#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_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_ORegAnno_bin	i_TTotCov	i_TVarCov	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_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
NPHP4	261734	hgsc.bcm.edu	37	1	6046337	6046337	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:6046337G>A	ENST00000378156.4	-	2	278	c.13C>T	c.(13-15)Cac>Tac	p.H5Y	NPHP4_ENST00000478423.2_Intron	NM_015102.3	NP_055917.1	O75161	NPHP4_HUMAN	nephronophthisis 4	5					actin cytoskeleton organization (GO:0030036)|hippo signaling (GO:0035329)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|visual behavior (GO:0007632)	cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytosol (GO:0005829)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|tight junction (GO:0005923)	structural molecule activity (GO:0005198)			NS(1)|breast(2)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(15)|ovary(2)|pancreas(1)|prostate(4)	47	Ovarian(185;0.0634)	all_cancers(23;7.53e-41)|all_epithelial(116;3.96e-23)|all_lung(118;5.12e-09)|all_hematologic(16;5.45e-07)|Lung NSC(185;5.49e-07)|all_neural(13;3.21e-06)|Acute lymphoblastic leukemia(12;3.44e-05)|Breast(487;0.000601)|Renal(390;0.0007)|Colorectal(325;0.00113)|Hepatocellular(190;0.00213)|Glioma(11;0.00223)|Myeloproliferative disorder(586;0.0256)|Ovarian(437;0.04)|Lung SC(97;0.128)|Medulloblastoma(700;0.213)		Epithelial(90;1.69e-36)|GBM - Glioblastoma multiforme(13;5.07e-29)|OV - Ovarian serous cystadenocarcinoma(86;1.05e-19)|Colorectal(212;4.54e-07)|COAD - Colon adenocarcinoma(227;3.14e-05)|Kidney(185;0.00012)|BRCA - Breast invasive adenocarcinoma(365;0.00102)|KIRC - Kidney renal clear cell carcinoma(229;0.00179)|STAD - Stomach adenocarcinoma(132;0.00472)|READ - Rectum adenocarcinoma(331;0.0649)		AAGATCCTGTGCCAGTCGTTC	0.577																																					p.H5Y		Atlas-SNP	.											.	NPHP4	119	.	0			c.C13T						.						53.0	57.0	56.0					1																	6046337		2015	4169	6184	SO:0001583	missense	261734	exon2			TCCTGTGCCAGTC	AB014573	CCDS44052.1	1p36	2010-03-26			ENSG00000131697	ENSG00000131697			19104	protein-coding gene	gene with protein product	"""nephroretinin"", ""nephrocystin-4"", ""POC10 centriolar protein homolog (Chlamydomonas)"""	607215				11920287, 12205563	Standard	XR_244787		Approved	SLSN4, KIAA0673, POC10	uc001alq.2	O75161	OTTHUMG00000000701	ENST00000378156.4:c.13C>T	chr1.hg19:g.6046337G>A	ENSP00000367398:p.His5Tyr	115.0	0.0		110.0	5.0	NM_015102	Q8IWC0	Missense_Mutation	SNP	ENST00000378156.4	hg19	CCDS44052.1	.	.	.	.	.	.	.	.	.	.	G	10.65	1.409964	0.25465	.	.	ENSG00000131697	ENST00000378156	D	0.86627	-2.15	5.41	4.47	0.54385	.	0.608208	0.16633	N	0.205999	T	0.77850	0.4192	L	0.44542	1.39	0.28107	N	0.931154	P	0.37864	0.61	B	0.35353	0.201	T	0.67879	-0.5556	10	0.02654	T	1	.	9.2336	0.37453	0.0:0.1593:0.6756:0.165	.	5	O75161	NPHP4_HUMAN	Y	5	ENSP00000367398:H5Y	ENSP00000367398:H5Y	H	-	1	0	NPHP4	5968924	1.000000	0.71417	0.936000	0.37596	0.119000	0.20118	2.207000	0.42788	1.367000	0.46095	0.655000	0.94253	CAC	.	.		0.577	NPHP4-001	KNOWN	non_canonical_polymorphism|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001715.2		
SPEN	23013	hgsc.bcm.edu	37	1	16260282	16260282	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:16260282C>T	ENST00000375759.3	+	11	7751	c.7547C>T	c.(7546-7548)cCa>cTa	p.P2516L		NM_015001.2	NP_055816.2	Q96T58	MINT_HUMAN	spen family transcriptional repressor	2516	Pro-rich.|RID.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|positive regulation of neurogenesis (GO:0050769)|positive regulation of transcription, DNA-templated (GO:0045893)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|transcription corepressor activity (GO:0003714)	p.P2516L(1)		NS(1)|breast(13)|central_nervous_system(3)|cervix(5)|endometrium(16)|kidney(18)|large_intestine(27)|liver(2)|lung(37)|ovary(7)|prostate(7)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	149		Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681)		ACTCCATCTCCAGCTCTTCCC	0.582																																					p.P2516L		Atlas-SNP	.											SPEN,NS,carcinoma,0,1	SPEN	374	.	1	Substitution - Missense(1)	lung(1)	c.C7547T						.						137.0	142.0	140.0					1																	16260282		2203	4300	6503	SO:0001583	missense	23013	exon11			CATCTCCAGCTCT		CCDS164.1	1p36	2013-10-17	2013-10-17		ENSG00000065526	ENSG00000065526		"""RNA binding motif (RRM) containing"""	17575	protein-coding gene	gene with protein product		613484	"""SPEN homolog, transcriptional regulator (Drosophila)"", ""spen homolog, transcriptional regulator (Drosophila)"""			10451362, 11331609	Standard	NM_015001		Approved	KIAA0929, MINT, SHARP, RBM15C	uc001axk.1	Q96T58	OTTHUMG00000009376	ENST00000375759.3:c.7547C>T	chr1.hg19:g.16260282C>T	ENSP00000364912:p.Pro2516Leu	34.0	0.0		35.0	2.0	NM_015001	Q9H9A8|Q9NWH5|Q9UQ01|Q9Y556	Missense_Mutation	SNP	ENST00000375759.3	hg19	CCDS164.1	.	.	.	.	.	.	.	.	.	.	C	15.79	2.937496	0.52972	.	.	ENSG00000065526	ENST00000375759	T	0.37915	1.17	5.16	5.16	0.70880	.	.	.	.	.	T	0.55561	0.1928	L	0.59436	1.845	0.80722	D	1	D	0.76494	0.999	D	0.64144	0.922	T	0.53542	-0.8424	9	0.42905	T	0.14	-11.4672	18.6444	0.91406	0.0:1.0:0.0:0.0	.	2516	Q96T58	MINT_HUMAN	L	2516	ENSP00000364912:P2516L	ENSP00000364912:P2516L	P	+	2	0	SPEN	16132869	1.000000	0.71417	1.000000	0.80357	0.831000	0.47069	6.357000	0.73051	2.418000	0.82041	0.561000	0.74099	CCA	.	.		0.582	SPEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025993.1	NM_015001	
CLCNKA	1187	hgsc.bcm.edu	37	1	16353907	16353907	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:16353907T>C	ENST00000331433.4	+	8	777	c.758T>C	c.(757-759)cTg>cCg	p.L253P	CLCNKA_ENST00000464764.1_3'UTR|CLCNKA_ENST00000420078.1_Missense_Mutation_p.L253P|CLCNKA_ENST00000375692.1_Missense_Mutation_p.L253P|CLCNKA_ENST00000439316.2_Missense_Mutation_p.L210P			P51800	CLCKA_HUMAN	chloride channel, voltage-sensitive Ka	253					excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|transmembrane transport (GO:0055085)|transport (GO:0006810)	chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	adenyl nucleotide binding (GO:0030554)|metal ion binding (GO:0046872)|voltage-gated chloride channel activity (GO:0005247)			breast(1)|kidney(1)|large_intestine(2)|lung(12)|ovary(2)|skin(1)	19		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Colorectal(212;8.04e-08)|COAD - Colon adenocarcinoma(227;5.46e-06)|BRCA - Breast invasive adenocarcinoma(304;9.02e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00655)|READ - Rectum adenocarcinoma(331;0.0649)	Niflumic Acid(DB04552)	TTCCGGCTCCTGGCAGTCTTC	0.642																																					p.L253P		Atlas-SNP	.											.	CLCNKA	56	.	0			c.T758C						.						63.0	69.0	67.0					1																	16353907		2203	4300	6503	SO:0001583	missense	1187	exon8			GGCTCCTGGCAGT		CCDS167.1, CCDS41269.1, CCDS57973.1	1p36	2012-09-26	2012-02-23		ENSG00000186510	ENSG00000186510		"""Ion channels / Chloride channels : Voltage-sensitive"""	2026	protein-coding gene	gene with protein product		602024	"""chloride channel Ka"""			8544406	Standard	NM_004070		Approved	hClC-Ka	uc001axu.3	P51800	OTTHUMG00000009529	ENST00000331433.4:c.758T>C	chr1.hg19:g.16353907T>C	ENSP00000332771:p.Leu253Pro	101.0	0.0		106.0	5.0	NM_004070	B4DPD3|E7EPH6|Q5T5P8|Q5T5Q4|Q7Z6D1|Q86VT1	Missense_Mutation	SNP	ENST00000331433.4	hg19	CCDS167.1	.	.	.	.	.	.	.	.	.	.	T	17.74	3.463288	0.63513	.	.	ENSG00000186510	ENST00000375692;ENST00000420078;ENST00000439316;ENST00000331433	D;D;D;D	0.95412	-3.7;-3.7;-3.7;-3.7	3.02	3.02	0.34903	Chloride channel, core (2);	0.078357	0.49305	D	0.000145	D	0.97838	0.9290	M	0.92923	3.36	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.97998	1.0358	10	0.87932	D	0	.	10.7799	0.46371	0.0:0.0:0.0:1.0	.	210;253;253	E7EPH6;Q5T5Q4;P51800	.;.;CLCKA_HUMAN	P	253;253;210;253	ENSP00000364844:L253P;ENSP00000410353:L253P;ENSP00000414445:L210P;ENSP00000332771:L253P	ENSP00000332771:L253P	L	+	2	0	CLCNKA	16226494	1.000000	0.71417	0.997000	0.53966	0.516000	0.34256	7.614000	0.82996	1.368000	0.46115	0.260000	0.18958	CTG	.	.		0.642	CLCNKA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026326.1		
KLHDC7A	127707	hgsc.bcm.edu	37	1	18808294	18808294	+	Missense_Mutation	SNP	T	T	A			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:18808294T>A	ENST00000400664.1	+	1	871	c.819T>A	c.(817-819)caT>caA	p.H273Q		NM_152375.2	NP_689588.2	Q5VTJ3	KLD7A_HUMAN	kelch domain containing 7A	273			H -> N (in dbSNP:rs2992753). {ECO:0000269|PubMed:14702039}.			integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	22		Colorectal(325;3.46e-05)|all_lung(284;0.000152)|Lung NSC(340;0.000185)|Breast(348;0.00046)|Renal(390;0.000518)|Ovarian(437;0.0014)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|BRCA - Breast invasive adenocarcinoma(304;1.41e-05)|Kidney(64;0.00017)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		TGGAGGAGCATTTCATACAGA	0.592																																					p.H273Q		Atlas-SNP	.											.	KLHDC7A	60	.	0			c.T819A						.						79.0	83.0	82.0					1																	18808294		2203	4300	6503	SO:0001583	missense	127707	exon1			GGAGCATTTCATA	AK096072	CCDS185.2	1p36.13	2008-02-05			ENSG00000179023	ENSG00000179023			26791	protein-coding gene	gene with protein product							Standard	NM_152375		Approved	FLJ38753	uc001bax.3	Q5VTJ3	OTTHUMG00000002431	ENST00000400664.1:c.819T>A	chr1.hg19:g.18808294T>A	ENSP00000383505:p.His273Gln	69.0	0.0		97.0	5.0	NM_152375	Q8N8W6	Missense_Mutation	SNP	ENST00000400664.1	hg19	CCDS185.2	.	.	.	.	.	.	.	.	.	.	T	10.46	1.355191	0.24512	.	.	ENSG00000179023	ENST00000400664;ENST00000540290	T	0.71461	-0.57	4.92	-3.68	0.04463	.	0.547006	0.17223	U	0.182256	T	0.46658	0.1404	N	0.08118	0	0.09310	N	1	B	0.12013	0.005	B	0.01281	0.0	T	0.32798	-0.9893	10	0.66056	D	0.02	.	13.1005	0.59218	0.0:0.6158:0.0:0.3842	.	273	Q5VTJ3	KLD7A_HUMAN	Q	273;210	ENSP00000383505:H273Q	ENSP00000383505:H273Q	H	+	3	2	KLHDC7A	18680881	0.000000	0.05858	0.019000	0.16419	0.298000	0.27526	-0.923000	0.04000	-0.682000	0.05197	0.260000	0.18958	CAT	.	.		0.592	KLHDC7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006923.3	NM_152375	
HSPG2	3339	hgsc.bcm.edu	37	1	22207984	22207984	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:22207984T>C	ENST00000374695.3	-	14	1745	c.1666A>G	c.(1666-1668)Aca>Gca	p.T556A		NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	556	Laminin IV type A 1. {ECO:0000255|PROSITE-ProRule:PRU00458}.				angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	GCAGGCATTGTCACATTCACA	0.637																																					p.T556A		Atlas-SNP	.											.	HSPG2	311	.	0			c.A1666G						.						91.0	91.0	91.0					1																	22207984		2203	4300	6503	SO:0001583	missense	3339	exon14			GCATTGTCACATT	M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"""Proteoglycans / Extracellular Matrix : Other"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5273	protein-coding gene	gene with protein product	"""perlecan proteoglycan"""	142461	"""Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"""	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.1666A>G	chr1.hg19:g.22207984T>C	ENSP00000363827:p.Thr556Ala	93.0	0.0		82.0	4.0	NM_005529	Q16287|Q5SZI3|Q9H3V5	Missense_Mutation	SNP	ENST00000374695.3	hg19	CCDS30625.1	.	.	.	.	.	.	.	.	.	.	T	5.321	0.244635	0.10077	.	.	ENSG00000142798	ENST00000374695	T	0.75154	-0.91	5.52	3.19	0.36642	Laminin B type IV (1);	0.785217	0.10745	N	0.639015	D	0.83862	0.5346	M	0.69823	2.125	0.25115	N	0.990681	D	0.58268	0.982	D	0.67548	0.952	T	0.70773	-0.4781	10	0.56958	D	0.05	.	10.783	0.46388	0.0:0.1472:0.0:0.8528	.	556	P98160	PGBM_HUMAN	A	556	ENSP00000363827:T556A	ENSP00000363827:T556A	T	-	1	0	HSPG2	22080571	1.000000	0.71417	0.058000	0.19502	0.000000	0.00434	2.119000	0.41958	0.123000	0.18342	-1.139000	0.01908	ACA	.	.		0.637	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529	
MYOM3	127294	hgsc.bcm.edu	37	1	24390564	24390564	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:24390564T>C	ENST00000374434.3	-	30	3782	c.3620A>G	c.(3619-3621)gAc>gGc	p.D1207G	RP11-293P20.4_ENST00000429191.1_RNA|MYOM3_ENST00000338909.5_Missense_Mutation_p.D100G|MYOM3_ENST00000330966.7_Missense_Mutation_p.D1210G|RP11-293P20.2_ENST00000439239.2_RNA	NM_152372.3	NP_689585.3	Q5VTT5	MYOM3_HUMAN	myomesin 3	1207						M band (GO:0031430)	protein homodimerization activity (GO:0042803)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(3)|lung(40)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	68		Colorectal(325;3.55e-05)|Renal(390;0.000703)|Lung NSC(340;0.001)|all_lung(284;0.0014)|Ovarian(437;0.00351)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;5.31e-24)|Colorectal(126;7.52e-08)|COAD - Colon adenocarcinoma(152;4.01e-06)|GBM - Glioblastoma multiforme(114;4.36e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00108)|KIRC - Kidney renal clear cell carcinoma(1967;0.00404)|STAD - Stomach adenocarcinoma(196;0.00966)|READ - Rectum adenocarcinoma(331;0.0678)|Lung(427;0.153)		GCTCCTACCGTCACCCGTGAG	0.527																																					p.D1207G		Atlas-SNP	.											.	MYOM3	131	.	0			c.A3620G						.						99.0	108.0	105.0					1																	24390564		2122	4238	6360	SO:0001583	missense	127294	exon30			CTACCGTCACCCG	AK093280	CCDS41281.1	1p36	2013-02-11	2012-10-17		ENSG00000142661	ENSG00000142661		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	26679	protein-coding gene	gene with protein product			"""myomesin family, member 3"""			18177667	Standard	NM_152372		Approved	FLJ35961	uc001bin.4	Q5VTT5	OTTHUMG00000002969	ENST00000374434.3:c.3620A>G	chr1.hg19:g.24390564T>C	ENSP00000363557:p.Asp1207Gly	88.0	0.0		87.0	4.0	NM_152372	A6NF75|Q5VTT6|Q6AWC0|Q6AWC1|Q6NXF9|Q6ZRG7|Q7Z3G9|Q8NA11|Q96C54	Missense_Mutation	SNP	ENST00000374434.3	hg19	CCDS41281.1	.	.	.	.	.	.	.	.	.	.	T	14.10	2.435411	0.43224	.	.	ENSG00000142661	ENST00000338909;ENST00000374434;ENST00000330966;ENST00000374442	T;T;T	0.56103	0.48;0.58;0.56	5.77	4.58	0.56647	Immunoglobulin subtype (1);	0.233454	0.43260	D	0.000593	T	0.27313	0.0670	N	0.08118	0	0.80722	D	1	B;B	0.06786	0.0;0.001	B;B	0.10450	0.0;0.005	T	0.12863	-1.0531	10	0.20519	T	0.43	.	6.2415	0.20793	0.0:0.0864:0.1632:0.7504	.	1207;100	Q5VTT5;Q5VTT5-3	MYOM3_HUMAN;.	G	100;1207;1210;102	ENSP00000342689:D100G;ENSP00000363557:D1207G;ENSP00000332670:D1210G	ENSP00000332670:D1210G	D	-	2	0	MYOM3	24263151	0.989000	0.36119	0.997000	0.53966	0.621000	0.37620	1.356000	0.34079	2.192000	0.70111	0.533000	0.62120	GAC	.	.		0.527	MYOM3-001	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000008272.2	NM_152372	
AHDC1	27245	hgsc.bcm.edu	37	1	27876868	27876868	+	Silent	SNP	G	G	T			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:27876868G>T	ENST00000247087.5	-	5	2355	c.1759C>A	c.(1759-1761)Cga>Aga	p.R587R	AHDC1_ENST00000374011.2_Silent_p.R587R			Q5TGY3	AHDC1_HUMAN	AT hook, DNA binding motif, containing 1	587							DNA binding (GO:0003677)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(8)|lung(20)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	42		all_lung(284;1.06e-05)|Lung NSC(340;1.86e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.00503)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0434)|OV - Ovarian serous cystadenocarcinoma(117;8.48e-25)|Colorectal(126;9.17e-09)|COAD - Colon adenocarcinoma(152;1.84e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00192)|BRCA - Breast invasive adenocarcinoma(304;0.00259)|STAD - Stomach adenocarcinoma(196;0.00311)|READ - Rectum adenocarcinoma(331;0.0291)		CGCCGCCGTCGTTTTTTTACC	0.652																																					p.R587R		Atlas-SNP	.											AHDC1,NS,carcinoma,0,1	AHDC1	98	.	0			c.C1759A						.						65.0	62.0	63.0					1																	27876868		2203	4300	6503	SO:0001819	synonymous_variant	27245	exon6			GCCGTCGTTTTTT	AK125431	CCDS30652.1	1p36.13	2008-02-05			ENSG00000126705	ENSG00000126705			25230	protein-coding gene	gene with protein product		615790				8619474, 9110174	Standard	XM_005245848		Approved	DJ159A19.3, RP1-159A19.1	uc009vsy.3	Q5TGY3	OTTHUMG00000003398	ENST00000247087.5:c.1759C>A	chr1.hg19:g.27876868G>T		236.0	0.0		257.0	33.0	NM_001029882	Q5TGY4|Q6PJK1|Q6ZUQ6|Q99769|Q9NUF5	Silent	SNP	ENST00000247087.5	hg19	CCDS30652.1																																																																																			.	.		0.652	AHDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009523.3		
PHACTR4	65979	hgsc.bcm.edu	37	1	28793167	28793167	+	Silent	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:28793167T>C	ENST00000373839.3	+	6	972	c.711T>C	c.(709-711)gcT>gcC	p.A237A	PHACTR4_ENST00000373836.3_Silent_p.A247A|PHACTR4_ENST00000493669.1_3'UTR	NM_001048183.1	NP_001041648.1	Q8IZ21	PHAR4_HUMAN	phosphatase and actin regulator 4	237	Pro-rich.				actin cytoskeleton organization (GO:0030036)|closure of optic fissure (GO:0061386)|enteric nervous system development (GO:0048484)|negative regulation of integrin-mediated signaling pathway (GO:2001045)|neural crest cell migration (GO:0001755)|neural tube closure (GO:0001843)|positive regulation of catalytic activity (GO:0043085)|regulation of cell cycle (GO:0051726)|Rho protein signal transduction (GO:0007266)	cytoplasm (GO:0005737)|lamellipodium (GO:0030027)	actin binding (GO:0003779)|protein phosphatase 1 binding (GO:0008157)|protein phosphatase type 1 activator activity (GO:0071862)			NS(1)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(6)|lung(10)|ovary(3)|skin(1)|urinary_tract(1)	32		Colorectal(325;3.46e-05)|Lung NSC(340;4.37e-05)|all_lung(284;7.01e-05)|Renal(390;0.00121)|Breast(348;0.00345)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0261)		OV - Ovarian serous cystadenocarcinoma(117;1.35e-21)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00273)|STAD - Stomach adenocarcinoma(196;0.00299)|BRCA - Breast invasive adenocarcinoma(304;0.0144)|READ - Rectum adenocarcinoma(331;0.0649)		TGCCTGCTGCTCCTGCCAGCA	0.577																																					p.A247A		Atlas-SNP	.											.	PHACTR4	64	.	0			c.T741C						.						52.0	60.0	57.0					1																	28793167		2080	4223	6303	SO:0001819	synonymous_variant	65979	exon5			TGCTGCTCCTGCC	AF130081	CCDS41293.1, CCDS41294.1	1p35.2	2014-06-13			ENSG00000204138	ENSG00000204138		"""Phosphatase and actin regulators"""	25793	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 124"""	608726				11483580, 15107502	Standard	NM_023923		Approved	FLJ13171, PPP1R124	uc001bpy.3	Q8IZ21	OTTHUMG00000003541	ENST00000373839.3:c.711T>C	chr1.hg19:g.28793167T>C		116.0	0.0		114.0	5.0	NM_023923	A2APK6|B9ZVW0|D3DPM3|Q68DD4|Q6NUN6|Q8N384|Q9H395|Q9H6X0|Q9H8W6	Silent	SNP	ENST00000373839.3	hg19	CCDS41293.1																																																																																			.	.		0.577	PHACTR4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000009868.4	NM_023923	
TXLNA	200081	hgsc.bcm.edu	37	1	32660695	32660695	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:32660695A>G	ENST00000373609.1	+	10	1821	c.1540A>G	c.(1540-1542)Agc>Ggc	p.S514G	TXLNA_ENST00000373610.3_Missense_Mutation_p.S514G			P40222	TXLNA_HUMAN	taxilin alpha	514					B cell activation (GO:0042113)|cell proliferation (GO:0008283)|exocytosis (GO:0006887)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	cytokine activity (GO:0005125)|high molecular weight B cell growth factor receptor binding (GO:0030372)			endometrium(1)|kidney(1)|large_intestine(4)|lung(2)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	13		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.101)|Breast(348;0.174)				TCAAGCACCCAGCTCCCCCAG	0.657																																					p.S514G		Atlas-SNP	.											.	TXLNA	34	.	0			c.A1540G						.						37.0	38.0	37.0					1																	32660695		2203	4300	6503	SO:0001583	missense	200081	exon11			GCACCCAGCTCCC	AF516206	CCDS353.1	1p35	2012-02-21			ENSG00000084652	ENSG00000084652			30685	protein-coding gene	gene with protein product		608676				15184072, 14623251	Standard	NM_175852		Approved	DKFZp451J0118	uc001bui.3	P40222	OTTHUMG00000004423	ENST00000373609.1:c.1540A>G	chr1.hg19:g.32660695A>G	ENSP00000362711:p.Ser514Gly	192.0	0.0		185.0	9.0	NM_175852	D3DPP6|Q5TFJ6|Q66K62|Q86T54|Q86T85|Q86T86|Q86Y86|Q86YW3|Q8N2Y3	Missense_Mutation	SNP	ENST00000373609.1	hg19	CCDS353.1	.	.	.	.	.	.	.	.	.	.	A	11.39	1.624997	0.28889	.	.	ENSG00000084652	ENST00000373610;ENST00000373609	T;T	0.34275	1.37;1.37	4.61	3.47	0.39725	.	1.237840	0.05167	N	0.498896	T	0.26376	0.0644	N	0.19112	0.55	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.20075	-1.0286	10	0.42905	T	0.14	-1.5236	7.202	0.25887	0.7733:0.0:0.2267:0.0	.	514	P40222	TXLNA_HUMAN	G	514	ENSP00000362712:S514G;ENSP00000362711:S514G	ENSP00000362711:S514G	S	+	1	0	TXLNA	32433282	0.006000	0.16342	0.151000	0.22473	0.965000	0.64279	1.793000	0.38764	0.913000	0.36797	0.460000	0.39030	AGC	.	.		0.657	TXLNA-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012844.1	NM_175852	
RRAGC	64121	hgsc.bcm.edu	37	1	39318159	39318159	+	Splice_Site	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:39318159A>G	ENST00000373001.3	-	4	819	c.643T>C	c.(643-645)Ttt>Ctt	p.F215L		NM_022157.2	NP_071440.1			Ras-related GTP binding C											endometrium(1)|kidney(1)|large_intestine(5)|lung(2)|ovary(1)	10	Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)				GTCAGATAAAAGCTGAAAAAC	0.294																																					p.F215L		Atlas-SNP	.											.	RRAGC	28	.	0			c.T643C						.						91.0	97.0	95.0					1																	39318159		2203	4299	6502	SO:0001630	splice_region_variant	64121	exon4			GATAAAAGCTGAA	AF323609	CCDS430.1	1p34	2008-02-05			ENSG00000116954	ENSG00000116954			19902	protein-coding gene	gene with protein product		608267				11073942	Standard	NM_022157		Approved	GTR2, FLJ13311	uc001ccq.3	Q9HB90	OTTHUMG00000000490	ENST00000373001.3:c.642-1T>C	chr1.hg19:g.39318159A>G		92.0	0.0		109.0	5.0	NM_022157		Missense_Mutation	SNP	ENST00000373001.3	hg19	CCDS430.1	.	.	.	.	.	.	.	.	.	.	A	34	5.386225	0.95967	.	.	ENSG00000116954	ENST00000373001	D	0.82711	-1.64	5.96	5.96	0.96718	.	0.000000	0.85682	D	0.000000	D	0.92593	0.7647	M	0.91717	3.235	0.80722	D	1	D;D;P	0.76494	0.975;0.999;0.912	P;D;P	0.66716	0.792;0.946;0.551	D	0.93720	0.7032	10	0.59425	D	0.04	-48.8638	16.4277	0.83824	1.0:0.0:0.0:0.0	.	181;149;215	E7ENI3;D3DPT8;Q9HB90	.;.;RRAGC_HUMAN	L	215	ENSP00000362092:F215L	ENSP00000362092:F215L	F	-	1	0	RRAGC	39090746	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.339000	0.96797	2.279000	0.76181	0.533000	0.62120	TTT	.	.		0.294	RRAGC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001222.2	NM_022157	Missense_Mutation
MAST2	23139	hgsc.bcm.edu	37	1	46487680	46487680	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:46487680A>G	ENST00000361297.2	+	12	1632	c.1349A>G	c.(1348-1350)gAg>gGg	p.E450G	MAST2_ENST00000372009.2_Missense_Mutation_p.E380G	NM_015112.2	NP_055927.2			microtubule associated serine/threonine kinase 2											breast(1)|lung(3)|ovary(5)|stomach(2)	11	Acute lymphoblastic leukemia(166;0.155)|Lung SC(450;0.184)					CACGCCAAAGAGGGACAAGGG	0.527																																					p.E450G		Atlas-SNP	.											.	MAST2	136	.	0			c.A1349G						.						198.0	203.0	201.0					1																	46487680		2049	4218	6267	SO:0001583	missense	23139	exon12			CCAAAGAGGGACA	AB047005	CCDS41326.1	1p34.1	2008-02-05			ENSG00000086015	ENSG00000086015			19035	protein-coding gene	gene with protein product		612257					Standard	NM_015112		Approved	MAST205, KIAA0807	uc001cov.3	Q6P0Q8	OTTHUMG00000008007	ENST00000361297.2:c.1349A>G	chr1.hg19:g.46487680A>G	ENSP00000354671:p.Glu450Gly	113.0	0.0		103.0	5.0	NM_015112		Missense_Mutation	SNP	ENST00000361297.2	hg19	CCDS41326.1	.	.	.	.	.	.	.	.	.	.	A	34	5.400533	0.96030	.	.	ENSG00000086015	ENST00000361297;ENST00000372009;ENST00000432341;ENST00000372008	T;T;T	0.30714	1.52;1.52;1.52	5.74	5.74	0.90152	Microtubule-associated serine/threonine-protein kinase, domain (1);	0.104885	0.64402	D	0.000007	T	0.62270	0.2414	M	0.87180	2.865	0.80722	D	1	B;D;B;D;D	0.89917	0.087;0.989;0.087;1.0;1.0	B;D;B;D;D	0.87578	0.168;0.979;0.168;0.998;0.994	T	0.68938	-0.5277	10	0.72032	D	0.01	-24.9249	16.3545	0.83230	1.0:0.0:0.0:0.0	.	124;380;124;380;450	B3KU51;Q6P0Q8-2;E7EWL1;E7ERL6;Q6P0Q8	.;.;.;.;MAST2_HUMAN	G	450;380;124;335	ENSP00000354671:E450G;ENSP00000361079:E380G;ENSP00000361078:E335G	ENSP00000354671:E450G	E	+	2	0	MAST2	46260267	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.274000	0.72587	2.326000	0.78906	0.533000	0.62120	GAG	.	.		0.527	MAST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021977.1	NM_015112	
SSBP3	23648	hgsc.bcm.edu	37	1	54870545	54870545	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:54870545T>C	ENST00000371320.3	-	2	525	c.115A>G	c.(115-117)Acc>Gcc	p.T39A	SSBP3_ENST00000357475.4_Missense_Mutation_p.T39A|SSBP3_ENST00000417664.2_5'UTR|SSBP3_ENST00000371319.3_Missense_Mutation_p.T39A	NM_145716.2	NP_663768.1	Q9BWW4	SSBP3_HUMAN	single stranded DNA binding protein 3	39	LisH. {ECO:0000255|PROSITE- ProRule:PRU00126}.				head morphogenesis (GO:0060323)|hematopoietic progenitor cell differentiation (GO:0002244)|midbrain-hindbrain boundary initiation (GO:0021547)|positive regulation of anterior head development (GO:2000744)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prechordal plate formation (GO:0021501)|protein complex assembly (GO:0006461)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|protein complex (GO:0043234)	single-stranded DNA binding (GO:0003697)			central_nervous_system(2)|endometrium(3)|large_intestine(1)|lung(3)|ovary(1)|urinary_tract(1)	11						GATAAGAAGGTCTGTGCAGAT	0.512																																					p.T39A		Atlas-SNP	.											.	SSBP3	65	.	0			c.A115G						.						55.0	53.0	54.0					1																	54870545		2203	4300	6503	SO:0001583	missense	23648	exon2			AGAAGGTCTGTGC		CCDS590.1, CCDS591.1, CCDS30726.1	1p32.3	2008-02-05	2001-11-28		ENSG00000157216	ENSG00000157216			15674	protein-coding gene	gene with protein product		607390	"""single-stranded DNA-binding protein 3"""			12079286	Standard	NM_145716		Approved	CSDP, SSDP, FLJ10355, SSDP1	uc001cxe.4	Q9BWW4	OTTHUMG00000008264	ENST00000371320.3:c.115A>G	chr1.hg19:g.54870545T>C	ENSP00000360371:p.Thr39Ala	89.0	0.0		120.0	5.0	NM_145716	A8K0A9|Q5T860|Q5T861|Q9BTM0|Q9BWW3	Missense_Mutation	SNP	ENST00000371320.3	hg19	CCDS591.1	.	.	.	.	.	.	.	.	.	.	T	19.18	3.777305	0.70107	.	.	ENSG00000157216	ENST00000371320;ENST00000371319;ENST00000357475	.	.	.	4.84	4.84	0.62591	LisH dimerisation motif (2);	0.074636	0.50627	U	0.000101	T	0.64962	0.2646	L	0.50333	1.59	0.58432	D	0.999997	B;P;P	0.50528	0.433;0.936;0.826	B;P;B	0.55577	0.107;0.779;0.424	T	0.67530	-0.5647	9	0.56958	D	0.05	-6.1723	13.7158	0.62695	0.0:0.0:0.0:1.0	.	39;39;39	Q9BWW4-2;Q9BWW4-3;Q9BWW4	.;.;SSBP3_HUMAN	A	39	.	ENSP00000350067:T39A	T	-	1	0	SSBP3	54643133	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.403000	0.79983	1.949000	0.56562	0.459000	0.35465	ACC	.	.		0.512	SSBP3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022721.1	NM_018070	
C1orf168	199920	hgsc.bcm.edu	37	1	57216837	57216837	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:57216837T>C	ENST00000343433.6	-	9	1347	c.1267A>G	c.(1267-1269)Acc>Gcc	p.T423A	C1orf168_ENST00000484327.1_5'UTR	NM_001004303.4	NP_001004303.3	Q5VWT5	CA168_HUMAN	chromosome 1 open reading frame 168	423										NS(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(13)|ovary(3)|skin(6)|stomach(1)|urinary_tract(2)	46						TGGACGTTGGTCATCTGAATT	0.473																																					p.T423A		Atlas-SNP	.											.	C1orf168	102	.	0			c.A1267G						.						127.0	108.0	115.0					1																	57216837		2203	4300	6503	SO:0001583	missense	199920	exon9			CGTTGGTCATCTG	BX648439	CCDS30729.1	1p32.2	2011-02-22			ENSG00000187889	ENSG00000187889			27295	protein-coding gene	gene with protein product						14702039	Standard	NM_001004303		Approved	RP4-758N20.2, FLJ43208	uc001cym.4	Q5VWT5	OTTHUMG00000008281	ENST00000343433.6:c.1267A>G	chr1.hg19:g.57216837T>C	ENSP00000345972:p.Thr423Ala	112.0	0.0		85.0	4.0	NM_001004303	Q63HM3|Q6ZUY6	Missense_Mutation	SNP	ENST00000343433.6	hg19	CCDS30729.1	.	.	.	.	.	.	.	.	.	.	T	2.033	-0.421864	0.04734	.	.	ENSG00000187889	ENST00000343433	T	0.27256	1.68	4.11	-5.64	0.02466	.	1.382770	0.04566	N	0.392460	T	0.07908	0.0198	N	0.04508	-0.205	0.09310	N	1	B	0.10296	0.003	B	0.06405	0.002	T	0.23119	-1.0197	10	0.07175	T	0.84	4.4247	2.2065	0.03937	0.1362:0.3874:0.2344:0.242	.	423	Q5VWT5	CA168_HUMAN	A	423	ENSP00000345972:T423A	ENSP00000345972:T423A	T	-	1	0	C1orf168	56989425	0.000000	0.05858	0.000000	0.03702	0.024000	0.10985	-0.639000	0.05446	-1.142000	0.02869	-0.274000	0.10170	ACC	.	.		0.473	C1orf168-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022751.2	NM_001004303	
INADL	10207	hgsc.bcm.edu	37	1	62483532	62483532	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:62483532A>G	ENST00000371158.2	+	29	3986	c.3872A>G	c.(3871-3873)aAc>aGc	p.N1291S	INADL_ENST00000543708.1_Missense_Mutation_p.N75S|INADL_ENST00000545929.1_Intron|INADL_ENST00000316485.6_Missense_Mutation_p.N1291S	NM_176877.2	NP_795352	Q8NI35	INADL_HUMAN	InaD-like (Drosophila)	1291	PDZ 7. {ECO:0000255|PROSITE- ProRule:PRU00143}.				cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|intracellular signal transduction (GO:0035556)|tight junction assembly (GO:0070830)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)				breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(8)|liver(1)|lung(51)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)	103						AAACAGATAAACAATCAGATT	0.328																																					p.N1291S		Atlas-SNP	.											.	INADL	179	.	0			c.A3872G						.						107.0	99.0	102.0					1																	62483532		2203	4300	6503	SO:0001583	missense	10207	exon29			AGATAAACAATCA	AB044807	CCDS617.2	1p31	2008-02-05			ENSG00000132849	ENSG00000132849			28881	protein-coding gene	gene with protein product		603199				9280290, 11374908	Standard	NM_176877		Approved	Cipp, PATJ	uc001dab.3	Q8NI35	OTTHUMG00000008560	ENST00000371158.2:c.3872A>G	chr1.hg19:g.62483532A>G	ENSP00000360200:p.Asn1291Ser	82.0	0.0		74.0	4.0	NM_176877	O15249|O43742|O60833|Q5VUA5|Q5VUA6|Q5VUA7|Q5VUA8|Q5VUA9|Q5VUB0|Q8WU78|Q9H3N9	Missense_Mutation	SNP	ENST00000371158.2	hg19	CCDS617.2	.	.	.	.	.	.	.	.	.	.	A	19.83	3.899556	0.72754	.	.	ENSG00000132849	ENST00000371158;ENST00000316485;ENST00000371156;ENST00000395513;ENST00000307297;ENST00000543708	T;T;T;T	0.59224	0.28;0.28;0.28;0.28	5.35	5.35	0.76521	PDZ/DHR/GLGF (4);	0.000000	0.85682	D	0.000000	T	0.79423	0.4443	M	0.89534	3.04	0.80722	D	1	P;P;P;D;D	0.61697	0.502;0.691;0.691;0.986;0.99	P;P;B;D;P	0.65684	0.505;0.488;0.36;0.937;0.86	D	0.84384	0.0551	10	0.87932	D	0	.	15.3286	0.74186	1.0:0.0:0.0:0.0	.	75;750;1291;1291;1291	B4DE90;Q8NI35-5;F8W8T2;Q8NI35;Q8NI35-4	.;.;.;INADL_HUMAN;.	S	1291;1291;1291;1291;75;75	ENSP00000360200:N1291S;ENSP00000326199:N1291S;ENSP00000307496:N75S;ENSP00000445790:N75S	ENSP00000307496:N75S	N	+	2	0	INADL	62256120	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.042000	0.89430	2.029000	0.59856	0.482000	0.46254	AAC	.	.		0.328	INADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023639.2	NM_170605	
KANK4	163782	hgsc.bcm.edu	37	1	62739460	62739460	+	Missense_Mutation	SNP	C	C	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:62739460C>G	ENST00000371153.4	-	3	1694	c.1316G>C	c.(1315-1317)aGc>aCc	p.S439T	KANK4_ENST00000371150.1_5'Flank|KANK4_ENST00000354381.3_Intron	NM_181712.4	NP_859063.3	Q5T7N3	KANK4_HUMAN	KN motif and ankyrin repeat domains 4	439						cytoplasm (GO:0005737)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(49)|ovary(3)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)	81						AGACTCCATGCTGCCTAGAAG	0.557																																					p.S439T		Atlas-SNP	.											.	KANK4	135	.	0			c.G1316C						.						191.0	183.0	186.0					1																	62739460		2203	4300	6503	SO:0001583	missense	163782	exon3			TCCATGCTGCCTA	AK096259	CCDS620.1	1p31.3	2013-10-11	2008-01-29	2008-01-29	ENSG00000132854	ENSG00000132854		"""KN motif and ankyrin repeat domain containing"", ""Ankyrin repeat domain containing"""	27263	protein-coding gene	gene with protein product		614612	"""ankyrin repeat domain 38"""	ANKRD38		17996375, 19554261	Standard	NM_181712		Approved	KIAA0172	uc001dah.4	Q5T7N3	OTTHUMG00000008971	ENST00000371153.4:c.1316G>C	chr1.hg19:g.62739460C>G	ENSP00000360195:p.Ser439Thr	121.0	0.0		199.0	47.0	NM_181712	B1ALP7|Q6P9A0|Q86T71|Q86VE6|Q8NAX3	Missense_Mutation	SNP	ENST00000371153.4	hg19	CCDS620.1	.	.	.	.	.	.	.	.	.	.	C	4.425	0.078600	0.08533	.	.	ENSG00000132854	ENST00000371153	T	0.46063	0.88	5.81	-2.06	0.07298	.	0.996520	0.08124	N	0.994228	T	0.21881	0.0527	N	0.15975	0.35	0.09310	N	1	B	0.12630	0.006	B	0.09377	0.004	T	0.29181	-1.0020	10	0.10902	T	0.67	-0.3381	9.8642	0.41134	0.1688:0.5557:0.2754:0.0	.	439	Q5T7N3	KANK4_HUMAN	T	439	ENSP00000360195:S439T	ENSP00000360195:S439T	S	-	2	0	KANK4	62512048	0.000000	0.05858	0.001000	0.08648	0.005000	0.04900	0.114000	0.15520	-0.006000	0.14370	-0.262000	0.10625	AGC	.	.		0.557	KANK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024877.1	NM_181712	
SLC35D1	23169	hgsc.bcm.edu	37	1	67512956	67512956	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:67512956C>T	ENST00000235345.5	-	7	713	c.628G>A	c.(628-630)Gat>Aat	p.D210N	SLC35D1_ENST00000506472.2_Missense_Mutation_p.D131N	NM_015139.2	NP_055954.1	Q9NTN3	S35D1_HUMAN	solute carrier family 35 (UDP-GlcA/UDP-GalNAc transporter), member D1	210					carbohydrate transport (GO:0008643)|cellular glucuronidation (GO:0052695)|chondroitin sulfate biosynthetic process (GO:0030206)|embryonic skeletal system development (GO:0048706)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|UDP-glucuronate biosynthetic process (GO:0006065)|UDP-glucuronic acid transport (GO:0015787)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	UDP-glucuronic acid transmembrane transporter activity (GO:0005461)			endometrium(2)|kidney(1)|large_intestine(3)|lung(4)	10						ACTTTTGAATCTAATTTTTGT	0.353																																					p.D210N		Atlas-SNP	.											.	SLC35D1	22	.	0			c.G628A						.						161.0	148.0	153.0					1																	67512956		2203	4300	6503	SO:0001583	missense	23169	exon7			TTGAATCTAATTT	AB044343	CCDS636.1	1p32-p31	2013-07-17	2013-07-17		ENSG00000116704	ENSG00000116704		"""Solute carriers"""	20800	protein-coding gene	gene with protein product		610804	"""solute carrier family 35 (UDP-glucuronic acid/UDP-N-acetylgalactosamine dual transporter), member D1"""			11322953	Standard	NM_015139		Approved	UGTREL7, KIAA0260	uc001ddk.2	Q9NTN3	OTTHUMG00000009360	ENST00000235345.5:c.628G>A	chr1.hg19:g.67512956C>T	ENSP00000235345:p.Asp210Asn	54.0	0.0		54.0	4.0	NM_015139	A8K185|B7Z3X2|Q52LU5|Q92548	Missense_Mutation	SNP	ENST00000235345.5	hg19	CCDS636.1	.	.	.	.	.	.	.	.	.	.	C	18.72	3.683636	0.68157	.	.	ENSG00000116704	ENST00000235345;ENST00000506472	T;T	0.63255	-0.03;-0.03	5.15	5.15	0.70609	Domain of unknown function DUF250 (1);	0.090486	0.85682	D	0.000000	T	0.40670	0.1126	L	0.35793	1.09	0.80722	D	1	B;B	0.20368	0.035;0.044	B;B	0.24269	0.05;0.052	T	0.27872	-1.0061	10	0.23302	T	0.38	-14.2744	17.7823	0.88527	0.0:1.0:0.0:0.0	.	131;210	B7Z3X2;Q9NTN3	.;S35D1_HUMAN	N	210;131	ENSP00000235345:D210N;ENSP00000445189:D131N	ENSP00000235345:D210N	D	-	1	0	SLC35D1	67285544	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.435000	0.80391	2.567000	0.86603	0.655000	0.94253	GAT	.	.		0.353	SLC35D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025948.1	NM_015139	
LRRC7	57554	hgsc.bcm.edu	37	1	70397188	70397188	+	Splice_Site	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:70397188A>G	ENST00000035383.5	+	6	563		c.e6-1		LRRC7_ENST00000415775.2_Splice_Site|LRRC7_ENST00000310961.5_Splice_Site	NM_020794.2	NP_065845.1	Q96NW7	LRRC7_HUMAN	leucine rich repeat containing 7							cell junction (GO:0030054)|cytoplasm (GO:0005737)|postsynaptic membrane (GO:0045211)				breast(11)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(3)|lung(81)|ovary(9)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	162						CATCTGTTGTAGGTCAATGCA	0.403																																					.		Atlas-SNP	.											.	LRRC7	400	.	0			c.534-2A>G						.						90.0	83.0	86.0					1																	70397188		2203	4300	6503	SO:0001630	splice_region_variant	57554	exon6			TGTTGTAGGTCAA		CCDS645.1	1p31.1	2008-02-05			ENSG00000033122	ENSG00000033122			18531	protein-coding gene	gene with protein product		614453				12525888	Standard	NM_020794		Approved	KIAA1365, densin-180	uc001dep.3	Q96NW7	OTTHUMG00000059194	ENST00000035383.5:c.534-1A>G	chr1.hg19:g.70397188A>G		85.0	0.0		119.0	5.0	NM_020794	Q5VXC2|Q5VXC3|Q68D07|Q86VE8|Q8WX20|Q9P2I2	Splice_Site	SNP	ENST00000035383.5	hg19	CCDS645.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	14.64|14.64	2.594771|2.594771	0.46318|0.46318	.|.	.|.	ENSG00000033122|ENSG00000033122	ENST00000310961;ENST00000035383|ENST00000370957	.|.	.|.	.|.	5.92|5.92	5.92|5.92	0.95590|0.95590	.|.	.|.	.|.	.|.	.|.	.|T	.|0.55033	.|0.1895	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.56896	.|-0.7903	.|4	.|.	.|.	.|.	.|.	12.7596|12.7596	0.57356|0.57356	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|.	.|.	.|.	.|G	-1|1	.|.	.|.	.|R	+|+	.|1	.|2	LRRC7|LRRC7	70169776|70169776	1.000000|1.000000	0.71417|0.71417	0.938000|0.938000	0.37757|0.37757	0.406000|0.406000	0.30931|0.30931	5.974000|5.974000	0.70465|0.70465	2.254000|2.254000	0.74563|0.74563	0.528000|0.528000	0.53228|0.53228	.|AGG	.	.		0.403	LRRC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131261.1	NM_020794	Intron
FUBP1	8880	hgsc.bcm.edu	37	1	78432435	78432435	+	Splice_Site	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:78432435T>C	ENST00000370768.2	-	7	497	c.416A>G	c.(415-417)gAc>gGc	p.D139G	FUBP1_ENST00000370767.1_Splice_Site_p.D139G|FUBP1_ENST00000436586.2_Splice_Site_p.D160G	NM_003902.3	NP_003893.2	Q96AE4	FUBP1_HUMAN	far upstream element (FUSE) binding protein 1	139	KH 1. {ECO:0000255|PROSITE- ProRule:PRU00117}.				positive regulation of gene expression (GO:0010628)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)			central_nervous_system(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(1)|upper_aerodigestive_tract(3)	17						GCCACCACTGTCTACAATTTA	0.323			"""F, N"""		oligodendroglioma																																p.D139G		Atlas-SNP	.		Rec	yes		1	1p13.1	8880	far upstream element (FUSE) binding protein 1		O	.	FUBP1	112	.	0			c.A416G						.						54.0	57.0	56.0					1																	78432435		2203	4300	6503	SO:0001630	splice_region_variant	8880	exon7			CCACTGTCTACAA	U05040	CCDS683.1	1p31.1	2008-02-05			ENSG00000162613	ENSG00000162613			4004	protein-coding gene	gene with protein product		603444		FUBP		8125259	Standard	XM_005271309		Approved	FBP	uc001dii.3	Q96AE4	OTTHUMG00000040799	ENST00000370768.2:c.416-1A>G	chr1.hg19:g.78432435T>C		69.0	0.0		87.0	4.0	NM_003902	Q12828	Missense_Mutation	SNP	ENST00000370768.2	hg19	CCDS683.1	.	.	.	.	.	.	.	.	.	.	T	27.6	4.845678	0.91197	.	.	ENSG00000162613	ENST00000370773;ENST00000370767;ENST00000370768;ENST00000394922;ENST00000436586;ENST00000421641	T;T;T;T	0.46063	1.4;1.4;1.4;0.88	5.67	5.67	0.87782	K Homology (1);K Homology, type 1, subgroup (1);K Homology, type 1 (1);	0.042455	0.85682	N	0.000000	T	0.49304	0.1549	M	0.71036	2.16	0.80722	D	1	B;P	0.46952	0.337;0.887	B;P	0.53722	0.346;0.733	T	0.54695	-0.8255	10	0.72032	D	0.01	.	16.1994	0.82060	0.0:0.0:0.0:1.0	.	160;139	B4DT31;Q96AE4	.;FUBP1_HUMAN	G	138;139;139;138;160;159	ENSP00000359803:D139G;ENSP00000359804:D139G;ENSP00000389536:D160G;ENSP00000402630:D159G	ENSP00000294623:D138G	D	-	2	0	FUBP1	78205023	1.000000	0.71417	0.998000	0.56505	0.969000	0.65631	5.919000	0.70005	2.281000	0.76405	0.528000	0.53228	GAC	.	.		0.323	FUBP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098030.3	NM_003902	Missense_Mutation
BCL10	8915	hgsc.bcm.edu	37	1	85733444	85733444	+	Missense_Mutation	SNP	T	T	C	rs556621354	byFrequency	TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:85733444T>C	ENST00000370580.1	-	3	1305	c.568A>G	c.(568-570)Act>Gct	p.T190A		NM_003921.4	NP_003912.1	O95999	BCL10_HUMAN	B-cell CLL/lymphoma 10	190					adaptive immune response (GO:0002250)|B cell apoptotic process (GO:0001783)|cell death (GO:0008219)|cellular defense response (GO:0006968)|cellular response to mechanical stimulus (GO:0071260)|Fc-epsilon receptor signaling pathway (GO:0038095)|immunoglobulin mediated immune response (GO:0016064)|innate immune response (GO:0045087)|interleukin-6 biosynthetic process (GO:0042226)|lymphotoxin A biosynthetic process (GO:0042109)|negative regulation of mature B cell apoptotic process (GO:0002906)|neural tube closure (GO:0001843)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|positive regulation of mast cell cytokine production (GO:0032765)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of T cell activation (GO:0050870)|positive regulation of transcription, DNA-templated (GO:0045893)|protein homooligomerization (GO:0051260)|protein oligomerization (GO:0051259)|regulation of T cell receptor signaling pathway (GO:0050856)|response to food (GO:0032094)|response to fungus (GO:0009620)|response to molecule of bacterial origin (GO:0002237)|T cell apoptotic process (GO:0070231)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor signaling pathway (GO:0002224)	CBM complex (GO:0032449)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|lysosome (GO:0005764)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	enzyme binding (GO:0019899)|kinase binding (GO:0019900)|NF-kappaB binding (GO:0051059)|protease binding (GO:0002020)|protein C-terminus binding (GO:0008022)|protein kinase B binding (GO:0043422)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)			haematopoietic_and_lymphoid_tissue(7)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|stomach(1)|urinary_tract(1)	19				all cancers(265;0.0114)|Epithelial(280;0.0311)		GGAAGTGTAGTTGAAGAGAAG	0.448			T	IGH@	MALT								T|||	2	0.000399361	0.0	0.0	5008	,	,		14905	0.0		0.0	False		,,,				2504	0.002				p.T190A	NSCLC(34;993 1034 12176 32621 50182)	Atlas-SNP	.		Dom	yes		1	1p22	8915	B-cell CLL/lymphoma 10		L	.	BCL10	39	.	0			c.A568G						.						96.0	102.0	100.0					1																	85733444		2203	4300	6503	SO:0001583	missense	8915	exon3			GTGTAGTTGAAGA	AJ006288	CCDS704.1	1p22	2008-07-18			ENSG00000142867	ENSG00000142867			989	protein-coding gene	gene with protein product	"""CARD-like apoptotic protein"", ""CARD-containing apoptotic signaling protein"", ""CARD containing molecule enhancing NF-kB"", ""caspase-recruiting domain-containing protein"", ""CARD-containing proapoptotic protein"""	603517				9989495	Standard	NM_003921		Approved	CARMEN, CIPER, mE10, c-E10, CLAP	uc021opd.1	O95999	OTTHUMG00000009965	ENST00000370580.1:c.568A>G	chr1.hg19:g.85733444T>C	ENSP00000359612:p.Thr190Ala	74.0	0.0		77.0	15.0	NM_003921	Q5VUF1	Missense_Mutation	SNP	ENST00000370580.1	hg19	CCDS704.1	.	.	.	.	.	.	.	.	.	.	T	8.104	0.777202	0.16120	.	.	ENSG00000142867	ENST00000370580;ENST00000271015	.	.	.	5.82	-1.91	0.07641	.	0.499537	0.23742	N	0.045015	T	0.04363	0.0120	N	0.04508	-0.205	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.38735	-0.9647	9	0.30854	T	0.27	-0.3714	6.7252	0.23353	0.1519:0.5344:0.0:0.3137	.	190	O95999	BCL10_HUMAN	A	190	.	ENSP00000271015:T190A	T	-	1	0	BCL10	85506032	0.056000	0.20664	0.026000	0.17262	0.985000	0.73830	0.587000	0.23909	-0.344000	0.08338	0.383000	0.25322	ACT	.	.		0.448	BCL10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027612.1	NM_003921	
CLCA1	1179	hgsc.bcm.edu	37	1	86957056	86957056	+	Splice_Site	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:86957056T>C	ENST00000234701.3	+	10	1815		c.e10+2		CLCA1_ENST00000394711.1_Splice_Site			A8K7I4	CLCA1_HUMAN	chloride channel accessory 1						calcium ion transport (GO:0006816)|cellular response to hypoxia (GO:0071456)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|transport (GO:0006810)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|microvillus (GO:0005902)|zymogen granule membrane (GO:0042589)	chloride channel activity (GO:0005254)			NS(1)|breast(3)|endometrium(1)|kidney(3)|large_intestine(9)|lung(14)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	38		Lung NSC(277;0.239)		all cancers(265;0.0249)|Epithelial(280;0.0476)		TCCATCCAGGTTGGAGTTCTT	0.398																																					.		Atlas-SNP	.											.	CLCA1	109	.	0			c.1464+2T>C						.						87.0	86.0	86.0					1																	86957056		2203	4300	6503	SO:0001630	splice_region_variant	1179	exon9			TCCAGGTTGGAGT		CCDS709.1	1p22.3	2012-02-26	2009-01-29		ENSG00000016490	ENSG00000016490			2015	protein-coding gene	gene with protein product		603906	"""chloride channel, calcium activated, family member 1"", ""chloride channel regulator 1"""			9828122	Standard	NM_001285		Approved	CaCC, CLCRG1	uc001dlt.3	A8K7I4	OTTHUMG00000010254	ENST00000234701.3:c.1464+2T>C	chr1.hg19:g.86957056T>C		82.0	0.0		108.0	5.0	NM_001285	B2RAV5|O95151|Q5TDF4|Q9UNF6|Q9UPC6	Splice_Site	SNP	ENST00000234701.3	hg19	CCDS709.1	.	.	.	.	.	.	.	.	.	.	T	17.23	3.336922	0.60963	.	.	ENSG00000016490	ENST00000234701;ENST00000394711;ENST00000539889	.	.	.	5.92	4.8	0.61643	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.9498	0.47323	0.0:0.074:0.0:0.926	.	.	.	.	.	-1	.	.	.	+	.	.	CLCA1	86729644	1.000000	0.71417	0.939000	0.37840	0.794000	0.44872	4.835000	0.62781	1.073000	0.40885	0.533000	0.62120	.	.	.		0.398	CLCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028277.1	NM_001285	Intron
PKN2	5586	hgsc.bcm.edu	37	1	89236054	89236054	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:89236054C>A	ENST00000370521.3	+	4	883	c.524C>A	c.(523-525)aCa>aAa	p.T175K	PKN2_ENST00000316005.7_Missense_Mutation_p.T175K|PKN2_ENST00000370513.5_Missense_Mutation_p.T175K|PKN2_ENST00000370505.3_Missense_Mutation_p.T18K	NM_006256.2	NP_006247.1	Q16513	PKN2_HUMAN	protein kinase N2	175					apical junction assembly (GO:0043297)|apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cell division (GO:0051301)|epithelial cell migration (GO:0010631)|positive regulation of cytokinesis (GO:0032467)|positive regulation of mitotic cell cycle (GO:0045931)|protein phosphorylation (GO:0006468)|regulation of cell motility (GO:2000145)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	apical junction complex (GO:0043296)|centrosome (GO:0005813)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium (GO:0030027)|membrane (GO:0016020)|midbody (GO:0030496)|nucleus (GO:0005634)	ATP binding (GO:0005524)|histone deacetylase binding (GO:0042826)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|endometrium(3)|kidney(3)|large_intestine(8)|lung(15)|prostate(1)|skin(1)	33		Lung NSC(277;0.123)		all cancers(265;0.0136)|Epithelial(280;0.0301)		CTCCATGGTACAGCTCAGCAA	0.353																																					p.T175K		Atlas-SNP	.											.	PKN2	109	.	0			c.C524A						.						98.0	92.0	94.0					1																	89236054		1890	4110	6000	SO:0001583	missense	5586	exon4			ATGGTACAGCTCA	U33052	CCDS714.1	1p22	2014-04-23	2004-07-01	2004-07-01	ENSG00000065243	ENSG00000065243			9406	protein-coding gene	gene with protein product	"""cardiolipin-activated protein kinase Pak2"""	602549	"""protein kinase C-like 2"""	PRKCL2		7988719, 7851406	Standard	NM_006256		Approved	PRK2, Pak-2, STK7	uc001dmn.3	Q16513	OTTHUMG00000010074	ENST00000370521.3:c.524C>A	chr1.hg19:g.89236054C>A	ENSP00000359552:p.Thr175Lys	132.0	0.0		141.0	34.0	NM_006256	B4DQ21|B4DTP5|B4DVG1|D3DT24|Q08AF4|Q9H1W4	Missense_Mutation	SNP	ENST00000370521.3	hg19	CCDS714.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.980601	0.74474	.	.	ENSG00000065243	ENST00000370521;ENST00000316005;ENST00000370505;ENST00000370513	T;T;T;T	0.28895	2.42;2.42;1.59;2.42	5.45	5.45	0.79879	.	0.000000	0.46442	U	0.000300	T	0.39358	0.1075	M	0.80616	2.505	0.80722	D	1	P;P;P;P	0.45126	0.851;0.586;0.82;0.608	P;B;B;B	0.47603	0.551;0.236;0.397;0.402	T	0.32903	-0.9889	10	0.48119	T	0.1	.	19.6523	0.95822	0.0:1.0:0.0:0.0	.	175;175;175;175	B4DTP5;E7ESL7;Q16513;B1AL79	.;.;PKN2_HUMAN;.	K	175;175;18;175	ENSP00000359552:T175K;ENSP00000317851:T175K;ENSP00000359536:T18K;ENSP00000359544:T175K	ENSP00000317851:T175K	T	+	2	0	PKN2	89008642	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.445000	0.80570	2.706000	0.92434	0.655000	0.94253	ACA	.	.		0.353	PKN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027828.3	NM_006256	
DNTTIP2	30836	hgsc.bcm.edu	37	1	94341253	94341253	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:94341253A>G	ENST00000436063.2	-	3	1811	c.1754T>C	c.(1753-1755)cTa>cCa	p.L585P	DNTTIP2_ENST00000460191.1_5'UTR	NM_014597.4	NP_055412.2	Q5QJE6	TDIF2_HUMAN	deoxynucleotidyltransferase, terminal, interacting protein 2	585	TdBR region; mediates interaction with DNTT.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(15)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	38		all_lung(203;0.0111)|Lung NSC(277;0.0347)		all cancers(265;0.00679)|GBM - Glioblastoma multiforme(16;0.0278)|Epithelial(280;0.128)		GTTAGACTGTAGTTTATCTGC	0.363																																					p.L585P		Atlas-SNP	.											.	DNTTIP2	59	.	0			c.T1754C						.						236.0	203.0	213.0					1																	94341253		1839	4085	5924	SO:0001583	missense	30836	exon3			GACTGTAGTTTAT	AY394925	CCDS44174.1	1p22.1	2008-02-05			ENSG00000067334	ENSG00000067334			24013	protein-coding gene	gene with protein product	"""acidic 82 kDa protein mRNA"""	611199				15047147	Standard	NM_014597		Approved	HSU15552, ERBP, TdIF2	uc001dqf.3	Q5QJE6	OTTHUMG00000010268	ENST00000436063.2:c.1754T>C	chr1.hg19:g.94341253A>G	ENSP00000411010:p.Leu585Pro	41.0	0.0		81.0	4.0	NM_014597	Q12987|Q53H59|Q5TFJ4|Q6TLI0|Q76MJ8|Q86WX9	Missense_Mutation	SNP	ENST00000436063.2	hg19	CCDS44174.1	.	.	.	.	.	.	.	.	.	.	A	10.48	1.363373	0.24684	.	.	ENSG00000067334	ENST00000436063	T	0.15487	2.42	5.93	2.28	0.28536	.	0.567223	0.16965	N	0.192349	T	0.03651	0.0104	L	0.39898	1.24	0.23704	N	0.997067	B	0.06786	0.001	B	0.08055	0.003	T	0.41910	-0.9482	10	0.25751	T	0.34	.	4.3301	0.11059	0.3615:0.0:0.1381:0.5004	.	585	Q5QJE6	TDIF2_HUMAN	P	585	ENSP00000411010:L585P	ENSP00000411010:L585P	L	-	2	0	DNTTIP2	94113841	1.000000	0.71417	0.421000	0.26609	0.963000	0.63663	2.802000	0.47916	0.443000	0.26582	0.533000	0.62120	CTA	.	.		0.363	DNTTIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028317.2	NM_014597	
SASS6	163786	hgsc.bcm.edu	37	1	100587007	100587007	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:100587007A>G	ENST00000287482.5	-	5	550	c.410T>C	c.(409-411)cTc>cCc	p.L137P	SASS6_ENST00000462159.1_5'UTR|SASS6_ENST00000535161.1_5'UTR	NM_194292.1	NP_919268.1	Q6UVJ0	SAS6_HUMAN	spindle assembly 6 homolog (C. elegans)	137					centriole replication (GO:0007099)|centrosome duplication (GO:0051298)	centriole (GO:0005814)|centrosome (GO:0005813)|deuterosome (GO:0098536)				breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(2)|lung(6)|ovary(1)|upper_aerodigestive_tract(2)	19		all_epithelial(167;4.58e-06)|all_lung(203;0.00125)|Lung NSC(277;0.00131)		Epithelial(280;0.085)|all cancers(265;0.139)|COAD - Colon adenocarcinoma(174;0.15)|Lung(183;0.197)		TTTTAGTGAGAGGTGTGTAAG	0.338																																					p.L137P		Atlas-SNP	.											.	SASS6	61	.	0			c.T410C						.						73.0	75.0	75.0					1																	100587007		2203	4299	6502	SO:0001583	missense	163786	exon5			AGTGAGAGGTGTG	AL834265	CCDS764.1	1p21.3	2008-02-05			ENSG00000156876	ENSG00000156876			25403	protein-coding gene	gene with protein product		609321				15665853, 14654843	Standard	NM_194292		Approved	DKFZp761A078, SAS-6, FLJ22097, SAS6	uc001dsu.3	Q6UVJ0	OTTHUMG00000010754	ENST00000287482.5:c.410T>C	chr1.hg19:g.100587007A>G	ENSP00000287482:p.Leu137Pro	87.0	0.0		124.0	5.0	NM_194292	D3DT55|Q8N3K0	Missense_Mutation	SNP	ENST00000287482.5	hg19	CCDS764.1	.	.	.	.	.	.	.	.	.	.	A	22.0	4.225033	0.79576	.	.	ENSG00000156876	ENST00000287482;ENST00000539329	T	0.39056	1.1	5.61	5.61	0.85477	.	0.128399	0.52532	D	0.000061	T	0.65238	0.2672	M	0.88181	2.935	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.73553	-0.3946	10	0.87932	D	0	-7.8256	16.1025	0.81194	1.0:0.0:0.0:0.0	.	137	Q6UVJ0	SAS6_HUMAN	P	137;110	ENSP00000287482:L137P	ENSP00000287482:L137P	L	-	2	0	SASS6	100359595	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.937000	0.87672	2.254000	0.74563	0.533000	0.62120	CTC	.	.		0.338	SASS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029656.2	NM_194292	
COL11A1	1301	hgsc.bcm.edu	37	1	103453237	103453237	+	Silent	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:103453237T>C	ENST00000370096.3	-	30	2766	c.2454A>G	c.(2452-2454)cgA>cgG	p.R818R	COL11A1_ENST00000358392.2_Silent_p.R830R|COL11A1_ENST00000512756.1_Silent_p.R702R|COL11A1_ENST00000353414.4_Silent_p.R779R	NM_001854.3	NP_001845.3	P12107	COBA1_HUMAN	collagen, type XI, alpha 1	818	Triple-helical region.				cartilage condensation (GO:0001502)|chondrocyte development (GO:0002063)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|embryonic skeletal system morphogenesis (GO:0048704)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|proteoglycan metabolic process (GO:0006029)|sensory perception of sound (GO:0007605)|tendon development (GO:0035989)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visual perception (GO:0007601)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)			NS(3)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(17)|kidney(8)|large_intestine(28)|lung(157)|ovary(6)|pancreas(2)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(1)	258		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)		TTGGGCCTGCTCGACCTTTGG	0.478																																					p.R830R		Atlas-SNP	.											COL11A1_ENST00000370096,NS,carcinoma,0,2	COL11A1	972	.	0			c.A2490G						.						92.0	87.0	88.0					1																	103453237		2203	4300	6503	SO:0001819	synonymous_variant	1301	exon30			GCCTGCTCGACCT	J04177	CCDS778.1, CCDS780.1, CCDS780.2, CCDS53348.1	1p21	2013-01-16			ENSG00000060718	ENSG00000060718		"""Collagens"""	2186	protein-coding gene	gene with protein product	"""collagen XI, alpha-1 polypeptide"""	120280		COLL6		3182841	Standard	NM_080630		Approved	STL2, CO11A1	uc001dul.3	P12107	OTTHUMG00000010872	ENST00000370096.3:c.2454A>G	chr1.hg19:g.103453237T>C		52.0	0.0		71.0	4.0	NM_080629	B1ASK7|D3DT73|E9PCU0|Q14034|Q149N0|Q9UIT4|Q9UIT5|Q9UIT6	Silent	SNP	ENST00000370096.3	hg19	CCDS778.1	.	.	.	.	.	.	.	.	.	.	T	8.092	0.774792	0.16051	.	.	ENSG00000060718	ENST00000370090	.	.	.	4.39	0.723	0.18231	.	.	.	.	.	T	0.22666	0.0547	.	.	.	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.09773	-1.0659	7	0.49607	T	0.09	.	3.6269	0.08116	0.3362:0.1692:0.0:0.4946	.	33	F5H5Z5	.	G	33	.	ENSP00000359108:E33G	E	-	2	0	COL11A1	103225825	1.000000	0.71417	0.999000	0.59377	0.733000	0.41908	0.666000	0.25097	0.012000	0.14892	0.377000	0.23210	GAG	.	.		0.478	COL11A1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029997.1	NM_080630	
VAV3	10451	hgsc.bcm.edu	37	1	108226149	108226149	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:108226149T>C	ENST00000370056.4	-	19	2012	c.1738A>G	c.(1738-1740)Acc>Gcc	p.T580A	VAV3_ENST00000371846.4_Missense_Mutation_p.T515A|VAV3_ENST00000527011.1_Missense_Mutation_p.T580A|VAV3_ENST00000544443.1_Intron|VAV3_ENST00000415432.2_Missense_Mutation_p.T20A|VAV3_ENST00000343258.4_5'UTR	NM_006113.4	NP_006104.4	Q9UKW4	VAV3_HUMAN	vav 3 guanine nucleotide exchange factor	580	Sufficient for interaction with ROS1.				angiogenesis (GO:0001525)|apoptotic signaling pathway (GO:0097190)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|cellular response to DNA damage stimulus (GO:0006974)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil chemotaxis (GO:0030593)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cell adhesion (GO:0045785)|positive regulation of GTPase activity (GO:0043547)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of signal transduction (GO:0009967)|regulation of Rac GTPase activity (GO:0032314)|regulation of small GTPase mediated signal transduction (GO:0051056)|response to drug (GO:0042493)|small GTPase mediated signal transduction (GO:0007264)|vesicle fusion (GO:0006906)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|SH3/SH2 adaptor activity (GO:0005070)			NS(2)|breast(5)|endometrium(4)|kidney(2)|large_intestine(14)|lung(20)|ovary(6)|prostate(3)|stomach(1)|urinary_tract(1)	58		all_epithelial(167;5.38e-05)|all_lung(203;0.000314)|Lung NSC(277;0.000594)		Colorectal(144;0.0331)|Lung(183;0.128)|Epithelial(280;0.204)		AGTCCATTGGTCCGTTTCTGT	0.363																																					p.T580A		Atlas-SNP	.											.	VAV3	176	.	0			c.A1738G						.						131.0	108.0	116.0					1																	108226149		2203	4300	6503	SO:0001583	missense	10451	exon19			CATTGGTCCGTTT	AF118886	CCDS785.1, CCDS44181.1	1p13.3	2013-02-14	2007-07-25		ENSG00000134215	ENSG00000134215		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	12659	protein-coding gene	gene with protein product		605541	"""vav 3 oncogene"""				Standard	NM_001079874		Approved		uc001dvk.1	Q9UKW4	OTTHUMG00000010995	ENST00000370056.4:c.1738A>G	chr1.hg19:g.108226149T>C	ENSP00000359073:p.Thr580Ala	108.0	0.0		130.0	7.0	NM_006113	B1AMM0|B1APV5|B4E232|B7ZLR1|E9PQ97|O60498|O95230|Q9Y5X8	Missense_Mutation	SNP	ENST00000370056.4	hg19	CCDS785.1	.	.	.	.	.	.	.	.	.	.	T	8.594	0.885170	0.17540	.	.	ENSG00000134215	ENST00000370056;ENST00000527011;ENST00000415432;ENST00000371846	T;T;T;T	0.77750	0.22;0.23;1.96;-1.12	5.5	1.84	0.25277	Src homology-3 domain (1);	0.536026	0.21020	N	0.081522	T	0.40956	0.1138	L	0.43152	1.355	0.29564	N	0.850424	B;B;B;B;B	0.14012	0.009;0.003;0.001;0.0;0.002	B;B;B;B;B	0.11329	0.004;0.006;0.002;0.001;0.002	T	0.14062	-1.0486	10	0.08599	T	0.76	.	5.2311	0.15422	0.0:0.1788:0.168:0.6532	.	580;580;515;580;20	B7ZLR1;E9PQ97;B4DHL6;Q9UKW4;Q9UKW4-3	.;.;.;VAV3_HUMAN;.	A	580;580;20;515	ENSP00000359073:T580A;ENSP00000432540:T580A;ENSP00000394897:T20A;ENSP00000360912:T515A	ENSP00000359073:T580A	T	-	1	0	VAV3	108027672	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	0.567000	0.23608	0.928000	0.37168	0.477000	0.44152	ACC	.	.		0.363	VAV3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030242.2	NM_006113	
OVGP1	5016	hgsc.bcm.edu	37	1	111957947	111957947	+	Silent	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:111957947T>C	ENST00000369732.3	-	11	1231	c.1176A>G	c.(1174-1176)ttA>ttG	p.L392L	OVGP1_ENST00000540696.1_3'UTR	NM_002557.3	NP_002548.3	Q12889	OVGP1_HUMAN	oviductal glycoprotein 1, 120kDa	392					binding of sperm to zona pellucida (GO:0007339)|carbohydrate metabolic process (GO:0005975)|chitin catabolic process (GO:0006032)|female pregnancy (GO:0007565)|multicellular organism reproduction (GO:0032504)|negative regulation of binding of sperm to zona pellucida (GO:2000360)|single fertilization (GO:0007338)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|egg coat (GO:0035805)|perivitelline space (GO:0098595)	chitinase activity (GO:0004568)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(13)|ovary(4)|prostate(1)|skin(4)|stomach(3)|urinary_tract(1)	39		all_cancers(81;8.18e-06)|all_epithelial(167;5.64e-06)|all_lung(203;0.000152)|Lung NSC(277;0.000302)		Lung(183;0.0253)|Colorectal(144;0.033)|all cancers(265;0.0552)|Epithelial(280;0.0802)|COAD - Colon adenocarcinoma(174;0.123)|LUSC - Lung squamous cell carcinoma(189;0.14)		AAAATTGTGGTAAAGAAGTTG	0.418																																					p.L392L		Atlas-SNP	.											.	OVGP1	177	.	0			c.A1176G						.						46.0	44.0	45.0					1																	111957947		2203	4300	6503	SO:0001819	synonymous_variant	5016	exon11			TTGTGGTAAAGAA	U09550	CCDS834.1	1p13.2	2008-07-31	2008-07-31		ENSG00000085465	ENSG00000085465		"""Mucins"""	8524	protein-coding gene	gene with protein product	"""oviductin"""	603578	"""mucin 9"""	MUC9		7819450, 9341614	Standard	NM_002557		Approved	CHIT5	uc001eba.3	Q12889	OTTHUMG00000011746	ENST00000369732.3:c.1176A>G	chr1.hg19:g.111957947T>C		84.0	0.0		95.0	29.0	NM_002557	A0AV19|B9EGE1|Q15841	Silent	SNP	ENST00000369732.3	hg19	CCDS834.1																																																																																			.	.		0.418	OVGP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032461.1	NM_002557	
PHTF1	10745	hgsc.bcm.edu	37	1	114252943	114252943	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:114252943T>C	ENST00000369604.1	-	11	1685	c.1202A>G	c.(1201-1203)gAg>gGg	p.E401G	PHTF1_ENST00000474926.1_5'UTR|PHTF1_ENST00000393357.2_Missense_Mutation_p.E401G|PHTF1_ENST00000447664.2_3'UTR|PHTF1_ENST00000357783.2_Missense_Mutation_p.E401G|PHTF1_ENST00000369596.2_Missense_Mutation_p.E348G|PHTF1_ENST00000369600.1_Missense_Mutation_p.E348G|PHTF1_ENST00000369598.1_Missense_Mutation_p.E356G			Q9UMS5	PHTF1_HUMAN	putative homeodomain transcription factor 1	401					transcription, DNA-templated (GO:0006351)	cis-Golgi network (GO:0005801)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(3)|kidney(2)|large_intestine(9)|liver(1)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	27	Lung SC(450;0.184)	all_cancers(81;3.78e-08)|all_epithelial(167;5.56e-08)|all_lung(203;6.97e-06)|Lung NSC(69;1.18e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		ATGGGCCCCCTCACTGTCACT	0.522																																					p.E401G		Atlas-SNP	.											.	PHTF1	69	.	0			c.A1202G						.						85.0	77.0	80.0					1																	114252943		2203	4300	6503	SO:0001583	missense	10745	exon10			GCCCCCTCACTGT	AJ011863	CCDS861.1	1p13-p11	2008-07-18			ENSG00000116793	ENSG00000116793			8939	protein-coding gene	gene with protein product		604950		PHTF		10395808	Standard	NM_006608		Approved		uc009wgp.1	Q9UMS5	OTTHUMG00000011800	ENST00000369604.1:c.1202A>G	chr1.hg19:g.114252943T>C	ENSP00000358617:p.Glu401Gly	144.0	0.0		136.0	6.0	NM_006608	Q5VWP7|Q5VWP8|Q9BUP2|Q9H1X8	Missense_Mutation	SNP	ENST00000369604.1	hg19	CCDS861.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	29.8|29.8	5.039560|5.039560	0.93630|0.93630	.|.	.|.	ENSG00000116793|ENSG00000116793	ENST00000369597;ENST00000393357;ENST00000369596;ENST00000369598;ENST00000369600;ENST00000369604;ENST00000357783|ENST00000412670	.|.	.|.	.|.	5.73|5.73	5.73|5.73	0.89815|0.89815	.|.	0.217764|.	0.46442|.	D|.	0.000282|.	T|T	0.47691|0.47691	0.1459|0.1459	L|L	0.38531|0.38531	1.155|1.155	0.80722|0.80722	D|D	1|1	D;P;D|.	0.58268|.	0.969;0.952;0.982|.	P;P;P|.	0.58970|.	0.585;0.724;0.849|.	T|T	0.45425|0.45425	-0.9262|-0.9262	9|5	0.87932|.	D|.	0|.	-24.3535|-24.3535	16.0225|16.0225	0.80509|0.80509	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	401;156;401|.	Q9UMS5;Q5TCR1;Q9UMS5-2|.	PHTF1_HUMAN;.;.|.	G|G	356;401;348;356;348;401;401|157	.|.	ENSP00000350428:E401G|.	E|R	-|-	2|1	0|2	PHTF1|PHTF1	114054466|114054466	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.944000|0.944000	0.59088|0.59088	5.033000|5.033000	0.64146|0.64146	2.198000|2.198000	0.70561|0.70561	0.533000|0.533000	0.62120|0.62120	GAG|AGG	.	.		0.522	PHTF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032666.1	NM_006608	
ATP1A4	480	hgsc.bcm.edu	37	1	160136351	160136351	+	Silent	SNP	C	C	A	rs143083729	byFrequency	TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:160136351C>A	ENST00000368081.4	+	8	1552	c.1081C>A	c.(1081-1083)Cgg>Agg	p.R361R		NM_144699.3	NP_653300.2	Q13733	AT1A4_HUMAN	ATPase, Na+/K+ transporting, alpha 4 polypeptide	361					ATP biosynthetic process (GO:0006754)|ATP hydrolysis coupled proton transport (GO:0015991)|fertilization (GO:0009566)|ion transmembrane transport (GO:0034220)|potassium ion transport (GO:0006813)|regulation of cellular pH (GO:0030641)|regulation of membrane potential (GO:0042391)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sodium:potassium-exchanging ATPase complex (GO:0005890)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|sodium:potassium-exchanging ATPase activity (GO:0005391)			breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(34)|ovary(2)|prostate(4)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	75	all_cancers(52;2.56e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			GCGCATGGCGCGGAAGAACTG	0.567																																					p.R361R		Atlas-SNP	.											ATP1A4,NS,carcinoma,0,1	ATP1A4	167	.	0			c.C1081A						.						89.0	80.0	83.0					1																	160136351		2203	4300	6503	SO:0001819	synonymous_variant	480	exon8			ATGGCGCGGAAGA	BC028297	CCDS1197.1, CCDS44255.1	1q23.2	2012-10-22	2002-02-25		ENSG00000132681	ENSG00000132681		"""ATPases / P-type"""	14073	protein-coding gene	gene with protein product	"""sodium/potassium-transporting ATPase subunit alpha-4"", ""sodium pump subunit alpha-4"", ""sodium-potassium ATPase catalytic subunit alpha-4"""	607321	"""ATPase, Na+/K+ transporting, alpha polypeptide-like 2"""	ATP1AL2		1981991, 3035563	Standard	NM_144699		Approved		uc001fve.4	Q13733	OTTHUMG00000031609	ENST00000368081.4:c.1081C>A	chr1.hg19:g.160136351C>A		152.0	0.0		393.0	0.0	NM_144699	Q504T2|Q7Z4I9|Q8TBN8|Q8WXA7|Q8WXH7|Q8WY13	Silent	SNP	ENST00000368081.4	hg19	CCDS1197.1																																																																																			.	C|0.999;T|0.001		0.567	ATP1A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077415.1	NM_144699	
KLHDC9	126823	hgsc.bcm.edu	37	1	161068653	161068653	+	Silent	SNP	C	C	T			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:161068653C>T	ENST00000368011.4	+	1	470	c.328C>T	c.(328-330)Ctg>Ttg	p.L110L	PFDN2_ENST00000468311.1_5'Flank|KLHDC9_ENST00000490724.2_3'UTR|KLHDC9_ENST00000392192.2_Silent_p.L110L	NM_152366.4	NP_689579.3	Q8NEP7	KLDC9_HUMAN	kelch domain containing 9	110										lung(5)|upper_aerodigestive_tract(1)	6	all_cancers(52;1.28e-19)|Breast(13;0.00188)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00165)			AGTGACCGCACTGGACACAGA	0.716																																					p.L110L		Atlas-SNP	.											.	KLHDC9	16	.	0			c.C328T						.						9.0	11.0	10.0					1																	161068653		2181	4270	6451	SO:0001819	synonymous_variant	126823	exon1			ACCGCACTGGACA	BC022077	CCDS30919.1, CCDS41425.1	1q23.3	2008-02-05			ENSG00000162755	ENSG00000162755			28489	protein-coding gene	gene with protein product	"""kelch/ankyrin repeat containing cyclin A1 interacting protein"""					15159402	Standard	NM_152366		Approved	KARCA1	uc001fxr.3	Q8NEP7	OTTHUMG00000031479	ENST00000368011.4:c.328C>T	chr1.hg19:g.161068653C>T		43.0	0.0		97.0	5.0	NM_001007255	Q5SY56|Q6NXT9|Q6PKN4|Q8N5E1|Q8NA16	Silent	SNP	ENST00000368011.4	hg19	CCDS30919.1																																																																																			.	.		0.716	KLHDC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077092.1	NM_152366	
C1orf226	400793	hgsc.bcm.edu	37	1	162351912	162351912	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:162351912T>C	ENST00000458626.2	+	1	393	c.221T>C	c.(220-222)cTg>cCg	p.L74P	C1orf226_ENST00000426197.2_Missense_Mutation_p.L117P	NM_001085375.1	NP_001078844.1	A1L170	CA226_HUMAN	chromosome 1 open reading frame 226	74										central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	12						CCCTCCAGCCTGGGCAGTGTG	0.597																																					p.L117P		Atlas-SNP	.											.	C1orf226	49	.	0			c.T350C						.						13.0	16.0	15.0					1																	162351912		2050	4197	6247	SO:0001583	missense	400793	exon2			CCAGCCTGGGCAG	AI480219, AK023199, AK125122, AL512785, BC127743	CCDS44268.1, CCDS53422.1	1q23.3	2013-10-11			ENSG00000239887	ENSG00000239887			34351	protein-coding gene	gene with protein product						14702039	Standard	NM_001085375		Approved	FLJ13137	uc010pkt.1	A1L170	OTTHUMG00000031376	ENST00000458626.2:c.221T>C	chr1.hg19:g.162351912T>C	ENSP00000437071:p.Leu74Pro	61.0	0.0		121.0	5.0	NM_001135240	B4DF31	Missense_Mutation	SNP	ENST00000458626.2	hg19	CCDS53422.1	.	.	.	.	.	.	.	.	.	.	T	13.80	2.346658	0.41599	.	.	ENSG00000239887	ENST00000420220;ENST00000426197;ENST00000458626	.	.	.	5.54	3.21	0.36854	.	0.300651	0.21136	N	0.079569	T	0.09335	0.0230	N	0.20986	0.625	.	.	.	B;B	0.27700	0.186;0.046	B;B	0.27170	0.077;0.03	T	0.15896	-1.0421	8	0.40728	T	0.16	-1.4367	1.2255	0.01932	0.149:0.1604:0.1553:0.5354	.	117;74	A1L170-2;A1L170	.;CA226_HUMAN	P	74;117;74	.	ENSP00000398035:L74P	L	+	2	0	C1orf226	160618536	0.409000	0.25368	0.004000	0.12327	0.592000	0.36648	2.274000	0.43390	0.382000	0.24878	0.533000	0.62120	CTG	.	.		0.597	C1orf226-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076793.2	NM_001085375	
ADCY10	55811	hgsc.bcm.edu	37	1	167874253	167874253	+	Silent	SNP	G	G	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:167874253G>C	ENST00000367851.4	-	2	310	c.126C>G	c.(124-126)gtC>gtG	p.V42V	ADCY10_ENST00000367848.1_5'UTR|ADCY10_ENST00000545172.1_Intron|ADCY10_ENST00000476818.2_Silent_p.V42V	NM_018417.4	NP_060887.2	Q96PN6	ADCYA_HUMAN	adenylate cyclase 10 (soluble)	42	Guanylate cyclase 1. {ECO:0000255|PROSITE-ProRule:PRU00099}.				cAMP biosynthetic process (GO:0006171)|intracellular signal transduction (GO:0035556)|positive regulation of apoptotic process (GO:0043065)|spermatogenesis (GO:0007283)	apical part of cell (GO:0045177)|axon (GO:0030424)|basal part of cell (GO:0045178)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|growth cone (GO:0030426)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)			autonomic_ganglia(1)|breast(1)|central_nervous_system(3)|cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(26)|ovary(2)|prostate(4)|skin(6)|stomach(1)|urinary_tract(1)	63						CAAACATCAGGACTCCGTCAA	0.453																																					p.V42V		Atlas-SNP	.											.	ADCY10	175	.	0			c.C126G						.						111.0	106.0	107.0					1																	167874253		2203	4300	6503	SO:0001819	synonymous_variant	55811	exon2			CATCAGGACTCCG	AF271058	CCDS1265.1, CCDS53426.1, CCDS72977.1	1q24	2013-02-04			ENSG00000143199	ENSG00000143199	4.6.1.1	"""Adenylate cyclases"""	21285	protein-coding gene	gene with protein product	"""soluble adenylyl cyclase"", ""Hypercalciuria, absorptive, 2"""	605205					Standard	XM_006711449		Approved	SAC, Sacy, SACI, HCA2, RP1-313L4.2	uc001ger.3	Q96PN6	OTTHUMG00000034573	ENST00000367851.4:c.126C>G	chr1.hg19:g.167874253G>C		167.0	0.0		372.0	84.0	NM_018417	B4DZF0|F5GWS5|O95558|Q5R329|Q5R330|Q8WXV4|Q9NNX0	Silent	SNP	ENST00000367851.4	hg19	CCDS1265.1																																																																																			.	.		0.453	ADCY10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083663.1	NM_018417	
TNN	63923	hgsc.bcm.edu	37	1	175113579	175113579	+	Missense_Mutation	SNP	G	G	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:175113579G>C	ENST00000239462.4	+	18	3765	c.3652G>C	c.(3652-3654)Gat>Cat	p.D1218H		NM_022093.1	NP_071376.1	Q9UQP3	TENN_HUMAN	tenascin N	1218	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				axonogenesis (GO:0007409)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|central_nervous_system(2)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(29)|liver(1)|lung(81)|ovary(5)|prostate(6)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	156		Breast(1374;0.000962)		KIRC - Kidney renal clear cell carcinoma(1967;0.00198)		CAGAGACAATGATATCGCACT	0.512																																					p.D1218H		Atlas-SNP	.											TNN,NS,carcinoma,0,1	TNN	297	.	0			c.G3652C						.						152.0	134.0	140.0					1																	175113579		2203	4300	6503	SO:0001583	missense	63923	exon18			GACAATGATATCG	AK127044	CCDS30943.1	1q23-q24	2013-02-11			ENSG00000120332	ENSG00000120332		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	22942	protein-coding gene	gene with protein product							Standard	NM_022093		Approved		uc001gkl.1	Q9UQP3	OTTHUMG00000034882	ENST00000239462.4:c.3652G>C	chr1.hg19:g.175113579G>C	ENSP00000239462:p.Asp1218His	155.0	0.0		217.0	0.0	NM_022093	B9EGP3|Q5R360	Missense_Mutation	SNP	ENST00000239462.4	hg19	CCDS30943.1	.	.	.	.	.	.	.	.	.	.	G	19.07	3.756837	0.69648	.	.	ENSG00000120332	ENST00000239462;ENST00000539081	D	0.83075	-1.68	5.01	5.01	0.66863	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 2 (1);	0.000000	0.85682	D	0.000000	D	0.95503	0.8539	H	0.99600	4.65	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.97983	1.0350	10	0.87932	D	0	.	17.9026	0.88909	0.0:0.0:1.0:0.0	.	1218	Q9UQP3	TENN_HUMAN	H	1218;1041	ENSP00000239462:D1218H	ENSP00000239462:D1218H	D	+	1	0	TNN	173380202	1.000000	0.71417	0.558000	0.28319	0.489000	0.33432	9.636000	0.98440	2.312000	0.78011	0.478000	0.44815	GAT	.	.		0.512	TNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084422.1	XM_040527	
HMCN1	83872	hgsc.bcm.edu	37	1	186086675	186086675	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:186086675T>C	ENST00000271588.4	+	77	11997	c.11768T>C	c.(11767-11769)gTt>gCt	p.V3923A	HMCN1_ENST00000367492.2_Missense_Mutation_p.V3923A	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	3923	Ig-like C2-type 38.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						GCTTCGGGAGTTCCATTTCCC	0.453																																					p.V3923A		Atlas-SNP	.											.	HMCN1	797	.	0			c.T11768C						.						108.0	103.0	104.0					1																	186086675		2203	4300	6503	SO:0001583	missense	83872	exon77			CGGGAGTTCCATT	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"""Fibulins"", ""Immunoglobulin superfamily / I-set domain containing"""	19194	protein-coding gene	gene with protein product	"""fibulin 6"""	608548	"""age-related macular degeneration 1 (senile macular degeneration)"""	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.11768T>C	chr1.hg19:g.186086675T>C	ENSP00000271588:p.Val3923Ala	73.0	0.0		145.0	6.0	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	hg19	CCDS30956.1	.	.	.	.	.	.	.	.	.	.	T	27.4	4.827410	0.90955	.	.	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.66815	-0.23;-0.23	5.65	5.65	0.86999	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.71247	0.3317	L	0.38733	1.17	0.80722	D	1	D	0.65815	0.995	D	0.78314	0.991	T	0.65463	-0.6162	10	0.06625	T	0.88	.	15.8909	0.79296	0.0:0.0:0.0:1.0	.	3923	Q96RW7	HMCN1_HUMAN	A	3923	ENSP00000271588:V3923A;ENSP00000356462:V3923A	ENSP00000271588:V3923A	V	+	2	0	HMCN1	184353298	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	6.223000	0.72257	2.146000	0.66826	0.533000	0.62120	GTT	.	.		0.453	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935	
PPP1R12B	4660	hgsc.bcm.edu	37	1	202394814	202394814	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:202394814T>C	ENST00000608999.1	+	4	815	c.662T>C	c.(661-663)cTt>cCt	p.L221P	PPP1R12B_ENST00000356764.2_Missense_Mutation_p.L221P|PPP1R12B_ENST00000336894.4_Missense_Mutation_p.L221P|PPP1R12B_ENST00000480184.1_Missense_Mutation_p.L221P	NM_001197131.1|NM_002481.3	NP_001184060.1|NP_002472.2	O60237	MYPT2_HUMAN	protein phosphatase 1, regulatory subunit 12B	221					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|positive regulation of catalytic activity (GO:0043085)|regulation of muscle contraction (GO:0006937)|signal transduction (GO:0007165)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	enzyme activator activity (GO:0008047)			central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(7)|lung(17)|ovary(4)|skin(3)|urinary_tract(1)	41			BRCA - Breast invasive adenocarcinoma(75;0.166)			GCTACAGCCCTTCATGTGGCT	0.512																																					p.L221P		Atlas-SNP	.											.	PPP1R12B	100	.	0			c.T662C						.						136.0	146.0	143.0					1																	202394814		2203	4300	6503	SO:0001583	missense	4660	exon4			CAGCCCTTCATGT	AB003062	CCDS1426.1, CCDS44294.1, CCDS44295.1, CCDS53458.1, CCDS53459.1, CCDS73005.1	1q32.1	2013-01-10	2011-10-04	2001-08-10	ENSG00000077157	ENSG00000077157		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Ankyrin repeat domain containing"""	7619	protein-coding gene	gene with protein product	"""myosin phosphatase regulatory subunit"", ""myosin phosphatase, target subunit 2"""	603768	"""protein phosphatase 1, regulatory (inhibitor) subunit 12B"""	MYPT2		9570949	Standard	NM_002481		Approved	MGC87886, MGC131980, PP1bp55	uc001gya.2	O60237	OTTHUMG00000041393	ENST00000608999.1:c.662T>C	chr1.hg19:g.202394814T>C	ENSP00000476755:p.Leu221Pro	65.0	0.0		174.0	7.0	NM_002481	A8MYF5|B7ZMN6|Q2TAI8|Q5T506|Q5VUK2|Q8N179|Q9HCB7|Q9HCB8	Missense_Mutation	SNP	ENST00000608999.1	hg19	CCDS1426.1	.	.	.	.	.	.	.	.	.	.	T	23.1	4.378634	0.82682	.	.	ENSG00000077157	ENST00000406302;ENST00000336894;ENST00000480184;ENST00000356764	T;T;T;T	0.79352	-1.26;-1.26;-1.26;-1.26	5.51	5.51	0.81932	Ankyrin repeat-containing domain (3);	0.000000	0.56097	D	0.000039	D	0.92603	0.7650	H	0.98199	4.17	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.95263	0.8370	10	0.87932	D	0	.	15.625	0.76848	0.0:0.0:0.0:1.0	.	221;221;221;221	O60237-2;O60237;F8W8M3;Q2TAI8	.;MYPT2_HUMAN;.;.	P	221	ENSP00000384496:L221P;ENSP00000337897:L221P;ENSP00000417159:L221P;ENSP00000349206:L221P	ENSP00000337897:L221P	L	+	2	0	PPP1R12B	200661437	1.000000	0.71417	0.717000	0.30585	0.908000	0.53690	8.027000	0.88791	2.094000	0.63399	0.383000	0.25322	CTT	.	.		0.512	PPP1R12B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000099166.3	NM_032105	
PARP1	142	hgsc.bcm.edu	37	1	226570841	226570841	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:226570841T>C	ENST00000366794.5	-	8	1198	c.1055A>G	c.(1054-1056)aAa>aGa	p.K352R		NM_001618.3	NP_001609.2	P09874	PARP1_HUMAN	poly (ADP-ribose) polymerase 1	352					base-excision repair (GO:0006284)|cellular response to insulin stimulus (GO:0032869)|DNA damage response, detection of DNA damage (GO:0042769)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|gene expression (GO:0010467)|macrophage differentiation (GO:0030225)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription regulatory region DNA binding (GO:2000679)|protein ADP-ribosylation (GO:0006471)|protein autoprocessing (GO:0016540)|protein poly-ADP-ribosylation (GO:0070212)|regulation of growth rate (GO:0040009)|signal transduction involved in regulation of gene expression (GO:0023019)|telomere maintenance (GO:0000723)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|NAD binding (GO:0051287)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|poly(A) RNA binding (GO:0044822)|protein N-terminus binding (GO:0047485)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			breast(2)|endometrium(4)|kidney(4)|large_intestine(8)|lung(15)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	44	Breast(184;0.133)			GBM - Glioblastoma multiforme(131;0.0531)		ACGGTCCTGTTTTTTAACCTT	0.502								Poly(ADP-ribose) polymerase (PARP) enzymes that bind to DNA																													p.K352R		Atlas-SNP	.											PARP1,NS,carcinoma,0,1	PARP1	100	.	0			c.A1055G						.						115.0	143.0	134.0					1																	226570841		2203	4300	6503	SO:0001583	missense	142	exon8			TCCTGTTTTTTAA	BC037545	CCDS1554.1	1q41-q42	2010-02-16	2008-07-28	2004-08-26	ENSG00000143799	ENSG00000143799	2.4.2.30	"""Poly (ADP-ribose) polymerases"""	270	protein-coding gene	gene with protein product		173870	"""ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)"", ""poly (ADP-ribose) polymerase family, member 1"""	PPOL, ADPRT		10964595	Standard	NM_001618		Approved	PARP	uc001hqd.4	P09874	OTTHUMG00000037556	ENST00000366794.5:c.1055A>G	chr1.hg19:g.226570841T>C	ENSP00000355759:p.Lys352Arg	78.0	0.0		148.0	0.0	NM_001618	B1ANJ4|Q8IUZ9	Missense_Mutation	SNP	ENST00000366794.5	hg19	CCDS1554.1	.	.	.	.	.	.	.	.	.	.	T	8.952	0.968513	0.18659	.	.	ENSG00000143799	ENST00000366794	T	0.10192	2.9	5.27	2.95	0.34219	.	0.147960	0.64402	N	0.000015	T	0.04724	0.0128	N	0.08118	0	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.42258	-0.9462	10	0.15952	T	0.53	-10.5467	7.8417	0.29402	0.0:0.2327:0.0:0.7673	.	352	P09874	PARP1_HUMAN	R	352	ENSP00000355759:K352R	ENSP00000355759:K352R	K	-	2	0	PARP1	224637464	0.897000	0.30589	0.987000	0.45799	0.573000	0.36030	0.922000	0.28734	0.323000	0.23307	0.459000	0.35465	AAA	.	.		0.502	PARP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091519.1	NM_001618	
WNT3A	89780	hgsc.bcm.edu	37	1	228238561	228238561	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:228238561G>A	ENST00000284523.1	+	3	596	c.518G>A	c.(517-519)cGg>cAg	p.R173Q	WNT3A_ENST00000366753.2_Missense_Mutation_p.R173Q	NM_033131.3	NP_149122.1	P56704	WNT3A_HUMAN	wingless-type MMTV integration site family, member 3A	173					axis elongation involved in somitogenesis (GO:0090245)|axon guidance (GO:0007411)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in cardiac muscle cell fate commitment (GO:0061317)|cell proliferation in forebrain (GO:0021846)|cellular protein localization (GO:0034613)|cellular response to retinoic acid (GO:0071300)|COP9 signalosome assembly (GO:0010387)|dorsal/ventral neural tube patterning (GO:0021904)|extracellular matrix organization (GO:0030198)|heart looping (GO:0001947)|hemopoiesis (GO:0030097)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|inner ear morphogenesis (GO:0042472)|mammary gland development (GO:0030879)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron projection development (GO:0010977)|neuron differentiation (GO:0030182)|osteoblast differentiation (GO:0001649)|palate development (GO:0060021)|paraxial mesodermal cell fate commitment (GO:0048343)|platelet aggregation (GO:0070527)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of canonical Wnt signaling pathway involved in controlling type B pancreatic cell proliferation (GO:2000081)|positive regulation of cardiac muscle cell differentiation (GO:2000727)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-cell adhesion mediated by cadherin (GO:2000049)|positive regulation of collateral sprouting in absence of injury (GO:0048697)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of dermatome development (GO:0061184)|positive regulation of mesodermal cell fate specification (GO:0048337)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of receptor internalization (GO:0002092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|post-anal tail morphogenesis (GO:0036342)|regulation of microtubule cytoskeleton organization (GO:0070507)|skeletal muscle cell differentiation (GO:0035914)|spinal cord association neuron differentiation (GO:0021527)|Wnt signaling pathway involved in forebrain neuroblast division (GO:0021874)	cell surface (GO:0009986)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)|receptor agonist activity (GO:0048018)|transcription coactivator activity (GO:0003713)			kidney(1)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)	12		Prostate(94;0.0405)				GCCGACGCCCGGGAGAACCGG	0.657																																					p.R173Q		Atlas-SNP	.											.	WNT3A	40	.	0			c.G518A						.						56.0	56.0	56.0					1																	228238561		2203	4300	6503	SO:0001583	missense	89780	exon3			ACGCCCGGGAGAA	AB060284	CCDS1564.1	1q42	2013-02-28			ENSG00000154342	ENSG00000154342		"""Wingless-type MMTV integration sites"", ""Endogenous ligands"""	15983	protein-coding gene	gene with protein product		606359				11414706	Standard	NM_033131		Approved		uc001hrq.2	P56704	OTTHUMG00000037593	ENST00000284523.1:c.518G>A	chr1.hg19:g.228238561G>A	ENSP00000284523:p.Arg173Gln	123.0	0.0		237.0	47.0	NM_033131	Q3SY79|Q3SY80|Q969P2	Missense_Mutation	SNP	ENST00000284523.1	hg19	CCDS1564.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.127804	0.77549	.	.	ENSG00000154342	ENST00000284523;ENST00000366753	T;T	0.76578	-1.03;-1.03	4.78	4.78	0.61160	.	0.000000	0.85682	D	0.000000	T	0.76169	0.3950	L	0.57130	1.785	0.80722	D	1	B;B	0.27416	0.059;0.178	B;B	0.28139	0.025;0.086	T	0.75181	-0.3408	10	0.45353	T	0.12	.	17.8158	0.88634	0.0:0.0:1.0:0.0	.	173;173	P56704;Q3SY79	WNT3A_HUMAN;.	Q	173	ENSP00000284523:R173Q;ENSP00000355715:R173Q	ENSP00000284523:R173Q	R	+	2	0	WNT3A	226305184	1.000000	0.71417	0.876000	0.34364	0.740000	0.42216	9.787000	0.99055	2.221000	0.72209	0.591000	0.81541	CGG	.	.		0.657	WNT3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091648.1	NM_033131	
SIPA1L2	57568	hgsc.bcm.edu	37	1	232568017	232568017	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:232568017T>C	ENST00000366630.1	-	15	4590	c.4232A>G	c.(4231-4233)gAg>gGg	p.E1411G	SIPA1L2_ENST00000262861.4_Missense_Mutation_p.E1411G|SIPA1L2_ENST00000308942.4_Missense_Mutation_p.E485G			Q9P2F8	SI1L2_HUMAN	signal-induced proliferation-associated 1 like 2	1411					regulation of small GTPase mediated signal transduction (GO:0051056)		GTPase activator activity (GO:0005096)			NS(1)|breast(5)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(49)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	103		all_cancers(173;0.00605)|Prostate(94;0.128)|all_epithelial(177;0.186)				CACTTCAGGCTCCTCGGGCGG	0.537																																					p.E1411G		Atlas-SNP	.											.	SIPA1L2	218	.	0			c.A4232G						.						51.0	49.0	50.0					1																	232568017		1888	4116	6004	SO:0001583	missense	57568	exon14			TCAGGCTCCTCGG	AB037810	CCDS41474.1	1q42.2	2008-02-05			ENSG00000116991	ENSG00000116991			23800	protein-coding gene	gene with protein product		611609					Standard	NM_020808		Approved	KIAA1389	uc001hvg.3	Q9P2F8	OTTHUMG00000037820	ENST00000366630.1:c.4232A>G	chr1.hg19:g.232568017T>C	ENSP00000355589:p.Glu1411Gly	105.0	0.0		180.0	8.0	NM_020808	Q2TV88|Q5VXR7|Q5VXR8|Q641Q4|Q8NA38|Q96DZ3|Q9H9F6	Missense_Mutation	SNP	ENST00000366630.1	hg19	CCDS41474.1	.	.	.	.	.	.	.	.	.	.	T	14.42	2.530028	0.45073	.	.	ENSG00000116991	ENST00000366630;ENST00000262861;ENST00000308942	T;T;T	0.79033	-1.23;-1.23;2.71	5.92	5.92	0.95590	.	0.207654	0.43579	D	0.000549	T	0.71584	0.3357	L	0.43152	1.355	0.54753	D	0.999984	B;B	0.14012	0.001;0.009	B;B	0.15484	0.003;0.013	T	0.65747	-0.6093	10	0.23302	T	0.38	-29.9839	16.3648	0.83312	0.0:0.0:0.0:1.0	.	1411;485	Q9P2F8;Q9P2F8-2	SI1L2_HUMAN;.	G	1411;1411;485	ENSP00000355589:E1411G;ENSP00000262861:E1411G;ENSP00000309102:E485G	ENSP00000262861:E1411G	E	-	2	0	SIPA1L2	230634640	1.000000	0.71417	0.996000	0.52242	0.895000	0.52256	4.830000	0.62745	2.263000	0.75096	0.533000	0.62120	GAG	.	.		0.537	SIPA1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092318.1	XM_045839	
OR2C3	81472	hgsc.bcm.edu	37	1	247695757	247695757	+	Silent	SNP	G	G	C	rs61746303|rs386641879	byFrequency	TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:247695757G>C	ENST00000366487.3	-	2	418	c.57C>G	c.(55-57)tcC>tcG	p.S19S	GCSAML_ENST00000366489.1_Intron|GCSAML_ENST00000463359.1_Intron|GCSAML_ENST00000527541.1_Intron|GCSAML_ENST00000366490.3_Intron|GCSAML_ENST00000527084.1_Intron|GCSAML_ENST00000366491.2_Intron|GCSAML_ENST00000531662.1_Intron	NM_198074.4	NP_932340	Q8N628	OR2C3_HUMAN	olfactory receptor, family 2, subfamily C, member 3	19						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S19S(1)|p.S18S(1)		breast(1)|endometrium(5)|large_intestine(2)|lung(31)|ovary(1)|prostate(1)|skin(2)	43	all_cancers(71;4.51e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.0242)	OV - Ovarian serous cystadenocarcinoma(106;0.0241)			AGGGTCGTGTGGAGAAGCCCA	0.488																																					p.S19S		Atlas-SNP	.											OR2C3,NS,carcinoma,0,2	OR2C3	92	.	2	Substitution - coding silent(2)	prostate(2)	c.C57G						.						78.0	73.0	74.0					1																	247695757		2203	4300	6503	SO:0001819	synonymous_variant	81472	exon2			TCGTGTGGAGAAG	BC030717	CCDS1634.2	1q44	2014-02-19	2002-02-28		ENSG00000196242	ENSG00000196242		"""GPCR / Class A : Olfactory receptors"""	15005	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily C, member 4"""	OR2C4, OR2C5P			Standard	NM_198074		Approved	OST742	uc009xgy.3	Q8N628	OTTHUMG00000040579	ENST00000366487.3:c.57C>G	chr1.hg19:g.247695757G>C		108.0	0.0		195.0	0.0	NM_198074	Q5JQS4|Q6IEZ1|Q8NGW7	Silent	SNP	ENST00000366487.3	hg19	CCDS1634.2																																																																																			.	G|0.996;A|0.004		0.488	OR2C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097626.2	NM_198074	
TAF1B	9014	hgsc.bcm.edu	37	2	10045015	10045015	+	Nonsense_Mutation	SNP	A	A	T			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:10045015A>T	ENST00000263663.5	+	9	1023	c.835A>T	c.(835-837)Aaa>Taa	p.K279*	TAF1B_ENST00000396242.3_Nonsense_Mutation_p.K24*	NM_005680.2	NP_005671	Q53T94	TAF1B_HUMAN	TATA box binding protein (TBP)-associated factor, RNA polymerase I, B, 63kDa	279	C-terminal cyclin fold.				gene expression (GO:0010467)|RNA polymerase I transcriptional preinitiation complex assembly at the promoter for the nuclear large rRNA transcript (GO:0001189)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|RNA polymerase I core factor complex (GO:0070860)	metal ion binding (GO:0046872)|RNA polymerase I CORE element sequence-specific DNA binding (GO:0001164)|RNA polymerase I CORE element sequence-specific DNA binding transcription factor recruiting transcription factor activity (GO:0001187)|sequence-specific DNA binding transcription factor activity (GO:0003700)|TBP-class protein binding (GO:0017025)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|lung(4)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	14	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					GGACATCTACAAAAAAACAGT	0.328																																					p.K279X		Atlas-SNP	.											TAF1B,NS,carcinoma,0,1	TAF1B	62	.	0			c.A835T						.						75.0	65.0	68.0					2																	10045015		2203	4300	6503	SO:0001587	stop_gained	9014	exon9			ATCTACAAAAAAA	L39061	CCDS33143.1	2p25	2008-06-02	2002-08-29		ENSG00000115750	ENSG00000115750			11533	protein-coding gene	gene with protein product		604904	"""TATA box binding protein (TBP)-associated factor, RNA polymerase I, B, 63kD"""			7801123	Standard	NM_005680		Approved	TAFI63, SL1, RAF1B, RAFI63	uc002qzz.3	Q53T94	OTTHUMG00000151673	ENST00000263663.5:c.835A>T	chr2.hg19:g.10045015A>T	ENSP00000263663:p.Lys279*	29.0	0.0		72.0	0.0	NM_005680	B4DI42|F8WD72|Q15574|Q8WVC3	Nonsense_Mutation	SNP	ENST00000263663.5	hg19	CCDS33143.1	.	.	.	.	.	.	.	.	.	.	A	25.5	4.648783	0.87958	.	.	ENSG00000115750	ENST00000263663;ENST00000396242	.	.	.	5.46	0.00658	0.14068	.	0.641420	0.17120	N	0.186264	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-14.238	2.8251	0.05483	0.6069:0.1237:0.1497:0.1198	.	.	.	.	X	279;24	.	.	K	+	1	0	TAF1B	9962466	0.964000	0.33143	0.630000	0.29268	0.414000	0.31173	0.565000	0.23578	0.355000	0.24131	0.383000	0.25322	AAA	.	.		0.328	TAF1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323426.2	NM_005680	
WDR35	57539	hgsc.bcm.edu	37	2	20162082	20162082	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:20162082T>C	ENST00000345530.3	-	11	1316	c.1201A>G	c.(1201-1203)Aac>Gac	p.N401D	WDR35_ENST00000281405.4_Intron|WDR35_ENST00000416055.2_Intron	NM_001006657.1	NP_001006658.1	Q9P2L0	WDR35_HUMAN	WD repeat domain 35	401					cilium assembly (GO:0042384)|intraciliary retrograde transport (GO:0035721)	axoneme (GO:0005930)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|intraciliary transport particle A (GO:0030991)				breast(1)|endometrium(5)|kidney(8)|large_intestine(8)|lung(16)|ovary(2)|prostate(1)|skin(1)|stomach(1)	43	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TCCATCTCGTTCTCCTCCTTT	0.333																																					p.N401D		Atlas-SNP	.											.	WDR35	92	.	0			c.A1201G						.						125.0	120.0	122.0					2																	20162082		2203	4300	6503	SO:0001583	missense	57539	exon11			TCTCGTTCTCCTC	AB037757	CCDS1695.1, CCDS33152.1	2p24.3	2014-02-21			ENSG00000118965	ENSG00000118965		"""WD repeat domain containing"", ""Intraflagellar transport homologs"""	29250	protein-coding gene	gene with protein product		613602				10718198	Standard	NM_001006657		Approved	MGC33196, KIAA1336, IFT121, IFTA1	uc002rdi.3	Q9P2L0	OTTHUMG00000090737	ENST00000345530.3:c.1201A>G	chr2.hg19:g.20162082T>C	ENSP00000314444:p.Asn401Asp	26.0	0.0		67.0	4.0	NM_001006657	B3KVI5|Q4ZG01|Q8NE11	Missense_Mutation	SNP	ENST00000345530.3	hg19	CCDS33152.1	.	.	.	.	.	.	.	.	.	.	T	9.584	1.124435	0.20959	.	.	ENSG00000118965	ENST00000345530	T	0.64438	-0.1	4.95	2.51	0.30379	.	0.627364	0.17343	N	0.177670	T	0.29190	0.0726	N	0.02539	-0.55	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.04495	-1.0947	10	0.33141	T	0.24	-7.5428	2.2218	0.03974	0.1562:0.0885:0.1619:0.5934	.	401	Q9P2L0	WDR35_HUMAN	D	401	ENSP00000314444:N401D	ENSP00000314444:N401D	N	-	1	0	WDR35	20025563	0.899000	0.30636	0.981000	0.43875	0.993000	0.82548	0.641000	0.24720	0.415000	0.25817	0.482000	0.46254	AAC	.	.		0.333	WDR35-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000207472.2	NM_020779	
