-SNP	.											.	UPF3B	74	.	0			c.A483G						PASS	.						161.0	144.0	150.0					X																	118977251		2202	4300	6502	SO:0001819	synonymous_variant	65109	exon5			AAACTTTCTATAT	AF318576	CCDS14587.1, CCDS14588.1	Xq25-q26	2014-01-31			ENSG00000125351	ENSG00000125351			20439	protein-coding gene	gene with protein product		300298	"""mental retardation, X-linked 62"""	MRX62		11113196, 11163187, 19238151	Standard	NM_023010		Approved	RENT3B, UPF3X, HUPF3B	uc004erz.2	Q9BZI7	OTTHUMG00000022282	ENST00000276201.2:c.483A>G	chrX.hg19:g.118977251T>C		23.0	0.0	.		31.0	17.0	.	NM_023010	D3DWI3|D3DWI4|Q0VAK8|Q9H1J0	Silent	SNP	ENST00000276201.2	hg19	CCDS14588.1																																																																																			.	.	.	none		0.279	UPF3B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058068.1		
NDC80	10403	hgsc.bcm.edu	37	18	2610806	2610806	+	Frame_Shift_Del	DEL	A	A	-			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr18:2610806delA	ENST00000261597.4	+	16	1919	c.1737delA	c.(1735-1737)ggafs	p.G579fs		NM_006101.2	NP_006092.1	O14777	NDC80_HUMAN	NDC80 kinetochore complex component	579	Interaction with NEK2 and ZWINT.|Interaction with the C-terminus of CDCA1 and the SPBC24-SPBC25 subcomplex.				attachment of spindle microtubules to kinetochore (GO:0008608)|chromosome segregation (GO:0007059)|establishment of mitotic spindle orientation (GO:0000132)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid segregation (GO:0000070)|mitotic spindle organization (GO:0007052)	chromosome, centromeric region (GO:0000775)|condensed chromosome kinetochore (GO:0000777)|condensed nuclear chromosome outer kinetochore (GO:0000942)|cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|Ndc80 complex (GO:0031262)|nucleus (GO:0005634)				NS(1)|biliary_tract(2)|breast(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(6)|ovary(2)|prostate(2)|urinary_tract(2)	22						GAAAAGTGGGAAATAACTTGC	0.368																																					p.G579fs		Atlas-Indel,Pindel	.											.	NDC80	62	.	0			c.1736delG						PASS	.						194.0	172.0	180.0					18																	2610806		2203	4300	6503	SO:0001589	frameshift_variant	10403	exon16			.	AF017790	CCDS11827.1	18p11.31	2013-01-17	2013-01-17	2007-03-02	ENSG00000080986	ENSG00000080986			16909	protein-coding gene	gene with protein product		607272	"""highly expressed in cancer, rich in leucine heptad repeats (yeast)"", ""kinetochore associated 2"", ""NDC80 kinetochore complex component homolog (S. cerevisiae)"""	KNTC2		9315664, 12351790	Standard	NM_006101		Approved	HEC, HEC1, hsNDC80, TID3	uc002kli.3	O14777	OTTHUMG00000131483	ENST00000261597.4:c.1737delA	chr18.hg19:g.2610806delA	ENSP00000261597:p.Gly579fs	151.0	0.0	0		157.0	36.0	0.229299	NM_006101	Q6PJX2	Frame_Shift_Del	DEL	ENST00000261597.4	hg19	CCDS11827.1																																																																																			.	.	.	none		0.368	NDC80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254327.1	NM_006101	
LSM1	27257	hgsc.bcm.edu	37	8	38027436	38027436	+	Splice_Site	DEL	C	C	-			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr8:38027436delC	ENST00000311351.4	-	3	511		c.e3-1		LSM1_ENST00000522515.1_Splice_Site|LSM1_ENST00000520755.1_Intron	NM_014462.2	NP_055277.1	O15116	LSM1_HUMAN	LSM1, U6 small nuclear RNA associated						exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|histone mRNA catabolic process (GO:0071044)|mRNA metabolic process (GO:0016071)|mRNA processing (GO:0006397)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)			kidney(2)|large_intestine(3)|lung(2)	7	Colorectal(12;0.000442)					ACTAAGTTTGCTGTAAGTGTA	0.363																																					p.A39fs		Atlas-Indel,Pindel	.											.	LSM1	14	.	0			c.116delC						PASS	.						127.0	118.0	121.0					8																	38027436		2203	4300	6503	SO:0001630	splice_region_variant	27257	exon3			.	AF000177	CCDS6103.1	8p11.2	2014-02-14	2014-02-14		ENSG00000175324	ENSG00000175324			20472	protein-coding gene	gene with protein product		607281	"""LSM1 homolog, U6 small nuclear RNA associated (S. cerevisiae)"""			12515382, 11953827	Standard	NM_014462		Approved	CASM, YJL124C	uc003xkw.3	O15116	OTTHUMG00000164051	ENST00000311351.4:c.116-1G>-	chr8.hg19:g.38027436delC		122.0	0.0	0		129.0	33.0	0.255814	NM_014462	B2R5E6	Frame_Shift_Del	DEL	ENST00000311351.4	hg19	CCDS6103.1																																																																																			.	.	.	none		0.363	LSM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376965.1	NM_014462	Intron
RBM28	55131	hgsc.bcm.edu	37	7	127958110	127958111	+	In_Frame_Ins	INS	-	-	GAC			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr7:127958110_127958111insGAC	ENST00000223073.2	-	15	1726_1727	c.1612_1613insGTC	c.(1612-1614)cag>cGTCag	p.537_538insR	RBM28_ENST00000481788.1_Intron|RBM28_ENST00000415472.2_In_Frame_Ins_p.396_397insR	NM_018077.2	NP_060547.2	Q9NW13	RBM28_HUMAN	RNA binding motif protein 28	537	RRM 4. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleolus (GO:0005730)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|kidney(7)|large_intestine(3)|lung(8)|ovary(2)	21						GCCCAGGGACTGACCCTTCATG	0.485																																					p.Q538delinsRQ		Atlas-Indel,Pindel	.											.	RBM28	71	.	0			c.1613_1614insGTC						PASS	.																																			SO:0001652	inframe_insertion	55131	exon15			.	AK001239	CCDS5801.1, CCDS55159.1	7q32.2	2013-02-12			ENSG00000106344	ENSG00000106344		"""RNA binding motif (RRM) containing"""	21863	protein-coding gene	gene with protein product		612074					Standard	NM_018077		Approved	FLJ10377	uc003vmp.2	Q9NW13	OTTHUMG00000157711	ENST00000223073.2:c.1610_1612dupGTC	chr7.hg19:g.127958111_127958113dupGAC	ENSP00000223073:p.Gly537_Gln538insArg	101.0	0.0	0		88.0	19.0	0.215909	NM_018077	A4D100|B4DU52|E9PDD9|Q53H65|Q96CV3	In_Frame_Ins	INS	ENST00000223073.2	hg19	CCDS5801.1																																																																																			.	.	.	none		0.485	RBM28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349442.2	NM_018077	
KCNJ15	3772	hgsc.bcm.edu	37	21	39671646	39671649	+	Frame_Shift_Del	DEL	TTGA	TTGA	-			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	TTGA	TTGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr21:39671646_39671649delTTGA	ENST00000328656.4	+	4	766_769	c.463_466delTTGA	c.(463-468)ttgattfs	p.LI155fs	KCNJ15_ENST00000398938.2_Frame_Shift_Del_p.LI155fs|KCNJ15_ENST00000398932.1_Frame_Shift_Del_p.LI155fs|KCNJ15_ENST00000398934.1_Frame_Shift_Del_p.LI155fs|KCNJ15_ENST00000398930.1_Frame_Shift_Del_p.LI155fs	NM_001276437.1|NM_001276438.1|NM_001276439.1|NM_002243.3	NP_001263366.1|NP_001263367.1|NP_001263368.1|NP_002234.2	Q99712	KCJ15_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 15	155					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(2)|skin(3)|urinary_tract(1)	24					Yohimbine(DB01392)	CATCACGACCTTGATTGAGATCTT	0.515																																					p.154_155del		Atlas-Indel,Pindel	.											