ITSN2	50618	hgsc.bcm.edu	37	2	24469141	24469141	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:24469141T>C	ENST00000355123.4	-	29	3877	c.3434A>G	c.(3433-3435)gAg>gGg	p.E1145G	ITSN2_ENST00000361999.3_Missense_Mutation_p.E1118G|ITSN2_ENST00000406921.3_Missense_Mutation_p.E1145G	NM_006277.2	NP_006268.2	Q9NZM3	ITSN2_HUMAN	intersectin 2	1145	SH3 5. {ECO:0000255|PROSITE- ProRule:PRU00192}.				endocytosis (GO:0006897)|positive regulation of signal transduction (GO:0009967)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|SH3/SH2 adaptor activity (GO:0005070)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(8)|large_intestine(11)|liver(3)|lung(28)|ovary(2)|stomach(1)	61	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GAAACTGAGCTCATCTTCATT	0.368																																					p.E1145G		Atlas-SNP	.											.	ITSN2	224	.	0			c.A3434G						.						150.0	137.0	141.0					2																	24469141		2203	4300	6503	SO:0001583	missense	50618	exon29			CTGAGCTCATCTT	AB033082	CCDS1710.2, CCDS1711.2, CCDS46230.1	2p23.3	2013-09-19	2002-10-30		ENSG00000198399	ENSG00000198399		"""Rho guanine nucleotide exchange factors"", ""EF-hand domain containing"""	6184	protein-coding gene	gene with protein product	"""SH3 domain protein 1B"", ""SH3P18-like WASP associated protein"""	604464	"""SH3 domain protein 1B"""	SH3D1B		10922467, 11748279	Standard	NM_006277		Approved	KIAA1256, SWAP, SH3P18, SWA, PRO2015	uc002rfe.2	Q9NZM3	OTTHUMG00000090818	ENST00000355123.4:c.3434A>G	chr2.hg19:g.24469141T>C	ENSP00000347244:p.Glu1145Gly	82.0	0.0		120.0	5.0	NM_147152	O95062|Q15812|Q9HAK4|Q9NXE6|Q9NYG0|Q9NZM2|Q9ULG4	Missense_Mutation	SNP	ENST00000355123.4	hg19	CCDS1710.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	28.1|28.1	4.893867|4.893867	0.91889|0.91889	.|.	.|.	ENSG00000198399|ENSG00000198399	ENST00000361999;ENST00000355123;ENST00000380868;ENST00000406921|ENST00000416160	T;T;T;T|.	0.65732|.	-0.17;-0.17;-0.17;-0.17|.	5.53|5.53	5.53|5.53	0.82687|0.82687	Src homology-3 domain (5);|.	0.000000|.	0.34245|.	U|.	0.004122|.	T|T	0.77519|0.77519	0.4142|0.4142	M|M	0.81802|0.81802	2.56|2.56	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.91635|.	0.999;0.999;0.999|.	T|T	0.79112|0.79112	-0.1937|-0.1937	10|5	0.87932|.	D|.	0|.	.|.	15.9649|15.9649	0.79961|0.79961	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	1145;1118;1145|.	Q9NZM3-3;Q9NZM3-2;Q9NZM3|.	.;.;ITSN2_HUMAN|.	G|G	1118;1145;1118;1145|73	ENSP00000354561:E1118G;ENSP00000347244:E1145G;ENSP00000370250:E1118G;ENSP00000384499:E1145G|.	ENSP00000347244:E1145G|.	E|S	-|-	2|1	0|0	ITSN2|ITSN2	24322645|24322645	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.978000|0.978000	0.69477|0.69477	7.649000|7.649000	0.83500|0.83500	2.239000|2.239000	0.73571|0.73571	0.383000|0.383000	0.25322|0.25322	GAG|AGC	.	.		0.368	ITSN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207620.2	NM_006277	
HADHB	3032	hgsc.bcm.edu	37	2	26505888	26505888	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:26505888T>C	ENST00000317799.5	+	12	1134	c.1030T>C	c.(1030-1032)Tct>Cct	p.S344P	HADHB_ENST00000405867.3_Missense_Mutation_p.S221P|HADHB_ENST00000545822.1_Missense_Mutation_p.S322P|HADHB_ENST00000537713.1_Missense_Mutation_p.S329P|HADHB_ENST00000494615.1_3'UTR	NM_000183.2	NP_000174.1	P55084	ECHB_HUMAN	hydroxyacyl-CoA dehydrogenase/3-ketoacyl-CoA thiolase/enoyl-CoA hydratase (trifunctional protein), beta subunit	344					cardiolipin acyl-chain remodeling (GO:0035965)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|glycerophospholipid biosynthetic process (GO:0046474)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|mitochondrial envelope (GO:0005740)|mitochondrial fatty acid beta-oxidation multienzyme complex (GO:0016507)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|acetyl-CoA C-acyltransferase activity (GO:0003988)|enoyl-CoA hydratase activity (GO:0004300)|fatty-acyl-CoA binding (GO:0000062)|long-chain-3-hydroxyacyl-CoA dehydrogenase activity (GO:0016509)|long-chain-enoyl-CoA hydratase activity (GO:0016508)|NAD binding (GO:0051287)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)|skin(1)	19	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TATGTATGTGTCTCAGGATCC	0.318																																					p.S344P		Atlas-SNP	.											.	HADHB	50	.	0			c.T1030C						.						158.0	160.0	159.0					2																	26505888		2203	4300	6503	SO:0001583	missense	3032	exon12			TATGTGTCTCAGG		CCDS1722.1, CCDS62871.1, CCDS62872.1	2p23	2010-04-30	2010-04-30		ENSG00000138029	ENSG00000138029	2.3.1.16		4803	protein-coding gene	gene with protein product	"""mitochondrial trifunctional protein, beta subunit"""	143450	"""hydroxyacyl-Coenzyme A dehydrogenase/3-ketoacyl-Coenzyme A thiolase/enoyl-Coenzyme A hydratase (trifunctional protein), beta subunit"""			9605857	Standard	NM_000183		Approved	MTPB	uc002rgz.3	P55084	OTTHUMG00000096978	ENST00000317799.5:c.1030T>C	chr2.hg19:g.26505888T>C	ENSP00000325136:p.Ser344Pro	87.0	0.0		129.0	6.0	NM_000183	B2RB16|B4E2W0|O14969|Q53TA6|Q96C77|Q9H3F5|Q9T2V8	Missense_Mutation	SNP	ENST00000317799.5	hg19	CCDS1722.1	.	.	.	.	.	.	.	.	.	.	T	19.86	3.905481	0.72868	.	.	ENSG00000138029	ENST00000317799;ENST00000405867;ENST00000537713;ENST00000545822	D;D;D;D	0.93019	-3.15;-3.15;-3.15;-3.15	5.95	5.95	0.96441	Thiolase-like, subgroup (1);Thiolase-like (1);Thiolase, C-terminal (1);	0.048692	0.85682	D	0.000000	D	0.97012	0.9024	M	0.86573	2.825	0.80722	D	1	P;P;D;D	0.76494	0.952;0.933;0.999;0.961	P;P;D;P	0.83275	0.713;0.811;0.996;0.811	D	0.97637	1.0146	10	0.87932	D	0	-14.1637	15.2563	0.73588	0.0:0.0:0.0:1.0	.	329;322;221;344	F5GZQ3;B4E2W0;B5MD38;P55084	.;.;.;ECHB_HUMAN	P	344;221;329;322	ENSP00000325136:S344P;ENSP00000385411:S221P;ENSP00000444295:S329P;ENSP00000442665:S322P	ENSP00000325136:S344P	S	+	1	0	HADHB	26359392	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	7.599000	0.82757	2.281000	0.76405	0.528000	0.53228	TCT	.	.		0.318	HADHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214050.2	NM_000183	
PLB1	151056	hgsc.bcm.edu	37	2	28788183	28788183	+	Silent	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:28788183T>C	ENST00000327757.5	+	19	1287	c.1243T>C	c.(1243-1245)Ttg>Ctg	p.L415L	PLB1_ENST00000422425.2_Silent_p.L426L|PLB1_ENST00000329020.6_Silent_p.L103L	NM_153021.4	NP_694566.4	Q6P1J6	PLB1_HUMAN	phospholipase B1	415	4 X 308-326 AA approximate repeats.				glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phospholipid metabolic process (GO:0006644)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	lysophospholipase activity (GO:0004622)|phospholipase A2 activity (GO:0004623)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(31)|ovary(6)|prostate(1)|skin(7)|stomach(2)	69	Acute lymphoblastic leukemia(172;0.155)					TGGGAACGTCTTGGACGTCTT	0.612																																					p.L426L		Atlas-SNP	.											.	PLB1	255	.	0			c.T1276C						.						69.0	61.0	64.0					2																	28788183		2203	4300	6503	SO:0001819	synonymous_variant	151056	exon19			AACGTCTTGGACG		CCDS33168.1, CCDS54340.1	2p23.3	2014-03-14			ENSG00000163803	ENSG00000163803	3.1.1.4, 3.1.1.5		30041	protein-coding gene	gene with protein product		610179				12150957	Standard	NM_153021		Approved	PLB, FLJ30866	uc002rmb.2	Q6P1J6	OTTHUMG00000152014	ENST00000327757.5:c.1243T>C	chr2.hg19:g.28788183T>C		86.0	0.0		99.0	4.0	NM_001170585	A8KAX2|Q53S03|Q8IUP7|Q96DP9	Silent	SNP	ENST00000327757.5	hg19	CCDS33168.1																																																																																			.	.		0.612	PLB1-012	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353348.2		
SPDYA	245711	hgsc.bcm.edu	37	2	29041943	29041943	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:29041943A>G	ENST00000334056.5	+	4	454	c.265A>G	c.(265-267)Atg>Gtg	p.M89V	SPDYA_ENST00000379579.4_Missense_Mutation_p.M89V|SPDYA_ENST00000462832.1_3'UTR	NM_182756.3	NP_877433.2			speedy/RINGO cell cycle regulator family member A											cervix(1)|endometrium(1)|large_intestine(2)|lung(1)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	9	Acute lymphoblastic leukemia(172;0.155)					TTTCTTGTGGATGGACTGCTG	0.303																																					p.M89V		Atlas-SNP	.											.	SPDYA	41	.	0			c.A265G						.						129.0	131.0	130.0					2																	29041943		2203	4300	6503	SO:0001583	missense	245711	exon3			TTGTGGATGGACT	AA424209	CCDS1767.2	2p23	2013-05-08	2013-05-08	2006-03-31	ENSG00000163806	ENSG00000163806		"""Speedy homologs"""	30613	protein-coding gene	gene with protein product		614029	"""speedy homolog 1 (Drosophila)"", ""speedy homolog A (Xenopus laevis)"""	SPDY1		11980914, 12839962, 15611625	Standard	NM_182756		Approved	SPY1, Ringo3	uc002rmk.3	Q5MJ70	OTTHUMG00000074041	ENST00000334056.5:c.265A>G	chr2.hg19:g.29041943A>G	ENSP00000335628:p.Met89Val	62.0	0.0		95.0	4.0	NM_001142634		Missense_Mutation	SNP	ENST00000334056.5	hg19	CCDS1767.2	.	.	.	.	.	.	.	.	.	.	A	18.87	3.716049	0.68844	.	.	ENSG00000163806	ENST00000379579;ENST00000334056;ENST00000449210	.	.	.	5.03	5.03	0.67393	.	0.000000	0.85682	U	0.000000	T	0.67468	0.2896	M	0.67953	2.075	0.58432	D	0.999996	D;P	0.54047	0.964;0.915	P;P	0.53102	0.718;0.596	T	0.71619	-0.4538	9	0.59425	D	0.04	-17.5259	15.054	0.71897	1.0:0.0:0.0:0.0	.	89;89	Q5MJ70;Q5MJ70-1	SPDYA_HUMAN;.	V	89	.	ENSP00000335628:M89V	M	+	1	0	SPDYA	28895447	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.343000	0.65976	2.016000	0.59253	0.533000	0.62120	ATG	.	.		0.303	SPDYA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157171.1	NM_182756	
BIRC6	57448	hgsc.bcm.edu	37	2	32733177	32733177	+	Silent	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:32733177T>C	ENST00000421745.2	+	51	9965	c.9831T>C	c.(9829-9831)gcT>gcC	p.A3277A		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	3277					apoptotic process (GO:0006915)|labyrinthine layer development (GO:0060711)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of cytokinesis (GO:0032465)|spongiotrophoblast layer development (GO:0060712)	endosome (GO:0005768)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|spindle pole (GO:0000922)|trans-Golgi network (GO:0005802)	acid-amino acid ligase activity (GO:0016881)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|ubiquitin-protein transferase activity (GO:0004842)			NS(4)|breast(8)|central_nervous_system(3)|endometrium(21)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(31)|lung(65)|ovary(7)|pancreas(1)|prostate(5)|skin(5)|stomach(1)|urinary_tract(5)	172	Acute lymphoblastic leukemia(172;0.155)					TAGCTTCTGCTGTCTGCCTTA	0.458																																					p.A3277A	Pancreas(94;175 1509 16028 18060 45422)	Atlas-SNP	.											.	BIRC6	838	.	0			c.T9831C						.						96.0	88.0	91.0					2																	32733177		2203	4300	6503	SO:0001819	synonymous_variant	57448	exon51			TTCTGCTGTCTGC	AF265555	CCDS33175.2	2p22.3	2011-01-25	2011-01-25		ENSG00000115760	ENSG00000115760		"""Baculoviral IAP repeat containing"", ""Ubiquitin-conjugating enzymes E2"""	13516	protein-coding gene	gene with protein product	"""apollon"""	605638	"""baculoviral IAP repeat-containing 6"""			10544019	Standard	NM_016252		Approved	BRUCE	uc010ezu.3	Q9NR09	OTTHUMG00000150528	ENST00000421745.2:c.9831T>C	chr2.hg19:g.32733177T>C		167.0	0.0		216.0	92.0	NM_016252	Q9ULD1	Silent	SNP	ENST00000421745.2	hg19	CCDS33175.2																																																																																			.	.		0.458	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252	
LTBP1	4052	hgsc.bcm.edu	37	2	33413701	33413701	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:33413701T>C	ENST00000404816.2	+	7	1837	c.1484T>C	c.(1483-1485)gTc>gCc	p.V495A	LTBP1_ENST00000390003.4_Missense_Mutation_p.V169A|LTBP1_ENST00000418533.2_Missense_Mutation_p.V169A|LTBP1_ENST00000407925.1_Missense_Mutation_p.V169A|LTBP1_ENST00000404525.1_Missense_Mutation_p.V169A|LTBP1_ENST00000402934.1_Missense_Mutation_p.V169A|LTBP1_ENST00000354476.3_Missense_Mutation_p.V495A			Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding protein 1	495					extracellular matrix organization (GO:0030198)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta-activated receptor activity (GO:0005024)			breast(2)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(13)|lung(60)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(3)	108	all_hematologic(175;0.115)	Medulloblastoma(90;0.215)				GAAGCTTCCGTCCAGATACAT	0.443																																					p.V495A		Atlas-SNP	.											.	LTBP1	317	.	0			c.T1484C						.						93.0	90.0	91.0					2																	33413701		2203	4300	6503	SO:0001583	missense	4052	exon7			CTTCCGTCCAGAT		CCDS33177.1, CCDS33178.1, CCDS33177.2, CCDS33178.2, CCDS54344.1, CCDS54345.1	2p22-p21	2008-05-23			ENSG00000049323	ENSG00000049323		"""Latent transforming growth factor, beta binding proteins"""	6714	protein-coding gene	gene with protein product	"""TGF-beta1-BP-1"""	150390				2350783, 11104663	Standard	NM_206943		Approved		uc021vft.1	Q14766	OTTHUMG00000152118	ENST00000404816.2:c.1484T>C	chr2.hg19:g.33413701T>C	ENSP00000386043:p.Val495Ala	37.0	0.0		59.0	4.0	NM_206943	A1L3V1|P22064|Q53SD8|Q53SF3|Q53SG1|Q59HF7|Q8TD95	Missense_Mutation	SNP	ENST00000404816.2	hg19	CCDS33177.2	.	.	.	.	.	.	.	.	.	.	T	22.2	4.258067	0.80246	.	.	ENSG00000049323	ENST00000404816;ENST00000354476;ENST00000432635;ENST00000390003;ENST00000418533;ENST00000402934;ENST00000404525;ENST00000407925	D;D;D;D;D;D;D	0.87650	-2.28;-2.19;-2.01;-2.02;-2.06;-2.05;-1.98	5.38	5.38	0.77491	.	.	.	.	.	D	0.92799	0.7710	M	0.69523	2.12	0.80722	D	1	D;D;D;D;D;D	0.89917	0.968;0.962;1.0;0.99;0.99;0.981	P;B;D;P;P;P	0.97110	0.708;0.339;1.0;0.624;0.624;0.694	D	0.93616	0.6943	9	0.87932	D	0	.	15.7502	0.77980	0.0:0.0:0.0:1.0	.	495;169;169;169;169;495	Q14766;E7EV71;Q14766-3;Q14766-2;Q14766-5;Q14766-4	LTBP1_HUMAN;.;.;.;.;.	A	495;495;184;169;169;169;169;169	ENSP00000386043:V495A;ENSP00000346467:V495A;ENSP00000374653:V169A;ENSP00000393057:V169A;ENSP00000384373:V169A;ENSP00000385359:V169A;ENSP00000384091:V169A	ENSP00000346467:V495A	V	+	2	0	LTBP1	33267205	1.000000	0.71417	0.954000	0.39281	0.612000	0.37316	7.350000	0.79385	2.192000	0.70111	0.449000	0.29647	GTC	.	.		0.443	LTBP1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326227.2	NM_206943	
NDUFAF7	55471	hgsc.bcm.edu	37	2	37475305	37475305	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:37475305T>C	ENST00000002125.4	+	10	1178	c.1138T>C	c.(1138-1140)Tca>Cca	p.S380P	NDUFAF7_ENST00000336237.6_Missense_Mutation_p.S282P	NM_144736.4	NP_653337.1	Q7L592	NDUF7_HUMAN	NADH dehydrogenase (ubiquinone) complex I, assembly factor 7	380					methylation (GO:0032259)|mitochondrial respiratory chain complex I assembly (GO:0032981)	extracellular space (GO:0005615)|mitochondrion (GO:0005739)	enzyme binding (GO:0019899)|methyltransferase activity (GO:0008168)										AAATGAGCCATCAGTGAGGCA	0.348																																					p.S380P		Atlas-SNP	.											.	.	.	.	0			c.T1138C						.						85.0	80.0	82.0					2																	37475305		2203	4300	6503	SO:0001583	missense	55471	exon10			GAGCCATCAGTGA		CCDS1788.1, CCDS42673.1	2p22.2	2012-10-12	2012-10-12	2012-10-12	ENSG00000003509	ENSG00000003509		"""Mitochondrial respiratory chain complex assembly factors"""	28816	protein-coding gene	gene with protein product	"""mitochondrial dysfunction protein A homolog"""	615898	"""chromosome 2 open reading frame 56"""	C2orf56			Standard	NM_144736		Approved	PRO1853, MidA	uc002rqa.4	Q7L592	OTTHUMG00000128468	ENST00000002125.4:c.1138T>C	chr2.hg19:g.37475305T>C	ENSP00000002125:p.Ser380Pro	80.0	0.0		125.0	5.0	NM_144736	Q7Z399|Q9P1G3	Missense_Mutation	SNP	ENST00000002125.4	hg19	CCDS1788.1	.	.	.	.	.	.	.	.	.	.	T	13.47	2.247530	0.39697	.	.	ENSG00000003509	ENST00000002125;ENST00000336237	T;T	0.77750	-1.12;-1.12	5.94	-3.35	0.04928	.	0.417340	0.28688	N	0.014471	T	0.65144	0.2663	L	0.60455	1.87	0.09310	N	0.999995	B;B;B;B	0.19331	0.007;0.016;0.035;0.007	B;B;B;B	0.22152	0.006;0.011;0.038;0.006	T	0.55088	-0.8195	10	0.51188	T	0.08	-9.3551	3.5821	0.07957	0.2383:0.0651:0.4088:0.2878	.	353;309;282;380	E7EUC2;B4DQY3;Q7L592-2;Q7L592	.;.;.;MIDA_HUMAN	P	380;282	ENSP00000002125:S380P;ENSP00000337431:S282P	ENSP00000002125:S380P	S	+	1	0	C2orf56	37328809	0.002000	0.14202	0.525000	0.27900	0.912000	0.54170	0.187000	0.16998	-0.131000	0.11578	0.482000	0.46254	TCA	.	.		0.348	NDUFAF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250267.1	NM_144736	
MSH2	4436	hgsc.bcm.edu	37	2	47639551	47639551	+	Splice_Site	SNP	A	A	T	rs587779169|rs267607929		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:47639551A>T	ENST00000233146.2	+	4	868		c.e4-1		MSH2_ENST00000543555.1_Splice_Site|MSH2_ENST00000406134.1_Splice_Site	NM_000251.2	NP_000242.1	P43246	MSH2_HUMAN	mutS homolog 2						ATP catabolic process (GO:0006200)|B cell differentiation (GO:0030183)|B cell mediated immunity (GO:0019724)|cell cycle arrest (GO:0007050)|determination of adult lifespan (GO:0008340)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|germ cell development (GO:0007281)|in utero embryonic development (GO:0001701)|intra-S DNA damage checkpoint (GO:0031573)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|isotype switching (GO:0045190)|maintenance of DNA repeat elements (GO:0043570)|male gonad development (GO:0008584)|meiotic gene conversion (GO:0006311)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of reciprocal meiotic recombination (GO:0045128)|oxidative phosphorylation (GO:0006119)|positive regulation of helicase activity (GO:0051096)|postreplication repair (GO:0006301)|response to UV-B (GO:0010224)|response to X-ray (GO:0010165)|somatic hypermutation of immunoglobulin genes (GO:0016446)|somatic recombination of immunoglobulin gene segments (GO:0016447)	membrane (GO:0016020)|MutSalpha complex (GO:0032301)|MutSbeta complex (GO:0032302)|nuclear chromosome (GO:0000228)	ATP binding (GO:0005524)|centromeric DNA binding (GO:0019237)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|double-strand/single-strand DNA junction binding (GO:0000406)|enzyme binding (GO:0019899)|guanine/thymine mispair binding (GO:0032137)|heteroduplex DNA loop binding (GO:0000404)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|Y-form DNA binding (GO:0000403)	p.0?(2)|p.?(1)		NS(1)|breast(4)|central_nervous_system(2)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(9)|kidney(5)|large_intestine(50)|lung(18)|ovary(5)|prostate(2)|skin(3)|small_intestine(1)|stomach(2)|urinary_tract(1)	112		all_hematologic(82;0.0359)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			CTTTCAAAATAGATAATTCAA	0.299			"""D, Mis, N, F, S"""		"""colorectal, endometrial, ovarian"""	"""colorectal, endometrial, ovarian"""		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome																												.		Atlas-SNP	.	yes	Rec	yes	Hereditary non-polyposis colorectal cancer	2	2p22-p21	4436	mutS homolog 2 (E. coli)		E	.	MSH2	198	.	3	Whole gene deletion(2)|Unknown(1)	haematopoietic_and_lymphoid_tissue(3)	c.646-2A>T						.						32.0	34.0	34.0					2																	47639551		2200	4300	6500	SO:0001630	splice_region_variant	4436	exon4	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome; ;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	CAAAATAGATAAT	U03911	CCDS1834.1, CCDS58709.1	2p21	2014-09-17	2013-09-12		ENSG00000095002	ENSG00000095002			7325	protein-coding gene	gene with protein product		609309	"""mutS (E. coli) homolog 2 (colon cancer, nonpolyposis type 1)"", ""mutS homolog 2, colon cancer, nonpolyposis type 1 (E. coli)"""	COCA1		8484120, 9843200	Standard	NM_000251		Approved	HNPCC, HNPCC1	uc002rvy.2	P43246	OTTHUMG00000128861	ENST00000233146.2:c.646-1A>T	chr2.hg19:g.47639551A>T		211.0	0.0		293.0	83.0	NM_000251	B4E2Z2|O75488	Splice_Site	SNP	ENST00000233146.2	hg19	CCDS1834.1	.	.	.	.	.	.	.	.	.	.	A	10.91	1.483210	0.26598	.	.	ENSG00000095002	ENST00000233146;ENST00000543555;ENST00000406134;ENST00000419559;ENST00000432737;ENST00000453755;ENST00000448533;ENST00000394792;ENST00000413880	.	.	.	5.0	5.0	0.66597	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.0583	0.71933	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	MSH2	47493055	1.000000	0.71417	0.932000	0.37286	0.041000	0.13682	8.975000	0.93437	2.037000	0.60232	0.456000	0.33151	.	.	.		0.299	MSH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250805.3		Intron
EML6	400954	hgsc.bcm.edu	37	2	55040425	55040425	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:55040425C>T	ENST00000356458.6	+	2	774	c.254C>T	c.(253-255)cCa>cTa	p.P85L		NM_001039753.2	NP_001034842.2	Q6ZMW3	EMAL6_HUMAN	echinoderm microtubule associated protein like 6	85						cytoplasm (GO:0005737)|microtubule (GO:0005874)				breast(1)|endometrium(6)	7						GGGAAGGAGCCATATATATGC	0.438																																					p.P85L		Atlas-SNP	.											.	EML6	85	.	0			c.C254T						.						159.0	124.0	135.0					2																	55040425		692	1591	2283	SO:0001583	missense	400954	exon2			AGGAGCCATATAT		CCDS46286.1	2p16.1	2013-01-10			ENSG00000214595	ENSG00000214595		"""WD repeat domain containing"""	35412	protein-coding gene	gene with protein product							Standard	NM_001039753		Approved	FLJ42562	uc002ryb.4	Q6ZMW3	OTTHUMG00000152035	ENST00000356458.6:c.254C>T	chr2.hg19:g.55040425C>T	ENSP00000348842:p.Pro85Leu	99.0	0.0		123.0	40.0	NM_001039753	A8MUB5|B6ZDG7	Missense_Mutation	SNP	ENST00000356458.6	hg19	CCDS46286.1	.	.	.	.	.	.	.	.	.	.	C	33	5.274834	0.95459	.	.	ENSG00000214595	ENST00000356458	T	0.41065	1.01	5.84	5.84	0.93424	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.27567	U	0.018788	T	0.74160	0.3680	M	0.90922	3.16	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.79179	-0.1910	10	0.87932	D	0	.	20.1434	0.98067	0.0:1.0:0.0:0.0	.	85	Q6ZMW3	EMAL6_HUMAN	L	85	ENSP00000348842:P85L	ENSP00000348842:P85L	P	+	2	0	EML6	54893929	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	7.400000	0.79949	2.760000	0.94817	0.591000	0.81541	CCA	.	.		0.438	EML6-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000324997.3	XM_001725002	
EML6	400954	hgsc.bcm.edu	37	2	55179820	55179820	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:55179820A>G	ENST00000356458.6	+	30	4823	c.4303A>G	c.(4303-4305)Agc>Ggc	p.S1435G		NM_001039753.2	NP_001034842.2	Q6ZMW3	EMAL6_HUMAN	echinoderm microtubule associated protein like 6	1435						cytoplasm (GO:0005737)|microtubule (GO:0005874)				breast(1)|endometrium(6)	7						GGTGGCCACCAGCCAGATAGG	0.577																																					p.S1435G		Atlas-SNP	.											.	EML6	85	.	0			c.A4303G						.						56.0	56.0	56.0					2																	55179820		692	1591	2283	SO:0001583	missense	400954	exon30			GCCACCAGCCAGA		CCDS46286.1	2p16.1	2013-01-10			ENSG00000214595	ENSG00000214595		"""WD repeat domain containing"""	35412	protein-coding gene	gene with protein product							Standard	NM_001039753		Approved	FLJ42562	uc002ryb.4	Q6ZMW3	OTTHUMG00000152035	ENST00000356458.6:c.4303A>G	chr2.hg19:g.55179820A>G	ENSP00000348842:p.Ser1435Gly	80.0	0.0		89.0	4.0	NM_001039753	A8MUB5|B6ZDG7	Missense_Mutation	SNP	ENST00000356458.6	hg19	CCDS46286.1	.	.	.	.	.	.	.	.	.	.	A	8.118	0.780294	0.16120	.	.	ENSG00000214595	ENST00000356458	T	0.28454	1.61	5.62	5.62	0.85841	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	.	.	.	.	T	0.05135	0.0137	N	0.00050	-2.41	0.48135	D	0.99959	B	0.02656	0.0	B	0.04013	0.001	T	0.36841	-0.9731	9	0.02654	T	1	.	10.211	0.43141	0.926:0.0:0.074:0.0	.	1435	Q6ZMW3	EMAL6_HUMAN	G	1435	ENSP00000348842:S1435G	ENSP00000348842:S1435G	S	+	1	0	EML6	55033324	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.812000	0.75226	2.135000	0.66039	0.533000	0.62120	AGC	.	.		0.577	EML6-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000324997.3	XM_001725002	
REL	5966	hgsc.bcm.edu	37	2	61149213	61149213	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:61149213A>G	ENST00000295025.8	+	11	1723	c.1403A>G	c.(1402-1404)gAc>gGc	p.D468G	REL_ENST00000394479.3_Missense_Mutation_p.D436G	NM_002908.2	NP_002899.1	Q04864	REL_HUMAN	v-rel avian reticuloendotheliosis viral oncogene homolog	468					cytokine production (GO:0001816)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|negative regulation of neuron death (GO:1901215)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|large_intestine(5)|lung(3)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	16	all_hematologic(2;0.0797)	Ovarian(717;0.0728)	LUSC - Lung squamous cell carcinoma(5;6.2e-08)|Lung(5;1.65e-06)|Epithelial(17;0.064)|all cancers(80;0.221)			AATGCCGATGACATAGTCGGA	0.403			A		Hodgkin Lymphoma																																p.D468G		Atlas-SNP	.		Dom	yes		2	2p13-p12	5966	v-rel reticuloendotheliosis viral oncogene homolog (avian)		L	.	REL	48	.	0			c.A1403G						.						111.0	97.0	102.0					2																	61149213		2203	4300	6503	SO:0001583	missense	5966	exon11			CCGATGACATAGT	M11595	CCDS1864.1, CCDS74515.1	2p13-p12	2013-07-09	2013-07-09		ENSG00000162924	ENSG00000162924			9954	protein-coding gene	gene with protein product		164910				1577270	Standard	XM_005264470		Approved	I-Rel, c-Rel	uc002sam.1	Q04864	OTTHUMG00000129418	ENST00000295025.8:c.1403A>G	chr2.hg19:g.61149213A>G	ENSP00000295025:p.Asp468Gly	90.0	0.0		100.0	4.0	NM_002908	Q17RU2|Q2PNZ7|Q6LDY0	Missense_Mutation	SNP	ENST00000295025.8	hg19	CCDS1864.1	.	.	.	.	.	.	.	.	.	.	A	6.162	0.398046	0.11696	.	.	ENSG00000162924	ENST00000295025;ENST00000394479	T;T	0.51071	0.72;0.82	5.4	4.27	0.50696	.	1.005800	0.07990	N	0.986987	T	0.27765	0.0683	N	0.12746	0.255	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.11767	-1.0574	10	0.30078	T	0.28	-14.0714	4.1185	0.10094	0.7971:0.0:0.2029:0.0	.	436;468	Q17RU2;Q04864	.;REL_HUMAN	G	468;436	ENSP00000295025:D468G;ENSP00000377989:D436G	ENSP00000295025:D468G	D	+	2	0	REL	61002717	0.981000	0.34729	0.184000	0.23157	0.115000	0.19883	1.999000	0.40806	2.044000	0.60594	0.528000	0.53228	GAC	.	.		0.403	REL-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251576.3	NM_002908	
COMMD1	150684	hgsc.bcm.edu	37	2	62132979	62132979	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:62132979A>G	ENST00000311832.5	+	1	198	c.166A>G	c.(166-168)Agg>Ggg	p.R56G	COMMD1_ENST00000538736.1_Missense_Mutation_p.R56G|COMMD1_ENST00000472729.1_Intron	NM_152516.2	NP_689729.1	Q8N668	COMD1_HUMAN	copper metabolism (Murr1) domain containing 1	56					copper ion homeostasis (GO:0055070)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|positive regulation of protein ubiquitination (GO:0031398)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)	Cul2-RING ubiquitin ligase complex (GO:0031462)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	copper ion binding (GO:0005507)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)			large_intestine(1)|liver(2)|lung(5)|ovary(1)	9	Lung NSC(7;0.035)|all_lung(7;0.0691)		LUSC - Lung squamous cell carcinoma(7;4.73e-07)|Epithelial(17;0.0216)|all cancers(80;0.0934)			GGCAAAGATGAGGGGGATTCT	0.592																																					p.R56G		Atlas-SNP	.											.	COMMD1	17	.	0			c.A166G						.						51.0	49.0	50.0					2																	62132979		2203	4300	6503	SO:0001583	missense	150684	exon1			AAGATGAGGGGGA	BC022046	CCDS1869.1	2p15	2004-03-02	2004-02-13	2004-02-18	ENSG00000173163	ENSG00000173163			23024	protein-coding gene	gene with protein product	"""copper metabolism gene MURR1"""	607238	"""chromosome 2 open reading frame 5 (MURR1)"""	C2orf5		9001233, 11809725	Standard	NM_152516		Approved	MURR1, MGC27155	uc002sbp.3	Q8N668	OTTHUMG00000129445	ENST00000311832.5:c.166A>G	chr2.hg19:g.62132979A>G	ENSP00000308236:p.Arg56Gly	81.0	0.0		85.0	5.0	NM_152516	B4DFQ4|Q96GS0	Missense_Mutation	SNP	ENST00000311832.5	hg19	CCDS1869.1	.	.	.	.	.	.	.	.	.	.	A	20.1	3.937999	0.73557	.	.	ENSG00000173163	ENST00000311832;ENST00000538736	T;T	0.09817	2.94;2.94	5.78	3.22	0.36961	.	0.248111	0.44688	D	0.000433	T	0.09247	0.0228	L	0.39397	1.21	0.46849	D	0.999227	B	0.13145	0.007	B	0.17979	0.02	T	0.12293	-1.0553	10	0.32370	T	0.25	.	9.9166	0.41439	0.7418:0.2581:0.0:0.0	.	56	Q8N668	COMD1_HUMAN	G	56	ENSP00000308236:R56G;ENSP00000438961:R56G	ENSP00000308236:R56G	R	+	1	2	COMMD1	61986483	0.997000	0.39634	0.996000	0.52242	0.973000	0.67179	0.240000	0.18042	2.220000	0.72140	0.533000	0.62120	AGG	.	.		0.592	COMMD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251607.2	NM_152516	
EHBP1	23301	hgsc.bcm.edu	37	2	62934345	62934345	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:62934345A>G	ENST00000263991.5	+	2	501	c.19A>G	c.(19-21)Aga>Gga	p.R7G	EHBP1_ENST00000405015.3_Missense_Mutation_p.R7G|EHBP1_ENST00000354487.3_Missense_Mutation_p.R7G|EHBP1_ENST00000405289.1_Missense_Mutation_p.R7G|EHBP1_ENST00000431489.1_Missense_Mutation_p.R7G	NM_015252.3	NP_056067.2	Q8NDI1	EHBP1_HUMAN	EH domain binding protein 1	7						cytoplasm (GO:0005737)|membrane (GO:0016020)				biliary_tract(1)|breast(3)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(8)|lung(22)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	47	Lung NSC(7;0.0951)|all_lung(7;0.169)		LUSC - Lung squamous cell carcinoma(7;7.74e-05)|Epithelial(17;0.189)			AGTTTGGAAGAGACTGCAGCG	0.473																																					p.R7G		Atlas-SNP	.											.	EHBP1	127	.	0			c.A19G						.						158.0	149.0	152.0					2																	62934345		2203	4300	6503	SO:0001583	missense	23301	exon2			TGGAAGAGACTGC	AL833968	CCDS1872.1, CCDS46299.1, CCDS46300.1	2p15	2008-02-05			ENSG00000115504	ENSG00000115504			29144	protein-coding gene	gene with protein product		609922				10048485	Standard	NM_015252		Approved	KIAA0903, NACSIN	uc002sby.3	Q8NDI1	OTTHUMG00000129453	ENST00000263991.5:c.19A>G	chr2.hg19:g.62934345A>G	ENSP00000263991:p.Arg7Gly	159.0	0.0		156.0	9.0	NM_001142616	O94977|Q53TG7|Q53TV6|Q580X2|Q6NX72|Q6PIT3|Q6QNV2|Q9NWI9	Missense_Mutation	SNP	ENST00000263991.5	hg19	CCDS1872.1	.	.	.	.	.	.	.	.	.	.	A	16.33	3.092655	0.56075	.	.	ENSG00000115504	ENST00000405015;ENST00000405482;ENST00000427809;ENST00000431489;ENST00000263991;ENST00000354487;ENST00000405289	D;T;D;D;D;D	0.81908	-1.55;0.28;-1.55;-1.54;-1.54;-1.54	4.85	3.67	0.42095	.	0.000000	0.64402	D	0.000001	D	0.89894	0.6847	M	0.78637	2.42	0.52501	D	0.999956	D;D;D;D	0.89917	0.996;0.967;1.0;0.995	D;P;D;D	0.83275	0.99;0.879;0.996;0.989	D	0.89685	0.3893	10	0.87932	D	0	.	11.3547	0.49609	0.8418:0.1582:0.0:0.0	.	7;7;7;7	Q8NDI1-2;A8K930;Q8NDI1-3;Q8NDI1	.;.;.;EHBP1_HUMAN	G	7	ENSP00000384143:R7G;ENSP00000384829:R7G;ENSP00000403783:R7G;ENSP00000263991:R7G;ENSP00000346482:R7G;ENSP00000385524:R7G	ENSP00000263991:R7G	R	+	1	2	EHBP1	62787849	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.971000	0.63749	0.673000	0.31224	0.460000	0.39030	AGA	.	.		0.473	EHBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251616.1	NM_015252	
DCTN1	1639	hgsc.bcm.edu	37	2	74597423	74597423	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:74597423T>C	ENST00000361874.3	-	12	1494	c.1177A>G	c.(1177-1179)Aag>Gag	p.K393E	DCTN1_ENST00000407639.2_Missense_Mutation_p.K259E|DCTN1_ENST00000409567.3_Missense_Mutation_p.K373E|DCTN1_ENST00000409438.1_Missense_Mutation_p.K259E|DCTN1_ENST00000409240.1_Missense_Mutation_p.K356E|DCTN1_ENST00000495643.1_5'Flank|DCTN1_ENST00000409868.1_Missense_Mutation_p.K376E|DCTN1_ENST00000394003.3_Missense_Mutation_p.K386E	NM_004082.4	NP_004073.2	Q14203	DCTN1_HUMAN	dynactin 1	393					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|G2/M transition of mitotic cell cycle (GO:0000086)|melanosome transport (GO:0032402)|microtubule-based transport (GO:0010970)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|nervous system development (GO:0007399)	cell leading edge (GO:0031252)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dynactin complex (GO:0005869)|dynein complex (GO:0030286)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|spindle pole (GO:0000922)	motor activity (GO:0003774)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(20)|ovary(4)|prostate(1)|skin(3)	45						TCCATGAGCTTCTGGAGCTTC	0.537																																					p.K393E		Atlas-SNP	.											.	DCTN1	110	.	0			c.A1177G						.						71.0	66.0	68.0					2																	74597423		2203	4300	6503	SO:0001583	missense	1639	exon12			TGAGCTTCTGGAG		CCDS1939.1, CCDS46341.1, CCDS46342.1, CCDS54368.1, CCDS54369.1	2p13	2014-09-17	2010-06-24		ENSG00000204843	ENSG00000204843			2711	protein-coding gene	gene with protein product	"""p150 glued homolog (Drosophila)"""	601143	"""dynactin 1 (p150, Glued (Drosophila) homolog)"""			1828535	Standard	NM_001190836		Approved		uc002skx.3	Q14203	OTTHUMG00000129963	ENST00000361874.3:c.1177A>G	chr2.hg19:g.74597423T>C	ENSP00000354791:p.Lys393Glu	83.0	0.0		96.0	4.0	NM_004082	A8MY36|B4DM45|E9PFS5|E9PGE1|G5E9H4|O95296|Q6IQ37|Q9BRM9|Q9UIU1|Q9UIU2	Missense_Mutation	SNP	ENST00000361874.3	hg19	CCDS1939.1	.	.	.	.	.	.	.	.	.	.	T	25.3	4.624418	0.87560	.	.	ENSG00000204843	ENST00000361874;ENST00000394003;ENST00000393999;ENST00000407639;ENST00000409438;ENST00000409240;ENST00000409868;ENST00000409567	T;T;T;T;T;T;T	0.76839	-1.0;-1.0;-1.0;-1.0;-1.0;-1.05;-1.0	4.97	4.97	0.65823	.	0.000000	0.45126	D	0.000383	D	0.86948	0.6056	M	0.78456	2.415	0.80722	D	1	D;P;D;B;P;D	0.76494	0.999;0.863;0.993;0.427;0.754;0.975	D;B;D;B;P;P	0.70935	0.971;0.445;0.956;0.436;0.71;0.833	D	0.87983	0.2744	10	0.54805	T	0.06	-8.0299	13.7753	0.63050	0.0:0.0:0.0:1.0	.	373;356;393;386;259;259	E9PGE1;E9PFS5;Q14203;A8MY36;Q14203-2;G5E9H4	.;.;DCTN1_HUMAN;.;.;.	E	393;386;376;259;259;356;376;373	ENSP00000354791:K393E;ENSP00000377571:K386E;ENSP00000384844:K259E;ENSP00000387270:K259E;ENSP00000386406:K356E;ENSP00000387327:K376E;ENSP00000386843:K373E	ENSP00000354791:K393E	K	-	1	0	DCTN1	74450931	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.845000	0.86875	2.076000	0.62316	0.528000	0.53228	AAG	.	.		0.537	DCTN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252227.3	NM_004082	
REG1B	5968	hgsc.bcm.edu	37	2	79313509	79313509	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:79313509A>G	ENST00000305089.3	-	4	385	c.305T>C	c.(304-306)cTc>cCc	p.L102P		NM_006507.3	NP_006498.1	P48304	REG1B_HUMAN	regenerating islet-derived 1 beta	102	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				cell proliferation (GO:0008283)	extracellular vesicular exosome (GO:0070062)	carbohydrate binding (GO:0030246)	p.I100fs*39(1)		central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(40)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	51						TGGGTCATGGAGGCCAATCCA	0.512																																					p.L102P		Atlas-SNP	.											.,1	REG1B	83	.	1	Deletion - Frameshift(1)	prostate(1)	c.T305C						.						114.0	101.0	106.0					2																	79313509		2203	4300	6503	SO:0001583	missense	5968	exon4			TCATGGAGGCCAA		CCDS1963.1	2p12	2008-06-04	2008-06-04		ENSG00000172023	ENSG00000172023			9952	protein-coding gene	gene with protein product	"""lithostathine 1 beta"", ""secretory pancreatic stone protein 2"""	167771	"""regenerating islet-derived 1 beta (pancreatic stone protein, pancreatic thread protein)"""			8110835	Standard	NM_006507		Approved	REGL, PSPS2, REGH, REGI-BETA	uc002sny.2	P48304	OTTHUMG00000130019	ENST00000305089.3:c.305T>C	chr2.hg19:g.79313509A>G	ENSP00000303206:p.Leu102Pro	117.0	0.0		142.0	7.0	NM_006507		Missense_Mutation	SNP	ENST00000305089.3	hg19	CCDS1963.1	.	.	.	.	.	.	.	.	.	.	a	12.18	1.859750	0.32884	.	.	ENSG00000172023	ENST00000454188;ENST00000305089	T;T	0.15372	2.43;2.43	3.51	2.29	0.28610	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.000000	0.33792	N	0.004541	T	0.53981	0.1830	H	0.99042	4.41	0.32787	N	0.501657	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.66760	-0.5842	10	0.87932	D	0	.	6.7304	0.23381	0.7573:0.2427:0.0:0.0	.	102;102	Q6ICS1;P48304	.;REG1B_HUMAN	P	53;102	ENSP00000387410:L53P;ENSP00000303206:L102P	ENSP00000303206:L102P	L	-	2	0	REG1B	79167017	0.116000	0.22171	0.024000	0.17045	0.013000	0.08279	2.145000	0.42207	0.501000	0.28013	-0.619000	0.04042	CTC	.	.		0.512	REG1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252292.2	NM_006507	
IMMT	10989	hgsc.bcm.edu	37	2	86393732	86393732	+	Missense_Mutation	SNP	T	T	C	rs556796647		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:86393732T>C	ENST00000410111.3	-	7	1078	c.691A>G	c.(691-693)Act>Gct	p.T231A	IMMT_ENST00000449247.2_Missense_Mutation_p.T220A|IMMT_ENST00000442664.2_Missense_Mutation_p.T230A|IMMT_ENST00000409051.2_Missense_Mutation_p.T184A|IMMT_ENST00000254636.5_Missense_Mutation_p.T132A|IMMT_ENST00000490238.1_5'UTR	NM_001100169.1|NM_001100170.1|NM_006839.2	NP_001093639.1|NP_001093640.1|NP_006830.2	Q16891	MIC60_HUMAN	inner membrane protein, mitochondrial	231					mitochondrial calcium ion homeostasis (GO:0051560)|response to cold (GO:0009409)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						ACACTTGCAGTTTGCCTCAGA	0.423													T|||	1	0.000199681	0.0	0.0	5008	,	,		15210	0.001		0.0	False		,,,				2504	0.0				p.T231A		Atlas-SNP	.											.	IMMT	65	.	0			c.A691G						.						55.0	52.0	53.0					2																	86393732		1887	4104	5991	SO:0001583	missense	10989	exon7			TTGCAGTTTGCCT	D21094	CCDS46355.1, CCDS46356.1, CCDS46357.1	2p11.2	2011-10-04	2010-04-29		ENSG00000132305	ENSG00000132305			6047	protein-coding gene	gene with protein product	"""mitofilin"", ""mitochondrial inner membrane organizing system 2"""	600378	"""inner membrane protein, mitochondrial (mitofilin)"""			9168817, 8039717	Standard	NM_001100169		Approved	P87, P89, HMP, MINOS2	uc002sqz.4	Q16891	OTTHUMG00000153170	ENST00000410111.3:c.691A>G	chr2.hg19:g.86393732T>C	ENSP00000387262:p.Thr231Ala	62.0	0.0		88.0	4.0	NM_006839	B1H0U5|B2R5N6|Q14539|Q15092|Q68D41|Q69HW5|Q6IBL0|Q7Z3X1|Q8TAJ5|Q9P0V2	Missense_Mutation	SNP	ENST00000410111.3	hg19	CCDS46355.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	11.94|11.94	1.787670|1.787670	0.31593|0.31593	.|.	.|.	ENSG00000132305|ENSG00000132305	ENST00000419070|ENST00000254636;ENST00000449247;ENST00000410111;ENST00000442664;ENST00000409051;ENST00000545283;ENST00000377310;ENST00000398211;ENST00000409715	.|T;T;T;T;T	.|0.30448	.|1.53;1.53;1.53;1.53;1.53	5.36|5.36	5.36|5.36	0.76844|0.76844	.|.	.|0.051776	.|0.85682	.|D	.|0.000000	T|T	0.39036|0.39036	0.1063|0.1063	L|L	0.39898|0.39898	1.24|1.24	0.47245|0.47245	D|D	0.999366|0.999366	.|B;P;B;P;D;P;B;P;P	.|0.55385	.|0.324;0.47;0.375;0.73;0.971;0.55;0.324;0.55;0.604	.|B;P;B;P;P;B;B;B;B	.|0.62298	.|0.273;0.512;0.394;0.644;0.9;0.273;0.273;0.273;0.394	T|T	0.11155|0.11155	-1.0599|-1.0599	5|10	.|0.06365	.|T	.|0.9	-19.9405|-19.9405	14.6434|14.6434	0.68742|0.68742	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|220;184;219;228;219;199;220;199;231	.|F5GZ32;B9A067;B4DKR1;Q05DN3;B4E2B5;F8W9I1;Q16891-2;Q16891-3;Q16891	.|.;.;.;.;.;.;.;.;IMMT_HUMAN	S|A	85|132;220;231;230;184;220;199;219;153	.|ENSP00000254636:T132A;ENSP00000396899:T220A;ENSP00000387262:T231A;ENSP00000407788:T230A;ENSP00000387227:T184A	.|ENSP00000254636:T132A	N|T	-|-	2|1	0|0	IMMT|IMMT	86247243|86247243	0.999000|0.999000	0.42202|0.42202	0.871000|0.871000	0.34182|0.34182	0.785000|0.785000	0.44390|0.44390	3.200000|3.200000	0.51051|0.51051	2.160000|2.160000	0.67779|0.67779	0.523000|0.523000	0.50628|0.50628	AAC|ACT	.	.		0.423	IMMT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000329909.2	NM_006839	
TMEM131	23505	hgsc.bcm.edu	37	2	98460710	98460710	+	Silent	SNP	T	T	C	rs202141365		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:98460710T>C	ENST00000186436.5	-	6	726	c.498A>G	c.(496-498)ggA>ggG	p.G166G	TMEM131_ENST00000425805.2_Silent_p.G117G	NM_015348.1	NP_056163.1	Q92545	TM131_HUMAN	transmembrane protein 131	166						integral component of membrane (GO:0016021)				NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(23)|ovary(4)|prostate(1)|skin(1)|stomach(1)	57						ATGTATTTCCTCCTGGAAGAA	0.274																																					p.G166G		Atlas-SNP	.											.	TMEM131	258	.	0			c.A498G						.						11.0	11.0	11.0					2																	98460710		1702	3855	5557	SO:0001819	synonymous_variant	23505	exon6			ATTTCCTCCTGGA	AK025852	CCDS46368.1	2q11.2	2006-04-12			ENSG00000075568	ENSG00000075568			30366	protein-coding gene	gene with protein product		615659				9039502, 10996388	Standard	NM_015348		Approved	CC28, YR-23, RW1, KIAA0257, PRO1048	uc002syh.4	Q92545	OTTHUMG00000153061	ENST00000186436.5:c.498A>G	chr2.hg19:g.98460710T>C		92.0	0.0		146.0	6.0	NM_015348		Silent	SNP	ENST00000186436.5	hg19	CCDS46368.1																																																																																			.	T|1.000;G|0.000		0.274	TMEM131-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329285.2	XM_371542	
TSGA10	80705	hgsc.bcm.edu	37	2	99721887	99721887	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:99721887T>C	ENST00000393483.3	-	9	1238	c.394A>G	c.(394-396)Aca>Gca	p.T132A	TSGA10_ENST00000410001.1_Missense_Mutation_p.T132A|TSGA10_ENST00000355053.4_Missense_Mutation_p.T132A|TSGA10_ENST00000539964.1_Missense_Mutation_p.T132A|TSGA10_ENST00000542655.1_Missense_Mutation_p.T132A|TSGA10_ENST00000478090.1_5'UTR	NM_025244.2	NP_079520.1	Q9BZW7	TSG10_HUMAN	testis specific, 10	132					cell projection assembly (GO:0030031)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|membrane (GO:0016020)|motile cilium (GO:0031514)|neuron projection (GO:0043005)|nucleus (GO:0005634)				NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(10)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	34						TTAAATGCTGTCTCTTGAGCA	0.318																																					p.T132A		Atlas-SNP	.											.	TSGA10	81	.	0			c.A394G						.						68.0	72.0	71.0					2																	99721887		2202	4300	6502	SO:0001583	missense	80705	exon8			ATGCTGTCTCTTG	AF254756	CCDS2037.1	2q11.2	2009-08-06			ENSG00000135951	ENSG00000135951			14927	protein-coding gene	gene with protein product	"""cancer/testis antigen 79"""	607166				11179690	Standard	NM_025244		Approved	CEP4L, CT79	uc002szi.4	Q9BZW7	OTTHUMG00000130637	ENST00000393483.3:c.394A>G	chr2.hg19:g.99721887T>C	ENSP00000377123:p.Thr132Ala	83.0	0.0		95.0	4.0	NM_182911	B7Z925|D3DVH7|Q8NEP0|Q9BWX0	Missense_Mutation	SNP	ENST00000393483.3	hg19	CCDS2037.1	.	.	.	.	.	.	.	.	.	.	T	16.89	3.246682	0.59103	.	.	ENSG00000135951	ENST00000393483;ENST00000410001;ENST00000355053;ENST00000539964;ENST00000409564;ENST00000393482;ENST00000542655	T;T;T;T;T;T;T	0.77620	0.95;0.95;0.95;0.95;-1.11;-1.11;-1.11	4.98	4.98	0.66077	.	0.000000	0.64402	D	0.000012	T	0.76004	0.3927	L	0.31065	0.9	0.35300	D	0.782925	D;D	0.64830	0.994;0.994	P;P	0.58520	0.791;0.84	T	0.75221	-0.3394	10	0.11182	T	0.66	-15.3955	13.6914	0.62549	0.0:0.0:0.0:1.0	.	132;132	B7Z925;Q9BZW7	.;TSG10_HUMAN	A	132	ENSP00000377123:T132A;ENSP00000386956:T132A;ENSP00000347161:T132A;ENSP00000444419:T132A;ENSP00000386508:T132A;ENSP00000377122:T132A;ENSP00000445623:T132A	ENSP00000347161:T132A	T	-	1	0	TSGA10	99088319	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	3.236000	0.51336	2.096000	0.63516	0.529000	0.55759	ACA	.	.		0.318	TSGA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253125.1	NM_182911	
RANBP2	5903	hgsc.bcm.edu	37	2	109379816	109379816	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:109379816C>A	ENST00000283195.6	+	20	2947	c.2821C>A	c.(2821-2823)Cct>Act	p.P941T		NM_006267.4	NP_006258.3	P49792	RBP2_HUMAN	RAN binding protein 2	941					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of glucokinase activity (GO:0033132)|protein folding (GO:0006457)|protein import into nucleus (GO:0006606)|protein sumoylation (GO:0016925)|regulation of gluconeogenesis involved in cellular glucose homeostasis (GO:0090526)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)	ligase activity (GO:0016874)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|Ran GTPase binding (GO:0008536)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)		RANBP2/ALK(34)	NS(1)|biliary_tract(1)|breast(3)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(21)|large_intestine(19)|lung(51)|pancreas(1)|prostate(8)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	129						GATGTATGGTCCTCCTGCATT	0.473																																					p.P941T		Atlas-SNP	.											.	RANBP2	488	.	0			c.C2821A						.						130.0	120.0	124.0					2																	109379816		2203	4300	6503	SO:0001583	missense	5903	exon20			TATGGTCCTCCTG	D42063	CCDS2079.1	2q13	2013-11-14			ENSG00000153201	ENSG00000153201		"""Tetratricopeptide (TTC) repeat domain containing"""	9848	protein-coding gene	gene with protein product		601181	"""acute necrotizing encephalopathy 1 (autosomal dominant)"""	ANE1		7724562, 19118815	Standard	NM_006267		Approved	NUP358, ADANE	uc002tem.4	P49792	OTTHUMG00000130981	ENST00000283195.6:c.2821C>A	chr2.hg19:g.109379816C>A	ENSP00000283195:p.Pro941Thr	174.0	0.0		247.0	11.0	NM_006267	Q13074|Q15280|Q53TE2|Q59FH7	Missense_Mutation	SNP	ENST00000283195.6	hg19	CCDS2079.1	.	.	.	.	.	.	.	.	.	.	C	13.96	2.392009	0.42410	.	.	ENSG00000153201	ENST00000283195	T	0.23147	1.92	5.19	5.19	0.71726	.	.	.	.	.	T	0.20292	0.0488	L	0.29908	0.895	0.32255	N	0.570945	B	0.22276	0.067	B	0.15052	0.012	T	0.08764	-1.0706	9	0.28530	T	0.3	-17.2047	14.6488	0.68780	0.2118:0.7882:0.0:0.0	.	941	P49792	RBP2_HUMAN	T	941	ENSP00000283195:P941T	ENSP00000283195:P941T	P	+	1	0	RANBP2	108746248	0.996000	0.38824	1.000000	0.80357	0.893000	0.52053	1.412000	0.34714	2.570000	0.86706	0.563000	0.77884	CCT	.	.		0.473	RANBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253594.1	NM_006267	
RANBP2	5903	hgsc.bcm.edu	37	2	109379840	109379840	+	Missense_Mutation	SNP	C	C	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:109379840C>G	ENST00000283195.6	+	20	2971	c.2845C>G	c.(2845-2847)Cct>Gct	p.P949A		NM_006267.4	NP_006258.3	P49792	RBP2_HUMAN	RAN binding protein 2	949					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of glucokinase activity (GO:0033132)|protein folding (GO:0006457)|protein import into nucleus (GO:0006606)|protein sumoylation (GO:0016925)|regulation of gluconeogenesis involved in cellular glucose homeostasis (GO:0090526)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)	ligase activity (GO:0016874)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|Ran GTPase binding (GO:0008536)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)		RANBP2/ALK(34)	NS(1)|biliary_tract(1)|breast(3)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(21)|large_intestine(19)|lung(51)|pancreas(1)|prostate(8)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	129						TTTTGAGTCTCCTGCAACGGG	0.468																																					p.P949A		Atlas-SNP	.											.	RANBP2	488	.	0			c.C2845G						.						121.0	115.0	117.0					2																	109379840		2203	4300	6503	SO:0001583	missense	5903	exon20			GAGTCTCCTGCAA	D42063	CCDS2079.1	2q13	2013-11-14			ENSG00000153201	ENSG00000153201		"""Tetratricopeptide (TTC) repeat domain containing"""	9848	protein-coding gene	gene with protein product		601181	"""acute necrotizing encephalopathy 1 (autosomal dominant)"""	ANE1		7724562, 19118815	Standard	NM_006267		Approved	NUP358, ADANE	uc002tem.4	P49792	OTTHUMG00000130981	ENST00000283195.6:c.2845C>G	chr2.hg19:g.109379840C>G	ENSP00000283195:p.Pro949Ala	140.0	0.0		223.0	10.0	NM_006267	Q13074|Q15280|Q53TE2|Q59FH7	Missense_Mutation	SNP	ENST00000283195.6	hg19	CCDS2079.1	.	.	.	.	.	.	.	.	.	.	C	19.43	3.826229	0.71143	.	.	ENSG00000153201	ENST00000283195	T	0.26660	1.72	5.08	5.08	0.68730	.	.	.	.	.	T	0.40979	0.1139	L	0.34521	1.04	0.49299	D	0.999771	D	0.89917	1.0	D	0.67548	0.952	T	0.18999	-1.0319	9	0.49607	T	0.09	-19.2482	18.8287	0.92128	0.0:1.0:0.0:0.0	.	949	P49792	RBP2_HUMAN	A	949	ENSP00000283195:P949A	ENSP00000283195:P949A	P	+	1	0	RANBP2	108746272	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	3.339000	0.52135	2.511000	0.84671	0.563000	0.77884	CCT	.	.		0.468	RANBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253594.1	NM_006267	
CCDC138	165055	hgsc.bcm.edu	37	2	109429147	109429147	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:109429147C>A	ENST00000295124.4	+	8	976	c.916C>A	c.(916-918)Cgt>Agt	p.R306S	CCDC138_ENST00000412964.2_Missense_Mutation_p.R306S	NM_144978.1	NP_659415.1	Q96M89	CC138_HUMAN	coiled-coil domain containing 138	306										endometrium(1)|large_intestine(3)|lung(7)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	14						AGTTCAAGCTCGTTTAGATAA	0.318																																					p.R306S		Atlas-SNP	.											CCDC138,caecum,carcinoma,0,1	CCDC138	49	.	0			c.C916A						.						114.0	124.0	121.0					2																	109429147		2203	4298	6501	SO:0001583	missense	165055	exon8			CAAGCTCGTTTAG	AK057307	CCDS2080.1	2q13	2008-02-05			ENSG00000163006	ENSG00000163006			26531	protein-coding gene	gene with protein product						12477932	Standard	NM_144978		Approved	FLJ32745	uc002ten.1	Q96M89	OTTHUMG00000130980	ENST00000295124.4:c.916C>A	chr2.hg19:g.109429147C>A	ENSP00000295124:p.Arg306Ser	110.0	0.0		162.0	0.0	NM_144978	Q05DF1|Q4ZG07|Q53TE1|Q6ZUY5|Q86VL7	Missense_Mutation	SNP	ENST00000295124.4	hg19	CCDS2080.1	.	.	.	.	.	.	.	.	.	.	C	21.3	4.131642	0.77662	.	.	ENSG00000163006	ENST00000412964;ENST00000295124	D;D	0.88741	-2.42;-2.42	5.72	4.8	0.61643	.	0.000000	0.85682	D	0.000000	D	0.93729	0.7996	M	0.74258	2.255	0.40555	D	0.981157	D;D	0.89917	1.0;0.988	D;P	0.87578	0.998;0.795	D	0.94349	0.7577	10	0.87932	D	0	2.2356	14.457	0.67423	0.148:0.852:0.0:0.0	.	306;306	Q96M89-2;Q96M89	.;CC138_HUMAN	S	306	ENSP00000411800:R306S;ENSP00000295124:R306S	ENSP00000295124:R306S	R	+	1	0	CCDC138	108795579	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.452000	0.52971	2.694000	0.91930	0.655000	0.94253	CGT	.	.		0.318	CCDC138-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253593.1	NM_144978	
DPP10	57628	hgsc.bcm.edu	37	2	116447448	116447448	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:116447448A>G	ENST00000410059.1	+	7	1007	c.527A>G	c.(526-528)gAg>gGg	p.E176G	DPP10_ENST00000409163.1_Missense_Mutation_p.E126G|DPP10_ENST00000393147.2_Missense_Mutation_p.E180G|DPP10_ENST00000310323.8_Missense_Mutation_p.E169G|DPP10_ENST00000488208.1_3'UTR	NM_001178037.1|NM_020868.3	NP_001171508.1|NP_065919	Q8N608	DPP10_HUMAN	dipeptidyl-peptidase 10 (non-functional)	176						integral component of membrane (GO:0016021)|membrane (GO:0016020)	serine-type peptidase activity (GO:0008236)			breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(24)|liver(2)|lung(48)|ovary(6)|prostate(1)|skin(5)|soft_tissue(1)	101						CCAGAAGTAGAGGACTCCGTC	0.438																																					p.E180G		Atlas-SNP	.											.	DPP10	415	.	0			c.A539G						.						88.0	95.0	93.0					2																	116447448		2203	4300	6503	SO:0001583	missense	57628	exon7			AAGTAGAGGACTC	AY172661	CCDS33278.1, CCDS46400.1, CCDS54388.1, CCDS54389.1	2q14.1	2010-05-04	2010-05-04		ENSG00000175497	ENSG00000175497			20823	protein-coding gene	gene with protein product		608209	"""dipeptidylpeptidase 10"", ""dipeptidyl-peptidase 10"""			10819331, 12662155	Standard	NM_020868		Approved	DPRP3	uc002tle.3	Q8N608	OTTHUMG00000153294	ENST00000410059.1:c.527A>G	chr2.hg19:g.116447448A>G	ENSP00000386565:p.Glu176Gly	57.0	0.0		71.0	5.0	NM_001178034	A8K1Q2|J3KPP2|J3KQ46|Q0GLB8|Q53QT3|Q53S86|Q53SL8|Q53SS4|Q6TTV4|Q86YR9|Q9P236	Missense_Mutation	SNP	ENST00000410059.1	hg19	CCDS46400.1	.	.	.	.	.	.	.	.	.	.	A	14.47	2.544759	0.45280	.	.	ENSG00000175497	ENST00000410059;ENST00000409163;ENST00000393146;ENST00000393147;ENST00000310323;ENST00000476155	T;T;D;T;T	0.95377	1.61;1.61;-3.69;1.61;1.61	5.44	4.26	0.50523	Peptidase S9B, dipeptidylpeptidase IV N-terminal (1);	0.353745	0.29286	N	0.012582	D	0.92084	0.7491	N	0.19112	0.55	0.35228	D	0.776657	P;D;P;P	0.53312	0.73;0.959;0.772;0.772	B;P;P;B	0.50049	0.284;0.629;0.526;0.407	D	0.92101	0.5688	10	0.34782	T	0.22	-17.821	10.5101	0.44857	0.8372:0.1628:0.0:0.0	.	169;180;172;176	Q8N608-2;Q0GLB8;Q0GLB9;Q8N608	.;.;.;DPP10_HUMAN	G	176;126;172;180;169;126	ENSP00000386565:E176G;ENSP00000387038:E126G;ENSP00000376854:E172G;ENSP00000376855:E180G;ENSP00000309066:E169G	ENSP00000309066:E169G	E	+	2	0	DPP10	116163918	0.812000	0.29077	0.999000	0.59377	0.988000	0.76386	1.342000	0.33919	0.865000	0.35603	0.477000	0.44152	GAG	.	.		0.438	DPP10-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330580.4	NM_020868	
WDR33	55339	hgsc.bcm.edu	37	2	128477145	128477145	+	Silent	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:128477145T>C	ENST00000322313.4	-	16	2612	c.2454A>G	c.(2452-2454)ggA>ggG	p.G818G		NM_018383.4	NP_060853.3	Q9C0J8	WDR33_HUMAN	WD repeat domain 33	818					mRNA processing (GO:0006397)|postreplication repair (GO:0006301)|spermatogenesis (GO:0007283)	collagen trimer (GO:0005581)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(9)|lung(17)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	39	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0695)		GTCCCAGTAGTCCACCTGGAG	0.632																																					p.G818G		Atlas-SNP	.											.	WDR33	136	.	0			c.A2454G						.						31.0	34.0	33.0					2																	128477145		2203	4300	6503	SO:0001819	synonymous_variant	55339	exon16			CAGTAGTCCACCT		CCDS2150.1, CCDS42746.1, CCDS46407.1	2q21.1	2013-01-09			ENSG00000136709	ENSG00000136709		"""WD repeat domain containing"""	25651	protein-coding gene	gene with protein product						11162572	Standard	NM_001006622		Approved	FLJ11294, WDC146, NET14	uc002tpg.2	Q9C0J8	OTTHUMG00000131534	ENST00000322313.4:c.2454A>G	chr2.hg19:g.128477145T>C		69.0	0.0		110.0	5.0	NM_018383	Q05DP8|Q53FG9|Q587J1|Q69YF7|Q6NUQ0|Q9NUL1	Silent	SNP	ENST00000322313.4	hg19	CCDS2150.1																																																																																			.	.		0.632	WDR33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331141.2	NM_018383	
NEB	4703	hgsc.bcm.edu	37	2	152424933	152424933	+	Splice_Site	SNP	T	T	A	rs3214503|rs397772995|rs539518038|rs75873810	byFrequency	TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:152424933T>A	ENST00000172853.10	-	84	12679		c.e84-2		NEB_ENST00000603639.1_Splice_Site|NEB_ENST00000604864.1_Splice_Site|NEB_ENST00000397345.3_Splice_Site|NEB_ENST00000409198.1_Splice_Site|NEB_ENST00000427231.2_Splice_Site			P20929	NEBU_HUMAN	nebulin						muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)			NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		GTATTTAATCTAAAAAAAAAA	0.423																																					.		Atlas-SNP	.											.,3	NEB	1697	.	0			c.17635-2A>T						.						47.0	51.0	49.0					2																	152424933		1813	4075	5888	SO:0001630	splice_region_variant	4703	exon113			TTAATCTAAAAAA	X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"""nemaline myopathy type 2"""	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.12532-2A>T	chr2.hg19:g.152424933T>A		59.0	2.0		70.0	5.0	NM_001164507	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Splice_Site	SNP	ENST00000172853.10	hg19		.	.	.	.	.	.	.	.	.	.	T	19.92	3.916138	0.73098	.	.	ENSG00000183091	ENST00000409198;ENST00000397345;ENST00000427231;ENST00000397342;ENST00000413693;ENST00000172853	.	.	.	6.17	6.17	0.99709	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.8222	0.85835	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	NEB	152133179	1.000000	0.71417	0.996000	0.52242	0.705000	0.40729	6.287000	0.72671	2.371000	0.80710	0.533000	0.62120	.	.	.		0.423	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543	Intron
XIRP2	129446	hgsc.bcm.edu	37	2	168101503	168101503	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:168101503A>G	ENST00000409195.1	+	9	3690	c.3601A>G	c.(3601-3603)Agg>Ggg	p.R1201G	XIRP2_ENST00000409273.1_Missense_Mutation_p.R979G|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000295237.9_Missense_Mutation_p.R1201G	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	1026					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						TTCCAGCATGAGGTATAAATT	0.338																																					p.R1201G		Atlas-SNP	.											.	XIRP2	914	.	0			c.A3601G						.						63.0	59.0	61.0					2																	168101503		1826	4078	5904	SO:0001583	missense	129446	exon9			AGCATGAGGTATA	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"""myomaxin"""	609778	"""cardiomyopathy associated 3"""	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.3601A>G	chr2.hg19:g.168101503A>G	ENSP00000386840:p.Arg1201Gly	62.0	0.0		74.0	5.0	NM_152381	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409195.1	hg19	CCDS42769.1	.	.	.	.	.	.	.	.	.	.	A	9.332	1.060875	0.19987	.	.	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273	T;T;T	0.03035	4.07;4.07;4.07	5.91	-2.05	0.07321	.	0.216956	0.44688	D	0.000426	T	0.04543	0.0124	L	0.59436	1.845	0.28443	N	0.916692	B;B;B	0.26258	0.09;0.145;0.145	B;B;B	0.27380	0.036;0.079;0.079	T	0.21724	-1.0237	10	0.72032	D	0.01	-0.1624	9.4277	0.38590	0.6968:0.1362:0.0:0.167	.	1026;1026;979	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	G	1201;1201;979	ENSP00000386840:R1201G;ENSP00000295237:R1201G;ENSP00000387255:R979G	ENSP00000295237:R1201G	R	+	1	2	XIRP2	167809749	1.000000	0.71417	0.251000	0.24312	0.712000	0.41017	1.734000	0.38166	-0.255000	0.09486	0.533000	0.62120	AGG	.	.		0.338	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381	
RAPGEF4	11069	hgsc.bcm.edu	37	2	173882175	173882175	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:173882175T>C	ENST00000397081.3	+	21	2094	c.1951T>C	c.(1951-1953)Ttc>Ctc	p.F651L	RAPGEF4_ENST00000397087.3_Missense_Mutation_p.F507L|RAPGEF4_ENST00000538974.1_Missense_Mutation_p.F480L|RAPGEF4_ENST00000535187.1_Missense_Mutation_p.F431L|RAPGEF4_ENST00000539331.1_Missense_Mutation_p.F498L|RAPGEF4_ENST00000540783.1_Missense_Mutation_p.F498L|RAPGEF4_ENST00000409036.1_Missense_Mutation_p.F651L|RAPGEF4_ENST00000264111.6_Missense_Mutation_p.F650L	NM_007023.3	NP_008954.2	Q8WZA2	RPGF4_HUMAN	Rap guanine nucleotide exchange factor (GEF) 4	651					blood coagulation (GO:0007596)|calcium ion-dependent exocytosis (GO:0017156)|cAMP-mediated signaling (GO:0019933)|energy reserve metabolic process (GO:0006112)|G-protein coupled receptor signaling pathway (GO:0007186)|insulin secretion (GO:0030073)|platelet activation (GO:0030168)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Ras GTPase activity (GO:0032320)|regulation of exocytosis (GO:0017157)|regulation of insulin secretion (GO:0050796)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	cAMP-dependent protein kinase complex (GO:0005952)|cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|cAMP-dependent protein kinase regulator activity (GO:0008603)|guanyl-nucleotide exchange factor activity (GO:0005085)|Ras GTPase binding (GO:0017016)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)			breast(1)|central_nervous_system(2)|endometrium(5)|kidney(5)|large_intestine(14)|lung(13)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	47			OV - Ovarian serous cystadenocarcinoma(117;0.194)			TTTGCAACAGTTCAATACGGG	0.473																																					p.F651L		Atlas-SNP	.											.	RAPGEF4	103	.	0			c.T1951C						.						85.0	80.0	82.0					2																	173882175		1912	4125	6037	SO:0001583	missense	11069	exon21			CAACAGTTCAATA	U78516	CCDS42775.1, CCDS42776.1, CCDS63060.1, CCDS63061.1, CCDS74604.1	2q31-q32	2008-02-05	2004-03-26		ENSG00000091428	ENSG00000091428			16626	protein-coding gene	gene with protein product	"""cAMP-regulated guanine nucleotide exchange factor II"", "" exchange protein directly activated by cAMP 2"""	606058	"""RAP guanine-nucleotide-exchange factor (GEF) 4"""			10777494, 9856955	Standard	NM_007023		Approved	cAMP-GEFII, CGEF2	uc002uhv.4	Q8WZA2	OTTHUMG00000133677	ENST00000397081.3:c.1951T>C	chr2.hg19:g.173882175T>C	ENSP00000380271:p.Phe651Leu	79.0	0.0		90.0	4.0	NM_007023	B2R7R3|B7Z283|B7Z3T6|B7Z912|O95636|Q8IXK6|Q8TAA4	Missense_Mutation	SNP	ENST00000397081.3	hg19	CCDS42775.1	.	.	.	.	.	.	.	.	.	.	T	12.54	1.967815	0.34754	.	.	ENSG00000091428	ENST00000264111;ENST00000397081;ENST00000409036;ENST00000397087;ENST00000538974;ENST00000540783;ENST00000539331;ENST00000535187	T;T;T;T;T;T;T;T	0.29142	1.58;1.58;1.58;1.58;1.58;1.58;1.58;1.58	5.46	5.46	0.80206	Ras guanine nucleotide exchange factor, domain (1);	0.090261	0.85682	D	0.000000	T	0.25158	0.0611	L	0.45228	1.405	0.80722	D	1	B;B	0.24651	0.108;0.066	B;B	0.25506	0.061;0.046	T	0.06661	-1.0814	10	0.02654	T	1	.	15.8863	0.79251	0.0:0.0:0.0:1.0	.	507;651	Q8WZA2-3;Q8WZA2	.;RPGF4_HUMAN	L	650;651;651;507;480;498;498;431	ENSP00000264111:F650L;ENSP00000380271:F651L;ENSP00000387104:F651L;ENSP00000380276:F507L;ENSP00000440135:F480L;ENSP00000440250:F498L;ENSP00000437384:F498L;ENSP00000438011:F431L	ENSP00000264111:F650L	F	+	1	0	RAPGEF4	173590421	1.000000	0.71417	1.000000	0.80357	0.895000	0.52256	7.655000	0.83696	2.223000	0.72356	0.454000	0.30748	TTC	.	.		0.473	RAPGEF4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257864.2	NM_007023	
TTN	7273	hgsc.bcm.edu	37	2	179397453	179397453	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:179397453T>C	ENST00000591111.1	-	308	99190	c.98966A>G	c.(98965-98967)gAg>gGg	p.E32989G	TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000591466.1_RNA|TTN-AS1_ENST00000585625.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000589842.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000588244.1_RNA|TTN-AS1_ENST00000588804.1_RNA|TTN-AS1_ENST00000588257.1_RNA|TTN-AS1_ENST00000592182.1_RNA|TTN-AS1_ENST00000585487.1_RNA|TTN-AS1_ENST00000590040.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000589355.1_RNA|TTN-AS1_ENST00000588716.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.E25757G|TTN_ENST00000589042.1_Missense_Mutation_p.E34630G|TTN-AS1_ENST00000587944.1_RNA|TTN-AS1_ENST00000591867.1_RNA|TTN-AS1_ENST00000431259.2_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.E32062G|TTN_ENST00000460472.2_Missense_Mutation_p.E25565G|TTN-AS1_ENST00000587568.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000592836.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000442329.2_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.E25690G|TTN-AS1_ENST00000589391.1_RNA|TTN-AS1_ENST00000604571.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000585358.1_RNA|TTN-AS1_ENST00000589434.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000450692.2_RNA|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	32989					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TCTCACTATCTCAAGATCATC	0.448																																					p.E34630G		Atlas-SNP	.											.	TTN	18412	.	0			c.A103889G						.						76.0	71.0	73.0					2																	179397453		1937	4124	6061	SO:0001583	missense	7273	exon358			ACTATCTCAAGAT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.98966A>G	chr2.hg19:g.179397453T>C	ENSP00000465570:p.Glu32989Gly	61.0	0.0		104.0	5.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	T	16.76	3.212556	0.58452	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.64991	-0.13;0.11;0.09;0.08	5.95	5.95	0.96441	Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);	.	.	.	.	T	0.68016	0.2955	N	0.19112	0.55	0.58432	D	0.999999	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	D;D;D;D	0.80764	0.994;0.994;0.994;0.994	T	0.73000	-0.4120	9	0.87932	D	0	.	16.0715	0.80940	0.0:0.0:0.0:1.0	.	25565;25690;25757;32989	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	G	32062;25565;25757;25690;25562	ENSP00000343764:E32062G;ENSP00000434586:E25565G;ENSP00000340554:E25757G;ENSP00000352154:E25690G	ENSP00000340554:E25757G	E	-	2	0	TTN	179105699	1.000000	0.71417	0.994000	0.49952	0.942000	0.58702	8.015000	0.88690	2.280000	0.76307	0.460000	0.39030	GAG	.	.		0.448	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
TTN	7273	hgsc.bcm.edu	37	2	179490077	179490077	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:179490077T>C	ENST00000591111.1	-	191	39772	c.39548A>G	c.(39547-39549)gAt>gGt	p.D13183G	TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.D5951G|TTN_ENST00000589042.1_Missense_Mutation_p.D14824G|TTN_ENST00000342992.6_Missense_Mutation_p.D12256G|TTN_ENST00000460472.2_Missense_Mutation_p.D5759G|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.D5884G|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	13183	Ig-like 87.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TAACTTTACATCCCTCAGAGT	0.368																																					p.D14824G		Atlas-SNP	.											.	TTN	18412	.	0			c.A44471G						.						234.0	223.0	226.0					2																	179490077		1842	4072	5914	SO:0001583	missense	7273	exon241			TTTACATCCCTCA	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.39548A>G	chr2.hg19:g.179490077T>C	ENSP00000465570:p.Asp13183Gly	83.0	0.0		99.0	4.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	T	17.10	3.302537	0.60195	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.44083	0.93;0.93;0.93;0.93	5.95	5.95	0.96441	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.39784	0.1091	N	0.26162	0.8	0.58432	D	0.999994	P;P;P;P	0.45715	0.865;0.865;0.865;0.865	P;P;P;P	0.45610	0.487;0.487;0.487;0.487	T	0.35251	-0.9796	9	0.87932	D	0	.	16.4116	0.83717	0.0:0.0:0.0:1.0	.	5759;5884;5951;13183	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	G	12256;5759;5951;5884;5759	ENSP00000343764:D12256G;ENSP00000434586:D5759G;ENSP00000340554:D5951G;ENSP00000352154:D5884G	ENSP00000340554:D5951G	D	-	2	0	TTN	179198322	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.612000	0.82975	2.276000	0.75962	0.528000	0.53228	GAT	.	.		0.368	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
TTN	7273	hgsc.bcm.edu	37	2	179501512	179501512	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:179501512T>C	ENST00000591111.1	-	175	36243	c.36019A>G	c.(36019-36021)Act>Gct	p.T12007A	TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000431752.1_RNA|TTN-AS1_ENST00000418062.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.T4775A|TTN_ENST00000589042.1_Missense_Mutation_p.T13648A|TTN_ENST00000342992.6_Missense_Mutation_p.T11080A|TTN_ENST00000460472.2_Missense_Mutation_p.T4583A|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.T4708A|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	12007	Pro-rich.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GGTGAAGGAGTCTTTTTGGGT	0.443																																					p.T13648A		Atlas-SNP	.											.	TTN	18412	.	0			c.A40942G						.						45.0	45.0	45.0					2																	179501512		1863	4099	5962	SO:0001583	missense	7273	exon225			AAGGAGTCTTTTT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.36019A>G	chr2.hg19:g.179501512T>C	ENSP00000465570:p.Thr12007Ala	72.0	0.0		125.0	5.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	T	15.82	2.947088	0.53186	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127;ENST00000414766	T;T;T;T	0.74315	-0.83;-0.23;-0.24;-0.25	5.77	5.77	0.91146	Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);	.	.	.	.	D	0.84853	0.5564	M	0.65498	2.005	0.58432	D	0.999995	D;D;D;D	0.69078	0.997;0.997;0.997;0.997	D;D;D;D	0.75020	0.985;0.985;0.985;0.985	D	0.86468	0.1783	9	0.87932	D	0	.	16.0836	0.81023	0.0:0.0:0.0:1.0	.	4583;4708;4775;12007	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	A	11080;4583;4775;4708;4583;952	ENSP00000343764:T11080A;ENSP00000434586:T4583A;ENSP00000340554:T4775A;ENSP00000352154:T4708A	ENSP00000340554:T4775A	T	-	1	0	TTN	179209757	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.959000	0.87885	2.196000	0.70406	0.528000	0.53228	ACT	.	.		0.443	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
CWC22	57703	hgsc.bcm.edu	37	2	180835748	180835748	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:180835748T>C	ENST00000410053.3	-	9	1159	c.860A>G	c.(859-861)gAt>gGt	p.D287G	CWC22_ENST00000295749.6_Missense_Mutation_p.D287G	NM_020943.2	NP_065994.1	Q9HCG8	CWC22_HUMAN	CWC22 spliceosome-associated protein	287	MIF4G. {ECO:0000255|PROSITE- ProRule:PRU00698}.				mRNA splicing, via spliceosome (GO:0000398)|regulation of mRNA splicing, via spliceosome (GO:0048024)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	RNA binding (GO:0003723)			NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(7)|kidney(2)|large_intestine(8)|liver(1)|lung(8)|stomach(1)	30						AACGCTATCATCTGTTGGTCT	0.358																																					p.D287G		Atlas-SNP	.											.	CWC22	62	.	0			c.A860G						.						113.0	107.0	109.0					2																	180835748		1871	4113	5984	SO:0001583	missense	57703	exon9			CTATCATCTGTTG		CCDS46465.1	2q31.3	2014-07-03	2014-07-03		ENSG00000163510	ENSG00000163510			29322	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein b"""	615186	"""CWC22 spliceosome-associated protein homolog (S. cerevisiae)"""			9136012, 23236153	Standard	NM_020943		Approved	KIAA1604, EIF4GL, fSAPb, NCM	uc010frh.1	Q9HCG8	OTTHUMG00000154244	ENST00000410053.3:c.860A>G	chr2.hg19:g.180835748T>C	ENSP00000387006:p.Asp287Gly	75.0	0.0		107.0	5.0	NM_020943	Q05DC2|Q4G135|Q52LF0|Q6PEX2|Q7Z6I0|Q9H5L3|Q9H6Q6	Missense_Mutation	SNP	ENST00000410053.3	hg19	CCDS46465.1	.	.	.	.	.	.	.	.	.	.	T	26.1	4.700738	0.88924	.	.	ENSG00000163510	ENST00000410053;ENST00000295749;ENST00000404136	T;T;T	0.23348	1.91;1.91;1.91	5.91	5.91	0.95273	MIF4G-like, type 3 (2);Armadillo-type fold (1);MIF4-like, type 1/2/3 (1);	0.000000	0.85682	D	0.000000	T	0.49983	0.1589	H	0.94582	3.555	0.80722	D	1	P	0.44816	0.844	P	0.45610	0.487	T	0.65249	-0.6214	10	0.87932	D	0	-39.4203	15.5295	0.75942	0.0:0.0:0.0:1.0	.	287	Q9HCG8	CWC22_HUMAN	G	287	ENSP00000387006:D287G;ENSP00000295749:D287G;ENSP00000384159:D287G	ENSP00000295749:D287G	D	-	2	0	CWC22	180543993	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.825000	0.86693	2.254000	0.74563	0.533000	0.62120	GAT	.	.		0.358	CWC22-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334537.1	NM_020943	
FAM171B	165215	hgsc.bcm.edu	37	2	187605011	187605011	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:187605011A>G	ENST00000304698.5	+	2	498	c.295A>G	c.(295-297)Agc>Ggc	p.S99G		NM_177454.3	NP_803237.3	Q6P995	F171B_HUMAN	family with sequence similarity 171, member B	99						integral component of membrane (GO:0016021)	DNA binding (GO:0003677)			NS(1)|breast(6)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(22)|ovary(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	54						TCAGTACCTGAGCCAAGCAGT	0.398																																					p.S99G		Atlas-SNP	.											.	FAM171B	146	.	0			c.A295G						.						112.0	96.0	102.0					2																	187605011		2203	4300	6503	SO:0001583	missense	165215	exon2			TACCTGAGCCAAG	AF361495	CCDS33347.1	2q32.2	2008-06-16	2008-06-16	2008-06-16	ENSG00000144369	ENSG00000144369			29412	protein-coding gene	gene with protein product			"""KIAA1946"""	KIAA1946		11853319	Standard	NM_177454		Approved	FLJ34104	uc002ups.3	Q6P995	OTTHUMG00000154278	ENST00000304698.5:c.295A>G	chr2.hg19:g.187605011A>G	ENSP00000304108:p.Ser99Gly	121.0	0.0		201.0	11.0	NM_177454	Q53SK3|Q8N1Y4|Q8N3K1|Q8N970|Q8NB81|Q8TF55|Q8WYR8	Missense_Mutation	SNP	ENST00000304698.5	hg19	CCDS33347.1	.	.	.	.	.	.	.	.	.	.	A	14.69	2.609599	0.46527	.	.	ENSG00000144369	ENST00000304698;ENST00000272804	T	0.35236	1.32	6.16	5.06	0.68205	.	0.292241	0.38663	N	0.001605	T	0.28333	0.0700	L	0.38175	1.15	0.28359	N	0.920569	B;B	0.20164	0.042;0.042	B;B	0.28385	0.089;0.089	T	0.14309	-1.0477	10	0.48119	T	0.1	-15.5391	6.7577	0.23523	0.6417:0.272:0.0863:0.0	.	99;100	Q6P995;A8K122	F171B_HUMAN;.	G	99	ENSP00000304108:S99G	ENSP00000272804:S99G	S	+	1	0	FAM171B	187313256	0.933000	0.31639	1.000000	0.80357	0.960000	0.62799	2.113000	0.41902	2.367000	0.80283	0.528000	0.53228	AGC	.	.		0.398	FAM171B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334679.1	NM_177454	
COL5A2	1290	hgsc.bcm.edu	37	2	189951464	189951464	+	Silent	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:189951464T>C	ENST00000374866.3	-	9	952	c.678A>G	c.(676-678)ttA>ttG	p.L226L		NM_000393.3	NP_000384.2	P05997	CO5A2_HUMAN	collagen, type V, alpha 2	226					axon guidance (GO:0007411)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|negative regulation of endodermal cell differentiation (GO:1903225)|skeletal system development (GO:0001501)|skin development (GO:0043588)	collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)			NS(3)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(16)|lung(53)|ovary(3)|prostate(2)|skin(6)|urinary_tract(3)	95			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.127)			GCTGTCCTTGTAAACCCTGTG	0.363																																					p.L226L		Atlas-SNP	.											.	COL5A2	230	.	0			c.A678G						.						46.0	44.0	45.0					2																	189951464		2203	4297	6500	SO:0001819	synonymous_variant	1290	exon9			TCCTTGTAAACCC	Y14690	CCDS33350.1	2q14-q32	2014-09-17			ENSG00000204262	ENSG00000204262		"""Collagens"""	2210	protein-coding gene	gene with protein product	"""AB collagen"""	120190				1572660	Standard	NM_000393		Approved		uc002uqk.3	P05997	OTTHUMG00000149842	ENST00000374866.3:c.678A>G	chr2.hg19:g.189951464T>C		30.0	0.0		60.0	4.0	NM_000393	P78440|Q13908|Q53WR4|Q59GR4|Q6LDJ5|Q7KZ55|Q86XF6|Q96QB0|Q96QB3	Silent	SNP	ENST00000374866.3	hg19	CCDS33350.1																																																																																			.	.		0.363	COL5A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313523.1	NM_000393	
HIBCH	26275	hgsc.bcm.edu	37	2	191159295	191159295	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:191159295A>G	ENST00000359678.5	-	4	575	c.281T>C	c.(280-282)tTc>tCc	p.F94S	HIBCH_ENST00000392332.3_Missense_Mutation_p.F94S	NM_014362.3|NM_198047.2	NP_055177.2|NP_932164.1	Q6NVY1	HIBCH_HUMAN	3-hydroxyisobutyryl-CoA hydrolase	94					branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)|valine catabolic process (GO:0006574)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)	3-hydroxyisobutyryl-CoA hydrolase activity (GO:0003860)			NS(1)|breast(2)|endometrium(1)|large_intestine(1)|lung(5)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(1)	13			OV - Ovarian serous cystadenocarcinoma(117;0.000586)|Epithelial(96;0.0286)|all cancers(119;0.0814)			CCCGGCACAGAAAGCCTTTCC	0.388																																					p.F94S		Atlas-SNP	.											.	HIBCH	28	.	0			c.T281C						.						85.0	82.0	83.0					2																	191159295		2203	4300	6503	SO:0001583	missense	26275	exon4			GCACAGAAAGCCT	U66669	CCDS2304.1, CCDS46475.1	2q32.3	2010-04-29	2010-04-29		ENSG00000198130	ENSG00000198130	3.1.2.4		4908	protein-coding gene	gene with protein product		610690	"""3-hydroxyisobutyryl-Coenzyme A hydrolase"""			8824301	Standard	NM_014362		Approved		uc002uru.3	Q6NVY1	OTTHUMG00000132673	ENST00000359678.5:c.281T>C	chr2.hg19:g.191159295A>G	ENSP00000352706:p.Phe94Ser	72.0	0.0		96.0	4.0	NM_014362	D3DPI4|Q53GA8|Q53GF2|Q53RF7|Q53TC6|Q92931|Q9BS94	Missense_Mutation	SNP	ENST00000359678.5	hg19	CCDS2304.1	.	.	.	.	.	.	.	.	.	.	A	23.8	4.453349	0.84209	.	.	ENSG00000198130	ENST00000392332;ENST00000359678;ENST00000409934	D;D;T	0.90563	-2.69;-2.69;-1.32	5.43	5.43	0.79202	Crotonase, core (1);	0.044752	0.85682	D	0.000000	D	0.97504	0.9183	H	0.99545	4.62	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.98652	1.0680	10	0.87932	D	0	-10.5228	13.4412	0.61114	1.0:0.0:0.0:0.0	.	94;94	Q6NVY1-2;Q6NVY1	.;HIBCH_HUMAN	S	94;94;148	ENSP00000376144:F94S;ENSP00000352706:F94S;ENSP00000387247:F148S	ENSP00000352706:F94S	F	-	2	0	HIBCH	190867540	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.743000	0.85020	2.053000	0.61076	0.460000	0.39030	TTC	.	.		0.388	HIBCH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255933.1		
ICA1L	130026	hgsc.bcm.edu	37	2	203650685	203650685	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:203650685T>C	ENST00000392237.2	-	13	1446	c.1289A>G	c.(1288-1290)gAt>gGt	p.D430G	ICA1L_ENST00000358299.2_Missense_Mutation_p.D430G	NM_138468.4	NP_612477.3	Q8NDH6	ICA1L_HUMAN	islet cell autoantigen 1,69kDa-like	430										breast(1)|endometrium(1)|large_intestine(7)|lung(7)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						TGGCTGGTTATCAGTGTGTGA	0.343																																					p.D430G		Atlas-SNP	.											.	ICA1L	33	.	0			c.A1289G						.						101.0	107.0	105.0					2																	203650685		2203	4300	6503	SO:0001583	missense	130026	exon13			TGGTTATCAGTGT	AB053317	CCDS2354.1, CCDS74632.1	2q33	2008-02-05	2006-05-26	2006-05-26	ENSG00000163596	ENSG00000163596			14442	protein-coding gene	gene with protein product			"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 15"", ""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 14"""	ALS2CR15, ALS2CR14		11586298	Standard	NM_138468		Approved		uc002uzh.1	Q8NDH6	OTTHUMG00000132856	ENST00000392237.2:c.1289A>G	chr2.hg19:g.203650685T>C	ENSP00000376070:p.Asp430Gly	39.0	0.0		55.0	5.0	NM_138468	B3KRW6|Q53P45|Q53QZ4|Q53T97|Q96N47|Q96Q32|Q9BVQ2	Missense_Mutation	SNP	ENST00000392237.2	hg19	CCDS2354.1	.	.	.	.	.	.	.	.	.	.	T	7.626	0.677752	0.14841	.	.	ENSG00000163596	ENST00000392237;ENST00000358299	.	.	.	4.99	2.54	0.30619	Islet cell autoantigen Ica1, C-terminal (1);	0.797344	0.11643	N	0.543540	T	0.34250	0.0891	N	0.25647	0.755	0.80722	D	1	B	0.23185	0.081	B	0.21917	0.037	T	0.07790	-1.0754	9	0.20519	T	0.43	.	4.8407	0.13489	0.0:0.0972:0.1899:0.7129	.	430	Q8NDH6	ICA1L_HUMAN	G	430	.	ENSP00000351047:D430G	D	-	2	0	ICA1L	203358930	0.786000	0.28738	0.562000	0.28370	0.688000	0.40055	0.933000	0.28897	0.357000	0.24183	0.456000	0.33151	GAT	.	.		0.343	ICA1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256330.1	NM_138468	
TTLL4	9654	hgsc.bcm.edu	37	2	219604821	219604821	+	Missense_Mutation	SNP	G	G	T	rs371385094	byFrequency	TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:219604821G>T	ENST00000392102.1	+	4	1868	c.1528G>T	c.(1528-1530)Gat>Tat	p.D510Y	TTLL4_ENST00000258398.4_Missense_Mutation_p.D510Y|TTLL4_ENST00000457313.1_Missense_Mutation_p.D345Y|TTLL4_ENST00000442769.1_Missense_Mutation_p.D510Y	NM_014640.4	NP_055455.3	Q14679	TTLL4_HUMAN	tubulin tyrosine ligase-like family, member 4	510					protein polyglutamylation (GO:0018095)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	ligase activity (GO:0016874)|tubulin binding (GO:0015631)			endometrium(3)|kidney(1)|large_intestine(6)|lung(21)|ovary(3)|skin(3)|upper_aerodigestive_tract(2)	39		Renal(207;0.0915)		Epithelial(149;5.03e-07)|all cancers(144;0.000106)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.0101)		TGAGACTGAAGATACAGAAGA	0.458																																					p.D510Y	GBM(172;1818 2053 15407 20943 49753)	Atlas-SNP	.											.	TTLL4	96	.	0			c.G1528T						.						122.0	117.0	118.0					2																	219604821		2203	4300	6503	SO:0001583	missense	9654	exon4			ACTGAAGATACAG		CCDS2422.1	2p24.3-p24.1	2013-02-14			ENSG00000135912	ENSG00000135912		"""Tubulin tyrosine ligase-like family"""	28976	protein-coding gene	gene with protein product						11054573	Standard	NM_014640		Approved	KIAA0173	uc002viy.3	Q14679	OTTHUMG00000133081	ENST00000392102.1:c.1528G>T	chr2.hg19:g.219604821G>T	ENSP00000375951:p.Asp510Tyr	185.0	0.0		231.0	25.0	NM_014640	A8K6V5|Q8WW29	Missense_Mutation	SNP	ENST00000392102.1	hg19	CCDS2422.1	.	.	.	.	.	.	.	.	.	.	G	19.28	3.796399	0.70567	.	.	ENSG00000135912	ENST00000457313;ENST00000392102;ENST00000442769;ENST00000258398	T;T;T;T	0.06294	3.49;3.71;3.32;3.71	4.69	4.69	0.59074	.	0.793840	0.11423	N	0.565537	T	0.16938	0.0407	L	0.34521	1.04	0.44531	D	0.997485	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.74023	0.936;0.927;0.982	T	0.01879	-1.1255	10	0.62326	D	0.03	.	14.4975	0.67700	0.0:0.0:1.0:0.0	.	345;510;510	E9PH58;E7EX20;Q14679	.;.;TTLL4_HUMAN	Y	345;510;510;510	ENSP00000393332:D345Y;ENSP00000375951:D510Y;ENSP00000396555:D510Y;ENSP00000258398:D510Y	ENSP00000258398:D510Y	D	+	1	0	TTLL4	219313065	1.000000	0.71417	0.996000	0.52242	0.908000	0.53690	5.584000	0.67490	2.433000	0.82419	0.561000	0.74099	GAT	.	.		0.458	TTLL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256726.1	NM_014640	
DNPEP	23549	hgsc.bcm.edu	37	2	220246820	220246820	+	Silent	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:220246820T>C	ENST00000273075.4	-	11	1198	c.978A>G	c.(976-978)acA>acG	p.T326T	DNPEP_ENST00000373972.1_Silent_p.T251T|DNPEP_ENST00000523282.1_Silent_p.T334T|DNPEP_ENST00000490371.1_5'Flank	NM_012100.2	NP_036232	Q9ULA0	DNPEP_HUMAN	aspartyl aminopeptidase	316					peptide metabolic process (GO:0006518)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(3)|endometrium(2)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		Renal(207;0.0474)		Epithelial(149;1.09e-06)|all cancers(144;0.000179)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GCACCAGCTCTGTCAGCAGTG	0.602																																					p.T326T		Atlas-SNP	.											.	DNPEP	40	.	0			c.A978G						.						50.0	57.0	55.0					2																	220246820		2134	4248	6382	SO:0001819	synonymous_variant	23549	exon11			CAGCTCTGTCAGC		CCDS42823.1	2q36.1	2008-05-22			ENSG00000123992	ENSG00000123992			2981	protein-coding gene	gene with protein product		611367				9632644	Standard	NM_012100		Approved	DAP, ASPEP	uc002vle.2	Q9ULA0	OTTHUMG00000058919	ENST00000273075.4:c.978A>G	chr2.hg19:g.220246820T>C		38.0	0.0		85.0	4.0	NM_012100	Q9BW44|Q9NUV5	Silent	SNP	ENST00000273075.4	hg19	CCDS42823.1																																																																																			.	.		0.602	DNPEP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000130212.1	NM_012100	
COL4A3	1285	hgsc.bcm.edu	37	2	228111436	228111436	+	Silent	SNP	G	G	C	rs559126084	byFrequency	TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:228111436G>C	ENST00000396578.3	+	7	585	c.423G>C	c.(421-423)ctG>ctC	p.L141L	AC097662.2_ENST00000396588.2_RNA|AC097662.2_ENST00000437673.1_RNA|AC097662.2_ENST00000439598.2_RNA|AC097662.2_ENST00000606119.1_RNA	NM_000091.4	NP_000082.2	Q01955	CO4A3_HUMAN	collagen, type IV, alpha 3 (Goodpasture antigen)	141	Triple-helical region.		L -> P (in dbSNP:rs10178458). {ECO:0000269|PubMed:11134255, ECO:0000269|PubMed:8083201}.		activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|axon guidance (GO:0007411)|blood circulation (GO:0008015)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|collagen catabolic process (GO:0030574)|endothelial cell apoptotic process (GO:0072577)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endopeptidase activity (GO:0010951)|sensory perception of sound (GO:0007605)	basement membrane (GO:0005604)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)|integrin binding (GO:0005178)|metalloendopeptidase inhibitor activity (GO:0008191)|structural molecule activity (GO:0005198)			NS(4)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	55		all_lung(227;0.00101)|Lung NSC(271;0.00278)|Renal(207;0.0112)|Ovarian(221;0.0129)|all_hematologic(139;0.211)|Esophageal squamous(248;0.247)		Epithelial(121;1.17e-46)|all cancers(144;6.87e-42)|Lung(261;0.0137)|LUSC - Lung squamous cell carcinoma(224;0.0187)		CAGGGACACTGGGCTACCCAG	0.413																																					p.L141L		Atlas-SNP	.											COL4A3_ENST00000328380,NS,carcinoma,0,2	COL4A3	293	.	0			c.G423C						.						65.0	64.0	64.0					2																	228111436		1839	4084	5923	SO:0001819	synonymous_variant	1285	exon7			GACACTGGGCTAC		CCDS42829.1	2q36-q37	2014-09-17			ENSG00000169031	ENSG00000169031		"""Collagens"""	2204	protein-coding gene	gene with protein product	"""tumstatin"""	120070				1737849	Standard	NM_000091		Approved		uc002vom.2	Q01955	OTTHUMG00000149891	ENST00000396578.3:c.423G>C	chr2.hg19:g.228111436G>C		135.0	0.0		180.0	0.0	NM_000091	Q53QQ1|Q53R14|Q53RW8|Q9BQT2|Q9NYC4|Q9UDJ9|Q9UDK9|Q9UDL0|Q9UDL1	Silent	SNP	ENST00000396578.3	hg19	CCDS42829.1																																																																																			.	.		0.413	COL4A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331409.2	NM_000091	
LRRFIP1	9208	hgsc.bcm.edu	37	2	238681566	238681566	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:238681566A>G	ENST00000308482.9	+	22	1754	c.1685A>G	c.(1684-1686)gAg>gGg	p.E562G	LRRFIP1_ENST00000468950.1_3'UTR	NM_001137550.1	NP_001131022.1	Q32MZ4	LRRF1_HUMAN	leucine rich repeat (in FLII) interacting protein 1	0	DNA-binding.			L -> F (in Ref. 4; AAI08915). {ECO:0000305}.	innate immune response (GO:0045087)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of type I interferon production (GO:0032481)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|protein homodimerization activity (GO:0042803)			NS(1)|breast(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)	29		Breast(86;0.00257)|Renal(207;0.00571)|Ovarian(221;0.17)|all_hematologic(139;0.182)		Epithelial(121;9.75e-23)|OV - Ovarian serous cystadenocarcinoma(60;1.01e-10)|Kidney(56;4.85e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.31e-07)|BRCA - Breast invasive adenocarcinoma(100;0.000151)|Lung(119;0.0137)|LUSC - Lung squamous cell carcinoma(224;0.0325)|COAD - Colon adenocarcinoma(134;0.228)		TCTGAGCAAGAGATAACTGCA	0.418																																					p.E562G		Atlas-SNP	.											LRRFIP1_ENST00000308482,NS,carcinoma,0,1	LRRFIP1	171	.	0			c.A1685G						.						91.0	81.0	84.0					2																	238681566		1568	3582	5150	SO:0001583	missense	9208	exon22			AGCAAGAGATAAC	AJ223075	CCDS2521.1, CCDS46551.1, CCDS46552.1, CCDS46553.1	2q37.3	2010-09-30			ENSG00000124831	ENSG00000124831			6702	protein-coding gene	gene with protein product	"""GC-binding factor 2"""	603256				9705290, 9525888, 16199883	Standard	NM_004735		Approved	FLAP-1, FLIIAP1, TRIP, GCF-2, HUFI-1	uc002vxe.3	Q32MZ4	OTTHUMG00000133339	ENST00000308482.9:c.1685A>G	chr2.hg19:g.238681566A>G	ENSP00000310109:p.Glu562Gly	86.0	0.0		113.0	5.0	NM_001137550	E9PGZ2|O75766|O75799|Q32MZ5|Q53T49|Q6PKG2|Q9Y607	Missense_Mutation	SNP	ENST00000308482.9	hg19	CCDS46551.1	.	.	.	.	.	.	.	.	.	.	A	25.5	4.640973	0.87859	.	.	ENSG00000124831	ENST00000308482;ENST00000391999	T	0.60040	0.22	5.44	5.44	0.79542	.	.	.	.	.	T	0.74076	0.3669	M	0.68593	2.085	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.77273	-0.2649	9	0.87932	D	0	.	14.6865	0.69052	1.0:0.0:0.0:0.0	.	316;562	B4DPC0;E9PGZ2	.;.	G	562;552	ENSP00000310109:E562G	ENSP00000310109:E562G	E	+	2	0	LRRFIP1	238346305	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	8.628000	0.90979	2.065000	0.61736	0.460000	0.39030	GAG	.	.		0.418	LRRFIP1-002	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000257169.3	NM_004735	
NKTR	4820	hgsc.bcm.edu	37	3	42679487	42679487	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:42679487A>G	ENST00000232978.8	+	13	2479	c.2291A>G	c.(2290-2292)aAa>aGa	p.K764R	RP4-613B23.1_ENST00000438017.1_RNA|RP4-613B23.1_ENST00000434363.1_RNA|RP4-613B23.1_ENST00000445452.1_RNA	NM_005385.3	NP_005376.2	P30414	NKTR_HUMAN	natural killer cell triggering receptor	764	Arg/Ser-rich.				protein folding (GO:0006457)	membrane (GO:0016020)	cyclosporin A binding (GO:0016018)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			breast(3)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(6)|lung(10)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	41				KIRC - Kidney renal clear cell carcinoma(284;0.24)		TCCAGTGGGAAAAAAAATAGC	0.383																																					p.K764R		Atlas-SNP	.											NKTR,NS,carcinoma,0,1	NKTR	116	.	0			c.A2291G						.						86.0	86.0	86.0					3																	42679487		2203	4300	6503	SO:0001583	missense	4820	exon13			GTGGGAAAAAAAA		CCDS2702.1	3p22.1	2014-01-20	2014-01-20		ENSG00000114857	ENSG00000114857			7833	protein-coding gene	gene with protein product	"""NK-tumor recognition protein"", ""natural-killer cells cyclophilin-related protein"", ""NK-TR protein"""	161565	"""natural killer-tumor recognition sequence"""			8314596, 8144875	Standard	XM_005265173		Approved	p104	uc003clo.3	P30414	OTTHUMG00000133037	ENST00000232978.8:c.2291A>G	chr3.hg19:g.42679487A>G	ENSP00000232978:p.Lys764Arg	88.0	0.0		133.0	0.0	NM_005385		Missense_Mutation	SNP	ENST00000232978.8	hg19	CCDS2702.1	.	.	.	.	.	.	.	.	.	.	A	4.945	0.175619	0.09391	.	.	ENSG00000114857	ENST00000232978	T	0.12147	2.71	5.64	1.93	0.25924	.	0.627824	0.17249	N	0.181233	T	0.11750	0.0286	L	0.49350	1.555	0.09310	N	1	B;B	0.11235	0.004;0.003	B;B	0.11329	0.006;0.002	T	0.22626	-1.0211	10	0.39692	T	0.17	-4.6749	5.8403	0.18629	0.5922:0.2633:0.1445:0.0	.	464;764	Q6M1B8;P30414	.;NKTR_HUMAN	R	764	ENSP00000232978:K764R	ENSP00000232978:K764R	K	+	2	0	NKTR	42654491	0.034000	0.19679	0.001000	0.08648	0.159000	0.22180	0.458000	0.21892	0.386000	0.24997	0.482000	0.46254	AAA	.	.		0.383	NKTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256642.2	NM_005385	
ZNF197	10168	hgsc.bcm.edu	37	3	44683956	44683956	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:44683956A>G	ENST00000396058.1	+	5	1501	c.1334A>G	c.(1333-1335)cAg>cGg	p.Q445R	ZNF197_ENST00000383745.2_Intron|ZNF197_ENST00000344387.4_Missense_Mutation_p.Q445R|ZNF197_ENST00000383744.4_Intron|RP11-944L7.4_ENST00000457331.1_RNA			O14709	ZN197_HUMAN	zinc finger protein 197	445					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(9)|ovary(3)|prostate(1)|skin(1)	25				KIRC - Kidney renal clear cell carcinoma(197;0.0478)|Kidney(197;0.0598)		CTAAACCATCAGAGGATCCAC	0.428																																					p.Q445R		Atlas-SNP	.											.	ZNF197	81	.	0			c.A1334G						.						63.0	67.0	66.0					3																	44683956		2203	4300	6503	SO:0001583	missense	10168	exon6			ACCATCAGAGGAT	AF011573	CCDS2717.1, CCDS33743.1	3p21	2013-01-09	2003-10-07		ENSG00000186448	ENSG00000186448		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	12988	protein-coding gene	gene with protein product			"""zinc finger protein 166"""	ZNF166		9380504, 8353497	Standard	XM_005264783		Approved	P18, D3S1363E, ZKSCAN9, ZSCAN41	uc003cnm.3	O14709	OTTHUMG00000133089	ENST00000396058.1:c.1334A>G	chr3.hg19:g.44683956A>G	ENSP00000379370:p.Gln445Arg	54.0	0.0		85.0	4.0	NM_006991	B2RAH8|Q86VG0	Missense_Mutation	SNP	ENST00000396058.1	hg19	CCDS2717.1	.	.	.	.	.	.	.	.	.	.	A	13.56	2.274445	0.40194	.	.	ENSG00000186448	ENST00000344387;ENST00000396058	T;T	0.17691	2.26;2.26	4.32	3.11	0.35812	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.33553	N	0.004789	T	0.12860	0.0312	N	0.02775	-0.495	0.09310	N	0.999994	D	0.62365	0.991	P	0.61592	0.891	T	0.05784	-1.0864	10	0.45353	T	0.12	.	5.899	0.18955	0.6627:0.1719:0.0:0.1654	.	445	O14709	ZN197_HUMAN	R	445	ENSP00000345809:Q445R;ENSP00000379370:Q445R	ENSP00000345809:Q445R	Q	+	2	0	ZNF197	44658960	0.001000	0.12720	1.000000	0.80357	0.988000	0.76386	1.083000	0.30815	0.757000	0.33036	0.374000	0.22700	CAG	.	.		0.428	ZNF197-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256747.4	NM_006991	