.	KCNJ15	43	.	0			c.462_465del						PASS	.																																			SO:0001589	frameshift_variant	3772	exon3			.	Y10745	CCDS13656.1	21q22.2	2011-07-05			ENSG00000157551	ENSG00000157551		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Inwardly rectifying"""	6261	protein-coding gene	gene with protein product		602106				9299242, 8995301, 16382105	Standard	NM_170736		Approved	Kir4.2, Kir1.3, IRKK	uc002ywx.4	Q99712	OTTHUMG00000090609	ENST00000328656.4:c.463_466delTTGA	chr21.hg19:g.39671650_39671653delTTGA	ENSP00000331698:p.Leu155fs	115.0	0.0	0		105.0	28.0	0.266667	NM_170736	D3DSH5|O00564|Q96L28|Q99446	Frame_Shift_Del	DEL	ENST00000328656.4	hg19	CCDS13656.1																																																																																			.	.	.	none		0.515	KCNJ15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207181.2	NM_002243	
GPR85	54329	hgsc.bcm.edu	37	7	112724144	112724146	+	In_Frame_Del	DEL	ATC	ATC	-			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	ATC	ATC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr7:112724144_112724146delATC	ENST00000297146.3	-	3	1234_1236	c.631_633delGAT	c.(631-633)gatdel	p.D211del	GPR85_ENST00000501255.2_In_Frame_Del_p.D211del|GPR85_ENST00000487573.1_5'Flank|GPR85_ENST00000424100.1_In_Frame_Del_p.D211del|GPR85_ENST00000449591.1_In_Frame_Del_p.D211del	NM_001146266.1	NP_001139738.1	P60893	GPR85_HUMAN	G protein-coupled receptor 85	211					signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	17						TTTTTCTTCGATCGTGGACGAAA	0.493																																					p.211_212del		Atlas-INDEL	.											GPR85,NS,carcinoma,0,1	GPR85	49	.	0			c.632_634del						PASS	.																																			SO:0001651	inframe_deletion	54329	exon3			.	AF250237	CCDS5758.1	7q31	2012-08-21			ENSG00000164604	ENSG00000164604		"""GPCR / Class A : Orphans"""	4536	protein-coding gene	gene with protein product		605188				10978537, 10833454	Standard	NM_018970		Approved	SREB2	uc003vgp.1	P60893	OTTHUMG00000156933	ENST00000297146.3:c.631_633delGAT	chr7.hg19:g.112724144_112724146delATC	ENSP00000297146:p.Asp211del	84.0	0.0	0		63.0	14.0	0.222222	NM_001146265	Q9JHI6|Q9NPD1	In_Frame_Del	DEL	ENST00000297146.3	hg19	CCDS5758.1																																																																																			.	.	.	none		0.493	GPR85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346650.2		
AK9	221264	hgsc.bcm.edu	37	6	109977966	109977966	+	Frame_Shift_Del	DEL	G	G	-			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr6:109977966delG	ENST00000424296.2	-	8	828	c.752delC	c.(751-753)actfs	p.T251fs	AK9_ENST00000368948.2_Frame_Shift_Del_p.T251fs|AK9_ENST00000341338.6_5'UTR|AK9_ENST00000285397.5_Frame_Shift_Del_p.T251fs	NM_001145128.2	NP_001138600.2	Q5TCS8	KAD9_HUMAN	adenylate kinase 9	251	Adenylate kinase 1.|Glu-rich.				ADP phosphorylation (GO:0006757)|AMP phosphorylation (GO:0006756)|CDP phosphorylation (GO:0061508)|CMP phosphorylation (GO:0061566)|dADP phosphorylation (GO:0006174)|dAMP phosphorylation (GO:0061565)|dCDP phosphorylation (GO:0061570)|dCMP phosphorylation (GO:0061567)|dGDP phosphorylation (GO:0006186)|GDP phosphorylation (GO:0061568)|TDP phosphorylation (GO:0061571)|UDP phosphorylation (GO:0061569)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|nucleoside diphosphate kinase activity (GO:0004550)|nucleoside phosphate kinase activity (GO:0050145)										TACTTCTAAAGTTTGGAGAAT	0.318																																					p.T251fs		Atlas-Indel,Pindel	.											