LZTFL1	54585	hgsc.bcm.edu	37	3	45874602	45874602	+	Silent	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:45874602A>G	ENST00000296135.6	-	5	570	c.396T>C	c.(394-396)gaT>gaC	p.D132D	LZTFL1_ENST00000536047.1_Silent_p.D115D|LZTFL1_ENST00000490463.1_5'UTR|LZTFL1_ENST00000539217.1_Silent_p.D128D	NM_001276378.1|NM_020347.2	NP_001263307.1|NP_065080.1	Q9NQ48	LZTL1_HUMAN	leucine zipper transcription factor-like 1	132					establishment of protein localization to organelle (GO:0072594)	BBSome (GO:0034464)|cytoplasm (GO:0005737)	identical protein binding (GO:0042802)			endometrium(1)|large_intestine(2)|lung(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	8				BRCA - Breast invasive adenocarcinoma(193;0.00867)|KIRC - Kidney renal clear cell carcinoma(197;0.0177)|Kidney(197;0.0208)		GCTTTGTGACATCTAAGATGG	0.353																																					p.D132D		Atlas-SNP	.											.	LZTFL1	37	.	0			c.T396C						.						119.0	117.0	118.0					3																	45874602		2203	4300	6503	SO:0001819	synonymous_variant	54585	exon5			TGTGACATCTAAG	AJ297351	CCDS2731.1, CCDS63608.1, CCDS63609.1	3p21.3	2014-01-28			ENSG00000163818	ENSG00000163818			6741	protein-coding gene	gene with protein product		606568				11352561, 22510444	Standard	NM_020347		Approved	BBS17	uc003cox.2	Q9NQ48	OTTHUMG00000133452	ENST00000296135.6:c.396T>C	chr3.hg19:g.45874602A>G		79.0	0.0		68.0	4.0	NM_020347	B3KSI9|B4E0K7|Q8TC61|Q9NQ56	Silent	SNP	ENST00000296135.6	hg19	CCDS2731.1	.	.	.	.	.	.	.	.	.	.	A	5.468	0.271472	0.10349	.	.	ENSG00000163818	ENST00000440576	.	.	.	5.77	-11.5	0.00074	.	.	.	.	.	T	0.54983	0.1892	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.67273	-0.5712	4	.	.	.	-14.0683	12.74	0.57246	0.2111:0.4242:0.3646:0.0	.	.	.	.	R	90	.	.	C	-	1	0	LZTFL1	45849606	0.000000	0.05858	0.000000	0.03702	0.084000	0.17831	-2.259000	0.01178	-2.136000	0.00810	-0.340000	0.08031	TGT	.	.		0.353	LZTFL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257326.3	NM_020347	
SETD2	29072	hgsc.bcm.edu	37	3	47164899	47164899	+	Silent	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:47164899A>G	ENST00000409792.3	-	3	1269	c.1227T>C	c.(1225-1227)tcT>tcC	p.S409S		NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	409	Arg-rich.				angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)			breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		AGCCTCTCTCAGACCTAGAGT	0.428			"""N, F, S, Mis"""		clear cell renal carcinoma																																p.S409S		Atlas-SNP	.		Rec	yes		3	3p21.31	29072	SET domain containing 2		E	.	SETD2	721	.	0			c.T1227C						.						80.0	64.0	69.0					3																	47164899		692	1591	2283	SO:0001819	synonymous_variant	29072	exon3			TCTCTCAGACCTA	AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"""Chromatin-modifying enzymes / K-methyltransferases"""	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.1227T>C	chr3.hg19:g.47164899A>G		113.0	0.0		142.0	7.0	NM_014159	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Silent	SNP	ENST00000409792.3	hg19	CCDS2749.2																																																																																			.	.		0.428	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159	
GMPPB	29925	hgsc.bcm.edu	37	3	49759218	49759218	+	Silent	SNP	G	G	A			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:49759218G>A	ENST00000480687.1	-	10	1166	c.1050C>T	c.(1048-1050)ggC>ggT	p.G350G	AMIGO3_ENST00000535833.1_5'UTR|AMIGO3_ENST00000320431.7_5'Flank|GMPPB_ENST00000308375.6_Silent_p.G377G|GMPPB_ENST00000308388.6_Silent_p.G350G			Q9Y5P6	GMPPB_HUMAN	GDP-mannose pyrophosphorylase B	350					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|GDP-mannose biosynthetic process (GO:0009298)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)|mannose-1-phosphate guanylyltransferase activity (GO:0004475)			endometrium(1)|kidney(2)|large_intestine(1)|lung(1)|skin(1)	6				BRCA - Breast invasive adenocarcinoma(193;4.53e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		GCACTGACTCGCCAATAGACT	0.577																																					p.G377G		Atlas-SNP	.											.	GMPPB	14	.	0			c.C1131T						.						50.0	48.0	49.0					3																	49759218		2203	4300	6503	SO:0001819	synonymous_variant	29925	exon8			TGACTCGCCAATA	AF135421	CCDS2802.1, CCDS2803.1	3p21.31	2008-02-05			ENSG00000173540	ENSG00000173540	2.7.7.22		22932	protein-coding gene	gene with protein product		615320					Standard	NM_013334		Approved	KIAA1851	uc003cxl.1	Q9Y5P6	OTTHUMG00000158151	ENST00000480687.1:c.1050C>T	chr3.hg19:g.49759218G>A		32.0	0.0		36.0	4.0	NM_013334	A8K6N5|Q9H7U3	Silent	SNP	ENST00000480687.1	hg19	CCDS2803.1																																																																																			.	.		0.577	GMPPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350291.1	NM_013334	
CACNA2D2	9254	hgsc.bcm.edu	37	3	50417242	50417242	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:50417242T>C	ENST00000479441.1	-	10	906	c.907A>G	c.(907-909)Agc>Ggc	p.S303G	CACNA2D2_ENST00000424201.2_Missense_Mutation_p.S303G|CACNA2D2_ENST00000435965.1_Missense_Mutation_p.S303G|CACNA2D2_ENST00000266039.3_Missense_Mutation_p.S303G|CACNA2D2_ENST00000360963.3_Missense_Mutation_p.S234G|CACNA2D2_ENST00000429770.1_Missense_Mutation_p.S303G|CACNA2D2_ENST00000395083.1_Missense_Mutation_p.S303G|CACNA2D2_ENST00000423994.2_Missense_Mutation_p.S303G			Q9NY47	CA2D2_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 2	303	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				energy reserve metabolic process (GO:0006112)|muscle fiber development (GO:0048747)|neuromuscular junction development (GO:0007528)|positive regulation of organ growth (GO:0046622)|regulation of insulin secretion (GO:0050796)|regulation of multicellular organism growth (GO:0040014)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			breast(3)|cervix(1)|endometrium(4)|large_intestine(4)|lung(8)|ovary(2)|prostate(4)|skin(4)|urinary_tract(1)	31				BRCA - Breast invasive adenocarcinoma(193;0.000365)|KIRC - Kidney renal clear cell carcinoma(197;0.00862)|Kidney(197;0.01)	Amiodarone(DB01118)|Bepridil(DB01244)|Felodipine(DB01023)|Gabapentin(DB00996)|Isradipine(DB00270)|Nitrendipine(DB01054)|Spironolactone(DB00421)	GTCAGGCCGCTCACACTGCCA	0.587																																					p.S303G		Atlas-SNP	.											.	CACNA2D2	82	.	0			c.A907G						.						98.0	83.0	88.0					3																	50417242		2203	4300	6503	SO:0001583	missense	9254	exon10			GGCCGCTCACACT	AF040709	CCDS33763.1, CCDS54588.1, CCDS63647.1	3p21.3	2004-02-27			ENSG00000007402	ENSG00000007402		"""Calcium channel subunits"""	1400	protein-coding gene	gene with protein product	"""gene 26"""	607082					Standard	XM_005265581		Approved	KIAA0558	uc003daq.3	Q9NY47	OTTHUMG00000156887	ENST00000479441.1:c.907A>G	chr3.hg19:g.50417242T>C	ENSP00000418081:p.Ser303Gly	130.0	0.0		158.0	7.0	NM_001174051	A7MD15|Q9NY48|Q9UEW0|Q9Y268	Missense_Mutation	SNP	ENST00000479441.1	hg19	CCDS54588.1	.	.	.	.	.	.	.	.	.	.	T	21.4	4.140503	0.77775	.	.	ENSG00000007402	ENST00000423994;ENST00000429770;ENST00000266039;ENST00000360963;ENST00000435965;ENST00000395083;ENST00000424201;ENST00000479441	D;D;D;D;D;D;D;D	0.81821	-1.54;-1.54;-1.54;-1.54;-1.54;-1.54;-1.54;-1.54	5.0	5.0	0.66597	von Willebrand factor, type A (3);	0.085016	0.85682	D	0.000000	D	0.87966	0.6311	M	0.65975	2.015	0.50171	D	0.999852	D;D	0.71674	0.998;0.997	D;D	0.72338	0.977;0.977	D	0.88920	0.3365	10	0.59425	D	0.04	-14.2627	14.7124	0.69244	0.0:0.0:0.0:1.0	.	303;303	Q9NY47;Q9NY47-2	CA2D2_HUMAN;.	G	303;303;303;234;303;303;303;303	ENSP00000407393:S303G;ENSP00000404631:S303G;ENSP00000266039:S303G;ENSP00000354228:S234G;ENSP00000390526:S303G;ENSP00000378519:S303G;ENSP00000390329:S303G;ENSP00000418081:S303G	ENSP00000266039:S303G	S	-	1	0	CACNA2D2	50392246	1.000000	0.71417	0.785000	0.31869	0.899000	0.52679	7.969000	0.87988	1.878000	0.54408	0.459000	0.35465	AGC	.	.		0.587	CACNA2D2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000346457.1	NM_006030	
GNL3	26354	hgsc.bcm.edu	37	3	52727059	52727059	+	Silent	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:52727059A>G	ENST00000418458.1	+	10	1214	c.1041A>G	c.(1039-1041)cgA>cgG	p.R347R	SNORD19B_ENST00000459623.1_RNA|SNORD69_ENST00000391150.1_RNA|SNORD19_ENST00000410413.1_RNA|GLT8D1_ENST00000463827.1_5'Flank|GNL3_ENST00000394799.2_Silent_p.R335R	NM_014366.4|NM_206826.1	NP_055181.3|NP_996562.1	Q9BVP2	GNL3_HUMAN	guanine nucleotide binding protein-like 3 (nucleolar)	347	Intermediate. {ECO:0000250}.				cell proliferation (GO:0008283)|GTP catabolic process (GO:0006184)|regulation of cell proliferation (GO:0042127)|ribosome biogenesis (GO:0042254)	extracellular space (GO:0005615)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)			breast(4)|endometrium(3)|large_intestine(3)|lung(2)	12				BRCA - Breast invasive adenocarcinoma(193;6.75e-05)|Kidney(197;0.000611)|KIRC - Kidney renal clear cell carcinoma(197;0.000773)|OV - Ovarian serous cystadenocarcinoma(275;0.048)		CTGATGCTCGACAGGTAAAAG	0.458																																					p.R347R		Atlas-SNP	.											.	GNL3	37	.	0			c.A1041G						.						63.0	61.0	62.0					3																	52727059		2203	4300	6503	SO:0001819	synonymous_variant	26354	exon10			TGCTCGACAGGTA	AK027514	CCDS2861.1, CCDS43100.1	3p21.1	2005-01-10			ENSG00000163938	ENSG00000163938			29931	protein-coding gene	gene with protein product		608011				11085516, 12464630	Standard	NM_014366		Approved	C77032, E2IG3, MGC800, NS, nucleostemin	uc003dfd.3	Q9BVP2	OTTHUMG00000158752	ENST00000418458.1:c.1041A>G	chr3.hg19:g.52727059A>G		64.0	0.0		98.0	4.0	NM_014366	B2RDC1|Q5PU80|Q96SV6|Q96SV7|Q9UJY0	Silent	SNP	ENST00000418458.1	hg19	CCDS2861.1																																																																																			.	.		0.458	GNL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352032.1	NM_014366	
FLNB	2317	hgsc.bcm.edu	37	3	58087998	58087998	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:58087998A>G	ENST00000295956.4	+	9	1579	c.1414A>G	c.(1414-1416)Acc>Gcc	p.T472A	FLNB_ENST00000493452.1_Missense_Mutation_p.T303A|FLNB_ENST00000358537.3_Missense_Mutation_p.T472A|FLNB_ENST00000357272.4_Missense_Mutation_p.T472A|FLNB_ENST00000348383.5_Missense_Mutation_p.T472A|FLNB_ENST00000490882.1_Missense_Mutation_p.T472A|FLNB_ENST00000429972.2_Missense_Mutation_p.T472A|FLNB_ENST00000419752.2_Missense_Mutation_p.T303A	NM_001457.3	NP_001448.2	O75369	FLNB_HUMAN	filamin B, beta	472					actin cytoskeleton organization (GO:0030036)|cell differentiation (GO:0030154)|cytokine-mediated signaling pathway (GO:0019221)|cytoskeletal anchoring at plasma membrane (GO:0007016)|signal transduction (GO:0007165)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	actin binding (GO:0003779)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(13)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(23)|liver(2)|lung(38)|ovary(6)|prostate(3)|skin(8)|upper_aerodigestive_tract(3)|urinary_tract(5)	120				BRCA - Breast invasive adenocarcinoma(55;0.000335)|KIRC - Kidney renal clear cell carcinoma(284;0.0726)|Kidney(284;0.0898)		TATCCGGGAGACCACAGATTT	0.517																																					p.T472A		Atlas-SNP	.											.	FLNB	430	.	0			c.A1414G						.						119.0	123.0	122.0					3																	58087998		2203	4300	6503	SO:0001583	missense	2317	exon9			CGGGAGACCACAG	AF043045	CCDS2885.1, CCDS54599.1, CCDS54600.1, CCDS54601.1	3p14.3	2011-02-11	2009-07-23		ENSG00000136068	ENSG00000136068			3755	protein-coding gene	gene with protein product	"""actin binding protein 278"""	603381	"""filamin B, beta (actin binding protein 278)"", ""Larsen syndrome 1 (autosomal dominant)"""	FLN1L, LRS1		8327473, 10449914, 14991055, 16801345	Standard	NM_001457		Approved	TAP, TABP, ABP-278, FH1	uc010hne.2	O75369	OTTHUMG00000159158	ENST00000295956.4:c.1414A>G	chr3.hg19:g.58087998A>G	ENSP00000295956:p.Thr472Ala	121.0	0.0		123.0	5.0	NM_001457	B2ZZ83|B2ZZ84|B2ZZ85|C9JKE6|C9JMC4|Q13706|Q59EC2|Q60FE7|Q6MZJ1|Q8WXS9|Q8WXT0|Q8WXT1|Q8WXT2|Q8WXT3|Q9NRB5|Q9NT26|Q9UEV9	Missense_Mutation	SNP	ENST00000295956.4	hg19	CCDS2885.1	.	.	.	.	.	.	.	.	.	.	A	10.40	1.338940	0.24253	.	.	ENSG00000136068	ENST00000295956;ENST00000490882;ENST00000358537;ENST00000429972;ENST00000348383;ENST00000357272;ENST00000493452;ENST00000419752	D;D;D;D;D;D;D;D	0.84370	-1.84;-1.84;-1.84;-1.84;-1.84;-1.84;-1.84;-1.84	5.43	5.43	0.79202	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.158239	0.56097	D	0.000025	T	0.79569	0.4468	N	0.20986	0.625	0.41804	D	0.989936	B;B;B;B;B;B	0.22604	0.059;0.025;0.072;0.001;0.04;0.04	B;B;B;B;B;B	0.32980	0.097;0.034;0.156;0.013;0.156;0.156	T	0.75059	-0.3451	10	0.30078	T	0.28	.	15.7645	0.78114	1.0:0.0:0.0:0.0	.	472;472;303;303;472;472	O75369-2;B2ZZ83;E7EN95;O75369-7;Q60FE7;O75369	.;.;.;.;.;FLNB_HUMAN	A	472;472;472;472;472;472;303;303	ENSP00000295956:T472A;ENSP00000420213:T472A;ENSP00000351339:T472A;ENSP00000415599:T472A;ENSP00000232447:T472A;ENSP00000349819:T472A;ENSP00000418510:T303A;ENSP00000414532:T303A	ENSP00000295956:T472A	T	+	1	0	FLNB	58063038	1.000000	0.71417	1.000000	0.80357	0.809000	0.45718	4.553000	0.60753	2.196000	0.70406	0.482000	0.46254	ACC	.	.		0.517	FLNB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353569.1	NM_001457	
SUCLG2	8801	hgsc.bcm.edu	37	3	67660015	67660015	+	Silent	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:67660015A>G	ENST00000307227.5	-	2	117	c.90T>C	c.(88-90)gtT>gtC	p.V30V	SUCLG2_ENST00000492795.1_Silent_p.V30V|SUCLG2_ENST00000493112.1_Silent_p.V30V	NM_003848.3	NP_003839.2	Q96I99	SUCB2_HUMAN	succinate-CoA ligase, GDP-forming, beta subunit	30					cellular metabolic process (GO:0044237)|small molecule metabolic process (GO:0044281)|succinate metabolic process (GO:0006105)|succinyl-CoA metabolic process (GO:0006104)|tricarboxylic acid cycle (GO:0006099)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|succinate-CoA ligase complex (GDP-forming) (GO:0045244)	ATP binding (GO:0005524)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|succinate-CoA ligase (GDP-forming) activity (GO:0004776)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(3)|skin(1)	10		Renal(2;0.00294)|Lung NSC(201;0.012)|Hepatocellular(537;0.121)		BRCA - Breast invasive adenocarcinoma(55;3.53e-05)|Epithelial(33;0.000153)	Succinic acid(DB00139)	AGGTTAATTGAACTGCCTACA	0.408																																					p.V30V		Atlas-SNP	.											.	SUCLG2	95	.	0			c.T90C						.						84.0	73.0	77.0					3																	67660015		1852	4092	5944	SO:0001819	synonymous_variant	8801	exon2			TAATTGAACTGCC	AF058954	CCDS43104.1, CCDS54605.1	3p14.3	2004-05-17			ENSG00000172340	ENSG00000172340	6.2.1.4		11450	protein-coding gene	gene with protein product		603922				9765291	Standard	NM_001177599		Approved		uc003dna.4	Q96I99	OTTHUMG00000158740	ENST00000307227.5:c.90T>C	chr3.hg19:g.67660015A>G		66.0	0.0		76.0	4.0	NM_001177599	C9JVT2|O95195|Q6NUH7|Q86VX8|Q8WUQ1	Silent	SNP	ENST00000307227.5	hg19	CCDS43104.1																																																																																			.	.		0.408	SUCLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351993.1	NM_003848	
FRMD4B	23150	hgsc.bcm.edu	37	3	69239069	69239069	+	Silent	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:69239069A>G	ENST00000398540.3	-	18	1832	c.1749T>C	c.(1747-1749)tcT>tcC	p.S583S	FRMD4B_ENST00000478263.1_Silent_p.S235S|FRMD4B_ENST00000542259.1_Silent_p.S529S	NM_015123.1	NP_055938	Q9Y2L6	FRM4B_HUMAN	FERM domain containing 4B	583					establishment of epithelial cell polarity (GO:0090162)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|ruffle (GO:0001726)				NS(2)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(1)|ovary(3)|prostate(3)|skin(2)	19		Lung NSC(201;0.0138)|Prostate(884;0.11)		BRCA - Breast invasive adenocarcinoma(55;0.000201)|Epithelial(33;0.00141)|LUSC - Lung squamous cell carcinoma(21;0.00999)|Lung(16;0.0182)		TGGTGGTGTCAGACAAAGAGC	0.323																																					p.S583S		Atlas-SNP	.											.	FRMD4B	90	.	0			c.T1749C						.						90.0	90.0	90.0					3																	69239069		1813	4082	5895	SO:0001819	synonymous_variant	23150	exon18			GGTGTCAGACAAA	AL832231	CCDS46863.1	3p14.2	2006-04-12			ENSG00000114541	ENSG00000114541			24886	protein-coding gene	gene with protein product						10231032, 11445584	Standard	XM_005264720		Approved	KIAA1013, GRSP1	uc003dnv.2	Q9Y2L6	OTTHUMG00000158772	ENST00000398540.3:c.1749T>C	chr3.hg19:g.69239069A>G		65.0	0.0		99.0	4.0	NM_015123	Q8TAI3	Silent	SNP	ENST00000398540.3	hg19	CCDS46863.1																																																																																			.	.		0.323	FRMD4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352111.1		
TOMM70A	9868	hgsc.bcm.edu	37	3	100093979	100093979	+	Silent	SNP	G	G	A			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:100093979G>A	ENST00000284320.5	-	7	1558	c.1110C>T	c.(1108-1110)ctC>ctT	p.L370L		NM_014820.4	NP_055635.3	O94826	TOM70_HUMAN	translocase of outer mitochondrial membrane 70 homolog A (S. cerevisiae)	370					cellular protein metabolic process (GO:0044267)|protein targeting to mitochondrion (GO:0006626)|protein transmembrane transport (GO:0071806)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial outer membrane translocase complex (GO:0005742)|mitochondrion (GO:0005739)	protein transmembrane transporter activity (GO:0008320)			endometrium(11)|large_intestine(5)|lung(10)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)	32						CTCTTTTGATGAGAGCATTTG	0.398																																					p.L370L		Atlas-SNP	.											.	TOMM70A	65	.	0			c.C1110T						.						129.0	126.0	127.0					3																	100093979		2203	4300	6503	SO:0001819	synonymous_variant	9868	exon7			TTTGATGAGAGCA	AB018262	CCDS33807.1	3q12.2	2013-01-10	2006-04-04		ENSG00000154174	ENSG00000154174		"""Tetratricopeptide (TTC) repeat domain containing"""	11985	protein-coding gene	gene with protein product		606081	"""translocase of outer mitochondrial membrane 70 (yeast) homolog A"", ""translocase of outer mitochondrial membrane 70 homolog A (yeast)"""			10582581	Standard	NM_014820		Approved	KIAA0719	uc003dtw.3	O94826	OTTHUMG00000159065	ENST00000284320.5:c.1110C>T	chr3.hg19:g.100093979G>A		58.0	0.0		54.0	19.0	NM_014820	D3DN48	Silent	SNP	ENST00000284320.5	hg19	CCDS33807.1																																																																																			.	.		0.398	TOMM70A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353141.2		
GPR156	165829	hgsc.bcm.edu	37	3	119887020	119887020	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:119887020T>C	ENST00000464295.1	-	10	1749	c.1304A>G	c.(1303-1305)gAt>gGt	p.D435G	GPR156_ENST00000315843.3_Missense_Mutation_p.D435G|GPR156_ENST00000461057.1_Missense_Mutation_p.D431G			Q8NFN8	GP156_HUMAN	G protein-coupled receptor 156	435						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled GABA receptor activity (GO:0004965)			breast(2)|endometrium(3)|kidney(1)|large_intestine(11)|lung(12)|ovary(1)|prostate(1)|skin(1)	32				GBM - Glioblastoma multiforme(114;0.19)		CATGCCAGGATCATTCTGAAA	0.627																																					p.D435G		Atlas-SNP	.											.	GPR156	85	.	0			c.A1304G						.						28.0	31.0	30.0					3																	119887020		2203	4300	6503	SO:0001583	missense	165829	exon9			CCAGGATCATTCT	AF488739	CCDS2997.1, CCDS54629.1	3q13.33	2012-08-21			ENSG00000175697	ENSG00000175697		"""GPCR / Class C : Orphans"""	20844	protein-coding gene	gene with protein product		610464				12591167	Standard	NM_153002		Approved	PGR28, GABABL	uc011bjf.2	Q8NFN8	OTTHUMG00000159406	ENST00000464295.1:c.1304A>G	chr3.hg19:g.119887020T>C	ENSP00000417261:p.Asp435Gly	119.0	0.0		146.0	6.0	NM_153002	B7ZL66|E9PFZ4|Q14CM1|Q86SN6	Missense_Mutation	SNP	ENST00000464295.1	hg19	CCDS2997.1	.	.	.	.	.	.	.	.	.	.	T	13.59	2.284076	0.40394	.	.	ENSG00000175697	ENST00000464295;ENST00000315843;ENST00000461057	T;T;T	0.26518	1.73;1.73;1.73	5.53	5.53	0.82687	.	0.510934	0.20398	N	0.093101	T	0.21674	0.0522	L	0.36672	1.1	0.29812	N	0.831588	P;P	0.47106	0.89;0.89	B;B	0.40066	0.318;0.318	T	0.08911	-1.0699	9	.	.	.	-3.0169	13.6518	0.62314	0.0:0.0:0.0:1.0	.	431;435	E9PFZ4;Q8NFN8	.;GP156_HUMAN	G	435;435;431	ENSP00000417261:D435G;ENSP00000324553:D435G;ENSP00000418758:D431G	.	D	-	2	0	GPR156	121369710	0.000000	0.05858	0.684000	0.30055	0.069000	0.16628	0.805000	0.27112	2.319000	0.78375	0.533000	0.62120	GAT	.	.		0.627	GPR156-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355139.1	NM_153002	
SLC15A2	6565	hgsc.bcm.edu	37	3	121613346	121613346	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:121613346A>G	ENST00000489711.1	+	1	411	c.23A>G	c.(22-24)gAg>gGg	p.E8G	SLC15A2_ENST00000295605.2_Missense_Mutation_p.E8G	NM_021082.3	NP_066568.3	Q16348	S15A2_HUMAN	solute carrier family 15 (oligopeptide transporter), member 2	8					drug transport (GO:0015893)|ion transport (GO:0006811)|protein transport (GO:0015031)|proton transport (GO:0015992)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	antibiotic transporter activity (GO:0042895)|dipeptide transporter activity (GO:0042936)|high-affinity oligopeptide transporter activity (GO:0015334)|peptide:proton symporter activity (GO:0015333)			NS(1)|endometrium(1)|kidney(4)|large_intestine(5)|lung(17)|skin(6)|upper_aerodigestive_tract(2)	36				GBM - Glioblastoma multiforme(114;0.0967)	Aminolevulinic acid(DB00855)|Amoxicillin(DB01060)|Ampicillin(DB00415)|Azidocillin(DB08795)|Benazepril(DB00542)|Benzylpenicillin(DB01053)|Cefaclor(DB00833)|Cefadroxil(DB01140)|Cefalotin(DB00456)|Cefdinir(DB00535)|Cefepime(DB01413)|Cefixime(DB00671)|Cefmetazole(DB00274)|Cefotaxime(DB00493)|Cefradine(DB01333)|Ceftazidime(DB00438)|Ceftibuten(DB01415)|Ceftriaxone(DB01212)|Cefuroxime(DB01112)|Cephalexin(DB00567)|Chlorpropamide(DB00672)|Cilazapril(DB01340)|Cloxacillin(DB01147)|Cyclacillin(DB01000)|Dicloxacillin(DB00485)|Fosinopril(DB00492)|Glyburide(DB01016)|Moexipril(DB00691)|Nateglinide(DB00731)|Oxacillin(DB00713)|Perindopril(DB00790)|Quinapril(DB00881)|Ramipril(DB00178)|Spirapril(DB01348)|Tolbutamide(DB01124)|Trandolapril(DB00519)|Tranexamic Acid(DB00302)|Valaciclovir(DB00577)|Valganciclovir(DB01610)	CAGAAAAATGAGTCCAAGGAA	0.483																																					p.E8G		Atlas-SNP	.											.	SLC15A2	92	.	0			c.A23G						.						161.0	174.0	169.0					3																	121613346		2203	4300	6503	SO:0001583	missense	6565	exon1			AAAATGAGTCCAA	BC044572	CCDS3007.1, CCDS54631.1	3q21.1	2013-07-18	2013-07-18		ENSG00000163406	ENSG00000163406		"""Solute carriers"""	10921	protein-coding gene	gene with protein product		602339	"""solute carrier family 15 (H+/peptide transporter), member 2"""			7756356	Standard	NM_021082		Approved	PEPT2	uc003eep.2	Q16348	OTTHUMG00000159423	ENST00000489711.1:c.23A>G	chr3.hg19:g.121613346A>G	ENSP00000417085:p.Glu8Gly	64.0	0.0		85.0	4.0	NM_001145998	A8K1A5|B4E2A7	Missense_Mutation	SNP	ENST00000489711.1	hg19	CCDS3007.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	15.38|15.38	2.815373|2.815373	0.50527|0.50527	.|.	.|.	ENSG00000163406|ENSG00000163406	ENST00000489711;ENST00000295605|ENST00000542599	T;T|.	0.03358|.	4.33;3.96|.	5.1|5.1	3.94|3.94	0.45596|0.45596	Major facilitator superfamily domain, general substrate transporter (1);|.	0.196743|.	0.35235|.	N|.	0.003355|.	T|T	0.44993|0.44993	0.1320|0.1320	L|L	0.31926|0.31926	0.97|0.97	0.36739|0.36739	D|D	0.882148|0.882148	P;P|.	0.39665|.	0.682;0.682|.	B;B|.	0.33890|.	0.172;0.172|.	T|T	0.46303|0.46303	-0.9201|-0.9201	10|5	0.87932|.	D|.	0|.	-5.1703|-5.1703	8.1849|8.1849	0.31333|0.31333	0.8228:0.0:0.0:0.1772|0.8228:0.0:0.0:0.1772	.|.	8;8|.	B4E2A7;Q16348|.	.;S15A2_HUMAN|.	G|G	8|2	ENSP00000417085:E8G;ENSP00000295605:E8G|.	ENSP00000295605:E8G|.	E|S	+|+	2|1	0|0	SLC15A2|SLC15A2	123096036|123096036	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	2.349000|2.349000	0.44054|0.44054	0.946000|0.946000	0.37632|0.37632	0.455000|0.455000	0.32223|0.32223	GAG|AGT	.	.		0.483	SLC15A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355239.1	NM_021082	
C3orf22	152065	hgsc.bcm.edu	37	3	126270923	126270923	+	Silent	SNP	G	G	A	rs34760151	byFrequency	TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:126270923G>A	ENST00000318225.2	-	3	510	c.132C>T	c.(130-132)ccC>ccT	p.P44P		NM_152533.1	NP_689746.1	Q8N5N4	CC022_HUMAN	chromosome 3 open reading frame 22	44										large_intestine(1)|lung(3)|ovary(2)|prostate(1)	7				GBM - Glioblastoma multiforme(114;0.147)		TGACCTCCCAGGGCTGCAGGG	0.602																																					p.P44P		Atlas-SNP	.											.	C3orf22	17	.	0			c.C132T						.						83.0	77.0	79.0					3																	126270923		2203	4300	6503	SO:0001819	synonymous_variant	152065	exon3			CTCCCAGGGCTGC		CCDS3040.1	3q21.3	2011-09-30			ENSG00000180697	ENSG00000180697			28534	protein-coding gene	gene with protein product						12477932	Standard	NM_152533		Approved	MGC34728	uc003ejb.3	Q8N5N4	OTTHUMG00000162731	ENST00000318225.2:c.132C>T	chr3.hg19:g.126270923G>A		93.0	0.0		113.0	31.0	NM_152533	B3KUS9	Silent	SNP	ENST00000318225.2	hg19	CCDS3040.1																																																																																			.	G|0.912;C|0.088		0.602	C3orf22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370231.2	NM_152533	
TXNRD3NB	645840	hgsc.bcm.edu	37	3	126291337	126291337	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:126291337T>C	ENST00000404489.2	-	1	142	c.50A>G	c.(49-51)gAg>gGg	p.E17G	TXNRD3NB_ENST00000383572.2_Missense_Mutation_p.E17G			Q6F5E7	TR3N_HUMAN	thioredoxin reductase 3 neighbor	17										endometrium(1)|large_intestine(2)|skin(2)	5						CATCTGCTGCTCAGCTTTCAG	0.602																																					p.E17G		Atlas-SNP	.											.	TXNRD3NB	13	.	0			c.A50G						.						42.0	39.0	40.0					3																	126291337		2203	4300	6503	SO:0001583	missense	645840	exon3			TGCTGCTCAGCTT	BC130546	CCDS33846.1	3q21.3	2011-04-13	2011-04-13	2011-04-13	ENSG00000206483	ENSG00000206483			33870	protein-coding gene	gene with protein product	"""thioredoxin reductase 3 new transcript 1"""		"""thioredoxin reductase 3 intronic transcript 1"""	TXNRD3IT1		15674732	Standard	NM_001039783		Approved	TR2IT1, TXNRD3NT1	uc003ejc.3	Q6F5E7	OTTHUMG00000162732	ENST00000404489.2:c.50A>G	chr3.hg19:g.126291337T>C	ENSP00000384071:p.Glu17Gly	80.0	0.0		121.0	5.0	NM_001039783		Missense_Mutation	SNP	ENST00000404489.2	hg19	CCDS33846.1	.	.	.	.	.	.	.	.	.	.	T	3.066	-0.192235	0.06259	.	.	ENSG00000206483	ENST00000383572;ENST00000404489	.	.	.	0.661	0.661	0.17874	.	.	.	.	.	T	0.32912	0.0845	N	0.08118	0	0.09310	N	1	D	0.69078	0.997	D	0.65140	0.932	T	0.19647	-1.0299	7	0.87932	D	0	.	.	.	.	.	17	Q6F5E7	TR3N_HUMAN	G	17	.	ENSP00000373066:E17G	E	-	2	0	TXNRD3NB	127774027	0.004000	0.15560	0.091000	0.20842	0.012000	0.07955	-0.033000	0.12246	0.536000	0.28733	0.383000	0.25322	GAG	.	.		0.602	TXNRD3NB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370233.2	NM_001039783	
COL6A6	131873	hgsc.bcm.edu	37	3	130284285	130284285	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:130284285C>A	ENST00000358511.6	+	3	1140	c.1109C>A	c.(1108-1110)gCc>gAc	p.A370D	COL6A6_ENST00000453409.2_Missense_Mutation_p.A370D	NM_001102608.1	NP_001096078.1	A6NMZ7	CO6A6_HUMAN	collagen, type VI, alpha 6	370	Nonhelical region.|VWFA 2. {ECO:0000255|PROSITE- ProRule:PRU00219}.		A -> T (in dbSNP:rs9830253).		cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(30)|lung(57)|ovary(8)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	134						ATAGAGGGCGCCAGCGACACC	0.547																																					p.A370D		Atlas-SNP	.											COL6A6_ENST00000358511,right_upper_lobe,carcinoma,0,2	COL6A6	497	.	0			c.C1109A						.						117.0	131.0	126.0					3																	130284285		2049	4205	6254	SO:0001583	missense	131873	exon3			AGGGCGCCAGCGA	AL713792	CCDS46911.1	3q22.1	2013-01-16			ENSG00000206384	ENSG00000206384		"""Collagens"""	27023	protein-coding gene	gene with protein product							Standard	NM_001102608		Approved		uc010htl.3	A6NMZ7	OTTHUMG00000159653	ENST00000358511.6:c.1109C>A	chr3.hg19:g.130284285C>A	ENSP00000351310:p.Ala370Asp	96.0	0.0		88.0	0.0	NM_001102608	A7DZQ0|A7DZQ1|A7DZQ2|Q69YT0	Missense_Mutation	SNP	ENST00000358511.6	hg19	CCDS46911.1	.	.	.	.	.	.	.	.	.	.	C	16.01	3.000937	0.54254	.	.	ENSG00000206384	ENST00000358511;ENST00000453409	T;T	0.80738	-1.41;-1.41	5.01	5.01	0.66863	von Willebrand factor, type A (3);	0.103399	0.42821	D	0.000652	D	0.87517	0.6197	M	0.77406	2.37	0.45194	D	0.998205	D	0.63880	0.993	D	0.65874	0.939	D	0.87045	0.2143	10	0.44086	T	0.13	.	11.035	0.47795	0.0:0.9126:0.0:0.0874	.	370	A6NMZ7	CO6A6_HUMAN	D	370	ENSP00000351310:A370D;ENSP00000399236:A370D	ENSP00000351310:A370D	A	+	2	0	COL6A6	131766975	0.998000	0.40836	0.551000	0.28230	0.043000	0.13939	4.381000	0.59587	2.492000	0.84095	0.561000	0.74099	GCC	.	.		0.547	COL6A6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356705.5	NM_001102608	
PIK3R4	30849	hgsc.bcm.edu	37	3	130454770	130454770	+	Silent	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:130454770T>C	ENST00000356763.3	-	3	1367	c.810A>G	c.(808-810)ggA>ggG	p.G270G		NM_014602.2	NP_055417.1	Q99570	PI3R4_HUMAN	phosphoinositide-3-kinase, regulatory subunit 4	270	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	axoneme (GO:0005930)|cytosol (GO:0005829)|late endosome (GO:0005770)|membrane (GO:0016020)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(6)|large_intestine(16)|lung(28)|ovary(6)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|urinary_tract(1)	77						GGAAAAAATGTCCATTTCTAT	0.323																																					p.G270G		Atlas-SNP	.											.	PIK3R4	145	.	0			c.A810G						.						120.0	129.0	126.0					3																	130454770		2203	4300	6503	SO:0001819	synonymous_variant	30849	exon3			AAAATGTCCATTT	Y08991	CCDS3067.1	3q22.1	2013-01-10	2008-02-04		ENSG00000196455	ENSG00000196455		"""WD repeat domain containing"""	8982	protein-coding gene	gene with protein product		602610				8999962	Standard	NM_014602		Approved	VPS15, p150	uc003enj.3	Q99570	OTTHUMG00000159645	ENST00000356763.3:c.810A>G	chr3.hg19:g.130454770T>C		58.0	0.0		64.0	4.0	NM_014602	Q2TBF4	Silent	SNP	ENST00000356763.3	hg19	CCDS3067.1																																																																																			.	.		0.323	PIK3R4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356668.1	NM_014602	
NPHP3	27031	hgsc.bcm.edu	37	3	132440946	132440946	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:132440946T>C	ENST00000337331.5	-	1	340	c.254A>G	c.(253-255)gAg>gGg	p.E85G	NPHP3_ENST00000383282.2_Missense_Mutation_p.E85G|NPHP3-AS1_ENST00000504440.1_RNA|NPHP3_ENST00000343113.4_Missense_Mutation_p.E85G|NPHP3_ENST00000326682.8_Missense_Mutation_p.E85G|NPHP3-AS1_ENST00000489343.1_RNA	NM_153240.4	NP_694972.3	Q7Z494	NPHP3_HUMAN	nephronophthisis 3 (adolescent)	85					atrial septum development (GO:0003283)|cilium morphogenesis (GO:0060271)|convergent extension involved in gastrulation (GO:0060027)|determination of intestine left/right asymmetry (GO:0071908)|determination of left/right symmetry (GO:0007368)|determination of liver left/right asymmetry (GO:0071910)|determination of pancreatic left/right asymmetry (GO:0035469)|determination of stomach left/right asymmetry (GO:0071909)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|establishment or maintenance of cell polarity (GO:0007163)|extracellular matrix organization (GO:0030198)|heart looping (GO:0001947)|kidney development (GO:0001822)|kidney morphogenesis (GO:0060993)|lipid metabolic process (GO:0006629)|lung development (GO:0030324)|maintenance of organ identity (GO:0048496)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|photoreceptor cell maintenance (GO:0045494)|regulation of cAMP metabolic process (GO:0030814)|regulation of planar cell polarity pathway involved in neural tube closure (GO:2000167)|regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000095)|ureter development (GO:0072189)|Wnt signaling pathway (GO:0016055)	cilium (GO:0005929)|primary cilium (GO:0072372)				NS(1)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(5)|lung(15)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						CGCCGCGTACTCCAGCTCTGG	0.706																																					p.E85G		Atlas-SNP	.											.	NPHP3	110	.	0			c.A254G						.						16.0	19.0	18.0					3																	132440946		2110	4112	6222	SO:0001583	missense	27031	exon1			GCGTACTCCAGCT	AB056657	CCDS3078.1	3q22	2014-07-18			ENSG00000113971	ENSG00000113971		"""Tetratricopeptide (TTC) repeat domain containing"""	7907	protein-coding gene	gene with protein product	"""nephrocystin-3"", ""Meckel syndrome, type 7"", ""cilia and flagella associated protein 31"""	608002				12872122, 15381417	Standard	NM_153240		Approved	NPH3, KIAA2000, FLJ30691, FLJ36696, MKS7, SLSN3, CFAP31	uc003epe.2	Q7Z494	OTTHUMG00000159713	ENST00000337331.5:c.254A>G	chr3.hg19:g.132440946T>C	ENSP00000338766:p.Glu85Gly	55.0	0.0		61.0	6.0	NM_153240	Q5JPE3|Q5JPE6|Q68D99|Q6NVH3|Q7Z492|Q7Z493|Q8N9R2|Q8NCM5|Q96N70|Q96NK2	Missense_Mutation	SNP	ENST00000337331.5	hg19	CCDS3078.1	.	.	.	.	.	.	.	.	.	.	T	17.87	3.494485	0.64186	.	.	ENSG00000113971	ENST00000326682;ENST00000337331;ENST00000343113;ENST00000383282	D;D;D;D	0.93426	-3.22;-3.13;-1.97;-1.99	3.6	3.6	0.41247	.	0.000000	0.64402	D	0.000001	D	0.93106	0.7805	N	0.24115	0.695	0.80722	D	1	D	0.76494	0.999	D	0.75484	0.986	D	0.93537	0.6874	10	0.62326	D	0.03	-18.1579	12.6567	0.56791	0.0:0.0:0.0:1.0	.	85	Q7Z494	NPHP3_HUMAN	G	85	ENSP00000319909:E85G;ENSP00000338766:E85G;ENSP00000344802:E85G;ENSP00000372769:E85G	ENSP00000319909:E85G	E	-	2	0	NPHP3	133923636	1.000000	0.71417	1.000000	0.80357	0.003000	0.03518	7.508000	0.81686	1.615000	0.50252	0.454000	0.30748	GAG	.	.		0.706	NPHP3-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357020.2	NM_153240	
PPP2R3A	5523	hgsc.bcm.edu	37	3	135745883	135745883	+	Silent	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:135745883T>C	ENST00000264977.3	+	3	2822	c.2205T>C	c.(2203-2205)gcT>gcC	p.A735A	PPP2R3A_ENST00000490467.1_5'UTR|PPP2R3A_ENST00000334546.2_Silent_p.A114A|PPP2R3A_ENST00000492624.2_5'UTR	NM_001190447.1|NM_002718.4	NP_001177376.1|NP_002709.2	Q06190	P2R3A_HUMAN	protein phosphatase 2, regulatory subunit B'', alpha	735					eye photoreceptor cell differentiation (GO:0001754)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of protein catabolic process (GO:0045732)|protein dephosphorylation (GO:0006470)|regulation of catalytic activity (GO:0050790)|regulation of cell motility involved in somitogenic axis elongation (GO:0090249)|somatic muscle development (GO:0007525)|somite development (GO:0061053)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	protein phosphatase type 2A complex (GO:0000159)	calcium ion binding (GO:0005509)|protein phosphatase type 2A regulator activity (GO:0008601)			breast(2)|cervix(1)|endometrium(2)|large_intestine(7)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						TTGAAACTGCTTTCATGGATA	0.368																																					p.A735A		Atlas-SNP	.											.	PPP2R3A	114	.	0			c.T2205C						.						48.0	46.0	46.0					3																	135745883		2203	4300	6503	SO:0001819	synonymous_variant	5523	exon3			AACTGCTTTCATG	L12146	CCDS3087.1, CCDS3088.1, CCDS54642.1	3q22.2-q22.3	2013-01-10	2010-06-18	2002-04-26	ENSG00000073711	ENSG00000073711	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"", ""EF-hand domain containing"""	9307	protein-coding gene	gene with protein product		604944	"""protein phosphatase 2 (formerly 2A), regulatory subunit B'' (PR 72), alpha isoform and (PR 130), beta isoform"", ""protein phosphatase 2 (formerly 2A), regulatory subunit B'', alpha"""	PPP2R3		8392071	Standard	NM_002718		Approved		uc003eqv.2	Q06190	OTTHUMG00000159766	ENST00000264977.3:c.2205T>C	chr3.hg19:g.135745883T>C		58.0	0.0		79.0	4.0	NM_002718	A8KAE7|B4DNU1|B7ZAE3|Q06189|Q9NPQ5	Silent	SNP	ENST00000264977.3	hg19	CCDS3087.1																																																																																			.	.		0.368	PPP2R3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357232.1	NM_002718	
GRK7	131890	hgsc.bcm.edu	37	3	141497152	141497152	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:141497152A>G	ENST00000264952.2	+	1	163	c.26A>G	c.(25-27)aAc>aGc	p.N9S		NM_139209.2	NP_631948.1	Q8WTQ7	GRK7_HUMAN	G protein-coupled receptor kinase 7	9					protein autophosphorylation (GO:0046777)|signal transduction (GO:0007165)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|visual perception (GO:0007601)	membrane (GO:0016020)	ATP binding (GO:0005524)|G-protein coupled receptor kinase activity (GO:0004703)|rhodopsin kinase activity (GO:0050254)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(14)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	26						GCCCTGGACAACCTGATCGCC	0.692																																					p.N9S		Atlas-SNP	.											.	GRK7	65	.	0			c.A26G						.						47.0	57.0	54.0					3																	141497152		2199	4300	6499	SO:0001583	missense	131890	exon1			TGGACAACCTGAT		CCDS3120.1	3q24	2004-02-04	2004-02-04	2004-02-04	ENSG00000114124	ENSG00000114124			17031	protein-coding gene	gene with protein product		606987		GPRK7		11717351, 11754336	Standard	NM_139209		Approved		uc011bnd.2	Q8WTQ7	OTTHUMG00000159068	ENST00000264952.2:c.26A>G	chr3.hg19:g.141497152A>G	ENSP00000264952:p.Asn9Ser	87.0	0.0		121.0	5.0	NM_139209		Missense_Mutation	SNP	ENST00000264952.2	hg19	CCDS3120.1	.	.	.	.	.	.	.	.	.	.	A	14.60	2.582379	0.46006	.	.	ENSG00000114124	ENST00000264952	T	0.61742	0.08	4.5	3.3	0.37823	.	0.099517	0.64402	D	0.000002	T	0.55940	0.1952	M	0.79123	2.44	0.40643	D	0.981967	P	0.43750	0.816	B	0.39185	0.293	T	0.59511	-0.7441	10	0.56958	D	0.05	-8.2697	10.1305	0.42676	0.85:0.0:0.0:0.15	.	9	Q8WTQ7	GRK7_HUMAN	S	9	ENSP00000264952:N9S	ENSP00000264952:N9S	N	+	2	0	GRK7	142979842	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.949000	0.56668	0.542000	0.28846	0.533000	0.62120	AAC	.	.		0.692	GRK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353168.1	NM_139209	
TM4SF18	116441	hgsc.bcm.edu	37	3	149051109	149051109	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:149051109T>C	ENST00000296059.2	-	2	326	c.61A>G	c.(61-63)Agt>Ggt	p.S21G	TM4SF18_ENST00000470080.1_Missense_Mutation_p.S21G|RP11-206M11.7_ENST00000489011.1_RNA	NM_138786.3	NP_620141.1	Q96CE8	T4S18_HUMAN	transmembrane 4 L six family member 18	21						integral component of membrane (GO:0016021)				lung(1)|ovary(1)|prostate(1)	3			LUSC - Lung squamous cell carcinoma(72;0.0378)|Lung(72;0.048)			ACGATTATACTCCAAAGTGCA	0.438																																					p.S21G		Atlas-SNP	.											.	TM4SF18	12	.	0			c.A61G						.						74.0	70.0	72.0					3																	149051109		2203	4300	6503	SO:0001583	missense	116441	exon1			TTATACTCCAAAG	BC014339	CCDS3142.1	3q25.1	2005-08-09			ENSG00000163762	ENSG00000163762			25181	protein-coding gene	gene with protein product						10975581	Standard	NM_001184723		Approved	L6D	uc021xfl.1	Q96CE8	OTTHUMG00000159582	ENST00000296059.2:c.61A>G	chr3.hg19:g.149051109T>C	ENSP00000296059:p.Ser21Gly	104.0	0.0		137.0	6.0	NM_001184723	B2R8K0|D3DNH5	Missense_Mutation	SNP	ENST00000296059.2	hg19	CCDS3142.1	.	.	.	.	.	.	.	.	.	.	T	11.19	1.566440	0.27915	.	.	ENSG00000163762	ENST00000296059;ENST00000470080;ENST00000474754	T;T;T	0.27557	1.66;1.66;1.66	4.81	4.81	0.61882	.	0.112361	0.64402	D	0.000009	T	0.25232	0.0613	L	0.34521	1.04	0.35286	D	0.781733	B	0.30542	0.284	B	0.34093	0.175	T	0.28586	-1.0039	10	0.19147	T	0.46	-13.1318	14.023	0.64568	0.0:0.0:0.0:1.0	.	21	Q96CE8	T4S18_HUMAN	G	21	ENSP00000296059:S21G;ENSP00000419278:S21G;ENSP00000418372:S21G	ENSP00000296059:S21G	S	-	1	0	TM4SF18	150533799	1.000000	0.71417	0.999000	0.59377	0.922000	0.55478	2.511000	0.45476	1.781000	0.52344	0.533000	0.62120	AGT	.	.		0.438	TM4SF18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356326.1	NM_138786	
MED12L	116931	hgsc.bcm.edu	37	3	150874054	150874054	+	Silent	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:150874054A>G	ENST00000474524.1	+	5	701	c.663A>G	c.(661-663)ccA>ccG	p.P221P	MED12L_ENST00000273432.4_Silent_p.P221P|MED12L_ENST00000422248.2_Silent_p.P221P|MED12L_ENST00000309237.4_Silent_p.P221P	NM_053002.4	NP_443728.3	Q86YW9	MD12L_HUMAN	mediator complex subunit 12-like	221						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)			CTGTGCCACCAGAGGTGGAGC	0.493																																					p.P221P		Atlas-SNP	.											.	MED12L	271	.	0			c.A663G						.						118.0	109.0	112.0					3																	150874054		2203	4300	6503	SO:0001819	synonymous_variant	116931	exon5			GCCACCAGAGGTG	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.663A>G	chr3.hg19:g.150874054A>G		82.0	0.0		97.0	5.0	NM_053002	Q96PC7|Q96PC8|Q9H9M5|Q9HCD7|Q9UI69	Silent	SNP	ENST00000474524.1	hg19	CCDS33876.1																																																																																			.	.		0.493	MED12L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357707.2	NM_053002	
WDR49	151790	hgsc.bcm.edu	37	3	167254660	167254660	+	Missense_Mutation	SNP	G	G	A	rs200695837		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:167254660G>A	ENST00000308378.3	-	7	1201	c.896C>T	c.(895-897)aCg>aTg	p.T299M	WDR49_ENST00000479765.1_Intron|WDR49_ENST00000453925.2_Missense_Mutation_p.T363M|WDR49_ENST00000476376.1_Missense_Mutation_p.T124M	NM_178824.3	NP_849146.1	Q8IV35	WDR49_HUMAN	WD repeat domain 49	299										breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(28)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	50						CAATTTACCCGTAACAAGAGT	0.373																																					p.T299M		Atlas-SNP	.											WDR49,bladder,carcinoma,0,2	WDR49	188	.	0			c.C896T						.						64.0	60.0	62.0					3																	167254660		2203	4300	6503	SO:0001583	missense	151790	exon7			TTACCCGTAACAA	AK097556	CCDS3201.1	3q26.1	2013-01-11			ENSG00000174776	ENSG00000174776		"""WD repeat domain containing"""	26587	protein-coding gene	gene with protein product						12477932	Standard	NM_178824		Approved	FLJ33620	uc003fev.1	Q8IV35	OTTHUMG00000158290	ENST00000308378.3:c.896C>T	chr3.hg19:g.167254660G>A	ENSP00000311343:p.Thr299Met	81.0	0.0		75.0	19.0	NM_178824	Q8N297	Missense_Mutation	SNP	ENST00000308378.3	hg19	CCDS3201.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.00|15.00	2.702932|2.702932	0.48412|0.48412	.|.	.|.	ENSG00000174776|ENSG00000174776	ENST00000472600|ENST00000308378;ENST00000476376;ENST00000453925	.|T;T;T	.|0.68181	.|-0.31;-0.31;-0.31	5.69|5.69	5.69|5.69	0.88448|0.88448	.|WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40 repeat, conserved site (1);WD40-repeat-containing domain (1);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.88559|0.88559	0.6469|0.6469	H|H	0.96633|0.96633	3.855|3.855	0.39988|0.39988	D|D	0.975001|0.975001	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.87578	.|0.998;0.997	D|D	0.92253|0.92253	0.5810|0.5810	5|10	.|0.87932	.|D	.|0	.|.	18.5851|18.5851	0.91187|0.91187	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|363;299	.|E7EQK3;Q8IV35	.|.;WDR49_HUMAN	W|M	375|299;124;363	.|ENSP00000311343:T299M;ENSP00000420508:T124M;ENSP00000410863:T363M	.|ENSP00000311343:T299M	R|T	-|-	1|2	2|0	WDR49|WDR49	168737354|168737354	1.000000|1.000000	0.71417|0.71417	0.995000|0.995000	0.50966|0.50966	0.003000|0.003000	0.03518|0.03518	6.671000|6.671000	0.74472|0.74472	2.700000|2.700000	0.92200|0.92200	0.655000|0.655000	0.94253|0.94253	CGG|ACG	.	G|0.999;A|0.001		0.373	WDR49-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000350592.3	NM_178824	
TNIK	23043	hgsc.bcm.edu	37	3	170805183	170805183	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:170805183T>C	ENST00000436636.2	-	24	3178	c.2834A>G	c.(2833-2835)gAg>gGg	p.E945G	TNIK_ENST00000475336.1_Missense_Mutation_p.E853G|TNIK_ENST00000357327.5_Missense_Mutation_p.E916G|TNIK_ENST00000488470.1_Missense_Mutation_p.E890G|TNIK_ENST00000460047.1_Missense_Mutation_p.E882G|TNIK_ENST00000284483.8_Missense_Mutation_p.E937G|TNIK_ENST00000341852.6_Missense_Mutation_p.E861G|TNIK_ENST00000470834.1_Missense_Mutation_p.E908G|TNIK_ENST00000538048.1_Missense_Mutation_p.E897G|TNIK_ENST00000369326.5_Missense_Mutation_p.E923G	NM_015028.2	NP_055843.1	Q9UKE5	TNIK_HUMAN	TRAF2 and NCK interacting kinase	945	Mediates interaction with NEDD4.				actin cytoskeleton reorganization (GO:0031532)|activation of JNKK activity (GO:0007256)|cytoskeleton organization (GO:0007010)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of dendrite morphogenesis (GO:0048814)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(14)|lung(22)|ovary(5)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(2)	62	all_cancers(22;2.55e-19)|all_lung(20;2.22e-14)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)			CCCCAGTCCCTCAGTCGGGGT	0.582																																					p.E945G		Atlas-SNP	.											.	TNIK	313	.	0			c.A2834G						.						82.0	84.0	84.0					3																	170805183		2006	4175	6181	SO:0001583	missense	23043	exon24			AGTCCCTCAGTCG	AF172264	CCDS46956.1, CCDS54673.1, CCDS54674.1, CCDS54675.1, CCDS54676.1, CCDS54677.1, CCDS54678.1, CCDS54679.1	3q26.31	2008-01-23			ENSG00000154310	ENSG00000154310			30765	protein-coding gene	gene with protein product		610005				9628581, 10521462	Standard	NR_027767		Approved	KIAA0551	uc003fhh.2	Q9UKE5	OTTHUMG00000159036	ENST00000436636.2:c.2834A>G	chr3.hg19:g.170805183T>C	ENSP00000399511:p.Glu945Gly	71.0	0.0		92.0	4.0	NM_015028	A7E2A3|A8K4U1|D3DNQ6|O60298|Q8WUY7|Q9UKD8|Q9UKD9|Q9UKE0|Q9UKE1|Q9UKE2|Q9UKE3|Q9UKE4	Missense_Mutation	SNP	ENST00000436636.2	hg19	CCDS46956.1	.	.	.	.	.	.	.	.	.	.	T	15.86	2.959234	0.53400	.	.	ENSG00000154310	ENST00000436636;ENST00000369326;ENST00000538048;ENST00000341852;ENST00000284483;ENST00000475336;ENST00000357327;ENST00000460047;ENST00000488470;ENST00000470834	T;T;T;T;T;T;T;T;T;T	0.73681	-0.76;-0.76;-0.75;-0.76;-0.76;-0.77;-0.77;-0.77;-0.76;-0.77	5.93	5.93	0.95920	.	0.129005	0.51477	D	0.000083	T	0.52306	0.1726	N	0.02539	-0.55	0.58432	D	0.999997	B;B;B;B;B;B;B;B	0.30281	0.275;0.002;0.275;0.275;0.002;0.003;0.275;0.001	B;B;B;B;B;B;B;B	0.25291	0.059;0.01;0.059;0.059;0.01;0.01;0.059;0.005	T	0.59359	-0.7469	10	0.59425	D	0.04	.	16.3943	0.83563	0.0:0.0:0.0:1.0	.	853;908;882;861;937;916;890;945	Q9UKE5-8;Q9UKE5-6;Q9UKE5-7;Q9UKE5-5;Q9UKE5-4;Q9UKE5-2;Q9UKE5-3;Q9UKE5	.;.;.;.;.;.;.;TNIK_HUMAN	G	945;923;897;861;937;853;916;882;890;908	ENSP00000399511:E945G;ENSP00000358332:E923G;ENSP00000443278:E897G;ENSP00000345352:E861G;ENSP00000284483:E937G;ENSP00000418156:E853G;ENSP00000349880:E916G;ENSP00000418916:E882G;ENSP00000418378:E890G;ENSP00000419990:E908G	ENSP00000284483:E937G	E	-	2	0	TNIK	172287877	1.000000	0.71417	0.997000	0.53966	0.610000	0.37248	6.155000	0.71833	2.281000	0.76405	0.533000	0.62120	GAG	.	.		0.582	TNIK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352973.2	XM_039796	
MCF2L2	23101	hgsc.bcm.edu	37	3	182946091	182946091	+	Silent	SNP	G	G	A			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:182946091G>A	ENST00000328913.3	-	18	2406	c.2109C>T	c.(2107-2109)ctC>ctT	p.L703L	MCF2L2_ENST00000447025.2_Silent_p.L703L|MCF2L2_ENST00000473233.1_Silent_p.L703L	NM_015078.2	NP_055893	Q86YR7	MF2L2_HUMAN	MCF.2 cell line derived transforming sequence-like 2	703	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.						Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|endometrium(5)|kidney(4)|large_intestine(22)|lung(25)|ovary(3)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	72	all_cancers(143;1.26e-12)|Ovarian(172;0.0355)		all cancers(12;3.35e-44)|Epithelial(37;6.48e-38)|LUSC - Lung squamous cell carcinoma(7;7.12e-25)|Lung(8;6.39e-23)|OV - Ovarian serous cystadenocarcinoma(80;6.75e-21)			TTACTCTCTTGAGAAAGCAAT	0.358																																					p.L703L		Atlas-SNP	.											.	MCF2L2	164	.	0			c.C2109T						.						86.0	84.0	84.0					3																	182946091		2203	4300	6503	SO:0001819	synonymous_variant	23101	exon18			TCTCTTGAGAAAG	AB020668	CCDS3243.1	3q27	2012-07-24			ENSG00000053524	ENSG00000053524		"""Rho guanine nucleotide exchange factors"""	30319	protein-coding gene	gene with protein product							Standard	NM_015078		Approved	KIAA0861, ARHGEF22	uc003fli.1	Q86YR7	OTTHUMG00000158388	ENST00000328913.3:c.2109C>T	chr3.hg19:g.182946091G>A		59.0	0.0		81.0	4.0	NM_015078	O94942|Q6P2B8|Q6ZVJ5|Q8N318	Silent	SNP	ENST00000328913.3	hg19	CCDS3243.1																																																																																			.	.		0.358	MCF2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350868.1	NM_015078	
GAK	2580	hgsc.bcm.edu	37	4	877197	877197	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:877197T>C	ENST00000314167.4	-	13	1420	c.1310A>G	c.(1309-1311)gAt>gGt	p.D437G	GAK_ENST00000511163.1_Missense_Mutation_p.D358G	NM_005255.2	NP_005246.2	O14976	GAK_HUMAN	cyclin G associated kinase	437	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.				cell cycle (GO:0007049)|cell development (GO:0048468)|clathrin coat disassembly (GO:0072318)|clathrin-mediated endocytosis (GO:0072583)|endoplasmic reticulum organization (GO:0007029)|epidermal cell differentiation (GO:0009913)|establishment of skin barrier (GO:0061436)|forebrain morphogenesis (GO:0048853)|Golgi organization (GO:0007030)|intrahepatic bile duct development (GO:0035622)|positive regulation of neural precursor cell proliferation (GO:2000179)	cell junction (GO:0030054)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(16)|skin(7)|urinary_tract(2)	39				Colorectal(103;0.219)		CAACCGCACATCTTCGATGTT	0.577																																					p.D437G		Atlas-SNP	.											.	GAK	104	.	0			c.A1310G						.						202.0	169.0	180.0					4																	877197		2203	4300	6503	SO:0001583	missense	2580	exon13			CGCACATCTTCGA	D88435	CCDS3340.1	4p16	2011-09-07			ENSG00000178950	ENSG00000178950		"""Heat shock proteins / DNAJ (HSP40)"""	4113	protein-coding gene	gene with protein product	"""auxilin-2"""	602052				9299234	Standard	NM_005255		Approved	DNAJC26	uc003gbm.4	O14976	OTTHUMG00000088301	ENST00000314167.4:c.1310A>G	chr4.hg19:g.877197T>C	ENSP00000314499:p.Asp437Gly	74.0	0.0		99.0	4.0	NM_005255	Q5U4P5|Q9BVY6	Missense_Mutation	SNP	ENST00000314167.4	hg19	CCDS3340.1	.	.	.	.	.	.	.	.	.	.	T	16.32	3.091156	0.55968	.	.	ENSG00000178950	ENST00000314167;ENST00000511163	D;D	0.98617	-5.03;-5.03	5.34	5.34	0.76211	Phosphatase tensin type (1);	0.000000	0.85682	D	0.000000	D	0.99214	0.9727	M	0.90870	3.155	0.80722	D	1	D;D;D;D	0.76494	0.999;0.983;0.999;0.997	D;P;D;D	0.74023	0.982;0.898;0.959;0.914	D	0.99239	1.0884	10	0.87932	D	0	-31.1922	13.2844	0.60235	0.0:0.0:0.0:1.0	.	358;358;437;333	Q5U4P5;E9PGR2;O14976;Q59HA5	.;.;GAK_HUMAN;.	G	437;358	ENSP00000314499:D437G;ENSP00000421361:D358G	ENSP00000314499:D437G	D	-	2	0	GAK	867197	1.000000	0.71417	0.103000	0.21229	0.023000	0.10783	7.874000	0.87199	2.022000	0.59522	0.482000	0.46254	GAT	.	.		0.577	GAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239188.1	NM_005255	
HTT	3064	hgsc.bcm.edu	37	4	3241656	3241656	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:3241656G>A	ENST00000355072.5	+	67	9444	c.9299G>A	c.(9298-9300)aGa>aAa	p.R3100K		NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	3100					anterior/posterior pattern specification (GO:0009952)|axon cargo transport (GO:0008088)|cell aging (GO:0007569)|citrulline metabolic process (GO:0000052)|determination of adult lifespan (GO:0008340)|dopamine receptor signaling pathway (GO:0007212)|endoplasmic reticulum organization (GO:0007029)|endosomal transport (GO:0016197)|ER to Golgi vesicle-mediated transport (GO:0006888)|establishment of mitotic spindle orientation (GO:0000132)|Golgi organization (GO:0007030)|grooming behavior (GO:0007625)|hormone metabolic process (GO:0042445)|insulin secretion (GO:0030073)|iron ion homeostasis (GO:0055072)|L-glutamate import (GO:0051938)|lactate biosynthetic process from pyruvate (GO:0019244)|locomotory behavior (GO:0007626)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|neural plate formation (GO:0021990)|neuron apoptotic process (GO:0051402)|neuron development (GO:0048666)|olfactory lobe development (GO:0021988)|organ development (GO:0048513)|paraxial mesoderm formation (GO:0048341)|positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031587)|protein import into nucleus (GO:0006606)|quinolinate biosynthetic process (GO:0019805)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of protein phosphatase type 2A activity (GO:0034047)|regulation of synaptic plasticity (GO:0048167)|response to calcium ion (GO:0051592)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|social behavior (GO:0035176)|spermatogenesis (GO:0007283)|striatum development (GO:0021756)|urea cycle (GO:0000050)|vesicle transport along microtubule (GO:0047496)|visual learning (GO:0008542)	autophagic vacuole (GO:0005776)|axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|late endosome (GO:0005770)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	beta-tubulin binding (GO:0048487)|diazepam binding (GO:0050809)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|p53 binding (GO:0002039)|transcription factor binding (GO:0008134)			breast(1)|cervix(2)|endometrium(14)|kidney(5)|large_intestine(23)|lung(28)|ovary(4)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	87		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)		GACTTCTACAGACACCAGATA	0.572																																					p.R3100K		Atlas-SNP	.											.	HTT	221	.	0			c.G9299A						.						39.0	43.0	41.0					4																	3241656		2170	4250	6420	SO:0001583	missense	3064	exon67			TCTACAGACACCA	L12392	CCDS43206.1	4p16.3	2014-09-17	2007-12-04	2007-12-04	ENSG00000197386	ENSG00000197386		"""Endogenous ligands"""	4851	protein-coding gene	gene with protein product		613004	"""huntingtin (Huntington disease)"""	HD		8458085	Standard	NM_002111		Approved	IT15	uc021xkv.1	P42858	OTTHUMG00000159916	ENST00000355072.5:c.9299G>A	chr4.hg19:g.3241656G>A	ENSP00000347184:p.Arg3100Lys	139.0	0.0		176.0	28.0	NM_002111	Q9UQB7	Missense_Mutation	SNP	ENST00000355072.5	hg19	CCDS43206.1	.	.	.	.	.	.	.	.	.	.	G	16.94	3.260136	0.59321	.	.	ENSG00000197386	ENST00000355072	T	0.04758	3.56	5.0	5.0	0.66597	.	0.000000	0.85682	D	0.000000	T	0.03695	0.0105	N	0.17723	0.515	0.45183	D	0.998196	B	0.13145	0.007	B	0.12837	0.008	T	0.50499	-0.8821	10	0.22109	T	0.4	.	10.8622	0.46833	0.0869:0.0:0.9131:0.0	.	3100	P42858	HD_HUMAN	K	3100	ENSP00000347184:R3100K	ENSP00000347184:R3100K	R	+	2	0	HTT	3211454	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.819000	0.75262	2.284000	0.76573	0.655000	0.94253	AGA	.	.		0.572	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111	
HGFAC	3083	hgsc.bcm.edu	37	4	3443797	3443797	+	Silent	SNP	C	C	G	rs538844201	byFrequency	TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:3443797C>G	ENST00000382774.3	+	1	184	c.69C>G	c.(67-69)ctC>ctG	p.L23L	HGFAC_ENST00000511533.1_Silent_p.L23L	NM_001528.2	NP_001519.1	Q04756	HGFA_HUMAN	HGF activator	23					proteolysis (GO:0006508)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|rough endoplasmic reticulum (GO:0005791)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			central_nervous_system(3)|cervix(1)|endometrium(4)|large_intestine(2)|lung(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	22				UCEC - Uterine corpus endometrioid carcinoma (64;0.163)		TCCTCCTCCTCCTGCTGCTGC	0.716													C|||	2	0.000399361	0.0008	0.0	5008	,	,		13350	0.0		0.0	False		,,,				2504	0.001				p.L23L		Atlas-SNP	.											HGFAC,NS,carcinoma,0,2	HGFAC	69	.	0			c.C69G						.						13.0	16.0	15.0					4																	3443797		1723	3604	5327	SO:0001819	synonymous_variant	3083	exon1			CCTCCTCCTGCTG	D14012	CCDS3369.1, CCDS75098.1	4p16	2008-02-07			ENSG00000109758	ENSG00000109758	3.4.21.-		4894	protein-coding gene	gene with protein product		604552				7683665, 8226803	Standard	XM_005247966		Approved	HGFAP, HGFA	uc003ghc.3	Q04756	OTTHUMG00000090281	ENST00000382774.3:c.69C>G	chr4.hg19:g.3443797C>G		16.0	0.0		26.0	2.0	NM_001528	Q14726|Q2M1W7|Q53X47	Silent	SNP	ENST00000382774.3	hg19	CCDS3369.1																																																																																			.	.		0.716	HGFAC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206607.3		
OTOP1	133060	hgsc.bcm.edu	37	4	4204211	4204211	+	Missense_Mutation	SNP	G	G	A	rs200612216		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:4204211G>A	ENST00000296358.4	-	4	718	c.694C>T	c.(694-696)Cgg>Tgg	p.R232W		NM_177998.1	NP_819056.1	Q7RTM1	OTOP1_HUMAN	otopetrin 1	232					biomineral tissue development (GO:0031214)|detection of gravity (GO:0009590)|inner ear morphogenesis (GO:0042472)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)		p.R232W(2)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(3)|liver(4)|lung(14)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	34				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		GTGATGAGCCGTTCCTTGTGC	0.507																																					p.R232W		Atlas-SNP	.											OTOP1,NS,carcinoma,0,3	OTOP1	118	.	2	Substitution - Missense(2)	prostate(1)|liver(1)	c.C694T						.						144.0	123.0	130.0					4																	4204211		2203	4300	6503	SO:0001583	missense	133060	exon4			TGAGCCGTTCCTT	BK000653	CCDS3372.1	4p16.2	2008-02-05			ENSG00000163982	ENSG00000163982			19656	protein-coding gene	gene with protein product		607806				12651873	Standard	NM_177998		Approved		uc003ghp.1	Q7RTM1	OTTHUMG00000090301	ENST00000296358.4:c.694C>T	chr4.hg19:g.4204211G>A	ENSP00000296358:p.Arg232Trp	119.0	0.0		141.0	6.0	NM_177998	A1L476	Missense_Mutation	SNP	ENST00000296358.4	hg19	CCDS3372.1	.	.	.	.	.	.	.	.	.	.	G	11.92	1.781817	0.31502	.	.	ENSG00000163982	ENST00000296358	T	0.09817	2.94	5.28	4.35	0.52113	.	0.000000	0.85682	D	0.000000	T	0.06690	0.0171	N	0.14661	0.345	0.80722	D	1	P	0.35328	0.495	B	0.32583	0.148	T	0.26224	-1.0109	10	0.72032	D	0.01	.	10.6877	0.45852	0.0:0.0:0.5681:0.4319	.	232	Q7RTM1	OTOP1_HUMAN	W	232	ENSP00000296358:R232W	ENSP00000296358:R232W	R	-	1	2	OTOP1	4255112	1.000000	0.71417	0.547000	0.28179	0.267000	0.26476	2.487000	0.45268	2.462000	0.83206	0.603000	0.83216	CGG	.	.		0.507	OTOP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206661.2	NM_177998	
OTOP1	133060	hgsc.bcm.edu	37	4	4204302	4204302	+	Missense_Mutation	SNP	A	A	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:4204302A>C	ENST00000296358.4	-	4	627	c.603T>G	c.(601-603)ttT>ttG	p.F201L		NM_177998.1	NP_819056.1	Q7RTM1	OTOP1_HUMAN	otopetrin 1	201					biomineral tissue development (GO:0031214)|detection of gravity (GO:0009590)|inner ear morphogenesis (GO:0042472)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)				NS(1)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(3)|liver(4)|lung(14)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	34				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		GGATCACTCCAAACCTGAAAA	0.527																																					p.F201L		Atlas-SNP	.											.	OTOP1	118	.	0			c.T603G						.						75.0	72.0	73.0					4																	4204302		2203	4299	6502	SO:0001583	missense	133060	exon4			CACTCCAAACCTG	BK000653	CCDS3372.1	4p16.2	2008-02-05			ENSG00000163982	ENSG00000163982			19656	protein-coding gene	gene with protein product		607806				12651873	Standard	NM_177998		Approved		uc003ghp.1	Q7RTM1	OTTHUMG00000090301	ENST00000296358.4:c.603T>G	chr4.hg19:g.4204302A>C	ENSP00000296358:p.Phe201Leu	66.0	0.0		91.0	5.0	NM_177998	A1L476	Missense_Mutation	SNP	ENST00000296358.4	hg19	CCDS3372.1	.	.	.	.	.	.	.	.	.	.	A	19.48	3.836374	0.71373	.	.	ENSG00000163982	ENST00000296358	T	0.32988	1.43	5.46	1.68	0.24146	.	0.000000	0.85682	D	0.000000	T	0.51601	0.1684	M	0.79926	2.475	0.58432	D	0.999997	D	0.89917	1.0	D	0.91635	0.999	T	0.47522	-0.9111	10	0.40728	T	0.16	.	9.2419	0.37502	0.789:0.0:0.211:0.0	.	201	Q7RTM1	OTOP1_HUMAN	L	201	ENSP00000296358:F201L	ENSP00000296358:F201L	F	-	3	2	OTOP1	4255203	0.998000	0.40836	0.997000	0.53966	0.852000	0.48524	0.634000	0.24614	0.394000	0.25230	0.491000	0.48974	TTT	.	.		0.527	OTOP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206661.2	NM_177998	
FBXL5	26234	hgsc.bcm.edu	37	4	15627530	15627530	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:15627530C>T	ENST00000341285.3	-	9	1319	c.1195G>A	c.(1195-1197)Gtg>Atg	p.V399M	FBXL5_ENST00000412094.2_Missense_Mutation_p.V382M|FBXL5_ENST00000382358.4_Missense_Mutation_p.V273M	NM_001193534.1|NM_001193535.1|NM_012161.3	NP_001180463.1|NP_001180464.1|NP_036293.1	Q9UKA1	FBXL5_HUMAN	F-box and leucine-rich repeat protein 5	399					iron ion homeostasis (GO:0055072)|protein ubiquitination (GO:0016567)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)	perinuclear region of cytoplasm (GO:0048471)|SCF ubiquitin ligase complex (GO:0019005)|ubiquitin ligase complex (GO:0000151)	iron ion binding (GO:0005506)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(2)|large_intestine(3)|lung(5)|ovary(1)|pancreas(1)|prostate(1)	13						TCTAGGGCCACATCTGTGATT	0.398																																					p.V399M		Atlas-SNP	.											.	FBXL5	52	.	0			c.G1195A						.						37.0	37.0	37.0					4																	15627530		2202	4298	6500	SO:0001583	missense	26234	exon9			GGGCCACATCTGT	AF174591	CCDS3415.1, CCDS54745.1	4p15.33	2011-06-09			ENSG00000118564	ENSG00000118564		"""F-boxes / Leucine-rich repeats"""	13602	protein-coding gene	gene with protein product		605655				10531035	Standard	NM_012161		Approved	FBL4, FBL5, FLR1	uc003goc.2	Q9UKA1	OTTHUMG00000097097	ENST00000341285.3:c.1195G>A	chr4.hg19:g.15627530C>T	ENSP00000344866:p.Val399Met	75.0	0.0		85.0	4.0	NM_012161	A8MSK4|B4DIB5|Q4W5A8|Q8NHP3|Q9NXN2|Q9P0I0|Q9P0X5|Q9UJT7|Q9UKC8	Missense_Mutation	SNP	ENST00000341285.3	hg19	CCDS3415.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	11.00|11.00	1.509797|1.509797	0.27036|0.27036	.|.	.|.	ENSG00000118564|ENSG00000118564	ENST00000513163|ENST00000341285;ENST00000412094;ENST00000382358	.|T;T;T	.|0.17370	.|2.28;2.28;2.28	5.92|5.92	4.18|4.18	0.49190|0.49190	.|.	.|0.785384	.|0.12899	.|N	.|0.429994	T|T	0.15176|0.15176	0.0366|0.0366	L|L	0.43152|0.43152	1.355|1.355	0.24901|0.24901	N|N	0.992104|0.992104	.|B;B	.|0.09022	.|0.001;0.002	.|B;B	.|0.11329	.|0.003;0.006	T|T	0.20605|0.20605	-1.0270|-1.0270	5|10	.|0.45353	.|T	.|0.12	-2.0215|-2.0215	7.0631|7.0631	0.25137|0.25137	0.139:0.7173:0.0:0.1437|0.139:0.7173:0.0:0.1437	.|.	.|382;399	.|Q9UKA1-2;Q9UKA1	.|.;FBXL5_HUMAN	Y|M	319|399;382;273	.|ENSP00000344866:V399M;ENSP00000408679:V382M;ENSP00000371795:V273M	.|ENSP00000344866:V399M	C|V	-|-	2|1	0|0	FBXL5|FBXL5	15236628|15236628	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.904000|0.904000	0.53231|0.53231	2.974000|2.974000	0.49272|0.49272	0.815000|0.815000	0.34398|0.34398	-0.157000|-0.157000	0.13467|0.13467	TGT|GTG	.	.		0.398	FBXL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214235.2		
KLB	152831	hgsc.bcm.edu	37	4	39436265	39436265	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:39436265A>G	ENST00000257408.4	+	2	1358	c.1261A>G	c.(1261-1263)Aca>Gca	p.T421A		NM_175737.3	NP_783864.1	Q86Z14	KLOTB_HUMAN	klotho beta	421	Glycosyl hydrolase-1 1.				carbohydrate metabolic process (GO:0005975)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	fibroblast growth factor binding (GO:0017134)|hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(11)|skin(6)	29						TGGCTGGTTCACAGACAGTCG	0.413																																					p.T421A		Atlas-SNP	.											.	KLB	95	.	0			c.A1261G						.						77.0	77.0	77.0					4																	39436265		2203	4300	6503	SO:0001583	missense	152831	exon2			TGGTTCACAGACA	AB079373	CCDS3451.1	4p14	2008-02-05			ENSG00000134962	ENSG00000134962			15527	protein-coding gene	gene with protein product		611135					Standard	NM_175737		Approved		uc003gua.3	Q86Z14	OTTHUMG00000128577	ENST00000257408.4:c.1261A>G	chr4.hg19:g.39436265A>G	ENSP00000257408:p.Thr421Ala	77.0	0.0		91.0	4.0	NM_175737	Q2M3K8	Missense_Mutation	SNP	ENST00000257408.4	hg19	CCDS3451.1	.	.	.	.	.	.	.	.	.	.	A	16.94	3.259851	0.59321	.	.	ENSG00000134962	ENST00000257408	T	0.28454	1.61	6.06	6.06	0.98353	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.109144	0.64402	D	0.000006	T	0.26666	0.0652	N	0.16098	0.37	0.37100	D	0.899867	P;P	0.51791	0.948;0.948	P;P	0.54499	0.754;0.754	T	0.13229	-1.0517	10	0.09338	T	0.73	-20.9716	11.6645	0.51366	0.8678:0.0:0.0:0.1322	.	421;421	B7ZL50;Q86Z14	.;KLOTB_HUMAN	A	421	ENSP00000257408:T421A	ENSP00000257408:T421A	T	+	1	0	KLB	39112660	1.000000	0.71417	0.998000	0.56505	0.974000	0.67602	3.182000	0.50910	2.315000	0.78130	0.533000	0.62120	ACA	.	.		0.413	KLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250429.1	NM_175737	
PHOX2B	8929	hgsc.bcm.edu	37	4	41750584	41750584	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:41750584T>C	ENST00000226382.2	-	1	403	c.44A>G	c.(43-45)gAg>gGg	p.E15G	RP11-227F19.1_ENST00000508038.1_RNA|RP11-227F19.2_ENST00000510602.1_lincRNA	NM_003924.3	NP_003915.2	Q99453	PHX2B_HUMAN	paired-like homeobox 2b	15					autonomic nervous system development (GO:0048483)|brainstem development (GO:0003360)|cell differentiation in hindbrain (GO:0021533)|cellular response to BMP stimulus (GO:0071773)|dopaminergic neuron differentiation (GO:0071542)|efferent axon development in a lateral line nerve (GO:0048894)|enteric nervous system development (GO:0048484)|glial cell differentiation (GO:0010001)|hindbrain tangential cell migration (GO:0021934)|inner ear development (GO:0048839)|medullary reticular formation development (GO:0021723)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron differentiation (GO:0045665)|neural crest cell migration involved in autonomic nervous system development (GO:1901166)|neuron migration (GO:0001764)|noradrenergic neuron development (GO:0003358)|noradrenergic neuron differentiation (GO:0003357)|parasympathetic nervous system development (GO:0048486)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of gene expression (GO:0010468)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|respiratory system development (GO:0060541)|retrotrapezoid nucleus neuron differentiation (GO:0061452)|skeletal muscle cell differentiation (GO:0035914)|sympathetic ganglion development (GO:0061549)|sympathetic nervous system development (GO:0048485)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)			autonomic_ganglia(7)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(11)|ovary(2)|skin(1)|urinary_tract(1)	30						CATACAGGACTCGTAGGCAGA	0.468			"""Mis, F"""		neuroblastoma	neuroblastoma	congenital central hypoventilation syndrome		Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome																												p.E15G		Atlas-SNP	.	yes	Rec	yes	familial neuroblastoma	4	4p12	8929	paired-like homeobox 2b	yes	O	.	PHOX2B	53	.	0			c.A44G						.						33.0	34.0	34.0					4																	41750584		2203	4300	6503	SO:0001583	missense	8929	exon1	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	CAGGACTCGTAGG	D82344	CCDS3463.1	4p13	2014-09-17	2003-02-10	2003-02-14	ENSG00000109132	ENSG00000109132		"""Homeoboxes / PRD class"""	9143	protein-coding gene	gene with protein product		603851	"""paired mesoderm homeobox 2b"""	PMX2B		9039501, 10395798	Standard	NM_003924		Approved	Phox2b, NBPhox	uc003gwf.4	Q99453	OTTHUMG00000099379	ENST00000226382.2:c.44A>G	chr4.hg19:g.41750584T>C	ENSP00000226382:p.Glu15Gly	86.0	0.0		99.0	4.0	NM_003924	Q6PJD9	Missense_Mutation	SNP	ENST00000226382.2	hg19	CCDS3463.1	.	.	.	.	.	.	.	.	.	.	T	14.64	2.596671	0.46318	.	.	ENSG00000109132	ENST00000226382	D	0.92149	-2.98	5.66	5.66	0.87406	.	0.000000	0.85682	D	0.000000	D	0.88941	0.6574	N	0.14661	0.345	0.80722	D	1	D	0.57257	0.979	P	0.49999	0.628	D	0.91078	0.4897	10	0.72032	D	0.01	.	15.8882	0.79269	0.0:0.0:0.0:1.0	.	15	Q99453	PHX2B_HUMAN	G	15	ENSP00000226382:E15G	ENSP00000226382:E15G	E	-	2	0	PHOX2B	41445341	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.845000	0.86875	2.166000	0.68216	0.454000	0.30748	GAG	.	.		0.468	PHOX2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216832.2		
SCFD2	152579	hgsc.bcm.edu	37	4	54231690	54231690	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:54231690A>G	ENST00000401642.3	-	1	552	c.419T>C	c.(418-420)cTg>cCg	p.L140P	SCFD2_ENST00000388940.4_Missense_Mutation_p.L140P	NM_152540.3	NP_689753.2	Q8WU76	SCFD2_HUMAN	sec1 family domain containing 2	140					protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)					breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	30			GBM - Glioblastoma multiforme(3;1.07e-26)|LUSC - Lung squamous cell carcinoma(32;0.0134)			CCATTCACACAGCTTCTCCTC	0.592																																					p.L140P		Atlas-SNP	.											.	SCFD2	78	.	0			c.T419C						.						93.0	76.0	82.0					4																	54231690		2203	4300	6503	SO:0001583	missense	152579	exon1			TCACACAGCTTCT	AY299407	CCDS33984.1	4q12	2004-01-15			ENSG00000184178	ENSG00000184178			30676	protein-coding gene	gene with protein product						12477932	Standard	NM_152540		Approved	STXBP1L1, FLJ39514	uc003gzu.3	Q8WU76	OTTHUMG00000160588	ENST00000401642.3:c.419T>C	chr4.hg19:g.54231690A>G	ENSP00000384182:p.Leu140Pro	95.0	0.0		121.0	5.0	NM_152540	Q8N5F3|Q8N8H0|Q96ED3	Missense_Mutation	SNP	ENST00000401642.3	hg19	CCDS33984.1	.	.	.	.	.	.	.	.	.	.	A	23.8	4.460545	0.84317	.	.	ENSG00000184178	ENST00000401642;ENST00000388940	T;T	0.54071	0.61;0.59	5.51	5.51	0.81932	.	0.070367	0.64402	D	0.000018	T	0.66684	0.2814	L	0.59436	1.845	0.80722	D	1	D;D	0.76494	0.999;0.992	D;P	0.65233	0.933;0.816	T	0.69752	-0.5060	10	0.87932	D	0	.	13.6279	0.62178	1.0:0.0:0.0:0.0	.	140;140	Q8WU76-2;Q8WU76	.;SCFD2_HUMAN	P	140	ENSP00000384182:L140P;ENSP00000373592:L140P	ENSP00000373592:L140P	L	-	2	0	SCFD2	53926447	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	8.172000	0.89677	2.317000	0.78254	0.459000	0.35465	CTG	.	.		0.592	SCFD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361311.3	NM_152540	
EPHA5	2044	hgsc.bcm.edu	37	4	66467955	66467955	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:66467955A>G	ENST00000273854.3	-	3	914	c.314T>C	c.(313-315)aTg>aCg	p.M105T	EPHA5_ENST00000354839.4_Missense_Mutation_p.M105T|EPHA5_ENST00000511294.1_Missense_Mutation_p.M105T|EPHA5_ENST00000432638.2_Missense_Mutation_p.M105T	NM_001281765.1|NM_004439.5	NP_001268694.1|NP_004430.4	P54756	EPHA5_HUMAN	EPH receptor A5	105	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.				axon guidance (GO:0007411)|cAMP-mediated signaling (GO:0019933)|ephrin receptor signaling pathway (GO:0048013)|hippocampus development (GO:0021766)|negative regulation of synapse assembly (GO:0051964)|neuron development (GO:0048666)|positive regulation of CREB transcription factor activity (GO:0032793)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of Rac GTPase activity (GO:0032314)	dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|GPI-linked ephrin receptor activity (GO:0005004)|transmembrane-ephrin receptor activity (GO:0005005)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(25)|liver(1)|lung(76)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	142						ATTCTGTTCCATCACTTTGCA	0.383										TSP Lung(17;0.13)																											p.M105T		Atlas-SNP	.											.	EPHA5	315	.	0			c.T314C						.						124.0	132.0	130.0					4																	66467955		2203	4300	6503	SO:0001583	missense	2044	exon3			TGTTCCATCACTT	L36644	CCDS3513.1, CCDS3514.1, CCDS75131.1, CCDS75132.1, CCDS75133.1	4q13.1	2013-02-11	2004-10-28		ENSG00000145242	ENSG00000145242		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3389	protein-coding gene	gene with protein product		600004	"""EphA5"""			9267020, 7528718	Standard	NM_004439		Approved	Hek7, TYRO4, CEK7, EHK1	uc003hcy.3	P54756	OTTHUMG00000129273	ENST00000273854.3:c.314T>C	chr4.hg19:g.66467955A>G	ENSP00000273854:p.Met105Thr	41.0	0.0		32.0	4.0	NM_004439	Q7Z3F2	Missense_Mutation	SNP	ENST00000273854.3	hg19	CCDS3513.1	.	.	.	.	.	.	.	.	.	.	A	18.13	3.554799	0.65425	.	.	ENSG00000145242	ENST00000273854;ENST00000432638;ENST00000354839;ENST00000511294	T;T;T;T	0.09538	2.97;2.97;2.97;2.97	5.68	5.68	0.88126	Ephrin receptor, ligand binding (2);Galactose-binding domain-like (1);	0.000000	0.85682	D	0.000000	T	0.30262	0.0759	L	0.58101	1.795	0.80722	D	1	D;P;D;P	0.63880	0.993;0.766;0.991;0.87	D;P;D;P	0.81914	0.995;0.565;0.991;0.613	T	0.00763	-1.1576	10	0.52906	T	0.07	.	15.9206	0.79562	1.0:0.0:0.0:0.0	.	105;105;105;105	B7ZKW7;B7ZKJ3;P54756-2;P54756	.;.;.;EPHA5_HUMAN	T	105	ENSP00000273854:M105T;ENSP00000389208:M105T;ENSP00000346899:M105T;ENSP00000427638:M105T	ENSP00000273854:M105T	M	-	2	0	EPHA5	66150550	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	9.339000	0.96797	2.166000	0.68216	0.533000	0.62120	ATG	.	.		0.383	EPHA5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251388.2	NM_004439	
TMPRSS11BNL	401136	hgsc.bcm.edu	37	4	69057170	69057170	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:69057170T>C	ENST00000432593.3	-	3	363	c.197A>G	c.(196-198)gAg>gGg	p.E66G	RP11-646E20.6_ENST00000510782.1_RNA|FTLP10_ENST00000503647.1_RNA					TMPRSS11B N-terminal like, pseudogene											autonomic_ganglia(1)	1						TGGTGATGTCTCCCTTTCATA	0.328																																					p.E66G		Atlas-SNP	.											.	TMPRSS11BNL	4	.	0			c.A197G						.						152.0	134.0	139.0					4																	69057170		692	1588	2280	SO:0001583	missense	401136	exon3			GATGTCTCCCTTT			4q13.2	2014-05-09	2014-05-08		ENSG00000226894	ENSG00000250026			37262	pseudogene	pseudogene			"""TMPRSS11B N terminal-like"", ""TMPRSS11B N-terminal like"""				Standard	NR_104048		Approved	FLJ41562	uc003hdv.1		OTTHUMG00000160802	ENST00000432593.3:c.197A>G	chr4.hg19:g.69057170T>C	ENSP00000391149:p.Glu66Gly	70.0	0.0		70.0	4.0	NM_001129907		Missense_Mutation	SNP	ENST00000432593.3	hg19	CCDS47066.1	.	.	.	.	.	.	.	.	.	.	T	6.361	0.434655	0.12045	.	.	ENSG00000226894	ENST00000432593	T	0.34275	1.37	4.52	-1.02	0.10135	.	.	.	.	.	T	0.23054	0.0557	L	0.39020	1.185	0.09310	N	1	P	0.36909	0.573	B	0.33521	0.165	T	0.13656	-1.0501	9	0.37606	T	0.19	.	6.5136	0.22236	0.0:0.0903:0.4592:0.4505	.	66	B3KVV0	TM11L_HUMAN	G	66	ENSP00000391149:E66G	ENSP00000391149:E66G	E	-	2	0	TMPRSS11BNL	68739765	0.843000	0.29541	0.846000	0.33378	0.001000	0.01503	0.775000	0.26689	-0.017000	0.14103	-2.201000	0.00304	GAG	.	.		0.328	TMPRSS11BNL-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001129907	
CSN2	1447	hgsc.bcm.edu	37	4	70824773	70824773	+	Silent	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:70824773T>C	ENST00000353151.3	-	3	104	c.93A>G	c.(91-93)gaA>gaG	p.E31E		NM_001891.2	NP_001882.1	P61201	CSN2_HUMAN	casein beta	0					cell proliferation (GO:0008283)|cullin deneddylation (GO:0010388)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron differentiation (GO:0030182)|signal transduction (GO:0007165)|skeletal muscle cell differentiation (GO:0035914)|transcription from RNA polymerase II promoter (GO:0006366)	COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)	signal transducer activity (GO:0004871)|transcription corepressor activity (GO:0003714)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(6)|skin(2)	12						TTACCTTGTATTCTGTAATAG	0.219																																					p.E31E		Atlas-SNP	.											.	CSN2	30	.	0			c.A93G						.						10.0	10.0	10.0					4																	70824773		2115	4158	6273	SO:0001819	synonymous_variant	1447	exon3			CTTGTATTCTGTA	X17070	CCDS3532.1	4q21.1	2008-02-05			ENSG00000135222	ENSG00000135222			2447	protein-coding gene	gene with protein product		115460		CASB		1577486	Standard	NM_001891		Approved		uc003hes.4	P05814	OTTHUMG00000129409	ENST00000353151.3:c.93A>G	chr4.hg19:g.70824773T>C		32.0	0.0		41.0	4.0	NM_001891	O88950|Q15647|Q6FGP4|Q9BY54|Q9R249|Q9UNI2|Q9UNQ5	Silent	SNP	ENST00000353151.3	hg19	CCDS3532.1																																																																																			.	.		0.219	CSN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251565.1		
PF4	5196	hgsc.bcm.edu	37	4	74847216	74847216	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:74847216T>C	ENST00000296029.3	-	2	306	c.136A>G	c.(136-138)Acc>Gcc	p.T46A		NM_002619.3	NP_002610.1	P02776	PLF4_HUMAN	platelet factor 4	46					blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|leukocyte chemotaxis (GO:0030595)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cytolysis (GO:0045918)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of megakaryocyte differentiation (GO:0045653)|negative regulation of MHC class II biosynthetic process (GO:0045347)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of cAMP metabolic process (GO:0030816)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of gene expression (GO:0010628)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of cell proliferation (GO:0042127)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|platelet alpha granule lumen (GO:0031093)	chemokine activity (GO:0008009)|CXCR3 chemokine receptor binding (GO:0048248)|heparin binding (GO:0008201)			kidney(1)|lung(1)	2	Breast(15;0.00136)		all cancers(17;0.0034)|Lung(101;0.196)		Drotrecogin alfa(DB00055)	TGGGAGGTGGTCTTCACACAC	0.602																																					p.T46A		Atlas-SNP	.											.	PF4	13	.	0			c.A136G						.						68.0	61.0	63.0					4																	74847216		2203	4296	6499	SO:0001583	missense	5196	exon2			AGGTGGTCTTCAC	M25897	CCDS3562.1	4q12-q21	2012-10-02	2008-08-29		ENSG00000163737	ENSG00000163737			8861	protein-coding gene	gene with protein product	"""chemokine (C-X-C motif) ligand 4"""	173460	"""platelet factor 4"""			3622011	Standard	NM_002619		Approved	SCYB4, CXCL4	uc003hhi.3	P02776	OTTHUMG00000130009	ENST00000296029.3:c.136A>G	chr4.hg19:g.74847216T>C	ENSP00000296029:p.Thr46Ala	180.0	0.0		147.0	6.0	NM_002619	Q53X61|Q9UC64|Q9UC65	Missense_Mutation	SNP	ENST00000296029.3	hg19	CCDS3562.1	.	.	.	.	.	.	.	.	.	.	T	19.53	3.845795	0.71603	.	.	ENSG00000163737	ENST00000296029	T	0.05319	3.46	2.63	2.63	0.31362	CXC chemokine, conserved site (1);Chemokine interleukin-8-like domain (3);	0.210963	0.43260	D	0.000587	T	0.22742	0.0549	M	0.89287	3.02	0.09310	N	1	D	0.69078	0.997	D	0.66196	0.942	T	0.02560	-1.1141	10	0.52906	T	0.07	.	7.0001	0.24805	0.0:0.0:0.0:1.0	.	46	P02776	PLF4_HUMAN	A	46	ENSP00000296029:T46A	ENSP00000296029:T46A	T	-	1	0	PF4	75066080	0.847000	0.29606	0.037000	0.18230	0.973000	0.67179	1.962000	0.40442	1.207000	0.43291	0.254000	0.18369	ACC	.	.		0.602	PF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252282.1		
CCNI	10983	hgsc.bcm.edu	37	4	77977228	77977228	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:77977228T>C	ENST00000237654.4	-	5	922	c.346A>G	c.(346-348)Aga>Gga	p.R116G	CCNI_ENST00000504697.1_5'UTR|CCNI_ENST00000537948.1_Missense_Mutation_p.R102G	NM_006835.2	NP_006826.1	Q14094	CCNI_HUMAN	cyclin I	116					regulation of cell cycle (GO:0051726)|spermatogenesis (GO:0007283)					NS(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(1)|ovary(1)|prostate(1)	9						AAACTGTCTCTTGCCAATACC	0.383																																					p.R116G		Atlas-SNP	.											.	CCNI	22	.	0			c.A346G						.						92.0	94.0	93.0					4																	77977228		2203	4300	6503	SO:0001583	missense	10983	exon5			TGTCTCTTGCCAA	D50310	CCDS3580.1	4q21.1	2014-07-03			ENSG00000118816	ENSG00000118816			1595	protein-coding gene	gene with protein product						7493655	Standard	NM_006835		Approved	CCNI1	uc003hkm.3	Q14094	OTTHUMG00000130106	ENST00000237654.4:c.346A>G	chr4.hg19:g.77977228T>C	ENSP00000237654:p.Arg116Gly	59.0	0.0		73.0	4.0	NM_006835	B2R6M0|B7Z6X4	Missense_Mutation	SNP	ENST00000237654.4	hg19	CCDS3580.1	.	.	.	.	.	.	.	.	.	.	T	11.25	1.583842	0.28268	.	.	ENSG00000118816	ENST00000237654;ENST00000537948;ENST00000505609	T;T;T	0.17691	2.75;2.75;2.26	6.16	6.16	0.99307	Cyclin, N-terminal (1);Cyclin-like (3);	0.241545	0.50627	D	0.000117	T	0.14743	0.0356	L	0.33792	1.035	0.36034	D	0.839633	B;B	0.23806	0.091;0.034	B;B	0.25987	0.065;0.038	T	0.19418	-1.0306	10	0.26408	T	0.33	-14.152	12.5783	0.56375	0.0:0.0:0.2408:0.7591	.	102;116	B7Z6X4;Q14094	.;CCNI_HUMAN	G	116;102;116	ENSP00000237654:R116G;ENSP00000441001:R102G;ENSP00000426467:R116G	ENSP00000237654:R116G	R	-	1	2	CCNI	78196252	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	1.651000	0.37302	2.367000	0.80283	0.528000	0.53228	AGA	.	.		0.383	CCNI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252412.2	NM_006835	
CDS1	1040	hgsc.bcm.edu	37	4	85555086	85555086	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:85555086T>C	ENST00000295887.5	+	7	1139	c.716T>C	c.(715-717)aTg>aCg	p.M239T		NM_001263.3	NP_001254.2	O96017	CHK2_HUMAN	CDP-diacylglycerol synthase (phosphatidate cytidylyltransferase) 1	0	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		E -> K (in prostate cancer; germline mutation). {ECO:0000269|PubMed:12533788}.		cellular protein catabolic process (GO:0044257)|cellular response to DNA damage stimulus (GO:0006974)|DNA damage checkpoint (GO:0000077)|DNA damage induced protein phosphorylation (GO:0006975)|double-strand break repair (GO:0006302)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|regulation of protein catabolic process (GO:0042176)|regulation of transcription, DNA-templated (GO:0006355)|replicative senescence (GO:0090399)|response to gamma radiation (GO:0010332)|signal transduction in response to DNA damage (GO:0042770)|signal transduction involved in intra-S DNA damage checkpoint (GO:0072428)|spindle assembly involved in mitosis (GO:0090307)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|PML body (GO:0016605)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(3)|kidney(1)|large_intestine(7)|liver(2)|lung(5)|ovary(1)	20		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.00101)		TTTGAAGGCATGATATGGTAA	0.353																																					p.M239T		Atlas-SNP	.											.	CDS1	58	.	0			c.T716C						.						169.0	139.0	149.0					4																	85555086		2203	4300	6503	SO:0001583	missense	1040	exon7			AAGGCATGATATG	U65887	CCDS3608.1	4q21	2008-02-05			ENSG00000163624	ENSG00000163624	2.7.7.41		1800	protein-coding gene	gene with protein product		603548				9806839, 9115637	Standard	NM_001263		Approved		uc011ccv.2	Q92903	OTTHUMG00000130428	ENST00000295887.5:c.716T>C	chr4.hg19:g.85555086T>C	ENSP00000295887:p.Met239Thr	70.0	0.0		89.0	4.0	NM_001263	A8K3Y9|B7ZBF3|B7ZBF4|B7ZBF5|Q6QA03|Q6QA04|Q6QA05|Q6QA06|Q6QA07|Q6QA08|Q6QA10|Q6QA11|Q6QA12|Q6QA13|Q9HBS5|Q9HCQ8|Q9UGF0|Q9UGF1	Missense_Mutation	SNP	ENST00000295887.5	hg19	CCDS3608.1	.	.	.	.	.	.	.	.	.	.	T	16.81	3.226338	0.58668	.	.	ENSG00000163624	ENST00000295887	T	0.42131	0.98	5.96	5.96	0.96718	.	0.035649	0.85682	D	0.000000	T	0.42494	0.1205	L	0.50919	1.6	0.80722	D	1	B	0.32968	0.392	B	0.33960	0.173	T	0.39418	-0.9615	10	0.72032	D	0.01	-25.9657	16.4221	0.83766	0.0:0.0:0.0:1.0	.	239	Q92903	CDS1_HUMAN	T	239	ENSP00000295887:M239T	ENSP00000295887:M239T	M	+	2	0	CDS1	85774110	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.040000	0.89188	2.283000	0.76528	0.477000	0.44152	ATG	.	.		0.353	CDS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252817.2		
SMARCAD1	56916	hgsc.bcm.edu	37	4	95129594	95129594	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:95129594A>G	ENST00000354268.4	+	2	122	c.49A>G	c.(49-51)Att>Gtt	p.I17V	SMARCAD1_ENST00000457823.2_Missense_Mutation_p.I17V|RP11-363G15.2_ENST00000501965.2_lincRNA			Q9H4L7	SMRCD_HUMAN	SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1	17					ATP-dependent chromatin remodeling (GO:0043044)|chromatin modification (GO:0016568)|chromatin remodeling (GO:0006338)|chromosome separation (GO:0051304)|DNA double-strand break processing (GO:0000729)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|nucleotide metabolic process (GO:0009117)|positive regulation of transcription, DNA-templated (GO:0045893)|protein homooligomerization (GO:0051260)|regulation of DNA recombination (GO:0000018)	heterochromatin (GO:0000792)|nuclear matrix (GO:0016363)|nuclear replication fork (GO:0043596)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(11)|liver(2)|lung(15)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	44				OV - Ovarian serous cystadenocarcinoma(123;4.33e-08)		AAGGAATAAGATTGAGGAAGC	0.473																																					p.I17V		Atlas-SNP	.											.	SMARCAD1	97	.	0			c.A49G						.						93.0	102.0	98.0					4																	95129594		2203	4300	6503	SO:0001583	missense	56916	exon2			AATAAGATTGAGG	AB032948	CCDS3639.1, CCDS47101.1, CCDS58914.1	4q22-q23	2008-02-05			ENSG00000163104	ENSG00000163104			18398	protein-coding gene	gene with protein product		612761				11031099	Standard	NM_001128430		Approved	ETL1, DKFZP762K2015, KIAA1122, DKFZp762K2015	uc003htb.4	Q9H4L7	OTTHUMG00000130971	ENST00000354268.4:c.49A>G	chr4.hg19:g.95129594A>G	ENSP00000346217:p.Ile17Val	107.0	0.0		90.0	4.0	NM_001128429	B7Z799|Q05D56|Q96SX1|Q9H017|Q9H860|Q9NPU9|Q9ULU7	Missense_Mutation	SNP	ENST00000354268.4	hg19	CCDS3639.1	.	.	.	.	.	.	.	.	.	.	A	10.03	1.240084	0.22711	.	.	ENSG00000163104	ENST00000359052;ENST00000457823;ENST00000536267;ENST00000354268	T;T;T	0.44482	0.92;0.92;0.92	4.83	-0.286	0.12862	.	0.249386	0.20883	N	0.083966	T	0.21468	0.0517	N	0.14661	0.345	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.03534	-1.1027	10	0.39692	T	0.17	-4.0883	7.4486	0.27225	0.6081:0.0:0.3919:0.0	.	17;17	Q9H4L7;Q9H4L7-2	SMRCD_HUMAN;.	V	17	ENSP00000351947:I17V;ENSP00000415576:I17V;ENSP00000346217:I17V	ENSP00000346217:I17V	I	+	1	0	SMARCAD1	95348617	0.054000	0.20591	0.988000	0.46212	0.620000	0.37586	0.179000	0.16840	0.059000	0.16252	0.459000	0.35465	ATT	.	.		0.473	SMARCAD1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253583.1	NM_020159	
BANK1	55024	hgsc.bcm.edu	37	4	102946503	102946503	+	Silent	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:102946503T>C	ENST00000322953.4	+	9	1705	c.1431T>C	c.(1429-1431)agT>agC	p.S477S	BANK1_ENST00000510950.1_3'UTR|BANK1_ENST00000508653.1_Silent_p.S344S|BANK1_ENST00000428908.1_Silent_p.S344S|BANK1_ENST00000504592.1_Silent_p.S462S|BANK1_ENST00000444316.2_Silent_p.S447S|RP11-498M5.2_ENST00000505091.1_RNA	NM_017935.4	NP_060405	Q8NDB2	BANK1_HUMAN	B-cell scaffold protein with ankyrin repeats 1	477					B cell activation (GO:0042113)					NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|liver(2)|lung(16)|ovary(2)|skin(2)|urinary_tract(1)	44		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;2.7e-07)		AGGTTGGCAGTGAGAGTTCTG	0.483																																					p.S477S		Atlas-SNP	.											.	BANK1	95	.	0			c.T1431C						.						215.0	177.0	190.0					4																	102946503		2203	4300	6503	SO:0001819	synonymous_variant	55024	exon9			TGGCAGTGAGAGT	AB063170	CCDS34038.1, CCDS47115.1, CCDS47116.1	4q23	2013-01-11						"""Ankyrin repeat domain containing"""	18233	protein-coding gene	gene with protein product		610292				11782428, 21208380, 21480188	Standard	NM_017935		Approved	BANK, FLJ20706	uc003hvy.4	Q8NDB2		ENST00000322953.4:c.1431T>C	chr4.hg19:g.102946503T>C		107.0	0.0		91.0	4.0	NM_017935	A8K7W8|B0F3S2|Q8N5K8|Q8NB56|Q8WYN5|Q9NWP2	Silent	SNP	ENST00000322953.4	hg19	CCDS34038.1																																																																																			.	.		0.483	BANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363161.1	NM_017935	
ALPK1	80216	hgsc.bcm.edu	37	4	113333009	113333009	+	Silent	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:113333009T>C	ENST00000458497.1	+	5	582	c.303T>C	c.(301-303)gcT>gcC	p.A101A	ALPK1_ENST00000177648.9_Silent_p.A101A|ALPK1_ENST00000505912.1_3'UTR|ALPK1_ENST00000504176.2_Silent_p.A23A	NM_001102406.1|NM_025144.3	NP_001095876.1|NP_079420.3	Q96QP1	ALPK1_HUMAN	alpha-kinase 1	101							ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(11)|lung(20)|ovary(6)|prostate(2)|urinary_tract(1)	53		Ovarian(17;0.0446)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00325)		CCATCCTCGCTCGGGACTGTG	0.632																																					p.A101A		Atlas-SNP	.											.	ALPK1	125	.	0			c.T303C						.						38.0	37.0	37.0					4																	113333009		2203	4300	6503	SO:0001819	synonymous_variant	80216	exon5			CCTCGCTCGGGAC	AY044164	CCDS3697.1, CCDS58923.1	4q26	2008-02-05			ENSG00000073331	ENSG00000073331			20917	protein-coding gene	gene with protein product	"""lymphocyte alpha-kinase"""	607347				10021370, 10819331	Standard	NM_025144		Approved	Lak, FLJ22670, KIAA1527	uc003ian.4	Q96QP1	OTTHUMG00000132911	ENST00000458497.1:c.303T>C	chr4.hg19:g.113333009T>C		155.0	0.0		138.0	6.0	NM_001102406	B4E3G1|F5H138|Q68CI9|Q6P9F9|Q6ZNK4|Q9P201	Silent	SNP	ENST00000458497.1	hg19	CCDS3697.1																																																																																			.	.		0.632	ALPK1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256421.2	NM_025144	
ALPK1	80216	hgsc.bcm.edu	37	4	113356354	113356354	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:113356354G>A	ENST00000458497.1	+	12	3364	c.3085G>A	c.(3085-3087)Gaa>Aaa	p.E1029K	ALPK1_ENST00000177648.9_Missense_Mutation_p.E1029K|ALPK1_ENST00000504176.2_Missense_Mutation_p.E951K	NM_001102406.1|NM_025144.3	NP_001095876.1|NP_079420.3	Q96QP1	ALPK1_HUMAN	alpha-kinase 1	1029	Alpha-type protein kinase. {ECO:0000255|PROSITE-ProRule:PRU00501}.						ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(11)|lung(20)|ovary(6)|prostate(2)|urinary_tract(1)	53		Ovarian(17;0.0446)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00325)		GACGGCCCAGGAAACTATTGT	0.353																																					p.E1029K		Atlas-SNP	.											.	ALPK1	125	.	0			c.G3085A						.						130.0	155.0	147.0					4																	113356354		2203	4300	6503	SO:0001583	missense	80216	exon12			GCCCAGGAAACTA	AY044164	CCDS3697.1, CCDS58923.1	4q26	2008-02-05			ENSG00000073331	ENSG00000073331			20917	protein-coding gene	gene with protein product	"""lymphocyte alpha-kinase"""	607347				10021370, 10819331	Standard	NM_025144		Approved	Lak, FLJ22670, KIAA1527	uc003ian.4	Q96QP1	OTTHUMG00000132911	ENST00000458497.1:c.3085G>A	chr4.hg19:g.113356354G>A	ENSP00000398048:p.Glu1029Lys	130.0	0.0		120.0	20.0	NM_001102406	B4E3G1|F5H138|Q68CI9|Q6P9F9|Q6ZNK4|Q9P201	Missense_Mutation	SNP	ENST00000458497.1	hg19	CCDS3697.1	.	.	.	.	.	.	.	.	.	.	G	25.6	4.653679	0.88056	.	.	ENSG00000073331	ENST00000458497;ENST00000177648;ENST00000504176	T;T;T	0.07114	3.22;3.22;3.22	5.84	5.84	0.93424	MHCK/EF2 kinase (2);Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.33614	0.0869	M	0.78801	2.425	0.52099	D	0.999943	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.997;0.995;0.994	T	0.01301	-1.1391	10	0.62326	D	0.03	-29.2293	20.1393	0.98055	0.0:0.0:1.0:0.0	.	951;951;1029	F5H138;B4E3G1;Q96QP1	.;.;ALPK1_HUMAN	K	1029;1029;951	ENSP00000398048:E1029K;ENSP00000177648:E1029K;ENSP00000426044:E951K	ENSP00000177648:E1029K	E	+	1	0	ALPK1	113575803	1.000000	0.71417	1.000000	0.80357	0.513000	0.34164	8.521000	0.90569	2.759000	0.94783	0.563000	0.77884	GAA	.	.		0.353	ALPK1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256421.2	NM_025144	
LARP7	51574	hgsc.bcm.edu	37	4	113565838	113565838	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:113565838A>G	ENST00000344442.5	+	2	291	c.13A>G	c.(13-15)Agt>Ggt	p.S5G	LARP7_ENST00000509061.1_Missense_Mutation_p.S12G|MIR302B_ENST00000505215.1_RNA|MIR302B_ENST00000510655.1_RNA|LARP7_ENST00000324052.6_Missense_Mutation_p.S5G|MIR302B_ENST00000509938.1_RNA	NM_016648.3	NP_057732.2	Q4G0J3	LARP7_HUMAN	La ribonucleoprotein domain family, member 7	5					RNA processing (GO:0006396)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(2)|large_intestine(2)|lung(8)|ovary(4)|skin(1)	17		Ovarian(17;0.0443)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000603)		GGAAACTGAAAGTGGAAATCA	0.308																																					p.S12G		Atlas-SNP	.											.	LARP7	54	.	0			c.A34G						.						47.0	44.0	45.0					4																	113565838		1802	4067	5869	SO:0001583	missense	51574	exon4			ACTGAAAGTGGAA	AF068284	CCDS3701.2, CCDS58924.1	4q25	2013-02-12			ENSG00000174720	ENSG00000174720		"""La ribonucleoprotein domain containing"", ""RNA binding motif (RRM) containing"""	24912	protein-coding gene	gene with protein product	"""P-TEFb-interaction protein for 7SK stability"""	612026				18191186, 18249148, 18281698, 22865833, 22488152	Standard	NM_016648		Approved	HDCMA18P, PIP7S, DKFZP564K112	uc003ibb.4	Q4G0J3	OTTHUMG00000132909	ENST00000344442.5:c.13A>G	chr4.hg19:g.113565838A>G	ENSP00000344950:p.Ser5Gly	47.0	0.0		45.0	4.0	NM_001267039	B2ZHN6|Q3B7A9|Q9P1S7|Q9Y3Z8	Missense_Mutation	SNP	ENST00000344442.5	hg19	CCDS3701.2	.	.	.	.	.	.	.	.	.	.	A	9.573	1.121416	0.20877	.	.	ENSG00000174720	ENST00000344442;ENST00000509061;ENST00000508577;ENST00000513553;ENST00000505034;ENST00000324052;ENST00000507443	T;T;T;T;T;T;T	0.49139	2.24;2.21;0.93;0.79;2.25;2.24;0.93	5.17	-4.86	0.03132	.	1.490870	0.03334	N	0.193878	T	0.33118	0.0852	L	0.40543	1.245	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.16335	-1.0406	10	0.41790	T	0.15	-1.3374	2.402	0.04404	0.3838:0.2079:0.3069:0.1014	.	5;5	D6RFF0;Q4G0J3	.;LARP7_HUMAN	G	5;12;5;5;5;5;5	ENSP00000344950:S5G;ENSP00000422626:S12G;ENSP00000426646:S5G;ENSP00000422013:S5G;ENSP00000421541:S5G;ENSP00000314311:S5G;ENSP00000421963:S5G	ENSP00000314311:S5G	S	+	1	0	LARP7	113785287	0.009000	0.17119	0.026000	0.17262	0.973000	0.67179	0.199000	0.17237	-0.617000	0.05664	-0.328000	0.08392	AGT	.	.		0.308	LARP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256417.2	NM_016648	