.	AKD1	223	.	0			c.753delT						PASS	.						57.0	58.0	58.0					6																	109977966		2203	4294	6497	SO:0001589	frameshift_variant	221264	exon8			.	AK131244, BC146443, BC087860	CCDS5077.1, CCDS55048.1	6q21	2013-04-29	2013-04-29	2013-04-29			2.7.4.3		33814	protein-coding gene	gene with protein product		615358	"""chromosome 6 open reading frame 224"", ""adenylate kinase domain containing 2"", ""chromosome 6 open reading frame 199"", ""adenylate kinase domain containing 1"""	C6orf224, AKD2, C6orf199, AKD1		23416111	Standard	NM_145025		Approved	FLJ42177, FLJ25791, dJ70A9.1, MGC26954		Q5TCS8		ENST00000424296.2:c.752delC	chr6.hg19:g.109977966delG	ENSP00000410186:p.Thr251fs	96.0	0.0	0		103.0	32.0	0.31068	NM_001145128	A6NL75|B2RDJ0|B6ZDM7|Q3MIS4|Q5I0W8|Q6ZNF1|Q6ZVR7|Q8N7C6|Q8WW00|Q96NF4	Frame_Shift_Del	DEL	ENST00000424296.2	hg19	CCDS55048.1																																																																																			.	.	.	none		0.318	AK9-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001145128	
C19orf40	91442	hgsc.bcm.edu	37	19	33464971	33464972	+	Frame_Shift_Ins	INS	-	-	A			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr19:33464971_33464972insA	ENST00000588258.1	+	4	359_360	c.249_250insA	c.(250-252)aatfs	p.N84fs	CEP89_ENST00000590597.2_5'Flank|CEP89_ENST00000591863.1_5'Flank|CEP89_ENST00000305768.5_5'Flank|C19orf40_ENST00000589646.1_5'UTR|C19orf40_ENST00000590281.1_Frame_Shift_Ins_p.N84fs|C19orf40_ENST00000590179.1_5'UTR	NM_152266.3	NP_689479.1	Q9BTP7	FAP24_HUMAN	chromosome 19 open reading frame 40	84					DNA repair (GO:0006281)	Fanconi anaemia nuclear complex (GO:0043240)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			endometrium(1)|large_intestine(2)|lung(2)|prostate(2)	7	Esophageal squamous(110;0.137)					TCAAGTCCAATAATCTTAAAGG	0.406								Direct reversal of damage																													p.N83fs		Atlas-Indel,Pindel	.											.	C19orf40	21	.	0			c.249_250insA						PASS	.																																			SO:0001589	frameshift_variant	91442	exon4			.	AK128668	CCDS12426.1, CCDS74327.1	19q13.11	2011-11-24			ENSG00000131944	ENSG00000131944			28467	protein-coding gene	gene with protein product	"""Fanconi anemia-associated protein, 24kDa"""	610884				17289582	Standard	XM_005259393		Approved	FLJ46828, MGC32020, FAAP24	uc002nud.4	Q9BTP7		ENST00000588258.1:c.251dupA	chr19.hg19:g.33464973_33464973dupA	ENSP00000466121:p.Asn84fs	145.0	0.0	0		170.0	43.0	0.252941	NM_152266	B3KY46|Q8WUJ7|Q96FX6	Frame_Shift_Ins	INS	ENST00000588258.1	hg19	CCDS12426.1																																																																																			.	.	.	none		0.406	C19orf40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450823.2	NM_152266	
SPTA1	6708	hgsc.bcm.edu	37	1	158639217	158639217	+	Frame_Shift_Del	DEL	G	G	-			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr1:158639217delG	ENST00000368147.4	-	14	1994	c.1814delC	c.(1813-1815)gcafs	p.A605fs		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	605					actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					TTCATCATCTGCCAACTTTTT	0.408																																					p.A605fs		Atlas-Indel,Pindel	.											.	SPTA1	720	.	0			c.1815delA						PASS	.						285.0	268.0	273.0					1																	158639217		1915	4136	6051	SO:0001589	frameshift_variant	6708	exon14			.	