NDST3	9348	hgsc.bcm.edu	37	4	119035960	119035960	+	Splice_Site	SNP	G	G	A			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:119035960G>A	ENST00000296499.5	+	4	1472		c.e4-1		NDST3_ENST00000433996.2_Intron	NM_004784.2	NP_004775.1	O95803	NDST3_HUMAN	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 3						heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparin biosynthetic process (GO:0030210)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine N-sulfotransferase activity (GO:0015016)|deacetylase activity (GO:0019213)			NS(1)|breast(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(23)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	54						CCCCCCTAAAGGAACTGAAGA	0.398																																					.		Atlas-SNP	.											.	NDST3	107	.	0			c.1070-1G>A						.						129.0	120.0	123.0					4																	119035960		2203	4300	6503	SO:0001630	splice_region_variant	9348	exon4			CCTAAAGGAACTG	AF074924	CCDS3708.1	4q26	2008-08-04			ENSG00000164100	ENSG00000164100		"""Sulfotransferases, membrane-bound"""	7682	protein-coding gene	gene with protein product		603950				9915799	Standard	NM_004784		Approved	HSST3	uc003ibx.3	O95803	OTTHUMG00000132959	ENST00000296499.5:c.1070-1G>A	chr4.hg19:g.119035960G>A		176.0	0.0		162.0	7.0	NM_004784	B4DI67|Q4W5C1|Q4W5D0|Q6UWC5|Q9UP21	Splice_Site	SNP	ENST00000296499.5	hg19	CCDS3708.1	.	.	.	.	.	.	.	.	.	.	G	19.94	3.920286	0.73098	.	.	ENSG00000164100	ENST00000296499	.	.	.	5.57	5.57	0.84162	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.9278	0.97110	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	NDST3	119255408	1.000000	0.71417	0.997000	0.53966	0.662000	0.39071	9.695000	0.98691	2.770000	0.95276	0.650000	0.86243	.	.	.		0.398	NDST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256517.4	NM_004784	Intron
SEC24D	9871	hgsc.bcm.edu	37	4	119736614	119736614	+	Missense_Mutation	SNP	G	G	T	rs138326987		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:119736614G>T	ENST00000280551.6	-	5	903	c.665C>A	c.(664-666)cCg>cAg	p.P222Q	SEC24D_ENST00000419654.2_5'UTR|SEC24D_ENST00000379735.5_Missense_Mutation_p.P222Q			O94855	SC24D_HUMAN	SEC24 family member D	222	Pro-rich.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|in utero embryonic development (GO:0001701)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)	zinc ion binding (GO:0008270)			breast(3)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(13)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	37						ACCCTGCTGCGGAGGATATCC	0.557																																					p.P222Q		Atlas-SNP	.											SEC24D,NS,carcinoma,0,1	SEC24D	96	.	0			c.C665A						.						73.0	71.0	71.0					4																	119736614		2203	4300	6503	SO:0001583	missense	9871	exon5			TGCTGCGGAGGAT	AB018298	CCDS3710.1	4q26	2013-10-21	2013-10-21		ENSG00000150961	ENSG00000150961			10706	protein-coding gene	gene with protein product		607186	"""SEC24 (S. cerevisiae) related gene family, member D"", ""SEC24 family, member D (S. cerevisiae)"""			9872452, 10075675	Standard	NM_014822		Approved	KIAA0755	uc003ici.4	O94855	OTTHUMG00000132957	ENST00000280551.6:c.665C>A	chr4.hg19:g.119736614G>T	ENSP00000280551:p.Pro222Gln	71.0	0.0		86.0	0.0	NM_014822	Q8IYI7	Missense_Mutation	SNP	ENST00000280551.6	hg19	CCDS3710.1	.	.	.	.	.	.	.	.	.	.	G	9.325	1.059060	0.19987	.	.	ENSG00000150961	ENST00000280551;ENST00000379735	T;T	0.19669	2.13;2.13	5.71	3.99	0.46301	.	0.285018	0.40385	N	0.001109	T	0.17152	0.0412	L	0.37750	1.13	0.80722	D	1	B;B	0.16166	0.016;0.008	B;B	0.17722	0.019;0.007	T	0.03268	-1.1054	10	0.46703	T	0.11	-4.68	10.2628	0.43436	0.1565:0.0:0.8435:0.0	.	222;222	O94855-2;O94855	.;SC24D_HUMAN	Q	222	ENSP00000280551:P222Q;ENSP00000369059:P222Q	ENSP00000280551:P222Q	P	-	2	0	SEC24D	119956062	0.998000	0.40836	0.266000	0.24541	0.145000	0.21501	3.054000	0.49908	0.778000	0.33520	-0.150000	0.13652	CCG	.	G|1.000;A|0.000		0.557	SEC24D-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256514.4		
CCNA2	890	hgsc.bcm.edu	37	4	122742218	122742218	+	Missense_Mutation	SNP	A	A	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:122742218A>C	ENST00000274026.5	-	3	789	c.486T>G	c.(484-486)atT>atG	p.I162M		NM_001237.3	NP_001228	P20248	CCNA2_HUMAN	cyclin A2	162					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic G2 DNA damage checkpoint (GO:0007095)|mitotic nuclear division (GO:0007067)|organ regeneration (GO:0031100)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of transcription, DNA-templated (GO:0045893)|Ras protein signal transduction (GO:0007265)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|response to estradiol (GO:0032355)|response to glucagon (GO:0033762)	cytoplasm (GO:0005737)|female pronucleus (GO:0001939)|male pronucleus (GO:0001940)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)|skin(1)	12						CTTCTAATATAATTGACATGT	0.343																																					p.I162M		Atlas-SNP	.											CCNA2,colon,carcinoma,0,1	CCNA2	30	.	0			c.T486G						.						196.0	187.0	190.0					4																	122742218		2203	4299	6502	SO:0001583	missense	890	exon3			TAATATAATTGAC		CCDS3723.1	4q27	2012-07-12			ENSG00000145386	ENSG00000145386			1578	protein-coding gene	gene with protein product		123835		CCNA, CCN1		1675006	Standard	NM_001237		Approved		uc003iec.4	P20248	OTTHUMG00000133072	ENST00000274026.5:c.486T>G	chr4.hg19:g.122742218A>C	ENSP00000274026:p.Ile162Met	149.0	0.0		156.0	0.0	NM_001237	A8K7B6|Q2M3U6|Q4W5P4|Q6LER8	Missense_Mutation	SNP	ENST00000274026.5	hg19	CCDS3723.1	.	.	.	.	.	.	.	.	.	.	A	13.05	2.121146	0.37436	.	.	ENSG00000145386	ENST00000274026	T	0.15256	2.44	5.86	3.55	0.40652	.	0.665471	0.12795	U	0.438573	T	0.14787	0.0357	L	0.58101	1.795	0.32550	N	0.532438	B	0.12630	0.006	B	0.12156	0.007	T	0.18429	-1.0337	10	0.33940	T	0.23	.	1.6245	0.02720	0.5393:0.1859:0.0894:0.1854	.	162	P20248	CCNA2_HUMAN	M	162	ENSP00000274026:I162M	ENSP00000274026:I162M	I	-	3	3	CCNA2	122961668	0.997000	0.39634	0.569000	0.28460	0.977000	0.68977	1.504000	0.35726	1.038000	0.40049	0.482000	0.46254	ATT	.	.		0.343	CCNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256712.2	NM_001237	
PCDH18	54510	hgsc.bcm.edu	37	4	138452456	138452456	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:138452456T>C	ENST00000344876.4	-	1	1173	c.787A>G	c.(787-789)Act>Gct	p.T263A	PCDH18_ENST00000507846.1_Missense_Mutation_p.T43A|PCDH18_ENST00000511115.1_Intron|PCDH18_ENST00000510305.1_Intron|PCDH18_ENST00000412923.2_Missense_Mutation_p.T263A	NM_019035.3	NP_061908.1	Q9HCL0	PCD18_HUMAN	protocadherin 18	263	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				brain development (GO:0007420)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(27)|lung(21)|ovary(2)|pancreas(4)|prostate(3)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	86	all_hematologic(180;0.24)					AAGAGCAAAGTGCCAACCGGG	0.413																																					p.T263A		Atlas-SNP	.											PCDH18,NS,carcinoma,0,1	PCDH18	229	.	0			c.A787G						.						61.0	64.0	63.0					4																	138452456		2203	4300	6503	SO:0001583	missense	54510	exon1			GCAAAGTGCCAAC	AL137471	CCDS34064.1, CCDS75193.1	4q28.3	2010-01-26			ENSG00000189184	ENSG00000189184		"""Cadherins / Protocadherins : Non-clustered"""	14268	protein-coding gene	gene with protein product		608287				10835267, 11549318	Standard	XM_005263070		Approved	KIAA1562, PCDH68L	uc003ihe.4	Q9HCL0	OTTHUMG00000161348	ENST00000344876.4:c.787A>G	chr4.hg19:g.138452456T>C	ENSP00000355082:p.Thr263Ala	47.0	0.0		40.0	3.0	NM_019035	A8K7K3|B7ZKT1|Q52LS2	Missense_Mutation	SNP	ENST00000344876.4	hg19	CCDS34064.1	.	.	.	.	.	.	.	.	.	.	T	15.50	2.850980	0.51270	.	.	ENSG00000189184	ENST00000344876;ENST00000412923;ENST00000507846	T;T;T	0.57107	0.42;0.42;0.42	5.7	5.7	0.88788	Cadherin (4);Cadherin-like (1);	0.000000	0.42420	U	0.000710	T	0.63792	0.2541	L	0.58969	1.84	0.80722	D	1	P;P;P	0.47762	0.835;0.57;0.9	P;B;P	0.53518	0.728;0.253;0.484	T	0.66889	-0.5809	10	0.72032	D	0.01	.	15.9803	0.80105	0.0:0.0:0.0:1.0	.	43;263;263	D6RIG4;Q9HCL0-2;Q9HCL0	.;.;PCD18_HUMAN	A	263;263;43	ENSP00000355082:T263A;ENSP00000390688:T263A;ENSP00000425903:T43A	ENSP00000355082:T263A	T	-	1	0	PCDH18	138671906	1.000000	0.71417	0.994000	0.49952	0.714000	0.41099	6.143000	0.71756	2.170000	0.68504	0.455000	0.32223	ACT	.	.		0.413	PCDH18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364614.1	NM_019035	
TBC1D9	23158	hgsc.bcm.edu	37	4	141560268	141560268	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:141560268T>C	ENST00000442267.2	-	15	2551	c.2477A>G	c.(2476-2478)gAg>gGg	p.E826G		NM_015130.2	NP_055945.2	Q6ZT07	TBCD9_HUMAN	TBC1 domain family, member 9 (with GRAM domain)	826							calcium ion binding (GO:0005509)|Rab GTPase activator activity (GO:0005097)			endometrium(3)|kidney(2)|large_intestine(3)|lung(18)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	31	all_hematologic(180;0.162)	Medulloblastoma(177;0.00498)				TTCTTCCAGCTCATCAATGGT	0.348																																					p.E826G		Atlas-SNP	.											.	TBC1D9	198	.	0			c.A2477G						.						48.0	43.0	45.0					4																	141560268		1849	4086	5935	SO:0001583	missense	23158	exon15			TCCAGCTCATCAA	AB020689	CCDS47136.1	4q31.1	2013-01-10	2006-07-12		ENSG00000109436	ENSG00000109436		"""EF-hand domain containing"""	21710	protein-coding gene	gene with protein product			"""TBC1 domain family, member 9"""			12970790	Standard	NM_015130		Approved	KIAA0882, MDR1	uc010ioj.3	Q6ZT07	OTTHUMG00000161405	ENST00000442267.2:c.2477A>G	chr4.hg19:g.141560268T>C	ENSP00000411197:p.Glu826Gly	90.0	0.0		91.0	5.0	NM_015130	A6H8U8|D3DNZ1|O94958	Missense_Mutation	SNP	ENST00000442267.2	hg19	CCDS47136.1	.	.	.	.	.	.	.	.	.	.	T	27.6	4.845946	0.91277	.	.	ENSG00000109436	ENST00000442267	T	0.37235	1.21	5.69	5.69	0.88448	EF-hand-like domain (1);	0.000000	0.85682	D	0.000000	T	0.71921	0.3397	H	0.96547	3.84	0.80722	D	1	D	0.71674	0.998	D	0.70487	0.969	T	0.82137	-0.0606	10	0.87932	D	0	-11.2177	15.9538	0.79865	0.0:0.0:0.0:1.0	.	826	Q6ZT07	TBCD9_HUMAN	G	826	ENSP00000411197:E826G	ENSP00000411197:E826G	E	-	2	0	TBC1D9	141779718	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.967000	0.87967	2.163000	0.67991	0.533000	0.62120	GAG	.	.		0.348	TBC1D9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364806.1	NM_015130	
KLKB1	3818	hgsc.bcm.edu	37	4	187172371	187172371	+	Splice_Site	SNP	A	A	T			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:187172371A>T	ENST00000264690.6	+	8	945		c.e8-1		KLKB1_ENST00000513864.1_Splice_Site	NM_000892.3	NP_000883.2	P03952	KLKB1_HUMAN	kallikrein B, plasma (Fletcher factor) 1						blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|Factor XII activation (GO:0002542)|fibrinolysis (GO:0042730)|plasminogen activation (GO:0031639)|positive regulation of fibrinolysis (GO:0051919)|proteolysis (GO:0006508)|zymogen activation (GO:0031638)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(15)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	40		all_cancers(14;1.55e-52)|all_epithelial(14;7.69e-39)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.00664)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.243)		OV - Ovarian serous cystadenocarcinoma(60;1.29e-10)|BRCA - Breast invasive adenocarcinoma(30;3.8e-05)|GBM - Glioblastoma multiforme(59;0.000131)|STAD - Stomach adenocarcinoma(60;0.000292)|LUSC - Lung squamous cell carcinoma(40;0.00241)|READ - Rectum adenocarcinoma(43;0.168)		TAAAAAAAATAGAAATGTTTG	0.348																																					.		Atlas-SNP	.											.	KLKB1	155	.	0			c.759-2A>T						.						40.0	45.0	43.0					4																	187172371		2199	4296	6495	SO:0001630	splice_region_variant	3818	exon8			AAAAATAGAAATG	M13143	CCDS34120.1	4q35	2008-02-05			ENSG00000164344	ENSG00000164344		"""Kallikreins"""	6371	protein-coding gene	gene with protein product		229000		KLK3		9535413, 3521732	Standard	XM_005262987		Approved		uc003iyy.3	P03952	OTTHUMG00000150347	ENST00000264690.6:c.759-1A>T	chr4.hg19:g.187172371A>T		44.0	0.0		62.0	4.0	NM_000892	A6NH96|B2R8H9|Q17RE8|Q17RE9|Q4W5C3	Splice_Site	SNP	ENST00000264690.6	hg19	CCDS34120.1	.	.	.	.	.	.	.	.	.	.	a	11.20	1.569288	0.28003	.	.	ENSG00000164344	ENST00000511608;ENST00000264690;ENST00000513864;ENST00000418715	.	.	.	4.24	4.24	0.50183	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.459	0.67435	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	KLKB1	187409365	1.000000	0.71417	1.000000	0.80357	0.342000	0.28953	6.055000	0.71103	2.157000	0.67596	0.468000	0.43344	.	.	.		0.348	KLKB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317732.1	NM_000892	Intron
C5orf22	55322	hgsc.bcm.edu	37	5	31541441	31541441	+	Silent	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:31541441A>G	ENST00000325366.9	+	6	1051	c.924A>G	c.(922-924)gaA>gaG	p.E308E	C5orf22_ENST00000355907.3_5'UTR	NM_018356.2	NP_060826.2	Q49AR2	CE022_HUMAN	chromosome 5 open reading frame 22	308										kidney(3)|large_intestine(2)|lung(10)|ovary(2)|skin(1)	18						AGGATTTAGAAGCCACTTTCG	0.353																																					p.E308E		Atlas-SNP	.											.	C5orf22	48	.	0			c.A924G						.						118.0	120.0	119.0					5																	31541441		2203	4300	6503	SO:0001819	synonymous_variant	55322	exon6			TTTAGAAGCCACT	AK002055	CCDS3895.1	5p13.3	2012-02-22			ENSG00000082213	ENSG00000082213			25639	protein-coding gene	gene with protein product							Standard	NM_018356		Approved	FLJ11193	uc003jhj.4	Q49AR2	OTTHUMG00000131067	ENST00000325366.9:c.924A>G	chr5.hg19:g.31541441A>G		62.0	0.0		86.0	4.0	NM_018356	Q8ND28|Q8WU61|Q9NUR1	Silent	SNP	ENST00000325366.9	hg19	CCDS3895.1																																																																																			.	.		0.353	C5orf22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253726.2	NM_018356	
LMBRD2	92255	hgsc.bcm.edu	37	5	36108707	36108707	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:36108707T>C	ENST00000296603.4	-	16	2288	c.1826A>G	c.(1825-1827)gAt>gGt	p.D609G		NM_001007527.1	NP_001007528.1	Q68DH5	LMBD2_HUMAN	LMBR1 domain containing 2	609						integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(2)|endometrium(4)|kidney(3)|large_intestine(7)|lung(12)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	all_lung(31;0.000146)		Epithelial(62;0.0396)|Lung(74;0.111)|all cancers(62;0.115)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			CCTAGTGGAATCTTCTCTATT	0.328																																					p.D609G		Atlas-SNP	.											.	LMBRD2	89	.	0			c.A1826G						.						142.0	134.0	136.0					5																	36108707		2203	4300	6503	SO:0001583	missense	92255	exon16			GTGGAATCTTCTC		CCDS34145.1	5p13.2	2008-02-05			ENSG00000164187	ENSG00000164187			25287	protein-coding gene	gene with protein product							Standard	NM_001007527		Approved	DKFZp434H2226	uc003jkb.1	Q68DH5	OTTHUMG00000162150	ENST00000296603.4:c.1826A>G	chr5.hg19:g.36108707T>C	ENSP00000296603:p.Asp609Gly	125.0	0.0		188.0	8.0	NM_001007527	B3KRB6|Q9NTC7	Missense_Mutation	SNP	ENST00000296603.4	hg19	CCDS34145.1	.	.	.	.	.	.	.	.	.	.	T	15.36	2.811551	0.50527	.	.	ENSG00000164187	ENST00000296603;ENST00000546130	.	.	.	5.7	5.7	0.88788	.	0.177935	0.64402	D	0.000015	T	0.46718	0.1407	L	0.35723	1.085	0.46678	D	0.999159	B	0.31383	0.321	B	0.25759	0.063	T	0.39078	-0.9631	9	0.22109	T	0.4	-15.3148	16.2617	0.82550	0.0:0.0:0.0:1.0	.	609	Q68DH5	LMBD2_HUMAN	G	609;503	.	ENSP00000296603:D609G	D	-	2	0	LMBRD2	36144464	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.894000	0.63206	2.302000	0.77476	0.528000	0.53228	GAT	.	.		0.328	LMBRD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367552.1	NM_001007527	
C5orf42	65250	hgsc.bcm.edu	37	5	37115123	37115123	+	Silent	SNP	T	T	C	rs368603190		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:37115123T>C	ENST00000508244.1	-	49	9270	c.9177A>G	c.(9175-9177)aaA>aaG	p.K3059K	C5orf42_ENST00000425232.2_Silent_p.K3059K|C5orf42_ENST00000274258.7_Silent_p.K1957K			Q9H799	CE042_HUMAN	chromosome 5 open reading frame 42	3059						integral component of membrane (GO:0016021)				breast(5)|endometrium(3)|kidney(8)|large_intestine(24)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	79	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)			CTCCACCAGCTTTTTTCTGTA	0.363																																					p.K3059K		Atlas-SNP	.											.	C5orf42	422	.	0			c.A9177G						.	T		2,4404	4.2+/-10.8	0,2,2201	94.0	84.0	88.0		9177	3.6	0.1	5		88	0,8600		0,0,4300	no	coding-synonymous	C5orf42	NM_023073.3		0,2,6501	CC,CT,TT		0.0,0.0454,0.0154		3059/3198	37115123	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	65250	exon50			ACCAGCTTTTTTC		CCDS34146.1, CCDS34146.2	5p13.2	2014-01-28			ENSG00000197603	ENSG00000197603			25801	protein-coding gene	gene with protein product		614571				22264561	Standard	NM_023073		Approved	FLJ13231, JBTS17	uc011cpa.1	Q9H799	OTTHUMG00000160492	ENST00000508244.1:c.9177A>G	chr5.hg19:g.37115123T>C		55.0	0.0		65.0	4.0	NM_023073	A8MUB7|B7ZLV7|Q4G174|Q6DK46|Q8N8L4|Q9H5T1|Q9H8T9	Silent	SNP	ENST00000508244.1	hg19	CCDS34146.2																																																																																			.	.		0.363	C5orf42-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360806.1	NM_023073	
LIFR	3977	hgsc.bcm.edu	37	5	38510584	38510584	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:38510584T>C	ENST00000263409.4	-	7	1135	c.973A>G	c.(973-975)Acc>Gcc	p.T325A	LIFR_ENST00000453190.2_Missense_Mutation_p.T325A|LIFR_ENST00000503088.1_5'UTR	NM_002310.5	NP_002301.1	P42702	LIFR_HUMAN	leukemia inhibitory factor receptor alpha	325					cell surface receptor signaling pathway (GO:0007166)|ciliary neurotrophic factor-mediated signaling pathway (GO:0070120)|cytokine-mediated signaling pathway (GO:0019221)|leukemia inhibitory factor signaling pathway (GO:0048861)|oncostatin-M-mediated signaling pathway (GO:0038165)|positive regulation of cell proliferation (GO:0008284)|response to cytokine (GO:0034097)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	ciliary neurotrophic factor receptor binding (GO:0005127)|growth factor binding (GO:0019838)|leukemia inhibitory factor receptor activity (GO:0004923)			NS(2)|breast(4)|endometrium(6)|kidney(2)|large_intestine(30)|liver(2)|lung(21)|ovary(3)|skin(5)|stomach(1)|urinary_tract(2)	78	all_lung(31;0.00021)					AAAATAACGGTTCCAAATATG	0.348			T	PLAG1	salivary adenoma																																p.T325A	Melanoma(13;4 730 6426 9861 34751)	Atlas-SNP	.		Dom	yes		5	5p13-p12	3977	leukemia inhibitory factor receptor		E	.	LIFR	348	.	0			c.A973G						.						68.0	67.0	67.0					5																	38510584		2203	4300	6503	SO:0001583	missense	3977	exon7			TAACGGTTCCAAA	X61615	CCDS3927.1	5p13-p12	2013-02-11	2006-05-17		ENSG00000113594	ENSG00000113594		"""CD molecules"", ""Fibronectin type III domain containing"""	6597	protein-coding gene	gene with protein product		151443	"""leukemia inhibitory factor receptor"""			1915266	Standard	NM_001127671		Approved	CD118	uc003jli.2	P42702	OTTHUMG00000131138	ENST00000263409.4:c.973A>G	chr5.hg19:g.38510584T>C	ENSP00000263409:p.Thr325Ala	62.0	0.0		114.0	5.0	NM_002310	Q6LCD9	Missense_Mutation	SNP	ENST00000263409.4	hg19	CCDS3927.1	.	.	.	.	.	.	.	.	.	.	T	5.638	0.302460	0.10678	.	.	ENSG00000113594	ENST00000263409;ENST00000453190	T;T	0.61040	0.14;0.14	5.61	3.22	0.36961	Fibronectin, type III (1);	0.518280	0.22053	N	0.065296	T	0.33702	0.0872	L	0.35414	1.06	0.29968	N	0.818779	P	0.39520	0.676	B	0.26517	0.07	T	0.27262	-1.0079	10	0.12430	T	0.62	-8.1867	7.3052	0.26443	0.0:0.1742:0.0:0.8258	.	325	P42702	LIFR_HUMAN	A	325	ENSP00000263409:T325A;ENSP00000398368:T325A	ENSP00000263409:T325A	T	-	1	0	LIFR	38546341	1.000000	0.71417	0.976000	0.42696	0.049000	0.14656	3.009000	0.49552	0.425000	0.26087	-0.256000	0.11100	ACC	.	.		0.348	LIFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253823.1	NM_002310	
NDUFS4	4724	hgsc.bcm.edu	37	5	52899338	52899338	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:52899338T>C	ENST00000296684.5	+	2	183	c.155T>C	c.(154-156)cTc>cCc	p.L52P		NM_002495.2	NP_002486.1	O43181	NDUS4_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 4, 18kDa (NADH-coenzyme Q reductase)	52					brain development (GO:0007420)|cAMP-mediated signaling (GO:0019933)|cellular metabolic process (GO:0044237)|cellular respiration (GO:0045333)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|mitochondrial respiratory chain complex I assembly (GO:0032981)|positive regulation of fibroblast proliferation (GO:0048146)|reactive oxygen species metabolic process (GO:0072593)|regulation of protein phosphorylation (GO:0001932)|respiratory electron transport chain (GO:0022904)|response to cAMP (GO:0051591)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)	p.L52P(1)		central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(1)|ovary(1)|prostate(3)	10		Lung NSC(810;8.27e-05)|Breast(144;0.0848)				GACACACAACTCATAACAGTT	0.403																																					p.L52P		Atlas-SNP	.											NDUFS4,NS,carcinoma,0,1	NDUFS4	17	.	1	Substitution - Missense(1)	kidney(1)	c.T155C						.						126.0	116.0	120.0					5																	52899338		2203	4300	6503	SO:0001583	missense	4724	exon2			CACAACTCATAAC	AF020351	CCDS3960.1	5q11.1	2011-07-04	2002-08-29		ENSG00000164258	ENSG00000164258		"""Mitochondrial respiratory chain complex / Complex I"""	7711	protein-coding gene	gene with protein product	"""complex I 18kDa subunit"""	602694	"""NADH dehydrogenase (ubiquinone) Fe-S protein 4 (18kD) (NADH-coenzyme Q reductase)"""			9463323, 9763677	Standard	NM_002495		Approved	AQDQ, CI-18	uc003jpe.2	O43181	OTTHUMG00000096987	ENST00000296684.5:c.155T>C	chr5.hg19:g.52899338T>C	ENSP00000296684:p.Leu52Pro	49.0	0.0		51.0	3.0	NM_002495	Q9BS69	Missense_Mutation	SNP	ENST00000296684.5	hg19	CCDS3960.1	.	.	.	.	.	.	.	.	.	.	T	19.26	3.793957	0.70452	.	.	ENSG00000164258	ENST00000296684;ENST00000506765	T	0.66099	-0.19	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	T	0.77465	0.4134	M	0.74258	2.255	0.80722	D	1	D	0.76494	0.999	D	0.65233	0.933	T	0.78006	-0.2373	10	0.44086	T	0.13	.	16.1138	0.81283	0.0:0.0:0.0:1.0	.	52	O43181	NDUS4_HUMAN	P	52;48	ENSP00000296684:L52P	ENSP00000296684:L52P	L	+	2	0	NDUFS4	52935095	1.000000	0.71417	0.998000	0.56505	0.841000	0.47740	6.863000	0.75489	2.220000	0.72140	0.533000	0.62120	CTC	.	.		0.403	NDUFS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214062.2	NM_002495	
ELOVL7	79993	hgsc.bcm.edu	37	5	60050627	60050627	+	Nonsense_Mutation	SNP	G	G	A			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:60050627G>A	ENST00000508821.1	-	9	984	c.670C>T	c.(670-672)Cag>Tag	p.Q224*	ELOVL7_ENST00000438340.1_Nonsense_Mutation_p.Q224*|ELOVL7_ENST00000425382.1_Nonsense_Mutation_p.Q224*|ELOVL7_ENST00000505959.1_Nonsense_Mutation_p.Q211*	NM_024930.2	NP_079206.2	A1L3X0	ELOV7_HUMAN	ELOVL fatty acid elongase 7	224					cellular lipid metabolic process (GO:0044255)|fatty acid elongation, polyunsaturated fatty acid (GO:0034626)|fatty acid elongation, saturated fatty acid (GO:0019367)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|very long-chain fatty acid biosynthetic process (GO:0042761)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	transferase activity (GO:0016740)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|skin(1)|urinary_tract(1)	9		Lung NSC(810;2.56e-06)|Prostate(74;0.0115)|Breast(144;0.0244)|Ovarian(174;0.0481)				AAAAAGAACTGGCTTATGTGG	0.353																																					p.Q224X		Atlas-SNP	.											.	ELOVL7	24	.	0			c.C670T						.						97.0	89.0	92.0					5																	60050627		2203	4300	6503	SO:0001587	stop_gained	79993	exon8			AGAACTGGCTTAT	AK027216	CCDS34164.1	5q12	2011-05-25	2011-05-25			ENSG00000164181			26292	protein-coding gene	gene with protein product		614451	"""ELOVL family member 7, elongation of long chain fatty acids (yeast)"""			19826053	Standard	NM_024930		Approved	FLJ23563	uc010iwk.3	A1L3X0		ENST00000508821.1:c.670C>T	chr5.hg19:g.60050627G>A	ENSP00000424123:p.Gln224*	82.0	0.0		111.0	33.0	NM_001104558	Q589T3|Q9H5D0|Q9NT66	Nonsense_Mutation	SNP	ENST00000508821.1	hg19	CCDS34164.1	.	.	.	.	.	.	.	.	.	.	G	40	8.445576	0.98815	.	.	ENSG00000164181	ENST00000508821;ENST00000438340;ENST00000425382;ENST00000505959	.	.	.	5.89	5.89	0.94794	.	0.166857	0.53938	D	0.000041	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.45353	T	0.12	-2.6046	20.2469	0.98398	0.0:0.0:1.0:0.0	.	.	.	.	X	224;224;224;211	.	ENSP00000402634:Q224X	Q	-	1	0	ELOVL7	60086384	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.428000	0.97476	2.781000	0.95711	0.555000	0.69702	CAG	.	.		0.353	ELOVL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368195.1		
PPWD1	23398	hgsc.bcm.edu	37	5	64878960	64878960	+	Silent	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:64878960T>C	ENST00000261308.5	+	8	1518	c.1446T>C	c.(1444-1446)acT>acC	p.T482T	PPWD1_ENST00000538977.1_Silent_p.T326T|PPWD1_ENST00000535264.1_Silent_p.T452T	NM_015342.3	NP_056157.1	Q96BP3	PPWD1_HUMAN	peptidylprolyl isomerase domain and WD repeat containing 1	482					mRNA splicing, via spliceosome (GO:0000398)|protein folding (GO:0006457)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)	19		Lung NSC(167;7.21e-05)|Prostate(74;0.0174)|Ovarian(174;0.186)		Lung(70;0.00451)		TGGCAGCTACTCAAGCTGAAG	0.408																																					p.T482T		Atlas-SNP	.											.	PPWD1	47	.	0			c.T1446C						.						153.0	147.0	149.0					5																	64878960		2203	4300	6503	SO:0001819	synonymous_variant	23398	exon8			AGCTACTCAAGCT	AK025679	CCDS3985.1, CCDS64161.1, CCDS64162.1	5q12.3	2013-01-09			ENSG00000113593	ENSG00000113593		"""WD repeat domain containing"""	28954	protein-coding gene	gene with protein product						7584044	Standard	NM_015342		Approved	KIAA0073	uc003jtv.5	Q96BP3	OTTHUMG00000131226	ENST00000261308.5:c.1446T>C	chr5.hg19:g.64878960T>C		75.0	0.0		122.0	5.0	NM_015342	B4DWR9|Q15002|Q7KZ89	Silent	SNP	ENST00000261308.5	hg19	CCDS3985.1																																																																																			.	.		0.408	PPWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253970.2	NM_015342	
TRAPPC13	80006	hgsc.bcm.edu	37	5	64931772	64931772	+	Splice_Site	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:64931772A>G	ENST00000399438.3	+	3	462	c.117A>G	c.(115-117)ggA>ggG	p.G39G	TRAPPC13_ENST00000231526.4_Splice_Site_p.G39G|TRAPPC13_ENST00000545191.1_Splice_Site_p.G39G|TRAPPC13_ENST00000438419.2_Splice_Site_p.G39G|TRAPPC13_ENST00000505553.1_Splice_Site_p.G39G	NM_001093755.1|NM_024941.3	NP_001087224.1|NP_079217.2	A5PLN9	TPC13_HUMAN	trafficking protein particle complex 13	39																	TTCATTCAGGAGATCTCTTTA	0.328																																					p.G39G		Atlas-SNP	.											.	TRAPPC13	1	.	0			c.A117G						.						72.0	60.0	64.0					5																	64931772		1813	4086	5899	SO:0001630	splice_region_variant	80006	exon3			TTCAGGAGATCTC		CCDS47221.1, CCDS47222.1, CCDS47223.1, CCDS58950.1	5q12.3	2013-01-31	2013-01-24	2013-01-24	ENSG00000113597	ENSG00000113597			25828	protein-coding gene	gene with protein product	"""Trs65-related"""		"""chromosome 5 open reading frame 44"""	C5orf44		12477932	Standard	NM_024941		Approved	FLJ13611, FLJ26957, MGC48585	uc010iwu.1	A5PLN9	OTTHUMG00000163649	ENST00000399438.3:c.116-1A>G	chr5.hg19:g.64931772A>G		76.0	0.0		115.0	5.0	NM_001243737	Q17RZ9|Q49A23|Q4JHG0|Q6MZG4|Q8TCM2|Q9H8I3	Silent	SNP	ENST00000399438.3	hg19	CCDS47222.1																																																																																			.	.		0.328	TRAPPC13-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000370113.1	NM_024941	Silent
ERBB2IP	55914	hgsc.bcm.edu	37	5	65321734	65321734	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:65321734T>C	ENST00000284037.5	+	12	1338	c.949T>C	c.(949-951)Tct>Cct	p.S317P	ERBB2IP_ENST00000380936.1_Missense_Mutation_p.S317P|ERBB2IP_ENST00000380943.2_Missense_Mutation_p.S317P|ERBB2IP_ENST00000506030.1_Missense_Mutation_p.S317P|ERBB2IP_ENST00000511297.1_Missense_Mutation_p.S317P|ERBB2IP_ENST00000416865.2_Missense_Mutation_p.S317P|ERBB2IP_ENST00000380938.2_Missense_Mutation_p.S317P|ERBB2IP_ENST00000508515.1_Missense_Mutation_p.S317P|ERBB2IP_ENST00000380935.1_Missense_Mutation_p.S317P|ERBB2IP_ENST00000380939.2_Missense_Mutation_p.S317P	NM_001253697.1	NP_001240626.1	Q96RT1	LAP2_HUMAN	erbb2 interacting protein	317					basal protein localization (GO:0045175)|cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cell growth (GO:0016049)|epidermal growth factor receptor signaling pathway (GO:0007173)|establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|signal transduction (GO:0007165)	basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|hemidesmosome (GO:0030056)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ErbB-2 class receptor binding (GO:0005176)|integrin binding (GO:0005178)|structural constituent of cytoskeleton (GO:0005200)			breast(2)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(8)|lung(11)|ovary(3)|skin(2)	36		Lung NSC(167;9.45e-06)|Prostate(74;0.0139)|Ovarian(174;0.0547)|Breast(144;0.093)|Colorectal(97;0.234)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0767)|Lung(70;0.00191)		TTTGCCTTCATCTATTGGGCA	0.294																																					p.S317P		Atlas-SNP	.											.	ERBB2IP	120	.	0			c.T949C						.						55.0	54.0	54.0					5																	65321734		2202	4298	6500	SO:0001583	missense	55914	exon12			CCTTCATCTATTG		CCDS3990.1, CCDS34172.1, CCDS58951.1, CCDS58952.1, CCDS58953.1, CCDS58954.1	5p14.3-q12.3	2008-07-18	2001-11-29		ENSG00000112851	ENSG00000112851			15842	protein-coding gene	gene with protein product	"""densin-180-like protein"", ""ERBB2-interacting protein"""	606944	"""erbb2-interacting protein"""			10574462, 10878805	Standard	NM_001253697		Approved	ERBIN, LAP2	uc011cqx.2	Q96RT1	OTTHUMG00000097808	ENST00000284037.5:c.949T>C	chr5.hg19:g.65321734T>C	ENSP00000284037:p.Ser317Pro	155.0	0.0		170.0	7.0	NM_001253701	A0AVR1|B4E3F1|B7ZLV9|E7EQW9|E9PCR8|Q1RMD0|Q86W38|Q9NR18|Q9NW48|Q9ULJ5	Missense_Mutation	SNP	ENST00000284037.5	hg19	CCDS58953.1	.	.	.	.	.	.	.	.	.	.	T	26.4	4.736203	0.89482	.	.	ENSG00000112851	ENST00000284037;ENST00000380943;ENST00000416865;ENST00000380939;ENST00000380936;ENST00000380935;ENST00000380938;ENST00000511297;ENST00000506030;ENST00000508515	T;T;T;T;T;T;T;T;T;T	0.48201	1.04;1.03;2.31;1.03;1.22;0.82;1.1;1.03;1.06;0.82	5.66	5.66	0.87406	.	0.000000	0.85682	D	0.000000	T	0.63224	0.2493	L	0.48877	1.53	0.80722	D	1	D;D;D;D;D;D;D;D	0.76494	0.997;0.997;0.997;0.999;0.999;0.999;0.998;0.999	D;D;D;D;D;D;D;D	0.80764	0.922;0.928;0.929;0.926;0.939;0.994;0.975;0.962	T	0.65755	-0.6091	10	0.87932	D	0	.	16.188	0.81967	0.0:0.0:0.0:1.0	.	317;317;317;317;317;317;317;317	B4DIP2;Q96RT1-4;E9PCR8;B7ZLV9;E7EQW9;Q96RT1;Q96RT1-7;Q96RT1-2	.;.;.;.;.;LAP2_HUMAN;.;.	P	317	ENSP00000284037:S317P;ENSP00000370330:S317P;ENSP00000397833:S317P;ENSP00000370326:S317P;ENSP00000370323:S317P;ENSP00000370322:S317P;ENSP00000370325:S317P;ENSP00000422766:S317P;ENSP00000426632:S317P;ENSP00000422015:S317P	ENSP00000284037:S317P	S	+	1	0	ERBB2IP	65357490	0.995000	0.38212	1.000000	0.80357	0.995000	0.86356	2.230000	0.42999	2.270000	0.75569	0.533000	0.62120	TCT	.	.		0.294	ERBB2IP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000215070.1	NM_018695	
MCCC2	64087	hgsc.bcm.edu	37	5	70936850	70936850	+	Silent	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:70936850T>C	ENST00000340941.6	+	11	1149	c.1020T>C	c.(1018-1020)gaT>gaC	p.D340D	MCCC2_ENST00000323375.8_Silent_p.D302D|MCCC2_ENST00000509358.2_Silent_p.D340D	NM_022132.4	NP_071415.1	Q9HCC0	MCCB_HUMAN	methylcrotonoyl-CoA carboxylase 2 (beta)	340	Carboxyltransferase.				biotin metabolic process (GO:0006768)|branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|coenzyme A metabolic process (GO:0015936)|leucine catabolic process (GO:0006552)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|methylcrotonoyl-CoA carboxylase activity (GO:0004485)			endometrium(2)|kidney(15)|large_intestine(2)|lung(9)|ovary(1)|urinary_tract(1)	30		Lung NSC(167;0.000697)|Prostate(74;0.0107)|Ovarian(174;0.0175)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;2.04e-54)	Biotin(DB00121)	GAATCGTGGATGGAAGCAGAT	0.328																																					p.D340D		Atlas-SNP	.											.	MCCC2	47	.	0			c.T1020C						.						129.0	122.0	125.0					5																	70936850		2203	4300	6503	SO:0001819	synonymous_variant	64087	exon11			CGTGGATGGAAGC	AF310971	CCDS34184.1	5q12-q13	2010-04-30	2010-04-30		ENSG00000131844	ENSG00000131844	6.4.1.4		6937	protein-coding gene	gene with protein product		609014	"""methylcrotonoyl-Coenzyme A carboxylase 2 (beta)"""				Standard	NM_022132		Approved	MCCB	uc003kbs.4	Q9HCC0	OTTHUMG00000162505	ENST00000340941.6:c.1020T>C	chr5.hg19:g.70936850T>C		69.0	0.0		93.0	4.0	NM_022132	A6NIY9|Q96C27|Q9Y4L7	Silent	SNP	ENST00000340941.6	hg19	CCDS34184.1																																																																																			.	.		0.328	MCCC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369243.4		
MAP1B	4131	hgsc.bcm.edu	37	5	71492183	71492183	+	Missense_Mutation	SNP	G	G	A	rs144088322		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:71492183G>A	ENST00000296755.7	+	5	3299	c.3001G>A	c.(3001-3003)Gaa>Aaa	p.E1001K		NM_005909.3	NP_005900.2	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	1001					axon extension (GO:0048675)|cellular process (GO:0009987)|dendrite development (GO:0016358)|establishment of monopolar cell polarity (GO:0061162)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|positive regulation of axon extension (GO:0045773)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|plasma membrane (GO:0005886)|synapse (GO:0045202)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(42)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	104		Lung NSC(167;0.00202)|Ovarian(174;0.0175)|Prostate(461;0.142)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;7.99e-54)		TGACCGAGCCGAAGAAGACAT	0.542																																					p.E1001K	Melanoma(17;367 822 11631 31730 47712)	Atlas-SNP	.											MAP1B,colon,carcinoma,0,1	MAP1B	243	.	0			c.G3001A						.	G	LYS/GLU	1,4405	2.1+/-5.4	0,1,2202	92.0	91.0	91.0		3001	6.1	1.0	5	dbSNP_134	91	0,8600		0,0,4300	no	missense	MAP1B	NM_005909.3	56	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	1001/2469	71492183	1,13005	2203	4300	6503	SO:0001583	missense	4131	exon5			CGAGCCGAAGAAG	L06237	CCDS4012.1	5q13	2014-06-12			ENSG00000131711	ENSG00000131711			6836	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 102"""	157129				1881920	Standard	NM_005909		Approved	MAP5, PPP1R102	uc003kbw.4	P46821	OTTHUMG00000100952	ENST00000296755.7:c.3001G>A	chr5.hg19:g.71492183G>A	ENSP00000296755:p.Glu1001Lys	128.0	0.0		127.0	43.0	NM_005909	A2BDK5	Missense_Mutation	SNP	ENST00000296755.7	hg19	CCDS4012.1	.	.	.	.	.	.	.	.	.	.	G	19.68	3.872172	0.72180	2.27E-4	0.0	ENSG00000131711	ENST00000296755	T	0.03801	3.8	6.08	6.08	0.98989	.	0.000000	0.64402	D	0.000004	T	0.08935	0.0221	N	0.08118	0	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.80764	0.994;0.994	T	0.54556	-0.8276	10	0.10111	T	0.7	-23.6485	20.2738	0.98482	0.0:0.0:1.0:0.0	.	875;1001	A2BDK6;P46821	.;MAP1B_HUMAN	K	1001	ENSP00000296755:E1001K	ENSP00000296755:E1001K	E	+	1	0	MAP1B	71527939	1.000000	0.71417	0.957000	0.39632	0.861000	0.49209	5.156000	0.64905	2.894000	0.99253	0.655000	0.94253	GAA	.	G|1.000;A|0.000		0.542	MAP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218561.6	NM_005909	
MRPS27	23107	hgsc.bcm.edu	37	5	71519665	71519665	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:71519665C>T	ENST00000261413.5	-	10	889	c.850G>A	c.(850-852)Ggt>Agt	p.G284S	MRPS27_ENST00000513900.1_Missense_Mutation_p.G298S|MRPS27_ENST00000457646.4_Missense_Mutation_p.G228S|MRPS27_ENST00000522562.1_5'UTR	NM_015084.2	NP_055899.2	Q92552	RT27_HUMAN	mitochondrial ribosomal protein S27	284			G -> D (polymorphism confirmed at protein level; dbSNP:rs3209157). {ECO:0000269|PubMed:17488105, ECO:0000269|PubMed:9039502}.			mitochondrion (GO:0005739)|ribosome (GO:0005840)				breast(1)|endometrium(1)|large_intestine(2)|lung(2)	6		Lung NSC(167;0.00237)|Ovarian(174;0.0175)|Prostate(461;0.141)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;1.46e-53)		AGCACTGCACCCAGCACATCG	0.502																																					p.G284S		Atlas-SNP	.											MRPS27,NS,neuroblastoma,0,1	MRPS27	23	.	0			c.G850A						.						63.0	62.0	62.0					5																	71519665		2203	4300	6503	SO:0001583	missense	23107	exon10			CTGCACCCAGCAC	D87453	CCDS4013.1, CCDS68890.1, CCDS75257.1	5q13.2	2012-09-13			ENSG00000113048	ENSG00000113048		"""Mitochondrial ribosomal proteins / small subunits"""	14512	protein-coding gene	gene with protein product		611989					Standard	NM_015084		Approved	KIAA0264	uc003kbz.4	Q92552	OTTHUMG00000100951	ENST00000261413.5:c.850G>A	chr5.hg19:g.71519665C>T	ENSP00000261413:p.Gly284Ser	93.0	0.0		103.0	0.0	NM_015084	B4DRT2|Q6P1S1	Missense_Mutation	SNP	ENST00000261413.5	hg19	CCDS4013.1	.	.	.	.	.	.	.	.	.	.	C	11.67	1.708945	0.30322	.	.	ENSG00000113048	ENST00000261413;ENST00000457646;ENST00000513900;ENST00000508863	T;T;T;T	0.40476	1.03;1.03;1.03;1.03	6.16	5.3	0.74995	.	0.384491	0.32785	N	0.005656	T	0.27559	0.0677	N	0.14661	0.345	0.80722	D	1	B;B;B	0.20671	0.047;0.0;0.047	B;B;B	0.19148	0.024;0.0;0.024	T	0.05321	-1.0892	10	0.30078	T	0.28	-7.2913	13.9186	0.63916	0.0:0.9303:0.0:0.0697	.	298;65;284	B4DRT2;E7ETN4;Q92552	.;.;RT27_HUMAN	S	284;228;298;228	ENSP00000261413:G284S;ENSP00000428120:G228S;ENSP00000426941:G298S;ENSP00000426176:G228S	ENSP00000261413:G284S	G	-	1	0	MRPS27	71555421	0.999000	0.42202	0.931000	0.37212	0.004000	0.04260	3.247000	0.51422	1.628000	0.50416	-0.145000	0.13849	GGT	.	.		0.502	MRPS27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218560.2	NM_015084	
BHMT2	23743	hgsc.bcm.edu	37	5	78375194	78375194	+	Missense_Mutation	SNP	C	C	T	rs141648685		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:78375194C>T	ENST00000255192.3	+	3	235	c.169C>T	c.(169-171)Cgt>Tgt	p.R57C	BHMT2_ENST00000521567.1_Missense_Mutation_p.R57C|DMGDH_ENST00000520388.1_Intron	NM_017614.4	NP_060084.2	Q9H2M3	BHMT2_HUMAN	betaine--homocysteine S-methyltransferase 2	57	Hcy-binding. {ECO:0000255|PROSITE- ProRule:PRU00333}.				L-methionine salvage (GO:0071267)|S-adenosylmethionine metabolic process (GO:0046500)|S-methylmethionine metabolic process (GO:0033477)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	S-adenosylmethionine-homocysteine S-methyltransferase activity (GO:0008898)|S-methylmethionine-homocysteine S-methyltransferase activity (GO:0061627)|zinc ion binding (GO:0008270)	p.R57C(1)		endometrium(2)|large_intestine(8)|lung(2)|ovary(1)|skin(1)|urinary_tract(1)	15		all_lung(232;0.00063)|Lung NSC(167;0.00171)|Ovarian(174;0.0261)|Prostate(461;0.191)		OV - Ovarian serous cystadenocarcinoma(54;2.09e-45)|Epithelial(54;9.3e-41)|all cancers(79;4.09e-36)	L-Methionine(DB00134)	CTTTGTAGTTCGTCAACTTCA	0.368													C|||	1	0.000199681	0.0008	0.0	5008	,	,		18926	0.0		0.0	False		,,,				2504	0.0				p.R57C		Atlas-SNP	.											BHMT2,NS,carcinoma,0,2	BHMT2	44	.	1	Substitution - Missense(1)	large_intestine(1)	c.C169T						.	C	CYS/ARG,CYS/ARG	2,4404	4.2+/-10.8	0,2,2201	82.0	77.0	79.0		169,169	2.9	1.0	5	dbSNP_134	79	0,8600		0,0,4300	no	missense,missense	BHMT2	NM_001178005.1,NM_017614.4	180,180	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	probably-damaging,probably-damaging	57/300,57/364	78375194	2,13004	2203	4300	6503	SO:0001583	missense	23743	exon3			GTAGTTCGTCAAC		CCDS4045.1, CCDS54871.1	5q13	2010-04-28	2010-04-28		ENSG00000132840	ENSG00000132840	2.1.1.5		1048	protein-coding gene	gene with protein product		605932				11087663, 18230605	Standard	NM_017614		Approved		uc003kft.3	Q9H2M3	OTTHUMG00000108158	ENST00000255192.3:c.169C>T	chr5.hg19:g.78375194C>T	ENSP00000255192:p.Arg57Cys	51.0	0.0		49.0	2.0	NM_017614	B7Z516|Q9NXX7	Missense_Mutation	SNP	ENST00000255192.3	hg19	CCDS4045.1	.	.	.	.	.	.	.	.	.	.	C	19.39	3.818425	0.71028	4.54E-4	0.0	ENSG00000132840	ENST00000255192;ENST00000521567	T;T	0.14022	2.54;2.54	5.72	2.9	0.33743	Homocysteine S-methyltransferase (4);	0.181464	0.47852	D	0.000204	T	0.37517	0.1006	M	0.85710	2.77	0.34390	D	0.694072	B;D	0.89917	0.047;1.0	B;D	0.71184	0.012;0.972	T	0.56141	-0.8028	10	0.52906	T	0.07	-0.4777	11.419	0.49969	0.0:0.7013:0.2339:0.0648	.	57;57	B7Z516;Q9H2M3	.;BHMT2_HUMAN	C	57	ENSP00000255192:R57C;ENSP00000430278:R57C	ENSP00000255192:R57C	R	+	1	0	BHMT2	78410950	0.998000	0.40836	0.954000	0.39281	0.992000	0.81027	1.973000	0.40550	0.737000	0.32582	0.655000	0.94253	CGT	.	C|1.000;T|0.000		0.368	BHMT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226962.2	NM_017614	
VCAN	1462	hgsc.bcm.edu	37	5	82833962	82833962	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:82833962T>C	ENST00000265077.3	+	8	5705	c.5140T>C	c.(5140-5142)Tgg>Cgg	p.W1714R	VCAN_ENST00000502527.2_Intron|VCAN_ENST00000342785.4_Intron|VCAN_ENST00000513016.1_3'UTR|VCAN_ENST00000343200.5_Missense_Mutation_p.W727R|VCAN-AS1_ENST00000512090.1_RNA|VCAN_ENST00000512590.2_Intron	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	1714	GAG-beta.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)			NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)	Hyaluronan(DB08818)	CACTTCTGAGTGGATTTCCAG	0.428																																					p.W1714R		Atlas-SNP	.											.	VCAN	498	.	0			c.T5140C						.						85.0	86.0	86.0					5																	82833962		2203	4299	6502	SO:0001583	missense	1462	exon8			TCTGAGTGGATTT	X15998	CCDS4060.1, CCDS47242.1, CCDS54875.1, CCDS54876.1	5q14.2-q14.3	2013-05-07	2007-02-15	2007-02-15	ENSG00000038427	ENSG00000038427		"""Immunoglobulin superfamily / V-set domain containing"", ""Proteoglycans / Extracellular Matrix : Hyalectans"""	2464	protein-coding gene	gene with protein product	"""versican proteoglycan"""	118661	"""chondroitin sulfate proteoglycan 2"""	CSPG2		1478664, 21063030	Standard	NM_004385		Approved	PG-M	uc003kii.3	P13611	OTTHUMG00000131321	ENST00000265077.3:c.5140T>C	chr5.hg19:g.82833962T>C	ENSP00000265077:p.Trp1714Arg	77.0	0.0		89.0	30.0	NM_004385	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Missense_Mutation	SNP	ENST00000265077.3	hg19	CCDS4060.1	.	.	.	.	.	.	.	.	.	.	T	11.53	1.665094	0.29604	.	.	ENSG00000038427	ENST00000265077;ENST00000343200;ENST00000513960	D;D;T	0.84660	-1.86;-1.88;3.26	5.96	2.37	0.29283	.	0.511459	0.18635	N	0.135473	T	0.77631	0.4159	M	0.62723	1.935	0.09310	N	1	P;P	0.46457	0.878;0.806	B;B	0.40285	0.325;0.269	T	0.64943	-0.6288	10	0.12766	T	0.61	.	5.2198	0.15362	0.0:0.1645:0.3648:0.4707	.	727;1714	P13611-2;P13611	.;CSPG2_HUMAN	R	1714;727;727	ENSP00000265077:W1714R;ENSP00000340062:W727R;ENSP00000426251:W727R	ENSP00000265077:W1714R	W	+	1	0	VCAN	82869718	0.023000	0.18921	0.503000	0.27626	0.054000	0.15201	0.285000	0.18883	0.512000	0.28257	0.533000	0.62120	TGG	.	.		0.428	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385	
VCAN	1462	hgsc.bcm.edu	37	5	82836233	82836233	+	Missense_Mutation	SNP	G	G	T	rs370712172		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:82836233G>T	ENST00000265077.3	+	8	7976	c.7411G>T	c.(7411-7413)Gtg>Ttg	p.V2471L	VCAN_ENST00000502527.2_Intron|VCAN-AS1_ENST00000513899.1_RNA|VCAN_ENST00000342785.4_Intron|VCAN_ENST00000513016.1_3'UTR|VCAN_ENST00000343200.5_Missense_Mutation_p.V1484L|VCAN-AS1_ENST00000512090.1_RNA|VCAN_ENST00000512590.2_Intron	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	2471	GAG-beta.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)			NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)	Hyaluronan(DB08818)	ACATCCTGAGGTGCCAAGCGC	0.458																																					p.V2471L		Atlas-SNP	.											.	VCAN	498	.	0			c.G7411T						.						94.0	91.0	92.0					5																	82836233		2203	4300	6503	SO:0001583	missense	1462	exon8			CCTGAGGTGCCAA	X15998	CCDS4060.1, CCDS47242.1, CCDS54875.1, CCDS54876.1	5q14.2-q14.3	2013-05-07	2007-02-15	2007-02-15	ENSG00000038427	ENSG00000038427		"""Immunoglobulin superfamily / V-set domain containing"", ""Proteoglycans / Extracellular Matrix : Hyalectans"""	2464	protein-coding gene	gene with protein product	"""versican proteoglycan"""	118661	"""chondroitin sulfate proteoglycan 2"""	CSPG2		1478664, 21063030	Standard	NM_004385		Approved	PG-M	uc003kii.3	P13611	OTTHUMG00000131321	ENST00000265077.3:c.7411G>T	chr5.hg19:g.82836233G>T	ENSP00000265077:p.Val2471Leu	116.0	0.0		187.0	54.0	NM_004385	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Missense_Mutation	SNP	ENST00000265077.3	hg19	CCDS4060.1	.	.	.	.	.	.	.	.	.	.	G	8.393	0.840202	0.16891	.	.	ENSG00000038427	ENST00000265077;ENST00000343200	T;T	0.40476	1.03;1.03	5.97	1.77	0.24775	.	0.697942	0.12964	N	0.424758	T	0.35770	0.0943	M	0.64997	1.995	0.09310	N	1	B;B	0.17667	0.023;0.013	B;B	0.16722	0.016;0.007	T	0.24657	-1.0154	10	0.25106	T	0.35	.	6.7271	0.23363	0.1472:0.0:0.5844:0.2684	.	1484;2471	P13611-2;P13611	.;CSPG2_HUMAN	L	2471;1484	ENSP00000265077:V2471L;ENSP00000340062:V1484L	ENSP00000265077:V2471L	V	+	1	0	VCAN	82871989	0.000000	0.05858	0.001000	0.08648	0.128000	0.20619	0.194000	0.17135	0.819000	0.34492	0.655000	0.94253	GTG	.	.		0.458	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385	
GPR98	84059	hgsc.bcm.edu	37	5	90149916	90149916	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:90149916T>C	ENST00000405460.2	+	81	17588	c.17492T>C	c.(17491-17493)cTc>cCc	p.L5831P	GPR98_ENST00000425867.2_Missense_Mutation_p.L1492P	NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	5831					detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		AGTTCACAACTCCTGACTAAT	0.383																																					p.L5831P		Atlas-SNP	.											.	GPR98	605	.	0			c.T17492C						.						131.0	105.0	113.0					5																	90149916		1853	4090	5943	SO:0001583	missense	84059	exon81			CACAACTCCTGAC	AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"""-"", ""GPCR / Class B : Orphans"""	17416	protein-coding gene	gene with protein product		602851	"""monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"""	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.17492T>C	chr5.hg19:g.90149916T>C	ENSP00000384582:p.Leu5831Pro	68.0	0.0		70.0	4.0	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	hg19	CCDS47246.1	.	.	.	.	.	.	.	.	.	.	T	1.975	-0.435647	0.04669	.	.	ENSG00000164199	ENST00000405460;ENST00000296619;ENST00000425867	T;T	0.28069	1.69;1.63	5.3	-0.133	0.13485	.	0.279181	0.41097	N	0.000950	T	0.04407	0.0121	N	0.00104	-2.125	0.19300	N	0.99998	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.38394	-0.9663	9	.	.	.	.	3.7169	0.08441	0.1162:0.5088:0.1151:0.2599	.	1492;5831;1492	E7EML1;Q8WXG9;Q8WXG9-2	.;GPR98_HUMAN;.	P	5831;5831;1492	ENSP00000384582:L5831P;ENSP00000392618:L1492P	.	L	+	2	0	GPR98	90185672	0.006000	0.16342	0.255000	0.24374	0.258000	0.26162	1.228000	0.32588	-0.262000	0.09392	-0.624000	0.04008	CTC	.	.		0.383	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119	
PPIP5K2	23262	hgsc.bcm.edu	37	5	102472511	102472511	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:102472511A>G	ENST00000358359.3	+	4	895	c.386A>G	c.(385-387)tAt>tGt	p.Y129C	PPIP5K2_ENST00000513500.1_3'UTR|PPIP5K2_ENST00000321521.9_Missense_Mutation_p.Y129C|PPIP5K2_ENST00000414217.1_Missense_Mutation_p.Y129C	NM_001276277.1	NP_001263206.1	O43314	VIP2_HUMAN	diphosphoinositol pentakisphosphate kinase 2	129					inositol metabolic process (GO:0006020)|inositol phosphate metabolic process (GO:0043647)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	acid phosphatase activity (GO:0003993)|ATP binding (GO:0005524)|diphosphoinositol-pentakisphosphate kinase activity (GO:0033857)|inositol hexakisphosphate 1-kinase activity (GO:0052723)|inositol hexakisphosphate 3-kinase activity (GO:0052724)|inositol hexakisphosphate 5-kinase activity (GO:0000832)|inositol-1,3,4,5,6-pentakisphosphate kinase activity (GO:0000827)	p.Y129C(1)		NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(20)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	42						AATATGCAGTATCTCATACAA	0.363																																					p.Y129C		Atlas-SNP	.											PPIP5K2,NS,carcinoma,0,1	PPIP5K2	98	.	1	Substitution - Missense(1)	lung(1)	c.A386G						.						166.0	178.0	174.0					5																	102472511		2203	4299	6502	SO:0001583	missense	23262	exon3			TGCAGTATCTCAT	AB007893	CCDS34207.1, CCDS64212.1, CCDS75283.1	5q21.1	2014-05-06	2010-01-26	2010-01-26	ENSG00000145725	ENSG00000145725	2.7.4.24		29035	protein-coding gene	gene with protein product		611648	"""histidine acid phosphatase domain containing 1"""	HISPPD1		9455477, 17690096, 18981179	Standard	NM_001276277		Approved	KIAA0433, VIP2	uc003koe.4	O43314	OTTHUMG00000181461	ENST00000358359.3:c.386A>G	chr5.hg19:g.102472511A>G	ENSP00000351126:p.Tyr129Cys	57.0	0.0		69.0	3.0	NM_015216	A1NI53|A6NGS8|Q8TB50	Missense_Mutation	SNP	ENST00000358359.3	hg19		.	.	.	.	.	.	.	.	.	.	A	19.77	3.889958	0.72524	.	.	ENSG00000145725	ENST00000321521;ENST00000507921;ENST00000358359;ENST00000451606;ENST00000414217;ENST00000507310	T;T;T;T	0.14893	2.47;3.11;2.47;2.47	5.28	5.28	0.74379	.	0.000000	0.64402	D	0.000008	T	0.46600	0.1401	M	0.88570	2.965	0.80722	D	1	D;D;D	0.76494	0.994;0.999;0.999	P;P;P	0.62885	0.792;0.902;0.908	T	0.57341	-0.7828	10	0.87932	D	0	-17.488	15.4885	0.75587	1.0:0.0:0.0:0.0	.	51;129;129	D6RBU4;O43314-2;O43314	.;.;VIP2_HUMAN	C	129;51;129;129;129;59	ENSP00000313070:Y129C;ENSP00000422525:Y51C;ENSP00000351126:Y129C;ENSP00000416016:Y129C	ENSP00000313070:Y129C	Y	+	2	0	PPIP5K2	102500410	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.910000	0.92685	2.117000	0.64856	0.383000	0.25322	TAT	.	.		0.363	PPIP5K2-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000370487.1	NM_015216	
NR3C1	2908	hgsc.bcm.edu	37	5	142680214	142680214	+	Missense_Mutation	SNP	A	A	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:142680214A>C	ENST00000343796.2	-	5	2576	c.1583T>G	c.(1582-1584)cTc>cGc	p.L528R	NR3C1_ENST00000394464.2_Missense_Mutation_p.L528R|NR3C1_ENST00000394466.2_Missense_Mutation_p.L529R|NR3C1_ENST00000424646.2_Missense_Mutation_p.L502R|NR3C1_ENST00000416954.2_Missense_Mutation_p.L131R|NR3C1_ENST00000415690.2_Missense_Mutation_p.L528R|NR3C1_ENST00000504336.1_5'UTR|NR3C1_ENST00000503201.1_Missense_Mutation_p.L528R|NR3C1_ENST00000504572.1_Missense_Mutation_p.L529R|NR3C1_ENST00000231509.3_Missense_Mutation_p.L529R	NM_001018074.1|NM_001018075.1|NM_001018077.1	NP_001018084.1|NP_001018085.1|NP_001018087.1	P04150	GCR_HUMAN	nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor)	528	Interaction with CLOCK.|Steroid-binding.				adrenal gland development (GO:0030325)|chromatin modification (GO:0016568)|gene expression (GO:0010467)|glucocorticoid metabolic process (GO:0008211)|mammary gland duct morphogenesis (GO:0060603)|negative regulation of glucocorticoid mediated signaling pathway (GO:1900170)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of glucocorticoid biosynthetic process (GO:0031946)|regulation of gluconeogenesis (GO:0006111)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrial matrix (GO:0005759)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	glucocorticoid receptor activity (GO:0004883)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid binding (GO:0005496)|zinc ion binding (GO:0008270)			breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(10)|lung(7)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	35		Acute lymphoblastic leukemia(2;3.2e-05)|all_hematologic(2;0.000361)	KIRC - Kidney renal clear cell carcinoma(527;0.00111)|Kidney(363;0.00176)		Alclometasone(DB00240)|Amcinonide(DB00288)|Beclomethasone(DB00394)|Betamethasone(DB00443)|Budesonide(DB01222)|Ciclesonide(DB01410)|Clobetasol propionate(DB01013)|Clocortolone(DB00838)|Cortisone acetate(DB01380)|Desonide(DB01260)|Desoximetasone(DB00547)|Dexamethasone(DB01234)|Diflorasone(DB00223)|Difluprednate(DB06781)|Fludrocortisone(DB00687)|Flumethasone Pivalate(DB00663)|Flunisolide(DB00180)|Fluocinolone Acetonide(DB00591)|Fluocinonide(DB01047)|Fluorometholone(DB00324)|Fluoxymesterone(DB01185)|Flurandrenolide(DB00846)|Fluticasone furoate(DB08906)|Fluticasone Propionate(DB00588)|Halobetasol Propionate(DB00596)|Hydrocortamate(DB00769)|Hydrocortisone(DB00741)|Loteprednol(DB00873)|Medrysone(DB00253)|Megestrol acetate(DB00351)|Methylprednisolone(DB00959)|Mifepristone(DB00834)|Mometasone(DB00764)|Paramethasone(DB01384)|Prednicarbate(DB01130)|Prednisolone(DB00860)|Prednisone(DB00635)|Rimexolone(DB00896)|Spironolactone(DB00421)|Triamcinolone(DB00620)	GGTAGGGGTGAGTTGTGGTAA	0.423																																					p.L529R		Atlas-SNP	.											.	NR3C1	124	.	0			c.T1586G						.						217.0	197.0	204.0					5																	142680214		2203	4300	6503	SO:0001583	missense	2908	exon5			GGGGTGAGTTGTG	X03225	CCDS4278.1, CCDS34258.1, CCDS47298.1	5q31-q32	2013-01-16	2002-08-27		ENSG00000113580	ENSG00000113580		"""Nuclear hormone receptors"""	7978	protein-coding gene	gene with protein product		138040	"""nuclear receptor subfamily 3, group C, member 1"""	GRL		2867473	Standard	NM_001204258		Approved	GR	uc003lnb.3	P04150	OTTHUMG00000129677	ENST00000343796.2:c.1583T>G	chr5.hg19:g.142680214A>C	ENSP00000343205:p.Leu528Arg	234.0	0.0		251.0	76.0	NM_001024094	A0ZXF9|B0LPG8|D3DQF4|P04151|Q53EP5|Q6N0A4	Missense_Mutation	SNP	ENST00000343796.2	hg19	CCDS4278.1	.	.	.	.	.	.	.	.	.	.	A	26.6	4.751525	0.89753	.	.	ENSG00000113580	ENST00000394464;ENST00000343796;ENST00000415690;ENST00000424646;ENST00000504572;ENST00000394466;ENST00000231509;ENST00000416954;ENST00000503201	D;D;D;D;D;D;D;D;D	0.87491	-1.91;-1.91;-1.87;-1.88;-1.91;-1.91;-1.91;-2.26;-1.91	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	D	0.94830	0.8330	M	0.91561	3.22	0.80722	D	1	D;D;D	0.89917	1.0;0.987;0.997	D;P;D	0.85130	0.997;0.836;0.995	D	0.95753	0.8793	10	0.72032	D	0.01	.	15.94	0.79747	1.0:0.0:0.0:0.0	.	528;528;529	E5KQF5;P04150;E5KQF6	.;GCR_HUMAN;.	R	528;528;528;502;529;529;529;131;528	ENSP00000377977:L528R;ENSP00000343205:L528R;ENSP00000387672:L528R;ENSP00000405282:L502R;ENSP00000422518:L529R;ENSP00000377979:L529R;ENSP00000231509:L529R;ENSP00000404218:L131R;ENSP00000427672:L528R	ENSP00000231509:L529R	L	-	2	0	NR3C1	142660407	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	6.979000	0.76154	2.156000	0.67533	0.533000	0.62120	CTC	.	.		0.423	NR3C1-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000370829.1		
PPARGC1B	133522	hgsc.bcm.edu	37	5	149219630	149219630	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:149219630A>G	ENST00000309241.5	+	9	2677	c.2645A>G	c.(2644-2646)gAc>gGc	p.D882G	PPARGC1B_ENST00000403750.1_Missense_Mutation_p.D818G|PPARGC1B_ENST00000394320.3_Missense_Mutation_p.D882G|PPARGC1B_ENST00000360453.4_Missense_Mutation_p.D843G	NM_133263.3	NP_573570.3	Q86YN6	PRGC2_HUMAN	peroxisome proliferator-activated receptor gamma, coactivator 1 beta	882					actin filament organization (GO:0007015)|bone trabecula formation (GO:0060346)|cellular lipid metabolic process (GO:0044255)|cellular response to reactive oxygen species (GO:0034614)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription, DNA-templated (GO:0045892)|ossification (GO:0001503)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of bone resorption (GO:0045780)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of phosphorylation (GO:0042327)|positive regulation of receptor activity (GO:2000273)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to cAMP (GO:0051591)|response to glucocorticoid (GO:0051384)|small molecule metabolic process (GO:0044281)|transcription from mitochondrial promoter (GO:0006390)|transcription from RNA polymerase II promoter (GO:0006366)	mediator complex (GO:0016592)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	AF-2 domain binding (GO:0050682)|estrogen receptor binding (GO:0030331)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nucleotide binding (GO:0000166)|receptor activator activity (GO:0030546)|RNA binding (GO:0003723)|RNA polymerase II transcription cofactor activity (GO:0001104)			NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(1)|liver(2)|lung(15)|ovary(3)|prostate(2)|stomach(1)	30			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)			CCGTGTTCAGACAGAACGCCA	0.597																																					p.D882G		Atlas-SNP	.											.	PPARGC1B	74	.	0			c.A2645G						.						74.0	66.0	69.0					5																	149219630		2203	4300	6503	SO:0001583	missense	133522	exon9			GTTCAGACAGAAC	AF468496	CCDS4298.1, CCDS54933.1, CCDS54934.1	5q33.1	2013-02-12	2006-10-17		ENSG00000155846	ENSG00000155846		"""RNA binding motif (RRM) containing"""	30022	protein-coding gene	gene with protein product		608886	"""peroxisome proliferative activated receptor, gamma, coactivator 1, beta"""			11793024, 11854298	Standard	NM_133263		Approved	PERC, PGC1B	uc003lrc.3	Q86YN6	OTTHUMG00000130055	ENST00000309241.5:c.2645A>G	chr5.hg19:g.149219630A>G	ENSP00000312649:p.Asp882Gly	101.0	0.0		120.0	5.0	NM_133263	A2RUM8|A2RUN0|B3KVW0|Q86YN3|Q86YN4|Q86YN5|Q8N1N9|Q8TDE4|Q8TDE5	Missense_Mutation	SNP	ENST00000309241.5	hg19	CCDS4298.1	.	.	.	.	.	.	.	.	.	.	A	9.700	1.154333	0.21371	.	.	ENSG00000155846	ENST00000360453;ENST00000394320;ENST00000309241;ENST00000403750	T;T;T;T	0.41065	1.01;1.01;1.01;1.01	5.05	3.88	0.44766	.	0.508876	0.21102	N	0.080145	T	0.37758	0.1015	N	0.21448	0.665	0.19300	N	0.999977	B;P;B;B;B	0.50943	0.007;0.94;0.003;0.004;0.027	B;P;B;B;B	0.54629	0.009;0.757;0.023;0.006;0.019	T	0.10314	-1.0635	10	0.30078	T	0.28	-9.2187	7.2627	0.26212	0.7389:0.0:0.2611:0.0	.	861;861;843;882;882	Q86YN6-2;Q86YN6-4;Q86YN6-5;Q86YN6;Q86YN6-3	.;.;.;PRGC2_HUMAN;.	G	843;882;882;818	ENSP00000353638:D843G;ENSP00000377855:D882G;ENSP00000312649:D882G;ENSP00000384403:D818G	ENSP00000312649:D882G	D	+	2	0	PPARGC1B	149199823	0.966000	0.33281	0.989000	0.46669	0.989000	0.77384	2.090000	0.41682	0.774000	0.33427	0.379000	0.24179	GAC	.	.		0.597	PPARGC1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252334.1	NM_133263	
PDE6A	5145	hgsc.bcm.edu	37	5	149276290	149276290	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:149276290T>C	ENST00000255266.5	-	11	1576	c.1457A>G	c.(1456-1458)gAg>gGg	p.E486G		NM_000440.2	NP_000431.2	P16499	PDE6A_HUMAN	phosphodiesterase 6A, cGMP-specific, rod, alpha	486					cytosolic calcium ion homeostasis (GO:0051480)|GMP metabolic process (GO:0046037)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina development in camera-type eye (GO:0060041)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	photoreceptor disc membrane (GO:0097381)|plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(13)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)	44			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)		Caffeine(DB00201)	CTCAGCCAGCTCCTCTTCCTC	0.532																																					p.E486G		Atlas-SNP	.											.	PDE6A	98	.	0			c.A1457G						.						165.0	158.0	160.0					5																	149276290		2203	4300	6503	SO:0001583	missense	5145	exon11			GCCAGCTCCTCTT		CCDS4299.1	5q31.2-q34	2013-02-14			ENSG00000132915	ENSG00000132915	3.1.4.17	"""Phosphodiesterases"""	8785	protein-coding gene	gene with protein product		180071		PDEA		2155175	Standard	NM_000440		Approved	RP43	uc003lrg.4	P16499	OTTHUMG00000130047	ENST00000255266.5:c.1457A>G	chr5.hg19:g.149276290T>C	ENSP00000255266:p.Glu486Gly	125.0	0.0		101.0	7.0	NM_000440	Q0P638	Missense_Mutation	SNP	ENST00000255266.5	hg19	CCDS4299.1	.	.	.	.	.	.	.	.	.	.	T	21.0	4.078394	0.76528	.	.	ENSG00000132915	ENST00000255266	T	0.65178	-0.14	5.9	5.9	0.94986	.	0.162346	0.52532	D	0.000067	T	0.71213	0.3313	M	0.85373	2.75	0.53688	D	0.999975	P	0.35226	0.491	B	0.40825	0.341	T	0.75288	-0.3370	10	0.72032	D	0.01	.	14.2745	0.66170	0.0:0.0:0.0:1.0	.	486	P16499	PDE6A_HUMAN	G	486	ENSP00000255266:E486G	ENSP00000255266:E486G	E	-	2	0	PDE6A	149256483	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.556000	0.67307	2.263000	0.75096	0.533000	0.62120	GAG	.	.		0.532	PDE6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252326.2		
SLC36A3	285641	hgsc.bcm.edu	37	5	150666921	150666921	+	Silent	SNP	G	G	T			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:150666921G>T	ENST00000335230.3	-	6	1005	c.594C>A	c.(592-594)ccC>ccA	p.P198P	SLC36A3_ENST00000377713.3_Silent_p.P239P	NM_181774.3	NP_861439.3	Q495N2	S36A3_HUMAN	solute carrier family 36, member 3	198						integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(6)|ovary(2)|skin(1)|stomach(2)|urinary_tract(2)	21		Medulloblastoma(196;0.109)|all_hematologic(541;0.243)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GGATCAGGAAGGGCAGGATTA	0.527																																					p.P239P		Atlas-SNP	.											.	SLC36A3	54	.	0			c.C717A						.						168.0	156.0	160.0					5																	150666921		2203	4300	6503	SO:0001819	synonymous_variant	285641	exon7			CAGGAAGGGCAGG	AY162215	CCDS4314.1, CCDS47316.1	5q33.1	2013-07-17	2013-07-17		ENSG00000186334	ENSG00000186334		"""Solute carriers"""	19659	protein-coding gene	gene with protein product		608332				12809675	Standard	NM_181774		Approved	PAT3, TRAMD2, tramdorin2	uc003ltw.2	Q495N2	OTTHUMG00000130128	ENST00000335230.3:c.594C>A	chr5.hg19:g.150666921G>T		165.0	0.0		224.0	61.0	NM_001145017	Q495N3|Q6ZMU7|Q6ZRU4|Q7Z6B4	Silent	SNP	ENST00000335230.3	hg19	CCDS4314.1																																																																																			.	.		0.527	SLC36A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252436.1	NM_181774	
TENM2	57451	hgsc.bcm.edu	37	5	167553853	167553853	+	Silent	SNP	C	C	T			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:167553853C>T	ENST00000518659.1	+	12	2343	c.2304C>T	c.(2302-2304)cgC>cgT	p.R768R	CTB-178M22.1_ENST00000517408.1_RNA|TENM2_ENST00000403607.2_Silent_p.R601R|TENM2_ENST00000545108.1_Silent_p.R768R|TENM2_ENST00000519204.1_Silent_p.R647R|TENM2_ENST00000520394.1_Silent_p.R536R	NM_001122679.1	NP_001116151.1	Q9NT68	TEN2_HUMAN	teneurin transmembrane protein 2	768					axon guidance (GO:0007411)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|heterophilic cell-cell adhesion (GO:0007157)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of filopodium assembly (GO:0051491)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)										GTGACCAGCGCGTGTGCCACC	0.597																																					p.R768R		Atlas-SNP	.											.	.	.	.	0			c.C2304T						.						45.0	51.0	49.0					5																	167553853		2036	4168	6204	SO:0001819	synonymous_variant	57451	exon12			CCAGCGCGTGTGC	AB032953		5q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000145934	ENSG00000145934			29943	protein-coding gene	gene with protein product		610119	"""odz, odd Oz/ten-m homolog 2 (Drosophila)"""	ODZ2		10625539	Standard	NM_001122679		Approved	KIAA1127, Ten-M2	uc010jjd.3	Q9NT68	OTTHUMG00000162928	ENST00000518659.1:c.2304C>T	chr5.hg19:g.167553853C>T		199.0	0.0		231.0	66.0	NM_001122679	Q9ULU2	Silent	SNP	ENST00000518659.1	hg19																																																																																				.	.		0.597	TENM2-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376096.1	NM_001122679	
SLIT3	6586	hgsc.bcm.edu	37	5	168678426	168678426	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:168678426T>C	ENST00000519560.1	-	2	654	c.235A>G	c.(235-237)Atg>Gtg	p.M79V	SLIT3_ENST00000404867.3_Missense_Mutation_p.M79V|SLIT3_ENST00000332966.8_Missense_Mutation_p.M79V|SLIT3_ENST00000521130.1_5'UTR	NM_001271946.1|NM_003062.2	NP_001258875.1|NP_003053	O75094	SLIT3_HUMAN	slit homolog 3 (Drosophila)	79					apoptotic process involved in luteolysis (GO:0061364)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|cellular response to hormone stimulus (GO:0032870)|negative chemotaxis (GO:0050919)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of gene expression (GO:0010629)|organ morphogenesis (GO:0009887)|response to cortisol (GO:0051414)|Roundabout signaling pathway (GO:0035385)	extracellular space (GO:0005615)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|Roundabout binding (GO:0048495)			endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(15)|liver(2)|lung(48)|ovary(4)|prostate(7)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	100	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			GCGAAGTCCATCTTGGTGATC	0.413																																					p.M79V	Ovarian(29;311 847 10864 17279 24903)	Atlas-SNP	.											.	SLIT3	224	.	0			c.A235G						.						172.0	159.0	163.0					5																	168678426		2203	4300	6503	SO:0001583	missense	6586	exon2			AGTCCATCTTGGT	AB011538	CCDS4369.1, CCDS64311.1	5q35	2008-07-18	2001-11-28		ENSG00000184347	ENSG00000184347			11087	protein-coding gene	gene with protein product		603745	"""slit (Drosophila) homolog 3"""	SLIL2		9693030, 9813312	Standard	NM_001271946		Approved	slit2, MEGF5, SLIT1, Slit-3	uc010jjg.4	O75094	OTTHUMG00000130409	ENST00000519560.1:c.235A>G	chr5.hg19:g.168678426T>C	ENSP00000430333:p.Met79Val	57.0	0.0		85.0	4.0	NM_001271946	A6H8U9|J3KNP3|O95804|Q9UFH5	Missense_Mutation	SNP	ENST00000519560.1	hg19	CCDS4369.1	.	.	.	.	.	.	.	.	.	.	T	10.49	1.364632	0.24684	.	.	ENSG00000184347	ENST00000519560;ENST00000332966;ENST00000404867	T;T;T	0.75154	-0.91;-0.91;-0.9	4.95	3.79	0.43588	.	0.365925	0.25122	N	0.032962	T	0.55545	0.1927	N	0.17474	0.49	0.25971	N	0.982505	B;B	0.10296	0.003;0.0	B;B	0.09377	0.004;0.002	T	0.47195	-0.9136	10	0.45353	T	0.12	.	7.2019	0.25885	0.0:0.1015:0.0:0.8985	.	79;79	O75094-2;O75094	.;SLIT3_HUMAN	V	79	ENSP00000430333:M79V;ENSP00000332164:M79V;ENSP00000384890:M79V	ENSP00000332164:M79V	M	-	1	0	SLIT3	168611004	0.960000	0.32886	1.000000	0.80357	0.998000	0.95712	1.722000	0.38042	0.751000	0.32900	0.533000	0.62120	ATG	.	.		0.413	SLIT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252792.4	NM_003062	
TLX3	30012	hgsc.bcm.edu	37	5	170736706	170736706	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:170736706T>C	ENST00000296921.5	+	1	419	c.337T>C	c.(337-339)Tcc>Ccc	p.S113P		NM_021025.2	NP_066305.2	O43711	TLX3_HUMAN	T-cell leukemia homeobox 3	113					central nervous system development (GO:0007417)|negative regulation of neuron differentiation (GO:0045665)|neuron fate specification (GO:0048665)|neuron migration (GO:0001764)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|regulation of transcription, DNA-templated (GO:0006355)|respiratory gaseous exchange (GO:0007585)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			central_nervous_system(1)	1	Renal(175;0.000159)|Lung NSC(126;0.00576)|all_lung(126;0.00963)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			CGCCATGCCCTCCGTGCCCAC	0.706			T	BCL11B	T-ALL																																p.S113P	Esophageal Squamous(33;43 807 3116 3348 30094)	Atlas-SNP	.		Dom	yes		5	5q35.1	30012	"""T-cell leukemia, homeobox 3 (HOX11L2)"""		L	.	TLX3	23	.	0			c.T337C						.						13.0	15.0	14.0					5																	170736706		2165	4256	6421	SO:0001583	missense	30012	exon1			ATGCCCTCCGTGC	AJ223798	CCDS34288.1	5q35.1	2011-06-20	2005-12-22	2002-05-31	ENSG00000164438	ENSG00000164438		"""Homeoboxes / ANTP class : NKL subclass"""	13532	protein-coding gene	gene with protein product		604640	"""homeo box 11-like 2"", ""T-cell leukemia, homeobox 3"""	HOX11L2		11435718, 11435716	Standard	NM_021025		Approved	RNX	uc003mbf.3	O43711	OTTHUMG00000163207	ENST00000296921.5:c.337T>C	chr5.hg19:g.170736706T>C	ENSP00000296921:p.Ser113Pro	55.0	0.0		75.0	5.0	NM_021025	Q96AD3	Missense_Mutation	SNP	ENST00000296921.5	hg19	CCDS34288.1	.	.	.	.	.	.	.	.	.	.	T	12.60	1.987211	0.35036	.	.	ENSG00000164438	ENST00000296921	D	0.91686	-2.89	4.4	3.23	0.37069	.	0.157179	0.40144	N	0.001163	D	0.82793	0.5114	N	0.17082	0.46	0.25980	N	0.982389	P	0.45634	0.863	B	0.41988	0.372	T	0.74293	-0.3712	10	0.19590	T	0.45	.	8.8572	0.35236	0.0:0.0:0.3788:0.6212	.	113	O43711	TLX3_HUMAN	P	113	ENSP00000296921:S113P	ENSP00000296921:S113P	S	+	1	0	TLX3	170669311	0.846000	0.29590	1.000000	0.80357	0.994000	0.84299	0.797000	0.26999	1.861000	0.53984	0.454000	0.30748	TCC	.	.		0.706	TLX3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000372076.3		
TLX3	30012	hgsc.bcm.edu	37	5	170736779	170736779	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:170736779A>G	ENST00000296921.5	+	1	492	c.410A>G	c.(409-411)gAc>gGc	p.D137G		NM_021025.2	NP_066305.2	O43711	TLX3_HUMAN	T-cell leukemia homeobox 3	137					central nervous system development (GO:0007417)|negative regulation of neuron differentiation (GO:0045665)|neuron fate specification (GO:0048665)|neuron migration (GO:0001764)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|regulation of transcription, DNA-templated (GO:0006355)|respiratory gaseous exchange (GO:0007585)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			central_nervous_system(1)	1	Renal(175;0.000159)|Lung NSC(126;0.00576)|all_lung(126;0.00963)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			TTCGTGAAAGACCGCTTCACA	0.682			T	BCL11B	T-ALL																																p.D137G	Esophageal Squamous(33;43 807 3116 3348 30094)	Atlas-SNP	.		Dom	yes		5	5q35.1	30012	"""T-cell leukemia, homeobox 3 (HOX11L2)"""		L	.	TLX3	23	.	0			c.A410G						.						15.0	18.0	17.0					5																	170736779		2184	4277	6461	SO:0001583	missense	30012	exon1			TGAAAGACCGCTT	AJ223798	CCDS34288.1	5q35.1	2011-06-20	2005-12-22	2002-05-31	ENSG00000164438	ENSG00000164438		"""Homeoboxes / ANTP class : NKL subclass"""	13532	protein-coding gene	gene with protein product		604640	"""homeo box 11-like 2"", ""T-cell leukemia, homeobox 3"""	HOX11L2		11435718, 11435716	Standard	NM_021025		Approved	RNX	uc003mbf.3	O43711	OTTHUMG00000163207	ENST00000296921.5:c.410A>G	chr5.hg19:g.170736779A>G	ENSP00000296921:p.Asp137Gly	51.0	0.0		54.0	4.0	NM_021025	Q96AD3	Missense_Mutation	SNP	ENST00000296921.5	hg19	CCDS34288.1	.	.	.	.	.	.	.	.	.	.	A	18.55	3.649208	0.67358	.	.	ENSG00000164438	ENST00000296921	D	0.91843	-2.92	4.31	4.31	0.51392	.	0.051376	0.85682	D	0.000000	D	0.93383	0.7890	M	0.70595	2.14	0.44098	D	0.99686	P	0.42248	0.774	P	0.50896	0.653	D	0.93590	0.6920	10	0.56958	D	0.05	.	12.6052	0.56519	1.0:0.0:0.0:0.0	.	137	O43711	TLX3_HUMAN	G	137	ENSP00000296921:D137G	ENSP00000296921:D137G	D	+	2	0	TLX3	170669384	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	7.019000	0.76412	1.823000	0.53134	0.454000	0.30748	GAC	.	.		0.682	TLX3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000372076.3		
PRSS16	10279	hgsc.bcm.edu	37	6	27218543	27218543	+	Silent	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:27218543A>G	ENST00000230582.3	+	5	564	c.549A>G	c.(547-549)ggA>ggG	p.G183G	PRSS16_ENST00000421826.2_Intron	NM_005865.3	NP_005856.1	Q9NQE7	TSSP_HUMAN	protease, serine, 16 (thymus)	183					protein catabolic process (GO:0030163)	cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|lysosome (GO:0005764)	serine-type peptidase activity (GO:0008236)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	26						TCTGCTTCGGAGGCTCCTATG	0.672																																					p.G183G	NSCLC(178;1118 2105 17078 23587 44429)	Atlas-SNP	.											.	PRSS16	66	.	0			c.A549G						.						47.0	45.0	46.0					6																	27218543		2203	4300	6503	SO:0001819	synonymous_variant	10279	exon5			CTTCGGAGGCTCC	AF052514	CCDS4623.1	6p21	2010-05-07			ENSG00000112812	ENSG00000112812		"""Serine peptidases / Serine peptidases"""	9480	protein-coding gene	gene with protein product		607169				10527559	Standard	NM_005865		Approved	TSSP	uc003nja.3	Q9NQE7	OTTHUMG00000016167	ENST00000230582.3:c.549A>G	chr6.hg19:g.27218543A>G		90.0	0.0		119.0	5.0	NM_005865	O75416	Silent	SNP	ENST00000230582.3	hg19	CCDS4623.1	.	.	.	.	.	.	.	.	.	.	A	12.11	1.840679	0.32513	.	.	ENSG00000112812	ENST00000485993;ENST00000475106	.	.	.	4.4	3.18	0.36537	.	.	.	.	.	T	0.45577	0.1349	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.39901	-0.9591	4	.	.	.	-20.829	9.2991	0.37833	0.8183:0.1817:0.0:0.0	.	.	.	.	G	75	.	.	R	+	1	2	PRSS16	27326522	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	0.952000	0.29149	0.790000	0.33803	0.460000	0.39030	AGG	.	.		0.672	PRSS16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043418.2		
RPP21	79897	hgsc.bcm.edu	37	6	30313126	30313126	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:30313126T>C	ENST00000442966.2	+	2	122	c.109T>C	c.(109-111)Ttt>Ctt	p.F37L	TRIM39-RPP21_ENST00000513556.1_Missense_Mutation_p.F298L|RPP21_ENST00000428040.2_Missense_Mutation_p.F60L|RPP21_ENST00000433076.2_Missense_Mutation_p.F37L|RPP21_ENST00000436442.2_Missense_Mutation_p.F37L|RPP21_ENST00000466327.1_3'UTR			Q9H633	RPP21_HUMAN	ribonuclease P/MRP 21kDa subunit	37					response to drug (GO:0042493)|tRNA processing (GO:0008033)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|ribonuclease P activity (GO:0004526)			endometrium(2)|ovary(1)|prostate(1)	4						GCTGGCGAGGTTTTACTGCTA	0.697																																					p.F386L		Atlas-SNP	.											.	.	.	.	0			c.T1156C						.						43.0	50.0	48.0					6																	30313126		1511	2709	4220	SO:0001583	missense	202658	exon7			GCGAGGTTTTACT	AK026291	CCDS4679.1, CCDS56409.1, CCDS56410.1	6p21.32	2012-05-21	2007-06-26	2004-03-19	ENSG00000241370	ENSG00000241370			21300	protein-coding gene	gene with protein product		612524	"""chromosome 6 open reading frame 135"", ""ribonuclease P 21kDa subunit"""	C6orf135			Standard	NM_001199120		Approved	FLJ22638, Em:AB014085.3		Q9H633	OTTHUMG00000031220	ENST00000442966.2:c.109T>C	chr6.hg19:g.30313126T>C	ENSP00000403833:p.Phe37Leu	97.0	0.0		220.0	9.0	NM_001199119	A2AAZ8|B0S834|B0S835|Q5JPL9|Q5JPM1|Q5STF8|Q5STF9|Q5STG2|Q5SU41|Q5SU42|Q86Y49|Q86Y50|Q86Y51|Q96F16	Missense_Mutation	SNP	ENST00000442966.2	hg19	CCDS4679.1	.	.	.	.	.	.	.	.	.	.	T	29.1	4.974023	0.92919	.	.	ENSG00000204599;ENSG00000248167;ENSG00000241370;ENSG00000241370;ENSG00000241370;ENSG00000241370	ENST00000412529;ENST00000513556;ENST00000433076;ENST00000442966;ENST00000428040;ENST00000436442	T;T;T;T;T	0.40225	1.04;1.04;1.04;1.04;1.04	5.12	5.12	0.69794	.	0.000000	0.85682	D	0.000000	T	0.48040	0.1478	L	0.58101	1.795	0.46131	D	0.998889	D;D;D;D	0.69078	0.994;0.99;0.997;0.992	P;P;D;P	0.66196	0.877;0.853;0.942;0.902	T	0.53885	-0.8375	10	0.87932	D	0	-4.499	11.2433	0.48982	0.0:0.0:0.0:1.0	.	300;37;37;60	F5H2V3;Q9H633-3;Q9H633;Q9H633-2	.;.;RPP21_HUMAN;.	L	300;298;37;37;60;37	ENSP00000424048:F298L;ENSP00000409799:F37L;ENSP00000403833:F37L;ENSP00000394320:F60L;ENSP00000397778:F37L	ENSP00000394320:F60L	F	+	1	0	RPP21;TRIM39-RPP21;TRIM39	30421105	1.000000	0.71417	0.997000	0.53966	0.855000	0.48748	5.398000	0.66308	2.146000	0.66826	0.460000	0.39030	TTT	.	.		0.697	RPP21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076451.2	NM_024839	
DPCR1	135656	hgsc.bcm.edu	37	6	30918020	30918020	+	Silent	SNP	G	G	A			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:30918020G>A	ENST00000462446.1	+	2	1807	c.1779G>A	c.(1777-1779)aaG>aaA	p.K593K	DPCR1_ENST00000304311.2_5'UTR|HCG21_ENST00000419481.1_RNA			Q3MIW9	DPCR1_HUMAN	diffuse panbronchiolitis critical region 1	145						integral component of membrane (GO:0016021)				endometrium(1)|kidney(2)|large_intestine(3)|lung(3)|pancreas(1)	10						CCAATGAGAAGACCACATCAT	0.502																																					p.K593K		Atlas-SNP	.											.	DPCR1	99	.	0			c.G1779A						.						48.0	51.0	50.0					6																	30918020		692	1591	2283	SO:0001819	synonymous_variant	135656	exon2			TGAGAAGACCACA	AB064272	CCDS4692.1, CCDS4692.2	6p21.32	2008-02-05			ENSG00000168631	ENSG00000168631			21666	protein-coding gene	gene with protein product		613928				12185533, 10677310	Standard	NM_080870		Approved	PBLT, bCX105N19.6	uc003nsg.2	Q3MIW9	OTTHUMG00000031104	ENST00000462446.1:c.1779G>A	chr6.hg19:g.30918020G>A		98.0	0.0		222.0	9.0	NM_080870	C9IZC0|Q658M7|Q8WYN2	Silent	SNP	ENST00000462446.1	hg19	CCDS4692.2																																																																																			.	.		0.502	DPCR1-001	NOVEL	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076173.3	NM_080870	
MICA	100507436	hgsc.bcm.edu	37	6	31380100	31380101	+	Splice_Site	DNP	AG	AG	CA	rs41558418		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A|G	A|G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:31380100_31380101AG>CA	ENST00000449934.2	+	5	946		c.e5-1		HCP5_ENST00000414046.2_RNA	NM_001177519.1	NP_001170990.1			MHC class I polypeptide-related sequence A											breast(1)|endometrium(3)|kidney(1)	5		Ovarian(999;0.0253)				CCTTTTTTTCAGGGAAAGTGCT	0.5																																					.		Atlas-SNP	.											.	MICA	21	.	0			c.893-2A>C|c.893-1G>A						.																																			SO:0001630	splice_region_variant	100507436	exon5			TTTTTCAGGGAAA|TTTTCAGGGAAAG	L14848	CCDS56412.1, CCDS75421.1	6p21.3	2013-01-11			ENSG00000204520	ENSG00000204520		"""Immunoglobulin superfamily / C1-set domain containing"""	7090	protein-coding gene	gene with protein product		600169				8022771	Standard	NM_000247		Approved	PERB11.1	uc003ntk.1	Q29983	OTTHUMG00000031073	Exception_encountered	chr6.hg19:g.31380100_31380101delinsCA		138.0	0.0		219.0|218.0	13.0|10.0	NM_001177519		Splice_Site	SNP	ENST00000449934.2	hg19	CCDS56412.1																																																																																			.	.		0.500	MICA-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076101.7	NM_001177519	Intron
PRRC2A	7916	hgsc.bcm.edu	37	6	31603384	31603384	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:31603384A>G	ENST00000376033.2	+	24	5633	c.5399A>G	c.(5398-5400)gAg>gGg	p.E1800G	PRRC2A_ENST00000376007.4_Missense_Mutation_p.E1800G	NM_004638.3	NP_004629.3	P48634	PRC2A_HUMAN	proline-rich coiled-coil 2A	1800	4 X 57 AA type A repeats.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(6)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(14)|lung(19)|ovary(3)|pancreas(2)|prostate(4)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	70						CGAGACTGGGAGCTGCTTCCC	0.612																																					p.E1800G		Atlas-SNP	.											.	PRRC2A	152	.	0			c.A5399G						.						56.0	65.0	62.0					6																	31603384		1511	2708	4219	SO:0001583	missense	7916	exon24			ACTGGGAGCTGCT	M31293	CCDS4708.1	6p21.3	2010-12-09	2010-12-09	2010-12-09	ENSG00000204469	ENSG00000204469			13918	protein-coding gene	gene with protein product		142580	"""HLA-B associated transcript 2"""	BAT2		2156268, 8499947	Standard	NM_080686		Approved	G2, D6S51E	uc003nvc.4	P48634	OTTHUMG00000031168	ENST00000376033.2:c.5399A>G	chr6.hg19:g.31603384A>G	ENSP00000365201:p.Glu1800Gly	85.0	0.0		132.0	7.0	NM_004638	B0UX77|B0UZE9|B0UZL3|O95875|Q05BK4|Q4LE37|Q5SQ29|Q5SQ30|Q5ST84|Q5STX6|Q5STX7|Q68DW9|Q6P9P7|Q6PIN1|Q8MGQ9|Q96QC6	Missense_Mutation	SNP	ENST00000376033.2	hg19	CCDS4708.1	.	.	.	.	.	.	.	.	.	.	A	13.69	2.313751	0.40996	.	.	ENSG00000204469	ENST00000424184;ENST00000435052;ENST00000376007;ENST00000376033;ENST00000376010	T;T	0.02085	4.46;4.46	5.4	5.4	0.78164	.	0.106321	0.42172	D	0.000745	T	0.01627	0.0052	L	0.43152	1.355	0.41508	D	0.988325	P	0.40970	0.734	B	0.40329	0.326	T	0.57021	-0.7882	10	0.87932	D	0	-17.3397	13.0364	0.58875	1.0:0.0:0.0:0.0	.	1800	P48634	PRC2A_HUMAN	G	1794;1783;1800;1800;1025	ENSP00000365175:E1800G;ENSP00000365201:E1800G	ENSP00000365175:E1800G	E	+	2	0	PRRC2A	31711363	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	4.337000	0.59310	2.270000	0.75569	0.459000	0.35465	GAG	.	.		0.612	PRRC2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259319.1	NM_080686	
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32549502	32549502	+	Missense_Mutation	SNP	G	G	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:32549502G>C	ENST00000360004.5	-	3	589	c.484C>G	c.(484-486)Ctg>Gtg	p.L162V		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	162	Beta-2.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)		p.L162L(1)		large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(2)|stomach(1)	10						TGGCCGTTCAGGAACCACCTG	0.552										Multiple Myeloma(14;0.17)																											p.L162V		Atlas-SNP	.											HLA-DRB1,NS,carcinoma,0,1	HLA-DRB1	41	.	1	Substitution - coding silent(1)	prostate(1)	c.C484G						.						79.0	94.0	89.0					6																	32549502		1509	2709	4218	SO:0001583	missense	3123	exon3			CGTTCAGGAACCA	AJ297583	CCDS47409.1	6p21.3	2013-01-11			ENSG00000196126	ENSG00000196126		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4948	protein-coding gene	gene with protein product		142857		HLA-DR1B			Standard	NM_001243965		Approved		uc011eri.2	P01911	OTTHUMG00000031196	ENST00000360004.5:c.484C>G	chr6.hg19:g.32549502G>C	ENSP00000353099:p.Leu162Val	279.0	2.0		438.0	0.0	NM_002124	P01914|Q9MYF5	Missense_Mutation	SNP	ENST00000360004.5	hg19	CCDS47409.1	.	.	.	.	.	.	.	.	.	.	.	8.248	0.808286	0.16467	.	.	ENSG00000196126	ENST00000360004	T	0.08546	3.08	3.87	1.89	0.25635	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	0.305223	0.33180	N	0.005193	T	0.05364	0.0142	M	0.86502	2.82	0.18873	N	0.999984	B	0.20052	0.041	B	0.25759	0.063	T	0.21621	-1.0240	10	0.87932	D	0	.	5.3486	0.16024	0.1119:0.0:0.5869:0.3012	.	162	P01911	2B1F_HUMAN	V	162	ENSP00000353099:L162V	ENSP00000353099:L162V	L	-	1	2	HLA-DRB1	32657480	0.170000	0.23016	0.526000	0.27913	0.421000	0.31385	0.849000	0.27723	0.751000	0.32900	0.453000	0.30009	CTG	.	.		0.552	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124	
SYNGAP1	8831	hgsc.bcm.edu	37	6	33400496	33400496	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:33400496T>C	ENST00000418600.2	+	5	523	c.422T>C	c.(421-423)aTc>aCc	p.I141T	SYNGAP1_ENST00000293748.5_Missense_Mutation_p.I141T|SYNGAP1_ENST00000496374.1_3'UTR|SYNGAP1_ENST00000428982.2_Missense_Mutation_p.I82T	NM_006772.2	NP_006763.2	Q96PV0	SYGP1_HUMAN	synaptic Ras GTPase activating protein 1	141					dendrite development (GO:0016358)|negative regulation of axonogenesis (GO:0050771)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of Ras protein signal transduction (GO:0046580)|pattern specification process (GO:0007389)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|receptor clustering (GO:0043113)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of MAPK cascade (GO:0043408)|regulation of synapse structure and activity (GO:0050803)|regulation of synaptic plasticity (GO:0048167)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	Rab GTPase activator activity (GO:0005097)|Ras GTPase activator activity (GO:0005099)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(15)|ovary(7)|pancreas(1)|stomach(1)|urinary_tract(1)	43						AAAAGCTCCATCAAACGAACG	0.587																																					p.I141T		Atlas-SNP	.											.	SYNGAP1	202	.	0			c.T422C						.						68.0	58.0	62.0					6																	33400496		2203	4300	6503	SO:0001583	missense	8831	exon5			GCTCCATCAAACG	AB067525	CCDS34434.2	6p21.3	2010-06-25	2010-06-25		ENSG00000197283	ENSG00000197283			11497	protein-coding gene	gene with protein product		603384	"""synaptic Ras GTPase activating protein 1 homolog (rat)"""			9581761, 18323856	Standard	NM_006772		Approved	SYNGAP, RASA5, KIAA1938	uc011dri.2	Q96PV0	OTTHUMG00000031096	ENST00000418600.2:c.422T>C	chr6.hg19:g.33400496T>C	ENSP00000403636:p.Ile141Thr	76.0	0.0		99.0	4.0	NM_006772	A2AB17|A2BEL6|A2BEL7|A8MQC4|Q8TCS2|Q9UGE2	Missense_Mutation	SNP	ENST00000418600.2	hg19	CCDS34434.2	.	.	.	.	.	.	.	.	.	.	T	15.56	2.869711	0.51588	.	.	ENSG00000197283	ENST00000293748;ENST00000418600;ENST00000449372;ENST00000428982	T;T;T	0.26518	1.73;1.82;1.81	4.36	4.36	0.52297	Pleckstrin homology domain (1);	0.000000	0.85682	D	0.000000	T	0.23451	0.0567	M	0.69358	2.11	0.58432	D	0.999999	B;B;P	0.37688	0.272;0.392;0.605	B;B;P	0.44696	0.167;0.315;0.458	T	0.06320	-1.0833	10	0.87932	D	0	.	11.5483	0.50706	0.0:0.0:0.0:1.0	.	141;141;141	Q96PV0;Q96PV0-4;B7ZCA0	SYGP1_HUMAN;.;.	T	141;141;141;82	ENSP00000293748:I141T;ENSP00000403636:I141T;ENSP00000412475:I82T	ENSP00000293748:I141T	I	+	2	0	SYNGAP1	33508474	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.107000	0.77047	1.840000	0.53500	0.383000	0.25322	ATC	.	.		0.587	SYNGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076151.4	XM_166407	
ZBTB9	221504	hgsc.bcm.edu	37	6	33423129	33423129	+	Silent	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:33423129T>C	ENST00000395064.2	+	2	520	c.252T>C	c.(250-252)cgT>cgC	p.R84R		NM_152735.3	NP_689948.1	Q96C00	ZBTB9_HUMAN	zinc finger and BTB domain containing 9	84	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(6)|skin(1)|upper_aerodigestive_tract(2)	11						ATGCGCCTCGTCTCACTCTAC	0.582																																					p.R84R		Atlas-SNP	.											.	ZBTB9	23	.	0			c.T252C						.						172.0	177.0	176.0					6																	33423129		2203	4300	6503	SO:0001819	synonymous_variant	221504	exon2			GCCTCGTCTCACT	AK122644	CCDS4780.1	6p21.31	2013-01-09			ENSG00000213588	ENSG00000213588		"""-"", ""BTB/POZ domain containing"", ""Zinc fingers, C2H2-type"""	28323	protein-coding gene	gene with protein product						12477932	Standard	NM_152735		Approved	MGC23166, ZNF919	uc003oeq.3	Q96C00	OTTHUMG00000140180	ENST00000395064.2:c.252T>C	chr6.hg19:g.33423129T>C		66.0	0.0		140.0	6.0	NM_152735	A2AB19	Silent	SNP	ENST00000395064.2	hg19	CCDS4780.1																																																																																			.	.		0.582	ZBTB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276533.1	NM_152735	
ETV7	51513	hgsc.bcm.edu	37	6	36339181	36339181	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:36339181T>C	ENST00000340181.4	-	5	831	c.590A>G	c.(589-591)gAg>gGg	p.E197G	ETV7_ENST00000373737.4_Intron|ETV7_ENST00000339796.5_Missense_Mutation_p.E197G|ETV7_ENST00000538992.1_Missense_Mutation_p.E46G|ETV7_ENST00000373738.1_Missense_Mutation_p.E142G	NM_001207037.1|NM_001207040.1|NM_016135.3	NP_001193966.1|NP_001193969.1|NP_057219.1	Q9Y603	ETV7_HUMAN	ets variant 7	197					cell differentiation (GO:0030154)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|organ morphogenesis (GO:0009887)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|skin(4)	10						GCAGCCGAGCTCTGCACAGTG	0.647																																					p.E197G		Atlas-SNP	.											.	ETV7	31	.	0			c.A590G						.						52.0	45.0	47.0					6																	36339181		2203	4300	6503	SO:0001583	missense	51513	exon5			CCGAGCTCTGCAC	AF116508	CCDS4819.1, CCDS56422.1, CCDS56423.1, CCDS56424.1, CCDS56425.1, CCDS75440.1, CCDS75441.1	6p21	2008-09-12	2008-09-12		ENSG00000010030	ENSG00000010030			18160	protein-coding gene	gene with protein product	"""TEL2 oncogene"""	605255	"""ets variant gene 7 (TEL2 oncogene)"""			10828014, 11108721	Standard	NM_016135		Approved	TEL2, TEL-2	uc003omb.3	Q9Y603	OTTHUMG00000014594	ENST00000340181.4:c.590A>G	chr6.hg19:g.36339181T>C	ENSP00000341843:p.Glu197Gly	56.0	0.0		95.0	5.0	NM_001207035	B3KVC2|B4DVB6|B4E1G4|Q5R3L3|Q5R3L4|Q9NZ65|Q9NZ66|Q9NZ68|Q9NZR8|Q9UNJ7|Q9Y5K4|Q9Y604	Missense_Mutation	SNP	ENST00000340181.4	hg19	CCDS4819.1	.	.	.	.	.	.	.	.	.	.	T	10.95	1.496980	0.26861	.	.	ENSG00000010030	ENST00000339796;ENST00000340181;ENST00000373738;ENST00000538992	T;T;T;T	0.14266	2.52;2.52;2.52;2.52	3.26	3.26	0.37387	.	0.297121	0.31427	N	0.007661	T	0.08626	0.0214	L	0.34521	1.04	0.09310	N	1	B;P;P;D;B	0.71674	0.022;0.939;0.82;0.998;0.011	B;P;P;D;B	0.66351	0.037;0.565;0.496;0.943;0.03	T	0.13548	-1.0505	10	0.27082	T	0.32	.	5.4496	0.16556	0.0:0.1353:0.0:0.8647	.	138;142;197;142;197	Q9Y603-2;Q9Y603-4;Q9Y603;Q9Y603-6;Q9Y603-5	.;.;ETV7_HUMAN;.;.	G	197;197;142;46	ENSP00000342260:E197G;ENSP00000341843:E197G;ENSP00000362843:E142G;ENSP00000440592:E46G	ENSP00000342260:E197G	E	-	2	0	ETV7	36447159	0.030000	0.19436	0.101000	0.21167	0.098000	0.18820	1.827000	0.39102	1.264000	0.44198	0.460000	0.39030	GAG	.	.		0.647	ETV7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040341.1	NM_016135	
MDGA1	266727	hgsc.bcm.edu	37	6	37616904	37616904	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:37616904G>T	ENST00000434837.3	-	9	2926	c.1748C>A	c.(1747-1749)cCg>cAg	p.P583Q	MDGA1_ENST00000505425.1_Missense_Mutation_p.P583Q|MDGA1_ENST00000510077.1_5'Flank|MDGA1_ENST00000297153.7_Missense_Mutation_p.P586Q	NM_153487.3	NP_705691.1	Q8NFP4	MDGA1_HUMAN	MAM domain containing glycosylphosphatidylinositol anchor 1	583	Ig-like 6.				brain development (GO:0007420)|cerebral cortex radially oriented cell migration (GO:0021799)|neuron migration (GO:0001764)|spinal cord association neuron differentiation (GO:0021527)	anchored component of plasma membrane (GO:0046658)|extracellular space (GO:0005615)				central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(12)|lung(11)|prostate(1)|skin(2)|urinary_tract(1)	38						AGGCGGCGGCGGCAGCAGCTG	0.736																																					p.P583Q		Atlas-SNP	.											.	MDGA1	104	.	0			c.C1748A						.						2.0	2.0	2.0					6																	37616904		1356	2933	4289	SO:0001583	missense	266727	exon9			GGCGGCGGCAGCA	AF478693	CCDS47417.1	6p21	2013-01-29			ENSG00000112139	ENSG00000112139		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	19267	protein-coding gene	gene with protein product		609626				15922729, 15019943	Standard	NM_153487		Approved	GPIM, MAMDC3	uc003onu.1	Q8NFP4	OTTHUMG00000014626	ENST00000434837.3:c.1748C>A	chr6.hg19:g.37616904G>T	ENSP00000402584:p.Pro583Gln	0.0	0.0		9.0	8.0	NM_153487	A6NHG0|Q8NBE3	Missense_Mutation	SNP	ENST00000434837.3	hg19	CCDS47417.1	.	.	.	.	.	.	.	.	.	.	G	10.27	1.302747	0.23736	.	.	ENSG00000112139	ENST00000434837;ENST00000297153;ENST00000505425	T;T;T	0.65549	-0.16;-0.16;-0.16	3.73	3.73	0.42828	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.159905	0.29293	N	0.012576	T	0.28400	0.0702	L	0.27053	0.805	0.27978	N	0.936153	B	0.15719	0.014	B	0.24701	0.055	T	0.09975	-1.0650	10	0.13853	T	0.58	.	13.2016	0.59772	0.0:0.0:1.0:0.0	.	583	Q8NFP4	MDGA1_HUMAN	Q	583;586;583	ENSP00000402584:P583Q;ENSP00000297153:P586Q;ENSP00000422042:P583Q	ENSP00000297153:P586Q	P	-	2	0	MDGA1	37724882	0.071000	0.21146	0.991000	0.47740	0.898000	0.52572	1.972000	0.40540	2.089000	0.63090	0.561000	0.74099	CCG	.	.		0.736	MDGA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040419.3		
DNAH8	1769	hgsc.bcm.edu	37	6	38834389	38834389	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:38834389A>G	ENST00000359357.3	+	44	6124	c.5870A>G	c.(5869-5871)cAg>cGg	p.Q1957R	DNAH8_ENST00000449981.2_Missense_Mutation_p.Q2174R|DNAH8_ENST00000441566.1_Missense_Mutation_p.Q1957R			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	1957	AAA 1. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						GCTGGGCGCCAGGAACTACCA	0.323																																					p.Q2174R		Atlas-SNP	.											.	DNAH8	1239	.	0			c.A6521G						.						67.0	68.0	67.0					6																	38834389		2203	4300	6503	SO:0001583	missense	1769	exon46			GGCGCCAGGAACT	Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"""Axonemal dyneins"""	2952	protein-coding gene	gene with protein product		603337	"""dynein, axonemal, heavy polypeptide 8"""			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.5870A>G	chr6.hg19:g.38834389A>G	ENSP00000352312:p.Gln1957Arg	53.0	0.0		92.0	4.0	NM_001206927	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Missense_Mutation	SNP	ENST00000359357.3	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	24.0|24.0	4.478637|4.478637	0.84747|0.84747	.|.	.|.	ENSG00000124721|ENSG00000124721	ENST00000449981;ENST00000327475;ENST00000359357;ENST00000441566|ENST00000394393	T;T;T|.	0.09255|.	3.0;3.0;3.0|.	5.87|5.87	4.68|4.68	0.58851|0.58851	ATPase, AAA+ type, core (1);|.	0.054564|.	0.85682|.	D|.	0.000000|.	T|T	0.52224|0.52224	0.1721|0.1721	L|L	0.56396|0.56396	1.775|1.775	0.58432|0.58432	D|D	0.999998|0.999998	D|.	0.89917|.	1.0|.	D|.	0.97110|.	1.0|.	T|T	0.52668|0.52668	-0.8545|-0.8545	10|5	0.54805|.	T|.	0.06|.	.|.	13.2981|13.2981	0.60309|0.60309	0.8679:0.1321:0.0:0.0|0.8679:0.1321:0.0:0.0	.|.	1957|.	Q96JB1|.	DYH8_HUMAN|.	R|G	2162;2162;1957;1957|39	ENSP00000333363:Q2162R;ENSP00000352312:Q1957R;ENSP00000402294:Q1957R|.	ENSP00000333363:Q2162R|.	Q|R	+|+	2|1	0|2	DNAH8|DNAH8	38942367|38942367	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	9.277000|9.277000	0.95755|0.95755	1.104000|1.104000	0.41587|0.41587	0.533000|0.533000	0.62120|0.62120	CAG|AGG	.	.		0.323	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927	