M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"""EF-hand domain containing"""	11272	protein-coding gene	gene with protein product	"""elliptocytosis 2"""	182860	"""spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"""				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.1814delC	chr1.hg19:g.158639217delG	ENSP00000357129:p.Ala605fs	65.0	0.0	0		73.0	19.0	0.260274	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Frame_Shift_Del	DEL	ENST00000368147.4	hg19	CCDS41423.1																																																																																			.	.	.	none		0.408	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126	
DOK7	285489	hgsc.bcm.edu	37	4	3478120	3478121	+	Frame_Shift_Ins	INS	-	-	GGCTA	rs376659660|rs539942267		TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr4:3478120_3478121insGGCTA	ENST00000340083.5	+	4	448_449	c.383_384insGGCTA	c.(382-387)ccggctfs	p.-129fs	DOK7_ENST00000507039.1_Frame_Shift_Ins_p.-129fs|DOK7_ENST00000389653.2_Frame_Shift_Ins_p.-129fs	NM_173660.4	NP_775931.3	Q18PE1	DOK7_HUMAN	docking protein 7						neuromuscular junction development (GO:0007528)|positive regulation of protein tyrosine kinase activity (GO:0061098)|receptor clustering (GO:0043113)	cell junction (GO:0030054)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)	phosphatidylinositol binding (GO:0035091)|protein kinase binding (GO:0019901)			kidney(1)|large_intestine(1)|skin(2)|upper_aerodigestive_tract(1)	5				UCEC - Uterine corpus endometrioid carcinoma (64;0.163)		GAGAGCGGCCCGGCTACCCTGC	0.668																																					p.P128fs		Atlas-Indel,Pindel	.											.	DOK7	44	.	0			c.383_384insGGCTA						PASS	.																																			SO:0001589	frameshift_variant	285489	exon4			.	AK091037	CCDS3370.2, CCDS54717.1	4p16.2	2014-09-17	2006-08-24	2006-08-24	ENSG00000175920	ENSG00000175920			26594	protein-coding gene	gene with protein product		610285	"""chromosome 4 open reading frame 25"""	C4orf25		16794080	Standard	NM_173660		Approved	FLJ33718, FLJ39137, Dok-7	uc003ghd.3	Q18PE1	OTTHUMG00000122087	ENST00000340083.5:c.384_388dupGGCTA	chr4.hg19:g.3478121_3478125dupGGCTA	ENSP00000344432:p.Ala129fs	91.0	0.0	0		86.0	21.0	0.244186	NM_001164673	A2A499|A2RRD4|E9PB56|Q6P6A6|Q86XG5|Q8N2J3|Q8NBC1	Frame_Shift_Ins	INS	ENST00000340083.5	hg19	CCDS3370.2																																																																																			.	.	.	none		0.668	DOK7-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313538.1	NM_173660	
SRD5A1	6715	hgsc.bcm.edu	37	5	6663046	6663047	+	Frame_Shift_Ins	INS	-	-	T			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr5:6663046_6663047insT	ENST00000274192.5	+	4	914_915	c.680_681insT	c.(679-684)tgttttfs	p.CF227fs	SRD5A1_ENST00000538824.1_Frame_Shift_Ins_p.CF180fs|SRD5A1_ENST00000537411.1_3'UTR	NM_001047.2	NP_001038.1	P18405	S5A1_HUMAN	steroid-5-alpha-reductase, alpha polypeptide 1 (3-oxo-5 alpha-steroid delta 4-dehydrogenase alpha 1)	227					androgen biosynthetic process (GO:0006702)|cell differentiation (GO:0030154)|sex determination (GO:0007530)|sex differentiation (GO:0007548)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	3-oxo-5-alpha-steroid 4-dehydrogenase activity (GO:0003865)|cholestenone 5-alpha-reductase activity (GO:0047751)|electron carrier activity (GO:0009055)			endometrium(3)|kidney(1)|large_intestine(1)|lung(8)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	19					Dutasteride(DB01126)|Finasteride(DB01216)|Levonorgestrel(DB00367)|Spironolactone(DB00421)	TTCACGTTTTGTTTTTTATCTG	0.396																																					p.C227fs		Atlas-Indel,Pindel	.											