EFHC1	114327	hgsc.bcm.edu	37	6	52303144	52303144	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:52303144T>C	ENST00000371068.5	+	3	431	c.328T>C	c.(328-330)Tca>Cca	p.S110P	EFHC1_ENST00000538167.1_Missense_Mutation_p.S91P|EFHC1_ENST00000491749.1_3'UTR|EFHC1_ENST00000433625.2_Missense_Mutation_p.S19P	NM_018100.3	NP_060570.2	Q5JVL4	EFHC1_HUMAN	EF-hand domain (C-terminal) containing 1	110	DM10 1. {ECO:0000255|PROSITE- ProRule:PRU00665}.					axoneme (GO:0005930)|neuronal cell body (GO:0043025)	calcium ion binding (GO:0005509)|protein C-terminus binding (GO:0008022)			breast(3)|central_nervous_system(1)|endometrium(4)|large_intestine(8)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	27	Lung NSC(77;0.109)					TGTTCCTATGTCAACTGAGGA	0.368																																					p.S110P		Atlas-SNP	.											.	EFHC1	68	.	0			c.T328C						.						50.0	45.0	46.0					6																	52303144		2202	4300	6502	SO:0001583	missense	114327	exon3			CCTATGTCAACTG	AK001328	CCDS4942.1, CCDS55021.1	6p12.3	2014-02-04			ENSG00000096093	ENSG00000096093		"""EF-hand domain containing"""	16406	protein-coding gene	gene with protein product	"""myoclonin-1"""	608815	"""epilepsy, juvenile myoclonic 1"""	EJM1, EJM		15258581	Standard	NM_018100		Approved	FLJ10466	uc003pap.4	Q5JVL4	OTTHUMG00000014848	ENST00000371068.5:c.328T>C	chr6.hg19:g.52303144T>C	ENSP00000360107:p.Ser110Pro	58.0	0.0		104.0	5.0	NM_018100	B4DMU3|F5GZD8|Q5XKM4|Q6E1U7|Q6E1U8|Q8WUL2|Q9NVW6	Missense_Mutation	SNP	ENST00000371068.5	hg19	CCDS4942.1	.	.	.	.	.	.	.	.	.	.	T	27.0	4.791581	0.90367	.	.	ENSG00000096093	ENST00000371068;ENST00000433625;ENST00000538167	T;T;T	0.71341	-0.32;-0.56;-0.53	5.78	5.78	0.91487	Uncharacterised domain DM10 (2);	0.056069	0.64402	D	0.000001	D	0.86406	0.5925	M	0.94101	3.495	0.54753	D	0.999989	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.998;0.993	D	0.89968	0.4091	10	0.72032	D	0.01	-1.4504	16.1205	0.81351	0.0:0.0:0.0:1.0	.	91;19;110	F5GZD8;B7Z2S4;Q5JVL4	.;.;EFHC1_HUMAN	P	110;19;91	ENSP00000360107:S110P;ENSP00000416492:S19P;ENSP00000444521:S91P	ENSP00000360107:S110P	S	+	1	0	EFHC1	52411103	1.000000	0.71417	0.694000	0.30210	0.934000	0.57294	8.040000	0.89188	2.205000	0.71048	0.533000	0.62120	TCA	.	.		0.368	EFHC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040905.2	NM_018100	
LRRC1	55227	hgsc.bcm.edu	37	6	53787490	53787490	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:53787490A>G	ENST00000370888.1	+	14	1751	c.1474A>G	c.(1474-1476)Aca>Gca	p.T492A	RP3-523E19.2_ENST00000474641.2_RNA	NM_018214.4	NP_060684.4	Q9BTT6	LRRC1_HUMAN	leucine rich repeat containing 1	492						cytoplasm (GO:0005737)|membrane (GO:0016020)				cervix(1)|endometrium(3)|large_intestine(5)|lung(6)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20	Lung NSC(77;0.0147)			BRCA - Breast invasive adenocarcinoma(397;0.0745)		CATGAAAAAGACAGTGGAGAA	0.433																																					p.T492A		Atlas-SNP	.											.	LRRC1	59	.	0			c.A1474G						.						213.0	211.0	212.0					6																	53787490		1932	4145	6077	SO:0001583	missense	55227	exon14			AAAAAGACAGTGG	AF332199	CCDS4953.2	6p12.2	2014-07-30	2003-11-19		ENSG00000137269	ENSG00000137269			14307	protein-coding gene	gene with protein product		608195	"""leucine-rich repeat-containing 1"""				Standard	NM_018214		Approved	dJ523E19.1, LANO, FLJ10775, FLJ11834	uc003pcd.1	Q9BTT6	OTTHUMG00000014885	ENST00000370888.1:c.1474A>G	chr6.hg19:g.53787490A>G	ENSP00000359925:p.Thr492Ala	68.0	0.0		115.0	6.0	NM_018214	Q5TGN3|Q9HAC0|Q9NVF1	Missense_Mutation	SNP	ENST00000370888.1	hg19	CCDS4953.2	.	.	.	.	.	.	.	.	.	.	A	6.065	0.380386	0.11466	.	.	ENSG00000137269	ENST00000370888	T	0.78003	-1.14	5.91	4.76	0.60689	.	0.058928	0.64402	D	0.000002	T	0.43700	0.1259	N	0.20685	0.6	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.37220	-0.9715	10	0.15952	T	0.53	.	11.0763	0.48034	0.9281:0.0:0.0719:0.0	.	492	Q9BTT6	LRRC1_HUMAN	A	492	ENSP00000359925:T492A	ENSP00000359925:T492A	T	+	1	0	LRRC1	53895449	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.922000	0.56462	1.072000	0.40860	0.533000	0.62120	ACA	.	.		0.433	LRRC1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040970.2	NM_025168	
GFRAL	389400	hgsc.bcm.edu	37	6	55198671	55198671	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:55198671A>G	ENST00000340465.2	+	3	331	c.245A>G	c.(244-246)gAg>gGg	p.E82G		NM_207410.2	NP_997293.2	Q6UXV0	GFRAL_HUMAN	GDNF family receptor alpha like	82					negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of neuron apoptotic process (GO:0043524)|stress-activated protein kinase signaling cascade (GO:0031098)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(1)|endometrium(2)|kidney(5)|large_intestine(2)|liver(1)|lung(31)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	48	Lung NSC(77;0.0875)|Renal(3;0.122)		LUSC - Lung squamous cell carcinoma(124;0.23)			CAATTTAAAGAGTGTCTTTGC	0.338																																					p.E82G		Atlas-SNP	.											.	GFRAL	91	.	0			c.A245G						.						135.0	135.0	135.0					6																	55198671		2203	4300	6503	SO:0001583	missense	389400	exon3			TTAAAGAGTGTCT	AY358198	CCDS4957.1	6p12.1	2007-06-22			ENSG00000187871	ENSG00000187871			32789	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 144"""	C6orf144		16086688	Standard	NM_207410		Approved	GRAL, UNQ9356, bA360D14.1	uc003pcm.1	Q6UXV0	OTTHUMG00000014900	ENST00000340465.2:c.245A>G	chr6.hg19:g.55198671A>G	ENSP00000343636:p.Glu82Gly	73.0	0.0		94.0	4.0	NM_207410	Q5VTF6	Missense_Mutation	SNP	ENST00000340465.2	hg19	CCDS4957.1	.	.	.	.	.	.	.	.	.	.	A	7.176	0.588646	0.13812	.	.	ENSG00000187871	ENST00000340465	T	0.31769	1.48	5.12	3.92	0.45320	GDNF/GAS1 (1);	0.565954	0.17857	N	0.159657	T	0.04861	0.0131	N	0.08118	0	0.25933	N	0.982967	B	0.02656	0.0	B	0.04013	0.001	T	0.38714	-0.9648	10	0.25106	T	0.35	-19.2804	7.9232	0.29859	0.9045:0.0:0.0955:0.0	.	82	Q6UXV0	GFRAL_HUMAN	G	82	ENSP00000343636:E82G	ENSP00000343636:E82G	E	+	2	0	GFRAL	55306630	0.989000	0.36119	0.825000	0.32803	0.394000	0.30568	1.867000	0.39499	0.739000	0.32628	0.528000	0.53228	GAG	.	.		0.338	GFRAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040995.2	NM_207410	
UBE3D	90025	hgsc.bcm.edu	37	6	83667146	83667146	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:83667146T>C	ENST00000369747.3	-	9	1156	c.1034A>G	c.(1033-1035)gAc>gGc	p.D345G		NM_198920.1	NP_944602.1	Q7Z6J8	UBE3D_HUMAN	ubiquitin protein ligase E3D	345					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)										GACGCTGATGTCACTTTCCCA	0.418																																					p.D345G		Atlas-SNP	.											.	.	.	.	0			c.A1034G						.						115.0	97.0	103.0					6																	83667146		2203	4300	6503	SO:0001583	missense	90025	exon9			CTGATGTCACTTT	AL137544	CCDS34491.1	6q15	2012-02-24	2012-02-24	2012-02-24	ENSG00000118420	ENSG00000118420			21381	protein-coding gene	gene with protein product	"""UBCH10 binding protein with a hect-like domain"""	612495	"""chromosome 6 open reading frame 157"", ""ubiquitin-conjugating enzyme E2C binding protein"""	C6orf157, UBE2CBP		15749827	Standard	NM_198920		Approved	DKFZp434A1520, H10BH, YJR141W	uc003pjp.2	Q7Z6J8	OTTHUMG00000015108	ENST00000369747.3:c.1034A>G	chr6.hg19:g.83667146T>C	ENSP00000358762:p.Asp345Gly	99.0	0.0		88.0	4.0	NM_198920	B4DP63|Q5T4W2|Q6IPR4|Q75UG0|Q9NT42	Missense_Mutation	SNP	ENST00000369747.3	hg19	CCDS34491.1	.	.	.	.	.	.	.	.	.	.	T	18.88	3.716883	0.68844	.	.	ENSG00000118420	ENST00000369747	T	0.34275	1.37	5.57	5.57	0.84162	.	0.143601	0.64402	D	0.000007	T	0.51415	0.1673	M	0.73598	2.24	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.57751	-0.7757	10	0.66056	D	0.02	-14.4416	13.2543	0.60070	0.0:0.0:0.0:1.0	.	345	Q7Z6J8	UB2CB_HUMAN	G	345	ENSP00000358762:D345G	ENSP00000358762:D345G	D	-	2	0	UBE2CBP	83723865	1.000000	0.71417	1.000000	0.80357	0.746000	0.42486	4.374000	0.59543	2.123000	0.65237	0.379000	0.24179	GAC	.	.		0.418	UBE3D-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041347.7	NM_198920	
ASCC3	10973	hgsc.bcm.edu	37	6	101163393	101163393	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:101163393T>C	ENST00000369162.2	-	13	2440	c.2096A>G	c.(2095-2097)aAc>aGc	p.N699S	ASCC3_ENST00000522650.1_Missense_Mutation_p.N699S	NM_006828.2	NP_006819.2	Q8N3C0	ASCC3_HUMAN	activating signal cointegrator 1 complex subunit 3	699					cell proliferation (GO:0008283)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA duplex unwinding (GO:0032508)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|poly(A) RNA binding (GO:0044822)			breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(20)|liver(1)|lung(36)|ovary(6)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	92		all_cancers(76;1.45e-07)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(87;0.00149)|Hepatocellular(1;0.0893)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0539)|all cancers(137;0.103)|GBM - Glioblastoma multiforme(226;0.199)		TTCATCCATGTTATTCAACTG	0.279																																					p.N699S		Atlas-SNP	.											.	ASCC3	205	.	0			c.A2096G						.						81.0	78.0	79.0					6																	101163393		2200	4291	6491	SO:0001583	missense	10973	exon13			TCCATGTTATTCA	AJ223948	CCDS5046.1, CCDS5047.1, CCDS75497.1	6q16	2008-02-05		2004-07-28	ENSG00000112249	ENSG00000112249			18697	protein-coding gene	gene with protein product	"""RNA helicase family"""	614217	"""helicase, ATP binding 1"""	HELIC1		10218103	Standard	NM_006828		Approved	RNAH, ASC1p200, dJ121G13.4, dJ467N11.1	uc003pqk.3	Q8N3C0	OTTHUMG00000015279	ENST00000369162.2:c.2096A>G	chr6.hg19:g.101163393T>C	ENSP00000358159:p.Asn699Ser	71.0	0.0		75.0	4.0	NM_006828	E7EW23|O43738|Q4G1A0|Q5VTN2|Q9H1I9|Q9H5A2|Q9NTR0	Missense_Mutation	SNP	ENST00000369162.2	hg19	CCDS5046.1	.	.	.	.	.	.	.	.	.	.	T	10.38	1.335422	0.24253	.	.	ENSG00000112249	ENST00000369162;ENST00000522650	T;T	0.57273	0.44;0.41	4.84	4.84	0.62591	Helicase, C-terminal (1);	0.221701	0.45867	D	0.000324	T	0.22551	0.0544	L	0.33137	0.985	0.80722	D	1	B;B	0.20052	0.041;0.041	B;B	0.20184	0.026;0.028	T	0.10451	-1.0629	10	0.08599	T	0.76	.	14.7165	0.69272	0.0:0.0:0.0:1.0	.	699;699	E7EW23;Q8N3C0	.;HELC1_HUMAN	S	699	ENSP00000358159:N699S;ENSP00000430769:N699S	ENSP00000358159:N699S	N	-	2	0	ASCC3	101270114	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	5.736000	0.68597	1.943000	0.56356	0.477000	0.44152	AAC	.	.		0.279	ASCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041632.2	NM_006828	
REV3L	5980	hgsc.bcm.edu	37	6	111686477	111686477	+	Silent	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:111686477T>C	ENST00000358835.3	-	16	7198	c.6744A>G	c.(6742-6744)acA>acG	p.T2248T	REV3L_ENST00000368802.3_Silent_p.T2248T|REV3L_ENST00000368805.1_Silent_p.T2248T|REV3L_ENST00000435970.1_Silent_p.T2170T			O60673	DPOLZ_HUMAN	REV3-like, polymerase (DNA directed), zeta, catalytic subunit	2248					DNA-dependent DNA replication (GO:0006261)|translesion synthesis (GO:0019985)	chromosome (GO:0005694)|nucleus (GO:0005634)|zeta DNA polymerase complex (GO:0016035)	4 iron, 4 sulfur cluster binding (GO:0051539)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			NS(2)|breast(1)|endometrium(6)|kidney(7)|large_intestine(30)|lung(25)|ovary(3)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	88		all_cancers(87;7.57e-06)|Acute lymphoblastic leukemia(125;2.46e-08)|all_hematologic(75;1.08e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.0314)|Epithelial(106;0.057)|all cancers(137;0.0663)		CCTTTGCTTGTGTTAACAGTA	0.294								DNA polymerases (catalytic subunits)																													p.T2248T		Atlas-SNP	.											.	REV3L	386	.	0			c.A6744G						.						129.0	120.0	123.0					6																	111686477		2198	4297	6495	SO:0001819	synonymous_variant	5980	exon15			TGCTTGTGTTAAC	AF058701	CCDS5091.2, CCDS69177.1	6q22	2012-05-18	2012-05-18		ENSG00000009413	ENSG00000009413		"""DNA polymerases"""	9968	protein-coding gene	gene with protein product	"""polymerase, DNA, zeta"""	602776	"""REV3 (yeast homolog)-like, catalytic subunit of DNA polymerase zeta"", ""REV3-like, catalytic subunit of DNA polymerase zeta (yeast)"""			9618506, 9925914	Standard	NM_001286431		Approved	POLZ, REV3	uc003puy.4	O60673	OTTHUMG00000016318	ENST00000358835.3:c.6744A>G	chr6.hg19:g.111686477T>C		33.0	0.0		51.0	4.0	NM_002912	O43214|Q5TC33	Silent	SNP	ENST00000358835.3	hg19	CCDS5091.2																																																																																			.	.		0.294	REV3L-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043695.1	NM_002912	
GOPC	57120	hgsc.bcm.edu	37	6	117923306	117923306	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:117923306T>C	ENST00000368498.2	-	1	221	c.146A>G	c.(145-147)gAt>gGt	p.D49G	GOPC_ENST00000052569.6_Missense_Mutation_p.D49G|GOPC_ENST00000535237.1_Missense_Mutation_p.D49G	NM_020399.3	NP_065132.1	Q9HD26	GOPC_HUMAN	golgi-associated PDZ and coiled-coil motif containing	49					apical protein localization (GO:0045176)|cytoplasmic sequestering of CFTR protein (GO:0043004)|ER to Golgi vesicle-mediated transport (GO:0006888)|Golgi to plasma membrane transport (GO:0006893)|protein homooligomerization (GO:0051260)|protein transport (GO:0015031)|spermatid nucleus differentiation (GO:0007289)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|trans-Golgi network transport vesicle (GO:0030140)	ion channel binding (GO:0044325)|small GTPase regulator activity (GO:0005083)		GOPC/ROS1(14)	endometrium(1)|large_intestine(3)|lung(4)|ovary(1)	9		all_cancers(87;0.00844)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0363)|OV - Ovarian serous cystadenocarcinoma(136;0.0821)|all cancers(137;0.0976)		CAGGAGCAGATCCACATCCAC	0.602			O	ROS1	glioblastoma						OREG0017633	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D49G		Atlas-SNP	.		Dom	yes		6	6q21	57120	golgi associated PDZ and coiled-coil motif containing		O	.	GOPC	29	.	0			c.A146G						.						89.0	81.0	84.0					6																	117923306		2203	4300	6503	SO:0001583	missense	57120	exon1			AGCAGATCCACAT	AF287894	CCDS5117.1, CCDS34523.1	6q21	2010-02-12	2010-02-12		ENSG00000047932	ENSG00000047932			17643	protein-coding gene	gene with protein product		606845				11162552, 11520064	Standard	NM_020399		Approved	dJ94G16.2, PIST, FIG, GOPC1, CAL		Q9HD26	OTTHUMG00000015457	ENST00000368498.2:c.146A>G	chr6.hg19:g.117923306T>C	ENSP00000357484:p.Asp49Gly	74.0	0.0	1484	63.0	4.0	NM_001017408	A6NM30|Q59FS4|Q969U8	Missense_Mutation	SNP	ENST00000368498.2	hg19	CCDS5117.1	.	.	.	.	.	.	.	.	.	.	T	23.2	4.392147	0.83011	.	.	ENSG00000047932	ENST00000052569;ENST00000368498;ENST00000535237	T;T;T	0.32515	1.46;1.45;1.46	5.71	4.55	0.56014	.	0.096929	0.64402	D	0.000002	T	0.43919	0.1269	M	0.73962	2.25	0.53688	D	0.999976	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.50355	-0.8838	10	0.87932	D	0	.	11.5711	0.50834	0.0:0.0697:0.0:0.9303	.	49;49	Q9HD26-2;Q9HD26	.;GOPC_HUMAN	G	49	ENSP00000052569:D49G;ENSP00000357484:D49G;ENSP00000445690:D49G	ENSP00000052569:D49G	D	-	2	0	GOPC	118029999	1.000000	0.71417	1.000000	0.80357	0.800000	0.45204	7.355000	0.79434	0.996000	0.38943	-0.250000	0.11733	GAT	.	.		0.602	GOPC-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041988.1	NM_020399	
TMEM244	253582	hgsc.bcm.edu	37	6	130182310	130182310	+	Silent	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:130182310A>G	ENST00000368143.1	-	1	106	c.24T>C	c.(22-24)gcT>gcC	p.A8A	TMEM244_ENST00000438392.1_Silent_p.A8A	NM_001010876.1	NP_001010876.1	Q5VVB8	TM244_HUMAN	transmembrane protein 244	8						integral component of membrane (GO:0016021)											CCTTGCTTGGAGCAACTCTGA	0.443																																					p.A8A		Atlas-SNP	.											.	.	.	.	0			c.T24C						.						164.0	147.0	153.0					6																	130182310		2203	4300	6503	SO:0001819	synonymous_variant	253582	exon1			GCTTGGAGCAACT		CCDS34536.1	6q22.33	2012-02-21	2012-02-21	2012-02-21	ENSG00000203756	ENSG00000203756			21571	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 191"""	C6orf191			Standard	NM_001010876		Approved	bA174C7.4	uc003qbs.3	Q5VVB8	OTTHUMG00000015553	ENST00000368143.1:c.24T>C	chr6.hg19:g.130182310A>G		91.0	0.0		102.0	5.0	NM_001010876		Silent	SNP	ENST00000368143.1	hg19	CCDS34536.1																																																																																			.	.		0.443	TMEM244-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042194.1	NM_001010876	
HBS1L	10767	hgsc.bcm.edu	37	6	135323883	135323883	+	Silent	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:135323883A>G	ENST00000367837.5	-	5	734	c.528T>C	c.(526-528)ttT>ttC	p.F176F	HBS1L_ENST00000415177.2_Silent_p.F111F|HBS1L_ENST00000314674.3_3'UTR|HBS1L_ENST00000367826.2_Silent_p.F134F|HBS1L_ENST00000367824.4_Silent_p.F12F|HBS1L_ENST00000445176.2_Intron|HBS1L_ENST00000527578.1_Silent_p.F12F	NM_001145158.1|NM_006620.3	NP_001138630.1|NP_006611.1	Q9Y450	HBS1L_HUMAN	HBS1-like translational GTPase	176					signal transduction (GO:0007165)|translation (GO:0006412)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|translation elongation factor activity (GO:0003746)			NS(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	20	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.0046)|GBM - Glioblastoma multiforme(68;0.00702)		CAGGCACTTCAAATCCCATAG	0.428																																					p.F176F		Atlas-SNP	.											.	HBS1L	75	.	0			c.T528C						.						112.0	100.0	104.0					6																	135323883		2203	4300	6503	SO:0001819	synonymous_variant	10767	exon5			CACTTCAAATCCC	U87791	CCDS5173.1, CCDS47479.1, CCDS47480.1	6q23.3	2014-04-30	2014-04-30		ENSG00000112339	ENSG00000112339			4834	protein-coding gene	gene with protein product	"""eRF3 family member"""	612450	"""HBS1 (S. cerevisiae)-like"", ""HBS1-like (S. cerevisiae)"""			9872408, 23667253	Standard	NM_006620		Approved	ERFS, HBS1, HSPC276, KIAA1038, DKFZp434g247, EF-1a, eRF3c	uc003qez.2	Q9Y450	OTTHUMG00000015626	ENST00000367837.5:c.528T>C	chr6.hg19:g.135323883A>G		118.0	0.0		124.0	5.0	NM_006620	B7Z365|Q4VX89|Q4VX90|Q5T7G3|Q8NDW9|Q9UPW3	Silent	SNP	ENST00000367837.5	hg19	CCDS5173.1																																																																																			.	.		0.428	HBS1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042339.2		
VTA1	51534	hgsc.bcm.edu	37	6	142525139	142525139	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:142525139A>G	ENST00000367630.4	+	7	773	c.715A>G	c.(715-717)Atc>Gtc	p.I239V	VTA1_ENST00000452973.2_Intron|VTA1_ENST00000367621.1_Missense_Mutation_p.I181V	NM_016485.3	NP_057569.2	Q9NP79	VTA1_HUMAN	vesicle (multivesicular body) trafficking 1	239	Interaction with VPS4B. {ECO:0000250}.		I -> M (in dbSNP:rs2232307).		endosomal transport (GO:0016197)|membrane organization (GO:0061024)|protein transport (GO:0015031)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)				endometrium(2)|large_intestine(1)|lung(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	12	Breast(32;0.155)			OV - Ovarian serous cystadenocarcinoma(155;1.34e-05)|GBM - Glioblastoma multiforme(68;0.00182)		AAGTAATACTATCCAACCTAC	0.383																																					p.I239V		Atlas-SNP	.											.	VTA1	29	.	0			c.A715G						.						143.0	127.0	132.0					6																	142525139		2203	4300	6503	SO:0001583	missense	51534	exon7			AATACTATCCAAC	AF060225	CCDS5197.1, CCDS69214.1, CCDS75531.1	6q24.1	2013-08-05	2013-08-05	2007-04-03	ENSG00000009844	ENSG00000009844			20954	protein-coding gene	gene with protein product		610902	"""chromosome 6 open reading frame 55"", ""Vps20-associated 1 homolog (S. cerevisiae)"""	C6orf55		11489251, 15644320	Standard	NM_001286372		Approved	HSPC228, My012	uc003qiw.3	Q9NP79	OTTHUMG00000015707	ENST00000367630.4:c.715A>G	chr6.hg19:g.142525139A>G	ENSP00000356602:p.Ile239Val	102.0	0.0		80.0	4.0	NM_016485	B4DW55|E1P594|E7ETQ7|Q5TGM1|Q6IAE8|Q9H0R2|Q9H3K9|Q9P0Q0	Missense_Mutation	SNP	ENST00000367630.4	hg19	CCDS5197.1	.	.	.	.	.	.	.	.	.	.	A	4.862	0.160165	0.09287	.	.	ENSG00000009844	ENST00000367630;ENST00000367621	T;T	0.40756	1.02;1.02	5.79	1.63	0.23807	.	0.268964	0.42172	N	0.000745	T	0.07503	0.0189	N	0.11560	0.145	0.80722	D	1	B	0.02656	0.0	B	0.06405	0.002	T	0.16158	-1.0412	10	0.26408	T	0.33	-3.3433	5.0273	0.14391	0.631:0.1599:0.2091:0.0	.	239	Q9NP79	VTA1_HUMAN	V	239;181	ENSP00000356602:I239V;ENSP00000356593:I181V	ENSP00000356593:I181V	I	+	1	0	VTA1	142566832	1.000000	0.71417	0.997000	0.53966	0.934000	0.57294	1.452000	0.35156	0.028000	0.15324	0.533000	0.62120	ATC	.	.		0.383	VTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042483.2	NM_016485	
LATS1	9113	hgsc.bcm.edu	37	6	150001577	150001577	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:150001577T>C	ENST00000543571.1	-	5	2574	c.2027A>G	c.(2026-2028)gAt>gGt	p.D676G	LATS1_ENST00000542747.1_5'UTR|LATS1_ENST00000253339.5_Missense_Mutation_p.D676G	NM_004690.3	NP_004681.1			large tumor suppressor kinase 1											central_nervous_system(1)|lung(5)	6		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;6.93e-13)|GBM - Glioblastoma multiforme(68;0.116)		ATCCTGGGCATCTTGAGATAA	0.318																																					p.D676G		Atlas-SNP	.											.	LATS1	241	.	0			c.A2027G						.						70.0	76.0	74.0					6																	150001577		2190	4288	6478	SO:0001583	missense	9113	exon5			TGGGCATCTTGAG	AF104413	CCDS34551.1, CCDS59040.1	6q25.1	2013-04-25	2013-04-25		ENSG00000131023	ENSG00000131023			6514	protein-coding gene	gene with protein product		603473	"""LATS (large tumor suppressor, Drosophila) homolog 1"", ""LATS, large tumor suppressor, homolog 1 (Drosophila)"""			9988268, 15122335	Standard	NM_004690		Approved	WARTS	uc003qmu.2	O95835	OTTHUMG00000016437	ENST00000543571.1:c.2027A>G	chr6.hg19:g.150001577T>C	ENSP00000437550:p.Asp676Gly	60.0	0.0		77.0	4.0	NM_004690		Missense_Mutation	SNP	ENST00000543571.1	hg19	CCDS34551.1	.	.	.	.	.	.	.	.	.	.	T	13.33	2.204434	0.38905	.	.	ENSG00000131023	ENST00000543571;ENST00000253339	T;T	0.42900	0.96;0.96	5.49	5.49	0.81192	.	0.202990	0.34046	N	0.004319	T	0.11665	0.0284	N	0.08118	0	0.80722	D	1	B	0.02656	0.0	B	0.06405	0.002	T	0.11131	-1.0600	9	.	.	.	.	15.8809	0.79205	0.0:0.0:0.0:1.0	.	676	O95835	LATS1_HUMAN	G	676	ENSP00000437550:D676G;ENSP00000253339:D676G	.	D	-	2	0	LATS1	150043270	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.929000	0.70096	2.205000	0.71048	0.455000	0.32223	GAT	.	.		0.318	LATS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043923.4	NM_004690	
RAET1L	154064	hgsc.bcm.edu	37	6	150343212	150343212	+	Missense_Mutation	SNP	T	T	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:150343212T>G	ENST00000367341.1	-	2	252	c.253A>C	c.(253-255)Atg>Ctg	p.M85L	RAET1L_ENST00000286380.2_Missense_Mutation_p.M85L			Q5VY80	RET1L_HUMAN	retinoic acid early transcript 1L	85	MHC class I alpha-1 like. {ECO:0000250}.		M -> T (in dbSNP:rs912565). {ECO:0000269|PubMed:11827464, ECO:0000269|PubMed:15489334}.		antigen processing and presentation (GO:0019882)|immune response (GO:0006955)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				endometrium(1)|large_intestine(1)|lung(1)|ovary(1)|skin(1)	5		Ovarian(120;0.028)	BRCA - Breast invasive adenocarcinoma(37;0.193)	OV - Ovarian serous cystadenocarcinoma(155;2.4e-12)		TTCCAGGCCATTGTGACATTT	0.483																																					p.M85L		Atlas-SNP	.											RAET1L,NS,carcinoma,0,2	RAET1L	21	.	0			c.A253C						.																																			SO:0001583	missense	154064	exon2			AGGCCATTGTGAC	AY039682	CCDS5224.1	6q24.1-25.1	2008-02-05			ENSG00000155918	ENSG00000155918			16798	protein-coding gene	gene with protein product		611047				11827464	Standard	NM_130900		Approved		uc011eei.2	Q5VY80	OTTHUMG00000015809	ENST00000367341.1:c.253A>C	chr6.hg19:g.150343212T>G	ENSP00000356310:p.Met85Leu	263.0	0.0		247.0	0.0	NM_130900	A3KME4|Q8TE74	Missense_Mutation	SNP	ENST00000367341.1	hg19	CCDS5224.1	.	.	.	.	.	.	.	.	.	.	t	6.430	0.447513	0.12223	.	.	ENSG00000155918	ENST00000367341;ENST00000286380	T;T	0.06218	3.33;3.33	1.91	-2.05	0.07321	MHC class I, alpha chain, alpha1/alpha2 (1);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	.	.	.	.	T	0.00967	0.0032	N	0.08118	0	0.09310	N	1	B	0.11235	0.004	B	0.04013	0.001	T	0.47548	-0.9109	9	0.87932	D	0	.	5.9233	0.19094	0.0:0.5665:0.0:0.4335	.	85	Q5VY80	RET1L_HUMAN	L	85	ENSP00000356310:M85L;ENSP00000286380:M85L	ENSP00000286380:M85L	M	-	1	0	RAET1L	150384905	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.287000	0.01151	-0.549000	0.06191	0.402000	0.26972	ATG	.	.		0.483	RAET1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042676.1	NM_130900	
MTHFD1L	25902	hgsc.bcm.edu	37	6	151209073	151209073	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:151209073A>G	ENST00000367321.3	+	7	1010	c.736A>G	c.(736-738)Atg>Gtg	p.M246V	MTHFD1L_ENST00000367307.4_Missense_Mutation_p.M246V	NM_001242767.1|NM_001242768.1|NM_015440.4	NP_001229696.1|NP_001229697.1|NP_056255.2	Q6UB35	C1TM_HUMAN	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1-like	246	Methylenetetrahydrofolate dehydrogenase and cyclohydrolase.				folic acid-containing compound biosynthetic process (GO:0009396)|folic acid-containing compound metabolic process (GO:0006760)|formate metabolic process (GO:0015942)|one-carbon metabolic process (GO:0006730)|oxidation-reduction process (GO:0055114)|tetrahydrofolate interconversion (GO:0035999)|tetrahydrofolate metabolic process (GO:0046653)	membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|formate-tetrahydrofolate ligase activity (GO:0004329)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(12)|lung(8)|ovary(3)|prostate(1)|upper_aerodigestive_tract(2)	29		Ovarian(120;0.128)		OV - Ovarian serous cystadenocarcinoma(155;8.7e-12)		AAAAGGGTCCATGACAATGAG	0.438																																					p.M247V		Atlas-SNP	.											.	MTHFD1L	75	.	0			c.A739G						.						101.0	101.0	101.0					6																	151209073		2203	4300	6503	SO:0001583	missense	25902	exon7			GGGTCCATGACAA	BC017477	CCDS5228.1, CCDS56457.1, CCDS75535.1, CCDS75536.1	6q25.1	2010-07-19	2004-12-13	2004-12-14	ENSG00000120254	ENSG00000120254	6.3.4.3		21055	protein-coding gene	gene with protein product	"""10-formyl-THF synthetase"", ""mitochondrial C1-tetrahydrofolate synthase"", ""monofunctional C1-tetrahydrofolate synthase, mitochondrial"""	611427	"""formyltetrahydrofolate synthetase domain containing 1"""	FTHFSDC1		18804703	Standard	NM_015440		Approved	DKFZP586G1517, FLJ21145	uc021zgs.1	Q6UB35	OTTHUMG00000015828	ENST00000367321.3:c.736A>G	chr6.hg19:g.151209073A>G	ENSP00000356290:p.Met246Val	105.0	0.0		84.0	4.0	NM_001242767	Q2TBF3|Q8WVW0|Q96HG8|Q9H789|Q9UFU8	Missense_Mutation	SNP	ENST00000367321.3	hg19	CCDS5228.1	.	.	.	.	.	.	.	.	.	.	A	5.497	0.276697	0.10403	.	.	ENSG00000120254	ENST00000367321;ENST00000367307;ENST00000443074;ENST00000425276	T;T;T;T	0.56444	0.46;0.46;0.46;0.46	5.37	1.49	0.22878	Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain (1);NAD(P)-binding domain (1);	0.624222	0.18361	N	0.143566	T	0.14227	0.0344	N	0.12182	0.205	0.27183	N	0.960617	B;B;B;B	0.21309	0.002;0.0;0.002;0.054	B;B;B;B	0.20577	0.003;0.002;0.003;0.03	T	0.19976	-1.0289	10	0.72032	D	0.01	.	7.9037	0.29750	0.4834:0.4421:0.0745:0.0	.	247;1;246;246	B7ZM99;B2RD24;Q6UB35;Q6UB35-2	.;.;C1TM_HUMAN;.	V	246;246;91;91	ENSP00000356290:M246V;ENSP00000356276:M246V;ENSP00000415039:M91V;ENSP00000414412:M91V	ENSP00000356276:M246V	M	+	1	0	MTHFD1L	151250766	0.997000	0.39634	0.952000	0.39060	0.768000	0.43524	0.781000	0.26774	0.100000	0.17581	-0.340000	0.08031	ATG	.	.		0.438	MTHFD1L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042699.1	NM_015440	
SYNE1	23345	hgsc.bcm.edu	37	6	152472763	152472763	+	Silent	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:152472763T>C	ENST00000367255.5	-	135	24976	c.24375A>G	c.(24373-24375)acA>acG	p.T8125T	SYNE1_ENST00000539504.1_Silent_p.T280T|SYNE1_ENST00000356820.4_Silent_p.T2649T|SYNE1_ENST00000354674.4_Silent_p.T280T|SYNE1_ENST00000265368.4_Silent_p.T8125T|SYNE1_ENST00000448038.1_Silent_p.T8054T|SYNE1_ENST00000347037.5_5'UTR|SYNE1_ENST00000341594.5_Silent_p.T7737T|SYNE1_ENST00000423061.1_Silent_p.T8054T	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	8125					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		GATCCATCTCTGTGAGCCAGA	0.393										HNSCC(10;0.0054)																											p.T8125T		Atlas-SNP	.											.	SYNE1	3227	.	0			c.A24375G						.						47.0	47.0	47.0					6																	152472763		2203	4300	6503	SO:0001819	synonymous_variant	23345	exon135			CATCTCTGTGAGC	AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"""myocyte nuclear envelope protein 1"", ""nuclear envelope spectrin repeat-1"""	608441	"""chromosome 6 open reading frame 98"""	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.24375A>G	chr6.hg19:g.152472763T>C		86.0	0.0		71.0	4.0	NM_182961	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Silent	SNP	ENST00000367255.5	hg19	CCDS5236.2																																																																																			.	.		0.393	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961	
CNKSR3	154043	hgsc.bcm.edu	37	6	154731499	154731499	+	Silent	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:154731499T>C	ENST00000607772.1	-	12	1891	c.1347A>G	c.(1345-1347)agA>agG	p.R449R	CNKSR3_ENST00000479339.1_Silent_p.R369R|CNKSR3_ENST00000433165.2_Silent_p.R274R	NM_173515.2	NP_775786.2	Q6P9H4	CNKR3_HUMAN	CNKSR family member 3	449	DUF1170.				negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)	cytoplasm (GO:0005737)|membrane (GO:0016020)				breast(2)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|skin(1)|stomach(1)|urinary_tract(1)	15		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;5.03e-11)|BRCA - Breast invasive adenocarcinoma(81;0.00627)		GACCTCGAGGTCTGGCAAAAG	0.532																																					p.R449R		Atlas-SNP	.											.	CNKSR3	56	.	0			c.A1347G						.						107.0	97.0	101.0					6																	154731499		2203	4300	6503	SO:0001819	synonymous_variant	154043	exon12			TCGAGGTCTGGCA	AK055911	CCDS5246.1	6q25.2	2013-01-10	2005-04-11	2005-04-11	ENSG00000153721	ENSG00000153721		"""Sterile alpha motif (SAM) domain containing"""	23034	protein-coding gene	gene with protein product			"""membrane associated guanylate kinase interacting protein-like 1"""	MAGI1			Standard	NM_173515		Approved	FLJ31349		Q6P9H4	OTTHUMG00000015873	ENST00000607772.1:c.1347A>G	chr6.hg19:g.154731499T>C		67.0	0.0		88.0	5.0	NM_173515	Q5SGD5|Q96N65	Silent	SNP	ENST00000607772.1	hg19	CCDS5246.1																																																																																			.	.		0.532	CNKSR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042792.2	NM_173515	
T	6862	hgsc.bcm.edu	37	6	166578153	166578153	+	Splice_Site	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:166578153T>C	ENST00000296946.2	-	6	1138	c.670A>G	c.(670-672)Agt>Ggt	p.S224G	T_ENST00000366871.3_Splice_Site_p.S224G	NM_003181.3	NP_003172.1	O15178	BRAC_HUMAN	T, brachyury homolog (mouse)	224					anterior/posterior axis specification, embryo (GO:0008595)|BMP signaling pathway (GO:0030509)|bone morphogenesis (GO:0060349)|canonical Wnt signaling pathway (GO:0060070)|determination of heart left/right asymmetry (GO:0061371)|embryonic skeletal system development (GO:0048706)|heart morphogenesis (GO:0003007)|mesoderm development (GO:0007498)|mesoderm migration involved in gastrulation (GO:0007509)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural plate morphogenesis (GO:0001839)|neural tube closure (GO:0001843)|notochord formation (GO:0014028)|penetration of zona pellucida (GO:0007341)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003257)|post-anal tail morphogenesis (GO:0036342)|primitive streak formation (GO:0090009)|signal transduction (GO:0007165)|signal transduction involved in regulation of gene expression (GO:0023019)|SMAD protein signal transduction (GO:0060395)|somitogenesis (GO:0001756)|transcription from RNA polymerase II promoter (GO:0006366)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(23)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	39		Prostate(117;4.48e-07)|Ovarian(120;1.78e-06)|Breast(66;2.54e-06)|Lung SC(201;0.0225)|Esophageal squamous(34;0.0559)		OV - Ovarian serous cystadenocarcinoma(33;1.09e-113)|GBM - Glioblastoma multiforme(31;1.51e-108)|BRCA - Breast invasive adenocarcinoma(81;8.45e-09)|LUAD - Lung adenocarcinoma(999;0.0407)		TTGTGATCACTTCTATCAAAA	0.378									Chordoma, Familial Clustering of																												p.S224G		Atlas-SNP	.											.	T	77	.	0			c.A670G						.						81.0	84.0	83.0					6																	166578153		2203	4300	6503	SO:0001630	splice_region_variant	6862	exon6	Familial Cancer Database		GATCACTTCTATC	AJ001699	CCDS5290.1, CCDS59045.1	6q27	2011-06-13	2001-11-28		ENSG00000164458	ENSG00000164458		"""T-boxes"""	11515	protein-coding gene	gene with protein product		601397	"""T brachyury (mouse) homolog"""			8963900	Standard	NM_003181		Approved		uc003quu.2	O15178	OTTHUMG00000015991	ENST00000296946.2:c.669-1A>G	chr6.hg19:g.166578153T>C		59.0	0.0		71.0	4.0	NM_003181	E7ERD6|Q4KMP4	Missense_Mutation	SNP	ENST00000296946.2	hg19	CCDS5290.1	.	.	.	.	.	.	.	.	.	.	T	11.68	1.711687	0.30322	.	.	ENSG00000164458	ENST00000366876;ENST00000296946;ENST00000366871	D;D;D	0.83755	-1.74;-1.76;-1.76	5.44	5.44	0.79542	p53-like transcription factor, DNA-binding (1);	0.377574	0.30126	N	0.010358	T	0.78426	0.4281	M	0.85299	2.745	0.40635	D	0.98189	B;B;B	0.18968	0.032;0.001;0.032	B;B;B	0.19946	0.027;0.003;0.027	T	0.77205	-0.2673	10	0.32370	T	0.25	.	14.707	0.69198	0.0:0.0:0.0:1.0	.	224;224;224	E7ERD6;O15178;Q4KMP4	.;BRAC_HUMAN;.	G	224	ENSP00000355841:S224G;ENSP00000296946:S224G;ENSP00000355836:S224G	ENSP00000296946:S224G	S	-	1	0	T	166498143	1.000000	0.71417	0.969000	0.41365	0.069000	0.16628	7.008000	0.76341	2.061000	0.61500	0.528000	0.53228	AGT	.	.		0.378	T-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043037.2	NM_003181	Missense_Mutation
INTS1	26173	hgsc.bcm.edu	37	7	1542815	1542815	+	Missense_Mutation	SNP	G	G	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:1542815G>C	ENST00000404767.3	-	3	156	c.71C>G	c.(70-72)cCa>cGa	p.P24R	INTS1_ENST00000389470.4_Missense_Mutation_p.P152R|INTS1_ENST00000493531.1_5'Flank	NM_001080453.2	NP_001073922.2	Q8N201	INT1_HUMAN	integrator complex subunit 1	24					inner cell mass cell proliferation (GO:0001833)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|snRNA processing (GO:0016180)|U2 snRNA 3'-end processing (GO:0034474)	integral component of membrane (GO:0016021)|integrator complex (GO:0032039)|membrane (GO:0016020)		p.P152Q(1)		autonomic_ganglia(1)|cervix(1)|endometrium(14)|kidney(3)|large_intestine(7)|lung(24)|ovary(1)|prostate(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	62		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|OV - Ovarian serous cystadenocarcinoma(56;6.99e-15)		GAAGTCTCCTGGGGGAGGGTG	0.562																																					p.P24R		Atlas-SNP	.											INTS1,colon,carcinoma,0,1	INTS1	145	.	1	Substitution - Missense(1)	lung(1)	c.C71G						.						43.0	49.0	47.0					7																	1542815		1905	4123	6028	SO:0001583	missense	26173	exon3			TCTCCTGGGGGAG	AB037861	CCDS47526.1	7p22.3	2009-11-06			ENSG00000164880	ENSG00000164880			24555	protein-coding gene	gene with protein product		611345				16239144	Standard	NM_001080453		Approved	DKFZp586J0619, KIAA1440, INT1, NET28	uc003skn.2	Q8N201	OTTHUMG00000151449	ENST00000404767.3:c.71C>G	chr7.hg19:g.1542815G>C	ENSP00000385722:p.Pro24Arg	115.0	0.0		156.0	0.0	NM_001080453	A6NJ44|Q6NT70|Q6UX74|Q8WV40|Q96D36|Q9NTD1|Q9P2A8|Q9Y3W8	Missense_Mutation	SNP	ENST00000404767.3	hg19	CCDS47526.1	.	.	.	.	.	.	.	.	.	.	G	14.92	2.679394	0.47886	.	.	ENSG00000164880	ENST00000404767;ENST00000389470	T;T	0.52526	0.66;0.67	4.75	4.75	0.60458	.	0.000000	0.85682	D	0.000000	T	0.46833	0.1413	L	0.55481	1.735	0.58432	D	0.999999	P;P	0.51240	0.725;0.943	B;B	0.41813	0.135;0.367	T	0.56275	-0.8006	10	0.72032	D	0.01	.	16.6607	0.85240	0.0:0.0:1.0:0.0	.	152;24	A4D212;Q8N201	.;INT1_HUMAN	R	24;152	ENSP00000385722:P24R;ENSP00000374121:P152R	ENSP00000374121:P152R	P	-	2	0	INTS1	1509341	1.000000	0.71417	0.145000	0.22337	0.617000	0.37484	8.978000	0.93450	2.455000	0.83008	0.563000	0.77884	CCA	.	.		0.562	INTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323683.1		
CYTH3	9265	hgsc.bcm.edu	37	7	6210573	6210573	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:6210573A>G	ENST00000350796.3	-	8	735	c.599T>C	c.(598-600)cTc>cCc	p.L200P	CYTH3_ENST00000488964.1_5'UTR|CYTH3_ENST00000396741.2_Missense_Mutation_p.L115P	NM_004227.3	NP_004218.1	O43739	CYH3_HUMAN	cytohesin 3	200	SEC7. {ECO:0000255|PROSITE- ProRule:PRU00189}.				establishment of epithelial cell polarity (GO:0090162)|Golgi vesicle transport (GO:0048193)|positive regulation of cell adhesion (GO:0045785)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)|regulation of cell adhesion (GO:0030155)	cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(7)|urinary_tract(1)	19						GCTGGTGTTGAGCATGATGAT	0.627																																					p.L200P		Atlas-SNP	.											.	CYTH3	44	.	0			c.T599C						.						176.0	126.0	143.0					7																	6210573		2203	4300	6503	SO:0001583	missense	9265	exon8			GTGTTGAGCATGA	AJ223957	CCDS5346.1	7p22.1	2014-05-02	2008-08-14	2008-08-14	ENSG00000008256	ENSG00000008256		"""Pleckstrin homology (PH) domain containing"""	9504	protein-coding gene	gene with protein product		605081	"""pleckstrin homology, Sec7 and coiled-coil domains 3"""	PSCD3		9072969	Standard	NM_004227		Approved	GRP1, ARNO3, cytohesin-3	uc003spt.3	O43739	OTTHUMG00000023440	ENST00000350796.3:c.599T>C	chr7.hg19:g.6210573A>G	ENSP00000297044:p.Leu200Pro	94.0	0.0		150.0	7.0	NM_004227	A4D2N8	Missense_Mutation	SNP	ENST00000350796.3	hg19	CCDS5346.1	.	.	.	.	.	.	.	.	.	.	A	27.0	4.786967	0.90367	.	.	ENSG00000008256	ENST00000350796;ENST00000396741	D;D	0.81821	-1.54;-1.54	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	D	0.93779	0.8011	H	0.98351	4.21	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.96116	0.9081	10	0.87932	D	0	.	15.1785	0.72934	1.0:0.0:0.0:0.0	.	115;200	B7Z2V9;O43739-2	.;.	P	200;115	ENSP00000297044:L200P;ENSP00000379967:L115P	ENSP00000297044:L200P	L	-	2	0	CYTH3	6177098	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.092000	0.94157	1.996000	0.58369	0.533000	0.62120	CTC	.	.		0.627	CYTH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207396.2	NM_004227	
AVL9	23080	hgsc.bcm.edu	37	7	32535339	32535339	+	Silent	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:32535339A>G	ENST00000318709.4	+	1	239	c.18A>G	c.(16-18)agA>agG	p.R6R	LSM5_ENST00000409952.3_5'Flank|AVL9_ENST00000409301.1_Silent_p.R6R|LSM5_ENST00000409909.3_5'Flank|AVL9_ENST00000404479.1_Silent_p.R6R|AVL9_ENST00000459629.1_3'UTR	NM_015060.1	NP_055875.1	Q8NBF6	AVL9_HUMAN	AVL9 homolog (S. cerevisiase)	6					cell migration (GO:0016477)	integral component of membrane (GO:0016021)|recycling endosome (GO:0055037)				endometrium(3)|kidney(1)|large_intestine(3)|lung(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	18						AGGCCAGGAGAGGCGGGGATG	0.721																																					p.R6R		Atlas-SNP	.											.	AVL9	66	.	0			c.A18G						.						8.0	12.0	11.0					7																	32535339		1821	3622	5443	SO:0001819	synonymous_variant	23080	exon1			CAGGAGAGGCGGG	D87682	CCDS34613.1	7p14.3	2013-05-01	2008-10-03	2008-10-03	ENSG00000105778	ENSG00000105778			28994	protein-coding gene	gene with protein product		612927	"""KIAA0241"""	KIAA0241		17229886, 22595670	Standard	XM_005249668		Approved		uc003tcv.1	Q8NBF6	OTTHUMG00000152929	ENST00000318709.4:c.18A>G	chr7.hg19:g.32535339A>G		41.0	0.0		125.0	8.0	NM_015060	Q92573	Silent	SNP	ENST00000318709.4	hg19	CCDS34613.1																																																																																			.	.		0.721	AVL9-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328643.1	NM_015060	
BMPER	168667	hgsc.bcm.edu	37	7	33976905	33976905	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:33976905A>G	ENST00000297161.2	+	4	598	c.224A>G	c.(223-225)aAg>aGg	p.K75R	BMPER_ENST00000426693.1_Missense_Mutation_p.K75R	NM_133468.4	NP_597725.1	Q8N8U9	BMPER_HUMAN	BMP binding endothelial regulator	75	VWFC 1. {ECO:0000255|PROSITE- ProRule:PRU00220}.				blood vessel endothelial cell proliferation involved in sprouting angiogenesis (GO:0002043)|endothelial cell activation (GO:0042118)|inner ear development (GO:0048839)|negative regulation of BMP signaling pathway (GO:0030514)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|regulation of endothelial cell migration (GO:0010594)|regulation of pathway-restricted SMAD protein phosphorylation (GO:0060393)|ureteric bud development (GO:0001657)	extracellular space (GO:0005615)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(24)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48						GTCTAGAACAAGGAAGTGACA	0.488																																					p.K75R		Atlas-SNP	.											.	BMPER	131	.	0			c.A224G						.						92.0	88.0	89.0					7																	33976905		2203	4300	6503	SO:0001583	missense	168667	exon4			AGAACAAGGAAGT		CCDS5442.1	7p14.3	2009-02-18			ENSG00000164619	ENSG00000164619			24154	protein-coding gene	gene with protein product	"""crossveinless-2"""	608699				12897139, 14766204	Standard	NM_133468		Approved	Cv2, CRIM3	uc011kap.2	Q8N8U9	OTTHUMG00000128675	ENST00000297161.2:c.224A>G	chr7.hg19:g.33976905A>G	ENSP00000297161:p.Lys75Arg	73.0	0.0		98.0	4.0	NM_133468	A8K1P8|Q8TF36	Missense_Mutation	SNP	ENST00000297161.2	hg19	CCDS5442.1	.	.	.	.	.	.	.	.	.	.	A	21.5	4.153705	0.78114	.	.	ENSG00000164619	ENST00000297161;ENST00000426693	T;T	0.64618	-0.11;-0.11	5.09	5.09	0.68999	von Willebrand factor, type C (2);	0.204689	0.41938	D	0.000788	T	0.52789	0.1756	L	0.44542	1.39	0.48236	D	0.999613	P	0.39282	0.666	B	0.33339	0.162	T	0.58434	-0.7637	10	0.52906	T	0.07	.	14.84	0.70217	1.0:0.0:0.0:0.0	.	75	Q8N8U9	BMPER_HUMAN	R	75	ENSP00000297161:K75R;ENSP00000393950:K75R	ENSP00000297161:K75R	K	+	2	0	BMPER	33943430	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.522000	0.67092	1.898000	0.54952	0.460000	0.39030	AAG	.	.		0.488	BMPER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250570.2	NM_133468	
BMPER	168667	hgsc.bcm.edu	37	7	33976996	33976996	+	Nonsense_Mutation	SNP	C	C	A			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:33976996C>A	ENST00000297161.2	+	4	689	c.315C>A	c.(313-315)tgC>tgA	p.C105*	BMPER_ENST00000426693.1_Nonsense_Mutation_p.C105*	NM_133468.4	NP_597725.1	Q8N8U9	BMPER_HUMAN	BMP binding endothelial regulator	105	VWFC 1. {ECO:0000255|PROSITE- ProRule:PRU00220}.				blood vessel endothelial cell proliferation involved in sprouting angiogenesis (GO:0002043)|endothelial cell activation (GO:0042118)|inner ear development (GO:0048839)|negative regulation of BMP signaling pathway (GO:0030514)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|regulation of endothelial cell migration (GO:0010594)|regulation of pathway-restricted SMAD protein phosphorylation (GO:0060393)|ureteric bud development (GO:0001657)	extracellular space (GO:0005615)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(24)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48						GTGAACAGTGCAAAGGTGATT	0.502																																					p.C105X		Atlas-SNP	.											.	BMPER	131	.	0			c.C315A						.						118.0	106.0	110.0					7																	33976996		2203	4300	6503	SO:0001587	stop_gained	168667	exon4			ACAGTGCAAAGGT		CCDS5442.1	7p14.3	2009-02-18			ENSG00000164619	ENSG00000164619			24154	protein-coding gene	gene with protein product	"""crossveinless-2"""	608699				12897139, 14766204	Standard	NM_133468		Approved	Cv2, CRIM3	uc011kap.2	Q8N8U9	OTTHUMG00000128675	ENST00000297161.2:c.315C>A	chr7.hg19:g.33976996C>A	ENSP00000297161:p.Cys105*	109.0	0.0		97.0	24.0	NM_133468	A8K1P8|Q8TF36	Nonsense_Mutation	SNP	ENST00000297161.2	hg19	CCDS5442.1	.	.	.	.	.	.	.	.	.	.	C	16.35	3.098639	0.56183	.	.	ENSG00000164619	ENST00000297161;ENST00000426693	.	.	.	5.18	3.37	0.38596	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.5775	0.33607	0.0:0.6989:0.0:0.3011	.	.	.	.	X	105	.	ENSP00000297161:C105X	C	+	3	2	BMPER	33943521	1.000000	0.71417	1.000000	0.80357	0.620000	0.37586	0.978000	0.29488	1.165000	0.42670	0.563000	0.77884	TGC	.	.		0.502	BMPER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250570.2	NM_133468	
CDK13	8621	hgsc.bcm.edu	37	7	40027428	40027428	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:40027428A>G	ENST00000181839.4	+	2	2047	c.1442A>G	c.(1441-1443)gAg>gGg	p.E481G	CDK13_ENST00000340829.5_Missense_Mutation_p.E481G	NM_003718.4|NM_031267.3	NP_003709.3|NP_112557.2	Q14004	CDK13_HUMAN	cyclin-dependent kinase 13	481					alternative mRNA splicing, via spliceosome (GO:0000380)|hemopoiesis (GO:0030097)|multicellular organismal development (GO:0007275)|phosphorylation of RNA polymerase II C-terminal domain (GO:0070816)|positive regulation of cell proliferation (GO:0008284)|regulation of mitosis (GO:0007088)|viral process (GO:0016032)	cyclin K-CDK13 complex (GO:0002945)|extracellular space (GO:0005615)|nuclear cyclin-dependent protein kinase holoenzyme complex (GO:0019908)|nuclear speck (GO:0016607)	ATP binding (GO:0005524)|cyclin binding (GO:0030332)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)			cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(19)|ovary(1)|pancreas(2)|prostate(2)|skin(5)|stomach(2)|urinary_tract(1)	49						AAGGCTGCTGAGGCTGCTGCC	0.502																																					p.E481G		Atlas-SNP	.											.	CDK13	114	.	0			c.A1442G						.						43.0	42.0	42.0					7																	40027428		2203	4300	6503	SO:0001583	missense	8621	exon2			CTGCTGAGGCTGC	M80629	CCDS5461.1, CCDS5462.1	7p14.1	2011-11-08	2009-12-16	2009-12-16	ENSG00000065883	ENSG00000065883		"""Cyclin-dependent kinases"""	1733	protein-coding gene	gene with protein product	"""cholinesterase-related cell division controller"""	603309	"""cell division cycle 2-like 5 (cholinesterase-related cell division controller)"""	CDC2L5		1731328, 19884882	Standard	NM_003718		Approved	CHED, CDC2L, KIAA1791	uc003thh.4	Q14004	OTTHUMG00000023726	ENST00000181839.4:c.1442A>G	chr7.hg19:g.40027428A>G	ENSP00000181839:p.Glu481Gly	70.0	0.0		89.0	4.0	NM_003718	Q53G78|Q6DKQ9|Q75MH4|Q75MH5|Q96JN4|Q9H4A0|Q9H4A1|Q9UDR4	Missense_Mutation	SNP	ENST00000181839.4	hg19	CCDS5461.1	.	.	.	.	.	.	.	.	.	.	A	14.05	2.419165	0.42918	.	.	ENSG00000065883	ENST00000181839;ENST00000340829	T;T	0.70631	-0.5;-0.5	4.56	4.56	0.56223	.	.	.	.	.	T	0.55097	0.1899	L	0.29908	0.895	0.34445	D	0.700002	P;P	0.40731	0.728;0.608	B;B	0.36186	0.219;0.109	T	0.64558	-0.6379	8	.	.	.	-9.874	10.6057	0.45392	1.0:0.0:0.0:0.0	.	481;481	Q14004-2;Q14004	.;CDK13_HUMAN	G	481	ENSP00000181839:E481G;ENSP00000340557:E481G	.	E	+	2	0	CDK13	39993953	1.000000	0.71417	1.000000	0.80357	0.891000	0.51852	2.298000	0.43602	2.280000	0.76307	0.460000	0.39030	GAG	.	.		0.502	CDK13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250726.2	NM_003718	
MYO1G	64005	hgsc.bcm.edu	37	7	45006272	45006272	+	Splice_Site	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:45006272T>C	ENST00000258787.7	-	15	2084	c.1948A>G	c.(1948-1950)Agg>Ggg	p.R650G		NM_033054.2	NP_149043.2	B0I1T2	MYO1G_HUMAN	myosin IG	650	Myosin motor.					extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|myosin complex (GO:0016459)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|pancreas(1)|skin(4)	28						TGCCAGTACCTGAGCAGGAAT	0.617																																					p.R650G		Atlas-SNP	.											.	MYO1G	86	.	0			c.A1948G						.						55.0	54.0	55.0					7																	45006272		2203	4300	6503	SO:0001630	splice_region_variant	64005	exon15			AGTACCTGAGCAG	AF380932	CCDS34629.1	7p13-p11.2	2011-09-27			ENSG00000136286	ENSG00000136286		"""Myosins / Myosin superfamily : Class I"""	13880	protein-coding gene	gene with protein product	"""minor histocompatibility antigen HA-2"""	600642					Standard	NM_033054		Approved	HA-2	uc003tmh.2	B0I1T2	OTTHUMG00000155821	ENST00000258787.7:c.1949+1A>G	chr7.hg19:g.45006272T>C		83.0	0.0		82.0	4.0	NM_033054	Q8TEI9|Q8TES2|Q96BE2|Q96RI5|Q96RI6	Missense_Mutation	SNP	ENST00000258787.7	hg19	CCDS34629.1	.	.	.	.	.	.	.	.	.	.	T	18.02	3.530275	0.64860	.	.	ENSG00000136286	ENST00000258787	D	0.91295	-2.82	4.61	4.61	0.57282	Myosin head, motor domain (2);	0.000000	0.42682	D	0.000676	D	0.96519	0.8864	H	0.96662	3.86	0.58432	D	0.99999	D;D	0.89917	0.999;1.0	D;D	0.97110	0.999;1.0	D	0.96806	0.9593	10	0.87932	D	0	.	10.0732	0.42345	0.0:0.0:0.1685:0.8315	.	650;650	B0I1T2-4;B0I1T2	.;MYO1G_HUMAN	G	650	ENSP00000258787:R650G	ENSP00000258787:R650G	R	-	1	2	MYO1G	44972797	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	1.812000	0.38952	1.829000	0.53265	0.482000	0.46254	AGG	.	.		0.617	MYO1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341832.2		Missense_Mutation
SUN3	256979	hgsc.bcm.edu	37	7	48026998	48026998	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:48026998T>C	ENST00000297325.4	-	10	1162	c.1003A>G	c.(1003-1005)Aac>Gac	p.N335D	SUN3_ENST00000412142.1_Missense_Mutation_p.N247D|SUN3_ENST00000473723.1_5'UTR|SUN3_ENST00000395572.2_Missense_Mutation_p.N335D|SUN3_ENST00000453192.2_Missense_Mutation_p.N323D	NM_001030019.1	NP_001025190.1	Q8TAQ9	SUN3_HUMAN	Sad1 and UNC84 domain containing 3	335	SUN. {ECO:0000255|PROSITE- ProRule:PRU00802}.					integral component of membrane (GO:0016021)|SUN-KASH complex (GO:0034993)				central_nervous_system(1)|endometrium(3)|large_intestine(8)|liver(1)|lung(15)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						TGTCCCCAGTTGCTAAAGATA	0.378																																					p.N335D		Atlas-SNP	.											.	SUN3	52	.	0			c.A1003G						.						134.0	137.0	136.0					7																	48026998		2203	4300	6503	SO:0001583	missense	256979	exon11			CCCAGTTGCTAAA	AF429967	CCDS34636.1, CCDS64647.1	7p12.3	2010-01-27	2010-01-27	2010-01-27	ENSG00000164744	ENSG00000164744			22429	protein-coding gene	gene with protein product			"""Sad1 and UNC84 domain containing 1"""	SUNC1			Standard	NM_001284350		Approved	MGC33329	uc003tof.3	Q8TAQ9	OTTHUMG00000155646	ENST00000297325.4:c.1003A>G	chr7.hg19:g.48026998T>C	ENSP00000297325:p.Asn335Asp	89.0	0.0		108.0	5.0	NM_152782	A4D2F3|B4DXK1|D3DVM3|E7EWC8|Q4F965|Q7Z4U8	Missense_Mutation	SNP	ENST00000297325.4	hg19	CCDS34636.1	.	.	.	.	.	.	.	.	.	.	T	27.6	4.844774	0.91197	.	.	ENSG00000164744	ENST00000297325;ENST00000412142;ENST00000395572;ENST00000453192;ENST00000438771	T;T;T;T;T	0.53857	0.6;0.6;0.6;0.6;0.6	5.64	5.64	0.86602	Sad1/UNC-like, C-terminal (2);	0.000000	0.85682	D	0.000000	T	0.79707	0.4492	H	0.94847	3.59	0.54753	D	0.999982	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.998;0.999	D	0.85379	0.1118	10	0.87932	D	0	.	13.8147	0.63283	0.0:0.0:0.0:1.0	.	323;247;335	E7EWC8;Q8TAQ9-2;Q8TAQ9	.;.;SUN3_HUMAN	D	335;247;335;323;247	ENSP00000297325:N335D;ENSP00000410204:N247D;ENSP00000378939:N335D;ENSP00000387525:N323D;ENSP00000409077:N247D	ENSP00000297325:N335D	N	-	1	0	SUN3	47993523	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	7.443000	0.80521	2.151000	0.67156	0.477000	0.44152	AAC	.	.		0.378	SUN3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340962.1	NM_152782	
ABCA13	154664	hgsc.bcm.edu	37	7	48313397	48313397	+	Silent	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:48313397A>G	ENST00000435803.1	+	17	4158	c.4134A>G	c.(4132-4134)ttA>ttG	p.L1378L		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	1378					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						TAGACACGTTAAATTCCACAT	0.343																																					p.L1378L		Atlas-SNP	.											.	ABCA13	1192	.	0			c.A4134G						.						52.0	49.0	50.0					7																	48313397		1867	4093	5960	SO:0001819	synonymous_variant	154664	exon17			CACGTTAAATTCC	AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"""ATP binding cassette transporters / subfamily A"""	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.4134A>G	chr7.hg19:g.48313397A>G		66.0	0.0		82.0	21.0	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Silent	SNP	ENST00000435803.1	hg19	CCDS47584.1																																																																																			.	.		0.343	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701	
IKZF1	10320	hgsc.bcm.edu	37	7	50467992	50467992	+	Silent	SNP	C	C	T			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:50467992C>T	ENST00000331340.3	+	8	1382	c.1227C>T	c.(1225-1227)agC>agT	p.S409S	IKZF1_ENST00000440768.2_3'UTR|IKZF1_ENST00000357364.4_Silent_p.S322S|IKZF1_ENST00000349824.4_Silent_p.S266S|IKZF1_ENST00000346667.4_Silent_p.S179S|IKZF1_ENST00000359197.5_Silent_p.S367S|IKZF1_ENST00000439701.1_Silent_p.S367S|IKZF1_ENST00000438033.1_Silent_p.S322S|IKZF1_ENST00000343574.5_Silent_p.S322S	NM_001220769.1|NM_001220772.1|NM_001220773.1|NM_001220775.1|NM_006060.4	NP_001207698.1|NP_001207701.1|NP_001207702.1|NP_001207704.1|NP_006051.1	Q13422	IKZF1_HUMAN	IKAROS family zinc finger 1 (Ikaros)	409					B cell differentiation (GO:0030183)|cell cycle (GO:0007049)|chromatin modification (GO:0016568)|forebrain development (GO:0030900)|lymph node development (GO:0048535)|mesoderm development (GO:0007498)|natural killer cell differentiation (GO:0001779)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Peyer's patch development (GO:0048541)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of neutrophil differentiation (GO:0045660)|positive regulation of NK T cell differentiation (GO:0051138)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|retina development in camera-type eye (GO:0060041)|T cell differentiation (GO:0030217)|thymus development (GO:0048538)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.?(28)		haematopoietic_and_lymphoid_tissue(275)|lung(1)	276	Glioma(55;0.08)|all_neural(89;0.245)	Acute lymphoblastic leukemia(4;7.29e-10)|all_hematologic(4;4.8e-07)				AGCAGCGCAGCGGTCTCATCT	0.677			"""D,T"""	BCL6	"""ALL, DLBCL"""																																p.S409S		Atlas-SNP	.		"""Rec,Dom"""	yes		7	7p12.2	10320	IKAROS family zinc finger 1		L	.	IKZF1	613	.	28	Unknown(28)	haematopoietic_and_lymphoid_tissue(28)	c.C1227T						.						31.0	39.0	36.0					7																	50467992		2178	4258	6436	SO:0001819	synonymous_variant	10320	exon8			GCGCAGCGGTCTC	U40462	CCDS59055.1, CCDS69299.1, CCDS75596.1, CCDS75597.1	7p12.2	2014-06-12	2006-08-25	2006-08-25	ENSG00000185811	ENSG00000185811		"""Zinc fingers, C2H2-type"", ""IKAROS zinc fingers"""	13176	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 92"""	603023	"""zinc finger protein, subfamily 1A, 1 (Ikaros)"""	ZNFN1A1		1439790, 7935426	Standard	NM_006060		Approved	hIk-1, LyF-1, Hs.54452, IKAROS, PPP1R92	uc003tow.4	Q13422	OTTHUMG00000155907	ENST00000331340.3:c.1227C>T	chr7.hg19:g.50467992C>T		71.0	0.0		117.0	20.0	NM_006060	A4D260|B4E0Z1|D3DVM5|O00598|Q53XL2|Q69BM4|Q8WVA3	Silent	SNP	ENST00000331340.3	hg19																																																																																				.	.		0.677	IKZF1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000342242.1	NM_006060	
GTF2IRD2	84163	hgsc.bcm.edu	37	7	74212037	74212037	+	Missense_Mutation	SNP	T	T	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:74212037T>G	ENST00000405086.2	-	16	2003	c.1814A>C	c.(1813-1815)aAg>aCg	p.K605T	GTF2IRD2_ENST00000451013.2_Missense_Mutation_p.K152T	NM_173537.2	NP_775808	Q86UP8	GTD2A_HUMAN	GTF2I repeat domain containing 2	605					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|endometrium(3)|large_intestine(2)|lung(2)|ovary(2)|skin(1)	11						gatacagaactttttcaggct	0.502																																					p.K605T	NSCLC(40;560 1096 7501 40315 49546)	Atlas-SNP	.											GTF2IRD2,colon,carcinoma,+1,1	GTF2IRD2	38	.	0			c.A1814C						.						39.0	39.0	39.0					7																	74212037		2203	4299	6502	SO:0001583	missense	84163	exon16			CAGAACTTTTTCA	BC047706	CCDS5576.1, CCDS64682.1	7q11.23	2014-05-06			ENSG00000196275	ENSG00000196275			30775	protein-coding gene	gene with protein product	"""transcription factor GTF2IRD2"""	608899				15243160	Standard	NM_173537		Approved	FLJ37938, GTF2IRD2A	uc003ubd.1	Q86UP8	OTTHUMG00000181527	ENST00000405086.2:c.1814A>C	chr7.hg19:g.74212037T>G	ENSP00000385491:p.Lys605Thr	601.0	1.0		736.0	0.0	NM_173537	A8K5W6|B3KUZ2|Q69G40|Q6EKI8|Q6EKI9|Q6NVW2|Q6P7N8|Q86WX4|Q8ND85|Q8NDE5	Missense_Mutation	SNP	ENST00000405086.2	hg19	CCDS5576.1	.	.	.	.	.	.	.	.	.	.	t	7.862	0.726215	0.15439	.	.	ENSG00000196275	ENST00000405086;ENST00000451013	D;D	0.85955	-2.05;-2.05	1.74	0.525	0.17072	Ribonuclease H-like (1);	.	.	.	.	T	0.71500	0.3347	L	0.37630	1.12	0.58432	D	0.999999	P	0.36065	0.535	B	0.32805	0.153	T	0.60026	-0.7343	9	0.30078	T	0.28	-13.8646	3.6893	0.08340	0.0:0.2067:0.0:0.7933	.	605	Q86UP8	GTD2A_HUMAN	T	605;152	ENSP00000385491:K605T;ENSP00000406723:K152T	ENSP00000385491:K605T	K	-	2	0	GTF2IRD2	73849973	0.912000	0.30974	0.826000	0.32828	0.704000	0.40688	0.249000	0.18216	0.158000	0.19367	0.363000	0.22086	AAG	.	.		0.502	GTF2IRD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252712.3	NM_173537	
ZNF804B	219578	hgsc.bcm.edu	37	7	88389389	88389389	+	Silent	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:88389389T>C	ENST00000333190.4	+	1	708	c.99T>C	c.(97-99)tcT>tcC	p.S33S		NM_181646.2	NP_857597.1	A4D1E1	Z804B_HUMAN	zinc finger protein 804B	33							metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(5)|kidney(5)|large_intestine(20)|lung(78)|ovary(5)|pancreas(5)|prostate(2)|skin(11)|soft_tissue(1)|upper_aerodigestive_tract(9)	144	all_hematologic(106;0.125)|Lung NSC(181;0.15)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0513)			AGAACGGATCTCCCTCTCCGG	0.478										HNSCC(36;0.09)																											p.S33S		Atlas-SNP	.											.	ZNF804B	322	.	0			c.T99C						.						108.0	98.0	101.0					7																	88389389		2203	4300	6503	SO:0001819	synonymous_variant	219578	exon1			CGGATCTCCCTCT	AK056672	CCDS5613.1	7q21.13	2012-10-05	2006-12-18		ENSG00000182348	ENSG00000182348			21958	protein-coding gene	gene with protein product			"""zinc finger 804B"""				Standard	NM_181646		Approved	FLJ32110	uc011khi.2	A4D1E1	OTTHUMG00000131037	ENST00000333190.4:c.99T>C	chr7.hg19:g.88389389T>C		128.0	0.0		144.0	6.0	NM_181646	B2RTV2|Q7Z714|Q96MN7	Silent	SNP	ENST00000333190.4	hg19	CCDS5613.1																																																																																			.	.		0.478	ZNF804B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253683.2	NM_181646	
ANKIB1	54467	hgsc.bcm.edu	37	7	91980374	91980374	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:91980374A>G	ENST00000265742.3	+	8	1572	c.1196A>G	c.(1195-1197)gAg>gGg	p.E399G		NM_019004.1	NP_061877.1	Q9P2G1	AKIB1_HUMAN	ankyrin repeat and IBR domain containing 1	399							zinc ion binding (GO:0008270)			cervix(1)|endometrium(7)|kidney(3)|large_intestine(10)|lung(19)|skin(1)	41	all_cancers(62;2.06e-09)|all_epithelial(64;9.24e-09)|Breast(17;0.0034)|all_lung(186;0.0509)|Lung NSC(181;0.0692)		STAD - Stomach adenocarcinoma(171;6.16e-05)|all cancers(6;0.00183)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			GTTTCAAAGGAGATGGACAAA	0.333																																					p.E399G		Atlas-SNP	.											.	ANKIB1	92	.	0			c.A1196G						.						88.0	83.0	85.0					7																	91980374		1855	4098	5953	SO:0001583	missense	54467	exon8			CAAAGGAGATGGA	AB037807	CCDS47639.1	7q21.3	2013-01-10			ENSG00000001629	ENSG00000001629		"""Ankyrin repeat domain containing"""	22215	protein-coding gene	gene with protein product							Standard	NM_019004		Approved	DKFZP434A0225, KIAA1386	uc003ulw.2	Q9P2G1	OTTHUMG00000155859	ENST00000265742.3:c.1196A>G	chr7.hg19:g.91980374A>G	ENSP00000265742:p.Glu399Gly	81.0	0.0		98.0	5.0	NM_019004	Q6GMS4|Q6P3S9|Q9NTD7|Q9NW49	Missense_Mutation	SNP	ENST00000265742.3	hg19	CCDS47639.1	.	.	.	.	.	.	.	.	.	.	A	26.2	4.710258	0.89018	.	.	ENSG00000001629	ENST00000265742	T	0.13657	2.57	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	T	0.27629	0.0679	M	0.73962	2.25	0.58432	D	0.999998	P	0.41214	0.742	P	0.46237	0.508	T	0.01951	-1.1241	10	0.72032	D	0.01	.	16.0698	0.80914	1.0:0.0:0.0:0.0	.	399	Q9P2G1	AKIB1_HUMAN	G	399	ENSP00000265742:E399G	ENSP00000265742:E399G	E	+	2	0	ANKIB1	91818310	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.650000	0.91073	2.245000	0.73994	0.455000	0.32223	GAG	.	.		0.333	ANKIB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342018.1		
COL1A2	1278	hgsc.bcm.edu	37	7	94043219	94043219	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:94043219G>T	ENST00000297268.6	+	28	2096	c.1625G>T	c.(1624-1626)gGa>gTa	p.G542V		NM_000089.3	NP_000080.2	P08123	CO1A2_HUMAN	collagen, type I, alpha 2	542					blood coagulation (GO:0007596)|blood vessel development (GO:0001568)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|odontogenesis (GO:0042476)|platelet activation (GO:0030168)|protein heterotrimerization (GO:0070208)|regulation of blood pressure (GO:0008217)|Rho protein signal transduction (GO:0007266)|skeletal system development (GO:0001501)|skin morphogenesis (GO:0043589)|transforming growth factor beta receptor signaling pathway (GO:0007179)	collagen type I trimer (GO:0005584)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|protein binding, bridging (GO:0030674)		COL1A2/PLAG1(3)	NS(2)|breast(2)|central_nervous_system(4)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(21)|lung(51)|ovary(2)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	115	all_cancers(62;2.46e-09)|all_epithelial(64;2.7e-08)		STAD - Stomach adenocarcinoma(171;0.0031)		Collagenase(DB00048)	GTTCAAGGTGGAAAAGGTGAA	0.443										HNSCC(75;0.22)																											p.G542V		Atlas-SNP	.											.	COL1A2	240	.	0			c.G1625T						.						137.0	123.0	128.0					7																	94043219		2203	4300	6503	SO:0001583	missense	1278	exon28			AAGGTGGAAAAGG	Z74616	CCDS34682.1	7q21.3	2014-09-17	2002-02-13		ENSG00000164692	ENSG00000164692		"""Collagens"""	2198	protein-coding gene	gene with protein product	"""alpha 2(I)-collagen"", ""alpha-2 collagen type I"", ""type I procollagen"", ""collagen I, alpha-2 polypeptide"", ""collagen of skin, tendon and bone, alpha-2 chain"""	120160	"""osteogenesis imperfecta type IV"""	OI4		3857213, 2897363	Standard	NM_000089		Approved		uc003ung.1	P08123	OTTHUMG00000148675	ENST00000297268.6:c.1625G>T	chr7.hg19:g.94043219G>T	ENSP00000297268:p.Gly542Val	157.0	0.0		183.0	20.0	NM_000089	P02464|Q13897|Q13997|Q13998|Q14038|Q14057|Q15177|Q15947|Q16480|Q16511|Q7Z5S6|Q9UEB6|Q9UEF9|Q9UM83|Q9UMI1|Q9UML5|Q9UMM6|Q9UPH0	Missense_Mutation	SNP	ENST00000297268.6	hg19	CCDS34682.1	.	.	.	.	.	.	.	.	.	.	G	15.51	2.853704	0.51270	.	.	ENSG00000164692	ENST00000297268;ENST00000545487	D	0.93366	-3.21	5.66	5.66	0.87406	.	0.112949	0.64402	D	0.000011	D	0.84083	0.5394	N	0.03209	-0.39	0.53005	D	0.999965	B	0.22800	0.075	B	0.26864	0.074	T	0.80725	-0.1254	10	0.87932	D	0	.	10.3124	0.43716	0.0718:0.2067:0.7215:0.0	.	542	P08123	CO1A2_HUMAN	V	542;543	ENSP00000297268:G542V	ENSP00000297268:G542V	G	+	2	0	COL1A2	93881155	1.000000	0.71417	1.000000	0.80357	0.892000	0.51952	2.969000	0.49232	2.840000	0.97914	0.655000	0.94253	GGA	.	.		0.443	COL1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309045.2	NM_000089	
RELN	5649	hgsc.bcm.edu	37	7	103202088	103202088	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:103202088T>C	ENST00000428762.1	-	36	5579	c.5420A>G	c.(5419-5421)gAt>gGt	p.D1807G	RELN_ENST00000343529.5_Missense_Mutation_p.D1807G|RELN_ENST00000424685.2_Missense_Mutation_p.D1807G	NM_005045.3	NP_005036.2	P78509	RELN_HUMAN	reelin	1807					associative learning (GO:0008306)|axon guidance (GO:0007411)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|central nervous system development (GO:0007417)|cerebral cortex tangential migration (GO:0021800)|dendrite development (GO:0016358)|glial cell differentiation (GO:0010001)|hippocampus development (GO:0021766)|lateral motor column neuron migration (GO:0097477)|layer formation in cerebral cortex (GO:0021819)|long-term memory (GO:0007616)|N-methyl-D-aspartate receptor clustering (GO:0097114)|neuron migration (GO:0001764)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of lateral motor column neuron migration (GO:1902078)|positive regulation of long-term synaptic potentiation (GO:1900273)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of TOR signaling (GO:0032008)|postsynaptic density protein 95 clustering (GO:0097119)|receptor localization to synapse (GO:0097120)|reelin-mediated signaling pathway (GO:0038026)|regulation of behavior (GO:0050795)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of synaptic transmission (GO:0050804)|response to pain (GO:0048265)|spinal cord patterning (GO:0021511)|ventral spinal cord development (GO:0021517)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	lipoprotein particle receptor binding (GO:0070325)|metal ion binding (GO:0046872)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|serine-type peptidase activity (GO:0008236)|very-low-density lipoprotein particle receptor binding (GO:0070326)			NS(3)|breast(8)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|lung(101)|ovary(9)|pancreas(2)|prostate(4)|skin(14)|stomach(2)|upper_aerodigestive_tract(12)|urinary_tract(2)	227				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		CCCATTGAAATCGTCTTTAAG	0.453																																					p.D1807G	NSCLC(146;835 1944 15585 22231 52158)	Atlas-SNP	.											.	RELN	593	.	0			c.A5420G						.						99.0	95.0	97.0					7																	103202088		2203	4300	6503	SO:0001583	missense	5649	exon36			TTGAAATCGTCTT		CCDS34722.1, CCDS47680.1	7q22	2008-07-18			ENSG00000189056	ENSG00000189056			9957	protein-coding gene	gene with protein product		600514				9049633	Standard	NM_005045		Approved	RL, PRO1598	uc010liz.3	P78509	OTTHUMG00000157247	ENST00000428762.1:c.5420A>G	chr7.hg19:g.103202088T>C	ENSP00000392423:p.Asp1807Gly	97.0	0.0		96.0	5.0	NM_173054	A4D0P9|A4D0Q0|Q86UJ0|Q86UJ8|Q8NDV0|Q9UDQ2	Missense_Mutation	SNP	ENST00000428762.1	hg19	CCDS47680.1	.	.	.	.	.	.	.	.	.	.	T	22.6	4.311650	0.81358	.	.	ENSG00000189056	ENST00000428762;ENST00000343529;ENST00000424685;ENST00000448171	T;T;T	0.26957	1.7;1.7;1.7	5.86	5.86	0.93980	Neuraminidase (1);	0.000000	0.85682	D	0.000000	T	0.49270	0.1547	L	0.61387	1.9	0.58432	D	0.999999	D;P	0.76494	0.999;0.512	D;B	0.72625	0.978;0.263	T	0.47983	-0.9074	10	0.62326	D	0.03	.	16.2555	0.82515	0.0:0.0:0.0:1.0	.	1807;1807	P78509-2;P78509	.;RELN_HUMAN	G	1807	ENSP00000392423:D1807G;ENSP00000345694:D1807G;ENSP00000388446:D1807G	ENSP00000345694:D1807G	D	-	2	0	RELN	102989324	1.000000	0.71417	1.000000	0.80357	0.776000	0.43924	7.499000	0.81566	2.242000	0.73789	0.460000	0.39030	GAT	.	.		0.453	RELN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348148.1	NM_005045	
RINT1	60561	hgsc.bcm.edu	37	7	105190572	105190572	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:105190572A>G	ENST00000257700.2	+	8	1298	c.1067A>G	c.(1066-1068)cAg>cGg	p.Q356R		NM_021930.4	NP_068749.3	Q6NUQ1	RINT1_HUMAN	RAD50 interactor 1	356	RINT1/TIP20. {ECO:0000255|PROSITE- ProRule:PRU00717}.				G2 DNA damage checkpoint (GO:0031572)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)				central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(9)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22						GAGAAGATTCAGCCAATATTA	0.378																																					p.Q356R		Atlas-SNP	.											.	RINT1	65	.	0			c.A1067G						.						126.0	127.0	126.0					7																	105190572		2203	4300	6503	SO:0001583	missense	60561	exon8			AGATTCAGCCAAT	AF317622	CCDS34726.1	7q22.2	2007-05-03			ENSG00000135249	ENSG00000135249			21876	protein-coding gene	gene with protein product		610089				11096100, 15029241	Standard	NM_021930		Approved	FLJ11785, RINT-1	uc003vda.1	Q6NUQ1	OTTHUMG00000157400	ENST00000257700.2:c.1067A>G	chr7.hg19:g.105190572A>G	ENSP00000257700:p.Gln356Arg	115.0	0.0		148.0	6.0	NM_021930	Q75MG9|Q75MH0|Q96IW8|Q9H229|Q9HAD9	Missense_Mutation	SNP	ENST00000257700.2	hg19	CCDS34726.1	.	.	.	.	.	.	.	.	.	.	A	24.0	4.476680	0.84640	.	.	ENSG00000135249	ENST00000257700	T	0.41758	0.99	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	T	0.63236	0.2494	M	0.65498	2.005	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.64214	-0.6460	10	0.49607	T	0.09	-14.3338	15.8976	0.79346	1.0:0.0:0.0:0.0	.	356	Q6NUQ1	RINT1_HUMAN	R	356	ENSP00000257700:Q356R	ENSP00000257700:Q356R	Q	+	2	0	RINT1	104977808	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	6.843000	0.75384	2.212000	0.71576	0.528000	0.53228	CAG	.	.		0.378	RINT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348686.1	NM_021930	
C7orf60	154743	hgsc.bcm.edu	37	7	112461887	112461887	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:112461887T>C	ENST00000297145.4	-	5	1295	c.1130A>G	c.(1129-1131)gAt>gGt	p.D377G	C7orf60_ENST00000485446.1_5'Flank	NM_152556.2	NP_689769.2	Q1RMZ1	BMT2_HUMAN	chromosome 7 open reading frame 60	377							rRNA (adenine) methyltransferase activity (GO:0016433)			breast(1)|endometrium(2)|lung(7)|ovary(3)|prostate(2)|skin(1)|urinary_tract(1)	17						ATATGGCGCATCAGGGAgttc	0.378																																					p.D377G		Atlas-SNP	.											.	C7orf60	55	.	0			c.A1130G						.						68.0	66.0	67.0					7																	112461887		1851	4100	5951	SO:0001583	missense	154743	exon5			GGCGCATCAGGGA		CCDS43634.1	7q31.1	2011-01-11	2008-06-19		ENSG00000164603	ENSG00000164603			26475	protein-coding gene	gene with protein product	"""hypothetical protein FLJ31818"""						Standard	NM_152556		Approved	DKFZp762M126, FLJ31818	uc003vgo.1	Q1RMZ1	OTTHUMG00000155233	ENST00000297145.4:c.1130A>G	chr7.hg19:g.112461887T>C	ENSP00000297145:p.Asp377Gly	84.0	0.0		104.0	5.0	NM_152556	Q8N3D0|Q96MV7	Missense_Mutation	SNP	ENST00000297145.4	hg19	CCDS43634.1	.	.	.	.	.	.	.	.	.	.	T	17.94	3.510788	0.64522	.	.	ENSG00000164603	ENST00000297145;ENST00000432572;ENST00000358032	.	.	.	5.83	5.83	0.93111	.	0.044615	0.85682	D	0.000000	T	0.51941	0.1704	N	0.19112	0.55	0.80722	D	1	P;D	0.56968	0.7;0.978	B;P	0.53224	0.221;0.721	T	0.57940	-0.7724	9	0.72032	D	0.01	-14.2384	16.1967	0.82036	0.0:0.0:0.0:1.0	.	324;377	B4DST1;Q1RMZ1	.;CG060_HUMAN	G	377;359;324	.	ENSP00000297145:D377G	D	-	2	0	C7orf60	112249123	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	6.275000	0.72594	2.217000	0.71921	0.477000	0.44152	GAT	.	.		0.378	C7orf60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338923.1	NM_152556	
CTTNBP2	83992	hgsc.bcm.edu	37	7	117398002	117398002	+	Silent	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:117398002A>G	ENST00000160373.3	-	11	3286	c.3195T>C	c.(3193-3195)ggT>ggC	p.G1065G		NM_033427.2	NP_219499.1	Q8WZ74	CTTB2_HUMAN	cortactin binding protein 2	1065					brain development (GO:0007420)	cell projection (GO:0042995)|synaptic vesicle (GO:0008021)				breast(3)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(36)|ovary(4)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	83	Lung NSC(10;0.0018)|all_lung(10;0.002)			LUSC - Lung squamous cell carcinoma(290;0.133)		CGAAGCTCTGACCCACTGACC	0.448																																					p.G1065G		Atlas-SNP	.											.	CTTNBP2	200	.	0			c.T3195C						.						71.0	57.0	62.0					7																	117398002		2203	4300	6503	SO:0001819	synonymous_variant	83992	exon11			GCTCTGACCCACT		CCDS5774.1	7q31	2013-01-10	2004-06-08	2004-06-09	ENSG00000077063	ENSG00000077063		"""Ankyrin repeat domain containing"""	15679	protein-coding gene	gene with protein product		609772	"""cortactin binding protein 2"""	CORTBP2, C7orf8		11707066	Standard	XM_005250635		Approved	KIAA1758, Orf4	uc003vjf.3	Q8WZ74	OTTHUMG00000022880	ENST00000160373.3:c.3195T>C	chr7.hg19:g.117398002A>G		59.0	0.0		33.0	4.0	NM_033427	O43389|Q7LG11|Q9C0A5	Silent	SNP	ENST00000160373.3	hg19	CCDS5774.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	3.803|3.803	-0.041242|-0.041242	0.07452|0.07452	.|.	.|.	ENSG00000077063|ENSG00000077063	ENST00000446636|ENST00000435233;ENST00000416239	.|.	.|.	.|.	5.73|5.73	0.331|0.331	0.15933|0.15933	.|.	.|.	.|.	.|.	.|.	T|T	0.50274|0.50274	0.1606|0.1606	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.35699|0.35699	-0.9778|-0.9778	4|4	.|.	.|.	.|.	-0.5958|-0.5958	4.7776|4.7776	0.13187|0.13187	0.6041:0.2254:0.062:0.1085|0.6041:0.2254:0.062:0.1085	.|.	.|.	.|.	.|.	P|A	553|79;61	.|.	.|.	S|V	-|-	1|2	0|0	CTTNBP2|CTTNBP2	117185238|117185238	1.000000|1.000000	0.71417|0.71417	0.991000|0.991000	0.47740|0.47740	0.232000|0.232000	0.25224|0.25224	1.637000|1.637000	0.37155|0.37155	0.117000|0.117000	0.18138|0.18138	0.533000|0.533000	0.62120|0.62120	TCA|GTC	.	.		0.448	CTTNBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059201.4	NM_033427	
NRF1	4899	hgsc.bcm.edu	37	7	129297391	129297391	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:129297391T>C	ENST00000393232.1	+	2	317	c.200T>C	c.(199-201)gTg>gCg	p.V67A	NRF1_ENST00000393231.3_Missense_Mutation_p.V67A|NRF1_ENST00000539636.1_5'UTR|NRF1_ENST00000311967.2_Missense_Mutation_p.V67A|NRF1_ENST00000353868.4_Missense_Mutation_p.V67A|NRF1_ENST00000393230.2_Missense_Mutation_p.V67A|NRF1_ENST00000223190.4_Missense_Mutation_p.V67A	NM_005011.3	NP_005002.3	Q16656	NRF1_HUMAN	nuclear respiratory factor 1	67	Dimerization.				cellular lipid metabolic process (GO:0044255)|generation of precursor metabolites and energy (GO:0006091)|mitochondrion organization (GO:0007005)|organ regeneration (GO:0031100)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to electrical stimulus (GO:0051602)|response to estradiol (GO:0032355)|response to folic acid (GO:0051593)|response to hypoxia (GO:0001666)|response to lipopolysaccharide (GO:0032496)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(2)|central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(5)|lung(12)|ovary(1)|prostate(1)	24						GCTGATGAGGTGACAGCTCAT	0.443																																					p.V67A		Atlas-SNP	.											.	NRF1	40	.	0			c.T200C						.						80.0	72.0	75.0					7																	129297391		2203	4300	6503	SO:0001583	missense	4899	exon2			ATGAGGTGACAGC	L22454	CCDS5813.2	7q32	2008-07-18			ENSG00000106459	ENSG00000106459			7996	protein-coding gene	gene with protein product	"""alpha palindromic-binding protein"""	600879				2584221	Standard	NM_005011		Approved	EWG, ALPHA-PAL	uc003voz.3	Q16656	OTTHUMG00000143736	ENST00000393232.1:c.200T>C	chr7.hg19:g.129297391T>C	ENSP00000376924:p.Val67Ala	62.0	0.0		81.0	4.0	NM_005011	A8K4C6|B4DDV6|Q15305|Q96AN2	Missense_Mutation	SNP	ENST00000393232.1	hg19	CCDS5813.2	.	.	.	.	.	.	.	.	.	.	T	17.50	3.404457	0.62288	.	.	ENSG00000106459	ENST00000393232;ENST00000353868;ENST00000454688;ENST00000223190;ENST00000311967;ENST00000393230;ENST00000393231	.	.	.	5.23	5.23	0.72850	.	0.112091	0.64402	D	0.000013	T	0.36635	0.0974	N	0.14661	0.345	0.80722	D	1	P;B	0.34562	0.457;0.392	B;B	0.31390	0.129;0.125	T	0.42258	-0.9462	9	0.87932	D	0	-15.8507	14.5973	0.68415	0.0:0.0:0.0:1.0	.	67;67	Q96AN2;Q16656	.;NRF1_HUMAN	A	67	.	ENSP00000223190:V67A	V	+	2	0	NRF1	129084627	1.000000	0.71417	0.999000	0.59377	0.835000	0.47333	7.563000	0.82314	2.115000	0.64714	0.477000	0.44152	GTG	.	.		0.443	NRF1-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289813.1	NM_001040110	
DENND2A	27147	hgsc.bcm.edu	37	7	140244510	140244510	+	Silent	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:140244510A>G	ENST00000275884.6	-	13	2652	c.2235T>C	c.(2233-2235)tcT>tcC	p.S745S	DENND2A_ENST00000537639.1_Silent_p.S745S|DENND2A_ENST00000496613.1_Silent_p.S745S|DENND2A_ENST00000492720.1_Silent_p.S745S			Q9ULE3	DEN2A_HUMAN	DENN/MADD domain containing 2A	745	DENN. {ECO:0000255|PROSITE- ProRule:PRU00304}.				positive regulation of Rab GTPase activity (GO:0032851)|protein transport (GO:0015031)|retrograde transport, endosome to Golgi (GO:0042147)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(22)|ovary(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	49	Melanoma(164;0.00956)					AGGAGAAGAGAGACTCAAAGT	0.617																																					p.S745S		Atlas-SNP	.											.	DENND2A	132	.	0			c.T2235C						.						42.0	51.0	48.0					7																	140244510		2184	4284	6468	SO:0001819	synonymous_variant	27147	exon12			GAAGAGAGACTCA	AB033103	CCDS43659.1	7q34	2012-10-03	2005-08-17	2005-08-17	ENSG00000146966	ENSG00000146966		"""DENN/MADD domain containing"""	22212	protein-coding gene	gene with protein product			"""KIAA1277"""	KIAA1277			Standard	NM_015689		Approved	FAM31D	uc010lnj.3	Q9ULE3	OTTHUMG00000157411	ENST00000275884.6:c.2235T>C	chr7.hg19:g.140244510A>G		89.0	0.0		128.0	8.0	NM_015689	C9JUI3|Q1RMD5|Q86XY0	Silent	SNP	ENST00000275884.6	hg19	CCDS43659.1																																																																																			.	.		0.617	DENND2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348742.1	NM_015689	
AGK	55750	hgsc.bcm.edu	37	7	141333731	141333731	+	Missense_Mutation	SNP	A	A	T	rs561898521	byFrequency	TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:141333731A>T	ENST00000355413.4	+	10	879	c.619A>T	c.(619-621)Acc>Tcc	p.T207S	AGK_ENST00000473247.1_Missense_Mutation_p.T179S|AGK_ENST00000535825.1_Missense_Mutation_p.T204S	NM_018238.3	NP_060708.1	Q53H12	AGK_HUMAN	acylglycerol kinase	207					ceramide biosynthetic process (GO:0046513)|glycerolipid metabolic process (GO:0046486)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)	intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)	acylglycerol kinase activity (GO:0047620)|ATP binding (GO:0005524)|ceramide kinase activity (GO:0001729)|diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951)			breast(1)|endometrium(1)|large_intestine(4)|lung(6)|ovary(1)|pancreas(1)|prostate(3)	17	Melanoma(164;0.0171)					ATTTGCAATGACCGGCCTTCG	0.348																																					p.T207S		Atlas-SNP	.											.	AGK	43	.	0			c.A619T						.						122.0	122.0	122.0					7																	141333731		2203	4300	6503	SO:0001583	missense	55750	exon10			GCAATGACCGGCC	BC022777	CCDS5865.1	7q34	2010-05-04	2007-01-11	2007-01-11	ENSG00000006530	ENSG00000006530	2.7.1.94		21869	protein-coding gene	gene with protein product		610345	"""multiple substrate lipid kinase"""	MULK		15252046, 15939762, 17135245	Standard	NM_018238		Approved	FLJ10842	uc003vwi.2	Q53H12	OTTHUMG00000157499	ENST00000355413.4:c.619A>T	chr7.hg19:g.141333731A>T	ENSP00000347581:p.Thr207Ser	34.0	0.0		58.0	20.0	NM_018238	Q75KN1|Q96GC3|Q9NP48	Missense_Mutation	SNP	ENST00000355413.4	hg19	CCDS5865.1	.	.	.	.	.	.	.	.	.	.	A	7.523	0.657045	0.14580	.	.	ENSG00000006530	ENST00000355413;ENST00000473247;ENST00000535825	T;T;T	0.40756	2.61;2.61;1.02	5.85	4.59	0.56863	.	0.356129	0.35436	N	0.003216	T	0.18045	0.0433	N	0.04090	-0.28	0.27369	N	0.955738	B	0.02656	0.0	B	0.06405	0.002	T	0.13072	-1.0523	10	0.06625	T	0.88	.	11.1992	0.48730	0.8531:0.0:0.0:0.1469	.	207	Q53H12	AGK_HUMAN	S	207;179;204	ENSP00000347581:T207S;ENSP00000420776:T179S;ENSP00000444349:T204S	ENSP00000347581:T207S	T	+	1	0	AGK	140980200	1.000000	0.71417	0.980000	0.43619	0.982000	0.71751	3.263000	0.51546	2.246000	0.74042	0.533000	0.62120	ACC	.	.		0.348	AGK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348969.1	NM_018238	
MGAM	8972	hgsc.bcm.edu	37	7	141727459	141727459	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:141727459T>C	ENST00000549489.2	+	10	1240	c.1145T>C	c.(1144-1146)cTc>cCc	p.L382P	MGAM_ENST00000475668.2_Missense_Mutation_p.L382P	NM_004668.2	NP_004659.2	O43451	MGA_HUMAN	maltase-glucoamylase (alpha-glucosidase)	382	Maltase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			cervix(1)|endometrium(1)|large_intestine(4)|lung(3)|ovary(2)|skin(2)	13	Melanoma(164;0.0272)				Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	GGATTTCACCTCAGTCGTTAC	0.443																																					p.L382P		Atlas-SNP	.											.	MGAM	767	.	0			c.T1145C						.						64.0	62.0	63.0					7																	141727459		1858	4102	5960	SO:0001583	missense	8972	exon10			TTCACCTCAGTCG	AF016833	CCDS47727.1	7q34	2012-10-03			ENSG00000257335	ENSG00000257335			7043	protein-coding gene	gene with protein product		154360				9446624	Standard	NM_004668		Approved	MGA	uc003vwy.3	O43451	OTTHUMG00000158395	ENST00000549489.2:c.1145T>C	chr7.hg19:g.141727459T>C	ENSP00000447378:p.Leu382Pro	57.0	0.0		79.0	4.0	NM_004668	Q0VAX6|Q75ME7|Q86UM5	Missense_Mutation	SNP	ENST00000549489.2	hg19	CCDS47727.1	.	.	.	.	.	.	.	.	.	.	T	22.7	4.323594	0.81580	.	.	ENSG00000257335	ENST00000549489;ENST00000475668;ENST00000548812	D	0.91996	-2.95	5.55	5.55	0.83447	Glycoside hydrolase, superfamily (1);	0.000000	0.49916	D	0.000140	D	0.97365	0.9138	H	0.96777	3.88	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98389	1.0562	10	0.87932	D	0	.	13.6922	0.62553	0.0:0.0:0.0:1.0	.	382	O43451	MGA_HUMAN	P	382;382;259	ENSP00000447378:L382P	ENSP00000316431:L259P	L	+	2	0	MGAM	141373928	0.987000	0.35691	0.989000	0.46669	0.765000	0.43378	7.457000	0.80775	2.326000	0.78906	0.533000	0.62120	CTC	.	.		0.443	MGAM-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351244.3		
KRBA1	84626	hgsc.bcm.edu	37	7	149420823	149420823	+	Splice_Site	SNP	A	A	T			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:149420823A>T	ENST00000485033.2	+	7	772		c.e7-1		KRBA1_ENST00000255992.10_Splice_Site|KRBA1_ENST00000479560.1_Splice_Site|KRBA1_ENST00000319551.8_Splice_Site			A5PL33	KRBA1_HUMAN	KRAB-A domain containing 1											breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(17)|ovary(1)|prostate(1)	27	Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			CTTTTTCCTTAGTGAAGACCG	0.557																																					.		Atlas-SNP	.											.	KRBA1	68	.	0			c.773-2A>T						.						48.0	52.0	51.0					7																	149420823		1978	4140	6118	SO:0001630	splice_region_variant	84626	exon8			TTCCTTAGTGAAG	AB058765	CCDS75674.1	7q36	2014-02-12	2006-08-15		ENSG00000133619	ENSG00000133619		"""-"""	22228	protein-coding gene	gene with protein product			"""KRAB A domain containing 1"""				Standard	NM_001290187		Approved	KIAA1862	uc003wfz.3	A5PL33	OTTHUMG00000157886	ENST00000485033.2:c.773-1A>T	chr7.hg19:g.149420823A>T		95.0	0.0		103.0	5.0	NM_032534	A7E2F5|E7ENE9|Q8N4X0|Q96JG5	Splice_Site	SNP	ENST00000485033.2	hg19		.	.	.	.	.	.	.	.	.	.	A	16.55	3.155080	0.57259	.	.	ENSG00000133619	ENST00000255992;ENST00000319551;ENST00000485033	.	.	.	5.26	5.26	0.73747	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.5898	0.50939	1.0:0.0:0.0:0.0	rs11462346	.	.	.	.	-1	.	.	.	+	.	.	KRBA1	149051756	0.978000	0.34361	0.920000	0.36463	0.793000	0.44817	2.679000	0.46909	1.996000	0.58369	0.533000	0.62120	.	.	.		0.557	KRBA1-004	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000349841.3	NM_032534	Intron
ZNF862	643641	hgsc.bcm.edu	37	7	149558251	149558251	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:149558251G>A	ENST00000223210.4	+	7	2247	c.2002G>A	c.(2002-2004)Gat>Aat	p.D668N	RP4-751H13.7_ENST00000608963.1_RNA	NM_001099220.1	NP_001092690.1	O60290	ZN862_HUMAN	zinc finger protein 862	668					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|skin(1)	34						TGAGACAGCAGATGGGTACTT	0.587																																					p.D668N		Atlas-SNP	.											.	ZNF862	97	.	0			c.G2002A						.						28.0	30.0	29.0					7																	149558251		2070	4216	6286	SO:0001583	missense	643641	exon7			ACAGCAGATGGGT	AB011115	CCDS47741.1	7q36.1	2013-01-11			ENSG00000106479	ENSG00000106479		"""Zinc fingers, C2H2-type"", ""-"""	34519	protein-coding gene	gene with protein product							Standard	NM_001099220		Approved		uc010lpn.3	O60290	OTTHUMG00000158093	ENST00000223210.4:c.2002G>A	chr7.hg19:g.149558251G>A	ENSP00000223210:p.Asp668Asn	177.0	0.0		187.0	64.0	NM_001099220	A0AUL8	Missense_Mutation	SNP	ENST00000223210.4	hg19	CCDS47741.1	.	.	.	.	.	.	.	.	.	.	G	12.14	1.848402	0.32699	.	.	ENSG00000106479	ENST00000223210	T	0.22539	1.95	5.17	5.17	0.71159	Ribonuclease H-like (1);	0.000000	0.52532	D	0.000075	T	0.39489	0.1080	L	0.50333	1.59	0.34382	D	0.693181	D	0.89917	1.0	D	0.80764	0.994	T	0.48559	-0.9025	10	0.41790	T	0.15	-21.8278	14.1976	0.65682	0.0:0.0:1.0:0.0	.	668	O60290	ZN862_HUMAN	N	668	ENSP00000223210:D668N	ENSP00000223210:D668N	D	+	1	0	ZNF862	149189184	0.985000	0.35326	0.163000	0.22734	0.026000	0.11368	4.329000	0.59260	2.407000	0.81776	0.655000	0.94253	GAT	.	.		0.587	ZNF862-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350165.1	NM_001099220	
MYOM2	9172	hgsc.bcm.edu	37	8	2092705	2092705	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr8:2092705T>C	ENST00000262113.4	+	37	4339	c.4198T>C	c.(4198-4200)Tac>Cac	p.Y1400H	MYOM2_ENST00000523438.1_Missense_Mutation_p.Y825H|MYOM2_ENST00000520298.1_3'UTR	NM_003970.2	NP_003961.2	P54296	MYOM2_HUMAN	myomesin 2	1400	Ig-like C2-type 5.				muscle contraction (GO:0006936)	M band (GO:0031430)|mitochondrion (GO:0005739)|myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)			autonomic_ganglia(2)|breast(4)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(11)|kidney(2)|large_intestine(17)|lung(39)|ovary(5)|prostate(1)|skin(10)|upper_aerodigestive_tract(3)	104		Ovarian(12;0.0572)|Colorectal(14;0.0844)|Hepatocellular(245;0.217)		BRCA - Breast invasive adenocarcinoma(11;1.85e-05)|Colorectal(4;0.0101)|READ - Rectum adenocarcinoma(4;0.148)|COAD - Colon adenocarcinoma(4;0.179)		GCAGGCCAAGTACGTCAGCAT	0.537																																					p.Y1400H		Atlas-SNP	.											.	MYOM2	251	.	0			c.T4198C						.						128.0	105.0	113.0					8																	2092705		2203	4300	6503	SO:0001583	missense	9172	exon37			GCCAAGTACGTCA		CCDS5957.1	8p23.3	2014-06-06	2012-10-17		ENSG00000036448	ENSG00000036448		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	7614	protein-coding gene	gene with protein product		603509	"""myomesin (M-protein) 2 (165kD)"", ""myomesin (M-protein) 2, 165kDa"""				Standard	XM_006716237		Approved		uc003wpx.4	P54296	OTTHUMG00000129175	ENST00000262113.4:c.4198T>C	chr8.hg19:g.2092705T>C	ENSP00000262113:p.Tyr1400His	112.0	0.0		96.0	5.0	NM_003970	Q7Z3Y2	Missense_Mutation	SNP	ENST00000262113.4	hg19	CCDS5957.1	.	.	.	.	.	.	.	.	.	.	T	17.30	3.354298	0.61293	.	.	ENSG00000036448	ENST00000262113;ENST00000523438	T;T	0.66280	-0.2;-0.2	5.24	4.05	0.47172	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.183408	0.49916	D	0.000129	T	0.67392	0.2888	L	0.47016	1.485	0.40680	D	0.982295	D	0.58970	0.984	P	0.62491	0.903	T	0.63143	-0.6703	10	0.21540	T	0.41	.	11.4574	0.50189	0.1351:0.0:0.0:0.8649	.	1400	P54296	MYOM2_HUMAN	H	1400;825	ENSP00000262113:Y1400H;ENSP00000428396:Y825H	ENSP00000262113:Y1400H	Y	+	1	0	MYOM2	2080112	1.000000	0.71417	0.985000	0.45067	0.988000	0.76386	3.261000	0.51530	0.875000	0.35847	0.533000	0.62120	TAC	.	.		0.537	MYOM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251249.1	NM_003970	
TUSC3	7991	hgsc.bcm.edu	37	8	15398006	15398006	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr8:15398006G>A	ENST00000503731.1	+	1	215	c.67G>A	c.(67-69)Ggg>Agg	p.G23R	TUSC3_ENST00000382020.4_Missense_Mutation_p.G23R|TUSC3_ENST00000509380.1_Missense_Mutation_p.G23R|TUSC3_ENST00000503191.1_Intron|TUSC3_ENST00000506802.1_Missense_Mutation_p.G23R	NM_006765.3	NP_006756.2	Q13454	TUSC3_HUMAN	tumor suppressor candidate 3	23					cell redox homeostasis (GO:0045454)|cellular protein metabolic process (GO:0044267)|cognition (GO:0050890)|magnesium ion transport (GO:0015693)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|oligosaccharyltransferase complex (GO:0008250)	magnesium ion transmembrane transporter activity (GO:0015095)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(10)|lung(10)|ovary(2)	28				Colorectal(111;0.113)		CCTGCCCACCGGGAGCTTTCC	0.672																																					p.G23R		Atlas-SNP	.											.	TUSC3	98	.	0			c.G67A						.						26.0	26.0	26.0					8																	15398006		2200	4298	6498	SO:0001583	missense	7991	exon1			CCCACCGGGAGCT	AK026149	CCDS5993.1, CCDS5994.1	8p22	2010-10-22			ENSG00000104723	ENSG00000104723			30242	protein-coding gene	gene with protein product	"""oligosaccharyltransferase 3 homolog A (S. cerevisiae)"""	601385				8661104, 10097140	Standard	NM_178234		Approved	MGC13453, N33, OST3A, MRT7	uc003wwt.3	Q13454	OTTHUMG00000094803	ENST00000503731.1:c.67G>A	chr8.hg19:g.15398006G>A	ENSP00000424544:p.Gly23Arg	152.0	0.0		198.0	81.0	NM_178234	A8MSM0|D3DSP2|Q14911|Q14912|Q96FW0	Missense_Mutation	SNP	ENST00000503731.1	hg19	CCDS5994.1	.	.	.	.	.	.	.	.	.	.	G	15.29	2.788938	0.49997	.	.	ENSG00000104723	ENST00000382020;ENST00000506802;ENST00000509380;ENST00000503731	T;T;T;T	0.46819	0.87;0.86;0.86;0.86	4.2	3.31	0.37934	.	0.301186	0.27645	N	0.018454	T	0.23766	0.0575	N	0.08118	0	0.29524	N	0.853302	B;B;B;B;B;B	0.26195	0.031;0.012;0.021;0.012;0.012;0.144	B;B;B;B;B;B	0.13407	0.001;0.001;0.003;0.001;0.001;0.009	T	0.12502	-1.0545	10	0.25106	T	0.35	-5.3103	10.034	0.42118	0.0:0.2049:0.7951:0.0	.	23;23;23;23;23;23	D6RDV0;D6RIY7;Q13454-2;Q13454;D6RA37;A8MSM0	.;.;.;TUSC3_HUMAN;.;.	R	23	ENSP00000371450:G23R;ENSP00000425777:G23R;ENSP00000423426:G23R;ENSP00000424544:G23R	ENSP00000221167:G23R	G	+	1	0	TUSC3	15442377	1.000000	0.71417	0.999000	0.59377	0.980000	0.70556	3.994000	0.56994	1.335000	0.45486	0.563000	0.77884	GGG	.	.		0.672	TUSC3-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000365367.1	NM_006765	
GOT1L1	137362	hgsc.bcm.edu	37	8	37791908	37791908	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr8:37791908T>C	ENST00000307599.4	-	9	1268	c.1169A>G	c.(1168-1170)tAc>tGc	p.Y390C		NM_152413.2	NP_689626.2	Q8NHS2	AATC2_HUMAN	glutamic-oxaloacetic transaminase 1-like 1	390					biosynthetic process (GO:0009058)|cellular amino acid metabolic process (GO:0006520)	cytoplasm (GO:0005737)	pyridoxal phosphate binding (GO:0030170)|transaminase activity (GO:0008483)			central_nervous_system(1)|endometrium(3)|lung(8)|ovary(1)|prostate(1)	14	Colorectal(12;0.00627)	Lung NSC(58;0.118)|all_lung(54;0.195)	LUSC - Lung squamous cell carcinoma(8;1.37e-11)			CTCAGTGATGTAATTTATGTT	0.423																																					p.Y390C		Atlas-SNP	.											.	GOT1L1	87	.	0			c.A1169G						.						251.0	241.0	244.0					8																	37791908		1910	4139	6049	SO:0001583	missense	137362	exon9			GTGATGTAATTTA	BC029504	CCDS47839.1	8p12	2005-09-22			ENSG00000169154	ENSG00000169154			28487	protein-coding gene	gene with protein product						12477932	Standard	NM_152413		Approved	MGC33309	uc011lbj.1	Q8NHS2	OTTHUMG00000164027	ENST00000307599.4:c.1169A>G	chr8.hg19:g.37791908T>C	ENSP00000303077:p.Tyr390Cys	331.0	0.0		301.0	67.0	NM_152413	A8MWL4	Missense_Mutation	SNP	ENST00000307599.4	hg19	CCDS47839.1	.	.	.	.	.	.	.	.	.	.	T	14.25	2.480254	0.44044	.	.	ENSG00000169154	ENST00000307599	T	0.26660	1.72	5.37	5.37	0.77165	Aminotransferase, class I/classII (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.098157	0.42053	D	0.000761	T	0.59032	0.2164	M	0.92169	3.28	0.80722	D	1	D	0.89917	1.0	D	0.72982	0.979	T	0.69224	-0.5201	10	0.87932	D	0	-21.863	13.0005	0.58672	0.0:0.0:0.0:1.0	.	390	Q8NHS2	AATC2_HUMAN	C	390	ENSP00000303077:Y390C	ENSP00000303077:Y390C	Y	-	2	0	GOT1L1	37911066	1.000000	0.71417	1.000000	0.80357	0.101000	0.19017	5.628000	0.67791	2.266000	0.75297	0.528000	0.53228	TAC	.	.		0.423	GOT1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376823.1	NM_152413	
PXDNL	137902	hgsc.bcm.edu	37	8	52396242	52396242	+	Missense_Mutation	SNP	G	G	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr8:52396242G>C	ENST00000356297.4	-	6	585	c.485C>G	c.(484-486)cCa>cGa	p.P162R	PXDNL_ENST00000543296.1_Missense_Mutation_p.P162R	NM_144651.4	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog (Drosophila)-like	162					hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	endonuclease activity (GO:0004519)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)	p.P162L(1)		NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	48		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)				GCTCCCAGCTGGAATTTTAGA	0.284																																					p.P162R		Atlas-SNP	.											PXDNL_ENST00000356297,rectum,carcinoma,0,1	PXDNL	414	.	1	Substitution - Missense(1)	large_intestine(1)	c.C485G						.						29.0	26.0	27.0					8																	52396242		1578	3669	5247	SO:0001583	missense	137902	exon6			CCAGCTGGAATTT		CCDS47855.1	8q11.21-q11.22	2013-02-18	2007-01-12		ENSG00000147485	ENSG00000147485		"""Immunoglobulin superfamily / I-set domain containing"""	26359	protein-coding gene	gene with protein product	"""polysomal ribonuclease 1 homolog (Xenopus)"""	615904	"""peroxidasin homolog-like (Drosophila)"""			22543864	Standard	NM_144651		Approved	FLJ25471, PMR1	uc003xqu.4	A1KZ92	OTTHUMG00000164244	ENST00000356297.4:c.485C>G	chr8.hg19:g.52396242G>C	ENSP00000348645:p.Pro162Arg	167.0	0.0		300.0	0.0	NM_144651	B5ME43|B6CGZ3|H0YBM9|Q6ZMR2|Q96LH9	Missense_Mutation	SNP	ENST00000356297.4	hg19	CCDS47855.1	.	.	.	.	.	.	.	.	.	.	G	8.607	0.888212	0.17540	.	.	ENSG00000147485	ENST00000356297;ENST00000543296	T;T	0.60299	0.2;0.2	4.6	-0.399	0.12415	.	.	.	.	.	T	0.51160	0.1658	L	0.56769	1.78	0.20074	N	0.999937	P	0.42010	0.768	B	0.43445	0.42	T	0.41251	-0.9519	9	0.20046	T	0.44	.	8.0724	0.30697	0.4475:0.0:0.5525:0.0	.	162	A1KZ92	PXDNL_HUMAN	R	162	ENSP00000348645:P162R;ENSP00000444865:P162R	ENSP00000348645:P162R	P	-	2	0	PXDNL	52558795	0.061000	0.20836	0.007000	0.13788	0.098000	0.18820	0.545000	0.23268	-0.355000	0.08199	-0.742000	0.03525	CCA	.	.		0.284	PXDNL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377905.1	NM_144651	
MTERF3	51001	hgsc.bcm.edu	37	8	97258633	97258633	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr8:97258633T>C	ENST00000287025.3	-	5	825	c.727A>G	c.(727-729)Atg>Gtg	p.M243V	MTERFD1_ENST00000522822.1_Missense_Mutation_p.M122V|MTERFD1_ENST00000524341.1_Missense_Mutation_p.M53V|MTERFD1_ENST00000523821.1_Missense_Mutation_p.M243V	NM_015942.3	NP_057026.3	Q96E29	MTEF3_HUMAN		243					negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	mitochondrion (GO:0005739)	transcription regulatory region DNA binding (GO:0044212)			endometrium(1)|kidney(1)|large_intestine(7)|lung(7)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	24	Breast(36;5.16e-05)					TTTCTGACCATCTGTGCAACA	0.348																																					p.M243V		Atlas-SNP	.											.	MTERFD1	50	.	0			c.A727G						.						88.0	84.0	85.0					8																	97258633		2203	4300	6503	SO:0001583	missense	51001	exon5			TGACCATCTGTGC																												ENST00000287025.3:c.727A>G	chr8.hg19:g.97258633T>C	ENSP00000287025:p.Met243Val	53.0	0.0		174.0	7.0	NM_015942	B3KMG6|G3V130|Q9Y301	Missense_Mutation	SNP	ENST00000287025.3	hg19	CCDS6270.1	.	.	.	.	.	.	.	.	.	.	T	21.7	4.193889	0.78902	.	.	ENSG00000156469	ENST00000523821;ENST00000522822;ENST00000524341;ENST00000287025	T;T;T;T	0.20738	2.05;2.05;2.05;2.05	6.02	6.02	0.97574	.	0.000000	0.85682	D	0.000000	T	0.36276	0.0961	M	0.78637	2.42	0.80722	D	1	D;D	0.55385	0.971;0.971	P;P	0.53185	0.72;0.72	T	0.28396	-1.0045	10	0.09084	T	0.74	-8.8963	15.1204	0.72438	0.0:0.0:0.0:1.0	.	243;243	E5RIK9;Q96E29	.;MTER1_HUMAN	V	243;122;53;243	ENSP00000429400:M243V;ENSP00000430138:M122V;ENSP00000429267:M53V;ENSP00000287025:M243V	ENSP00000287025:M243V	M	-	1	0	MTERFD1	97327809	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.641000	0.83368	2.299000	0.77371	0.528000	0.53228	ATG	.	.		0.348	MTERFD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379876.1		
EMC2	9694	hgsc.bcm.edu	37	8	109468100	109468100	+	Splice_Site	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr8:109468100A>G	ENST00000220853.3	+	5	340		c.e5-1			NM_014673.3	NP_055488.1	Q15006	EMC2_HUMAN	ER membrane protein complex subunit 2							cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|ER membrane protein complex (GO:0072546)|mitochondrion (GO:0005739)|nucleus (GO:0005634)											CTTTTTAAATAGATATGATGA	0.229																																					.		Atlas-SNP	.											.	.	.	.	0			c.306-2A>G						.						15.0	17.0	17.0					8																	109468100		2109	4128	6237	SO:0001630	splice_region_variant	9694	exon5			TTAAATAGATATG	BC021667	CCDS6309.1	8q23.2	2012-05-23	2012-05-23	2012-05-23	ENSG00000104412	ENSG00000104412			28963	protein-coding gene	gene with protein product		607722	"""tetratricopeptide repeat domain 35"""	KIAA0103, TTC35		7788527, 22119785	Standard	NM_014673		Approved		uc003ymw.1	Q15006	OTTHUMG00000164873	ENST00000220853.3:c.306-1A>G	chr8.hg19:g.109468100A>G		54.0	0.0		117.0	6.0	NM_014673	Q8WUE1	Splice_Site	SNP	ENST00000220853.3	hg19	CCDS6309.1	.	.	.	.	.	.	.	.	.	.	A	19.65	3.867002	0.72065	.	.	ENSG00000104412	ENST00000524143;ENST00000220853;ENST00000519642	.	.	.	5.4	5.4	0.78164	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.716	0.77670	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	TTC35	109537276	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.688000	0.84153	2.167000	0.68274	0.528000	0.53228	.	.	.		0.229	EMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380717.1	NM_014673	Intron
FER1L6	654463	hgsc.bcm.edu	37	8	125103757	125103757	+	Silent	SNP	C	C	T			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr8:125103757C>T	ENST00000522917.1	+	34	4691	c.4485C>T	c.(4483-4485)caC>caT	p.H1495H	FER1L6_ENST00000399018.1_Silent_p.H1495H|FER1L6-AS2_ENST00000520031.1_RNA	NM_001039112.2	NP_001034201.2	Q2WGJ9	FR1L6_HUMAN	fer-1-like family member 6	1495						integral component of membrane (GO:0016021)				NS(2)|breast(3)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(18)|liver(1)|lung(49)|ovary(5)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(1)	118	Lung NSC(37;4.1e-12)|Ovarian(258;0.00438)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00186)			CCTACTTTCACCCTGGGAAAA	0.453																																					p.H1495H		Atlas-SNP	.											.	FER1L6	268	.	0			c.C4485T						.						122.0	113.0	116.0					8																	125103757		1879	4104	5983	SO:0001819	synonymous_variant	654463	exon34			CTTTCACCCTGGG	AB196633	CCDS43767.1	8q24.13	2014-06-27	2014-06-27		ENSG00000214814	ENSG00000214814			28065	protein-coding gene	gene with protein product			"""fer-1-like 6 (C. elegans)"""				Standard	NM_001039112		Approved	C8ORFK23	uc003yqw.3	Q2WGJ9	OTTHUMG00000164998	ENST00000522917.1:c.4485C>T	chr8.hg19:g.125103757C>T		99.0	0.0		206.0	123.0	NM_001039112		Silent	SNP	ENST00000522917.1	hg19	CCDS43767.1																																																																																			.	.		0.453	FER1L6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381400.1	NM_001039112	
KCNQ3	3786	hgsc.bcm.edu	37	8	133192520	133192520	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr8:133192520C>T	ENST00000388996.4	-	4	1081	c.661G>A	c.(661-663)Gtt>Att	p.V221I	KCNQ3_ENST00000519445.1_Missense_Mutation_p.V221I|KCNQ3_ENST00000521134.1_Missense_Mutation_p.V101I	NM_004519.3	NP_004510.1	O43525	KCNQ3_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 3	221					axon guidance (GO:0007411)|membrane hyperpolarization (GO:0060081)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	axon initial segment (GO:0043194)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	70	Esophageal squamous(12;0.00507)|Ovarian(258;0.00579)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000311)		Amitriptyline(DB00321)|Diclofenac(DB00586)|Ezogabine(DB04953)|Meclofenamic acid(DB00939)	GTGGCCAGAACATTGCCTTGG	0.587																																					p.V221I		Atlas-SNP	.											.	KCNQ3	164	.	0			c.G661A						.						108.0	93.0	98.0					8																	133192520		2203	4300	6503	SO:0001583	missense	3786	exon4			CCAGAACATTGCC	AB208890	CCDS34943.1, CCDS56554.1	8q24	2012-07-05			ENSG00000184156	ENSG00000184156		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6297	protein-coding gene	gene with protein product		602232		EBN2		9425900, 16382104	Standard	NM_004519		Approved	Kv7.3	uc003ytj.3	O43525	OTTHUMG00000137472	ENST00000388996.4:c.661G>A	chr8.hg19:g.133192520C>T	ENSP00000373648:p.Val221Ile	38.0	0.0		99.0	4.0	NM_004519	A2VCT8|B4DJY4|E7EQ89	Missense_Mutation	SNP	ENST00000388996.4	hg19	CCDS34943.1	.	.	.	.	.	.	.	.	.	.	C	14.44	2.535878	0.45176	.	.	ENSG00000184156	ENST00000388996;ENST00000521134;ENST00000519445;ENST00000542679;ENST00000423790	D;D;D	0.97404	-4.37;-4.37;-4.37	5.52	5.52	0.82312	Ion transport (1);	0.182209	0.46758	D	0.000267	D	0.92331	0.7567	N	0.11845	0.185	0.51767	D	0.999933	P;P	0.48089	0.905;0.905	B;B	0.43331	0.416;0.416	D	0.91376	0.5123	10	0.05833	T	0.94	-20.0986	18.4101	0.90549	0.0:1.0:0.0:0.0	.	221;221	E7ET42;O43525	.;KCNQ3_HUMAN	I	221;101;221;210;100	ENSP00000373648:V221I;ENSP00000429799:V101I;ENSP00000428790:V221I	ENSP00000373648:V221I	V	-	1	0	KCNQ3	133261702	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.822000	0.62686	2.610000	0.88304	0.561000	0.74099	GTT	.	.		0.587	KCNQ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268621.2	NM_004519	
SLC45A4	57210	hgsc.bcm.edu	37	8	142231725	142231725	+	Silent	SNP	G	G	A			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr8:142231725G>A	ENST00000024061.3	-	2	535	c.228C>T	c.(226-228)tgC>tgT	p.C76C	SLC45A4_ENST00000519067.1_Silent_p.C76C|SLC45A4_ENST00000433583.2_Silent_p.C69C|SLC45A4_ENST00000517878.1_Silent_p.C127C	NM_001080431.1	NP_001073900.1	Q5BKX6	S45A4_HUMAN	solute carrier family 45, member 4						transport (GO:0006810)	integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(9)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	31	all_cancers(97;1.52e-15)|all_epithelial(106;2.92e-14)|Lung NSC(106;1.23e-05)|all_lung(105;1.75e-05)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0493)			GGACGCCAACGCAGAGGGCGA	0.622																																					p.C76C		Atlas-SNP	.											.	SLC45A4	71	.	0			c.C228T						.						74.0	81.0	79.0					8																	142231725		2203	4300	6503	SO:0001819	synonymous_variant	57210	exon2			GCCAACGCAGAGG	AB032952	CCDS34948.1, CCDS69550.1, CCDS75795.1	8q24.3	2013-05-22						"""Solute carriers"""	29196	protein-coding gene	gene with protein product							Standard	NM_001080431		Approved	KIAA1126	uc003ywd.1	Q5BKX6		ENST00000024061.3:c.228C>T	chr8.hg19:g.142231725G>A		101.0	0.0		216.0	32.0	NM_001080431	Q6ZRI2|Q9ULU3	Silent	SNP	ENST00000024061.3	hg19	CCDS34948.1																																																																																			.	.		0.622	SLC45A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378571.3	XM_050325	
DENND4C	55667	hgsc.bcm.edu	37	9	19361944	19361944	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:19361944T>C	ENST00000380432.2	+	25	4685	c.4652T>C	c.(4651-4653)gTc>gCc	p.V1551A	DENND4C_ENST00000602925.1_Missense_Mutation_p.V1787A|DENND4C_ENST00000434457.2_Missense_Mutation_p.V1836A			Q5VZ89	DEN4C_HUMAN	DENN/MADD domain containing 4C	1551					cellular response to insulin stimulus (GO:0032869)|positive regulation of Rab GTPase activity (GO:0032851)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)	cytosol (GO:0005829)|insulin-responsive compartment (GO:0032593)|plasma membrane (GO:0005886)|retromer complex (GO:0030904)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|endometrium(8)|kidney(1)|large_intestine(7)|liver(2)|lung(13)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40						CCTCTGTATGTCTCATGGAGG	0.438																																					p.V1787A		Atlas-SNP	.											.	DENND4C	120	.	0			c.T5360C						.						86.0	82.0	83.0					9																	19361944		2203	4300	6503	SO:0001583	missense	55667	exon29			TGTATGTCTCATG	AK000693	CCDS6491.2, CCDS6491.3	9p22.1	2012-10-03	2006-01-27	2006-01-27	ENSG00000137145	ENSG00000137145		"""DENN/MADD domain containing"""	26079	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 55B"", ""chromosome 9 open reading frame 55"""	C9orf55B, C9orf55		12906859	Standard	NM_017925		Approved	FLJ20686, bA513M16.3	uc031tcw.1	Q5VZ89	OTTHUMG00000019627	ENST00000380432.2:c.4652T>C	chr9.hg19:g.19361944T>C	ENSP00000369797:p.Val1551Ala	61.0	0.0		97.0	4.0	NM_017925	A2A3R1|A2A3R2|A2A3R3|A2A3R9|Q6AI48|Q6ZUB3|Q8NCY7|Q9H6N4|Q9NUT1|Q9NWA5|Q9NWT3	Missense_Mutation	SNP	ENST00000380432.2	hg19		.	.	.	.	.	.	.	.	.	.	T	6.248	0.413951	0.11870	.	.	ENSG00000137145	ENST00000380437;ENST00000307015;ENST00000453857;ENST00000540671;ENST00000380432;ENST00000380427;ENST00000361024	T;T	0.24151	1.88;1.87	5.02	2.71	0.32032	.	0.813120	0.11399	N	0.568016	T	0.19446	0.0467	L	0.42686	1.345	0.09310	N	1	B;B;B	0.11235	0.002;0.004;0.0	B;B;B	0.12837	0.008;0.008;0.002	T	0.29912	-0.9996	9	.	.	.	-1.8163	5.178	0.15145	0.0:0.1578:0.1516:0.6905	.	881;733;1551	B7Z660;Q5VZ89-3;Q5VZ89	.;.;DEN4C_HUMAN	A	1551;1024;733;881;1024;733;548	ENSP00000305795:V1024A;ENSP00000443804:V881A	.	V	+	2	0	DENND4C	19351944	0.998000	0.40836	0.949000	0.38748	0.152000	0.21847	2.811000	0.47986	0.410000	0.25675	-0.334000	0.08254	GTC	.	.		0.438	DENND4C-201	KNOWN	basic	protein_coding	protein_coding		NM_017925	
DNAI1	27019	hgsc.bcm.edu	37	9	34500786	34500787	+	Missense_Mutation	DNP	GG	GG	AT			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:34500786_34500787GG>AT	ENST00000242317.4	+	11	1139_1140	c.968_969GG>AT	c.(967-969)tGG>tAT	p.W323Y		NM_001281428.1|NM_012144.2	NP_001268357.1|NP_036276.1	Q9UI46	DNAI1_HUMAN	dynein, axonemal, intermediate chain 1	323					cell projection organization (GO:0030030)|epithelial cilium movement (GO:0003351)|metabolic process (GO:0008152)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	motor activity (GO:0003774)			autonomic_ganglia(1)|endometrium(7)|kidney(1)|large_intestine(8)|lung(13)|prostate(1)|skin(2)|urinary_tract(1)	34	all_epithelial(49;0.244)		LUSC - Lung squamous cell carcinoma(29;0.0107)|STAD - Stomach adenocarcinoma(86;0.212)	GBM - Glioblastoma multiforme(74;0.0222)		CTGCCGCTCTGGAAGTTCCAAA	0.53									Kartagener syndrome		OREG0019152	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.W323X|p.W323C		Atlas-SNP	.											.	DNAI1	72	.	0			c.G968A|c.G969T						.																																			SO:0001583	missense	27019	exon11	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	CGCTCTGGAAGTT|GCTCTGGAAGTTC	AF091619	CCDS6557.1, CCDS75829.1	9p13.3	2013-02-19	2006-09-04		ENSG00000122735	ENSG00000122735		"""Axonemal dyneins"", ""WD repeat domain containing"""	2954	protein-coding gene	gene with protein product		604366	"""dynein, axonemal, intermediate polypeptide 1"""			10577904, 21953912	Standard	NM_012144		Approved	DIC1, PCD, CILD1	uc003zum.3	Q9UI46	OTTHUMG00000019825	Exception_encountered	chr9.hg19:g.34500786_34500787delinsAT	ENSP00000242317:p.Trp323Tyr	83.0|82.0	0.0	848	98.0	4.0	NM_012144	B7Z7U1|Q5T8G7|Q8NHQ7|Q9UEZ8	Nonsense_Mutation|Missense_Mutation	SNP	ENST00000242317.4	hg19	CCDS6557.1																																																																																			.	.		0.530	DNAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052192.1		
TPM2	7169	hgsc.bcm.edu	37	9	35683240	35683240	+	Splice_Site	SNP	T	T	G	rs368128547|rs149115565	byFrequency	TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:35683240T>G	ENST00000360958.2	-	9	877		c.e9-2		TPM2_ENST00000378300.5_Intron|TPM2_ENST00000378292.3_Intron|TPM2_ENST00000329305.2_Intron	NM_003289.3	NP_003280.2	P07951	TPM2_HUMAN	tropomyosin 2 (beta)						muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|regulation of ATPase activity (GO:0043462)	cytosol (GO:0005829)|muscle thin filament tropomyosin (GO:0005862)	actin binding (GO:0003779)|structural constituent of muscle (GO:0008307)			NS(1)|breast(1)|cervix(1)|kidney(1)|large_intestine(6)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15	all_epithelial(49;0.121)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			AGACTTCATCTGGGGGGGGTC	0.547																																					.		Atlas-SNP	.											.,1	TPM2	64	.	0			c.773-2A>C						.						95.0	66.0	76.0					9																	35683240		2186	4268	6454	SO:0001630	splice_region_variant	7169	exon10			TTCATCTGGGGGG		CCDS6586.1, CCDS6587.1	9p13	2014-09-17	2003-12-02		ENSG00000198467	ENSG00000198467		"""Tropomyosins"""	12011	protein-coding gene	gene with protein product	"""nemaline myopathy type 4"""	190990	"""arthrogryposis multiplex congenital, distal, type 1"""	AMCD1		7606936	Standard	NM_003289		Approved	DA1, NEM4	uc003zxq.3	P07951	OTTHUMG00000019878	ENST00000360958.2:c.773-2A>C	chr9.hg19:g.35683240T>G		216.0	2.0		237.0	14.0	NM_003289	A6NM85|P06468|Q13894|Q53FM4|Q5TCU4|Q5TCU7|Q9UH67	Splice_Site	SNP	ENST00000360958.2	hg19	CCDS6587.1	.	.	.	.	.	.	.	.	.	.	T	22.4	4.285674	0.80803	.	.	ENSG00000198467	ENST00000360958	.	.	.	4.98	4.98	0.66077	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.286	0.66247	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	TPM2	35673240	1.000000	0.71417	1.000000	0.80357	0.908000	0.53690	7.793000	0.85851	2.224000	0.72417	0.533000	0.62120	.	.	.		0.547	TPM2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052376.1	NM_003289	Intron
DAPK1	1612	hgsc.bcm.edu	37	9	90296403	90296403	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:90296403T>C	ENST00000408954.3	+	20	2421	c.2086T>C	c.(2086-2088)Tcg>Ccg	p.S696P	DAPK1_ENST00000472284.1_Missense_Mutation_p.S696P|DAPK1_ENST00000469640.2_Missense_Mutation_p.S696P|DAPK1_ENST00000491893.1_Missense_Mutation_p.S696P|DAPK1_ENST00000358077.5_Missense_Mutation_p.S696P	NM_004938.2	NP_004929.2	P53355	DAPK1_HUMAN	death-associated protein kinase 1	696					apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cellular response to interferon-gamma (GO:0071346)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of translation (GO:0017148)|positive regulation of apoptotic process (GO:0043065)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of autophagy (GO:0010506)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|identical protein binding (GO:0042802)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(27)|liver(2)|lung(17)|ovary(1)|prostate(2)|skin(3)|stomach(1)	72						GTTTGGCCACTCGGGATCCGG	0.547									Chronic Lymphocytic Leukemia, Familial Clustering of																												p.S696P		Atlas-SNP	.											.	DAPK1	329	.	0			c.T2086C						.						108.0	111.0	110.0					9																	90296403		1949	4154	6103	SO:0001583	missense	1612	exon20	Familial Cancer Database	Familial CLL	GGCCACTCGGGAT	X76104	CCDS43842.1	9q34.1	2013-01-10			ENSG00000196730	ENSG00000196730		"""Ankyrin repeat domain containing"""	2674	protein-coding gene	gene with protein product		600831				8530096	Standard	XM_005251757		Approved	DAPK	uc004apd.3	P53355	OTTHUMG00000020150	ENST00000408954.3:c.2086T>C	chr9.hg19:g.90296403T>C	ENSP00000386135:p.Ser696Pro	109.0	0.0		112.0	6.0	NM_004938	B7ZLD2|B7ZLE7|Q14CQ7|Q1W5W0|Q68CP8|Q6ZRZ3|Q9BTL8	Missense_Mutation	SNP	ENST00000408954.3	hg19	CCDS43842.1	.	.	.	.	.	.	.	.	.	.	T	11.79	1.742742	0.30865	.	.	ENSG00000196730	ENST00000358077;ENST00000472284;ENST00000469640;ENST00000408954;ENST00000491893	T;T;T;T;T	0.68181	-0.31;-0.31;-0.3;-0.31;-0.25	5.17	5.17	0.71159	.	0.336419	0.21420	N	0.074823	T	0.51381	0.1671	N	0.21448	0.665	0.48901	D	0.999726	B;B;B	0.18310	0.001;0.027;0.001	B;B;B	0.15484	0.001;0.013;0.001	T	0.50717	-0.8795	10	0.51188	T	0.08	.	10.1557	0.42820	0.1488:0.0:0.0:0.8511	.	696;250;696	B7ZLE7;P53355-2;P53355	.;.;DAPK1_HUMAN	P	696	ENSP00000350785:S696P;ENSP00000417076:S696P;ENSP00000418885:S696P;ENSP00000386135:S696P;ENSP00000419026:S696P	ENSP00000350785:S696P	S	+	1	0	DAPK1	89486223	1.000000	0.71417	0.997000	0.53966	0.437000	0.31866	1.944000	0.40263	2.189000	0.69895	0.459000	0.35465	TCG	.	.		0.547	DAPK1-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356843.1	NM_004938	
SPATA31E1	286234	hgsc.bcm.edu	37	9	90502871	90502871	+	Missense_Mutation	SNP	T	T	C	rs201052734		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:90502871T>C	ENST00000325643.5	+	4	3535	c.3469T>C	c.(3469-3471)Tct>Cct	p.S1157P		NM_178828.4	NP_849150.3	Q6ZUB1	S31E1_HUMAN	SPATA31 subfamily E, member 1	1157					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											CCAGAGTGTGTCTGGTAAGAA	0.637																																					p.S1157P		Atlas-SNP	.											.	.	.	.	0			c.T3469C						.						36.0	40.0	39.0					9																	90502871		2203	4300	6503	SO:0001583	missense	286234	exon4			AGTGTGTCTGGTA	AK093185	CCDS6676.1	9q22.1-q22.2	2012-10-12	2012-10-12	2012-10-12	ENSG00000177992	ENSG00000177992			26672	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 79"", ""family with sequence similarity 75, member E1"""	C9orf79, FAM75E1			Standard	NM_178828		Approved	FLJ35866	uc004app.4	Q6ZUB1	OTTHUMG00000020157	ENST00000325643.5:c.3469T>C	chr9.hg19:g.90502871T>C	ENSP00000322640:p.Ser1157Pro	82.0	0.0		87.0	5.0	NM_178828	B2RPB1|Q5SQC9|Q8NA41|Q8ND27	Missense_Mutation	SNP	ENST00000325643.5	hg19	CCDS6676.1	.	.	.	.	.	.	.	.	.	.	t	11.91	1.780467	0.31502	.	.	ENSG00000177992	ENST00000325643	T	0.05258	3.47	3.03	-4.74	0.03249	.	1.526110	0.04322	N	0.350822	T	0.08223	0.0205	N	0.12182	0.205	0.09310	N	1	D	0.76494	0.999	D	0.71656	0.974	T	0.21484	-1.0244	10	0.31617	T	0.26	.	4.5911	0.12307	0.6368:0.1188:0.0:0.2444	.	1157	Q6ZUB1	CI079_HUMAN	P	1157	ENSP00000322640:S1157P	ENSP00000322640:S1157P	S	+	1	0	C9orf79	89692691	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.864000	0.04254	-0.879000	0.04002	0.533000	0.62120	TCT	.	T|0.999;A|0.001		0.637	SPATA31E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052954.2	NM_178828	
RP13-60M5.2	0	hgsc.bcm.edu	37	9	91262355	91262355	+	lincRNA	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:91262355A>G	ENST00000418343.2	-	0	396																											GGAGAAGATGACACGCTGGCC	0.433																																					p.C96C		Atlas-SNP	.											.	.	.	.	0			c.T288C						.						73.0	76.0	75.0					9																	91262355		1938	4151	6089			0	exon2			AAGATGACACGCT																													chr9.hg19:g.91262355A>G		99.0	0.0		89.0	5.0	NM_001100111		Silent	SNP	ENST00000418343.2	hg19																																																																																				.	.		0.433	RP13-60M5.2-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000052976.2		
ZNF782	158431	hgsc.bcm.edu	37	9	99581649	99581649	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:99581649T>C	ENST00000481138.1	-	6	1317	c.656A>G	c.(655-657)gAa>gGa	p.E219G	ZNF782_ENST00000466833.1_5'Flank|ZNF782_ENST00000535338.1_Missense_Mutation_p.E87G	NM_001001662.1	NP_001001662.1	Q6ZMW2	ZN782_HUMAN	zinc finger protein 782	219					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(2)|kidney(2)|large_intestine(12)|lung(8)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)	33		Acute lymphoblastic leukemia(62;0.0527)				TTTTCTACTTTCATTATATTC	0.343																																					p.E219G		Atlas-SNP	.											.	ZNF782	64	.	0			c.A656G						.						51.0	54.0	53.0					9																	99581649		2201	4297	6498	SO:0001583	missense	158431	exon6			CTACTTTCATTAT	AK131468	CCDS35075.1	9q22.33	2013-01-08			ENSG00000196597	ENSG00000196597		"""Zinc fingers, C2H2-type"", ""-"""	33110	protein-coding gene	gene with protein product							Standard	NM_001001662		Approved	FLJ16636	uc004awp.1	Q6ZMW2	OTTHUMG00000020310	ENST00000481138.1:c.656A>G	chr9.hg19:g.99581649T>C	ENSP00000419397:p.Glu219Gly	61.0	0.0		75.0	4.0	NM_001001662	B2RNR0	Missense_Mutation	SNP	ENST00000481138.1	hg19	CCDS35075.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	11.43|11.43	1.636755|1.636755	0.29068|0.29068	.|.	.|.	ENSG00000196597|ENSG00000196597	ENST00000481138;ENST00000535338|ENST00000289032	T;T|.	0.07327|.	3.37;3.2|.	3.38|3.38	2.25|2.25	0.28309|0.28309	.|.	.|.	.|.	.|.	.|.	T|.	0.41604|.	0.1166|.	L|L	0.56199|0.56199	1.76|1.76	0.09310|0.09310	N|N	1|1	B|.	0.09022|.	0.002|.	B|.	0.06405|.	0.002|.	T|.	0.27365|.	-1.0076|.	9|.	0.66056|.	D|.	0.02|.	.|.	6.9339|6.9339	0.24457|0.24457	0.0:0.1156:0.0:0.8843|0.0:0.1156:0.0:0.8843	.|.	219|.	Q6ZMW2|.	ZN782_HUMAN|.	G|W	219;87|207	ENSP00000419397:E219G;ENSP00000440624:E87G|.	ENSP00000419397:E219G|.	E|X	-|-	2|3	0|0	ZNF782|ZNF782	98621470|98621470	0.000000|0.000000	0.05858|0.05858	0.059000|0.059000	0.19551|0.19551	0.307000|0.307000	0.27823|0.27823	0.451000|0.451000	0.21779|0.21779	0.691000|0.691000	0.31592|0.31592	0.529000|0.529000	0.55759|0.55759	GAA|TGA	.	.		0.343	ZNF782-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356810.1	NM_001001662	
SVEP1	79987	hgsc.bcm.edu	37	9	113191515	113191515	+	Silent	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:113191515A>G	ENST00000401783.2	-	35	6051	c.5715T>C	c.(5713-5715)tgT>tgC	p.C1905C	SVEP1_ENST00000374469.1_Silent_p.C1882C|SVEP1_ENST00000297826.5_5'Flank	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	1905	Sushi 9. {ECO:0000255|PROSITE- ProRule:PRU00302}.				cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)			NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(2)|endometrium(19)|kidney(8)|large_intestine(24)|lung(58)|ovary(7)|prostate(7)|skin(1)|stomach(4)|upper_aerodigestive_tract(5)|urinary_tract(4)	147						CCGGACTAGAACACTTCACTG	0.393																																					p.C1905C		Atlas-SNP	.											.	SVEP1	326	.	0			c.T5715C						.						38.0	36.0	37.0					9																	113191515		1840	4089	5929	SO:0001819	synonymous_variant	79987	exon35			ACTAGAACACTTC	AK027870		9q31-q32	2008-02-05	2005-03-15	2005-03-17	ENSG00000165124	ENSG00000165124			15985	protein-coding gene	gene with protein product		611691	"""chromosome 9 open reading frame 13"""	C9orf13			Standard	NM_153366		Approved	bA427L11.3, POLYDOM, FLJ13529	uc010mtz.3	Q4LDE5	OTTHUMG00000020482	ENST00000401783.2:c.5715T>C	chr9.hg19:g.113191515A>G		57.0	0.0		43.0	4.0	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Silent	SNP	ENST00000401783.2	hg19	CCDS48004.1																																																																																			.	.		0.393	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
KIAA0368	23392	hgsc.bcm.edu	37	9	114213753	114213753	+	Silent	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:114213753A>G	ENST00000338205.5	-	2	324	c.105T>C	c.(103-105)ccT>ccC	p.P35P	KIAA0368_ENST00000259335.4_Silent_p.P213P			Q5VYK3	ECM29_HUMAN	KIAA0368	41					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)	centrosome (GO:0005813)|cytoplasmic membrane-bounded vesicle (GO:0016023)|early endosome (GO:0005769)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle (GO:0030134)|late endosome (GO:0005770)|membrane (GO:0016020)|multivesicular body (GO:0005771)|nucleus (GO:0005634)|proteasome complex (GO:0000502)				NS(2)|breast(3)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(23)|prostate(3)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	65						GCAAAACAGGAGGAAGGAATT	0.358																																					p.P213P		Atlas-SNP	.											.	KIAA0368	144	.	0			c.T639C						.						59.0	55.0	56.0					9																	114213753		1831	4091	5922	SO:0001819	synonymous_variant	23392	exon4			AACAGGAGGAAGG	AK025689	CCDS48006.1	9q32	2012-11-29	2006-11-23	2006-11-23	ENSG00000136813	ENSG00000136813			29020	protein-coding gene	gene with protein product	"""ECM29 homolog (S. cerevisiae)"""					9205841, 15496406, 20682791	Standard	NM_001080398		Approved	FLJ22036, ECM29	uc004bfe.1	Q5VYK3	OTTHUMG00000020489	ENST00000338205.5:c.105T>C	chr9.hg19:g.114213753A>G		60.0	0.0		75.0	5.0	NM_001080398	O15074|Q8WU82	Silent	SNP	ENST00000338205.5	hg19																																																																																				.	.		0.358	KIAA0368-001	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000053637.2	NM_014686	
TLR4	7099	hgsc.bcm.edu	37	9	120476060	120476060	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:120476060A>G	ENST00000355622.6	+	3	1755	c.1654A>G	c.(1654-1656)Agt>Ggt	p.S552G	TLR4_ENST00000472304.1_3'UTR|TLR4_ENST00000394487.4_Missense_Mutation_p.S512G	NM_138554.4|NM_138557.2	NP_612564.1|NP_612567.1	O00206	TLR4_HUMAN	toll-like receptor 4	552					activation of MAPK activity (GO:0000187)|B cell proliferation involved in immune response (GO:0002322)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to lipoteichoic acid (GO:0071223)|cellular response to mechanical stimulus (GO:0071260)|defense response to bacterium (GO:0042742)|defense response to Gram-negative bacterium (GO:0050829)|detection of fungus (GO:0016046)|detection of lipopolysaccharide (GO:0032497)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|immune response (GO:0006955)|innate immune response (GO:0045087)|interferon-gamma production (GO:0032609)|intestinal epithelial structure maintenance (GO:0060729)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|macrophage activation (GO:0042116)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-17 production (GO:0032700)|negative regulation of interleukin-23 production (GO:0032707)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of tumor necrosis factor production (GO:0032720)|nitric oxide production involved in inflammatory response (GO:0002537)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of chemokine production (GO:0032722)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-1 production (GO:0032732)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of JNK cascade (GO:0046330)|positive regulation of macrophage cytokine production (GO:0060907)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway (GO:0070430)|positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070434)|positive regulation of platelet activation (GO:0010572)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of cytokine secretion (GO:0050707)|response to lipopolysaccharide (GO:0032496)|T-helper 1 type immune response (GO:0042088)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|endosome membrane (GO:0010008)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|lipopolysaccharide receptor complex (GO:0046696)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	lipopolysaccharide binding (GO:0001530)|lipopolysaccharide receptor activity (GO:0001875)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(12)|lung(66)|ovary(4)|pancreas(1)|skin(6)|upper_aerodigestive_tract(5)|urinary_tract(1)	103					Naloxone(DB01183)	TCTTGATTACAGTCTCAATCA	0.373																																					p.S552G		Atlas-SNP	.											.	TLR4	220	.	0			c.A1654G						.						91.0	82.0	85.0					9																	120476060		2203	4300	6503	SO:0001583	missense	7099	exon3			GATTACAGTCTCA	U88880	CCDS6818.1	9q33.1	2013-01-23			ENSG00000136869	ENSG00000136869		"""CD molecules"""	11850	protein-coding gene	gene with protein product		603030				9435236, 9237759	Standard	NM_138554		Approved	hToll, CD284, TLR-4, ARMD10	uc004bjz.4	O00206	OTTHUMG00000021046	ENST00000355622.6:c.1654A>G	chr9.hg19:g.120476060A>G	ENSP00000363089:p.Ser552Gly	61.0	0.0		91.0	4.0	NM_138554	A8K1Y8|A9XLP9|A9XLQ0|A9XLQ1|B4E194|D1CS52|D1CS53|Q5VZI8|Q5VZI9|Q9UK78|Q9UM57	Missense_Mutation	SNP	ENST00000355622.6	hg19	CCDS6818.1	.	.	.	.	.	.	.	.	.	.	A	11.37	1.619216	0.28801	.	.	ENSG00000136869	ENST00000394487;ENST00000355622	T;T	0.01126	5.3;5.3	6.02	6.02	0.97574	.	0.000000	0.85682	D	0.000000	T	0.02012	0.0063	L	0.58510	1.815	0.34300	D	0.684272	P	0.38535	0.635	B	0.36092	0.217	T	0.44937	-0.9295	10	0.62326	D	0.03	.	12.9843	0.58583	0.8654:0.1346:0.0:0.0	.	552	O00206	TLR4_HUMAN	G	512;552	ENSP00000377997:S512G;ENSP00000363089:S552G	ENSP00000363089:S552G	S	+	1	0	TLR4	119515881	0.997000	0.39634	0.929000	0.37066	0.035000	0.12851	3.156000	0.50708	2.304000	0.77564	0.528000	0.53228	AGT	.	.		0.373	TLR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055549.3	NM_138554	
SCAI	286205	hgsc.bcm.edu	37	9	127904935	127904935	+	Silent	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:127904935T>C	ENST00000336505.6	-	2	133	c.75A>G	c.(73-75)aaA>aaG	p.K25K	SCAI_ENST00000373549.4_Silent_p.K25K	NM_001144877.2	NP_001138349.1	Q8N9R8	SCAI_HUMAN	suppressor of cancer cell invasion	25	Necessary to inhibit MKL1-induced SRF transcriptional activity. {ECO:0000250}.				negative regulation of cell migration (GO:0030336)|negative regulation of Rho protein signal transduction (GO:0035024)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	transcription corepressor activity (GO:0003714)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(7)|large_intestine(4)|lung(8)|ovary(2)|pancreas(1)|prostate(5)|stomach(1)|urinary_tract(1)	35						TTCGAGGCGGTTTCTCCACTG	0.463																																					p.K25K		Atlas-SNP	.											.	SCAI	84	.	0			c.A75G						.						84.0	89.0	88.0					9																	127904935		1929	4124	6053	SO:0001819	synonymous_variant	286205	exon2			AGGCGGTTTCTCC	AK093983	CCDS43877.1, CCDS48017.1	9q34.11	2009-11-06	2009-07-09	2009-07-09	ENSG00000173611	ENSG00000173611			26709	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 126"""	C9orf126			Standard	NM_173690		Approved	FLJ36664, NET40	uc004bpd.3	Q8N9R8	OTTHUMG00000020667	ENST00000336505.6:c.75A>G	chr9.hg19:g.127904935T>C		96.0	0.0		72.0	4.0	NM_173690	Q3SXZ1|Q3SXZ2|Q5T163|Q8N1I4	Silent	SNP	ENST00000336505.6	hg19	CCDS48017.1																																																																																			.	.		0.463	SCAI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054055.3	NM_173690	
TTC16	158248	hgsc.bcm.edu	37	9	130491908	130491908	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:130491908A>G	ENST00000373289.3	+	13	1893	c.1813A>G	c.(1813-1815)Agc>Ggc	p.S605G	TOR2A_ENST00000472723.1_5'Flank|TTC16_ENST00000489226.1_3'UTR	NM_144965.1	NP_659402.1	Q8NEE8	TTC16_HUMAN	tetratricopeptide repeat domain 16	605										central_nervous_system(2)|endometrium(3)|lung(7)|ovary(3)|pancreas(2)|prostate(4)|skin(1)	22						CCTGTCTGACAGCTACCTTGA	0.542																																					p.S605G		Atlas-SNP	.											.	TTC16	55	.	0			c.A1813G						.						107.0	92.0	98.0					9																	130491908		2203	4300	6503	SO:0001583	missense	158248	exon13			TCTGACAGCTACC	AK057342	CCDS6875.1	9q34.13	2013-01-10			ENSG00000167094	ENSG00000167094		"""Tetratricopeptide (TTC) repeat domain containing"""	26536	protein-coding gene	gene with protein product						12477932	Standard	NM_144965		Approved	FLJ32780	uc004brq.1	Q8NEE8	OTTHUMG00000020711	ENST00000373289.3:c.1813A>G	chr9.hg19:g.130491908A>G	ENSP00000362386:p.Ser605Gly	68.0	0.0		78.0	5.0	NM_144965	B4DYG4|B5ME24|Q5JU66|Q96M72	Missense_Mutation	SNP	ENST00000373289.3	hg19	CCDS6875.1	.	.	.	.	.	.	.	.	.	.	A	13.19	2.164593	0.38217	.	.	ENSG00000167094	ENST00000373289	T	0.25912	1.77	3.8	0.0857	0.14443	.	0.247869	0.29198	N	0.012841	T	0.21509	0.0518	L	0.36672	1.1	0.09310	N	1	D;D	0.58268	0.982;0.982	P;P	0.48598	0.583;0.583	T	0.11446	-1.0587	10	0.72032	D	0.01	-17.2498	6.1433	0.20271	0.6681:0.0:0.3319:0.0	.	592;605	B4DZ42;Q8NEE8	.;TTC16_HUMAN	G	605	ENSP00000362386:S605G	ENSP00000362386:S605G	S	+	1	0	TTC16	129531729	0.270000	0.24152	0.025000	0.17156	0.001000	0.01503	0.395000	0.20850	0.012000	0.14892	-0.388000	0.06559	AGC	.	.		0.542	TTC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054224.1	NM_144965	
TTC16	158248	hgsc.bcm.edu	37	9	130492952	130492952	+	Silent	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:130492952T>C	ENST00000373289.3	+	14	1970	c.1890T>C	c.(1888-1890)gcT>gcC	p.A630A	TOR2A_ENST00000472723.1_5'Flank|TTC16_ENST00000489226.1_3'UTR	NM_144965.1	NP_659402.1	Q8NEE8	TTC16_HUMAN	tetratricopeptide repeat domain 16	630										central_nervous_system(2)|endometrium(3)|lung(7)|ovary(3)|pancreas(2)|prostate(4)|skin(1)	22						AGATGTCGGCTATCTGCCAGG	0.592																																					p.A630A		Atlas-SNP	.											.	TTC16	55	.	0			c.T1890C						.						61.0	51.0	54.0					9																	130492952		2203	4300	6503	SO:0001819	synonymous_variant	158248	exon14			GTCGGCTATCTGC	AK057342	CCDS6875.1	9q34.13	2013-01-10			ENSG00000167094	ENSG00000167094		"""Tetratricopeptide (TTC) repeat domain containing"""	26536	protein-coding gene	gene with protein product						12477932	Standard	NM_144965		Approved	FLJ32780	uc004brq.1	Q8NEE8	OTTHUMG00000020711	ENST00000373289.3:c.1890T>C	chr9.hg19:g.130492952T>C		94.0	0.0		97.0	4.0	NM_144965	B4DYG4|B5ME24|Q5JU66|Q96M72	Silent	SNP	ENST00000373289.3	hg19	CCDS6875.1																																																																																			.	.		0.592	TTC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054224.1	NM_144965	
TRUB2	26995	hgsc.bcm.edu	37	9	131076096	131076096	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:131076096T>C	ENST00000372890.4	-	5	784	c.451A>G	c.(451-453)Aca>Gca	p.T151A	TRUB2_ENST00000546104.1_Missense_Mutation_p.T95A|RP11-339B21.13_ENST00000609315.1_RNA|TRUB2_ENST00000460320.1_5'UTR	NM_015679.1	NP_056494.1	O95900	TRUB2_HUMAN	TruB pseudouridine (psi) synthase family member 2	151					pseudouridine synthesis (GO:0001522)|tRNA processing (GO:0008033)		poly(A) RNA binding (GO:0044822)|pseudouridine synthase activity (GO:0009982)			kidney(2)|large_intestine(2)|lung(3)|ovary(1)	8						CCATAGGTTGTCTTCTCTACC	0.592																																					p.T151A		Atlas-SNP	.											.	TRUB2	26	.	0			c.A451G						.						192.0	156.0	168.0					9																	131076096		2203	4300	6503	SO:0001583	missense	26995	exon5			AGGTTGTCTTCTC	AK001956	CCDS6897.1	9q34.11	2014-01-28	2013-09-02		ENSG00000167112	ENSG00000167112			17170	protein-coding gene	gene with protein product		610727	"""TruB pseudouridine (psi) synthase homolog 2 (E. coli)"""			12736709	Standard	NM_015679		Approved	CLONE24922	uc004buq.1	O95900	OTTHUMG00000020741	ENST00000372890.4:c.451A>G	chr9.hg19:g.131076096T>C	ENSP00000361982:p.Thr151Ala	107.0	0.0		119.0	5.0	NM_015679	B7Z7G5	Missense_Mutation	SNP	ENST00000372890.4	hg19	CCDS6897.1	.	.	.	.	.	.	.	.	.	.	T	14.10	2.434736	0.43224	.	.	ENSG00000167112	ENST00000372890;ENST00000546104	T;T	0.49720	0.77;0.77	5.53	4.37	0.52481	Pseudouridine synthase, catalytic domain (1);	0.188576	0.47455	D	0.000228	T	0.45094	0.1325	L	0.29908	0.895	0.49798	D	0.999823	P	0.51653	0.947	P	0.57502	0.822	T	0.36187	-0.9758	10	0.05833	T	0.94	-9.4758	11.827	0.52273	0.1315:0.0:0.0:0.8685	.	151	O95900	TRUB2_HUMAN	A	151;95	ENSP00000361982:T151A;ENSP00000438084:T95A	ENSP00000361982:T151A	T	-	1	0	TRUB2	130115917	1.000000	0.71417	0.952000	0.39060	0.593000	0.36681	2.194000	0.42668	0.896000	0.36366	0.459000	0.35465	ACA	.	.		0.592	TRUB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054419.1	NM_015679	
FNBP1	23048	hgsc.bcm.edu	37	9	132662819	132662819	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:132662819A>G	ENST00000446176.2	-	14	1622	c.1436T>C	c.(1435-1437)cTg>cCg	p.L479P	FNBP1_ENST00000355681.3_Missense_Mutation_p.L450P|FNBP1_ENST00000443566.2_Missense_Mutation_p.L107P|FNBP1_ENST00000478129.1_5'UTR|FNBP1_ENST00000420781.1_Missense_Mutation_p.L470P	NM_015033.2	NP_055848.1	Q96RU3	FNBP1_HUMAN	formin binding protein 1	479	Interaction with RND2. {ECO:0000250}.|Required for self-association and induction of membrane tubulation.				endocytosis (GO:0006897)	coated pit (GO:0005905)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|lipid binding (GO:0008289)						Ovarian(14;0.000536)		GBM - Glioblastoma multiforme(294;0.0378)		AACCTCAGCCAGCCAGGCCTG	0.627			T	MLL	AML																																p.L479P		Atlas-SNP	.		Dom	yes		9	9q23	23048	formin binding protein 1 (FBP17)		L	.	FNBP1	51	.	0			c.T1436C						.						23.0	24.0	24.0					9																	132662819		1967	4154	6121	SO:0001583	missense	23048	exon14			TCAGCCAGCCAGG	AB011126	CCDS48040.1	9q34	2008-02-05			ENSG00000187239	ENSG00000187239			17069	protein-coding gene	gene with protein product		606191				9628581, 11438682	Standard	XM_005251815		Approved	FBP17, KIAA0554	uc004byw.1	Q96RU3	OTTHUMG00000020800	ENST00000446176.2:c.1436T>C	chr9.hg19:g.132662819A>G	ENSP00000413625:p.Leu479Pro	70.0	0.0		59.0	4.0	NM_015033	O60301|Q3MIN8|Q5TC87|Q5TC88|Q6P658|Q7LGG2|Q9H8H8|Q9NWD1	Missense_Mutation	SNP	ENST00000446176.2	hg19	CCDS48040.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	19.92|19.92	3.916158|3.916158	0.73098|0.73098	.|.	.|.	ENSG00000187239|ENSG00000187239	ENST00000372416;ENST00000446176;ENST00000420781;ENST00000372415;ENST00000443566;ENST00000355681|ENST00000449089	T;T;T;T|.	0.78364|.	-1.17;-1.17;-1.17;-1.17|.	4.24|4.24	4.24|4.24	0.50183|0.50183	.|.	0.000000|.	0.64402|.	D|.	0.000001|.	T|T	0.77857|0.77857	0.4193|0.4193	M|M	0.87269|0.87269	2.87|2.87	0.80722|0.80722	D|D	1|1	B;D;D;D;D;D;D;D|.	0.89917|.	0.435;0.999;0.999;1.0;1.0;0.999;1.0;1.0|.	B;D;D;D;D;D;D;D|.	0.79108|.	0.155;0.982;0.987;0.992;0.99;0.968;0.992;0.982|.	T|T	0.81413|0.81413	-0.0944|-0.0944	10|5	0.87932|.	D|.	0|.	-24.3011|-24.3011	12.942|12.942	0.58350|0.58350	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	474;469;107;413;450;430;474;479|.	B7ZL12;B7ZL13;E7EPB7;B7ZL14;Q96RU3-3;Q5QP69;Q96RU3-2;Q96RU3|.	.;.;.;.;.;.;.;FNBP1_HUMAN|.	P|R	479;479;470;479;107;450|431	ENSP00000413625:L479P;ENSP00000407548:L470P;ENSP00000389117:L107P;ENSP00000347907:L450P|.	ENSP00000347907:L450P|.	L|W	-|-	2|1	0|0	FNBP1|FNBP1	131702640|131702640	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.950000|0.950000	0.60333|0.60333	8.203000|8.203000	0.89739|0.89739	1.895000|1.895000	0.54865|0.54865	0.260000|0.260000	0.18958|0.18958	CTG|TGG	.	.		0.627	FNBP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054630.2		
SURF1	6834	hgsc.bcm.edu	37	9	136218808	136218808	+	Missense_Mutation	SNP	A	A	G	rs200841752		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:136218808A>G	ENST00000371974.3	-	9	894	c.863T>C	c.(862-864)cTg>cCg	p.L288P	SURF1_ENST00000495952.1_5'UTR|SNORD36A_ENST00000362874.1_RNA|SNORD24_ENST00000383884.1_RNA|SNORD36C_ENST00000516733.1_RNA|SNORD36B_ENST00000363961.1_RNA	NM_001280787.1|NM_003172.2	NP_001267716.1|NP_003163.1	Q15526	SURF1_HUMAN	surfeit 1	288					aerobic respiration (GO:0009060)|ATP biosynthetic process (GO:0006754)|oxidation-reduction process (GO:0055114)|oxidative phosphorylation (GO:0006119)|respiratory chain complex IV assembly (GO:0008535)	integral component of membrane (GO:0016021)|mitochondrial respiratory chain (GO:0005746)	cytochrome-c oxidase activity (GO:0004129)			breast(2)|endometrium(1)|ovary(2)|stomach(1)	6				OV - Ovarian serous cystadenocarcinoma(145;5.06e-07)|Epithelial(140;4.25e-06)|all cancers(34;3.93e-05)		CTTAAACCACAGGTAGGATGT	0.532											OREG0019585	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L288P		Atlas-SNP	.											.	SURF1	15	.	0			c.T863C						.						72.0	68.0	70.0					9																	136218808		2203	4300	6503	SO:0001583	missense	6834	exon9			AACCACAGGTAGG		CCDS6966.1, CCDS75928.1	9q33-q34	2012-10-12			ENSG00000148290	ENSG00000148290		"""Mitochondrial respiratory chain complex assembly factors"""	11474	protein-coding gene	gene with protein product	"""surfeit locus protein 1"""	185620				8499913, 9843204	Standard	NM_003172		Approved		uc004cdh.1	Q15526	OTTHUMG00000020866	ENST00000371974.3:c.863T>C	chr9.hg19:g.136218808A>G	ENSP00000361042:p.Leu288Pro	83.0	0.0	1624	83.0	4.0	NM_003172	Q5T8T3|Q5T8T4	Missense_Mutation	SNP	ENST00000371974.3	hg19	CCDS6966.1	.	.	.	.	.	.	.	.	.	.	A	19.02	3.745721	0.69418	.	.	ENSG00000148290	ENST00000371974;ENST00000437995	D	0.95001	-3.58	5.27	5.27	0.74061	.	0.120040	0.56097	D	0.000032	D	0.96300	0.8793	M	0.83774	2.66	0.80722	D	1	D	0.55605	0.972	P	0.55667	0.781	D	0.96637	0.9471	10	0.72032	D	0.01	-17.5262	13.2078	0.59807	1.0:0.0:0.0:0.0	.	288	Q15526	SURF1_HUMAN	P	288;258	ENSP00000361042:L288P	ENSP00000361042:L288P	L	-	2	0	SURF1	135208629	1.000000	0.71417	0.939000	0.37840	0.429000	0.31625	6.581000	0.74045	2.118000	0.64928	0.379000	0.24179	CTG	.	A|1.000;C|0.000		0.532	SURF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054879.1	NM_003172	
GLT6D1	360203	hgsc.bcm.edu	37	9	138516016	138516016	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:138516016T>C	ENST00000371763.1	-	5	1011	c.758A>G	c.(757-759)gAc>gGc	p.D253G		NM_182974.2	NP_892019.2	Q7Z4J2	GL6D1_HUMAN	glycosyltransferase 6 domain containing 1	253					carbohydrate metabolic process (GO:0005975)	integral component of membrane (GO:0016021)	transferase activity, transferring hexosyl groups (GO:0016758)			endometrium(2)|large_intestine(5)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	15		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;4.3e-07)|Epithelial(140;1.58e-06)|all cancers(34;5.36e-05)		ATTTTTGATGTCATGAATAAC	0.373																																					p.D253G		Atlas-SNP	.											.	GLT6D1	56	.	0			c.A758G						.						165.0	162.0	163.0					9																	138516016		1849	4099	5948	SO:0001583	missense	360203	exon5			TTGATGTCATGAA	AY336054	CCDS43900.1	9q34.3	2013-02-22	2004-09-16	2004-09-17	ENSG00000204007	ENSG00000204007		"""Glycosyltransferase family 6 domain containing"""	23671	protein-coding gene	gene with protein product		613699	"""galactosyltransferase family 6 domain containing 1"""	GLTDC1			Standard	NM_182974		Approved		uc010nbd.1	Q7Z4J2	OTTHUMG00000020911	ENST00000371763.1:c.758A>G	chr9.hg19:g.138516016T>C	ENSP00000360829:p.Asp253Gly	102.0	0.0		126.0	6.0	NM_182974		Missense_Mutation	SNP	ENST00000371763.1	hg19	CCDS43900.1	.	.	.	.	.	.	.	.	.	.	T	16.23	3.064491	0.55432	.	.	ENSG00000204007	ENST00000371763	T	0.02472	4.28	2.8	2.8	0.32819	.	0.000000	0.56097	D	0.000023	T	0.14874	0.0359	M	0.86420	2.815	0.39432	D	0.967096	D	0.89917	1.0	D	0.97110	1.0	T	0.00948	-1.1504	10	0.87932	D	0	-62.4897	9.3621	0.38201	0.0:0.0:0.0:1.0	.	253	Q7Z4J2	GL6D1_HUMAN	G	253	ENSP00000360829:D253G	ENSP00000360829:D253G	D	-	2	0	GLT6D1	137655837	1.000000	0.71417	0.012000	0.15200	0.010000	0.07245	5.826000	0.69293	1.526000	0.49068	0.482000	0.46254	GAC	.	.		0.373	GLT6D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055005.2	NM_182974	
QSOX2	169714	hgsc.bcm.edu	37	9	139100989	139100989	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:139100989T>C	ENST00000358701.5	-	12	1719	c.1682A>G	c.(1681-1683)cAc>cGc	p.H561R		NM_181701.3	NP_859052.3	Q6ZRP7	QSOX2_HUMAN	quiescin Q6 sulfhydryl oxidase 2	561					cell redox homeostasis (GO:0045454)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	thiol oxidase activity (GO:0016972)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(10)|ovary(4)|prostate(1)|upper_aerodigestive_tract(1)	22		Myeloproliferative disorder(178;0.0511)		Epithelial(140;7.78e-08)|OV - Ovarian serous cystadenocarcinoma(145;1.55e-07)		GCGGCCATAGTGCTGCTTCAA	0.582																																					p.H561R		Atlas-SNP	.											.	QSOX2	63	.	0			c.A1682G						.						101.0	103.0	102.0					9																	139100989		2203	4300	6503	SO:0001583	missense	169714	exon12			CCATAGTGCTGCT	AJ318051	CCDS35178.1	9q34.3	2008-02-05	2007-04-23	2007-04-23	ENSG00000165661	ENSG00000165661			30249	protein-coding gene	gene with protein product		612860	"""quiescin Q6-like 1"""	QSCN6L1		12176051	Standard	NM_181701		Approved	SOXN, DKFZp762A2013	uc010nbi.2	Q6ZRP7	OTTHUMG00000020923	ENST00000358701.5:c.1682A>G	chr9.hg19:g.139100989T>C	ENSP00000351536:p.His561Arg	91.0	0.0		87.0	4.0	NM_181701	A2CEE0|A6NLB0|Q5TB37|Q7Z7B6|Q86VV7|Q8N3G2	Missense_Mutation	SNP	ENST00000358701.5	hg19	CCDS35178.1	.	.	.	.	.	.	.	.	.	.	T	12.21	1.870040	0.33069	.	.	ENSG00000165661	ENST00000358701	T	0.15256	2.44	4.91	3.69	0.42338	.	0.376195	0.28908	N	0.013745	T	0.35770	0.0943	M	0.75615	2.305	0.43494	D	0.99573	D	0.76494	0.999	D	0.66196	0.942	T	0.07578	-1.0765	10	0.40728	T	0.16	-28.9019	9.8401	0.40993	0.1533:0.0:0.0:0.8467	.	561	Q6ZRP7	QSOX2_HUMAN	R	561	ENSP00000351536:H561R	ENSP00000351536:H561R	H	-	2	0	QSOX2	138240810	1.000000	0.71417	0.984000	0.44739	0.072000	0.16883	5.469000	0.66749	1.831000	0.53308	0.456000	0.33151	CAC	.	.		0.582	QSOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055046.2	NM_181701	
PMPCA	23203	hgsc.bcm.edu	37	9	139313097	139313097	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:139313097T>C	ENST00000371717.3	+	9	1090	c.1081T>C	c.(1081-1083)Tcc>Ccc	p.S361P	PMPCA_ENST00000462616.1_3'UTR|PMPCA_ENST00000399219.3_Missense_Mutation_p.S230P	NM_001282946.1|NM_015160.1	NP_001269875.1|NP_055975.1	Q10713	MPPA_HUMAN	peptidase (mitochondrial processing) alpha	361					cellular protein metabolic process (GO:0044267)|protein targeting to mitochondrion (GO:0006626)|proteolysis (GO:0006508)	extracellular space (GO:0005615)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			endometrium(3)|kidney(1)|large_intestine(1)|lung(6)|ovary(2)|urinary_tract(1)	14		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;9.3e-06)|Epithelial(140;1.15e-05)		GGGCATGTTCTCCAGGCTCTA	0.587																																					p.S361P		Atlas-SNP	.											.	PMPCA	29	.	0			c.T1081C						.						94.0	86.0	89.0					9																	139313097		2203	4300	6503	SO:0001583	missense	23203	exon9			ATGTTCTCCAGGC	D21064	CCDS35180.1, CCDS65192.1	9q34.3	2008-02-05	2003-06-13	2003-06-20	ENSG00000165688	ENSG00000165688			18667	protein-coding gene	gene with protein product		613036	"""inositol polyphosphate-5-phosphatase, 72 kD"""	INPP5E		8590280, 7788527	Standard	NM_015160		Approved	KIAA0123, Alpha-MPP	uc004chl.3	Q10713	OTTHUMG00000020926	ENST00000371717.3:c.1081T>C	chr9.hg19:g.139313097T>C	ENSP00000360782:p.Ser361Pro	117.0	0.0		154.0	7.0	NM_015160	B4DKL3|E7ET61|Q16639|Q5SXM9|Q8N513	Missense_Mutation	SNP	ENST00000371717.3	hg19	CCDS35180.1	.	.	.	.	.	.	.	.	.	.	t	22.6	4.304958	0.81247	.	.	ENSG00000165688	ENST00000371717;ENST00000399219;ENST00000444897	T;T;T	0.15718	2.4;2.4;2.4	5.23	4.08	0.47627	Peptidase M16, C-terminal (1);Peptidase M16, core (1);Metalloenzyme, LuxS/M16 peptidase-like, metal-binding (1);	0.044808	0.85682	D	0.000000	T	0.42921	0.1224	M	0.86651	2.83	0.40934	D	0.984415	D;P;D;P	0.67145	0.996;0.845;0.992;0.845	D;P;D;P	0.71184	0.972;0.742;0.917;0.742	T	0.44421	-0.9329	10	0.87932	D	0	.	8.9403	0.35725	0.7686:0.0:0.0:0.2314	.	230;361;69;361	B4DKL3;Q5SXM9;Q5SXN9;Q10713	.;.;.;MPPA_HUMAN	P	361;230;69	ENSP00000360782:S361P;ENSP00000416702:S230P;ENSP00000408393:S69P	ENSP00000360782:S361P	S	+	1	0	PMPCA	138432918	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	7.082000	0.76851	0.829000	0.34733	0.454000	0.30748	TCC	.	.		0.587	PMPCA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055054.1	NM_015160	
MCM10	55388	hgsc.bcm.edu	37	10	13239739	13239739	+	Silent	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:13239739A>G	ENST00000484800.2	+	15	2197	c.2094A>G	c.(2092-2094)gtA>gtG	p.V698V	MCM10_ENST00000378694.1_Silent_p.V697V|MCM10_ENST00000378714.3_Silent_p.V697V			Q7L590	MCM10_HUMAN	minichromosome maintenance complex component 10	698					cell proliferation (GO:0008283)|DNA replication (GO:0006260)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)			central_nervous_system(1)|large_intestine(4)|ovary(2)|skin(1)|stomach(1)	9						AGGAACGTGTAGAAAAAAACA	0.398																																					p.V698V		Atlas-SNP	.											.	MCM10	76	.	0			c.A2094G						.						88.0	78.0	82.0					10																	13239739		2203	4300	6503	SO:0001819	synonymous_variant	55388	exon15			ACGTGTAGAAAAA	AB042719	CCDS7095.1, CCDS7096.1	10p13	2008-08-01	2007-04-04		ENSG00000065328	ENSG00000065328			18043	protein-coding gene	gene with protein product		609357	"""MCM10 minichromosome maintenance deficient 10 (S. cerevisiae)"""			11095689, 17699597	Standard	NM_018518		Approved	PRO2249, CNA43, DNA43	uc001ima.3	Q7L590	OTTHUMG00000017694	ENST00000484800.2:c.2094A>G	chr10.hg19:g.13239739A>G		59.0	0.0		93.0	4.0	NM_182751	A8K9I6|B7ZKZ8|Q3MIR3|Q7LD55|Q96GX4|Q96NB6|Q9H0D7|Q9H3P9|Q9P177	Silent	SNP	ENST00000484800.2	hg19	CCDS7096.1																																																																																			.	.		0.398	MCM10-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356853.1	NM_182751	
MASTL	84930	hgsc.bcm.edu	37	10	27448581	27448581	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:27448581T>C	ENST00000375940.4	+	3	415	c.358T>C	c.(358-360)Tct>Cct	p.S120P	MASTL_ENST00000342386.6_Missense_Mutation_p.S120P|MASTL_ENST00000375946.4_Missense_Mutation_p.S120P			Q96GX5	GWL_HUMAN	microtubule associated serine/threonine kinase-like	120	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular response to DNA damage stimulus (GO:0006974)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of protein phosphatase type 2A activity (GO:0034048)|regulation of cell cycle (GO:0051726)	centrosome (GO:0005813)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|protein phosphatase 2A binding (GO:0051721)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|cervix(2)|endometrium(2)|large_intestine(7)|lung(9)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						AGATGTCAAGTCTCTCCTACA	0.308																																					p.S120P		Atlas-SNP	.											.	MASTL	81	.	0			c.T358C						.						68.0	74.0	72.0					10																	27448581		2203	4298	6501	SO:0001583	missense	84930	exon3			GTCAAGTCTCTCC	BC009107	CCDS7153.1, CCDS53502.1, CCDS53503.1	10p12.1	2005-11-03			ENSG00000120539	ENSG00000120539			19042	protein-coding gene	gene with protein product		608221					Standard	NM_001172303		Approved	FLJ14813, THC2	uc001itm.3	Q96GX5	OTTHUMG00000017855	ENST00000375940.4:c.358T>C	chr10.hg19:g.27448581T>C	ENSP00000365107:p.Ser120Pro	54.0	0.0		62.0	4.0	NM_032844	Q5T8D5|Q5T8D7|Q8NCD6|Q96SJ5	Missense_Mutation	SNP	ENST00000375940.4	hg19	CCDS53502.1	.	.	.	.	.	.	.	.	.	.	T	22.5	4.293671	0.80914	.	.	ENSG00000120539	ENST00000375946;ENST00000342386;ENST00000375940	T;T;T	0.41758	0.99;0.99;0.99	5.7	4.55	0.56014	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.047398	0.85682	D	0.000000	T	0.66356	0.2781	M	0.83483	2.645	0.80722	D	1	D;D;D	0.89917	0.998;0.999;1.0	D;D;D	0.91635	0.994;0.997;0.999	T	0.71052	-0.4704	10	0.87932	D	0	-17.7169	13.0503	0.58950	0.0:0.0:0.1343:0.8657	.	120;120;120	Q96GX5-2;Q96GX5;Q96GX5-3	.;GWL_HUMAN;.	P	120	ENSP00000365113:S120P;ENSP00000343446:S120P;ENSP00000365107:S120P	ENSP00000343446:S120P	S	+	1	0	MASTL	27488587	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	7.493000	0.81493	0.979000	0.38497	0.459000	0.35465	TCT	.	.		0.308	MASTL-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047320.1	NM_032844	
A1CF	29974	hgsc.bcm.edu	37	10	52603752	52603752	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:52603752T>C	ENST00000373993.1	-	2	274	c.230A>G	c.(229-231)gAa>gGa	p.E77G	A1CF_ENST00000374001.2_Missense_Mutation_p.E77G|A1CF_ENST00000373995.3_Missense_Mutation_p.E85G|A1CF_ENST00000395489.2_Missense_Mutation_p.E70G|A1CF_ENST00000395495.1_Missense_Mutation_p.E77G|A1CF_ENST00000373997.3_Missense_Mutation_p.E77G|A1CF_ENST00000282641.2_Missense_Mutation_p.E77G			Q9NQ94	A1CF_HUMAN	APOBEC1 complementation factor	77	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				cytidine to uridine editing (GO:0016554)|gene expression (GO:0010467)|mRNA modification (GO:0016556)|mRNA processing (GO:0006397)|protein stabilization (GO:0050821)	apolipoprotein B mRNA editing enzyme complex (GO:0030895)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)			NS(1)|breast(1)|central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(14)|prostate(2)|skin(3)	29						ACTCACTTTTTCACATAATGG	0.403																																					p.E85G		Atlas-SNP	.											.	A1CF	190	.	0			c.A254G						.						104.0	122.0	116.0					10																	52603752		2202	4300	6502	SO:0001583	missense	29974	exon5			ACTTTTTCACATA	AF271790	CCDS7241.1, CCDS7242.1, CCDS7243.1, CCDS73133.1	10q21.1	2013-02-12			ENSG00000148584	ENSG00000148584		"""RNA binding motif (RRM) containing"""	24086	protein-coding gene	gene with protein product						11815617, 11072063	Standard	NM_014576		Approved	ACF, ASP, ACF64, ACF65, APOBEC1CF	uc001jjj.3	Q9NQ94	OTTHUMG00000018240	ENST00000373993.1:c.230A>G	chr10.hg19:g.52603752T>C	ENSP00000363105:p.Glu77Gly	82.0	0.0		90.0	4.0	NM_001198820	A1L4F2|A8K7G7|B7ZM14|Q5SZQ0|Q9NQ93|Q9NQX8|Q9NQX9|Q9NXC9|Q9NZD3	Missense_Mutation	SNP	ENST00000373993.1	hg19	CCDS7242.1	.	.	.	.	.	.	.	.	.	.	T	24.8	4.571540	0.86542	.	.	ENSG00000148584	ENST00000374001;ENST00000373993;ENST00000373997;ENST00000373995;ENST00000282641;ENST00000395495;ENST00000395488;ENST00000395489;ENST00000414883	T;T;T;T;T;T;T;T	0.16196	2.36;2.36;2.36;2.36;2.36;2.36;2.36;2.36	5.55	5.55	0.83447	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	T	0.32224	0.0822	L	0.37561	1.115	0.80722	D	1	D;D;D;D	0.89917	0.964;0.971;1.0;0.983	P;D;D;P	0.85130	0.839;0.93;0.997;0.889	T	0.03981	-1.0987	10	0.87932	D	0	.	13.6488	0.62299	0.0:0.0:0.0:1.0	.	70;77;77;85	F8W9F8;Q9NQ94;Q9NQ94-2;Q9NQ94-4	.;A1CF_HUMAN;.;.	G	77;77;77;85;77;77;60;70;77	ENSP00000363113:E77G;ENSP00000363105:E77G;ENSP00000363109:E77G;ENSP00000363107:E85G;ENSP00000282641:E77G;ENSP00000378873:E77G;ENSP00000378868:E70G;ENSP00000397953:E77G	ENSP00000282641:E77G	E	-	2	0	A1CF	52273758	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.698000	0.84413	2.112000	0.64535	0.528000	0.53228	GAA	.	.		0.403	A1CF-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048086.2	NM_014576	
IPMK	253430	hgsc.bcm.edu	37	10	59986874	59986874	+	Silent	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:59986874A>G	ENST00000373935.3	-	3	625	c.303T>C	c.(301-303)ggT>ggC	p.G101G		NM_152230.4	NP_689416.1	Q8NFU5	IPMK_HUMAN	inositol polyphosphate multikinase	101					inositol phosphate biosynthetic process (GO:0032958)|inositol phosphate metabolic process (GO:0043647)|neural tube formation (GO:0001841)|small molecule metabolic process (GO:0044281)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|inositol tetrakisphosphate 3-kinase activity (GO:0000824)|inositol-1,4,5-trisphosphate 3-kinase activity (GO:0008440)|inositol-1,4,5-trisphosphate 6-kinase activity (GO:0000823)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(11)|ovary(1)	22						CTAGAAGAACACCATCAAAAC	0.358																																					p.G101G		Atlas-SNP	.											.	IPMK	45	.	0			c.T303C						.						95.0	94.0	95.0					10																	59986874		2203	4300	6503	SO:0001819	synonymous_variant	253430	exon3			AAGAACACCATCA	AF432853	CCDS7250.1	10q21.1	2010-11-29		2004-07-22	ENSG00000151151	ENSG00000151151			20739	protein-coding gene	gene with protein product		609851				12223481, 12027805	Standard	NM_152230		Approved		uc001jkb.3	Q8NFU5	OTTHUMG00000018268	ENST00000373935.3:c.303T>C	chr10.hg19:g.59986874A>G		57.0	0.0		58.0	4.0	NM_152230		Silent	SNP	ENST00000373935.3	hg19	CCDS7250.1																																																																																			.	.		0.358	IPMK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048142.1	NM_152230	
BICC1	80114	hgsc.bcm.edu	37	10	60549664	60549664	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:60549664T>C	ENST00000373886.3	+	8	1022	c.1018T>C	c.(1018-1020)Tct>Cct	p.S340P		NM_001080512.1	NP_001073981.1	Q9H694	BICC1_HUMAN	BicC family RNA binding protein 1	340	KH 2. {ECO:0000255|PROSITE- ProRule:PRU00117}.				multicellular organismal development (GO:0007275)|negative regulation of canonical Wnt signaling pathway (GO:0090090)	cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(22)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	44						CACCATTGAGTCTGTCTGTCT	0.408																																					p.S340P		Atlas-SNP	.											.	BICC1	121	.	0			c.T1018C						.						156.0	145.0	149.0					10																	60549664		2203	4300	6503	SO:0001583	missense	80114	exon8			ATTGAGTCTGTCT	AK026129	CCDS31206.1	10q21.3	2014-09-17	2014-02-03		ENSG00000122870	ENSG00000122870		"""Sterile alpha motif (SAM) domain containing"""	19351	protein-coding gene	gene with protein product		614295	"""bicaudal C homolog 1 (Drosophila)"""				Standard	XM_005270166		Approved		uc001jki.1	Q9H694	OTTHUMG00000018271	ENST00000373886.3:c.1018T>C	chr10.hg19:g.60549664T>C	ENSP00000362993:p.Ser340Pro	80.0	0.0		96.0	5.0	NM_001080512		Missense_Mutation	SNP	ENST00000373886.3	hg19	CCDS31206.1	.	.	.	.	.	.	.	.	.	.	T	22.1	4.247095	0.80024	.	.	ENSG00000122870	ENST00000373886	T	0.34667	1.35	5.67	5.67	0.87782	K Homology (1);K Homology, type 1, subgroup (1);K Homology, type 1 (1);	0.000000	0.85682	D	0.000000	T	0.60025	0.2237	M	0.74647	2.275	0.80722	D	1	D	0.76494	0.999	D	0.69824	0.966	T	0.61212	-0.7108	10	0.45353	T	0.12	-13.0028	15.9271	0.79628	0.0:0.0:0.0:1.0	.	340	Q9H694	BICC1_HUMAN	P	340	ENSP00000362993:S340P	ENSP00000362993:S340P	S	+	1	0	BICC1	60219670	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.081000	0.71309	2.159000	0.67721	0.533000	0.62120	TCT	.	.		0.408	BICC1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048150.2	NM_025044	
SLC16A9	220963	hgsc.bcm.edu	37	10	61413574	61413574	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:61413574T>C	ENST00000395348.3	-	5	1846	c.1210A>G	c.(1210-1212)Atc>Gtc	p.I404V	SLC16A9_ENST00000395347.1_Missense_Mutation_p.I404V	NM_194298.2	NP_919274.1	Q7RTY1	MOT9_HUMAN	solute carrier family 16, member 9	404					urate metabolic process (GO:0046415)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	symporter activity (GO:0015293)			kidney(3)|large_intestine(5)|lung(5)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	23						AACCCTAGGATCCCAGAAAGC	0.413																																					p.I404V		Atlas-SNP	.											.	SLC16A9	58	.	0			c.A1210G						.						138.0	129.0	132.0					10																	61413574		2203	4300	6503	SO:0001583	missense	220963	exon5			CTAGGATCCCAGA	AK125791	CCDS7256.1	10q21.3	2013-07-18	2013-07-18	2004-01-21	ENSG00000165449	ENSG00000165449		"""Solute carriers"""	23520	protein-coding gene	gene with protein product	"""monocarboxylic acid transporter 9"""	614242	"""chromosome 10 open reading frame 36"", ""solute carrier family 16 (monocarboxylic acid transporters), member 9"", ""solute carrier family 16, member 9 (monocarboxylic acid transporter 9)"""	C10orf36			Standard	NM_194298		Approved	FLJ43803, MCT9	uc010qig.1	Q7RTY1	OTTHUMG00000018283	ENST00000395348.3:c.1210A>G	chr10.hg19:g.61413574T>C	ENSP00000378757:p.Ile404Val	70.0	0.0		97.0	4.0	NM_194298	Q6ZMI2|Q9UFH8	Missense_Mutation	SNP	ENST00000395348.3	hg19	CCDS7256.1	.	.	.	.	.	.	.	.	.	.	T	0.007	-2.009250	0.00426	.	.	ENSG00000165449	ENST00000395348;ENST00000395347	T;T	0.60299	0.2;0.2	5.2	1.38	0.22167	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.463258	0.26019	N	0.026834	T	0.25644	0.0624	N	0.04355	-0.22	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.17715	-1.0360	10	0.09590	T	0.72	.	5.4943	0.16793	0.128:0.1438:0.0:0.7282	.	404	Q7RTY1	MOT9_HUMAN	V	404	ENSP00000378757:I404V;ENSP00000378756:I404V	ENSP00000378756:I404V	I	-	1	0	SLC16A9	61083580	0.008000	0.16893	0.001000	0.08648	0.002000	0.02628	0.103000	0.15292	0.310000	0.22990	-0.326000	0.08463	ATC	.	.		0.413	SLC16A9-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048174.2	NM_194298	
ANK3	288	hgsc.bcm.edu	37	10	61819139	61819139	+	Silent	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:61819139A>G	ENST00000280772.2	-	41	12836	c.12645T>C	c.(12643-12645)gcT>gcC	p.A4215A	ANK3_ENST00000355288.2_Silent_p.A839A|ANK3_ENST00000373827.2_Silent_p.A1699A|RP11-388P9.2_ENST00000414383.1_RNA|ANK3_ENST00000503366.1_Silent_p.A1706A	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	4215					axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization (GO:0045184)|Golgi to plasma membrane protein transport (GO:0043001)|maintenance of protein location in plasma membrane (GO:0072660)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|neuromuscular junction development (GO:0007528)|neuronal action potential (GO:0019228)|plasma membrane organization (GO:0007009)|positive regulation of cell communication by electrical coupling (GO:0010650)|positive regulation of gene expression (GO:0010628)|positive regulation of homotypic cell-cell adhesion (GO:0034112)|positive regulation of membrane depolarization during cardiac muscle cell action potential (GO:1900827)|positive regulation of membrane potential (GO:0045838)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein localization to plasma membrane (GO:0072659)|protein targeting to plasma membrane (GO:0072661)|regulation of potassium ion transport (GO:0043266)|signal transduction (GO:0007165)	axon initial segment (GO:0043194)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|costamere (GO:0043034)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|lysosome (GO:0005764)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|T-tubule (GO:0030315)|Z disc (GO:0030018)	cadherin binding (GO:0045296)|cytoskeletal protein binding (GO:0008092)|ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(4)|breast(7)|central_nervous_system(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(5)|kidney(14)|large_intestine(30)|liver(2)|lung(59)|ovary(8)|pancreas(2)|prostate(5)|skin(26)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	196						TTACTCTTCGAGCTTGAGCGC	0.413																																					p.A4215A		Atlas-SNP	.											.	ANK3	703	.	0			c.T12645C						.						201.0	175.0	184.0					10																	61819139		2203	4300	6503	SO:0001819	synonymous_variant	288	exon41			TCTTCGAGCTTGA	U13616	CCDS7258.1, CCDS7259.1, CCDS55711.1, CCDS55712.1	10q21	2013-01-10			ENSG00000151150	ENSG00000151150		"""Ankyrin repeat domain containing"""	494	protein-coding gene	gene with protein product	"""ankyrin-3, node of Ranvier"", ""ankyrin-G"""	600465				7665168	Standard	NM_020987		Approved		uc001jky.3	Q12955	OTTHUMG00000018288	ENST00000280772.2:c.12645T>C	chr10.hg19:g.61819139A>G		165.0	0.0		173.0	7.0	NM_020987	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Silent	SNP	ENST00000280772.2	hg19	CCDS7258.1																																																																																			.	.		0.413	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987	
TET1	80312	hgsc.bcm.edu	37	10	70333306	70333306	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:70333306T>C	ENST00000373644.4	+	2	1420	c.1211T>C	c.(1210-1212)gTc>gCc	p.V404A		NM_030625.2	NP_085128.2	Q8NFU7	TET1_HUMAN	tet methylcytosine dioxygenase 1	404					chromatin modification (GO:0016568)|DNA demethylation (GO:0080111)|inner cell mass cell differentiation (GO:0001826)|negative regulation of methylation-dependent chromatin silencing (GO:0090310)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein O-linked glycosylation (GO:0006493)|regulation of DNA methylation (GO:0044030)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	iron ion binding (GO:0005506)|methylcytosine dioxygenase activity (GO:0070579)|structure-specific DNA binding (GO:0043566)|zinc ion binding (GO:0008270)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(2)|ovary(5)|prostate(1)|upper_aerodigestive_tract(2)	21						GCTATTCCAGTCCAAGGAGAG	0.507																																					p.V404A		Atlas-SNP	.											.	TET1	255	.	0			c.T1211C						.						150.0	157.0	154.0					10																	70333306		2203	4300	6503	SO:0001583	missense	80312	exon2			TTCCAGTCCAAGG	AF430147	CCDS7281.1	10q21	2014-02-18	2011-09-30	2008-03-12	ENSG00000138336	ENSG00000138336			29484	protein-coding gene	gene with protein product	"""leukemia-associated protein with a CXXC domain"", ""ten-eleven translocation-1"""	607790	"""CXXC zinc finger 6"", ""tet oncogene 1"""	CXXC6		12124344, 12646957	Standard	NM_030625		Approved	LCX, KIAA1676, bA119F7.1	uc001jok.4	Q8NFU7	OTTHUMG00000018359	ENST00000373644.4:c.1211T>C	chr10.hg19:g.70333306T>C	ENSP00000362748:p.Val404Ala	99.0	0.0		111.0	5.0	NM_030625	Q5VUP7|Q7Z6B6|Q8TCR1|Q9C0I7	Missense_Mutation	SNP	ENST00000373644.4	hg19	CCDS7281.1	.	.	.	.	.	.	.	.	.	.	T	7.745	0.702023	0.15172	.	.	ENSG00000138336	ENST00000373644	T	0.07688	3.17	4.48	1.92	0.25849	.	0.363501	0.20071	N	0.099866	T	0.03915	0.0110	N	0.24115	0.695	0.22017	N	0.999413	B	0.06786	0.001	B	0.04013	0.001	T	0.43750	-0.9372	10	0.07644	T	0.81	.	3.424	0.07403	0.1975:0.1082:0.0:0.6943	.	404	Q8NFU7	TET1_HUMAN	A	404	ENSP00000362748:V404A	ENSP00000362748:V404A	V	+	2	0	TET1	70003312	0.995000	0.38212	0.998000	0.56505	0.649000	0.38597	0.204000	0.17335	0.813000	0.34350	-0.400000	0.06385	GTC	.	.		0.507	TET1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048354.1	NM_030625	
NEUROG3	50674	hgsc.bcm.edu	37	10	71332756	71332756	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:71332756C>T	ENST00000242462.4	-	2	73	c.44G>A	c.(43-45)cGt>cAt	p.R15H	RP11-343J3.2_ENST00000428753.1_RNA	NM_020999.3	NP_066279.2	Q9Y4Z2	NGN3_HUMAN	neurogenin 3	15					central nervous system development (GO:0007417)|endocrine pancreas development (GO:0031018)|epithelial cell differentiation (GO:0030855)|forebrain development (GO:0030900)|hindbrain development (GO:0030902)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|peripheral nervous system development (GO:0007422)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of dendrite morphogenesis (GO:0048814)|spinal cord development (GO:0021510)|transdifferentiation (GO:0060290)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|double-stranded DNA binding (GO:0003690)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|transcription coactivator activity (GO:0003713)			endometrium(4)|large_intestine(2)|lung(6)|prostate(1)	13						CTCCGTCTCACGGGTCACTTG	0.677																																					p.R15H		Atlas-SNP	.											NEUROG3,NS,carcinoma,0,1	NEUROG3	33	.	0			c.G44A						.						43.0	48.0	47.0					10																	71332756		2203	4300	6503	SO:0001583	missense	50674	exon2			GTCTCACGGGTCA	AJ133776	CCDS31212.1	10q21.3	2013-05-21			ENSG00000122859	ENSG00000122859		"""Basic helix-loop-helix proteins"""	13806	protein-coding gene	gene with protein product		604882				9000438, 10677506	Standard	NM_020999		Approved	Atoh5, Math4B, ngn3, bHLHa7	uc001jpp.3	Q9Y4Z2	OTTHUMG00000018391	ENST00000242462.4:c.44G>A	chr10.hg19:g.71332756C>T	ENSP00000242462:p.Arg15His	97.0	0.0		74.0	3.0	NM_020999	Q5VVI0|Q6DJX6|Q9BY24	Missense_Mutation	SNP	ENST00000242462.4	hg19	CCDS31212.1	.	.	.	.	.	.	.	.	.	.	C	1.655	-0.513026	0.04200	.	.	ENSG00000122859	ENST00000242462	D	0.94280	-3.39	4.69	-8.44	0.00950	.	17.827300	0.00166	U	0.000006	T	0.79452	0.4448	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.75224	-0.3393	10	0.14656	T	0.56	2.4082	0.7377	0.00968	0.3346:0.3365:0.111:0.218	.	15	Q9Y4Z2	NGN3_HUMAN	H	15	ENSP00000242462:R15H	ENSP00000242462:R15H	R	-	2	0	NEUROG3	71002762	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	-2.014000	0.01449	-2.087000	0.00862	-0.150000	0.13652	CGT	.	.		0.677	NEUROG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048464.1	NM_020999	
ASCC1	51008	hgsc.bcm.edu	37	10	73862147	73862147	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:73862147T>C	ENST00000342444.4	-	12	1284	c.1183A>G	c.(1183-1185)Agc>Ggc	p.S395G	ASCC1_ENST00000317168.6_Intron|ASCC1_ENST00000394919.1_Intron|ASCC1_ENST00000394915.3_Missense_Mutation_p.S395G|ASCC1_ENST00000317126.4_Intron|ASCC1_ENST00000545550.1_Intron	NM_001198799.2	NP_001185728.1	Q8N9N2	ASCC1_HUMAN	activating signal cointegrator 1 complex subunit 1	395					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|transcription factor complex (GO:0005667)	catalytic activity (GO:0003824)|RNA binding (GO:0003723)			endometrium(1)|kidney(1)|large_intestine(1)|liver(1)|lung(2)|skin(1)	7						CCTGGTAGGCTCTGAGAATAT	0.438																																					p.S395G		Atlas-SNP	.											.	ASCC1	18	.	0			c.A1183G						.																																			SO:0001583	missense	51008	exon12			GTAGGCTCTGAGA	AY013290	CCDS31219.1, CCDS55713.1	10q22.1	2012-09-20			ENSG00000138303	ENSG00000138303			24268	protein-coding gene	gene with protein product		614215				10810093, 12077347	Standard	NM_001198799		Approved	CGI-18, ASC1p50, Em:AC022392.3	uc001jst.2	Q8N9N2	OTTHUMG00000018434	ENST00000342444.4:c.1183A>G	chr10.hg19:g.73862147T>C	ENSP00000339404:p.Ser395Gly	121.0	0.0		115.0	5.0	NM_001198799	Q5SW06|Q5SW07|Q96EI8|Q9Y307	Missense_Mutation	SNP	ENST00000342444.4	hg19	CCDS55713.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	9.856|9.856	1.194911|1.194911	0.22037|0.22037	.|.	.|.	ENSG00000138303|ENSG00000138303	ENST00000530394|ENST00000342444;ENST00000394915	.|T;T	.|0.12879	.|2.64;2.64	1.97|1.97	1.97|1.97	0.26223|0.26223	.|.	.|0.558137	.|0.15354	.|N	.|0.266790	T|T	0.09642|0.09642	0.0237|0.0237	L|L	0.39514|0.39514	1.22|1.22	0.09310|0.09310	N|N	1|1	.|B	.|0.20261	.|0.043	.|B	.|0.17098	.|0.017	T|T	0.29671|0.29671	-1.0004|-1.0004	5|10	.|0.20519	.|T	.|0.43	.|.	5.999|5.999	0.19509|0.19509	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|395	.|Q8N9N2	.|ASCC1_HUMAN	G|G	125|395	.|ENSP00000339404:S395G;ENSP00000378373:S395G	.|ENSP00000339404:S395G	E|S	-|-	2|1	0|0	ASCC1|ASCC1	73532153|73532153	0.048000|0.048000	0.20356|0.20356	0.011000|0.011000	0.14972|0.14972	0.041000|0.041000	0.13682|0.13682	1.024000|1.024000	0.30077|0.30077	1.169000|1.169000	0.42739|0.42739	0.528000|0.528000	0.53228|0.53228	GAG|AGC	.	.		0.438	ASCC1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048573.2	NM_015947	
SYNPO2L	79933	hgsc.bcm.edu	37	10	75407601	75407601	+	Silent	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:75407601A>G	ENST00000394810.2	-	4	1958	c.1809T>C	c.(1807-1809)gcT>gcC	p.A603A	SYNPO2L_ENST00000372873.4_Silent_p.A379A	NM_001114133.1	NP_001107605.1	Q9H987	SYP2L_HUMAN	synaptopodin 2-like	603	Pro-rich.					cytoskeleton (GO:0005856)|nucleus (GO:0005634)|Z disc (GO:0030018)				breast(2)|endometrium(3)|kidney(3)|large_intestine(5)|lung(6)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	26	Prostate(51;0.0112)					GGGGCTCAGGAGCCCCTGGGC	0.701																																					p.A603A		Atlas-SNP	.											.	SYNPO2L	118	.	0			c.T1809C						.						18.0	22.0	21.0					10																	75407601		2006	4174	6180	SO:0001819	synonymous_variant	79933	exon4			CTCAGGAGCCCCT	AK022983	CCDS7331.1, CCDS44438.1	10q22.3	2007-12-19			ENSG00000166317	ENSG00000166317			23532	protein-coding gene	gene with protein product							Standard	XM_005270158		Approved	FLJ12921	uc001jut.4	Q9H987	OTTHUMG00000018471	ENST00000394810.2:c.1809T>C	chr10.hg19:g.75407601A>G		42.0	0.0		62.0	4.0	NM_001114133	A5PKV9|Q68A20	Silent	SNP	ENST00000394810.2	hg19	CCDS44438.1																																																																																			.	.		0.701	SYNPO2L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316562.2	NM_024875	
FAM213A	84293	hgsc.bcm.edu	37	10	82182254	82182254	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:82182254T>C	ENST00000372181.1	+	2	730	c.260T>C	c.(259-261)cTc>cCc	p.L87P	FAM213A_ENST00000372188.1_Missense_Mutation_p.L87P|FAM213A_ENST00000372185.1_Missense_Mutation_p.L76P|FAM213A_ENST00000372187.5_Missense_Mutation_p.L87P	NM_001243778.1|NM_001243782.1	NP_001230707.1|NP_001230711.1	Q9BRX8	F213A_HUMAN	family with sequence similarity 213, member A	87	Thioredoxin fold. {ECO:0000250}.				oxidation-reduction process (GO:0055114)|regulation of osteoclast differentiation (GO:0045670)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	antioxidant activity (GO:0016209)										GGCTGTTTCCTCTGTCGAGAG	0.498																																					p.L87P		Atlas-SNP	.											.	.	.	.	0			c.T260C						.						80.0	88.0	85.0					10																	82182254		2203	4300	6503	SO:0001583	missense	84293	exon3			GTTTCCTCTGTCG	AF086462	CCDS7368.1, CCDS58089.1	10q23.1	2011-12-08	2011-12-08	2011-12-08	ENSG00000122378	ENSG00000122378			28651	protein-coding gene	gene with protein product	"""peroxiredoxin-like 2 activated in M-CSF stimulated monocytes"""		"""chromosome 10 open reading frame 58"""	C10orf58		11483580, 19951071	Standard	NM_032333		Approved	MGC4248, PAMM	uc001kce.4	Q9BRX8	OTTHUMG00000018614	ENST00000372181.1:c.260T>C	chr10.hg19:g.82182254T>C	ENSP00000361254:p.Leu87Pro	62.0	0.0		69.0	4.0	NM_032333	B2RD81|Q6UW08|Q8N2K3|Q8NBK9|Q96JR0	Missense_Mutation	SNP	ENST00000372181.1	hg19	CCDS7368.1	.	.	.	.	.	.	.	.	.	.	T	24.0	4.481600	0.84747	.	.	ENSG00000122378	ENST00000372188;ENST00000372187;ENST00000372185;ENST00000372181	.	.	.	5.56	5.56	0.83823	.	0.000000	0.64402	D	0.000001	T	0.78629	0.4313	M	0.81497	2.545	0.80722	D	1	D	0.76494	0.999	D	0.69654	0.965	T	0.81055	-0.1106	9	0.56958	D	0.05	0.1713	13.6543	0.62328	0.0:0.0:0.0:1.0	.	87	Q9BRX8	PAMM_HUMAN	P	87;87;76;87	.	ENSP00000361254:L87P	L	+	2	0	C10orf58	82172234	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.507000	0.81676	2.113000	0.64589	0.533000	0.62120	CTC	.	.		0.498	FAM213A-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049077.2		
GHITM	27069	hgsc.bcm.edu	37	10	85904722	85904722	+	Missense_Mutation	SNP	A	A	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:85904722A>C	ENST00000372134.3	+	5	626	c.433A>C	c.(433-435)Atc>Ctc	p.I145L		NM_014394.2	NP_055209.2	Q9H3K2	GHITM_HUMAN	growth hormone inducible transmembrane protein	145					apoptotic process (GO:0006915)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				breast(1)|endometrium(1)|large_intestine(3)|lung(3)|prostate(2)	10						TGCCATAGCAATCAGCAGAAC	0.388																																					p.I145L		Atlas-SNP	.											.	GHITM	30	.	0			c.A433C						.						181.0	167.0	172.0					10																	85904722		1897	4115	6012	SO:0001583	missense	27069	exon5			ATAGCAATCAGCA	AB009685	CCDS41542.1	10q23.1	2008-02-01			ENSG00000165678	ENSG00000165678			17281	protein-coding gene	gene with protein product	"""transmembrane BAX inhibitor motif containing 5"""					8619474, 9110174	Standard	NM_014394		Approved	HSPC282, PTD010, DERP2, My021, TMBIM5	uc001kcs.1	Q9H3K2	OTTHUMG00000018637	ENST00000372134.3:c.433A>C	chr10.hg19:g.85904722A>C	ENSP00000361207:p.Ile145Leu	175.0	0.0		182.0	67.0	NM_014394	A8K9Z9|D3DWE0|O95894|Q5VT95|Q9H0P2	Missense_Mutation	SNP	ENST00000372134.3	hg19	CCDS41542.1	.	.	.	.	.	.	.	.	.	.	A	11.31	1.601023	0.28534	.	.	ENSG00000165678	ENST00000372134;ENST00000538477;ENST00000436406;ENST00000339736	T	0.40476	1.03	6.17	-4.32	0.03688	.	0.565075	0.19863	N	0.104385	T	0.14570	0.0352	N	0.10945	0.07	0.18873	N	0.999982	B;B	0.12013	0.005;0.0	B;B	0.15484	0.013;0.001	T	0.31024	-0.9958	10	0.07325	T	0.83	-31.854	5.9594	0.19291	0.3654:0.0:0.4463:0.1883	.	76;145	B4DNL0;Q9H3K2	.;GHITM_HUMAN	L	145;132;145;125	ENSP00000361207:I145L	ENSP00000342214:I125L	I	+	1	0	GHITM	85894702	0.998000	0.40836	0.017000	0.16124	0.390000	0.30446	1.230000	0.32612	-0.828000	0.04273	-0.290000	0.09829	ATC	.	.		0.388	GHITM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049125.1	NM_014394	
WAPAL	23063	hgsc.bcm.edu	37	10	88230752	88230752	+	Silent	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:88230752A>G	ENST00000298767.5	-	8	2611	c.2139T>C	c.(2137-2139)caT>caC	p.H713H	WAPAL_ENST00000263070.7_5'UTR	NM_015045.2	NP_055860.1	Q7Z5K2	WAPL_HUMAN	wings apart-like homolog (Drosophila)	713	WAPL. {ECO:0000255|PROSITE- ProRule:PRU00603}.				mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of chromatin binding (GO:0035562)|negative regulation of DNA replication (GO:0008156)|negative regulation of sister chromatid cohesion (GO:0045875)|positive regulation of fibroblast proliferation (GO:0048146)|protein localization to chromatin (GO:0071168)|regulation of chromosome condensation (GO:0060623)|regulation of cohesin localization to chromatin (GO:0071922)|response to toxic substance (GO:0009636)|viral process (GO:0016032)	chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cohesin complex (GO:0008278)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)				breast(2)|endometrium(2)|kidney(5)|large_intestine(6)|lung(13)|ovary(2)|stomach(1)	31						AAAATACCTGATGGTGCTGGG	0.373																																					p.H713H		Atlas-SNP	.											.	WAPAL	81	.	0			c.T2139C						.						66.0	61.0	62.0					10																	88230752		2203	4300	6503	SO:0001819	synonymous_variant	23063	exon8			TACCTGATGGTGC	AB065003	CCDS7375.1	10q23.31	2006-12-08	2006-03-16	2006-03-16	ENSG00000062650	ENSG00000062650			23293	protein-coding gene	gene with protein product	"""friend of EBNA2"""	610754	"""KIAA0261"""	KIAA0261		9039502, 17112726	Standard	XM_006717726		Approved	FOE, WAPL	uc001kdo.3	Q7Z5K2	OTTHUMG00000018651	ENST00000298767.5:c.2139T>C	chr10.hg19:g.88230752A>G		92.0	0.0		92.0	4.0	NM_015045	A7E2B5|Q5VSK5|Q8IX10|Q92549	Silent	SNP	ENST00000298767.5	hg19	CCDS7375.1																																																																																			.	.		0.373	WAPAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049151.2	NM_015045	
MYOF	26509	hgsc.bcm.edu	37	10	95111559	95111559	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:95111559C>T	ENST00000359263.4	-	33	3525	c.3526G>A	c.(3526-3528)Gag>Aag	p.E1176K	MYOF_ENST00000371502.4_Missense_Mutation_p.E1176K|MYOF_ENST00000358334.5_Missense_Mutation_p.E1163K|MYOF_ENST00000371501.4_Missense_Mutation_p.E1176K	NM_013451.3	NP_038479.1	Q9NZM1	MYOF_HUMAN	myoferlin	1176	C2 4. {ECO:0000255|PROSITE- ProRule:PRU00041}.				blood circulation (GO:0008015)|cellular response to heat (GO:0034605)|muscle contraction (GO:0006936)|plasma membrane repair (GO:0001778)|regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030947)	caveola (GO:0005901)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	phospholipid binding (GO:0005543)			NS(2)|autonomic_ganglia(1)|breast(3)|endometrium(7)|kidney(7)|large_intestine(15)|lung(14)|ovary(4)|prostate(4)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	67						TGGATGATCTCAGTGGTTTTG	0.433																																					p.E1176K		Atlas-SNP	.											.	MYOF	177	.	0			c.G3526A						.						118.0	110.0	113.0					10																	95111559		1858	4099	5957	SO:0001583	missense	26509	exon33			TGATCTCAGTGGT	AB033033	CCDS41550.1, CCDS41551.1	10q24	2014-06-27	2008-11-26	2008-11-26	ENSG00000138119	ENSG00000138119			3656	protein-coding gene	gene with protein product	"""fer-1-like family member 3"""	604603	"""fer-1 (C.elegans)-like 3 (myoferlin)"", ""fer-1-like 3, myoferlin (C. elegans)"""	FER1L3		10607832, 10995573, 17702744	Standard	NM_013451		Approved	KIAA1207	uc001kin.3	Q9NZM1	OTTHUMG00000018772	ENST00000359263.4:c.3526G>A	chr10.hg19:g.95111559C>T	ENSP00000352208:p.Glu1176Lys	58.0	0.0		79.0	5.0	NM_013451	B3KQN5|Q5VWW2|Q5VWW3|Q5VWW4|Q5VWW5|Q7Z642|Q8IWH0|Q9HBU3|Q9NZM0|Q9ULL3|Q9Y4U4	Missense_Mutation	SNP	ENST00000359263.4	hg19	CCDS41551.1	.	.	.	.	.	.	.	.	.	.	C	8.823	0.938041	0.18206	.	.	ENSG00000138119	ENST00000358334;ENST00000359263;ENST00000371501;ENST00000371502	T;T;T;T	0.67523	-0.27;-0.27;-0.27;-0.27	5.77	5.77	0.91146	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	T	0.53722	0.1814	N	0.20357	0.565	0.80722	D	1	B;B	0.24368	0.008;0.102	B;B	0.31337	0.026;0.128	T	0.51204	-0.8735	10	0.02654	T	1	-27.5578	19.9826	0.97334	0.0:1.0:0.0:0.0	.	1163;1176	Q9NZM1-6;Q9NZM1	.;MYOF_HUMAN	K	1163;1176;1176;1176	ENSP00000351094:E1163K;ENSP00000352208:E1176K;ENSP00000360556:E1176K;ENSP00000360557:E1176K	ENSP00000351094:E1163K	E	-	1	0	MYOF	95101549	1.000000	0.71417	0.999000	0.59377	0.777000	0.43975	6.050000	0.71063	2.734000	0.93682	0.650000	0.86243	GAG	.	.		0.433	MYOF-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049423.2	NM_013451	
FFAR4	338557	hgsc.bcm.edu	37	10	95338962	95338962	+	Splice_Site	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:95338962A>G	ENST00000371483.4	+	3	799	c.743A>G	c.(742-744)gAg>gGg	p.E248G	FFAR4_ENST00000371481.4_Intron|FFAR4_ENST00000604414.1_Intron	NM_181745.3	NP_859529.2	Q5NUL3	FFAR4_HUMAN	free fatty acid receptor 4	248					hormone secretion (GO:0046879)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of inflammatory response (GO:0050728)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|regulation of glucose transport (GO:0010827)	endocytic vesicle (GO:0030139)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	fatty acid binding (GO:0005504)|taste receptor activity (GO:0008527)										ACTCACAGTGAGGTAAAAGGG	0.517																																					p.E248G		Atlas-SNP	.											.	.	.	.	0			c.A743G						.						116.0	98.0	104.0					10																	95338962		2203	4300	6503	SO:0001630	splice_region_variant	338557	exon3			ACAGTGAGGTAAA		CCDS31248.1, CCDS55720.1	10q23.33	2012-11-16	2012-11-16	2012-11-16	ENSG00000186188	ENSG00000186188		"""GPCR / Class A : Fatty acid receptors"""	19061	protein-coding gene	gene with protein product		609044	"""G protein-coupled receptor 129"", ""G protein-coupled receptor 120"", ""omega-3 fatty acid receptor 1"""	GPR129, GPR120, O3FAR1		20471368, 19723586, 15619630, 20813258	Standard	NM_181745		Approved	PGR4	uc010qnt.2	Q5NUL3	OTTHUMG00000034409	ENST00000371483.4:c.744+1A>G	chr10.hg19:g.95338962A>G		53.0	0.0		80.0	5.0	NM_181745	Q495H1|Q5VY25|Q5VY26|Q7Z605|Q86SM7	Missense_Mutation	SNP	ENST00000371483.4	hg19	CCDS31248.1	.	.	.	.	.	.	.	.	.	.	A	0.109	-1.141138	0.01728	.	.	ENSG00000186188	ENST00000371483	T	0.65732	-0.17	0.893	-1.79	0.07932	GPCR, rhodopsin-like superfamily (1);	9.965130	0.00166	N	0.000001	T	0.42314	0.1197	N	0.17082	0.46	0.80722	D	1	B	0.09022	0.002	B	0.06405	0.002	T	0.04607	-1.0939	10	0.31617	T	0.26	27.4512	2.0073	0.03480	0.2646:0.3067:0.0:0.4286	.	248	Q5NUL3	O3FA1_HUMAN	G	248	ENSP00000360538:E248G	ENSP00000360538:E248G	E	+	2	0	O3FAR1	95328952	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.953000	0.03877	-1.247000	0.02507	-0.783000	0.03347	GAG	.	.		0.517	FFAR4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000083179.1	NM_181745	Missense_Mutation
ZFYVE27	118813	hgsc.bcm.edu	37	10	99517436	99517436	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:99517436G>T	ENST00000393677.4	+	12	1331	c.1127G>T	c.(1126-1128)cGa>cTa	p.R376L	ZFYVE27_ENST00000357540.4_Missense_Mutation_p.R283L|ZFYVE27_ENST00000477521.1_3'UTR|ZFYVE27_ENST00000359980.3_Missense_Mutation_p.R369L|ZFYVE27_ENST00000356257.4_Missense_Mutation_p.R381L|ZFYVE27_ENST00000370613.3_Missense_Mutation_p.R251L|ZFYVE27_ENST00000337540.7_Missense_Mutation_p.R337L|ZFYVE27_ENST00000370610.3_Missense_Mutation_p.R276L|ZFYVE27_ENST00000453958.2_3'UTR	NM_144588.6	NP_653189.3	Q5T4F4	ZFY27_HUMAN	zinc finger, FYVE domain containing 27	376					cell death (GO:0008219)|neuron projection development (GO:0031175)|neurotrophin TRK receptor signaling pathway (GO:0048011)|protein localization to plasma membrane (GO:0072659)	axon (GO:0030424)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|growth cone membrane (GO:0032584)|integral component of membrane (GO:0016021)|recycling endosome membrane (GO:0055038)	metal ion binding (GO:0046872)			endometrium(1)|kidney(2)|large_intestine(1)|lung(1)|ovary(1)|prostate(1)|urinary_tract(1)	8		Colorectal(252;0.0846)		Epithelial(162;7.08e-10)|all cancers(201;5.18e-08)		TTCTGCTCTCGATGCTGCTCC	0.592																																					p.R381L		Atlas-SNP	.											.	ZFYVE27	31	.	0			c.G1142T						.						123.0	118.0	120.0					10																	99517436		2203	4300	6503	SO:0001583	missense	118813	exon11			GCTCTCGATGCTG	BC030621	CCDS31263.1, CCDS31264.1, CCDS53562.1, CCDS53563.1, CCDS53564.1, CCDS53565.1	10q24.2	2013-09-11			ENSG00000155256	ENSG00000155256		"""Zinc fingers, FYVE domain containing"""	26559	protein-coding gene	gene with protein product	"""protrudin"""	610243				14702039	Standard	NM_144588		Approved	FLJ32919, SPG33	uc001kol.2	Q5T4F4	OTTHUMG00000018867	ENST00000393677.4:c.1127G>T	chr10.hg19:g.99517436G>T	ENSP00000377282:p.Arg376Leu	158.0	0.0		172.0	57.0	NM_001002261	B7Z3S0|B7Z404|B7Z626|G8JLC3|G8JLF0|J3KP98|Q5T4F1|Q5T4F2|Q5T4F3|Q8N1K0|Q8N6D6|Q8NCA0|Q8NDE4|Q96M08	Missense_Mutation	SNP	ENST00000393677.4	hg19	CCDS31263.1	.	.	.	.	.	.	.	.	.	.	G	33	5.208201	0.95033	.	.	ENSG00000155256	ENST00000337540;ENST00000357540;ENST00000370613;ENST00000370610;ENST00000393677;ENST00000359980;ENST00000356257;ENST00000423811	T;T;T;T;T;T;T;T	0.77098	-1.07;-1.07;-1.07;-1.07;-1.07;-1.07;-1.07;-1.07	5.52	5.52	0.82312	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, FYVE-type (2);Zinc finger, FYVE-related (1);Zinc finger, FYVE/PHD-type (1);	0.000000	0.85682	D	0.000000	D	0.87261	0.6133	M	0.67953	2.075	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;0.997;0.996;1.0;0.999;1.0	D;D;D;D;D;D;D	0.91635	0.998;0.999;0.994;0.995;0.998;0.996;0.999	D	0.87894	0.2686	10	0.66056	D	0.02	-20.3208	17.6242	0.88090	0.0:0.0:1.0:0.0	.	337;276;251;283;381;369;376	B7Z404;B7Z3S0;B7Z626;Q5T4F4-5;Q5T4F4-3;Q5T4F4-2;Q5T4F4	.;.;.;.;.;.;ZFY27_HUMAN	L	337;283;251;276;376;369;381;359	ENSP00000337993:R337L;ENSP00000350148:R283L;ENSP00000359646:R251L;ENSP00000359642:R276L;ENSP00000377282:R376L;ENSP00000353069:R369L;ENSP00000348593:R381L;ENSP00000409594:R359L	ENSP00000337993:R337L	R	+	2	0	ZFYVE27	99507426	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.507000	0.90522	2.600000	0.87896	0.561000	0.74099	CGA	.	.		0.592	ZFYVE27-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049745.2	NM_144588	
R3HCC1L	27291	hgsc.bcm.edu	37	10	99991437	99991437	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:99991437A>G	ENST00000298999.3	+	6	2257	c.1954A>G	c.(1954-1956)Agt>Ggt	p.S652G	R3HCC1L_ENST00000370584.3_Missense_Mutation_p.S652G|R3HCC1L_ENST00000314594.5_Missense_Mutation_p.S68G|R3HCC1L_ENST00000370586.2_Missense_Mutation_p.S58G	NM_014472.4	NP_055287	Q7Z5L2	R3HCL_HUMAN	R3H domain and coiled-coil containing 1-like	666							nucleotide binding (GO:0000166)										GGTTTTCTGCAGTTATCAGTG	0.363																																					p.S666G		Atlas-SNP	.											.	R3HCC1L	3	.	0			c.A1996G						.						93.0	92.0	93.0					10																	99991437		2203	4300	6503	SO:0001583	missense	27291	exon7			TTCTGCAGTTATC	AF525304	CCDS31267.1, CCDS58093.1, CCDS73178.1	10q24.2	2012-05-23	2012-05-23	2012-05-23	ENSG00000166024	ENSG00000166024			23512	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 28"""	C10orf28			Standard	NM_014472		Approved	GIDRP86, PSORT	uc001kox.4	Q7Z5L2	OTTHUMG00000018873	ENST00000298999.3:c.1954A>G	chr10.hg19:g.99991437A>G	ENSP00000298999:p.Ser652Gly	79.0	0.0		109.0	5.0	NM_001256619	O60598|Q5W0B4|Q5W0B5|Q86VT9|Q8N9H0	Missense_Mutation	SNP	ENST00000298999.3	hg19	CCDS31267.1	.	.	.	.	.	.	.	.	.	.	A	14.84	2.655847	0.47467	.	.	ENSG00000166024	ENST00000370584;ENST00000298999;ENST00000370586;ENST00000314594;ENST00000544834	T;T;T;T	0.27402	1.67;1.67;1.67;1.67	5.73	5.73	0.89815	Nucleotide-binding, alpha-beta plait (1);	0.130755	0.64402	D	0.000002	T	0.35770	0.0943	L	0.42245	1.32	0.49130	D	0.999758	B;P;B	0.50943	0.042;0.94;0.332	B;P;B	0.49012	0.033;0.598;0.156	T	0.04005	-1.0985	9	.	.	.	-7.0369	14.9743	0.71257	1.0:0.0:0.0:0.0	.	58;666;652	Q7Z5L2-3;Q7Z5L2;Q7Z5L2-2	.;GIDRP_HUMAN;.	G	652;652;58;68;59	ENSP00000359616:S652G;ENSP00000298999:S652G;ENSP00000359618:S58G;ENSP00000314018:S68G	.	S	+	1	0	C10orf28	99981427	1.000000	0.71417	1.000000	0.80357	0.929000	0.56500	1.865000	0.39479	2.169000	0.68431	0.533000	0.62120	AGT	.	.		0.363	R3HCC1L-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049764.1	NM_014472	
PSD	5662	hgsc.bcm.edu	37	10	104163074	104163074	+	Silent	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:104163074T>C	ENST00000020673.5	-	17	3484	c.2958A>G	c.(2956-2958)ggA>ggG	p.G986G	PSD_ENST00000406432.1_Silent_p.G986G	NM_001270966.1|NM_002779.4	NP_001257895.1|NP_002770.3	A5PKW4	PSD1_HUMAN	pleckstrin and Sec7 domain containing	986					neuron differentiation (GO:0030182)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|phospholipid binding (GO:0005543)|signal transducer activity (GO:0004871)			breast(4)|endometrium(2)|large_intestine(5)|liver(1)|lung(14)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	34				Epithelial(162;1.27e-08)|all cancers(201;2.85e-07)		AAGGAGGGAGTCCATCCTCTG	0.667																																					p.G986G		Atlas-SNP	.											.	PSD	164	.	0			c.A2958G						.						82.0	59.0	67.0					10																	104163074		2203	4300	6503	SO:0001819	synonymous_variant	5662	exon18			AGGGAGTCCATCC	X99688	CCDS31272.1, CCDS73187.1	10q24	2013-01-10	2004-04-28		ENSG00000059915	ENSG00000059915		"""Pleckstrin homology (PH) domain containing"""	9507	protein-coding gene	gene with protein product		602327	"""pleckstrin and Sec7 domain protein"""			9417912	Standard	NM_002779		Approved	KIAA2011, TYL, PSD1	uc009xxd.2	A5PKW4	OTTHUMG00000018954	ENST00000020673.5:c.2958A>G	chr10.hg19:g.104163074T>C		132.0	0.0		133.0	6.0	NM_001270965	B1AKX7|D3DR87|Q15673|Q8IVG0	Silent	SNP	ENST00000020673.5	hg19	CCDS31272.1																																																																																			.	.		0.667	PSD-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050041.2		