.	SRD5A1	31	.	0			c.680_681insT						PASS	.																																			SO:0001589	frameshift_variant	6715	exon4			.	M32313	CCDS3870.1	5p15.31	2008-02-05			ENSG00000145545	ENSG00000145545	1.3.99.5		11284	protein-coding gene	gene with protein product		184753				1686016	Standard	XR_427663		Approved		uc003jdw.3	P18405	OTTHUMG00000090456	ENST00000274192.5:c.686dupT	chr5.hg19:g.6663052_6663052dupT	ENSP00000274192:p.Cys227fs	92.0	0.0	0		91.0	23.0	0.252747	NM_001047	B2R7Q1|Q9UHY4|Q9UP36|Q9UP37	Frame_Shift_Ins	INS	ENST00000274192.5	hg19	CCDS3870.1																																																																																			.	.	.	none		0.396	SRD5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206903.1	NM_001047	
EFCAB13	124989	hgsc.bcm.edu	37	17	45468874	45468875	+	Frame_Shift_Ins	INS	-	-	G			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr17:45468874_45468875insG	ENST00000331493.2	+	15	2065_2066	c.1654_1655insG	c.(1654-1656)tgtfs	p.C552fs	EFCAB13_ENST00000517484.1_Frame_Shift_Ins_p.C456fs	NM_152347.4	NP_689560.3	Q8IY85	EFC13_HUMAN	EF-hand calcium binding domain 13	552	EF-hand 2.					cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)										TCTAAATACTTGTCTTCAAAAT	0.327																																					p.C552fs		Pindel	.											.	.	.	.	0			c.1654_1655insG						PASS	.																																			SO:0001589	frameshift_variant	124989	exon15			.	BC036407	CCDS11512.1, CCDS56034.1	17q21.32	2013-01-11	2012-07-20	2012-07-20	ENSG00000178852	ENSG00000178852		"""EF-hand domain containing"""	26864	protein-coding gene	gene with protein product			"""chromosome 17 open reading frame 57"""	C17orf57			Standard	NM_152347		Approved	FLJ40342	uc002iln.3	Q8IY85	OTTHUMG00000164767	ENST00000331493.2:c.1655dupG	chr17.hg19:g.45468875_45468875dupG	ENSP00000332111:p.Cys552fs	277.0	0.0	.		342.0	63.0	0.184	NM_152347	G3V128|Q49AG9	Frame_Shift_Ins	INS	ENST00000331493.2	hg19	CCDS11512.1																																																																																			.	.	.	none		0.327	EFCAB13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380147.4	NM_152347	
GPR174	84636	hgsc.bcm.edu	37	X	78426874	78426874	+	Frame_Shift_Del	DEL	T	T	-	rs137871290		TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chrX:78426874delT	ENST00000276077.1	+	1	406	c.370delT	c.(370-372)tttfs	p.F124fs		NM_032553.1	NP_115942.1	Q9BXC1	GP174_HUMAN	G protein-coupled receptor 174	124						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|liver(1)|lung(19)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	38						CATGTACCCCTTTCGCTTCCA	0.458										HNSCC(63;0.18)																											p.P123fs		Pindel	.											.	GPR174	79	.	0			c.369delC						PASS	.						217.0	194.0	202.0					X																	78426874		2203	4300	6503	SO:0001589	frameshift_variant	84636	exon1			.	AF345567	CCDS14443.1	Xq13.3	2012-08-21			ENSG00000147138	ENSG00000147138		"""GPCR / Class A : Orphans"""	30245	protein-coding gene	gene with protein product		300903					Standard	NM_032553		Approved	FKSG79	uc004edg.1	Q9BXC1	OTTHUMG00000021898	ENST00000276077.1:c.370delT	chrX.hg19:g.78426874delT	ENSP00000276077:p.Phe124fs	128.0	0.0	.		144.0	59.0	0.410	NM_032553	Q2M3F7	Frame_Shift_Del	DEL	ENST00000276077.1	hg19	CCDS14443.1																																																																																			.	.	.	none		0.458	GPR174-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057327.1	NM_032553	