PLEKHS1	79949	hgsc.bcm.edu	37	10	115537241	115537241	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:115537241T>C	ENST00000369310.3	+	12	1802	c.1240T>C	c.(1240-1242)Ttc>Ctc	p.F414L	PLEKHS1_ENST00000369312.4_Intron|PLEKHS1_ENST00000361048.1_Intron|PLEKHS1_ENST00000354462.3_Intron|PLEKHS1_ENST00000369309.1_Intron	NM_182601.1	NP_872407.1	Q5SXH7	PKHS1_HUMAN	pleckstrin homology domain containing, family S member 1	0																	AGCACCTGGGTTCAGGACCTC	0.453																																					p.F414L		Atlas-SNP	.											.	PLEKHS1	19	.	0			c.T1240C						.						21.0	18.0	19.0					10																	115537241		876	1991	2867	SO:0001583	missense	79949	exon12			CCTGGGTTCAGGA	AK027190	CCDS7583.1, CCDS53580.1, CCDS53581.1	10q26.11	2013-01-11	2012-05-31	2012-05-31	ENSG00000148735	ENSG00000148735		"""Pleckstrin homology (PH) domain containing"""	26285	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 81"""	C10orf81		12477932	Standard	NM_024889		Approved	FLJ23537, bA211N11.2	uc001lat.2	Q5SXH7	OTTHUMG00000019074	ENST00000369310.3:c.1240T>C	chr10.hg19:g.115537241T>C	ENSP00000358316:p.Phe414Leu	126.0	0.0		92.0	4.0	NM_182601	A8KA02|B3KX00|B6EDE1|Q5SXH8|Q5SXI0|Q6ZQR5|Q8NE42|Q9H5D9	Missense_Mutation	SNP	ENST00000369310.3	hg19	CCDS53580.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	15.91|15.91	2.971066|2.971066	0.53614|0.53614	.|.	.|.	ENSG00000148735|ENSG00000148735	ENST00000369310|ENST00000448805	T|.	0.46063|.	0.88|.	5.01|5.01	0.862|0.862	0.19056|0.19056	.|.	1.475580|.	0.04563|.	N|.	0.391864|.	T|T	0.36413|0.36413	0.0966|0.0966	L|L	0.36672|0.36672	1.1|1.1	0.09310|0.09310	N|N	1|1	B|.	0.09022|.	0.002|.	B|.	0.09377|.	0.004|.	T|T	0.29792|0.29792	-1.0000|-1.0000	10|5	0.10902|.	T|.	0.67|.	0.0291|0.0291	10.8924|10.8924	0.47002|0.47002	0.0:0.0:0.6002:0.3998|0.0:0.0:0.6002:0.3998	.|.	414|.	Q5SXH7-5|.	.|.	L|A	414|144	ENSP00000358316:F414L|.	ENSP00000358316:F414L|.	F|V	+|+	1|2	0|0	C10orf81|C10orf81	115527231|115527231	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.487000|0.487000	0.33371|0.33371	0.165000|0.165000	0.16564|0.16564	0.369000|0.369000	0.24510|0.24510	0.528000|0.528000	0.53228|0.53228	TTC|GTT	.	.		0.453	PLEKHS1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050432.1	NM_024889	
PRDX3	10935	hgsc.bcm.edu	37	10	120933332	120933332	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:120933332A>G	ENST00000298510.2	-	4	406	c.364T>C	c.(364-366)Ttt>Ctt	p.F122L	PRDX3_ENST00000494433.1_5'Flank|PRDX3_ENST00000356951.3_Missense_Mutation_p.F104L	NM_006793.2	NP_006784.1	P30048	PRDX3_HUMAN	peroxiredoxin 3	122	Thioredoxin. {ECO:0000255|PROSITE- ProRule:PRU00691}.				cellular response to oxidative stress (GO:0034599)|cellular response to reactive oxygen species (GO:0034614)|hydrogen peroxide catabolic process (GO:0042744)|maternal placenta development (GO:0001893)|mitochondrion organization (GO:0007005)|myeloid cell differentiation (GO:0030099)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of kinase activity (GO:0033673)|peptidyl-cysteine oxidation (GO:0018171)|positive regulation of cell proliferation (GO:0008284)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|regulation of mitochondrial membrane potential (GO:0051881)|response to hydrogen peroxide (GO:0042542)|response to lipopolysaccharide (GO:0032496)|response to oxidative stress (GO:0006979)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	alkyl hydroperoxide reductase activity (GO:0008785)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|kinase binding (GO:0019900)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|thioredoxin peroxidase activity (GO:0008379)			endometrium(1)|lung(2)	3		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.0245)		ACGTCGTGAAATTCGTTAGCT	0.403																																					p.F122L	Pancreas(36;562 1096 2447 42526)	Atlas-SNP	.											.	PRDX3	15	.	0			c.T364C						.						102.0	95.0	98.0					10																	120933332		2203	4300	6503	SO:0001583	missense	10935	exon4			CGTGAAATTCGTT	D49396	CCDS7611.1	10q25-q26	2010-11-24			ENSG00000165672	ENSG00000165672			9354	protein-coding gene	gene with protein product		604769	"""antioxidant protein 1"""	AOP1		7733872, 9363753	Standard	NM_006793		Approved	MER5, AOP-1, SP-22	uc001lec.3	P30048	OTTHUMG00000019146	ENST00000298510.2:c.364T>C	chr10.hg19:g.120933332A>G	ENSP00000298510:p.Phe122Leu	53.0	0.0		77.0	4.0	NM_006793	B2R7Z0|D3DRC9|E9PH29|P35690|Q0D2H1|Q13776|Q5T5V2|Q96HK4	Missense_Mutation	SNP	ENST00000298510.2	hg19	CCDS7611.1	.	.	.	.	.	.	.	.	.	.	A	33	5.202622	0.94997	.	.	ENSG00000165672	ENST00000356951;ENST00000298510	T;T	0.19532	2.14;2.14	4.81	4.81	0.61882	Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant (1);Thioredoxin-like fold (3);	0.044938	0.85682	D	0.000000	T	0.46014	0.1371	M	0.72118	2.19	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.49312	-0.8953	10	0.87932	D	0	-20.3557	14.676	0.68981	1.0:0.0:0.0:0.0	.	122	P30048	PRDX3_HUMAN	L	104;122	ENSP00000349432:F104L;ENSP00000298510:F122L	ENSP00000298510:F122L	F	-	1	0	PRDX3	120923322	1.000000	0.71417	0.996000	0.52242	0.909000	0.53808	9.107000	0.94261	1.926000	0.55796	0.533000	0.62120	TTT	.	.		0.403	PRDX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050639.1	NM_006793	
MCMBP	79892	hgsc.bcm.edu	37	10	121607167	121607167	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:121607167A>G	ENST00000360003.3	-	8	954	c.785T>C	c.(784-786)cTg>cCg	p.L262P	MCMBP_ENST00000369077.3_Missense_Mutation_p.L262P|MCMBP_ENST00000466047.1_5'UTR	NM_001256378.1|NM_001256379.1|NM_024834.3	NP_001243307.1|NP_001243308.1|NP_079110.1	Q9BTE3	MCMBP_HUMAN	minichromosome maintenance complex binding protein	262					DNA-dependent DNA replication (GO:0006261)|mitotic nuclear division (GO:0007067)|sister chromatid cohesion (GO:0007062)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chromatin binding (GO:0003682)			breast(1)|endometrium(3)|large_intestine(4)|lung(9)|ovary(2)|skin(2)	21						ATCCACAGACAGTATGCCATA	0.348																																					p.L262P		Atlas-SNP	.											.	MCMBP	49	.	0			c.T785C						.						152.0	135.0	141.0					10																	121607167		2203	4300	6503	SO:0001583	missense	79892	exon8			ACAGACAGTATGC	BC007219	CCDS7617.1, CCDS58099.1	10q26.13	2013-10-11	2011-01-05	2011-01-05	ENSG00000197771	ENSG00000197771			25782	protein-coding gene	gene with protein product		610909	"""chromosome 10 open reading frame 119"""	C10orf119		17296731	Standard	NM_024834		Approved	FLJ13081, MCM-BP	uc001ler.3	Q9BTE3	OTTHUMG00000019159	ENST00000360003.3:c.785T>C	chr10.hg19:g.121607167A>G	ENSP00000353098:p.Leu262Pro	72.0	0.0		78.0	4.0	NM_024834	B3KSP7|Q6IA56|Q9BVT9|Q9H916	Missense_Mutation	SNP	ENST00000360003.3	hg19	CCDS7617.1	.	.	.	.	.	.	.	.	.	.	A	20.3	3.974558	0.74246	.	.	ENSG00000197771	ENST00000360003;ENST00000369077	T;T	0.67171	-0.25;-0.25	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	T	0.80803	0.4693	M	0.72894	2.215	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.82938	-0.0209	10	0.87932	D	0	-23.0419	14.7194	0.69294	1.0:0.0:0.0:0.0	.	262;262	Q9BTE3-2;Q9BTE3	.;MCMBP_HUMAN	P	262	ENSP00000353098:L262P;ENSP00000358073:L262P	ENSP00000353098:L262P	L	-	2	0	MCMBP	121597157	0.998000	0.40836	0.027000	0.17364	0.983000	0.72400	7.675000	0.84002	2.272000	0.75746	0.459000	0.35465	CTG	.	.		0.348	MCMBP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000050684.1	NM_024834	
WDR11	55717	hgsc.bcm.edu	37	10	122643322	122643322	+	Silent	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:122643322A>G	ENST00000263461.6	+	14	2016	c.1770A>G	c.(1768-1770)aaA>aaG	p.K590K	WDR11_ENST00000604509.1_3'UTR	NM_018117.11	NP_060587.8	Q8WWQ0	PHIP_HUMAN	WD repeat domain 11	247					cytoskeleton organization (GO:0007010)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell morphogenesis (GO:0022604)|regulation of growth (GO:0040008)|regulation of protein phosphorylation (GO:0001932)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin receptor binding (GO:0005158)|lysine-acetylated histone binding (GO:0070577)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(9)|prostate(2)|skin(2)|stomach(5)	38						TCAGAGATAAACCCCTGGAGC	0.338																																					p.K590K		Atlas-SNP	.											WDR11,colon,carcinoma,0,1	WDR11	95	.	0			c.A1770G						.						108.0	104.0	106.0					10																	122643322		2203	4300	6503	SO:0001819	synonymous_variant	55717	exon14			AGATAAACCCCTG	AF320223	CCDS7619.1	10q26	2013-01-21	2010-01-06	2010-01-06	ENSG00000120008	ENSG00000120008		"""WD repeat domain containing"""	13831	protein-coding gene	gene with protein product		606417	"""bromodomain and WD repeat domain containing 2"""	BRWD2		10718198, 11536051	Standard	NM_018117		Approved	KIAA1351, FLJ10506, WDR15, HH14, DR11	uc021pzt.1	Q9BZH6	OTTHUMG00000019171	ENST00000263461.6:c.1770A>G	chr10.hg19:g.122643322A>G		63.0	0.0		71.0	3.0	NM_018117	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Silent	SNP	ENST00000263461.6	hg19	CCDS7619.1																																																																																			.	.		0.338	WDR11-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050707.2		
MUC2	4583	hgsc.bcm.edu	37	11	1094691	1094691	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:1094691G>T	ENST00000441003.2	+	31	5806	c.5779G>T	c.(5779-5781)Ggg>Tgg	p.G1927W	MUC2_ENST00000361558.6_Missense_Mutation_p.G65W|MUC2_ENST00000333592.6_Missense_Mutation_p.G215W	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	4289					cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	TACCACGACCGGGTCATCTTC	0.632																																					p.G1923W		Atlas-SNP	.											.	MUC2	614	.	0			c.G5767T						.						78.0	97.0	90.0					11																	1094691		2117	4220	6337	SO:0001583	missense	4583	exon32			ACGACCGGGTCAT	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.5779G>T	chr11.hg19:g.1094691G>T	ENSP00000415183:p.Gly1927Trp	108.0	0.0		146.0	7.0	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	hg19		.	.	.	.	.	.	.	.	.	.	G	10.79	1.449554	0.26074	.	.	ENSG00000198788	ENST00000441003;ENST00000361558;ENST00000333592	T;T;T	0.41758	2.56;0.99;2.9	1.97	-1.24	0.09435	.	.	.	.	.	T	0.40171	0.1106	L	0.51422	1.61	0.09310	N	1	D	0.63880	0.993	P	0.49665	0.618	T	0.31613	-0.9937	9	0.66056	D	0.02	.	5.8132	0.18477	0.5036:0.0:0.4964:0.0	.	1927	E7EUV1	.	W	1927;65;215	ENSP00000415183:G1927W;ENSP00000354885:G65W;ENSP00000331373:G215W	ENSP00000331373:G215W	G	+	1	0	MUC2	1084691	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	-2.996000	0.00655	-0.225000	0.09913	0.479000	0.44913	GGG	.	.		0.632	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
KCNQ1	3784	hgsc.bcm.edu	37	11	2609986	2609986	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:2609986C>T	ENST00000155840.5	+	10	1403	c.1295C>T	c.(1294-1296)aCt>aTt	p.T432I	KCNQ1_ENST00000335475.5_Missense_Mutation_p.T305I	NM_000218.2	NP_000209.2	P51787	KCNQ1_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 1	432					atrial cardiac muscle cell action potential (GO:0086014)|cardiac muscle contraction (GO:0060048)|cardiovascular system development (GO:0072358)|cellular response to cAMP (GO:0071320)|cellular response to drug (GO:0035690)|cellular response to epinephrine stimulus (GO:0071872)|gene silencing (GO:0016458)|male gonad development (GO:0008584)|membrane repolarization during action potential (GO:0086011)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|negative regulation of insulin secretion (GO:0046676)|positive regulation of gastric acid secretion (GO:0060454)|positive regulation of potassium ion transmembrane transport (GO:1901381)|potassium ion export (GO:0071435)|potassium ion transmembrane transport (GO:0071805)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of heart contraction (GO:0008016)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of membrane repolarization (GO:0060306)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|sensory perception of sound (GO:0007605)|synaptic transmission (GO:0007268)|ventricular cardiac muscle cell action potential (GO:0086005)	basolateral plasma membrane (GO:0016323)|early endosome (GO:0005769)|late endosome (GO:0005770)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|voltage-gated potassium channel complex (GO:0008076)|zymogen granule membrane (GO:0042589)	calmodulin binding (GO:0005516)|delayed rectifier potassium channel activity (GO:0005251)|ion channel binding (GO:0044325)|outward rectifier potassium channel activity (GO:0015271)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|protein phosphatase 1 binding (GO:0008157)|scaffold protein binding (GO:0097110)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated potassium channel activity involved in atrial cardiac muscle cell action potential repolarization (GO:0086089)|voltage-gated potassium channel activity involved in cardiac muscle cell action potential repolarization (GO:0086008)|voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization (GO:1902282)			endometrium(1)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(2)	21		all_epithelial(84;3.26e-05)|Breast(177;0.001)|Medulloblastoma(188;0.00111)|Ovarian(85;0.00158)|all_neural(188;0.00725)|all_lung(207;0.11)|Lung NSC(207;0.159)		BRCA - Breast invasive adenocarcinoma(625;0.00251)|Lung(200;0.131)	Bepridil(DB01244)|Indapamide(DB00808)	AATGGGGTGACTCCTGGAGAG	0.512																																					p.T432I		Atlas-SNP	.											.	KCNQ1	60	.	0			c.C1295T						.						67.0	66.0	66.0					11																	2609986		2202	4299	6501	SO:0001583	missense	3784	exon10			GGGTGACTCCTGG	AF000571	CCDS7736.1	11p15.5	2014-09-17			ENSG00000053918	ENSG00000053918		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6294	protein-coding gene	gene with protein product	"""Jervell and Lange-Nielsen syndrome 1"""	607542		LQT, KCNA9		8528244, 16382104	Standard	NM_181798		Approved	Kv7.1, KCNA8, KVLQT1, JLNS1, LQT1	uc001lwn.3	P51787	OTTHUMG00000009900	ENST00000155840.5:c.1295C>T	chr11.hg19:g.2609986C>T	ENSP00000155840:p.Thr432Ile	51.0	0.0		100.0	5.0	NM_000218	O00347|O60607|O94787|Q14D14|Q7Z6G9|Q92960|Q9UMN8|Q9UMN9	Missense_Mutation	SNP	ENST00000155840.5	hg19	CCDS7736.1	.	.	.	.	.	.	.	.	.	.	C	10.87	1.472772	0.26423	.	.	ENSG00000053918	ENST00000155840;ENST00000335475	D;D	0.99264	-5.65;-5.58	5.02	3.16	0.36331	.	1.079220	0.07093	N	0.839072	D	0.97099	0.9052	N	0.22421	0.69	0.09310	N	1	B;B;B	0.12630	0.006;0.004;0.002	B;B;B	0.17722	0.019;0.008;0.004	D	0.94232	0.7477	10	0.87932	D	0	-9.5083	7.2776	0.26294	0.0929:0.1723:0.7348:0.0	.	305;305;432	P51787-2;Q14D14;P51787	.;.;KCNQ1_HUMAN	I	432;305	ENSP00000155840:T432I;ENSP00000334497:T305I	ENSP00000155840:T432I	T	+	2	0	KCNQ1	2566562	0.003000	0.15002	0.113000	0.21522	0.893000	0.52053	0.558000	0.23469	0.658000	0.30925	-0.359000	0.07587	ACT	.	.		0.512	KCNQ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027382.2	NM_000218	
SMPD1	6609	hgsc.bcm.edu	37	11	6411960	6411960	+	Silent	SNP	G	G	T			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:6411960G>T	ENST00000342245.4	+	1	300	c.132G>T	c.(130-132)gcG>gcT	p.A44A	SMPD1_ENST00000356761.2_Silent_p.A44A|SMPD1_ENST00000527275.1_Silent_p.A44A|SMPD1_ENST00000299397.3_Silent_p.A44A|SMPD1_ENST00000533196.1_3'UTR	NM_000543.4|NM_001007593.2	NP_000534.3|NP_001007594.2	P17405	ASM_HUMAN	sphingomyelin phosphodiesterase 1, acid lysosomal	44					cell death (GO:0008219)|ceramide biosynthetic process (GO:0046513)|glycosphingolipid metabolic process (GO:0006687)|negative regulation of MAP kinase activity (GO:0043407)|nervous system development (GO:0007399)|positive regulation of apoptotic process (GO:0043065)|positive regulation of protein dephosphorylation (GO:0035307)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)|sphingomyelin catabolic process (GO:0006685)|sphingomyelin metabolic process (GO:0006684)|termination of signal transduction (GO:0023021)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lamellar body (GO:0042599)|lysosomal lumen (GO:0043202)	hydrolase activity, acting on glycosyl bonds (GO:0016798)|sphingomyelin phosphodiesterase activity (GO:0004767)			breast(1)|central_nervous_system(2)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(3)	23		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;4.9e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)	Amlodipine(DB00381)|Chlorpromazine(DB00477)|Desipramine(DB01151)	tggcgctggcgctggcgctgg	0.692																																					p.A44A		Atlas-SNP	.											.	SMPD1	108	.	0			c.G132T						.						19.0	22.0	21.0					11																	6411960		2199	4295	6494	SO:0001819	synonymous_variant	6609	exon1			GCTGGCGCTGGCG	AB209775	CCDS31409.1, CCDS44531.1, CCDS31409.2	11p15.4-p15.1	2010-04-28	2008-02-04		ENSG00000166311	ENSG00000166311	3.1.4.12		11120	protein-coding gene	gene with protein product	"""acid sphingomyelinase"""	607608				1711683	Standard	NM_000543		Approved	ASM	uc001mcw.3	P17405	OTTHUMG00000165453	ENST00000342245.4:c.132G>T	chr11.hg19:g.6411960G>T		18.0	0.0		46.0	6.0	NM_000543	A8K8M3|E9PKS3|P17406|Q13811|Q16837|Q16841	Silent	SNP	ENST00000342245.4	hg19	CCDS44531.1																																																																																			.	.		0.692	SMPD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384205.1	NM_000543	
DNHD1	144132	hgsc.bcm.edu	37	11	6592498	6592498	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:6592498T>C	ENST00000527990.2	+	40	13756	c.13756T>C	c.(13756-13758)Ttt>Ctt	p.F4586L	DNHD1_ENST00000254579.6_Missense_Mutation_p.F4586L			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	4586					microtubule-based movement (GO:0007018)	dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)	microtubule motor activity (GO:0003777)			NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(13)|kidney(6)|large_intestine(11)|lung(14)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	55		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.171)		Epithelial(150;3.93e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)		CCTGTCAGCCTTTCGCCACCC	0.647																																					p.F4586L		Atlas-SNP	.											.	DNHD1	198	.	0			c.T13756C						.						31.0	37.0	35.0					11																	6592498		2149	4255	6404	SO:0001583	missense	144132	exon42			TCAGCCTTTCGCC	AK128064	CCDS44532.1, CCDS7767.1	11p15.4	2011-02-10		2005-11-28	ENSG00000179532	ENSG00000179532			26532	protein-coding gene	gene with protein product			"""chromosome 11 open reading frame 47"", ""dynein heavy chain domain 1-like"", ""coiled-coil domain containing 35"""	DHCD1, C11orf47, DNHD1L, CCDC35		12975309	Standard	NM_173589		Approved	FLJ32752, FLJ46184, FLJ35709, DKFZp686J0796	uc001mdw.4	Q96M86	OTTHUMG00000133403	ENST00000527990.2:c.13756T>C	chr11.hg19:g.6592498T>C	ENSP00000436180:p.Phe4586Leu	62.0	0.0		88.0	4.0	NM_144666	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Missense_Mutation	SNP	ENST00000527990.2	hg19	CCDS44532.1	.	.	.	.	.	.	.	.	.	.	T	26.5	4.742265	0.89573	.	.	ENSG00000179532	ENST00000254579;ENST00000527990;ENST00000530197	T;T	0.07908	3.15;3.15	4.27	4.27	0.50696	Dynein heavy chain (1);	0.000000	0.64402	D	0.000001	T	0.23727	0.0574	M	0.67953	2.075	0.30964	N	0.723378	D;D;D	0.76494	0.997;0.999;0.997	D;D;D	0.87578	0.983;0.998;0.983	T	0.04128	-1.0975	10	0.51188	T	0.08	-10.0864	9.9508	0.41638	0.0:0.0:0.0:1.0	.	3674;639;4586	B0I1S4;Q9NSW8;Q96M86	.;.;DNHD1_HUMAN	L	4586;4586;854	ENSP00000254579:F4586L;ENSP00000436180:F4586L	ENSP00000254579:F4586L	F	+	1	0	DNHD1	6549074	1.000000	0.71417	0.995000	0.50966	0.927000	0.56198	3.992000	0.56980	1.915000	0.55452	0.455000	0.32223	TTT	.	.		0.647	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666	
FAR1	84188	hgsc.bcm.edu	37	11	13732397	13732397	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:13732397A>G	ENST00000354817.3	+	5	847	c.703A>G	c.(703-705)Agt>Ggt	p.S235G	FAR1_ENST00000527202.1_3'UTR	NM_032228.5	NP_115604.1	Q8WVX9	FACR1_HUMAN	fatty acyl CoA reductase 1	235					cellular lipid metabolic process (GO:0044255)|ether lipid biosynthetic process (GO:0008611)|glycerophospholipid biosynthetic process (GO:0046474)|long-chain fatty-acyl-CoA metabolic process (GO:0035336)|small molecule metabolic process (GO:0044281)|wax biosynthetic process (GO:0010025)	integral component of membrane (GO:0016021)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	fatty-acyl-CoA reductase (alcohol-forming) activity (GO:0080019)|long-chain-fatty-acyl-CoA reductase activity (GO:0050062)			breast(1)|endometrium(1)|kidney(3)|large_intestine(1)|liver(1)|lung(3)|ovary(1)|prostate(1)|skin(1)	13						TGTTGGTGCCAGTTGGAAAGA	0.348																																					p.S235G		Atlas-SNP	.											.	FAR1	40	.	0			c.A703G						.						84.0	80.0	82.0					11																	13732397		2200	4294	6494	SO:0001583	missense	84188	exon5			GGTGCCAGTTGGA	AK026381	CCDS7813.1	11p15.2	2011-09-14	2008-06-06	2008-06-06	ENSG00000197601	ENSG00000197601	1.2.1.-	"""Short chain dehydrogenase/reductase superfamily / Atypical members"""	26222	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 10E, member 1"""		"""male sterility domain containing 2"""	MLSTD2		15220348, 15220349, 19027726	Standard	NM_032228		Approved	FLJ22728, SDR10E1	uc001mld.3	Q8WVX9	OTTHUMG00000165743	ENST00000354817.3:c.703A>G	chr11.hg19:g.13732397A>G	ENSP00000346874:p.Ser235Gly	104.0	0.0		119.0	5.0	NM_032228	D3DQW8|Q5CZA3	Missense_Mutation	SNP	ENST00000354817.3	hg19	CCDS7813.1	.	.	.	.	.	.	.	.	.	.	A	32	5.142686	0.94560	.	.	ENSG00000197601	ENST00000354817;ENST00000532701;ENST00000355107	T;T	0.30182	1.54;1.54	5.79	5.79	0.91817	NAD(P)-binding domain (1);Male sterility, NAD-binding (1);	0.000000	0.85682	D	0.000000	T	0.57607	0.2065	M	0.87038	2.855	0.80722	D	1	P;D	0.56287	0.949;0.975	P;P	0.58660	0.796;0.843	T	0.65627	-0.6122	10	0.72032	D	0.01	-17.5084	15.7869	0.78310	1.0:0.0:0.0:0.0	.	235;235	E7ETC1;Q8WVX9	.;FACR1_HUMAN	G	235	ENSP00000346874:S235G;ENSP00000437111:S235G	ENSP00000346874:S235G	S	+	1	0	FAR1	13688973	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.339000	0.96797	2.205000	0.71048	0.477000	0.44152	AGT	.	.		0.348	FAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385990.2	NM_032228	
COPB1	1315	hgsc.bcm.edu	37	11	14487826	14487826	+	Splice_Site	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:14487826A>G	ENST00000249923.3	-	17	2591		c.e17+1		COPB1_ENST00000439561.2_Splice_Site	NM_016451.4	NP_057535.1	P53618	COPB_HUMAN	coatomer protein complex, subunit beta 1						COPI coating of Golgi vesicle (GO:0048205)|intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|viral process (GO:0016032)	COPI vesicle coat (GO:0030126)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi-associated vesicle (GO:0005798)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(12)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(2)	36						AAGTTTCCTCACCTAGTGTAG	0.378																																					.		Atlas-SNP	.											.	COPB1	81	.	0			c.2290+2T>C						.						209.0	196.0	201.0					11																	14487826		2200	4294	6494	SO:0001630	splice_region_variant	1315	exon18			TTCCTCACCTAGT	BC037280	CCDS7815.1	11p15.2	2011-05-20	2006-06-30	2006-06-30	ENSG00000129083	ENSG00000129083			2231	protein-coding gene	gene with protein product		600959	"""coatomer protein complex, subunit beta"""	COPB		7982906	Standard	NM_016451		Approved		uc001mlg.2	P53618	OTTHUMG00000165824	ENST00000249923.3:c.2290+1T>C	chr11.hg19:g.14487826A>G		66.0	0.0		97.0	4.0	NM_001144062	D3DQX0|Q6GTT7|Q9NTK2|Q9UNW7	Splice_Site	SNP	ENST00000249923.3	hg19	CCDS7815.1	.	.	.	.	.	.	.	.	.	.	A	26.7	4.762212	0.89932	.	.	ENSG00000129083	ENST00000249923;ENST00000439561	.	.	.	5.56	5.56	0.83823	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.7062	0.77583	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	COPB1	14444402	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	9.339000	0.96797	2.117000	0.64856	0.533000	0.62120	.	.	.		0.378	COPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386410.1	NM_016451	Intron
NDUFS3	4722	hgsc.bcm.edu	37	11	47603658	47603658	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:47603658T>C	ENST00000263774.4	+	5	482	c.400T>C	c.(400-402)Tct>Cct	p.S134P	NDUFS3_ENST00000533507.1_3'UTR	NM_004551.2	NP_004542.1	O75489	NDUS3_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 3, 30kDa (NADH-coenzyme Q reductase)	134					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|negative regulation of cell growth (GO:0030308)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|reactive oxygen species metabolic process (GO:0072593)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)	mitochondrial inner membrane (GO:0005743)|mitochondrial membrane (GO:0031966)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	electron carrier activity (GO:0009055)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)|NADH dehydrogenase activity (GO:0003954)			breast(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(2)	9					Doxorubicin(DB00997)	CAACCTGTTGTCTCTGCGCTT	0.522																																					p.S134P	Pancreas(15;551 601 22438 23457 52512)	Atlas-SNP	.											.	NDUFS3	19	.	0			c.T400C						.						169.0	158.0	162.0					11																	47603658		2201	4298	6499	SO:0001583	missense	4722	exon5			CTGTTGTCTCTGC	AF067139	CCDS7941.1	11p11.11	2011-08-03	2002-08-29		ENSG00000213619	ENSG00000213619	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7710	protein-coding gene	gene with protein product	"""complex I 30kDa subunit"", ""NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial"""	603846	"""NADH dehydrogenase (ubiquinone) Fe-S protein 3 (30kD) (NADH-coenzyme Q reductase)"""			9763677	Standard	NM_004551		Approved	CI-30	uc001nga.2	O75489	OTTHUMG00000166893	ENST00000263774.4:c.400T>C	chr11.hg19:g.47603658T>C	ENSP00000263774:p.Ser134Pro	207.0	0.0		219.0	9.0	NM_004551	B2R9J1|B4DFM8|Q9UNQ8	Missense_Mutation	SNP	ENST00000263774.4	hg19	CCDS7941.1	.	.	.	.	.	.	.	.	.	.	T	24.6	4.547972	0.86022	.	.	ENSG00000213619	ENST00000263774	D	0.88586	-2.4	6.08	6.08	0.98989	NADH:ubiquinone oxidoreductase, 30kDa subunit (1);	0.000000	0.85682	D	0.000000	D	0.97495	0.9180	H	0.99874	4.875	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.99490	1.0950	10	0.87932	D	0	-38.2705	16.6438	0.85155	0.0:0.0:0.0:1.0	.	134;60	O75489;Q9UF24	NDUS3_HUMAN;.	P	134	ENSP00000263774:S134P	ENSP00000263774:S134P	S	+	1	0	NDUFS3	47560234	1.000000	0.71417	0.932000	0.37286	0.680000	0.39746	7.468000	0.80943	2.333000	0.79357	0.533000	0.62120	TCT	.	.		0.522	NDUFS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391749.1	NM_004551	
OR4C16	219428	hgsc.bcm.edu	37	11	55339830	55339830	+	Missense_Mutation	SNP	C	C	G	rs372108090		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:55339830C>G	ENST00000314634.3	+	1	227	c.227C>G	c.(226-228)aCc>aGc	p.T76S		NM_001004701.2	NP_001004701.2	Q8NGL9	OR4CG_HUMAN	olfactory receptor, family 4, subfamily C, member 16 (gene/pseudogene)	76			T -> A (in dbSNP:rs557590). {ECO:0000269|Ref.1}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.T76S(1)		central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(1)|lung(28)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	41		all_epithelial(135;0.0748)				ACTTCCATAACCCCTAGAATG	0.428																																					p.T76S		Atlas-SNP	.											OR4C16,mouth,carcinoma,0,3	OR4C16	104	.	1	Substitution - Missense(1)	upper_aerodigestive_tract(1)	c.C227G						.						262.0	243.0	249.0					11																	55339830		2201	4296	6497	SO:0001583	missense	219428	exon1			CCATAACCCCTAG	AB065773	CCDS31502.1	11q11	2013-10-10	2013-10-10		ENSG00000181935	ENSG00000181935		"""GPCR / Class A : Olfactory receptors"""	15172	protein-coding gene	gene with protein product			"""olfactory receptor, family 4, subfamily C, member 16"""				Standard	NM_001004701		Approved		uc010rih.2	Q8NGL9	OTTHUMG00000165198	ENST00000314634.3:c.227C>G	chr11.hg19:g.55339830C>G	ENSP00000324913:p.Thr76Ser	145.0	0.0		217.0	11.0	NM_001004701	Q6IEV8	Missense_Mutation	SNP	ENST00000314634.3	hg19	CCDS31502.1	.	.	.	.	.	.	.	.	.	.	C	10.01	1.234160	0.22626	.	.	ENSG00000181935	ENST00000314634	T	0.03035	4.07	4.98	4.98	0.66077	GPCR, rhodopsin-like superfamily (1);	0.092864	0.47852	D	0.000208	T	0.04998	0.0134	L	0.43701	1.375	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.30592	-0.9973	10	0.29301	T	0.29	.	15.7881	0.78326	0.0:1.0:0.0:0.0	.	76	Q8NGL9	OR4CG_HUMAN	S	76	ENSP00000324913:T76S	ENSP00000324913:T76S	T	+	2	0	OR4C16	55096406	0.000000	0.05858	0.278000	0.24718	0.584000	0.36387	-0.144000	0.10280	2.595000	0.87683	0.549000	0.68633	ACC	.	.		0.428	OR4C16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382627.1	NM_001004701	
AHNAK	79026	hgsc.bcm.edu	37	11	62300880	62300880	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:62300880A>G	ENST00000378024.4	-	5	1283	c.1009T>C	c.(1009-1011)Tct>Cct	p.S337P	AHNAK_ENST00000257247.7_Intron|AHNAK_ENST00000530124.1_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	337					protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)			NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				TGCCCCACAGAGACTTCAGGT	0.552																																					p.S337P		Atlas-SNP	.											.	AHNAK	532	.	0			c.T1009C						.						53.0	57.0	56.0					11																	62300880		2202	4299	6501	SO:0001583	missense	79026	exon5			CCACAGAGACTTC	M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"""desmoyokin"""	103390	"""AHNAK nucleoprotein (desmoyokin)"""			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.1009T>C	chr11.hg19:g.62300880A>G	ENSP00000367263:p.Ser337Pro	85.0	0.0		143.0	7.0	NM_001620	A1A586	Missense_Mutation	SNP	ENST00000378024.4	hg19	CCDS31584.1	.	.	.	.	.	.	.	.	.	.	A	14.11	2.437034	0.43224	.	.	ENSG00000124942	ENST00000378024	T	0.00912	5.55	5.05	5.05	0.67936	.	0.239940	0.21619	U	0.071678	T	0.02342	0.0072	L	0.59436	1.845	0.09310	N	1	D	0.58620	0.983	P	0.53861	0.736	T	0.49652	-0.8917	10	0.34782	T	0.22	-6.36	9.1238	0.36803	0.8158:0.1841:0.0:0.0	.	337	Q09666	AHNK_HUMAN	P	337	ENSP00000367263:S337P	ENSP00000367263:S337P	S	-	1	0	AHNAK	62057456	0.003000	0.15002	0.967000	0.41034	0.810000	0.45777	-0.347000	0.07750	1.904000	0.55121	0.528000	0.53228	TCT	.	.		0.552	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060	
RCOR2	283248	hgsc.bcm.edu	37	11	63675749	63675749	+	IGR	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:63675749A>G	ENST00000301459.4	-	0	2604				MARK2_ENST00000361128.5_Intron|MARK2_ENST00000377810.3_Missense_Mutation_p.E563G|MARK2_ENST00000402010.2_Missense_Mutation_p.E660G|MARK2_ENST00000508192.1_Missense_Mutation_p.E596G|MARK2_ENST00000413835.2_Missense_Mutation_p.E606G|MARK2_ENST00000502399.3_Missense_Mutation_p.E650G|MARK2_ENST00000315032.8_Missense_Mutation_p.E651G|MARK2_ENST00000425897.2_Missense_Mutation_p.E571G|MARK2_ENST00000350490.7_Intron|MARK2_ENST00000513765.2_Missense_Mutation_p.E627G|MARK2_ENST00000377809.4_Intron|MARK2_ENST00000509502.2_Missense_Mutation_p.E617G|MARK2_ENST00000408948.3_Missense_Mutation_p.E563G	NM_173587.3	NP_775858.2	Q8IZ40	RCOR2_HUMAN	REST corepressor 2						negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			kidney(2)|large_intestine(3)|liver(1)|lung(5)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	17						AATGAACCTGAAAGCAAAGAC	0.607																																					p.E660G		Atlas-SNP	.											.	MARK2	91	.	0			c.A1979G						.						46.0	42.0	43.0					11																	63675749		2192	4291	6483	SO:0001628	intergenic_variant	2011	exon18			AACCTGAAAGCAA	BC010608	CCDS8052.1	11q13.1	2008-02-05			ENSG00000167771	ENSG00000167771			27455	protein-coding gene	gene with protein product						12477932	Standard	NM_173587		Approved		uc001nyc.3	Q8IZ40	OTTHUMG00000150472		chr11.hg19:g.63675749A>G		85.0	0.0		82.0	4.0	NM_001039469	Q96FP3	Missense_Mutation	SNP	ENST00000301459.4	hg19	CCDS8052.1	.	.	.	.	.	.	.	.	.	.	A	17.47	3.398225	0.62177	.	.	ENSG00000072518	ENST00000402010;ENST00000315032;ENST00000413835;ENST00000377810;ENST00000508192;ENST00000502399;ENST00000509502;ENST00000513765;ENST00000408948;ENST00000425897	T;T;T;T;T;T;T;T;T	0.50813	0.73;0.73;0.73;0.73;0.73;0.73;0.73;0.73;0.73	4.43	4.43	0.53597	.	0.293370	0.30293	N	0.009945	T	0.40815	0.1132	L	0.48362	1.52	0.80722	D	1	B;B;B;B	0.26902	0.001;0.163;0.037;0.004	B;B;B;B	0.20384	0.005;0.029;0.028;0.018	T	0.38520	-0.9657	10	0.51188	T	0.08	.	13.1231	0.59338	1.0:0.0:0.0:0.0	.	571;617;660;596	E7ETY4;Q7KZI7-14;Q7KZI7;Q7KZI7-16	.;.;MARK2_HUMAN;.	G	660;651;606;563;596;652;617;627;563;571	ENSP00000385751:E660G;ENSP00000326632:E651G;ENSP00000389184:E606G;ENSP00000367041:E563G;ENSP00000425765:E596G;ENSP00000423974:E617G;ENSP00000421075:E627G;ENSP00000386128:E563G;ENSP00000415494:E571G	ENSP00000326632:E651G	E	+	2	0	MARK2	63432325	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.589000	0.67523	2.003000	0.58678	0.454000	0.30748	GAA	.	.		0.607	RCOR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318233.1	NM_173587	
ATG2A	23130	hgsc.bcm.edu	37	11	64664282	64664282	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:64664282C>A	ENST00000377264.3	-	38	5322	c.5210G>T	c.(5209-5211)cGc>cTc	p.R1737L	ATG2A_ENST00000421419.2_Missense_Mutation_p.R1739L	NM_015104.2	NP_055919.2	Q2TAZ0	ATG2A_HUMAN	autophagy related 2A	1737					autophagic vacuole assembly (GO:0000045)|cellular response to nitrogen starvation (GO:0006995)|mitochondrion degradation (GO:0000422)|nucleophagy (GO:0044804)	extrinsic component of membrane (GO:0019898)|lipid particle (GO:0005811)|pre-autophagosomal structure (GO:0000407)				breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(19)|ovary(3)|prostate(5)|skin(1)|stomach(1)|urinary_tract(3)	55						CTGGTTCTTGCGGATGTCCTG	0.622											OREG0004026	type=REGULATORY REGION|Gene=BC027481|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.R1737L		Atlas-SNP	.											.	ATG2A	133	.	0			c.G5210T						.						54.0	54.0	54.0					11																	64664282		2201	4297	6498	SO:0001583	missense	23130	exon38			TTCTTGCGGATGT		CCDS31602.1	11q13.1	2014-02-12	2012-06-06		ENSG00000110046	ENSG00000110046			29028	protein-coding gene	gene with protein product			"""ATG2 autophagy related 2 homolog A (S. cerevisiae)"""			21887408	Standard	NM_015104		Approved	KIAA0404	uc001obx.3	Q2TAZ0	OTTHUMG00000066831	ENST00000377264.3:c.5210G>T	chr11.hg19:g.64664282C>A	ENSP00000366475:p.Arg1737Leu	109.0	0.0	1078	143.0	27.0	NM_015104	O43154|Q14DM2|Q6ZTV2|Q7Z6K8|Q8IVY5|Q8TAI8|Q96HH7	Missense_Mutation	SNP	ENST00000377264.3	hg19	CCDS31602.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.165441	0.78339	.	.	ENSG00000110046	ENST00000421419;ENST00000377262;ENST00000377264	T;T	0.07327	3.2;3.2	4.05	3.11	0.35812	.	0.000000	0.64402	D	0.000001	T	0.18964	0.0455	L	0.44542	1.39	0.51482	D	0.99992	D;D	0.89917	1.0;1.0	D;D	0.87578	0.995;0.998	T	0.00557	-1.1672	10	0.52906	T	0.07	.	11.0151	0.47685	0.1878:0.8122:0.0:0.0	.	1737;1739	Q2TAZ0;Q2TAZ0-3	ATG2A_HUMAN;.	L	1739;130;1737	ENSP00000410522:R1739L;ENSP00000366475:R1737L	ENSP00000366473:R130L	R	-	2	0	ATG2A	64420858	0.920000	0.31207	1.000000	0.80357	0.877000	0.50540	1.424000	0.34848	1.042000	0.40150	-0.314000	0.08810	CGC	.	.		0.622	ATG2A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000143224.1	NM_015104	
EHBP1L1	254102	hgsc.bcm.edu	37	11	65350589	65350589	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:65350589A>G	ENST00000309295.4	+	9	2711	c.2446A>G	c.(2446-2448)Act>Gct	p.T816A		NM_001099409.1	NP_001092879.1	Q8N3D4	EH1L1_HUMAN	EH domain binding protein 1-like 1	816	Glu-rich.					membrane (GO:0016020)				central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	23						GACAGCAGAAACTGAGATATT	0.557																																					p.T816A		Atlas-SNP	.											.	EHBP1L1	64	.	0			c.A2446G						.						45.0	47.0	46.0					11																	65350589		1872	4093	5965	SO:0001583	missense	254102	exon9			GCAGAAACTGAGA	AL834433	CCDS44649.1	11q13.1	2008-02-05			ENSG00000173442	ENSG00000173442			30682	protein-coding gene	gene with protein product							Standard	NM_001099409		Approved	DKFZp762C186, TANGERIN	uc001oeo.4	Q8N3D4	OTTHUMG00000166520	ENST00000309295.4:c.2446A>G	chr11.hg19:g.65350589A>G	ENSP00000312671:p.Thr816Ala	92.0	0.0		135.0	6.0	NM_001099409	Q8TB89|Q9H7M7	Missense_Mutation	SNP	ENST00000309295.4	hg19	CCDS44649.1	.	.	.	.	.	.	.	.	.	.	A	5.751	0.323072	0.10900	.	.	ENSG00000173442	ENST00000309295	T	0.61627	0.09	4.81	-5.02	0.02982	.	1.470350	0.04895	N	0.450284	T	0.19446	0.0467	N	0.01874	-0.695	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.28618	-1.0038	10	0.02654	T	1	.	0.9903	0.01455	0.3781:0.112:0.2832:0.2268	.	816	Q8N3D4	EH1L1_HUMAN	A	816	ENSP00000312671:T816A	ENSP00000312671:T816A	T	+	1	0	EHBP1L1	65107165	0.000000	0.05858	0.000000	0.03702	0.248000	0.25809	-2.366000	0.01078	-0.482000	0.06782	-0.177000	0.13119	ACT	.	.		0.557	EHBP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390145.1	XM_170658	
PCNXL3	399909	hgsc.bcm.edu	37	11	65391400	65391400	+	Splice_Site	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:65391400A>G	ENST00000355703.3	+	13	3051	c.2512A>G	c.(2512-2514)Agc>Ggc	p.S838G		NM_032223.2	NP_115599.2	Q9H6A9	PCX3_HUMAN	pecanex-like 3 (Drosophila)	838						integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)	13						TCTCTTCCAGAGCGTGCAGCC	0.642																																					p.S838G		Atlas-SNP	.											.	PCNXL3	140	.	0			c.A2512G						.						55.0	63.0	60.0					11																	65391400		2056	4191	6247	SO:0001630	splice_region_variant	399909	exon13			TTCCAGAGCGTGC	BX640978	CCDS44650.1	11q12.1	2008-07-21			ENSG00000197136	ENSG00000197136			18760	protein-coding gene	gene with protein product						15146197	Standard	NM_032223		Approved	FLJ22427	uc001oey.2	Q9H6A9	OTTHUMG00000166539	ENST00000355703.3:c.2512-1A>G	chr11.hg19:g.65391400A>G		98.0	0.0		124.0	5.0	NM_032223	Q6MZN8	Missense_Mutation	SNP	ENST00000355703.3	hg19	CCDS44650.1	.	.	.	.	.	.	.	.	.	.	A	17.87	3.494570	0.64186	.	.	ENSG00000197136	ENST00000355703	T	0.76839	-1.05	4.82	4.82	0.62117	.	.	.	.	.	D	0.85062	0.5611	M	0.82132	2.575	0.43430	D	0.995598	P	0.49447	0.924	P	0.57776	0.827	D	0.85850	0.1403	8	.	.	.	.	10.7496	0.46200	1.0:0.0:0.0:0.0	.	838	Q9H6A9	PCX3_HUMAN	G	838	ENSP00000347931:S838G	.	S	+	1	0	PCNXL3	65147976	1.000000	0.71417	0.997000	0.53966	0.188000	0.23474	8.106000	0.89555	1.813000	0.52934	0.379000	0.24179	AGC	.	.		0.642	PCNXL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390321.1	NM_032223	Missense_Mutation
SYT12	91683	hgsc.bcm.edu	37	11	66811279	66811279	+	Silent	SNP	G	G	A			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:66811279G>A	ENST00000393946.2	+	8	1954	c.792G>A	c.(790-792)ccG>ccA	p.P264P	SYT12_ENST00000525457.1_Silent_p.P264P|SYT12_ENST00000527043.1_Silent_p.P264P			Q8IV01	SYT12_HUMAN	synaptotagmin XII	264	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.					cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|synapse (GO:0045202)				NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(1)|urinary_tract(1)	20						TTGACCTCCCGCTGCAGCCCT	0.552																																					p.P264P	Ovarian(65;2862 3307)	Atlas-SNP	.											.	SYT12	60	.	0			c.G792A						.						97.0	74.0	82.0					11																	66811279		2200	4295	6495	SO:0001819	synonymous_variant	91683	exon5			CCTCCCGCTGCAG	AK024280	CCDS8154.1	11q13.2	2014-07-02			ENSG00000173227	ENSG00000173227		"""Synaptotagmins"""	18381	protein-coding gene	gene with protein product		606436				8987811	Standard	NM_177963		Approved	SRG1	uc001oju.3	Q8IV01	OTTHUMG00000167101	ENST00000393946.2:c.792G>A	chr11.hg19:g.66811279G>A		84.0	0.0		109.0	17.0	NM_001177880		Silent	SNP	ENST00000393946.2	hg19	CCDS8154.1																																																																																			.	.		0.552	SYT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393129.1	NM_177963	
AIP	9049	hgsc.bcm.edu	37	11	67258394	67258394	+	Missense_Mutation	SNP	C	C	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:67258394C>G	ENST00000279146.3	+	6	1041	c.923C>G	c.(922-924)gCc>gGc	p.A308G	PITPNM1_ENST00000526450.1_5'Flank	NM_003977.2	NP_003968.2	O00170	AIP_HUMAN	aryl hydrocarbon receptor interacting protein	308					negative regulation of cyclic-nucleotide phosphodiesterase activity (GO:0051344)|protein maturation by protein folding (GO:0022417)|protein targeting to mitochondrion (GO:0006626)|regulation of protein kinase A signaling (GO:0010738)|signal transduction (GO:0007165)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	GAF domain binding (GO:0036004)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|unfolded protein binding (GO:0051082)			central_nervous_system(1)|large_intestine(1)|lung(3)|skin(2)	7						GAGCTGCAGGCCCTGGAGGCA	0.652									Familial Isolated Pituitary Adenoma																												p.A308G		Atlas-SNP	.											.	AIP	26	.	0			c.C923G						.						22.0	22.0	22.0					11																	67258394		2195	4289	6484	SO:0001583	missense	9049	exon6	Familial Cancer Database	FIPA, incl. Familial Isolated Somatotropinomas, FIS, IFS, Familial Acromegaly	TGCAGGCCCTGGA	U31913	CCDS8168.1	11q13.3	2014-09-17	2001-11-29		ENSG00000110711	ENSG00000110711			358	protein-coding gene	gene with protein product		605555	"""aryl hydrocarbon receptor-interacting protein"""			8972861, 9111057	Standard	NM_003977		Approved	XAP2, ARA9, FKBP16	uc001olv.3	O00170	OTTHUMG00000167674	ENST00000279146.3:c.923C>G	chr11.hg19:g.67258394C>G	ENSP00000279146:p.Ala308Gly	125.0	0.0		192.0	8.0	NM_003977	A0SZW3|A0SZW4|A0SZW5|A0SZW6|Q2M3Q2|Q99606	Missense_Mutation	SNP	ENST00000279146.3	hg19	CCDS8168.1	.	.	.	.	.	.	.	.	.	.	C	10.38	1.332847	0.24167	.	.	ENSG00000110711	ENST00000279146	T	0.74209	-0.82	5.39	3.42	0.39159	.	0.737123	0.13434	N	0.388207	T	0.58047	0.2095	L	0.39898	1.24	0.30196	N	0.799055	B	0.27264	0.173	B	0.23275	0.045	T	0.49204	-0.8964	10	0.23302	T	0.38	-18.9647	3.1863	0.06602	0.274:0.4925:0.1448:0.0887	.	308	O00170	AIP_HUMAN	G	308	ENSP00000279146:A308G	ENSP00000279146:A308G	A	+	2	0	AIP	67014970	0.760000	0.28428	1.000000	0.80357	0.718000	0.41266	0.510000	0.22723	2.703000	0.92315	0.561000	0.74099	GCC	.	.		0.652	AIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395516.1		
SHANK2	22941	hgsc.bcm.edu	37	11	70332097	70332097	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:70332097A>G	ENST00000423696.2	-	15	3200	c.3164T>C	c.(3163-3165)cTc>cCc	p.L1055P	SHANK2_ENST00000338508.4_Missense_Mutation_p.L1435P|SHANK2_ENST00000449833.2_Missense_Mutation_p.L839P|SHANK2_ENST00000409161.1_Missense_Mutation_p.L838P			Q9UPX8	SHAN2_HUMAN	SH3 and multiple ankyrin repeat domains 2	1055					adult behavior (GO:0030534)|learning (GO:0007612)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|vocalization behavior (GO:0071625)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|cell junction (GO:0030054)|ciliary membrane (GO:0060170)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|growth cone (GO:0030426)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	GKAP/Homer scaffold activity (GO:0030160)|ionotropic glutamate receptor binding (GO:0035255)			NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(30)|ovary(3)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	62			LUSC - Lung squamous cell carcinoma(11;4.72e-09)|STAD - Stomach adenocarcinoma(18;0.071)			TAAGTCTGAGAGAGCCGGGAC	0.502																																					p.L846P		Atlas-SNP	.											.	SHANK2	340	.	0			c.T2537C						.						80.0	91.0	88.0					11																	70332097		2200	4294	6494	SO:0001583	missense	22941	exon10			TCTGAGAGAGCCG	AF141901		11q13.2	2013-01-10			ENSG00000162105	ENSG00000162105		"""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	14295	protein-coding gene	gene with protein product		603290	"""cortactin binding protein 1"""	CORTBP1		10506216	Standard	XM_005277930		Approved	CTTNBP1, ProSAP1, SHANK, SPANK-3	uc001oqc.3	Q9UPX8	OTTHUMG00000154615	ENST00000423696.2:c.3164T>C	chr11.hg19:g.70332097A>G	ENSP00000394536:p.Leu1055Pro	63.0	0.0		107.0	5.0	NM_133266	C0SPG8|C0SPG9|Q3Y8G9|Q52LK2|Q9UKP1	Missense_Mutation	SNP	ENST00000423696.2	hg19		.	.	.	.	.	.	.	.	.	.	A	11.78	1.741649	0.30865	.	.	ENSG00000162105	ENST00000449833;ENST00000409161;ENST00000424924;ENST00000338508;ENST00000423696;ENST00000433693;ENST00000294018	T;T;T;T;T;T	0.44083	2.17;2.2;2.86;0.93;2.31;2.31	5.42	1.97	0.26223	.	1.267120	0.04920	N	0.454912	T	0.58991	0.2161	L	0.58810	1.83	0.20074	N	0.999937	P;D;D	0.69078	0.954;0.997;0.959	P;D;P	0.67382	0.736;0.951;0.812	T	0.41502	-0.9505	10	0.41790	T	0.15	.	9.1686	0.37067	0.7972:0.0:0.2028:0.0	.	1055;1434;839	Q9UPX8;Q9UPX8-3;Q9UPX8-4	SHAN2_HUMAN;.;.	P	839;838;713;1435;1055;1073;1058	ENSP00000399423:L839P;ENSP00000386491:L838P;ENSP00000402944:L713P;ENSP00000345193:L1435P;ENSP00000394536:L1055P;ENSP00000294018:L1058P	ENSP00000294018:L1058P	L	-	2	0	SHANK2	70009745	0.576000	0.26700	0.134000	0.22075	0.923000	0.55619	2.706000	0.47135	0.922000	0.37019	0.533000	0.62120	CTC	.	.		0.502	SHANK2-203	KNOWN	basic	protein_coding	protein_coding		NM_012309	
CAPN5	726	hgsc.bcm.edu	37	11	76834767	76834767	+	Silent	SNP	C	C	T			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:76834767C>T	ENST00000278559.3	+	13	1963	c.1774C>T	c.(1774-1776)Ctg>Ttg	p.L592L	CAPN5_ENST00000529629.1_Silent_p.L592L|CAPN5_ENST00000531028.1_Intron|CAPN5_ENST00000456580.2_Silent_p.L632L	NM_004055.4	NP_004046.2	O15484	CAN5_HUMAN	calpain 5	592	C2.				proteolysis (GO:0006508)|signal transduction (GO:0007165)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			NS(1)|breast(2)|endometrium(2)|large_intestine(7)|lung(17)|urinary_tract(1)	30						GGATGAATTTCTGGGCCAGGT	0.602																																					p.L592L		Atlas-SNP	.											.	CAPN5	67	.	0			c.C1774T						.						113.0	114.0	114.0					11																	76834767		2200	4292	6492	SO:0001819	synonymous_variant	726	exon13			GAATTTCTGGGCC		CCDS8248.1	11q14	2014-01-29				ENSG00000149260			1482	protein-coding gene	gene with protein product		602537	"""vitreoretinopathy, neovascular inflammatory"""	VRNI		9503024, 9367857, 23055945	Standard	NM_004055		Approved	nCL-3, HTRA3, ADNIV	uc001oxx.3	O15484		ENST00000278559.3:c.1774C>T	chr11.hg19:g.76834767C>T		98.0	0.0		96.0	4.0	NM_004055	O00263	Silent	SNP	ENST00000278559.3	hg19	CCDS8248.1																																																																																			.	.		0.602	CAPN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382564.2	NM_004055	
KIAA1731	85459	hgsc.bcm.edu	37	11	93432541	93432541	+	Missense_Mutation	SNP	T	T	A			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:93432541T>A	ENST00000325212.6	+	15	4625	c.4463T>A	c.(4462-4464)tTt>tAt	p.F1488Y	KIAA1731_ENST00000531700.1_Intron|KIAA1731_ENST00000411936.1_Missense_Mutation_p.F1488Y|KIAA1731_ENST00000344196.4_5'UTR			Q9C0D2	K1731_HUMAN	KIAA1731	1488						centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)	11		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				CCATGTAAATTTGAGGAAAAG	0.383																																					p.F1488Y		Atlas-SNP	.											.	KIAA1731	173	.	0			c.T4463A						.						87.0	69.0	74.0					11																	93432541		692	1591	2283	SO:0001583	missense	85459	exon15			GTAAATTTGAGGA	AB051518	CCDS44708.1	11q21	2014-03-11			ENSG00000166004	ENSG00000166004			29366	protein-coding gene	gene with protein product						20844083	Standard	NM_033395		Approved		uc009ywb.1	Q9C0D2	OTTHUMG00000167449	ENST00000325212.6:c.4463T>A	chr11.hg19:g.93432541T>A	ENSP00000316681:p.Phe1488Tyr	106.0	0.0		149.0	43.0	NM_033395	C9J5H9|C9JQY8|Q8N7L4|Q8N919|Q8N9B0|Q96LT8	Missense_Mutation	SNP	ENST00000325212.6	hg19	CCDS44708.1	.	.	.	.	.	.	.	.	.	.	T	14.28	2.488399	0.44249	.	.	ENSG00000166004	ENST00000325212;ENST00000411936	T;T	0.21932	1.98;1.98	4.93	-0.153	0.13403	.	0.789539	0.11146	N	0.594641	T	0.15955	0.0384	L	0.48642	1.525	0.38903	D	0.957363	B	0.11235	0.004	B	0.11329	0.006	T	0.13415	-1.0510	10	0.66056	D	0.02	-3.3414	2.7885	0.05380	0.3597:0.188:0.0:0.4523	.	1488	Q9C0D2	K1731_HUMAN	Y	1488	ENSP00000316681:F1488Y;ENSP00000406505:F1488Y	ENSP00000316681:F1488Y	F	+	2	0	KIAA1731	93072189	0.173000	0.23056	0.195000	0.23364	0.592000	0.36648	-0.118000	0.10692	-0.189000	0.10482	0.533000	0.62120	TTT	.	.		0.383	KIAA1731-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000394640.1	NM_033395	
C11orf54	28970	hgsc.bcm.edu	37	11	93488394	93488394	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:93488394A>G	ENST00000331239.4	+	6	528	c.349A>G	c.(349-351)Aca>Gca	p.T117A	C11orf54_ENST00000528288.1_Missense_Mutation_p.T117A|C11orf54_ENST00000528099.1_Missense_Mutation_p.T117A|C11orf54_ENST00000540113.1_Missense_Mutation_p.T98A|C11orf54_ENST00000354421.3_Missense_Mutation_p.T117A			Q9H0W9	CK054_HUMAN	chromosome 11 open reading frame 54	117					metabolic process (GO:0008152)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	hydrolase activity, acting on ester bonds (GO:0016788)|zinc ion binding (GO:0008270)			NS(1)|endometrium(1)|large_intestine(1)|lung(5)	8		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				AGTTATTCAGACAGAAAGTGA	0.378																																					p.T117A		Atlas-SNP	.											.	C11orf54	23	.	0			c.A349G						.						90.0	85.0	86.0					11																	93488394		2201	4298	6499	SO:0001583	missense	28970	exon6			ATTCAGACAGAAA	AF092133	CCDS8294.1, CCDS66204.1, CCDS73365.1, CCDS73366.1	11q21	2012-08-09			ENSG00000182919	ENSG00000182919			30204	protein-coding gene	gene with protein product		615810				16522806	Standard	NM_014039		Approved	PTD012	uc001pef.3	Q9H0W9	OTTHUMG00000167452	ENST00000331239.4:c.349A>G	chr11.hg19:g.93488394A>G	ENSP00000331209:p.Thr117Ala	55.0	0.0		95.0	4.0	NM_014039	A8K850|Q6FI88|Q6XYB0|Q96EI3|Q96IX1|Q9Y6B4	Missense_Mutation	SNP	ENST00000331239.4	hg19		.	.	.	.	.	.	.	.	.	.	A	13.39	2.223398	0.39300	.	.	ENSG00000182919	ENST00000528288;ENST00000331239;ENST00000528099;ENST00000354421;ENST00000540113;ENST00000530620;ENST00000524485;ENST00000527363;ENST00000526335;ENST00000533154	.	.	.	5.94	3.65	0.41850	Domain of unknown function DUF1907 (1);	0.183784	0.64402	N	0.000016	T	0.43897	0.1268	L	0.42581	1.335	0.53005	D	0.999966	B;B	0.06786	0.001;0.001	B;B	0.10450	0.004;0.005	T	0.22208	-1.0223	9	0.16896	T	0.51	-6.3971	7.8365	0.29374	0.7181:0.0:0.2819:0.0	.	117;117	Q9H0W9;Q9H0W9-3	CK054_HUMAN;.	A	117;117;117;117;98;98;98;117;117;6	.	ENSP00000331209:T117A	T	+	1	0	C11orf54	93128042	0.998000	0.40836	0.999000	0.59377	0.989000	0.77384	2.450000	0.44943	1.063000	0.40649	0.482000	0.46254	ACA	.	.		0.378	C11orf54-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000394671.1	NM_014039	
DYNC2H1	79659	hgsc.bcm.edu	37	11	103173919	103173919	+	Silent	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:103173919T>C	ENST00000375735.2	+	76	11337	c.11193T>C	c.(11191-11193)gcT>gcC	p.A3731A	DYNC2H1_ENST00000398093.3_Silent_p.A3738A|DYNC2H1_ENST00000334267.7_Intron	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	3731	AAA 6. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|asymmetric protein localization (GO:0008105)|cilium assembly (GO:0042384)|determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|forebrain development (GO:0030900)|Golgi organization (GO:0007030)|intraciliary retrograde transport (GO:0035721)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|spinal cord motor neuron differentiation (GO:0021522)	apical part of cell (GO:0045177)|axoneme (GO:0005930)|cytosol (GO:0005829)|dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile primary cilium (GO:0031512)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	33		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		CTCCGGGTGCTGATCCTTCTC	0.413																																					p.A3738A		Atlas-SNP	.											.	DYNC2H1	246	.	0			c.T11214C						.						100.0	97.0	98.0					11																	103173919		1826	4086	5912	SO:0001819	synonymous_variant	79659	exon77			GGGTGCTGATCCT	AB082528	CCDS44717.1, CCDS53701.1	11q21-q22.1	2011-06-02	2005-11-24	2005-11-24	ENSG00000187240	ENSG00000187240		"""Cytoplasmic dyneins"""	2962	protein-coding gene	gene with protein product		603297	"""dynein, cytoplasmic, heavy polypeptide 2"""	DNCH2		9763680, 9373155	Standard	NM_001080463		Approved	hdhc11, DHC2, DHC1b, DYH1B	uc001phn.1	Q8NCM8	OTTHUMG00000165941	ENST00000375735.2:c.11193T>C	chr11.hg19:g.103173919T>C		74.0	0.0		95.0	4.0	NM_001080463	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Silent	SNP	ENST00000375735.2	hg19	CCDS53701.1																																																																																			.	.		0.413	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652	
CASP5	838	hgsc.bcm.edu	37	11	104871171	104871171	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:104871171A>G	ENST00000260315.3	-	6	768	c.769T>C	c.(769-771)Tct>Cct	p.S257P	CASP5_ENST00000444749.2_Missense_Mutation_p.S199P|CASP5_ENST00000526056.1_Missense_Mutation_p.S270P|CASP5_ENST00000393141.2_Missense_Mutation_p.S270P|CASP5_ENST00000393139.2_3'UTR|CASP5_ENST00000418434.1_Missense_Mutation_p.S115P|CASP5_ENST00000531367.1_Missense_Mutation_p.S115P			P51878	CASP5_HUMAN	caspase 5, apoptosis-related cysteine peptidase	257					apoptotic process (GO:0006915)|cellular response to mechanical stimulus (GO:0071260)|execution phase of apoptosis (GO:0097194)|proteolysis (GO:0006508)|regulation of apoptotic process (GO:0042981)|regulation of inflammatory response (GO:0050727)|substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)|NLRP1 inflammasome complex (GO:0072558)	cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)			NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(15)|ovary(3)|skin(1)|urinary_tract(1)	35		Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Melanoma(852;0.0047)		BRCA - Breast invasive adenocarcinoma(274;0.000943)|Epithelial(105;0.0104)|all cancers(92;0.042)		GTGCTGTCAGAGGACTTGTGC	0.453																																					p.S270P		Atlas-SNP	.											.	CASP5	213	.	0			c.T808C						.						116.0	105.0	109.0					11																	104871171		2202	4299	6501	SO:0001583	missense	838	exon6			TGTCAGAGGACTT		CCDS8328.2, CCDS44718.1, CCDS44719.1, CCDS44720.1	11q22.2-q22.3	2006-02-17	2005-08-17		ENSG00000137757	ENSG00000137757		"""Caspases"""	1506	protein-coding gene	gene with protein product		602665	"""caspase 5, apoptosis-related cysteine protease"""			7797592, 9250871	Standard	NM_004347		Approved	ICE(rel)III	uc010ruz.1	P51878	OTTHUMG00000048073	ENST00000260315.3:c.769T>C	chr11.hg19:g.104871171A>G	ENSP00000260315:p.Ser257Pro	134.0	0.0		171.0	7.0	NM_001136112	B4DKP5|Q0QVY7|Q0QVY8|Q0QVZ0|Q0QVZ1|Q0QVZ2|Q14DD6|Q1HBJ3|Q6DJV7	Missense_Mutation	SNP	ENST00000260315.3	hg19	CCDS8328.2	.	.	.	.	.	.	.	.	.	.	.	11.35	1.613899	0.28712	.	.	ENSG00000137757	ENST00000393141;ENST00000418434;ENST00000260315;ENST00000444749;ENST00000526056;ENST00000531367	T;T;T;T;T;T	0.22743	1.94;1.94;1.94;1.94;1.94;1.94	4.21	3.04	0.35103	Peptidase C14, caspase catalytic (1);Peptidase C14, caspase precursor p45, core (1);Peptidase C14, ICE, catalytic subunit p20 (1);	0.067331	0.64402	D	0.000009	T	0.51432	0.1674	M	0.92077	3.27	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;1.0;1.0;0.999	T	0.55829	-0.8079	10	0.72032	D	0.01	.	9.0406	0.36316	0.8133:0.1867:0.0:0.0	.	115;199;257;270	P51878-3;P51878-2;P51878;P51878-5	.;.;CASP5_HUMAN;.	P	270;115;257;199;270;115	ENSP00000376849:S270P;ENSP00000398130:S115P;ENSP00000260315:S257P;ENSP00000388365:S199P;ENSP00000436877:S270P;ENSP00000434471:S115P	ENSP00000260315:S257P	S	-	1	0	CASP5	104376381	0.996000	0.38824	0.144000	0.22314	0.035000	0.12851	3.443000	0.52907	0.569000	0.29329	0.172000	0.16884	TCT	.	.		0.453	CASP5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109397.2	NM_004347	
CWF19L2	143884	hgsc.bcm.edu	37	11	107197734	107197734	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:107197734T>C	ENST00000282251.5	-	18	2614	c.2587A>G	c.(2587-2589)Aaa>Gaa	p.K863E		NM_152434.2	NP_689647.2	Q2TBE0	C19L2_HUMAN	CWF19-like 2, cell cycle control (S. pombe)	863							catalytic activity (GO:0003824)			endometrium(4)|kidney(2)|large_intestine(13)|lung(21)	40		Melanoma(852;1.75e-05)|all_epithelial(67;6.27e-05)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Breast(348;0.0258)		Epithelial(105;7.18e-06)|BRCA - Breast invasive adenocarcinoma(274;1.65e-05)|all cancers(92;1.76e-05)		CGGATGCCTTTCCTCCAAAGT	0.383																																					p.K863E		Atlas-SNP	.											.	CWF19L2	135	.	0			c.A2587G						.						143.0	147.0	146.0					11																	107197734		2201	4298	6499	SO:0001583	missense	143884	exon18			TGCCTTTCCTCCA	AK056905	CCDS8336.2	11q23.1	2005-09-22			ENSG00000152404	ENSG00000152404			26508	protein-coding gene	gene with protein product						14702039	Standard	NM_152434		Approved	FLJ32343	uc010rvp.2	Q2TBE0	OTTHUMG00000152975	ENST00000282251.5:c.2587A>G	chr11.hg19:g.107197734T>C	ENSP00000282251:p.Lys863Glu	65.0	0.0		74.0	4.0	NM_152434	A4FU66|A4FU67|A4FU68|Q6PHW1|Q96MI1	Missense_Mutation	SNP	ENST00000282251.5	hg19	CCDS8336.2	.	.	.	.	.	.	.	.	.	.	T	28.9	4.962710	0.92791	.	.	ENSG00000152404	ENST00000282251	T	0.32272	1.46	5.57	5.57	0.84162	Cwf19-like protein, C-terminal domain-2 (1);	0.044248	0.85682	D	0.000000	T	0.54367	0.1854	M	0.76328	2.33	0.80722	D	1	D	0.60575	0.988	D	0.64877	0.93	T	0.58951	-0.7545	10	0.72032	D	0.01	-18.2671	14.921	0.70838	0.0:0.0:0.0:1.0	.	863	Q2TBE0	C19L2_HUMAN	E	863	ENSP00000282251:K863E	ENSP00000282251:K863E	K	-	1	0	CWF19L2	106702944	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.940000	0.87693	2.127000	0.65507	0.528000	0.53228	AAA	.	.		0.383	CWF19L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328825.2	NM_152434	
ZC3H12C	85463	hgsc.bcm.edu	37	11	110035965	110035965	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:110035965T>C	ENST00000278590.3	+	6	2206	c.2155T>C	c.(2155-2157)Tcc>Ccc	p.S719P	ZC3H12C_ENST00000528673.1_Missense_Mutation_p.S720P|ZC3H12C_ENST00000453089.2_Missense_Mutation_p.S688P	NM_033390.1	NP_203748.1	Q9C0D7	ZC12C_HUMAN	zinc finger CCCH-type containing 12C	719							endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)			endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(16)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	37		all_cancers(61;3.24e-13)|all_epithelial(67;1.27e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;3.95e-05)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;1.72e-06)|BRCA - Breast invasive adenocarcinoma(274;1.17e-05)|all cancers(92;9e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0279)		GGGCGCCCGGTCCAGCTGTCC	0.592																																					p.S719P		Atlas-SNP	.											.	ZC3H12C	83	.	0			c.T2155C						.						142.0	161.0	155.0					11																	110035965		2149	4237	6386	SO:0001583	missense	85463	exon6			GCCCGGTCCAGCT		CCDS44727.1	11q22.3	2012-07-05			ENSG00000149289	ENSG00000149289		"""Zinc fingers, CCCH-type domain containing"""	29362	protein-coding gene	gene with protein product	"""MCP induced protein 3"""	615001				11214970, 18178554	Standard	NM_033390		Approved	KIAA1726, MCPIP3	uc009yxw.3	Q9C0D7	OTTHUMG00000166572	ENST00000278590.3:c.2155T>C	chr11.hg19:g.110035965T>C	ENSP00000278590:p.Ser719Pro	113.0	0.0		137.0	6.0	NM_033390	B4DI65|B4DR47	Missense_Mutation	SNP	ENST00000278590.3	hg19	CCDS44727.1	.	.	.	.	.	.	.	.	.	.	T	19.49	3.836541	0.71373	.	.	ENSG00000149289	ENST00000278590;ENST00000528673;ENST00000453089	T;T;T	0.43294	0.95;0.95;0.98	5.94	5.94	0.96194	.	0.055406	0.85682	D	0.000000	T	0.63988	0.2558	M	0.66939	2.045	0.40146	D	0.976894	D;D;D	0.71674	0.998;0.998;0.998	D;D;D	0.75484	0.986;0.986;0.986	T	0.67669	-0.5611	10	0.72032	D	0.01	-20.3697	16.3947	0.83586	0.0:0.0:0.0:1.0	.	720;719;719	B4DR47;B4DI65;Q9C0D7	.;.;ZC12C_HUMAN	P	719;720;688	ENSP00000278590:S719P;ENSP00000431821:S720P;ENSP00000413094:S688P	ENSP00000278590:S719P	S	+	1	0	ZC3H12C	109541175	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.827000	0.55745	2.272000	0.75746	0.459000	0.35465	TCC	.	.		0.592	ZC3H12C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000390491.1	NM_033390	
PPP2R1B	5519	hgsc.bcm.edu	37	11	111618722	111618722	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:111618722T>C	ENST00000527614.1	-	11	1420	c.1355A>G	c.(1354-1356)gAt>gGt	p.D452G	PPP2R1B_ENST00000311129.5_Missense_Mutation_p.D452G|PPP2R1B_ENST00000426998.2_Missense_Mutation_p.D388G|PPP2R1B_ENST00000341980.6_Missense_Mutation_p.D407G|PPP2R1B_ENST00000427203.2_Missense_Mutation_p.D291G|PPP2R1B_ENST00000393055.2_Missense_Mutation_p.D325G	NM_001177562.1|NM_002716.4	NP_001171033.1|NP_002707.3	P30154	2AAB_HUMAN	protein phosphatase 2, regulatory subunit A, beta	452					apoptotic process involved in morphogenesis (GO:0060561)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)	extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|liver(1)|lung(10)|prostate(1)|urinary_tract(2)	22		all_cancers(61;2.34e-15)|all_epithelial(67;1.72e-09)|Melanoma(852;1.91e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|Epithelial(105;2.36e-06)|all cancers(92;3.78e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0761)		CAGCTTTTCATCAAAGAATTC	0.343																																					p.D452G		Atlas-SNP	.											.	PPP2R1B	44	.	0			c.A1355G						.						110.0	99.0	103.0					11																	111618722		2201	4296	6497	SO:0001583	missense	5519	exon11			TTTTCATCAAAGA	AF087438	CCDS8348.1, CCDS8349.1, CCDS53706.1, CCDS53707.1, CCDS53708.1	11q23.1	2010-06-18	2010-04-14		ENSG00000137713	ENSG00000137713	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"""	9303	protein-coding gene	gene with protein product	"""PP2A-A-beta"", ""protein phosphatase 2A, regulatory subunit A, beta isoform"""	603113	"""protein phosphatase 2 (formerly 2A), regulatory subunit A (PR 65), beta isoform"", ""protein phosphatase 2 (formerly 2A), regulatory subunit A, beta isoform"""			2159327, 9795170	Standard	NM_181699		Approved	PR65B, PP2A-Abeta	uc001plw.1	P30154	OTTHUMG00000166741	ENST00000527614.1:c.1355A>G	chr11.hg19:g.111618722T>C	ENSP00000437193:p.Asp452Gly	56.0	0.0		66.0	4.0	NM_002716	A8MY67|B0YJ69|B4DGQ6|B4DK91|B4DWW5|F8W8G1|O75620|Q8NHV8	Missense_Mutation	SNP	ENST00000527614.1	hg19	CCDS8349.1	.	.	.	.	.	.	.	.	.	.	T	18.11	3.551621	0.65311	.	.	ENSG00000137713	ENST00000311129;ENST00000412902;ENST00000426998;ENST00000527614;ENST00000427203;ENST00000341980;ENST00000393055	T;T;T;T;T;T	0.31510	2.23;2.23;2.23;2.23;1.49;2.23	5.73	5.73	0.89815	Armadillo-like helical (1);Armadillo-type fold (1);	0.044662	0.85682	D	0.000000	T	0.45498	0.1345	M	0.75884	2.315	0.80722	D	1	B;B;B;B;B;B	0.27013	0.166;0.01;0.026;0.09;0.016;0.041	B;B;B;B;B;B	0.40602	0.209;0.049;0.053;0.334;0.053;0.08	T	0.48031	-0.9070	10	0.87932	D	0	-22.5378	14.2586	0.66070	0.0:0.0:0.0:1.0	.	325;407;291;388;452;452	A8MY67;F8W8G1;B7Z1G3;B4DWW5;P30154;P30154-2	.;.;.;.;2AAB_HUMAN;.	G	452;325;388;452;291;407;325	ENSP00000311344:D452G;ENSP00000410671:D388G;ENSP00000437193:D452G;ENSP00000415759:D291G;ENSP00000343317:D407G;ENSP00000376775:D325G	ENSP00000311344:D452G	D	-	2	0	PPP2R1B	111123932	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.387000	0.79785	2.308000	0.77769	0.533000	0.62120	GAT	.	.		0.343	PPP2R1B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391298.1	NM_002716	
FDXACB1	91893	hgsc.bcm.edu	37	11	111747356	111747356	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:111747356C>T	ENST00000260257.4	-	4	588	c.541G>A	c.(541-543)Gat>Aat	p.D181N	C11orf1_ENST00000530214.1_5'Flank|FDXACB1_ENST00000542429.1_Missense_Mutation_p.D32N|C11orf1_ENST00000260276.3_5'Flank|ALG9_ENST00000524880.1_Missense_Mutation_p.D181N|ALG9_ENST00000527377.1_5'UTR|C11orf1_ENST00000528125.1_5'Flank	NM_138378.2	NP_612387.1	Q9BRP7	FDXA1_HUMAN	ferredoxin-fold anticodon binding domain containing 1	181					phenylalanyl-tRNA aminoacylation (GO:0006432)|tRNA processing (GO:0008033)		ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|phenylalanine-tRNA ligase activity (GO:0004826)|tRNA binding (GO:0000049)			endometrium(1)|kidney(3)|large_intestine(2)|lung(9)|ovary(1)|upper_aerodigestive_tract(3)	19						AAGGACTTATCTTGACTCCTG	0.383																																					p.D181N		Atlas-SNP	.											.	FDXACB1	74	.	0			c.G541A						.						77.0	74.0	75.0					11																	111747356		1882	4110	5992	SO:0001583	missense	91893	exon4			ACTTATCTTGACT		CCDS44729.1	11q23.1	2011-04-15			ENSG00000255561	ENSG00000255561			25110	protein-coding gene	gene with protein product	"""hypothetical protein BC006136"""						Standard	NR_038364		Approved	LOC91893, hCG_2033039	uc001pmc.4	Q9BRP7	OTTHUMG00000166795	ENST00000260257.4:c.541G>A	chr11.hg19:g.111747356C>T	ENSP00000260257:p.Asp181Asn	56.0	0.0		86.0	4.0	NM_138378	A0PJW7|B4DUU2	Missense_Mutation	SNP	ENST00000260257.4	hg19	CCDS44729.1	.	.	.	.	.	.	.	.	.	.	C	14.02	2.409998	0.42715	.	.	ENSG00000086848;ENSG00000255561;ENSG00000255561;ENSG00000255561	ENST00000428306;ENST00000260257;ENST00000542429;ENST00000528274	T;T;T	0.77229	0.27;-1.08;0.63	5.91	2.22	0.28083	.	0.144081	0.64402	N	0.000009	T	0.72187	0.3429	L	0.58810	1.83	0.54753	D	0.999984	B	0.18968	0.032	B	0.17722	0.019	T	0.69716	-0.5070	10	0.59425	D	0.04	.	11.3577	0.49625	0.0:0.7457:0.0:0.2543	.	181	Q9BRP7	FDXA1_HUMAN	N	181;181;32;92	ENSP00000260257:D181N;ENSP00000441304:D32N;ENSP00000435572:D92N	ENSP00000387627:D181N	D	-	1	0	FDXACB1;ALG9	111252566	0.999000	0.42202	1.000000	0.80357	0.992000	0.81027	1.784000	0.38674	0.655000	0.30866	0.655000	0.94253	GAT	.	.		0.383	FDXACB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391497.1	NM_138378	
REXO2	25996	hgsc.bcm.edu	37	11	114316717	114316717	+	Silent	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:114316717A>G	ENST00000265881.5	+	5	581	c.438A>G	c.(436-438)gaA>gaG	p.E146E	REXO2_ENST00000539275.1_Intron|REXO2_ENST00000538791.1_Silent_p.E56E|REXO2_ENST00000539754.1_Silent_p.E131E	NM_015523.3	NP_056338.2	Q9Y3B8	ORN_HUMAN	RNA exonuclease 2	146	Exonuclease.				nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleobase-containing compound metabolic process (GO:0006139)|nucleotide metabolic process (GO:0009117)	focal adhesion (GO:0005925)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|nucleic acid binding (GO:0003676)			cervix(1)|endometrium(1)|kidney(1)|lung(1)	4		all_cancers(61;5.06e-12)|all_epithelial(67;5.3e-06)|all_hematologic(158;7.68e-05)|Acute lymphoblastic leukemia(157;0.000966)|Melanoma(852;0.00153)|Medulloblastoma(222;0.0523)|all_neural(223;0.0663)|Breast(348;0.0818)|Prostate(24;0.104)		BRCA - Breast invasive adenocarcinoma(274;2.65e-06)|Epithelial(105;6.09e-05)|all cancers(92;0.000494)		CAGTTCATGAAGATAAGAAGT	0.328																																					p.E146E		Atlas-SNP	.											.	REXO2	12	.	0			c.A438G						.						133.0	138.0	136.0					11																	114316717		2201	4296	6497	SO:0001819	synonymous_variant	25996	exon5			TCATGAAGATAAG	AF151872	CCDS8371.1	11q23.2	2013-06-10	2013-06-10		ENSG00000076043	ENSG00000076043			17851	protein-coding gene	gene with protein product		607149	"""REX2, RNA exonuclease 2 homolog (S. cerevisiae)"""			10851236, 10810093, 23741365	Standard	NM_015523		Approved	DKFZP566E144, SFN, CGI-114	uc001poy.3	Q9Y3B8	OTTHUMG00000168271	ENST00000265881.5:c.438A>G	chr11.hg19:g.114316717A>G		49.0	0.0		98.0	5.0	NM_015523	B2R532|Q32Q18|Q53FT1|Q6FIC6|Q9UFY7	Silent	SNP	ENST00000265881.5	hg19	CCDS8371.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	2.690|2.690	-0.273420|-0.273420	0.05679|0.05679	.|.	.|.	ENSG00000076043|ENSG00000076043	ENST00000544827|ENST00000539119;ENST00000538403	.|.	.|.	.|.	5.59|5.59	4.4|4.4	0.53042|0.53042	.|.	.|.	.|.	.|.	.|.	T|T	0.62974|0.62974	0.2472|0.2472	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.61662|0.61662	-0.7017|-0.7017	5|4	0.02654|.	T|.	1|.	-1.8711|-1.8711	11.6412|11.6412	0.51233|0.51233	0.8517:0.1483:0.0:0.0|0.8517:0.1483:0.0:0.0	.|.	.|.	.|.	.|.	R|G	106|101;63	.|.	ENSP00000442703:K109R|.	K|R	+|+	2|1	0|2	REXO2|REXO2	113821927|113821927	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	1.346000|1.346000	0.33964|0.33964	2.133000|2.133000	0.65898|0.65898	0.455000|0.455000	0.32223|0.32223	AAG|AGA	.	.		0.328	REXO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399087.1	NM_015523	
CADM1	23705	hgsc.bcm.edu	37	11	115099840	115099840	+	Silent	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:115099840T>C	ENST00000452722.3	-	5	734	c.714A>G	c.(712-714)gaA>gaG	p.E238E	CADM1_ENST00000542447.2_Silent_p.E238E|CADM1_ENST00000537140.1_5'UTR|CADM1_ENST00000536727.1_Silent_p.E238E|CADM1_ENST00000331581.6_Silent_p.E238E|CADM1_ENST00000537058.1_Silent_p.E238E	NM_014333.3	NP_055148.3			cell adhesion molecule 1											cervix(1)|endometrium(4)|kidney(4)|large_intestine(11)|lung(9)|ovary(2)|skin(1)	32	all_hematologic(175;0.0628)	all_cancers(61;2.98e-14)|all_epithelial(67;2.64e-08)|all_hematologic(158;0.000154)|Melanoma(852;0.000952)|Acute lymphoblastic leukemia(157;0.00101)|Breast(348;0.0102)|Medulloblastoma(222;0.0429)|Prostate(24;0.145)|all_neural(223;0.237)		BRCA - Breast invasive adenocarcinoma(274;5.01e-06)|Epithelial(105;0.000305)|all cancers(92;0.00303)		CACACTGTACTTCTAGATACC	0.478																																					p.E238E		Atlas-SNP	.											.	CADM1	74	.	0			c.A714G						.						65.0	54.0	58.0					11																	115099840		2201	4296	6497	SO:0001819	synonymous_variant	23705	exon5			CTGTACTTCTAGA	AB017563	CCDS8373.1, CCDS53711.1, CCDS73397.1, CCDS73398.1, CCDS73399.1	11q23.2	2013-01-29	2007-02-07	2007-02-07	ENSG00000182985	ENSG00000182985		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5951	protein-coding gene	gene with protein product	"""nectin-like 2"""	605686	"""tumor suppressor in lung cancer 1"", ""immunoglobulin superfamily, member 4"""	TSLC1, IGSF4		10610705	Standard	NM_014333		Approved	NECL2, ST17, BL2, SYNCAM, IGSF4A, Necl-2, SYNCAM1, RA175	uc001ppi.4	Q9BY67	OTTHUMG00000168202	ENST00000452722.3:c.714A>G	chr11.hg19:g.115099840T>C		54.0	0.0		72.0	6.0	NM_014333		Silent	SNP	ENST00000452722.3	hg19	CCDS8373.1	.	.	.	.	.	.	.	.	.	.	T	9.852	1.193982	0.22037	.	.	ENSG00000182985	ENST00000545380	.	.	.	6.17	5.05	0.67936	.	.	.	.	.	T	0.56093	0.1962	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.54282	-0.8317	4	.	.	.	.	6.1386	0.20247	0.0:0.1356:0.1368:0.7276	.	.	.	.	G	237	.	.	S	-	1	0	CADM1	114605050	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	0.850000	0.27737	1.159000	0.42565	0.533000	0.62120	AGT	.	.		0.478	CADM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000398753.2	NM_014333	
IL10RA	3587	hgsc.bcm.edu	37	11	117860327	117860327	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:117860327T>C	ENST00000227752.3	+	3	479	c.359T>C	c.(358-360)gTg>gCg	p.V120A	IL10RA_ENST00000541785.1_Missense_Mutation_p.V100A|IL10RA_ENST00000533700.1_3'UTR|IL10RA_ENST00000545409.1_Intron	NM_001558.3	NP_001549.2	Q13651	I10R1_HUMAN	interleukin 10 receptor, alpha	120					cytokine-mediated signaling pathway (GO:0019221)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-10 receptor activity (GO:0004920)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(10)|ovary(2)|prostate(1)	19	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.07e-05)|Epithelial(105;0.00108)		CGCTTCTCTGTGGATGAAGGT	0.552																																					p.V120A		Atlas-SNP	.											.	IL10RA	46	.	0			c.T359C						.						49.0	46.0	47.0					11																	117860327		2200	4296	6496	SO:0001583	missense	3587	exon3			TCTCTGTGGATGA	U00672	CCDS8388.1	11q23	2014-09-17			ENSG00000110324	ENSG00000110324		"""Interleukins and interleukin receptors"", ""CD molecules"""	5964	protein-coding gene	gene with protein product		146933		IL10R		8120391	Standard	NR_026691		Approved	HIL-10R, CDW210A, CD210a, CD210	uc001prv.3	Q13651	OTTHUMG00000166523	ENST00000227752.3:c.359T>C	chr11.hg19:g.117860327T>C	ENSP00000227752:p.Val120Ala	80.0	0.0		73.0	4.0	NM_001558	A8K6I0|B0YJ27	Missense_Mutation	SNP	ENST00000227752.3	hg19	CCDS8388.1	.	.	.	.	.	.	.	.	.	.	T	14.57	2.575457	0.45902	.	.	ENSG00000110324	ENST00000227752;ENST00000541785;ENST00000536858	T;T	0.57907	0.37;0.37	4.95	-0.957	0.10350	Fibronectin, type III (1);Immunoglobulin-like fold (1);	1.775030	0.03457	N	0.211530	T	0.43523	0.1251	L	0.56769	1.78	0.09310	N	1	B;B	0.34290	0.447;0.319	B;B	0.30029	0.11;0.083	T	0.14364	-1.0475	10	0.17832	T	0.49	0.3079	5.4281	0.16438	0.5307:0.0823:0.0:0.3869	.	100;120	F5GYV8;Q13651	.;I10R1_HUMAN	A	120;100;100	ENSP00000227752:V120A;ENSP00000441397:V100A	ENSP00000227752:V120A	V	+	2	0	IL10RA	117365537	0.000000	0.05858	0.021000	0.16686	0.791000	0.44710	-0.527000	0.06200	-0.019000	0.14055	0.460000	0.39030	GTG	.	.		0.552	IL10RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390167.1		
BCL9L	283149	hgsc.bcm.edu	37	11	118771996	118771996	+	Missense_Mutation	SNP	C	C	T	rs374181286		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:118771996C>T	ENST00000334801.3	-	6	3420	c.2456G>A	c.(2455-2457)cGg>cAg	p.R819Q	BCL9L_ENST00000526143.1_5'UTR	NM_182557.2	NP_872363.1	Q86UU0	BCL9L_HUMAN	B-cell CLL/lymphoma 9-like	819	Met-rich.				canonical Wnt signaling pathway (GO:0060070)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell morphogenesis (GO:0022604)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	beta-catenin binding (GO:0008013)|transcription coactivator activity (GO:0003713)			NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(2)	56	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.103)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.66e-05)		GGCCCGAACCCGGGCCATCTC	0.647																																					p.R819Q		Atlas-SNP	.											.	BCL9L	254	.	0			c.G2456A						.	C	GLN/ARG	1,4399		0,1,2199	43.0	43.0	43.0		2456	4.3	1.0	11		43	0,8590		0,0,4295	no	missense	BCL9L	NM_182557.2	43	0,1,6494	TT,TC,CC		0.0,0.0227,0.0077	possibly-damaging	819/1500	118771996	1,12989	2200	4295	6495	SO:0001583	missense	283149	exon6			CGAACCCGGGCCA	AB094091	CCDS8403.1	11q23.3	2012-06-06				ENSG00000186174			23688	protein-coding gene	gene with protein product		609004				12964048	Standard	NM_182557		Approved	DLNB11	uc001pug.3	Q86UU0		ENST00000334801.3:c.2456G>A	chr11.hg19:g.118771996C>T	ENSP00000335320:p.Arg819Gln	74.0	0.0		80.0	5.0	NM_182557	A1A4C1|Q67FY1|Q6ZWJ0|Q6ZWK2	Missense_Mutation	SNP	ENST00000334801.3	hg19	CCDS8403.1	.	.	.	.	.	.	.	.	.	.	C	19.41	3.821447	0.71028	2.27E-4	0.0	ENSG00000186174	ENST00000334801;ENST00000526143;ENST00000525300;ENST00000392849;ENST00000431085	T	0.41065	1.01	5.21	4.29	0.51040	.	0.000000	0.45867	D	0.000327	T	0.30008	0.0751	L	0.38531	1.155	0.43061	D	0.994683	P;P	0.48016	0.904;0.846	B;B	0.36666	0.23;0.115	T	0.14952	-1.0454	10	0.42905	T	0.14	-21.2794	12.8474	0.57837	0.0:0.9208:0.0:0.0792	.	814;819	Q86UU0-2;Q86UU0	.;BCL9L_HUMAN	Q	819;782;112;819;819	ENSP00000335320:R819Q	ENSP00000335320:R819Q	R	-	2	0	BCL9L	118277206	0.994000	0.37717	0.981000	0.43875	0.955000	0.61496	3.106000	0.50322	2.415000	0.81967	0.655000	0.94253	CGG	.	.		0.647	BCL9L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389653.1	NM_182557	
HYOU1	10525	hgsc.bcm.edu	37	11	118926262	118926262	+	Silent	SNP	C	C	T	rs376675681		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:118926262C>T	ENST00000404233.3	-	4	331	c.207G>A	c.(205-207)ccG>ccA	p.P69P	HYOU1_ENST00000525859.1_Silent_p.P69P|HYOU1_ENST00000529972.1_Silent_p.P69P|HYOU1_ENST00000543287.1_5'UTR	NM_001130991.1|NM_006389.3	NP_001124463.1|NP_006380.1	Q9Y4L1	HYOU1_HUMAN	hypoxia up-regulated 1	69					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|response to ischemia (GO:0002931)|response to stress (GO:0006950)	endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)	ATP binding (GO:0005524)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(10)|prostate(1)|skin(2)	33	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)|all_hematologic(192;0.207)		BRCA - Breast invasive adenocarcinoma(274;7.78e-05)		TCACGATCACCGGTGTTTTCC	0.517																																					p.P69P		Atlas-SNP	.											.	HYOU1	88	.	0			c.G207A						.	C	,	1,4399	2.1+/-5.4	0,1,2199	99.0	99.0	99.0		207,207	-7.8	0.9	11		99	0,8590		0,0,4295	no	coding-synonymous,coding-synonymous	HYOU1	NM_001130991.1,NM_006389.3	,	0,1,6494	TT,TC,CC		0.0,0.0227,0.0077	,	69/1000,69/1000	118926262	1,12989	2200	4295	6495	SO:0001819	synonymous_variant	10525	exon4			GATCACCGGTGTT	U65785	CCDS8408.1	11q23.1-q23.3	2011-09-02			ENSG00000149428	ENSG00000149428		"""Heat shock proteins / HSP70"""	16931	protein-coding gene	gene with protein product	"""glucose-regulated protein 170"""	601746				9020069, 10037731	Standard	XM_005271390		Approved	ORP150, HSP12A, Grp170	uc001pux.3	Q9Y4L1	OTTHUMG00000166354	ENST00000404233.3:c.207G>A	chr11.hg19:g.118926262C>T		107.0	0.0		152.0	20.0	NM_006389	A8C1Z0|B7Z909|Q2I204|Q53H25	Silent	SNP	ENST00000404233.3	hg19	CCDS8408.1																																																																																			.	.		0.517	HYOU1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389353.1	NM_006389	
TECTA	7007	hgsc.bcm.edu	37	11	120989419	120989419	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:120989419A>G	ENST00000392793.1	+	7	1466	c.1195A>G	c.(1195-1197)Aga>Gga	p.R399G	TECTA_ENST00000264037.2_Missense_Mutation_p.R399G			O75443	TECTA_HUMAN	tectorin alpha	399	VWFD 1. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cell-matrix adhesion (GO:0007160)|sensory perception of sound (GO:0007605)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)			TECTA/TBCEL(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|liver(1)|lung(46)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	135	all_hematologic(175;0.208)	Breast(109;0.000766)|Medulloblastoma(222;0.0427)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;8.04e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.166)		AAGCTATGGAAGAGTCAAGGT	0.512																																					p.R399G		Atlas-SNP	.											.	TECTA	329	.	0			c.A1195G						.						55.0	59.0	58.0					11																	120989419		2203	4298	6501	SO:0001583	missense	7007	exon6			TATGGAAGAGTCA	AF055136	CCDS8434.1	11q22-q24	2008-02-05			ENSG00000109927	ENSG00000109927			11720	protein-coding gene	gene with protein product		602574		DFNA12, DFNA8, DFNB21		9503015, 9590290	Standard	NM_005422		Approved		uc010rzo.2	O75443	OTTHUMG00000149908	ENST00000392793.1:c.1195A>G	chr11.hg19:g.120989419A>G	ENSP00000376543:p.Arg399Gly	40.0	0.0		76.0	4.0	NM_005422		Missense_Mutation	SNP	ENST00000392793.1	hg19	CCDS8434.1	.	.	.	.	.	.	.	.	.	.	A	10.30	1.313395	0.23908	.	.	ENSG00000109927	ENST00000392793;ENST00000264037	T;T	0.59224	0.28;0.28	5.72	4.54	0.55810	von Willebrand factor, type D domain (3);	0.372961	0.27912	N	0.017350	T	0.41003	0.1140	N	0.16862	0.45	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.19679	-1.0298	10	0.28530	T	0.3	.	14.1639	0.65464	0.8672:0.1328:0.0:0.0	.	399	O75443	TECTA_HUMAN	G	399	ENSP00000376543:R399G;ENSP00000264037:R399G	ENSP00000264037:R399G	R	+	1	2	TECTA	120494629	1.000000	0.71417	0.956000	0.39512	0.947000	0.59692	3.980000	0.56895	2.180000	0.69256	0.460000	0.39030	AGA	.	.		0.512	TECTA-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313850.1	NM_005422	
OR8D1	283159	hgsc.bcm.edu	37	11	124180206	124180206	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:124180206A>G	ENST00000357821.2	-	1	527	c.457T>C	c.(457-459)Ttt>Ctt	p.F153L		NM_001002917.1	NP_001002917.1	Q8WZ84	OR8D1_HUMAN	olfactory receptor, family 8, subfamily D, member 1	153						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			kidney(1)|large_intestine(1)|lung(7)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0528)		GCAGAGAGAAAGCCCAAGAAG	0.458																																					p.F153L		Atlas-SNP	.											.	OR8D1	53	.	0			c.T457C						.						73.0	64.0	67.0					11																	124180206		2201	4299	6500	SO:0001583	missense	283159	exon1			AGAGAAAGCCCAA	AF238489	CCDS31706.1	11q25	2012-08-09			ENSG00000196341	ENSG00000196341		"""GPCR / Class A : Olfactory receptors"""	8481	protein-coding gene	gene with protein product				OR8D3			Standard	NM_001002917		Approved	OST004	uc010sag.2	Q8WZ84	OTTHUMG00000165977	ENST00000357821.2:c.457T>C	chr11.hg19:g.124180206A>G	ENSP00000350474:p.Phe153Leu	61.0	0.0		81.0	4.0	NM_001002917	B2RNL4|Q6IEW1|Q8NGH0	Missense_Mutation	SNP	ENST00000357821.2	hg19	CCDS31706.1	.	.	.	.	.	.	.	.	.	.	c	6.379	0.438002	0.12104	.	.	ENSG00000196341	ENST00000357821	T	0.00039	8.85	4.29	-8.35	0.00984	GPCR, rhodopsin-like superfamily (1);	0.670897	0.12166	N	0.493560	T	0.00073	0.0002	L	0.28344	0.845	0.09310	N	1	B	0.06786	0.001	B	0.09377	0.004	T	0.30149	-0.9988	10	0.25751	T	0.34	.	1.8553	0.03177	0.1601:0.3845:0.1856:0.2698	.	153	Q8WZ84	OR8D1_HUMAN	L	153	ENSP00000350474:F153L	ENSP00000350474:F153L	F	-	1	0	OR8D1	123685416	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.077000	0.01371	-2.024000	0.00936	-0.456000	0.05471	TTT	.	.		0.458	OR8D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387285.1	NM_001002917	
HEPN1	641654	hgsc.bcm.edu	37	11	124789756	124789756	+	Missense_Mutation	SNP	G	G	C	rs201178398		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:124789756G>C	ENST00000408930.5	+	1	611	c.110G>C	c.(109-111)tGg>tCg	p.W37S	HEPACAM_ENST00000298251.4_3'UTR	NM_001037558.2	NP_001032647.2	Q6WQI6	HEPN1_HUMAN	hepatocellular carcinoma, down-regulated 1	37			W -> R (in dbSNP:rs3802904). {ECO:0000269|PubMed:12971969}.			cytoplasm (GO:0005737)				large_intestine(1)|lung(1)|stomach(1)	3	all_hematologic(175;0.215)	Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|Breast(109;0.171)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0287)		AGGAGGGAATGGAATACACAG	0.502																																					p.W37S		Atlas-SNP	.											HEPN1,NS,carcinoma,0,1	HEPN1	11	.	0			c.G110C						.						121.0	124.0	123.0					11																	124789756		1967	4153	6120	SO:0001583	missense	641654	exon1			GGGAATGGAATAC	BC148521	CCDS41729.1	11q24	2013-07-02	2011-02-11		ENSG00000221932	ENSG00000221932			34400	protein-coding gene	gene with protein product	"""cancer susceptibility gene HEPN1"""	611641	"""HEPACAM opposite strand 1"""			12971969, 23548416	Standard	NM_001037558		Approved		uc001qbj.1	Q6WQI6	OTTHUMG00000165939	ENST00000408930.5:c.110G>C	chr11.hg19:g.124789756G>C	ENSP00000386143:p.Trp37Ser	170.0	0.0		167.0	0.0	NM_001037558		Missense_Mutation	SNP	ENST00000408930.5	hg19	CCDS41729.1	.	.	.	.	.	.	.	.	.	.	G	2.538	-0.306935	0.05458	.	.	ENSG00000221932	ENST00000408930	T	0.56941	0.43	4.85	-0.241	0.13043	.	.	.	.	.	T	0.40222	0.1108	.	.	.	0.09310	N	1	B	0.06786	0.001	B	0.09377	0.004	T	0.33979	-0.9847	8	0.87932	D	0	.	8.4933	0.33112	0.749:0.0:0.251:0.0	.	37	Q6WQI6	HEPN1_HUMAN	S	37	ENSP00000386143:W37S	ENSP00000386143:W37S	W	+	2	0	HEPN1	124294966	0.000000	0.05858	0.011000	0.14972	0.002000	0.02628	-0.123000	0.10611	-0.328000	0.08539	-1.232000	0.01568	TGG	.	.		0.502	HEPN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387129.1	NM_001037558	
SPATA19	219938	hgsc.bcm.edu	37	11	133711936	133711936	+	Nonstop_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:133711936A>G	ENST00000299140.3	-	6	556	c.502T>C	c.(502-504)Tga>Cga	p.*168R	SPATA19_ENST00000532889.1_Nonstop_Mutation_p.*168R	NM_174927.1	NP_777587.1	Q7Z5L4	SPT19_HUMAN	spermatogenesis associated 19	0					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	mitochondrial outer membrane (GO:0005741)				cervix(1)|endometrium(2)|large_intestine(2)|lung(5)|prostate(1)	11	all_hematologic(175;0.127)	all_cancers(12;5.59e-17)|all_epithelial(12;2.65e-12)|all_lung(97;0.00045)|Lung NSC(97;0.000861)|Breast(109;0.000873)|Medulloblastoma(222;0.0425)|Esophageal squamous(93;0.0844)|all_neural(223;0.117)		Epithelial(10;4.36e-10)|all cancers(11;7.1e-09)|BRCA - Breast invasive adenocarcinoma(10;8.45e-09)|OV - Ovarian serous cystadenocarcinoma(99;0.00286)|Lung(977;0.207)		TGTTGCTCTCAGCAGTCTGAG	0.562																																					p.X168R		Atlas-SNP	.											.	SPATA19	36	.	0			c.T502C						.						136.0	126.0	129.0					11																	133711936		2201	4297	6498	SO:0001578	stop_lost	219938	exon6			GCTCTCAGCAGTC	AK098717	CCDS8493.1	11q25	2010-04-23				ENSG00000166118			30614	protein-coding gene	gene with protein product	"""spergen 1"", ""cancer/testis antigen 132"""	609805				12477932	Standard	XM_005271448		Approved	FLJ25851, spergen1, SPAS1, CT132	uc001qgv.1	Q7Z5L4		ENST00000299140.3:c.502T>C	chr11.hg19:g.133711936A>G	ENSP00000299140:p.*168Glyext*61	66.0	0.0		117.0	41.0	NM_174927	Q8N7A9	Missense_Mutation	SNP	ENST00000299140.3	hg19	CCDS8493.1	.	.	.	.	.	.	.	.	.	.	A	10.17	1.277183	0.23307	.	.	ENSG00000166118	ENST00000299140;ENST00000532889	.	.	.	5.45	5.45	0.79879	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.9127	0.52747	1.0:0.0:0.0:0.0	.	.	.	.	R	168	.	.	X	-	1	0	SPATA19	133217146	0.998000	0.40836	1.000000	0.80357	0.530000	0.34684	4.100000	0.57762	2.062000	0.61559	0.459000	0.35465	TGA	.	.		0.562	SPATA19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393281.1	NM_174927	
CRACR2A	84766	hgsc.bcm.edu	37	12	3789421	3789421	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:3789421T>C	ENST00000252322.1	-	5	791	c.323A>G	c.(322-324)gAg>gGg	p.E108G	EFCAB4B_ENST00000440314.2_Missense_Mutation_p.E108G|EFCAB4B_ENST00000444507.1_Missense_Mutation_p.E108G	NM_032680.3	NP_116069.1	Q9BSW2	EFC4B_HUMAN		108	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.				activation of store-operated calcium channel activity (GO:0032237)|immune system process (GO:0002376)|positive regulation of calcium ion transport (GO:0051928)|store-operated calcium entry (GO:0002115)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			breast(1)|endometrium(3)|large_intestine(2)|liver(1)|lung(12)|ovary(1)|pancreas(2)|prostate(1)|upper_aerodigestive_tract(1)	24			OV - Ovarian serous cystadenocarcinoma(31;0.00287)|COAD - Colon adenocarcinoma(12;0.0264)			AGTAGTGAACTCCTGTGGGGT	0.512																																					p.E108G		Atlas-SNP	.											.	EFCAB4B	100	.	0			c.A323G						.						114.0	90.0	98.0					12																	3789421		2203	4300	6503	SO:0001583	missense	84766	exon5			GTGAACTCCTGTG																												ENST00000252322.1:c.323A>G	chr12.hg19:g.3789421T>C	ENSP00000252322:p.Glu108Gly	134.0	0.0		158.0	7.0	NM_001144958	B4E1X0|B9EK63	Missense_Mutation	SNP	ENST00000252322.1	hg19	CCDS8522.1	.	.	.	.	.	.	.	.	.	.	T	15.49	2.847989	0.51164	.	.	ENSG00000130038	ENST00000440314;ENST00000444507;ENST00000252322	D;D;D	0.90261	-2.64;-2.17;-2.64	4.69	4.69	0.59074	EF-hand-like domain (1);	0.187168	0.45606	D	0.000351	D	0.96685	0.8918	H	0.96916	3.905	0.46564	D	0.999103	D;D;D	0.89917	0.993;1.0;0.989	P;D;P	0.85130	0.905;0.997;0.9	D	0.97464	1.0036	10	0.87932	D	0	-26.3189	12.1539	0.54066	0.0:0.0:0.0:1.0	.	108;108;108	D7UEQ6;Q9BSW2-2;Q9BSW2	.;.;EFC4B_HUMAN	G	108	ENSP00000409382:E108G;ENSP00000412496:E108G;ENSP00000252322:E108G	ENSP00000252322:E108G	E	-	2	0	EFCAB4B	3659682	1.000000	0.71417	0.998000	0.56505	0.492000	0.33523	3.631000	0.54280	1.991000	0.58162	0.459000	0.35465	GAG	.	.		0.512	EFCAB4B-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000398673.1		
CD163L1	283316	hgsc.bcm.edu	37	12	7521548	7521548	+	Silent	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:7521548T>C	ENST00000313599.3	-	16	4110	c.4053A>G	c.(4051-4053)aaA>aaG	p.K1351K	CD163L1_ENST00000416109.2_Silent_p.K1361K|CD163L1_ENST00000396630.1_Silent_p.K1351K			Q9NR16	C163B_HUMAN	CD163 molecule-like 1	1351						extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	scavenger receptor activity (GO:0005044)			breast(5)|central_nervous_system(3)|endometrium(8)|kidney(3)|large_intestine(18)|lung(37)|ovary(8)|prostate(3)|skin(6)|stomach(1)|urinary_tract(4)	96						CATTCAGTGATTTCAGCGACT	0.453																																					p.K1351K		Atlas-SNP	.											.	CD163L1	238	.	0			c.A4053G						.						132.0	119.0	124.0					12																	7521548		2203	4300	6503	SO:0001819	synonymous_variant	283316	exon16			CAGTGATTTCAGC	AF264014	CCDS8577.1, CCDS73434.1	12p13.31	2006-03-28	2006-03-28			ENSG00000177675			30375	protein-coding gene	gene with protein product		606079	"""CD163 antigen-like 1"""			11124526, 11086079	Standard	XM_005253348		Approved	M160, CD163B	uc001qsy.3	Q9NR16		ENST00000313599.3:c.4053A>G	chr12.hg19:g.7521548T>C		43.0	0.0		61.0	5.0	NM_174941	B4E0G7|C9JHR7|E7EVK4|Q2M3B7|Q6UWC2	Silent	SNP	ENST00000313599.3	hg19	CCDS8577.1	.	.	.	.	.	.	.	.	.	.	T	1.607	-0.525079	0.04141	.	.	ENSG00000177675	ENST00000539726	.	.	.	0.802	-0.499	0.12015	.	.	.	.	.	T	0.21227	0.0511	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.24512	-1.0158	4	.	.	.	.	2.9066	0.05722	0.0:0.3328:0.0:0.6672	.	.	.	.	V	7	.	.	I	-	1	0	CD163L1	7412815	0.002000	0.14202	0.001000	0.08648	0.044000	0.14063	-0.049000	0.11924	-0.204000	0.10235	-0.475000	0.04921	ATC	.	.		0.453	CD163L1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399329.1	NM_174941	
SLC2A3	6515	hgsc.bcm.edu	37	12	8085609	8085609	+	Silent	SNP	G	G	A			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:8085609G>A	ENST00000075120.7	-	3	483	c.243C>T	c.(241-243)gtC>gtT	p.V81V		NM_006931.2	NP_008862.1	P11169	GTR3_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 3	81					carbohydrate metabolic process (GO:0005975)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|L-ascorbic acid metabolic process (GO:0019852)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	glucose transmembrane transporter activity (GO:0005355)			central_nervous_system(1)|cervix(2)|endometrium(1)|kidney(3)|large_intestine(2)|lung(14)|ovary(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30				Kidney(36;0.0866)		CGAAGAGTCCGACGGAAAAGG	0.547											OREG0021656	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V81V	Colon(96;424 1461 14416 20933 23688)	Atlas-SNP	.											.	SLC2A3	83	.	0			c.C243T						.						94.0	87.0	89.0					12																	8085609		2203	4300	6503	SO:0001819	synonymous_variant	6515	exon3			GAGTCCGACGGAA	M20681	CCDS8586.1	12p13.3	2013-05-22			ENSG00000059804	ENSG00000059804		"""Solute carriers"""	11007	protein-coding gene	gene with protein product		138170		GLUT3			Standard	NM_006931		Approved		uc001qtr.3	P11169	OTTHUMG00000133685	ENST00000075120.7:c.243C>T	chr12.hg19:g.8085609G>A		109.0	0.0	646	89.0	4.0	NM_006931	B2R606|D3DUU6|Q6I9U2|Q9UG15	Silent	SNP	ENST00000075120.7	hg19	CCDS8586.1																																																																																			.	.		0.547	SLC2A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257914.1	NM_006931	
TAS2R42	353164	hgsc.bcm.edu	37	12	11338615	11338615	+	Missense_Mutation	SNP	T	T	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:11338615T>G	ENST00000334266.1	-	1	928	c.929A>C	c.(928-930)aAt>aCt	p.N310T		NM_181429.1	NP_852094.1	Q7RTR8	T2R42_HUMAN	taste receptor, type 2, member 42	310					sensory perception of taste (GO:0050909)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(1)|kidney(2)|lung(4)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11			OV - Ovarian serous cystadenocarcinoma(49;0.0455)			AGGTAAAGCATTTGGTGTTTT	0.413																																					p.N310T	Melanoma(15;352 722 10077 19546 48810)	Atlas-SNP	.											.	TAS2R42	30	.	0			c.A929C						.						58.0	54.0	55.0					12																	11338615		2203	4300	6503	SO:0001583	missense	353164	exon1			AAAGCATTTGGTG	AX097739, AB199241	CCDS31747.1	12p13	2012-08-22			ENSG00000186136	ENSG00000186136		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	18888	protein-coding gene	gene with protein product		613966				12679530	Standard	NM_181429		Approved	T2R24, T2R55, hT2R55, TAS2R55	uc001qzr.1	Q7RTR8	OTTHUMG00000168567	ENST00000334266.1:c.929A>C	chr12.hg19:g.11338615T>G	ENSP00000334050:p.Asn310Thr	103.0	0.0		99.0	6.0	NM_181429	A2RRP4|Q645X0	Missense_Mutation	SNP	ENST00000334266.1	hg19	CCDS31747.1	.	.	.	.	.	.	.	.	.	.	T	7.528	0.658085	0.14645	.	.	ENSG00000186136	ENST00000334266	T	0.00784	5.7	2.9	0.223	0.15292	.	1.148940	0.06597	U	0.753108	T	0.00496	0.0016	N	0.08118	0	0.09310	N	1	P	0.39480	0.675	B	0.27887	0.084	T	0.50118	-0.8865	10	0.54805	T	0.06	.	6.8753	0.24143	0.0:0.0:0.4872:0.5128	.	310	Q7RTR8	T2R42_HUMAN	T	310	ENSP00000334050:N310T	ENSP00000334050:N310T	N	-	2	0	TAS2R42	11229882	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	0.039000	0.13884	0.048000	0.15891	0.528000	0.53228	AAT	.	.		0.413	TAS2R42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400243.1	NM_181429	
GUCY2C	2984	hgsc.bcm.edu	37	12	14829894	14829894	+	Missense_Mutation	SNP	A	A	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:14829894A>C	ENST00000261170.3	-	7	978	c.842T>G	c.(841-843)tTt>tGt	p.F281C	RP11-174G6.1_ENST00000501178.2_RNA	NM_004963.3	NP_004954.2	P25092	GUC2C_HUMAN	guanylate cyclase 2C (heat stable enterotoxin receptor)	281			F -> L (in dbSNP:rs1420635). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:1680854, ECO:0000269|PubMed:1718270, ECO:0000269|PubMed:8381596, ECO:0000269|Ref.4}.		intracellular signal transduction (GO:0035556)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of cell proliferation (GO:0042127)|response to toxic substance (GO:0009636)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|protein kinase activity (GO:0004672)|toxic substance binding (GO:0015643)			breast(3)|endometrium(7)|kidney(3)|large_intestine(9)|lung(17)|ovary(4)|skin(7)|urinary_tract(1)	51					Linaclotide(DB08890)	ATTGTCCTCAAAGTACTGGTC	0.388																																					p.F281C		Atlas-SNP	.											GUCY2C,NS,carcinoma,0,1	GUCY2C	126	.	0			c.T842G						.						76.0	76.0	76.0					12																	14829894		2203	4300	6503	SO:0001583	missense	2984	exon7			TCCTCAAAGTACT		CCDS8664.1	12p12	2008-08-18			ENSG00000070019	ENSG00000070019			4688	protein-coding gene	gene with protein product		601330		GUC2C		8661067	Standard	NM_004963		Approved	STAR	uc001rcd.3	P25092	OTTHUMG00000168732	ENST00000261170.3:c.842T>G	chr12.hg19:g.14829894A>C	ENSP00000261170:p.Phe281Cys	151.0	0.0		206.0	0.0	NM_004963	B2RMY6	Missense_Mutation	SNP	ENST00000261170.3	hg19	CCDS8664.1	.	.	.	.	.	.	.	.	.	.	A	13.03	2.115603	0.37339	.	.	ENSG00000070019	ENST00000261170	T	0.74842	-0.88	5.77	5.77	0.91146	Extracellular ligand-binding receptor (1);	0.053419	0.85682	D	0.000000	T	0.81148	0.4762	L	0.54323	1.7	0.42978	D	0.994453	D	0.67145	0.996	P	0.62813	0.907	T	0.82493	-0.0430	10	0.56958	D	0.05	.	12.5394	0.56161	1.0:0.0:0.0:0.0	.	281	P25092	GUC2C_HUMAN	C	281	ENSP00000261170:F281C	ENSP00000261170:F281C	F	-	2	0	GUCY2C	14721161	0.997000	0.39634	0.922000	0.36590	0.026000	0.11368	4.745000	0.62125	2.213000	0.71641	0.529000	0.55759	TTT	.	.		0.388	GUCY2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400835.1		
SLCO1C1	53919	hgsc.bcm.edu	37	12	20885932	20885932	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:20885932A>G	ENST00000266509.2	+	10	1644	c.1276A>G	c.(1276-1278)Aaa>Gaa	p.K426E	SLCO1C1_ENST00000545604.1_Missense_Mutation_p.K426E|SLCO1C1_ENST00000545102.1_Missense_Mutation_p.K308E|SLCO1C1_ENST00000381552.1_Missense_Mutation_p.K426E|SLCO1C1_ENST00000540354.1_Missense_Mutation_p.K377E	NM_017435.4	NP_059131.1	Q9NYB5	SO1C1_HUMAN	solute carrier organic anion transporter family, member 1C1	426					sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			NS(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|liver(1)|lung(28)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	60	Esophageal squamous(101;0.149)				Conjugated Estrogens(DB00286)|Dextrothyroxine(DB00509)|Diclofenac(DB00586)|Digoxin(DB00390)|Dinoprostone(DB00917)|Estradiol(DB00783)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)|Meclofenamic acid(DB00939)|Methotrexate(DB00563)|Ouabain(DB01092)|Phenytoin(DB00252)|Probenecid(DB01032)	TGGAGCTGCAAAACTCTACTT	0.443																																					p.K426E		Atlas-SNP	.											SLCO1C1_ENST00000381552,NS,carcinoma,0,2	SLCO1C1	216	.	0			c.A1276G						.						204.0	180.0	189.0					12																	20885932		2203	4300	6503	SO:0001583	missense	53919	exon10			GCTGCAAAACTCT	AF260704	CCDS8683.1, CCDS53757.1, CCDS53758.1, CCDS53759.1	12p12.2	2013-05-22	2003-11-25	2003-11-26	ENSG00000139155	ENSG00000139155		"""Solute carriers"""	13819	protein-coding gene	gene with protein product		613389	"""solute carrier family 21 (organic anion transporter), member 14"""	SLC21A14			Standard	NM_017435		Approved	OATP-F, OATP1C1, OATP1	uc010sii.2	Q9NYB5	OTTHUMG00000168966	ENST00000266509.2:c.1276A>G	chr12.hg19:g.20885932A>G	ENSP00000266509:p.Lys426Glu	154.0	0.0		159.0	0.0	NM_017435	B7Z251|B7Z3Q3|B7Z8P1|F5GZD6|Q5JPA4	Missense_Mutation	SNP	ENST00000266509.2	hg19	CCDS8683.1	.	.	.	.	.	.	.	.	.	.	A	27.1	4.801568	0.90538	.	.	ENSG00000139155	ENST00000545604;ENST00000540354;ENST00000266509;ENST00000381552;ENST00000545102	T;T;T;T;D	0.82167	0.1;0.1;0.1;0.1;-1.58	5.11	5.11	0.69529	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.047896	0.85682	D	0.000000	D	0.92315	0.7562	M	0.91300	3.195	0.54753	D	0.999982	D;D;P;P	0.58620	0.982;0.983;0.815;0.607	P;D;P;P	0.67900	0.805;0.954;0.793;0.686	D	0.93834	0.7130	10	0.66056	D	0.02	.	15.0568	0.71921	1.0:0.0:0.0:0.0	.	308;377;426;426	F5GZD6;B7Z3Q3;Q5JPA4;Q9NYB5	.;.;.;SO1C1_HUMAN	E	426;377;426;426;308	ENSP00000444149:K426E;ENSP00000438665:K377E;ENSP00000266509:K426E;ENSP00000370964:K426E;ENSP00000444527:K308E	ENSP00000266509:K426E	K	+	1	0	SLCO1C1	20777199	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.774000	0.75012	2.134000	0.65973	0.482000	0.46254	AAA	.	.		0.443	SLCO1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401765.1	NM_017435	
OVCH1	341350	hgsc.bcm.edu	37	12	29626034	29626034	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:29626034A>G	ENST00000318184.5	-	15	1602	c.1603T>C	c.(1603-1605)Tct>Cct	p.S535P	OVCH1-AS1_ENST00000549411.1_Intron|OVCH1-AS1_ENST00000551108.1_Intron	NM_183378.2	NP_899234.2	Q7RTY7	OVCH1_HUMAN	ovochymase 1	535						extracellular region (GO:0005576)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)			NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(43)|ovary(5)|pancreas(3)|prostate(2)|skin(1)|soft_tissue(1)|stomach(3)	92	Lung NSC(12;1.84e-09)|Acute lymphoblastic leukemia(23;0.00885)|all_hematologic(23;0.0155)					TTGTTTAAAGACTCTGTAGAA	0.343																																					p.S535P		Atlas-SNP	.											.	OVCH1	195	.	0			c.T1603C						.						83.0	79.0	80.0					12																	29626034		1818	4078	5896	SO:0001583	missense	341350	exon15			TTAAAGACTCTGT	BN000128		12p11.23	2012-11-08			ENSG00000187950	ENSG00000187950			23080	protein-coding gene	gene with protein product						12838346	Standard	NM_183378		Approved	OVCH	uc001rix.1	Q7RTY7	OTTHUMG00000167741	ENST00000318184.5:c.1603T>C	chr12.hg19:g.29626034A>G	ENSP00000326708:p.Ser535Pro	35.0	0.0		48.0	4.0	NM_183378		Missense_Mutation	SNP	ENST00000318184.5	hg19		.	.	.	.	.	.	.	.	.	.	A	6.862	0.528315	0.13127	.	.	ENSG00000187950	ENST00000318184	D	0.86865	-2.18	2.46	1.25	0.21368	.	.	.	.	.	T	0.72890	0.3517	N	0.08118	0	0.09310	N	1	P	0.50617	0.937	P	0.45506	0.483	T	0.63739	-0.6569	9	0.29301	T	0.29	.	4.628	0.12488	0.6723:0.0:0.0:0.3277	.	535	Q7RTY7	OVCH1_HUMAN	P	535	ENSP00000326708:S535P	ENSP00000326708:S535P	S	-	1	0	OVCH1	29517301	0.005000	0.15991	0.000000	0.03702	0.001000	0.01503	1.049000	0.30392	0.344000	0.23847	-0.438000	0.05819	TCT	.	.		0.343	OVCH1-001	KNOWN	non_canonical_TEC|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395997.2	NM_183378	
BICD1	636	hgsc.bcm.edu	37	12	32369392	32369392	+	Splice_Site	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:32369392A>G	ENST00000281474.5	+	2	528	c.425A>G	c.(424-426)gAg>gGg	p.E142G	BICD1_ENST00000548411.1_Splice_Site_p.E142G	NM_001714.2	NP_001705.2	Q96G01	BICD1_HUMAN	bicaudal D homolog 1 (Drosophila)	142					anatomical structure morphogenesis (GO:0009653)|intracellular mRNA localization (GO:0008298)|microtubule anchoring at microtubule organizing center (GO:0072393)|minus-end-directed organelle transport along microtubule (GO:0072385)|negative regulation of phospholipase C activity (GO:1900275)|negative regulation of phospholipase C-activating G-protein coupled receptor signaling pathway (GO:1900737)|positive regulation of receptor-mediated endocytosis (GO:0048260)|protein localization to organelle (GO:0033365)|regulation of proteinase activated receptor activity (GO:1900276)|RNA processing (GO:0006396)|stress granule assembly (GO:0034063)|viral process (GO:0016032)	cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|host cell viral assembly compartment (GO:0072517)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network (GO:0005802)	cytoskeletal adaptor activity (GO:0008093)|dynactin binding (GO:0034452)|dynein binding (GO:0045502)|proteinase activated receptor binding (GO:0031871)|Rab GTPase binding (GO:0017137)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(2)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	46	all_cancers(9;5.13e-11)|all_epithelial(9;2.71e-11)|all_lung(12;6.66e-10)|Acute lymphoblastic leukemia(23;0.0122)|Lung SC(12;0.0213)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)		OV - Ovarian serous cystadenocarcinoma(6;0.0201)			GATCTGAAGGAGGTAAATAAA	0.443																																					p.E142G		Atlas-SNP	.											.	BICD1	89	.	0			c.A425G						.						48.0	45.0	46.0					12																	32369392		2203	4300	6503	SO:0001630	splice_region_variant	636	exon2			TGAAGGAGGTAAA	U90028	CCDS8726.1, CCDS44859.1	12p11.2-p11.1	2005-01-13	2001-11-28			ENSG00000151746			1049	protein-coding gene	gene with protein product		602204	"""Bicaudal D (Drosophila) homolog 1"""			9367685	Standard	NM_001714		Approved		uc001rku.3	Q96G01	OTTHUMG00000169307	ENST00000281474.5:c.426+1A>G	chr12.hg19:g.32369392A>G		53.0	0.0		76.0	4.0	NM_001714	A8K2C3|F8W113|O43892|O43893	Missense_Mutation	SNP	ENST00000281474.5	hg19	CCDS8726.1	.	.	.	.	.	.	.	.	.	.	A	24.6	4.546311	0.86022	.	.	ENSG00000151746	ENST00000548411;ENST00000281474	T;T	0.30182	1.54;1.54	5.58	5.58	0.84498	.	0.059936	0.64402	D	0.000003	T	0.58495	0.2126	M	0.81802	2.56	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.87578	0.996;0.998	T	0.61845	-0.6979	10	0.49607	T	0.09	.	15.7616	0.78087	1.0:0.0:0.0:0.0	.	142;142	F8W113;Q96G01	.;BICD1_HUMAN	G	142	ENSP00000446793:E142G;ENSP00000281474:E142G	ENSP00000281474:E142G	E	+	2	0	BICD1	32260659	1.000000	0.71417	1.000000	0.80357	0.786000	0.44442	8.987000	0.93497	2.121000	0.65114	0.533000	0.62120	GAG	.	.		0.443	BICD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403380.1	NM_001714	Missense_Mutation
SENP1	29843	hgsc.bcm.edu	37	12	48482714	48482714	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:48482714A>G	ENST00000004980.5	-	5	728	c.250T>C	c.(250-252)Tca>Cca	p.S84P	SENP1_ENST00000339976.6_Silent_p.A159A|SENP1_ENST00000549518.1_Missense_Mutation_p.S84P|SENP1_ENST00000551330.1_Missense_Mutation_p.S84P|SENP1_ENST00000547886.1_5'UTR|SENP1_ENST00000549595.1_Missense_Mutation_p.S84P|SENP1_ENST00000448372.1_Missense_Mutation_p.S84P			Q9P0U3	SENP1_HUMAN	SUMO1/sentrin specific peptidase 1	84	Ser-rich.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic signaling pathway (GO:0097190)|cellular protein metabolic process (GO:0044267)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-translational protein modification (GO:0043687)|protein desumoylation (GO:0016926)|protein sumoylation (GO:0016925)|proteolysis (GO:0006508)|regulation of definitive erythrocyte differentiation (GO:0010724)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	endopeptidase activity (GO:0004175)|SUMO-specific protease activity (GO:0016929)			large_intestine(3)|lung(1)|pancreas(2)|stomach(1)	7		Acute lymphoblastic leukemia(13;0.108)|all_hematologic(14;0.214)				AAATCGCCTGAGCCAAGAAAA	0.383																																					p.S84P		Atlas-SNP	.											.	SENP1	44	.	0			c.T250C						.						92.0	76.0	81.0					12																	48482714		1811	4071	5882	SO:0001583	missense	29843	exon5			CGCCTGAGCCAAG	AF149770	CCDS44868.1, CCDS44868.2	12q13.1	2008-02-05	2005-08-17			ENSG00000079387			17927	protein-coding gene	gene with protein product		612157	"""SUMO1/sentrin specific protease 1"""			10652325, 14563852	Standard	NM_001267595		Approved		uc009zkx.4	Q9P0U3	OTTHUMG00000169896	ENST00000004980.5:c.250T>C	chr12.hg19:g.48482714A>G	ENSP00000004980:p.Ser84Pro	67.0	0.0		100.0	38.0	NM_001267594	A8K7P5|Q86XC8	Missense_Mutation	SNP	ENST00000004980.5	hg19	CCDS44868.2	.	.	.	.	.	.	.	.	.	.	A	16.13	3.035373	0.54896	.	.	ENSG00000079387	ENST00000004980;ENST00000448372;ENST00000551330;ENST00000549595;ENST00000549518;ENST00000551798	T;T;T;T;T	0.17054	2.3;2.3;2.3;2.3;2.3	4.91	3.73	0.42828	.	0.394176	0.21727	N	0.070034	T	0.17408	0.0418	N	0.19112	0.55	0.80722	D	1	D;D	0.58268	0.969;0.982	P;P	0.53549	0.54;0.729	T	0.02358	-1.1171	10	0.36615	T	0.2	-9.3972	10.0544	0.42237	0.8303:0.1697:0.0:0.0	.	84;84	Q9P0U3;Q9P0U3-2	SENP1_HUMAN;.	P	84;84;84;84;84;77	ENSP00000004980:S84P;ENSP00000394791:S84P;ENSP00000446681:S84P;ENSP00000450076:S84P;ENSP00000447328:S84P	ENSP00000004980:S84P	S	-	1	0	SENP1	46768981	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.298000	0.43602	0.934000	0.37316	0.454000	0.30748	TCA	.	.		0.383	SENP1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000406471.1	NM_014554	
DNAJC22	79962	hgsc.bcm.edu	37	12	49743118	49743118	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:49743118A>G	ENST00000549441.2	+	3	1667	c.463A>G	c.(463-465)Att>Gtt	p.I155V	DNAJC22_ENST00000395069.3_Missense_Mutation_p.I155V			Q8N4W6	DJC22_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 22	155						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|liver(2)|lung(1)|ovary(1)|pancreas(1)	10						CATACTGCCCATTAGCGTGGC	0.562																																					p.I155V		Atlas-SNP	.											.	DNAJC22	29	.	0			c.A463G						.						76.0	74.0	75.0					12																	49743118		2203	4300	6503	SO:0001583	missense	79962	exon2			CTGCCCATTAGCG	AK055747	CCDS8785.1	12q13.12	2011-09-02		2008-07-08	ENSG00000178401	ENSG00000178401		"""Heat shock proteins / DNAJ (HSP40)"""	25802	protein-coding gene	gene with protein product	"""wurst homolog (Drosophila)"""					17558392	Standard	NM_024902		Approved	wus, FLJ13236	uc001rua.3	Q8N4W6		ENST00000549441.2:c.463A>G	chr12.hg19:g.49743118A>G	ENSP00000446830:p.Ile155Val	54.0	0.0		86.0	18.0	NM_024902	B3KP54	Missense_Mutation	SNP	ENST00000549441.2	hg19	CCDS8785.1	.	.	.	.	.	.	.	.	.	.	A	13.46	2.243418	0.39697	.	.	ENSG00000178401	ENST00000549441;ENST00000395069	T;T	0.46063	0.88;0.88	4.86	4.86	0.63082	.	0.000000	0.85682	D	0.000000	T	0.40670	0.1126	M	0.64997	1.995	0.50813	D	0.999898	P	0.39748	0.686	B	0.35607	0.206	T	0.46247	-0.9205	10	0.59425	D	0.04	-11.3242	13.7297	0.62781	1.0:0.0:0.0:0.0	.	155	Q8N4W6	DJC22_HUMAN	V	155	ENSP00000446830:I155V;ENSP00000378508:I155V	ENSP00000378508:I155V	I	+	1	0	DNAJC22	48029385	1.000000	0.71417	1.000000	0.80357	0.190000	0.23558	4.345000	0.59360	1.939000	0.56221	0.454000	0.30748	ATT	.	.		0.562	DNAJC22-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404302.2	NM_024902	
LARP4	113251	hgsc.bcm.edu	37	12	50822817	50822817	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:50822817C>T	ENST00000398473.2	+	3	378	c.266C>T	c.(265-267)aCt>aTt	p.T89I	LARP4_ENST00000522085.1_Missense_Mutation_p.T89I|LARP4_ENST00000518444.1_Missense_Mutation_p.T88I|LARP4_ENST00000293618.8_Missense_Mutation_p.T89I|LARP4_ENST00000518561.1_Missense_Mutation_p.T19I|LARP4_ENST00000429001.3_Missense_Mutation_p.T95I|LARP4_ENST00000347328.5_Missense_Mutation_p.T89I	NM_052879.4|NM_199188.2	NP_443111.4|NP_954658.2	Q71RC2	LARP4_HUMAN	La ribonucleoprotein domain family, member 4	89					cytoskeleton organization (GO:0007010)|regulation of cell morphogenesis (GO:0022604)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(3)|kidney(2)|large_intestine(2)|liver(2)|lung(7)|ovary(1)|skin(2)|urinary_tract(1)	23						GAAGAATCAACTGATGGGATG	0.333																																					p.T89I		Atlas-SNP	.											.	LARP4	58	.	0			c.C266T						.						119.0	112.0	114.0					12																	50822817		1827	4086	5913	SO:0001583	missense	113251	exon3			AATCAACTGATGG	AY004310	CCDS41782.1, CCDS44879.1, CCDS44880.1, CCDS44879.2, CCDS53789.1, CCDS53790.1	12q13.12	2005-08-09			ENSG00000161813	ENSG00000161813		"""La ribonucleoprotein domain containing"""	24320	protein-coding gene	gene with protein product						12477932	Standard	NM_052879		Approved	PP13296	uc001rwp.2	Q71RC2	OTTHUMG00000163724	ENST00000398473.2:c.266C>T	chr12.hg19:g.50822817C>T	ENSP00000381490:p.Thr89Ile	55.0	0.0		75.0	4.0	NM_001170808	A8K6T1|E9PDG5|G3XAA8|G5E976|Q5CZ97|Q6ZV14|Q96NF9	Missense_Mutation	SNP	ENST00000398473.2	hg19	CCDS41782.1	.	.	.	.	.	.	.	.	.	.	C	16.17	3.046455	0.55110	.	.	ENSG00000161813	ENST00000550522;ENST00000293618;ENST00000429001;ENST00000548174;ENST00000548697;ENST00000548993;ENST00000398473;ENST00000441650;ENST00000522085;ENST00000398464;ENST00000518444;ENST00000551886;ENST00000523389;ENST00000518561;ENST00000520064;ENST00000347328;ENST00000550260;ENST00000517559;ENST00000552445	T;T;T;T;T;T;T	0.45668	1.5;1.49;1.48;0.89;1.47;0.9;1.51	5.37	5.37	0.77165	.	0.265880	0.35903	N	0.002903	T	0.37732	0.1014	L	0.29908	0.895	0.25653	N	0.986074	B;B;B;B;B	0.30281	0.016;0.275;0.12;0.008;0.026	B;B;B;B;B	0.33196	0.015;0.159;0.099;0.012;0.019	T	0.37619	-0.9698	10	0.52906	T	0.07	.	18.7183	0.91684	0.0:1.0:0.0:0.0	.	88;89;89;89;95	Q71RC2-3;G3XAA8;G5E976;Q71RC2;Q71RC2-4	.;.;.;LARP4_HUMAN;.	I	19;89;95;97;19;19;89;19;89;89;88;89;19;19;88;89;88;19;19	ENSP00000293618:T89I;ENSP00000415464:T95I;ENSP00000381490:T89I;ENSP00000429781:T89I;ENSP00000429077:T88I;ENSP00000430851:T19I;ENSP00000340901:T89I	ENSP00000293618:T89I	T	+	2	0	LARP4	49109084	0.958000	0.32768	0.998000	0.56505	0.989000	0.77384	5.186000	0.65082	2.513000	0.84729	0.585000	0.79938	ACT	.	.		0.333	LARP4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374981.1	NM_052879	
KRT79	338785	hgsc.bcm.edu	37	12	53227932	53227932	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:53227932A>G	ENST00000330553.5	-	1	147	c.113T>C	c.(112-114)gTg>gCg	p.V38A		NM_175834.2	NP_787028.1	Q5XKE5	K2C79_HUMAN	keratin 79	38	Head.					extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	enzyme binding (GO:0019899)|structural molecule activity (GO:0005198)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(11)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						GCTCCGAGACACCGTCACTGA	0.632																																					p.V38A		Atlas-SNP	.											.	KRT79	78	.	0			c.T113C						.						35.0	38.0	37.0					12																	53227932		2202	4298	6500	SO:0001583	missense	338785	exon1			CGAGACACCGTCA	AJ564105	CCDS8839.1	12q13.13	2014-02-12	2007-07-03		ENSG00000185640	ENSG00000185640		"""-"", ""Intermediate filaments type II, keratins (basic)"""	28930	protein-coding gene	gene with protein product	"""keratin 6-like"""	611160				11683385	Standard	NM_175834		Approved	K6L, KRT6L	uc001sbb.3	Q5XKE5	OTTHUMG00000169878	ENST00000330553.5:c.113T>C	chr12.hg19:g.53227932A>G	ENSP00000328358:p.Val38Ala	80.0	0.0		93.0	4.0	NM_175834	Q6P465|Q7Z793	Missense_Mutation	SNP	ENST00000330553.5	hg19	CCDS8839.1	.	.	.	.	.	.	.	.	.	.	A	7.981	0.751258	0.15778	.	.	ENSG00000185640	ENST00000330553	T	0.75589	-0.95	3.98	3.98	0.46160	.	0.531595	0.16412	N	0.215553	T	0.62454	0.2429	L	0.28649	0.875	0.25847	N	0.983985	B	0.09022	0.002	B	0.06405	0.002	T	0.55630	-0.8111	10	0.45353	T	0.12	.	11.4762	0.50300	1.0:0.0:0.0:0.0	.	38	Q5XKE5	K2C79_HUMAN	A	38	ENSP00000328358:V38A	ENSP00000328358:V38A	V	-	2	0	KRT79	51514199	0.031000	0.19500	0.914000	0.36105	0.417000	0.31264	1.133000	0.31430	2.045000	0.60652	0.533000	0.62120	GTG	.	.		0.632	KRT79-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406376.1	NM_175834	
TENC1	23371	hgsc.bcm.edu	37	12	53453176	53453176	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:53453176A>G	ENST00000314250.6	+	18	2041	c.1751A>G	c.(1750-1752)cAt>cGt	p.H584R	TENC1_ENST00000546602.1_Missense_Mutation_p.H584R|TENC1_ENST00000314276.3_Missense_Mutation_p.H594R|TENC1_ENST00000552570.1_Missense_Mutation_p.H584R|TENC1_ENST00000549700.1_Missense_Mutation_p.H584R|TENC1_ENST00000451358.1_Missense_Mutation_p.H584R|TENC1_ENST00000379902.3_Missense_Mutation_p.H460R	NM_170754.2	NP_736610.2	Q63HR2	TENC1_HUMAN	tensin like C1 domain containing phosphatase (tensin 2)	584					cellular homeostasis (GO:0019725)|collagen metabolic process (GO:0032963)|intracellular signal transduction (GO:0035556)|kidney development (GO:0001822)|multicellular organism growth (GO:0035264)|multicellular organismal homeostasis (GO:0048871)|negative regulation of cell proliferation (GO:0008285)|response to muscle activity (GO:0014850)	focal adhesion (GO:0005925)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|phosphoprotein phosphatase activity (GO:0004721)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(2)|lung(19)|ovary(1)|pancreas(1)|stomach(3)	34						TATCCAGGCCATAGGCCTGGC	0.706																																					p.H594R		Atlas-SNP	.											.	TENC1	148	.	0			c.A1781G						.						3.0	4.0	4.0					12																	53453176		1798	3800	5598	SO:0001583	missense	23371	exon18			CAGGCCATAGGCC	AF518729	CCDS8842.1, CCDS8843.1, CCDS8844.1	12q13.13	2013-02-14	2004-03-05			ENSG00000111077		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"", ""SH2 domain containing"""	19737	protein-coding gene	gene with protein product	"""tensin 2"""	607717	"""tensin like C1 domain-containing phosphatase"""				Standard	NM_015319		Approved	KIAA1075, C1-TEN, TNS2	uc001sbp.3	Q63HR2	OTTHUMG00000169730	ENST00000314250.6:c.1751A>G	chr12.hg19:g.53453176A>G	ENSP00000319684:p.His584Arg	36.0	0.0		52.0	5.0	NM_015319	A2VDF2|A2VDF3|A2VDI8|A5PKY4|Q2NL80|Q76MW6|Q7Z5T9|Q8NFF9|Q8NFG0|Q96P25|Q9NT29|Q9UPS7	Missense_Mutation	SNP	ENST00000314250.6	hg19	CCDS8843.1	.	.	.	.	.	.	.	.	.	.	A	2.881	-0.231906	0.05983	.	.	ENSG00000111077	ENST00000379902;ENST00000314276;ENST00000314250;ENST00000451358;ENST00000443113;ENST00000546602;ENST00000552570;ENST00000549700	D;D;D;D;D;D;D	0.93859	-3.29;-3.3;-3.3;-3.3;-3.3;-3.3;-3.3	4.08	0.219	0.15274	.	0.614111	0.15823	N	0.242888	T	0.78394	0.4276	N	0.02539	-0.55	0.23653	N	0.997196	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.001;0.001;0.0;0.001	T	0.67971	-0.5532	10	0.33141	T	0.24	.	4.4517	0.11624	0.4175:0.3844:0.198:0.0	.	584;584;584;594	Q63HR2-6;Q63HR2-2;Q63HR2;Q63HR2-4	.;.;TENC1_HUMAN;.	R	460;594;584;584;584;584;584;584	ENSP00000369232:H460R;ENSP00000319756:H594R;ENSP00000319684:H584R;ENSP00000393362:H584R;ENSP00000449363:H584R;ENSP00000447021:H584R;ENSP00000449361:H584R	ENSP00000319684:H584R	H	+	2	0	TENC1	51739443	0.002000	0.14202	0.465000	0.27155	0.852000	0.48524	-0.041000	0.12084	-0.047000	0.13423	-0.689000	0.03729	CAT	.	.		0.706	TENC1-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405779.1	NM_170754	
HOXC10	3226	hgsc.bcm.edu	37	12	54383171	54383171	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:54383171A>G	ENST00000303460.4	+	2	1044	c.970A>G	c.(970-972)Aag>Gag	p.K324E	RP11-834C11.12_ENST00000513209.1_Intron|MIR196A2_ENST00000385189.1_RNA|HOXC10_ENST00000511575.1_3'UTR	NM_017409.3	NP_059105.2	Q9NYD6	HXC10_HUMAN	homeobox C10	324					anterior/posterior pattern specification (GO:0009952)|embryonic limb morphogenesis (GO:0030326)|neuromuscular process (GO:0050905)|positive regulation of cell proliferation (GO:0008284)|proximal/distal pattern formation (GO:0009954)|regulation of transcription, DNA-templated (GO:0006355)|skeletal system development (GO:0001501)|spinal cord motor neuron cell fate specification (GO:0021520)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			endometrium(2)|large_intestine(3)|lung(14)|pancreas(1)	20						AATGAAACTCAAGAAAATGAA	0.483											OREG0021882	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.K324E		Atlas-SNP	.											.	HOXC10	42	.	0			c.A970G						.						61.0	57.0	59.0					12																	54383171		2203	4300	6503	SO:0001583	missense	3226	exon2			AAACTCAAGAAAA		CCDS8868.1	12q13.13	2011-06-20	2005-12-22		ENSG00000180818	ENSG00000180818		"""Homeoboxes / ANTP class : HOXL subclass"""	5122	protein-coding gene	gene with protein product		605560	"""homeo box C10"""	HOX3I		1358459	Standard	NM_017409		Approved		uc001sen.3	Q9NYD6	OTTHUMG00000160031	ENST00000303460.4:c.970A>G	chr12.hg19:g.54383171A>G	ENSP00000307321:p.Lys324Glu	95.0	0.0	999	86.0	4.0	NM_017409	O15219|O15220|Q9BVD5	Missense_Mutation	SNP	ENST00000303460.4	hg19	CCDS8868.1	.	.	.	.	.	.	.	.	.	.	A	18.50	3.638476	0.67130	.	.	ENSG00000180818	ENST00000303460	D	0.98296	-4.85	3.81	3.81	0.43845	Homeobox, eukaryotic (1);Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);Homeobox, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.99381	0.9782	H	0.99182	4.46	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98098	1.0413	10	0.87932	D	0	.	12.2389	0.54532	1.0:0.0:0.0:0.0	.	324	Q9NYD6	HXC10_HUMAN	E	324	ENSP00000307321:K324E	ENSP00000307321:K324E	K	+	1	0	HOXC10	52669438	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.225000	0.95219	1.680000	0.50976	0.379000	0.24179	AAG	.	.		0.483	HOXC10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358952.2		
OR6C6	283365	hgsc.bcm.edu	37	12	55688668	55688668	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:55688668A>G	ENST00000358433.2	-	1	348	c.349T>C	c.(349-351)Tcc>Ccc	p.S117P		NM_001005493.1	NP_001005493.1	A6NF89	OR6C6_HUMAN	olfactory receptor, family 6, subfamily C, member 6	117						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(5)|lung(7)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	20						CGGTCATAGGACATGGCAGCC	0.408																																					p.S117P		Atlas-SNP	.											.	OR6C6	56	.	0			c.T349C						.						61.0	59.0	59.0					12																	55688668		2203	4300	6503	SO:0001583	missense	283365	exon1			CATAGGACATGGC		CCDS31817.1	12q13.13	2012-08-09			ENSG00000188324	ENSG00000188324		"""GPCR / Class A : Olfactory receptors"""	31293	protein-coding gene	gene with protein product							Standard	NM_001005493		Approved		uc010sph.2	A6NF89	OTTHUMG00000168101	ENST00000358433.2:c.349T>C	chr12.hg19:g.55688668A>G	ENSP00000351211:p.Ser117Pro	62.0	0.0		78.0	4.0	NM_001005493		Missense_Mutation	SNP	ENST00000358433.2	hg19	CCDS31817.1	.	.	.	.	.	.	.	.	.	.	-	16.53	3.149275	0.57151	.	.	ENSG00000188324	ENST00000358433	T	0.01369	4.97	4.24	4.24	0.50183	GPCR, rhodopsin-like superfamily (1);	0.000000	0.49916	D	0.000139	T	0.09686	0.0238	M	0.92923	3.36	0.36330	D	0.858817	D	0.67145	0.996	D	0.65874	0.939	T	0.01829	-1.1265	10	0.87932	D	0	.	9.7725	0.40598	0.8264:0.1736:0.0:0.0	.	117	A6NF89	OR6C6_HUMAN	P	117	ENSP00000351211:S117P	ENSP00000351211:S117P	S	-	1	0	OR6C6	53974935	1.000000	0.71417	1.000000	0.80357	0.845000	0.48019	0.927000	0.28818	1.908000	0.55244	0.473000	0.43528	TCC	.	.		0.408	OR6C6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398151.1		
OR6C1	390321	hgsc.bcm.edu	37	12	55714705	55714705	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:55714705A>G	ENST00000379668.2	+	1	360	c.322A>G	c.(322-324)Aca>Gca	p.T108A		NM_001005182.1	NP_001005182.1	Q96RD1	OR6C1_HUMAN	olfactory receptor, family 6, subfamily C, member 1	108						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|large_intestine(5)|liver(2)|lung(13)|ovary(1)|upper_aerodigestive_tract(1)	25						CTTGGGAGTCACAGAGTTTTA	0.408																																					p.T108A		Atlas-SNP	.											.	OR6C1	58	.	0			c.A322G						.						54.0	55.0	55.0					12																	55714705		2202	4300	6502	SO:0001583	missense	390321	exon1			GGAGTCACAGAGT	AF399506	CCDS31818.1	12q13.13	2012-08-09			ENSG00000205330	ENSG00000205330		"""GPCR / Class A : Olfactory receptors"""	8355	protein-coding gene	gene with protein product							Standard	NM_001005182		Approved	OST267	uc010spi.2	Q96RD1	OTTHUMG00000168102	ENST00000379668.2:c.322A>G	chr12.hg19:g.55714705A>G	ENSP00000368990:p.Thr108Ala	57.0	0.0		58.0	4.0	NM_001005182	B2RNM0	Missense_Mutation	SNP	ENST00000379668.2	hg19	CCDS31818.1	.	.	.	.	.	.	.	.	.	.	a	9.634	1.137090	0.21123	.	.	ENSG00000205330	ENST00000379668	T	0.00873	5.59	4.84	1.09	0.20402	GPCR, rhodopsin-like superfamily (1);	0.094648	0.46758	N	0.000279	T	0.00784	0.0026	L	0.28115	0.83	0.09310	N	1	B	0.15141	0.012	B	0.21151	0.033	T	0.48151	-0.9060	10	0.54805	T	0.06	.	4.1894	0.10414	0.6671:0.0:0.1792:0.1537	.	108	Q96RD1	OR6C1_HUMAN	A	108	ENSP00000368990:T108A	ENSP00000368990:T108A	T	+	1	0	OR6C1	54000972	0.000000	0.05858	0.658000	0.29665	0.647000	0.38526	0.360000	0.20250	0.869000	0.35703	0.374000	0.22700	ACA	.	.		0.408	OR6C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398152.1	NM_001005182	
OR10P1	121130	hgsc.bcm.edu	37	12	56031281	56031281	+	Silent	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:56031281A>G	ENST00000309675.2	+	1	638	c.606A>G	c.(604-606)acA>acG	p.T202T	RP11-644F5.16_ENST00000556606.1_RNA	NM_206899.1	NP_996782.1	Q8NGE3	O10P1_HUMAN	olfactory receptor, family 10, subfamily P, member 1	202						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			autonomic_ganglia(1)|central_nervous_system(2)|endometrium(4)|large_intestine(3)|lung(6)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	26						CCGTGATGACAGCCACCATAG	0.562																																					p.T202T		Atlas-SNP	.											.	OR10P1	48	.	0			c.A606G						.						123.0	100.0	107.0					12																	56031281		2203	4300	6503	SO:0001819	synonymous_variant	121130	exon1			GATGACAGCCACC	BK004259	CCDS31828.1	12q13.13	2012-08-09		2004-03-10		ENSG00000175398		"""GPCR / Class A : Olfactory receptors"""	15378	protein-coding gene	gene with protein product				OR10P1P, OR10P2P, OR10P3P			Standard	NM_206899		Approved	OST701	uc010spq.2	Q8NGE3	OTTHUMG00000169961	ENST00000309675.2:c.606A>G	chr12.hg19:g.56031281A>G		77.0	0.0		87.0	4.0	NM_206899	B9EGY4	Silent	SNP	ENST00000309675.2	hg19	CCDS31828.1																																																																																			.	.		0.562	OR10P1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406680.1		
SMARCC2	6601	hgsc.bcm.edu	37	12	56565643	56565643	+	Missense_Mutation	SNP	G	G	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:56565643G>C	ENST00000267064.4	-	20	1998	c.1912C>G	c.(1912-1914)Cat>Gat	p.H638D	RP11-977G19.5_ENST00000553176.1_RNA|SMARCC2_ENST00000394023.3_Missense_Mutation_p.H669D|SMARCC2_ENST00000347471.4_Missense_Mutation_p.H669D|SMARCC2_ENST00000550164.1_Missense_Mutation_p.H669D	NM_003075.3	NP_003066.2	Q8TAQ2	SMRC2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2	638	SANT. {ECO:0000255|PROSITE- ProRule:PRU00624}.				ATP-dependent chromatin remodeling (GO:0043044)|chromatin remodeling (GO:0006338)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome disassembly (GO:0006337)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase II promoter involved in forebrain neuron fate commitment (GO:0021882)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)			breast(1)|central_nervous_system(3)|endometrium(6)|kidney(3)|large_intestine(3)|lung(20)|ovary(1)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)	41			OV - Ovarian serous cystadenocarcinoma(18;0.123)			CGAAGAAAATGCAAGATGCAC	0.547																																					p.H669D		Atlas-SNP	.											.	SMARCC2	212	.	0			c.C2005G						.						98.0	85.0	89.0					12																	56565643		2203	4300	6503	SO:0001583	missense	6601	exon21			GAAAATGCAAGAT	U66616	CCDS8907.1, CCDS8908.1, CCDS55835.1	12q13.2	2008-05-14				ENSG00000139613			11105	protein-coding gene	gene with protein product		601734				8804307, 9693044	Standard	NM_001130420		Approved	BAF170, Rsc8, CRACC2	uc001skb.3	Q8TAQ2	OTTHUMG00000170288	ENST00000267064.4:c.1912C>G	chr12.hg19:g.56565643G>C	ENSP00000267064:p.His638Asp	93.0	0.0		106.0	21.0	NM_139067	F8VTJ5|Q59GV3|Q92923|Q96E12|Q96GY4	Missense_Mutation	SNP	ENST00000267064.4	hg19	CCDS8907.1	.	.	.	.	.	.	.	.	.	.	G	23.5	4.419195	0.83559	.	.	ENSG00000139613	ENST00000394023;ENST00000550164;ENST00000347471;ENST00000267064	T;T;T;T	0.55052	0.54;0.54;0.54;0.54	3.73	3.73	0.42828	Myb, DNA-binding (1);SANT domain, DNA binding (1);Homeodomain-related (1);Homeodomain-like (1);SANT, eukarya (1);	0.000000	0.85682	D	0.000000	T	0.77974	0.4211	M	0.92880	3.355	0.58432	D	0.999999	D;D;D;D;D	0.62365	0.991;0.96;0.968;0.968;0.96	D;D;D;D;D	0.76071	0.987;0.923;0.954;0.954;0.923	D	0.84481	0.0605	10	0.87932	D	0	-8.9217	15.4916	0.75611	0.0:0.0:1.0:0.0	.	558;669;673;638;669	B4DF22;F8VTJ5;Q59G16;Q8TAQ2;Q8TAQ2-2	.;.;.;SMRC2_HUMAN;.	D	669;669;669;638	ENSP00000377591:H669D;ENSP00000449396:H669D;ENSP00000302919:H669D;ENSP00000267064:H638D	ENSP00000267064:H638D	H	-	1	0	SMARCC2	54851910	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.601000	0.98297	2.385000	0.81259	0.655000	0.94253	CAT	.	.		0.547	SMARCC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408370.1		
SHMT2	6472	hgsc.bcm.edu	37	12	57627373	57627373	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:57627373T>C	ENST00000328923.3	+	9	1503	c.1051T>C	c.(1051-1053)Tcc>Ccc	p.S351P	SHMT2_ENST00000553474.1_Missense_Mutation_p.S330P|SHMT2_ENST00000557487.1_Missense_Mutation_p.S341P|SHMT2_ENST00000449049.3_Missense_Mutation_p.S330P|SHMT2_ENST00000393827.4_Missense_Mutation_p.S255P|SHMT2_ENST00000414700.3_Missense_Mutation_p.S330P	NM_001166356.1|NM_005412.5	NP_001159828.1|NP_005403.2	P34897	GLYM_HUMAN	serine hydroxymethyltransferase 2 (mitochondrial)	351					glycine biosynthetic process from serine (GO:0019264)|L-serine biosynthetic process (GO:0006564)|one-carbon metabolic process (GO:0006730)|positive regulation of cell proliferation (GO:0008284)|protein homotetramerization (GO:0051289)|tetrahydrofolate interconversion (GO:0035999)	extracellular vesicular exosome (GO:0070062)|microtubule cytoskeleton (GO:0015630)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	amino acid binding (GO:0016597)|chromatin binding (GO:0003682)|glycine hydroxymethyltransferase activity (GO:0004372)|L-allo-threonine aldolase activity (GO:0008732)|pyridoxal phosphate binding (GO:0030170)			breast(1)|central_nervous_system(1)|large_intestine(4)|liver(2)|lung(3)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	15					Glycine(DB00145)|Tetrahydrofolic acid(DB00116)	CCGGGAGTACTCCCTGCAGGT	0.617																																					p.S351P	Esophageal Squamous(150;1369 2416 49071 49364)	Atlas-SNP	.											.	SHMT2	40	.	0			c.T1051C						.						77.0	65.0	69.0					12																	57627373		2203	4300	6503	SO:0001583	missense	6472	exon9			GAGTACTCCCTGC	AK223555	CCDS8934.1, CCDS53805.1, CCDS55837.1	12q12-q14	2006-03-27				ENSG00000182199	2.1.2.1		10852	protein-coding gene	gene with protein product		138450		SHMT		8999870	Standard	NM_005412		Approved		uc001snf.2	P34897		ENST00000328923.3:c.1051T>C	chr12.hg19:g.57627373T>C	ENSP00000333667:p.Ser351Pro	94.0	0.0		76.0	5.0	NM_005412	B7Z9F1|E7EQ19|E7EU43|O00740|Q8N1A5	Missense_Mutation	SNP	ENST00000328923.3	hg19	CCDS8934.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.30|14.30	2.494793|2.494793	0.44352|0.44352	.|.	.|.	ENSG00000182199|ENSG00000182199	ENST00000557529|ENST00000328923;ENST00000557487;ENST00000555634;ENST00000414700;ENST00000553474;ENST00000449049;ENST00000393827	.|T;T;T;T;T;T;T	.|0.44881	.|1.54;0.91;0.91;1.54;1.54;1.54;0.91	4.32|4.32	3.17|3.17	0.36434|0.36434	.|Pyridoxal phosphate-dependent transferase, major region, subdomain 2 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	.|0.252384	.|0.40064	.|N	.|0.001187	T|T	0.42314|0.42314	0.1197|0.1197	L|L	0.49126|0.49126	1.545|1.545	0.30033|0.30033	N|N	0.813261|0.813261	.|P;B;P;P;B	.|0.44478	.|0.62;0.052;0.836;0.62;0.051	.|P;B;B;P;B	.|0.46885	.|0.53;0.167;0.439;0.53;0.131	T|T	0.45948|0.45948	-0.9226|-0.9226	5|10	.|0.66056	.|D	.|0.02	-23.9224|-23.9224	9.6897|9.6897	0.40120|0.40120	0.0:0.0:0.3633:0.6366|0.0:0.0:0.3633:0.6366	.|.	.|360;341;255;282;351	.|B4DWA7;Q8N1A5;B4DLV4;B4DP88;P34897	.|.;.;.;.;GLYM_HUMAN	P|P	150|351;341;190;330;330;330;255	.|ENSP00000333667:S351P;ENSP00000452315:S341P;ENSP00000450930:S190P;ENSP00000406881:S330P;ENSP00000452419:S330P;ENSP00000413770:S330P;ENSP00000377413:S255P	.|ENSP00000333667:S351P	L|S	+|+	2|1	0|0	SHMT2|SHMT2	55913640|55913640	0.000000|0.000000	0.05858|0.05858	0.999000|0.999000	0.59377|0.59377	0.989000|0.989000	0.77384|0.77384	0.093000|0.093000	0.15086|0.15086	0.810000|0.810000	0.34279|0.34279	0.459000|0.459000	0.35465|0.35465	CTC|TCC	.	.		0.617	SHMT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412525.2	NM_005412	
CAND1	55832	hgsc.bcm.edu	37	12	67698891	67698891	+	Silent	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:67698891T>C	ENST00000545606.1	+	10	1880	c.1443T>C	c.(1441-1443)atT>atC	p.I481I		NM_018448.3	NP_060918.2	Q86VP6	CAND1_HUMAN	cullin-associated and neddylation-dissociated 1	481					cell differentiation (GO:0030154)|negative regulation of catalytic activity (GO:0043086)|positive regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0045899)|protein ubiquitination (GO:0016567)|SCF complex assembly (GO:0010265)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)				NS(1)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(10)|lung(12)|prostate(1)|skin(2)|stomach(1)	35			GBM - Glioblastoma multiforme(1;1.13e-10)|Lung(24;0.000342)|LUSC - Lung squamous cell carcinoma(43;0.196)	GBM - Glioblastoma multiforme(28;0.0279)		TAGGAATCATTTTCTCACTGA	0.348																																					p.I481I		Atlas-SNP	.											.	CAND1	100	.	0			c.T1443C						.						94.0	91.0	92.0					12																	67698891		2203	4300	6503	SO:0001819	synonymous_variant	55832	exon10			AATCATTTTCTCA		CCDS8977.1	12q14	2008-02-05			ENSG00000111530	ENSG00000111530			30688	protein-coding gene	gene with protein product	"""TBP interacting protein"""	607727				10048485, 8954946	Standard	NM_018448		Approved	TIP120A, DKFZp434M1414, KIAA0829, TIP120	uc001stn.2	Q86VP6	OTTHUMG00000169060	ENST00000545606.1:c.1443T>C	chr12.hg19:g.67698891T>C		48.0	0.0		59.0	4.0	NM_018448	B2RAU3|O94918|Q6PIY4|Q8NDJ4|Q96JZ9|Q96T19|Q9BTC4|Q9H0G2|Q9P0H7|Q9UF85	Silent	SNP	ENST00000545606.1	hg19	CCDS8977.1																																																																																			.	.		0.348	CAND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402105.1	NM_018448	
NAV3	89795	hgsc.bcm.edu	37	12	78531131	78531131	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:78531131A>G	ENST00000397909.2	+	19	4789	c.4616A>G	c.(4615-4617)gAc>gGc	p.D1539G	NAV3_ENST00000266692.7_Missense_Mutation_p.D1362G|NAV3_ENST00000228327.6_Missense_Mutation_p.D1539G|NAV3_ENST00000536525.2_Missense_Mutation_p.D1539G			Q8IVL0	NAV3_HUMAN	neuron navigator 3	1539	Ser-rich.					membrane (GO:0016020)|nuclear envelope (GO:0005635)		p.D1539G(1)		NS(2)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(13)|kidney(16)|large_intestine(39)|liver(2)|lung(126)|ovary(5)|pancreas(3)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(1)	236						TCATTCAGAGACAGCATGGAA	0.468										HNSCC(70;0.22)																											p.D1539G		Atlas-SNP	.											NAV3,larynx,carcinoma,0,1	NAV3	506	.	1	Substitution - Missense(1)	upper_aerodigestive_tract(1)	c.A4616G						.						82.0	80.0	81.0					12																	78531131		1904	4130	6034	SO:0001583	missense	89795	exon19			TCAGAGACAGCAT	AB023155	CCDS41815.1, CCDS66432.1	12q14.3	2008-08-05				ENSG00000067798			15998	protein-coding gene	gene with protein product	"""pore membrane and/or filament interacting like protein 1"", ""steerin 3"""	611629				12079279, 12062803	Standard	XM_005269215		Approved	KIAA0938, POMFIL1	uc001syo.3	Q8IVL0	OTTHUMG00000170001	ENST00000397909.2:c.4616A>G	chr12.hg19:g.78531131A>G	ENSP00000381007:p.Asp1539Gly	31.0	0.0		39.0	2.0	NM_014903	Q8NFW7|Q9Y2E7	Missense_Mutation	SNP	ENST00000397909.2	hg19		.	.	.	.	.	.	.	.	.	.	A	25.2	4.612702	0.87258	.	.	ENSG00000067798	ENST00000536525;ENST00000397909;ENST00000228327;ENST00000266692;ENST00000378640;ENST00000550788	T;T;T;T;T	0.38077	1.16;1.18;1.21;1.3;2.18	5.87	5.87	0.94306	.	0.000000	0.41938	U	0.000792	T	0.56630	0.1998	L	0.54323	1.7	0.80722	D	1	P;D;D;D	0.89917	0.942;0.996;1.0;1.0	P;D;D;D	0.87578	0.636;0.993;0.998;0.998	T	0.56469	-0.7974	10	0.54805	T	0.06	-21.8703	16.2736	0.82632	1.0:0.0:0.0:0.0	.	1539;1362;1539;1539	E7EUC6;Q8IVL0-3;Q8IVL0;Q8IVL0-2	.;.;NAV3_HUMAN;.	G	1539;1539;1539;1362;160;168	ENSP00000446132:D1539G;ENSP00000381007:D1539G;ENSP00000228327:D1539G;ENSP00000266692:D1362G;ENSP00000448303:D168G	ENSP00000228327:D1539G	D	+	2	0	NAV3	77055262	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	8.963000	0.93385	2.247000	0.74100	0.477000	0.44152	GAC	.	.		0.468	NAV3-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000406812.1	NM_001024383	
FGD6	55785	hgsc.bcm.edu	37	12	95604472	95604472	+	Silent	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:95604472A>G	ENST00000343958.4	-	2	811	c.588T>C	c.(586-588)tcT>tcC	p.S196S	FGD6_ENST00000549499.1_Silent_p.S196S|FGD6_ENST00000546711.1_Silent_p.S196S|FGD6_ENST00000550368.1_5'Flank	NM_018351.3	NP_060821.3	Q6ZV73	FGD6_HUMAN	FYVE, RhoGEF and PH domain containing 6	196					actin cytoskeleton organization (GO:0030036)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)			breast(3)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(14)|liver(1)|lung(12)|ovary(3)|prostate(3)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	56						GCTTCTGTGCAGAAATAAAAG	0.438																																					p.S196S		Atlas-SNP	.											.	FGD6	127	.	0			c.T588C						.						90.0	84.0	86.0					12																	95604472		2203	4300	6503	SO:0001819	synonymous_variant	55785	exon2			CTGTGCAGAAATA	AB037783	CCDS31878.1	12q23.1	2013-01-10				ENSG00000180263		"""Zinc fingers, FYVE domain containing"", ""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	21740	protein-coding gene	gene with protein product		613520					Standard	NM_018351		Approved	ZFYVE24, FLJ11183	uc001tdp.4	Q6ZV73	OTTHUMG00000170133	ENST00000343958.4:c.588T>C	chr12.hg19:g.95604472A>G		131.0	0.0		146.0	6.0	NM_018351	Q6ZR53|Q7Z2Z7|Q96D44|Q9NUR8|Q9P2I5	Silent	SNP	ENST00000343958.4	hg19	CCDS31878.1																																																																																			.	.		0.438	FGD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407600.1	NM_018351	
APAF1	317	hgsc.bcm.edu	37	12	99042548	99042548	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:99042548T>C	ENST00000551964.1	+	3	1019	c.283T>C	c.(283-285)Tct>Cct	p.S95P	APAF1_ENST00000552268.1_Missense_Mutation_p.S95P|APAF1_ENST00000333991.1_Missense_Mutation_p.S95P|APAF1_ENST00000547743.1_Missense_Mutation_p.S95P|APAF1_ENST00000547045.1_Missense_Mutation_p.S95P|APAF1_ENST00000359972.2_Missense_Mutation_p.S95P|APAF1_ENST00000339433.3_Missense_Mutation_p.S95P|APAF1_ENST00000550527.1_Missense_Mutation_p.S95P|APAF1_ENST00000549007.1_Missense_Mutation_p.S95P|APAF1_ENST00000357310.1_Missense_Mutation_p.S95P	NM_181861.1	NP_863651.1	O14727	APAF_HUMAN	apoptotic peptidase activating factor 1	95	Poly-Ser.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c (GO:0008635)|apoptotic process (GO:0006915)|forebrain development (GO:0030900)|intrinsic apoptotic signaling pathway (GO:0097193)|nervous system development (GO:0007399)|neural tube closure (GO:0001843)|neuron apoptotic process (GO:0051402)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|regulation of apoptotic DNA fragmentation (GO:1902510)|regulation of apoptotic process (GO:0042981)|response to G1 DNA damage checkpoint signaling (GO:0072432)	apoptosome (GO:0043293)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|nucleotide binding (GO:0000166)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(13)|liver(1)|lung(15)|ovary(2)|prostate(2)|skin(1)	42					Adenosine triphosphate(DB00171)	TCCTGTTGTCTCTTCTTCCAG	0.358																																					p.S95P		Atlas-SNP	.											.	APAF1	111	.	0			c.T283C						.						204.0	201.0	202.0					12																	99042548		2203	4300	6503	SO:0001583	missense	317	exon3			GTTGTCTCTTCTT	AF013263	CCDS9069.1, CCDS9070.1, CCDS9071.1, CCDS55862.1, CCDS55863.1	12q23	2013-01-10	2006-10-23			ENSG00000120868		"""WD repeat domain containing"""	576	protein-coding gene	gene with protein product		602233	"""apoptotic protease activating factor"", ""apoptotic peptidase activating factor"""			9267021, 10702682	Standard	NM_181861		Approved	CED4, APAF-1	uc001tfz.3	O14727	OTTHUMG00000170214	ENST00000551964.1:c.283T>C	chr12.hg19:g.99042548T>C	ENSP00000448165:p.Ser95Pro	111.0	0.0		151.0	7.0	NM_001160	B2RMX8|O43297|Q7Z438|Q9BXZ6|Q9UBZ5|Q9UGN8|Q9UGN9|Q9UGP0|Q9UJ58|Q9UJ59|Q9UJ60|Q9UJ61|Q9UJ62|Q9UJ63|Q9UJ64|Q9UJ65|Q9UJ66|Q9UJ67|Q9UNC9	Missense_Mutation	SNP	ENST00000551964.1	hg19	CCDS9069.1	.	.	.	.	.	.	.	.	.	.	T	17.07	3.294126	0.60086	.	.	ENSG00000120868	ENST00000551964;ENST00000359972;ENST00000357310;ENST00000339433;ENST00000333991;ENST00000547743;ENST00000552268;ENST00000550527;ENST00000547045;ENST00000549007	T;T;T;T;T;T;T	0.61040	0.17;0.26;0.26;0.37;0.14;0.26;0.37	5.23	1.15	0.20763	DEATH-like (1);	0.679445	0.15917	N	0.238328	T	0.61974	0.2390	L	0.54323	1.7	0.09310	N	0.999999	P;P;P;P;D	0.63880	0.948;0.922;0.908;0.928;0.993	P;P;P;P;D	0.73708	0.62;0.804;0.641;0.641;0.981	T	0.49041	-0.8980	10	0.37606	T	0.19	-2.8146	1.7186	0.02907	0.1368:0.1485:0.1425:0.5723	.	95;95;95;95;95	O14727-6;O14727-4;O14727-3;O14727;O14727-2	.;.;.;APAF_HUMAN;.	P	95	ENSP00000448165:S95P;ENSP00000353059:S95P;ENSP00000349862:S95P;ENSP00000341830:S95P;ENSP00000448449:S95P;ENSP00000449791:S95P;ENSP00000448161:S95P	ENSP00000334558:S95P	S	+	1	0	APAF1	97566679	0.856000	0.29760	0.216000	0.23742	0.950000	0.60333	1.201000	0.32259	0.341000	0.23771	0.533000	0.62120	TCT	.	.		0.358	APAF1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408006.1	NM_181861.1	
WSCD2	9671	hgsc.bcm.edu	37	12	108589990	108589990	+	Splice_Site	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:108589990A>G	ENST00000332082.4	+	3	1199	c.381A>G	c.(379-381)cgA>cgG	p.R127R	WSCD2_ENST00000549903.1_Splice_Site_p.R127R|WSCD2_ENST00000547525.1_Splice_Site_p.R127R|WSCD2_ENST00000261400.3_Splice_Site_p.R127R			Q2TBF2	WSCD2_HUMAN	WSC domain containing 2	127	WSC 1. {ECO:0000255|PROSITE- ProRule:PRU00558}.					integral component of membrane (GO:0016021)				breast(4)|endometrium(3)|kidney(1)|large_intestine(16)|liver(2)|lung(23)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	57						AGGAAGAGCGAGGTAAGAGCG	0.542																																					p.R127R		Atlas-SNP	.											.	WSCD2	125	.	0			c.A381G						.						26.0	28.0	27.0					12																	108589990		1988	4153	6141	SO:0001630	splice_region_variant	9671	exon2			AGAGCGAGGTAAG		CCDS41828.1	12q23.3	2008-02-05				ENSG00000075035			29117	protein-coding gene	gene with protein product							Standard	NM_014653		Approved	KIAA0789	uc001tms.3	Q2TBF2		ENST00000332082.4:c.382+1A>G	chr12.hg19:g.108589990A>G		56.0	0.0		71.0	5.0	NM_014653	B2RN48|B4DES1|Q8IY35|Q9Y4B7	Silent	SNP	ENST00000332082.4	hg19	CCDS41828.1																																																																																			.	.		0.542	WSCD2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405554.1	NM_014653	Silent
ANAPC7	51434	hgsc.bcm.edu	37	12	110826388	110826388	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:110826388T>C	ENST00000455511.3	-	4	551	c.551A>G	c.(550-552)cAg>cGg	p.Q184R	RP11-478C19.2_ENST00000550231.1_RNA|ANAPC7_ENST00000450008.2_Missense_Mutation_p.Q184R	NM_016238.2	NP_057322.2	Q9UJX3	APC7_HUMAN	anaphase promoting complex subunit 7	184				Q -> R (in Ref. 1; AAF05754). {ECO:0000305}.	anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein phosphatase binding (GO:0019903)			breast(3)|endometrium(3)|kidney(1)|large_intestine(5)|lung(6)|prostate(1)	19						AGGGCGCTCCTGACCAGCCTT	0.443																																					p.Q184R		Atlas-SNP	.											.	ANAPC7	68	.	0			c.A551G						.						130.0	112.0	118.0					12																	110826388		2203	4300	6503	SO:0001583	missense	51434	exon4			CGCTCCTGACCAG	AF191340	CCDS9145.2, CCDS44971.1	12q13.12	2013-01-10			ENSG00000196510	ENSG00000196510		"""Anaphase promoting complex subunits"", ""Tetratricopeptide (TTC) repeat domain containing"""	17380	protein-coding gene	gene with protein product		606949					Standard	NM_016238		Approved	APC7	uc001tqo.2	Q9UJX3	OTTHUMG00000157009	ENST00000455511.3:c.551A>G	chr12.hg19:g.110826388T>C	ENSP00000394394:p.Gln184Arg	87.0	0.0		98.0	4.0	NM_016238	Q96AC4|Q96GF4|Q9BU24|Q9NT16	Missense_Mutation	SNP	ENST00000455511.3	hg19	CCDS9145.2	.	.	.	.	.	.	.	.	.	.	T	22.6	4.310656	0.81358	.	.	ENSG00000196510;ENSG00000196510;ENSG00000258210	ENST00000455511;ENST00000450008;ENST00000550231	T;T	0.73258	1.27;-0.73	5.74	5.74	0.90152	Tetratricopeptide-like helical (1);	0.000000	0.85682	D	0.000000	T	0.73697	0.3620	L	0.34521	1.04	0.80722	D	1	P;P	0.48294	0.908;0.753	P;B	0.61397	0.888;0.316	T	0.68108	-0.5496	10	0.13108	T	0.6	-19.9339	16.0294	0.80567	0.0:0.0:0.0:1.0	.	184;184	Q9UJX3-2;Q9UJX3	.;APC7_HUMAN	R	184;184;83	ENSP00000394394:Q184R;ENSP00000402314:Q184R	ENSP00000402314:Q184R	Q	-	2	0	RP11-478C19.2;ANAPC7	109310771	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.698000	0.84413	2.185000	0.69588	0.455000	0.32223	CAG	.	.		0.443	ANAPC7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347075.3	NM_016238	
TMEM116	89894	hgsc.bcm.edu	37	12	112374971	112374971	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:112374971T>C	ENST00000550831.3	-	6	534	c.166A>G	c.(166-168)Agc>Ggc	p.S56G	TMEM116_ENST00000355445.3_Missense_Mutation_p.S113G|TMEM116_ENST00000437003.2_Missense_Mutation_p.S56G|TMEM116_ENST00000549537.2_Missense_Mutation_p.E8G|TMEM116_ENST00000354825.3_Missense_Mutation_p.S56G|TMEM116_ENST00000552374.2_Missense_Mutation_p.S148G	NM_138341.2	NP_612350.1	Q8NCL8	TM116_HUMAN	transmembrane protein 116	56						integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(3)|lung(2)|ovary(1)|skin(1)	8						TACTTGTGGCTCTGACTGAAG	0.368																																					p.S148G		Atlas-SNP	.											.	TMEM116	17	.	0			c.A442G						.						139.0	148.0	145.0					12																	112374971		2203	4300	6503	SO:0001583	missense	89894	exon7			TGTGGCTCTGACT	AK074648	CCDS9157.1, CCDS55886.1, CCDS55887.1	12q24.13	2012-03-02			ENSG00000198270	ENSG00000198270			25084	protein-coding gene	gene with protein product						12477932	Standard	NM_001193453		Approved	FLJ90167	uc001ttd.2	Q8NCL8	OTTHUMG00000169606	ENST00000550831.3:c.166A>G	chr12.hg19:g.112374971T>C	ENSP00000450377:p.Ser56Gly	108.0	0.0		120.0	5.0	NM_001193531	G3V1W7|G5E985|Q6NSH5|Q8IZ66	Missense_Mutation	SNP	ENST00000550831.3	hg19	CCDS9157.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	t|t	5.843|5.843	0.339846|0.339846	0.11069|0.11069	.|.	.|.	ENSG00000198270|ENSG00000198270	ENST00000549537|ENST00000355445;ENST00000354825;ENST00000550831;ENST00000437003;ENST00000552374;ENST00000550037	.|T;T;T;T;T;T	.|0.47528	.|1.24;1.24;1.24;1.24;1.24;0.84	4.9|4.9	4.9|4.9	0.64082|0.64082	.|.	.|0.568027	.|0.19459	.|N	.|0.113751	T|T	0.43299|0.43299	0.1241|0.1241	L|L	0.48642|0.48642	1.525|1.525	0.27114|0.27114	N|N	0.962309|0.962309	D|B;B;P;B	0.76494|0.35272	0.999|0.105;0.313;0.493;0.177	D|B;B;B;B	0.68943|0.40702	0.961|0.131;0.165;0.338;0.09	T|T	0.32719|0.32719	-0.9896|-0.9896	7|10	.|0.22706	.|T	.|0.39	-0.762|-0.762	9.823|9.823	0.40894|0.40894	0.0:0.0:0.1726:0.8274|0.0:0.0:0.1726:0.8274	.|.	8|148;113;148;56	G3V1Z3|F8VNZ8;G5E985;G3V1W7;Q8NCL8	.|.;.;.;TM116_HUMAN	G|G	8|113;56;56;56;148;148	.|ENSP00000347620:S113G;ENSP00000346883:S56G;ENSP00000450377:S56G;ENSP00000395861:S56G;ENSP00000447731:S148G;ENSP00000446516:S148G	.|ENSP00000346883:S56G	E|S	-|-	2|1	0|0	TMEM116|TMEM116	110859354|110859354	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.076000|0.076000	0.17211|0.17211	4.105000|4.105000	0.57797|0.57797	1.848000|1.848000	0.53677|0.53677	0.383000|0.383000	0.25322|0.25322	GAG|AGC	.	.		0.368	TMEM116-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405026.3	NM_138341	
SUDS3	64426	hgsc.bcm.edu	37	12	118838515	118838515	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:118838515A>G	ENST00000543473.1	+	7	881	c.569A>G	c.(568-570)aAt>aGt	p.N190S	SUDS3_ENST00000397564.2_Missense_Mutation_p.N191S	NM_022491.2	NP_071936.2	Q9H7L9	SDS3_HUMAN	suppressor of defective silencing 3 homolog (S. cerevisiae)	190	Sin3 interaction domain (SID). {ECO:0000250|UniProtKB:Q8BR65}.				apoptotic process (GO:0006915)|histone deacetylation (GO:0016575)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|substantia nigra development (GO:0021762)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|Sin3 complex (GO:0016580)	enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)			breast(1)|lung(1)	2	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					AGGCGACCAAATGATCCCGTC	0.458																																					p.N190S		Atlas-SNP	.											.	SUDS3	26	.	0			c.A569G						.						128.0	126.0	126.0					12																	118838515		1889	4110	5999	SO:0001583	missense	64426	exon7			GACCAAATGATCC	AK023801	CCDS44993.1	12q24.23	2006-02-13	2006-02-13		ENSG00000111707	ENSG00000111707			29545	protein-coding gene	gene with protein product	"""sin3A-associated protein, 45kDa"""	608250	"""suppressor of defective silencing 3 homolog (SDS3, S. cerevisiae)"""			11909966	Standard	NM_022491		Approved	SDS3, FLJ00052, SAP45	uc001twz.3	Q9H7L9	OTTHUMG00000168884	ENST00000543473.1:c.569A>G	chr12.hg19:g.118838515A>G	ENSP00000443988:p.Asn190Ser	85.0	0.0		97.0	4.0	NM_022491	Q4KMQ5|Q8N6H0|Q9H8D2	Missense_Mutation	SNP	ENST00000543473.1	hg19	CCDS44993.1	.	.	.	.	.	.	.	.	.	.	A	16.70	3.195064	0.58017	.	.	ENSG00000111707	ENST00000543473;ENST00000397564	.	.	.	4.82	4.82	0.62117	.	0.000000	0.85682	D	0.000000	T	0.78298	0.4261	M	0.80183	2.485	0.80722	D	1	D	0.57257	0.979	D	0.71414	0.973	T	0.78578	-0.2150	9	0.35671	T	0.21	.	14.3469	0.66672	1.0:0.0:0.0:0.0	.	190	Q9H7L9	SDS3_HUMAN	S	190;191	.	ENSP00000380695:N191S	N	+	2	0	SUDS3	117322898	1.000000	0.71417	0.999000	0.59377	0.954000	0.61252	8.887000	0.92456	1.928000	0.55862	0.402000	0.26972	AAT	.	.		0.458	SUDS3-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401504.1	NM_022491	
DNAH10	196385	hgsc.bcm.edu	37	12	124413861	124413861	+	Missense_Mutation	SNP	A	A	G	rs537787991		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:124413861A>G	ENST00000409039.3	+	70	12017	c.11992A>G	c.(11992-11994)Agg>Ggg	p.R3998G	CCDC92_ENST00000544798.1_Intron|DNAH10OS_ENST00000514254.2_3'UTR	NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	3998	AAA 6. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		ACTCAACATGAGGGCAACTTA	0.537													A|||	1	0.000199681	0.0	0.0014	5008	,	,		20013	0.0		0.0	False		,,,				2504	0.0				p.R3998G		Atlas-SNP	.											.	DNAH10	888	.	0			c.A11992G						.						38.0	39.0	38.0					12																	124413861		2046	4198	6244	SO:0001583	missense	196385	exon70			AACATGAGGGCAA	AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"""Axonemal dyneins"""	2941	protein-coding gene	gene with protein product		605884	"""dynein, axonemal, heavy polypeptide 10"""				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.11992A>G	chr12.hg19:g.124413861A>G	ENSP00000386770:p.Arg3998Gly	83.0	0.0		98.0	6.0	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	hg19	CCDS9255.2	.	.	.	.	.	.	.	.	.	.	A	19.51	3.841923	0.71488	.	.	ENSG00000197653	ENST00000409039	T	0.08984	3.03	5.16	1.02	0.19986	Dynein heavy chain (1);	0.000000	0.85682	D	0.000000	T	0.30198	0.0757	M	0.87900	2.915	0.80722	D	1	D	0.76494	0.999	D	0.76575	0.988	T	0.20306	-1.0279	10	0.35671	T	0.21	.	14.6974	0.69132	0.6009:0.3991:0.0:0.0	.	3998	Q8IVF4	DYH10_HUMAN	G	3998	ENSP00000386770:R3998G	ENSP00000386770:R3998G	R	+	1	2	DNAH10	122979814	1.000000	0.71417	0.996000	0.52242	0.955000	0.61496	1.788000	0.38714	0.324000	0.23333	0.482000	0.46254	AGG	.	.		0.537	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3		
POLE	5426	hgsc.bcm.edu	37	12	133249252	133249252	+	Silent	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:133249252A>G	ENST00000320574.5	-	15	1690	c.1647T>C	c.(1645-1647)tcT>tcC	p.S549S	POLE_ENST00000535270.1_Silent_p.S522S	NM_006231.2	NP_006222.2	Q07864	DPOE1_HUMAN	polymerase (DNA directed), epsilon, catalytic subunit	549					base-excision repair, gap-filling (GO:0006287)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA synthesis involved in DNA repair (GO:0000731)|G1/S transition of mitotic cell cycle (GO:0000082)|in utero embryonic development (GO:0001701)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	cytoplasm (GO:0005737)|epsilon DNA polymerase complex (GO:0008622)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|nucleotide binding (GO:0000166)|zinc ion binding (GO:0008270)			NS(2)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(41)|ovary(3)|pancreas(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	89	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0416)		OV - Ovarian serous cystadenocarcinoma(86;5.22e-08)|Epithelial(86;4.03e-07)|all cancers(50;1.18e-05)	Cladribine(DB00242)	GGAAAACCCCAGACTCGAGGG	0.572								DNA polymerases (catalytic subunits)																													p.S549S		Atlas-SNP	.											.	POLE	416	.	0			c.T1647C						.						97.0	98.0	98.0					12																	133249252		2203	4300	6503	SO:0001819	synonymous_variant	5426	exon15			AACCCCAGACTCG		CCDS9278.1	12q24.3	2014-09-17	2012-05-18		ENSG00000177084	ENSG00000177084		"""DNA polymerases"""	9177	protein-coding gene	gene with protein product	"""DNA polymerase epsilon catalytic subunit A"""	174762	"""polymerase (DNA directed), epsilon"""			8020968	Standard	NM_006231		Approved	POLE1	uc001uks.1	Q07864	OTTHUMG00000168045	ENST00000320574.5:c.1647T>C	chr12.hg19:g.133249252A>G		73.0	0.0		54.0	4.0	NM_006231	Q13533|Q86VH9	Silent	SNP	ENST00000320574.5	hg19	CCDS9278.1																																																																																			.	.		0.572	POLE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397689.2	NM_006231	
ANKLE2	23141	hgsc.bcm.edu	37	12	133310972	133310972	+	Splice_Site	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:133310972A>G	ENST00000357997.5	-	10	1979	c.1890T>C	c.(1888-1890)tcT>tcC	p.S630S	ANKLE2_ENST00000542657.1_5'Flank|ANKLE2_ENST00000337516.5_Splice_Site_p.S630S|ANKLE2_ENST00000542282.1_5'Flank|ANKLE2_ENST00000542374.1_5'UTR|ANKLE2_ENST00000539605.1_Splice_Site_p.S568S	NM_015114.1	NP_055929.1	Q86XL3	ANKL2_HUMAN	ankyrin repeat and LEM domain containing 2	630					mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope reassembly (GO:0007084)|negative regulation of phosphorylation (GO:0042326)|positive regulation of protein dephosphorylation (GO:0035307)|regulation of catalytic activity (GO:0050790)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)	protein phosphatase 2A binding (GO:0051721)|protein phosphatase type 2A regulator activity (GO:0008601)			NS(2)|autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(4)|lung(20)|ovary(1)|urinary_tract(2)	45	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0176)|Lung NSC(355;0.204)		OV - Ovarian serous cystadenocarcinoma(86;2.3e-08)|Epithelial(86;1.56e-07)|all cancers(50;4.94e-06)		CATGCTTACCAGACGTGGTGG	0.542																																					p.S630S		Atlas-SNP	.											.	ANKLE2	76	.	0			c.T1890C						.						93.0	100.0	98.0					12																	133310972		1987	4159	6146	SO:0001630	splice_region_variant	23141	exon10			CTTACCAGACGTG	AB014592	CCDS41869.1	12q24.33	2013-01-11	2008-03-25	2008-03-25	ENSG00000176915	ENSG00000176915		"""Ankyrin repeat domain containing"""	29101	protein-coding gene	gene with protein product	"""LEM domain containing 7"""		"""KIAA0692"""	KIAA0692		9734811	Standard	XM_005266159		Approved	LEMD7, Lem4	uc001ukx.2	Q86XL3	OTTHUMG00000168046	ENST00000357997.5:c.1891+1T>C	chr12.hg19:g.133310972A>G		70.0	0.0		93.0	4.0	NM_015114	A8KAG3|B3KN97|B3KSF8|O75176|Q6P6A5|Q8TAZ9|Q96DH4	Silent	SNP	ENST00000357997.5	hg19	CCDS41869.1																																																																																			.	.		0.542	ANKLE2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397712.1		Silent
RNF17	56163	hgsc.bcm.edu	37	13	25363884	25363884	+	Silent	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr13:25363884A>G	ENST00000255324.5	+	9	961	c.909A>G	c.(907-909)ggA>ggG	p.G303G	RNF17_ENST00000381921.1_Silent_p.G303G|RNF17_ENST00000255325.6_Silent_p.G303G|RNF17_ENST00000255326.4_3'UTR	NM_001184993.1|NM_031277.2	NP_001171922.1|NP_112567.2	Q9BXT8	RNF17_HUMAN	ring finger protein 17	303					multicellular organismal development (GO:0007275)|spermatid development (GO:0007286)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	hydrolase activity, acting on ester bonds (GO:0016788)|nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(15)|ovary(1)|prostate(3)|skin(6)	36		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0114)|OV - Ovarian serous cystadenocarcinoma(117;0.0311)|Epithelial(112;0.0524)		ACAATATGGGAAAGATTGAAT	0.303																																					p.G303G		Atlas-SNP	.											.	RNF17	259	.	0			c.A909G						.						160.0	162.0	161.0					13																	25363884		2203	4296	6499	SO:0001819	synonymous_variant	56163	exon9			TATGGGAAAGATT	AF285602, AK001907	CCDS9308.2	13q12.13	2013-01-23			ENSG00000132972	ENSG00000132972		"""RING-type (C3HC4) zinc fingers"", ""Tudor domain containing"""	10060	protein-coding gene	gene with protein product	"""spermatogenesis associated 23"""	605793	"""tudor domain containing 4"""	TDRD4		11279525	Standard	NM_001184993		Approved	Mmip-2, SPATA23, FLJ11045	uc001upr.3	Q9BXT8	OTTHUMG00000016589	ENST00000255324.5:c.909A>G	chr13.hg19:g.25363884A>G		59.0	0.0		86.0	4.0	NM_001184993	Q5T2J9|Q6P1W3|Q9BXT7|Q9NUY9	Silent	SNP	ENST00000255324.5	hg19	CCDS9308.2																																																																																			.	.		0.303	RNF17-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044217.1	NM_031994	
VWA8	23078	hgsc.bcm.edu	37	13	42263625	42263625	+	Silent	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr13:42263625A>G	ENST00000379310.3	-	34	4064	c.3996T>C	c.(3994-3996)ccT>ccC	p.P1332P	VWA8_ENST00000478987.1_5'UTR	NM_015058.1	NP_055873.1	A3KMH1	VWA8_HUMAN	von Willebrand factor A domain containing 8	1332						extracellular region (GO:0005576)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)										AAATTTTATGAGGTATGCTGA	0.348																																					p.P1332P		Atlas-SNP	.											.	.	.	.	0			c.T3996C						.						89.0	80.0	83.0					13																	42263625		1823	4086	5909	SO:0001819	synonymous_variant	23078	exon34			TTTATGAGGTATG	AB011136	CCDS31963.1, CCDS41881.1	13q14.11	2013-11-18	2012-08-02	2012-08-02	ENSG00000102763	ENSG00000102763			29071	protein-coding gene	gene with protein product			"""KIAA0564"""	KIAA0564		9628581	Standard	NM_015058		Approved		uc001uyj.3	A3KMH1	OTTHUMG00000016799	ENST00000379310.3:c.3996T>C	chr13.hg19:g.42263625A>G		62.0	0.0		82.0	4.0	NM_015058	O60310|Q5JTP6|Q5VW08|Q7Z6I9|Q86YC9|Q8N3E4	Silent	SNP	ENST00000379310.3	hg19	CCDS41881.1																																																																																			.	.		0.348	VWA8-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354828.2	NM_015058	
RCBTB1	55213	hgsc.bcm.edu	37	13	50118925	50118925	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr13:50118925A>G	ENST00000378302.2	-	10	1380	c.1120T>C	c.(1120-1122)Ttt>Ctt	p.F374L	RCBTB1_ENST00000258646.3_Missense_Mutation_p.F374L	NM_018191.3	NP_060661.3	Q8NDN9	RCBT1_HUMAN	regulator of chromosome condensation (RCC1) and BTB (POZ) domain containing protein 1	374	BTB 1. {ECO:0000255|PROSITE- ProRule:PRU00037}.				cell cycle (GO:0007049)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|prostate(1)|urinary_tract(1)	16		Lung NSC(96;2.1e-05)|Breast(56;0.00015)|Prostate(109;0.00314)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;4.7e-09)		TCAATTCGAAACTTCAGATCA	0.328																																					p.F374L		Atlas-SNP	.											.	RCBTB1	34	.	0			c.T1120C						.						106.0	97.0	100.0					13																	50118925		2202	4300	6502	SO:0001583	missense	55213	exon10			TTCGAAACTTCAG	AF334406	CCDS9418.1	13q14	2013-01-08			ENSG00000136144	ENSG00000136144		"""BTB/POZ domain containing"""	18243	protein-coding gene	gene with protein product		607867				11306461	Standard	XM_005266441		Approved	FLJ10716, CLLD7, CLLL7	uc001vde.1	Q8NDN9	OTTHUMG00000016915	ENST00000378302.2:c.1120T>C	chr13.hg19:g.50118925A>G	ENSP00000367552:p.Phe374Leu	72.0	0.0		88.0	4.0	NM_018191	Q8IY29|Q969U9	Missense_Mutation	SNP	ENST00000378302.2	hg19	CCDS9418.1	.	.	.	.	.	.	.	.	.	.	A	29.4	5.001329	0.93227	.	.	ENSG00000136144	ENST00000258646;ENST00000378302	T;T	0.62498	0.02;0.02	5.44	5.44	0.79542	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.000000	0.85682	D	0.000000	T	0.70456	0.3226	L	0.53671	1.685	0.80722	D	1	P	0.51933	0.949	P	0.56648	0.803	T	0.69624	-0.5095	10	0.37606	T	0.19	-18.7715	15.5123	0.75793	1.0:0.0:0.0:0.0	.	374	Q8NDN9	RCBT1_HUMAN	L	374	ENSP00000258646:F374L;ENSP00000367552:F374L	ENSP00000258646:F374L	F	-	1	0	RCBTB1	49016926	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	8.962000	0.93254	2.056000	0.61249	0.528000	0.53228	TTT	.	.		0.328	RCBTB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044912.2	NM_018191	
PIBF1	10464	hgsc.bcm.edu	37	13	73482702	73482702	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr13:73482702T>C	ENST00000326291.6	+	12	1860	c.1522T>C	c.(1522-1524)Tct>Cct	p.S508P		NM_006346.2	NP_006337.2	Q8WXW3	PIBF1_HUMAN	progesterone immunomodulatory binding factor 1	508						centrosome (GO:0005813)				breast(2)|endometrium(2)|kidney(1)|large_intestine(1)|lung(10)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	24		Prostate(6;0.00191)|Breast(118;0.0736)|Acute lymphoblastic leukemia(28;0.0865)		GBM - Glioblastoma multiforme(99;0.000664)		TCTCCAAGCCTCTTCTGAAAA	0.348																																					p.S508P		Atlas-SNP	.											.	PIBF1	65	.	0			c.T1522C						.						61.0	61.0	61.0					13																	73482702		2203	4300	6503	SO:0001583	missense	10464	exon12			CAAGCCTCTTCTG	AF330046	CCDS31991.1	13q21.33	2014-02-20	2007-10-17	2007-10-17	ENSG00000083535	ENSG00000083535			23352	protein-coding gene	gene with protein product	"""progesterone-induced blocking factor 1"""	607532	"""chromosome 13 open reading frame 24"""	C13orf24		11935316	Standard	NM_006346		Approved	CEP90	uc001vjc.3	Q8WXW3	OTTHUMG00000017071	ENST00000326291.6:c.1522T>C	chr13.hg19:g.73482702T>C	ENSP00000317144:p.Ser508Pro	55.0	0.0		95.0	7.0	NM_006346	O95664|Q6U9V2|Q6UG50|Q86V07|Q96SF4	Missense_Mutation	SNP	ENST00000326291.6	hg19	CCDS31991.1	.	.	.	.	.	.	.	.	.	.	T	15.34	2.805039	0.50315	.	.	ENSG00000083535	ENST00000326291	T	0.55930	0.49	5.73	5.73	0.89815	.	0.176258	0.52532	D	0.000070	T	0.57066	0.2028	M	0.68593	2.085	0.49687	D	0.999811	P;P	0.51537	0.946;0.946	P;P	0.49012	0.598;0.598	T	0.59968	-0.7354	10	0.45353	T	0.12	-3.9568	9.9198	0.41457	0.2621:0.0:0.0:0.7379	.	508;508	Q8WXW3;Q4G0R1	PIBF1_HUMAN;.	P	508	ENSP00000317144:S508P	ENSP00000317144:S508P	S	+	1	0	PIBF1	72380703	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.944000	0.49034	2.179000	0.69175	0.528000	0.53228	TCT	.	.		0.348	PIBF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045255.1	NM_006346	
KLF5	688	hgsc.bcm.edu	37	13	73636093	73636093	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr13:73636093T>C	ENST00000377687.4	+	2	892	c.356T>C	c.(355-357)gTc>gCc	p.V119A	KLF5_ENST00000539231.1_Missense_Mutation_p.V28A|KLF5_ENST00000477333.1_3'UTR	NM_001730.3	NP_001721.2	Q13887	KLF5_HUMAN	Kruppel-like factor 5 (intestinal)	119					angiogenesis (GO:0001525)|cellular response to organic cyclic compound (GO:0071407)|cellular response to peptide (GO:1901653)|intestinal epithelial cell development (GO:0060576)|microvillus assembly (GO:0030033)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of microvillus assembly (GO:0032534)|skeletal muscle cell differentiation (GO:0035914)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(1)|endometrium(2)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		Prostate(6;0.00187)|Breast(118;0.0735)		GBM - Glioblastoma multiforme(99;0.0011)		AGTGCCTCAGTCGTAGACCAG	0.438																																					p.V119A		Atlas-SNP	.											.	KLF5	59	.	0			c.T356C						.						186.0	172.0	177.0					13																	73636093		2203	4300	6503	SO:0001583	missense	688	exon2			CCTCAGTCGTAGA	D14520	CCDS9448.1, CCDS66562.1	13q21.3	2013-01-08			ENSG00000102554	ENSG00000102554		"""Kruppel-like transcription factors"", ""Zinc fingers, C2H2-type"""	6349	protein-coding gene	gene with protein product		602903		BTEB2		8479902, 9973612	Standard	NM_001730		Approved	IKLF, CKLF	uc001vje.3	Q13887	OTTHUMG00000017074	ENST00000377687.4:c.356T>C	chr13.hg19:g.73636093T>C	ENSP00000366915:p.Val119Ala	83.0	0.0		100.0	4.0	NM_001730	L0R3U5|L0R4T9|Q9UHP8	Missense_Mutation	SNP	ENST00000377687.4	hg19	CCDS9448.1	.	.	.	.	.	.	.	.	.	.	T	12.65	2.002916	0.35320	.	.	ENSG00000102554	ENST00000539231;ENST00000377687;ENST00000545883	T;T	0.09350	3.24;2.99	6.04	6.04	0.98038	.	0.437392	0.26432	N	0.024416	T	0.13072	0.0317	L	0.55990	1.75	0.31999	N	0.603602	B	0.30406	0.278	B	0.30179	0.112	T	0.06058	-1.0848	10	0.42905	T	0.14	.	12.4367	0.55602	0.0:0.0:0.1397:0.8603	.	119	Q13887	KLF5_HUMAN	A	28;119;99	ENSP00000440407:V28A;ENSP00000366915:V119A	ENSP00000366915:V119A	V	+	2	0	KLF5	72534094	0.998000	0.40836	0.999000	0.59377	0.995000	0.86356	2.434000	0.44802	2.317000	0.78254	0.460000	0.39030	GTC	.	.		0.438	KLF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045263.1		
KLF5	688	hgsc.bcm.edu	37	13	73650024	73650024	+	Nonstop_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr13:73650024A>G	ENST00000377687.4	+	4	1910	c.1374A>G	c.(1372-1374)tgA>tgG	p.*458W	KLF5_ENST00000539231.1_Nonstop_Mutation_p.*367W	NM_001730.3	NP_001721.2	Q13887	KLF5_HUMAN	Kruppel-like factor 5 (intestinal)	0					angiogenesis (GO:0001525)|cellular response to organic cyclic compound (GO:0071407)|cellular response to peptide (GO:1901653)|intestinal epithelial cell development (GO:0060576)|microvillus assembly (GO:0030033)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of microvillus assembly (GO:0032534)|skeletal muscle cell differentiation (GO:0035914)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(1)|endometrium(2)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		Prostate(6;0.00187)|Breast(118;0.0735)		GBM - Glioblastoma multiforme(99;0.0011)		ACCAGAACTGAGCACTGCCCG	0.547																																					p.X458W		Atlas-SNP	.											.	KLF5	59	.	0			c.A1374G						.						38.0	34.0	36.0					13																	73650024		2203	4299	6502	SO:0001578	stop_lost	688	exon4			GAACTGAGCACTG	D14520	CCDS9448.1, CCDS66562.1	13q21.3	2013-01-08			ENSG00000102554	ENSG00000102554		"""Kruppel-like transcription factors"", ""Zinc fingers, C2H2-type"""	6349	protein-coding gene	gene with protein product		602903		BTEB2		8479902, 9973612	Standard	NM_001730		Approved	IKLF, CKLF	uc001vje.3	Q13887	OTTHUMG00000017074	ENST00000377687.4:c.1374A>G	chr13.hg19:g.73650024A>G	ENSP00000366915:p.*458Trpext*5	70.0	0.0		91.0	4.0	NM_001730	L0R3U5|L0R4T9|Q9UHP8	Missense_Mutation	SNP	ENST00000377687.4	hg19	CCDS9448.1	.	.	.	.	.	.	.	.	.	.	A	14.43	2.533803	0.45073	.	.	ENSG00000102554	ENST00000539231;ENST00000377687;ENST00000545883	.	.	.	5.47	5.47	0.80525	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.7963	0.40737	0.8767:0.0:0.1233:0.0	.	.	.	.	W	367;458;438	.	.	X	+	3	0	KLF5	72548025	1.000000	0.71417	0.997000	0.53966	0.855000	0.48748	2.990000	0.49401	2.057000	0.61298	0.533000	0.62120	TGA	.	.		0.547	KLF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045263.1		
LMO7	4008	hgsc.bcm.edu	37	13	76381924	76381924	+	Missense_Mutation	SNP	G	G	A	rs369620389		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr13:76381924G>A	ENST00000321797.8	+	8	1527	c.806G>A	c.(805-807)tGt>tAt	p.C269Y	LMO7_ENST00000357063.3_Missense_Mutation_p.C554Y|LMO7_ENST00000377534.3_Missense_Mutation_p.C554Y|LMO7_ENST00000341547.4_Intron|LMO7_ENST00000526202.1_Intron|LMO7_ENST00000465261.2_Missense_Mutation_p.C269Y|RP11-29G8.3_ENST00000563635.1_RNA			Q8WWI1	LMO7_HUMAN	LIM domain 7	554					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(20)|lung(15)|ovary(2)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	56		Breast(118;0.0992)		GBM - Glioblastoma multiforme(99;0.0109)		ATTTTACAGTGTAGAGAAGGT	0.433																																					p.C269Y		Atlas-SNP	.											.	LMO7	334	.	0			c.G806A						.						91.0	90.0	90.0					13																	76381924		1568	3582	5150	SO:0001583	missense	4008	exon7			TACAGTGTAGAGA	AF092557	CCDS9454.1, CCDS53876.1	13q22.2	2008-02-05	2004-06-15		ENSG00000136153	ENSG00000136153			6646	protein-coding gene	gene with protein product	"""F-box only protein 20"""	604362	"""LIM domain only 7"""	FBXO20		9826547, 10531035	Standard	NM_005358		Approved	FBX20, KIAA0858	uc021rkq.1	Q8WWI1	OTTHUMG00000017093	ENST00000321797.8:c.806G>A	chr13.hg19:g.76381924G>A	ENSP00000317802:p.Cys269Tyr	54.0	0.0		91.0	5.0	NM_015842	E9PLH4|O15462|O95346|Q5TBK6|Q9UKC1|Q9UQM5|Q9Y6A7	Missense_Mutation	SNP	ENST00000321797.8	hg19		.	.	.	.	.	.	.	.	.	.	G	5.512	0.279477	0.10458	.	.	ENSG00000136153	ENST00000357063;ENST00000377534;ENST00000321797;ENST00000465261	T;T;T;T	0.53640	0.61;0.61;0.61;0.61	5.53	4.45	0.53987	.	0.403718	0.26692	N	0.022982	T	0.31167	0.0788	L	0.47716	1.5	0.09310	N	0.99999	P;P	0.41265	0.744;0.744	B;B	0.30943	0.122;0.122	T	0.27226	-1.0080	10	0.30854	T	0.27	-15.7611	6.5405	0.22377	0.1286:0.3545:0.5169:0.0	.	554;269	Q8WWI1;E9PLH4	LMO7_HUMAN;.	Y	554;554;269;269	ENSP00000349571:C554Y;ENSP00000366757:C554Y;ENSP00000317802:C269Y;ENSP00000433352:C269Y	ENSP00000317802:C269Y	C	+	2	0	LMO7	75279925	0.070000	0.21116	0.992000	0.48379	0.984000	0.73092	0.622000	0.24433	2.756000	0.94617	0.655000	0.94253	TGT	.	.		0.433	LMO7-005	PUTATIVE	alternative_5_UTR|not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000045301.3	NM_005358	
SLITRK6	84189	hgsc.bcm.edu	37	13	86369434	86369434	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr13:86369434C>T	ENST00000400286.2	-	2	1808	c.1210G>A	c.(1210-1212)Gaa>Aaa	p.E404K		NM_032229.2	NP_115605.2	Q9H5Y7	SLIK6_HUMAN	SLIT and NTRK-like family, member 6	404					adult locomotory behavior (GO:0008344)|auditory behavior (GO:0031223)|auditory receptor cell morphogenesis (GO:0002093)|axonogenesis (GO:0007409)|cochlea development (GO:0090102)|innervation (GO:0060384)|lens development in camera-type eye (GO:0002088)|linear vestibuloocular reflex (GO:0060007)|multicellular organism growth (GO:0035264)|sensory perception of sound (GO:0007605)|startle response (GO:0001964)|synapse assembly (GO:0007416)|vestibulocochlear nerve development (GO:0021562)|visual perception (GO:0007601)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)				breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(18)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_neural(89;0.117)|Medulloblastoma(90;0.163)			GBM - Glioblastoma multiforme(99;0.0456)		AACGATCCTTCTTCAAGAACT	0.353																																					p.E404K		Atlas-SNP	.											.	SLITRK6	150	.	0			c.G1210A						.						74.0	69.0	71.0					13																	86369434		1846	4091	5937	SO:0001583	missense	84189	exon2			ATCCTTCTTCAAG	AK026427	CCDS41903.1	13q31.1	2006-04-12			ENSG00000184564	ENSG00000184564			23503	protein-coding gene	gene with protein product		609681				14557068	Standard	NM_032229		Approved	FLJ22774	uc001vll.1	Q9H5Y7	OTTHUMG00000017157	ENST00000400286.2:c.1210G>A	chr13.hg19:g.86369434C>T	ENSP00000383143:p.Glu404Lys	40.0	0.0		107.0	15.0	NM_032229	A8K9S8|Q495Q0|Q6AW93|Q9HAA8|Q9NT60	Missense_Mutation	SNP	ENST00000400286.2	hg19	CCDS41903.1	.	.	.	.	.	.	.	.	.	.	C	15.39	2.820070	0.50633	.	.	ENSG00000184564	ENST00000400286	T	0.02421	4.3	5.76	5.76	0.90799	.	0.151890	0.43747	U	0.000536	T	0.07234	0.0183	L	0.31371	0.925	0.52501	D	0.999956	D	0.53312	0.959	P	0.57846	0.828	T	0.54925	-0.8220	10	0.23302	T	0.38	-12.071	18.5388	0.91020	0.0:1.0:0.0:0.0	.	404	Q9H5Y7	SLIK6_HUMAN	K	404	ENSP00000383143:E404K	ENSP00000383143:E404K	E	-	1	0	SLITRK6	85267435	1.000000	0.71417	1.000000	0.80357	0.914000	0.54420	5.956000	0.70315	2.724000	0.93272	0.585000	0.79938	GAA	.	.		0.353	SLITRK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045404.2	NM_032229	
BIVM	54841	hgsc.bcm.edu	37	13	103486900	103486900	+	Silent	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr13:103486900A>G	ENST00000257336.1	+	9	1798	c.1119A>G	c.(1117-1119)aaA>aaG	p.K373K	BIVM_ENST00000419638.1_3'UTR|BIVM-ERCC5_ENST00000602836.1_Missense_Mutation_p.K345E|BIVM_ENST00000448849.2_Silent_p.K144K	NM_017693.3	NP_060163.2	Q86UB2	BIVM_HUMAN	basic, immunoglobulin-like variable motif containing	373						cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleus (GO:0005634)				endometrium(3)|kidney(2)|large_intestine(7)|lung(10)|skin(2)|urinary_tract(1)	25	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.211)					TTCACTGTAAAAAGTATGTTA	0.308																																					p.K373K		Atlas-SNP	.											.	.	.	.	0			c.A1119G						.						120.0	117.0	118.0					13																	103486900		2203	4299	6502	SO:0001819	synonymous_variant	0	exon7			CTGTAAAAAGTAT	AF411385	CCDS9505.1, CCDS53879.1	13q33.1	2008-05-14			ENSG00000134897	ENSG00000134897			16034	protein-coding gene	gene with protein product						12036287	Standard	NM_017693		Approved	FLJ20159		Q86UB2	OTTHUMG00000017309	ENST00000257336.1:c.1119A>G	chr13.hg19:g.103486900A>G		59.0	0.0		99.0	4.0	NM_001204425	Q2M1J2|Q9NXM4	Silent	SNP	ENST00000257336.1	hg19	CCDS9505.1																																																																																			.	.		0.308	BIVM-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045704.2		
OR11G2	390439	hgsc.bcm.edu	37	14	20665742	20665742	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:20665742T>C	ENST00000357366.3	+	1	248	c.248T>C	c.(247-249)aTc>aCc	p.I83T		NM_001005503.1	NP_001005503.1	Q8NGC1	O11G2_HUMAN	olfactory receptor, family 11, subfamily G, member 2	83						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|kidney(1)|large_intestine(4)|lung(7)|ovary(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	22	all_cancers(95;0.00108)		Epithelial(56;9.76e-07)|all cancers(55;5.61e-06)	GBM - Glioblastoma multiforme(265;0.0144)		AATGGTTCCATCATCTGTGCT	0.542																																					p.I83T		Atlas-SNP	.											.	OR11G2	73	.	0			c.T248C						.						122.0	99.0	107.0					14																	20665742		2203	4300	6503	SO:0001583	missense	390439	exon1			GTTCCATCATCTG		CCDS32032.1	14q11.2	2013-09-24			ENSG00000196832	ENSG00000196832		"""GPCR / Class A : Olfactory receptors"""	15346	protein-coding gene	gene with protein product							Standard	NM_001005503		Approved		uc010tlb.2	Q8NGC1	OTTHUMG00000167700	ENST00000357366.3:c.248T>C	chr14.hg19:g.20665742T>C	ENSP00000349930:p.Ile83Thr	110.0	0.0		105.0	5.0	NM_001005503	Q6IF09|Q96R33	Missense_Mutation	SNP	ENST00000357366.3	hg19	CCDS32032.1	.	.	.	.	.	.	.	.	.	.	t	17.07	3.294964	0.60086	.	.	ENSG00000196832	ENST00000357366	T	0.00531	6.76	4.53	4.53	0.55603	GPCR, rhodopsin-like superfamily (1);	0.000000	0.44285	U	0.000461	T	0.02267	0.0070	M	0.90145	3.09	0.27370	N	0.955714	D	0.89917	1.0	D	0.80764	0.994	T	0.05099	-1.0906	10	0.87932	D	0	.	12.9846	0.58583	0.0:0.0:0.0:1.0	.	83	Q8NGC1	O11G2_HUMAN	T	83	ENSP00000349930:I83T	ENSP00000349930:I83T	I	+	2	0	OR11G2	19735582	0.819000	0.29175	0.999000	0.59377	0.977000	0.68977	3.110000	0.50352	1.900000	0.55004	0.454000	0.30748	ATC	.	.		0.542	OR11G2-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395722.1		
OR6S1	341799	hgsc.bcm.edu	37	14	21109487	21109487	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:21109487C>T	ENST00000320704.3	-	1	363	c.364G>A	c.(364-366)Gcg>Acg	p.A122T		NM_001001968.1	NP_001001968.1	Q8NH40	OR6S1_HUMAN	olfactory receptor, family 6, subfamily S, member 1	122						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			kidney(1)|large_intestine(3)|lung(13)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	23	all_cancers(95;0.00304)		Epithelial(56;1.23e-06)|all cancers(55;1.01e-05)	GBM - Glioblastoma multiforme(265;0.0135)		TAGCGATCCGCAGACATGACA	0.542																																					p.A122T		Atlas-SNP	.											.	OR6S1	49	.	0			c.G364A						.						93.0	81.0	85.0					14																	21109487		2203	4300	6503	SO:0001583	missense	341799	exon1			GATCCGCAGACAT	AL163636	CCDS32038.1	14q11.2	2013-09-24			ENSG00000181803	ENSG00000181803		"""GPCR / Class A : Olfactory receptors"""	15363	protein-coding gene	gene with protein product							Standard	NM_001001968		Approved	OR6S1Q	uc001vxv.1	Q8NH40	OTTHUMG00000171010	ENST00000320704.3:c.364G>A	chr14.hg19:g.21109487C>T	ENSP00000313110:p.Ala122Thr	114.0	0.0		117.0	23.0	NM_001001968	Q6IFJ9	Missense_Mutation	SNP	ENST00000320704.3	hg19	CCDS32038.1	.	.	.	.	.	.	.	.	.	.	C	14.45	2.539756	0.45176	.	.	ENSG00000181803	ENST00000320704	T	0.01335	5.0	5.46	3.52	0.40303	GPCR, rhodopsin-like superfamily (1);	0.313169	0.22962	N	0.053534	T	0.01092	0.0036	N	0.14661	0.345	0.22305	N	0.999211	B	0.06786	0.001	B	0.04013	0.001	T	0.46898	-0.9158	10	0.87932	D	0	-5.6108	6.3811	0.21536	0.2803:0.6321:0.0:0.0876	.	122	Q8NH40	OR6S1_HUMAN	T	122	ENSP00000313110:A122T	ENSP00000313110:A122T	A	-	1	0	OR6S1	20179327	0.000000	0.05858	1.000000	0.80357	0.972000	0.66771	0.882000	0.28186	1.439000	0.47511	-0.140000	0.14226	GCG	.	.		0.542	OR6S1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411227.1		
HECTD1	25831	hgsc.bcm.edu	37	14	31575935	31575935	+	Silent	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:31575935T>C	ENST00000399332.1	-	38	7631	c.7143A>G	c.(7141-7143)gaA>gaG	p.E2381E	HECTD1_ENST00000553700.1_Silent_p.E2381E	NM_015382.2	NP_056197.2	Q9ULT8	HECD1_HUMAN	HECT domain containing E3 ubiquitin protein ligase 1	2381	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				neural tube closure (GO:0001843)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|metal ion binding (GO:0046872)|ubiquitin-protein transferase activity (GO:0004842)			breast(10)|endometrium(7)|kidney(5)|large_intestine(12)|lung(23)|ovary(4)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	70	Hepatocellular(127;0.0877)|Breast(36;0.176)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.111)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00617)		TCTTCTCATCTTCAGAAAGAC	0.378																																					p.E2381E		Atlas-SNP	.											.	HECTD1	159	.	0			c.A7143G						.						104.0	95.0	98.0					14																	31575935		1842	4097	5939	SO:0001819	synonymous_variant	25831	exon38			CTCATCTTCAGAA	AB032957	CCDS41939.1	14q12	2013-01-10	2012-02-23		ENSG00000092148	ENSG00000092148		"""Ankyrin repeat domain containing"""	20157	protein-coding gene	gene with protein product			"""HECT domain containing 1"""			10574461	Standard	XM_005267502		Approved	KIAA1131	uc001wrc.1	Q9ULT8	OTTHUMG00000170670	ENST00000399332.1:c.7143A>G	chr14.hg19:g.31575935T>C		82.0	0.0		95.0	4.0	NM_015382	D3DS86|Q6P445|Q86VJ1|Q96F34|Q9UFZ7	Silent	SNP	ENST00000399332.1	hg19	CCDS41939.1	.	.	.	.	.	.	.	.	.	.	T	6.222	0.409153	0.11812	.	.	ENSG00000092148	ENST00000554882;ENST00000399323	.	.	.	5.81	5.81	0.92471	.	.	.	.	.	T	0.39064	0.1064	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.24261	-1.0165	5	0.07990	T	0.79	-13.609	10.4936	0.44764	0.0:0.0722:0.0:0.9278	.	.	.	.	R	747;5	.	ENSP00000382263:K5R	K	-	2	0	HECTD1	30645686	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.137000	0.50562	2.210000	0.71456	0.533000	0.62120	AAG	.	.		0.378	HECTD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409942.1		
HECTD1	25831	hgsc.bcm.edu	37	14	31626433	31626433	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:31626433C>T	ENST00000399332.1	-	11	2187	c.1699G>A	c.(1699-1701)Gat>Aat	p.D567N	HECTD1_ENST00000553700.1_Missense_Mutation_p.D567N	NM_015382.2	NP_056197.2	Q9ULT8	HECD1_HUMAN	HECT domain containing E3 ubiquitin protein ligase 1	567					neural tube closure (GO:0001843)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|metal ion binding (GO:0046872)|ubiquitin-protein transferase activity (GO:0004842)			breast(10)|endometrium(7)|kidney(5)|large_intestine(12)|lung(23)|ovary(4)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	70	Hepatocellular(127;0.0877)|Breast(36;0.176)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.111)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00617)		TGACCAACATCAGAATCACAA	0.338																																					p.D567N		Atlas-SNP	.											.	HECTD1	159	.	0			c.G1699A						.						167.0	159.0	162.0					14																	31626433		1852	4095	5947	SO:0001583	missense	25831	exon11			CAACATCAGAATC	AB032957	CCDS41939.1	14q12	2013-01-10	2012-02-23		ENSG00000092148	ENSG00000092148		"""Ankyrin repeat domain containing"""	20157	protein-coding gene	gene with protein product			"""HECT domain containing 1"""			10574461	Standard	XM_005267502		Approved	KIAA1131	uc001wrc.1	Q9ULT8	OTTHUMG00000170670	ENST00000399332.1:c.1699G>A	chr14.hg19:g.31626433C>T	ENSP00000382269:p.Asp567Asn	194.0	0.0		186.0	70.0	NM_015382	D3DS86|Q6P445|Q86VJ1|Q96F34|Q9UFZ7	Missense_Mutation	SNP	ENST00000399332.1	hg19	CCDS41939.1	.	.	.	.	.	.	.	.	.	.	C	18.24	3.580644	0.65992	.	.	ENSG00000092148	ENST00000553700;ENST00000261312;ENST00000399332;ENST00000553957;ENST00000556224	T;T;T;T	0.64991	-0.13;-0.13;1.44;-0.13	6.17	6.17	0.99709	Armadillo-like helical (1);Armadillo-type fold (1);	0.089401	0.85682	N	0.000000	T	0.54271	0.1848	N	0.22421	0.69	0.80722	D	1	B;B	0.27498	0.008;0.18	B;B	0.27796	0.004;0.083	T	0.50320	-0.8842	10	0.54805	T	0.06	-19.9409	20.8794	0.99867	0.0:1.0:0.0:0.0	.	567;567	D3DS86;Q9ULT8	.;HECD1_HUMAN	N	567;567;567;41;567	ENSP00000450697:D567N;ENSP00000382269:D567N;ENSP00000451860:D41N;ENSP00000452015:D567N	ENSP00000261312:D567N	D	-	1	0	HECTD1	30696184	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.070000	0.71220	2.941000	0.99782	0.655000	0.94253	GAT	.	.		0.338	HECTD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409942.1		
NPAS3	64067	hgsc.bcm.edu	37	14	33684760	33684760	+	Intron	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:33684760T>C	ENST00000356141.4	+	3	385				NPAS3_ENST00000551492.1_Intron|NPAS3_ENST00000346562.2_Intron|NPAS3_ENST00000548645.1_Intron|NPAS3_ENST00000357798.5_Missense_Mutation_p.S105P|NPAS3_ENST00000551008.1_Intron|NPAS3_ENST00000547068.1_Intron|NPAS3_ENST00000341321.4_Intron			Q8IXF0	NPAS3_HUMAN	neuronal PAS domain protein 3						locomotory behavior (GO:0007626)|maternal behavior (GO:0042711)|positive regulation of transcription, DNA-templated (GO:0045893)|startle response (GO:0001964)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)			breast(4)|endometrium(3)|kidney(1)|large_intestine(6)|liver(2)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	40	Breast(36;0.0102)|Hepatocellular(127;0.133)		LUAD - Lung adenocarcinoma(48;0.00169)|Lung(238;0.00968)	GBM - Glioblastoma multiforme(1;1.31e-09)|all cancers(1;0.000112)|OV - Ovarian serous cystadenocarcinoma(311;0.115)		AATGTGGAAATCTGAACTCTG	0.333																																					p.S105P		Atlas-SNP	.											.	NPAS3	266	.	0			c.T313C						.						92.0	100.0	97.0					14																	33684760		2165	4280	6445	SO:0001627	intron_variant	64067	exon3			TGGAAATCTGAAC	AF164438	CCDS9645.1, CCDS53891.1, CCDS53892.1, CCDS55912.1	14q13.1	2013-08-23			ENSG00000151322	ENSG00000151322		"""Basic helix-loop-helix proteins"""	19311	protein-coding gene	gene with protein product		609430					Standard	NM_022123		Approved	MOP6, PASD6, bHLHe12	uc001wru.3	Q8IXF0	OTTHUMG00000140215	ENST00000356141.4:c.385+128T>C	chr14.hg19:g.33684760T>C		83.0	0.0		97.0	4.0	NM_173159	Q86US6|Q86US7|Q8IXF2|Q9BY81|Q9H323|Q9Y4L8	Missense_Mutation	SNP	ENST00000356141.4	hg19	CCDS53891.1	.	.	.	.	.	.	.	.	.	.	T	16.22	3.062697	0.55432	.	.	ENSG00000151322	ENST00000357798	T	0.07021	3.23	5.95	5.95	0.96441	.	.	.	.	.	T	0.23532	0.0569	.	.	.	0.80722	D	1	D	0.64830	0.994	P	0.59889	0.865	T	0.00286	-1.1847	8	0.41790	T	0.15	.	14.978	0.71289	0.0:0.0:0.0:1.0	.	105	Q8IXF0-3	.	P	105	ENSP00000350446:S105P	ENSP00000350446:S105P	S	+	1	0	NPAS3	32754511	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.771000	0.68881	2.272000	0.75746	0.460000	0.39030	TCT	.	.		0.333	NPAS3-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276645.1		
PPP2R3C	55012	hgsc.bcm.edu	37	14	35554856	35554856	+	Silent	SNP	C	C	T			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:35554856C>T	ENST00000261475.5	-	13	1655	c.1302G>A	c.(1300-1302)gaG>gaA	p.E434E		NM_017917.2	NP_060387.2	Q969Q6	P2R3C_HUMAN	protein phosphatase 2, regulatory subunit B'', gamma	434					activation of protein kinase activity (GO:0032147)|B cell homeostasis (GO:0001782)|positive regulation of B cell differentiation (GO:0045579)|regulation of antimicrobial humoral response (GO:0002759)|regulation of mitochondrial depolarization (GO:0051900)|spleen development (GO:0048536)|T cell homeostasis (GO:0043029)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			central_nervous_system(1)|kidney(1)|large_intestine(8)|lung(4)|ovary(1)	15	Breast(36;0.0545)|Hepatocellular(127;0.158)|Prostate(35;0.184)		Lung(238;8.62e-06)|LUAD - Lung adenocarcinoma(48;1.42e-05)|Epithelial(34;0.0177)|all cancers(34;0.0491)	GBM - Glioblastoma multiforme(112;0.0803)		CCTCTCTGTTCTCGTAAGTCC	0.383																																					p.E434E		Atlas-SNP	.											.	PPP2R3C	44	.	0			c.G1302A						.						137.0	128.0	131.0					14																	35554856		2203	4300	6503	SO:0001819	synonymous_variant	55012	exon13			TCTGTTCTCGTAA	AK000651	CCDS9654.1	14q13.2	2010-06-18	2010-06-18	2007-01-22	ENSG00000092020	ENSG00000092020		"""Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"""	17485	protein-coding gene	gene with protein product		615902	"""chromosome 14 open reading frame 10"", ""protein phosphatase 2 (formerly 2A), regulatory subunit B'', gamma"""	C14orf10		12167160, 16129705	Standard	NM_017917		Approved	FLJ20644, G4-1, G5PR	uc001wss.3	Q969Q6	OTTHUMG00000140224	ENST00000261475.5:c.1302G>A	chr14.hg19:g.35554856C>T		110.0	0.0		86.0	4.0	NM_017917	B4DEN7|D3DS97|D3DS98|Q5GJ55|Q5GJ56|Q6P4G2|Q86TZ3|Q9NWR9	Silent	SNP	ENST00000261475.5	hg19	CCDS9654.1																																																																																			.	.		0.383	PPP2R3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276687.1	NM_017917	
FBXO33	254170	hgsc.bcm.edu	37	14	39868748	39868748	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:39868748T>C	ENST00000298097.7	-	4	1977	c.1640A>G	c.(1639-1641)gAg>gGg	p.E547G		NM_203301.3	NP_976046.1	Q7Z6M2	FBX33_HUMAN	F-box protein 33	547					protein ubiquitination (GO:0016567)					endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(4)|urinary_tract(1)	9	Hepatocellular(127;0.213)		LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00121)|Epithelial(34;0.169)	GBM - Glioblastoma multiforme(112;0.0425)		GCTTTGCATCTCTCTGTAAAA	0.403																																					p.E547G		Atlas-SNP	.											.	FBXO33	21	.	0			c.A1640G						.						80.0	70.0	73.0					14																	39868748		2203	4300	6503	SO:0001583	missense	254170	exon4			TGCATCTCTCTGT	BI460761	CCDS9677.1	14q13.3	2004-08-24	2004-06-15		ENSG00000165355	ENSG00000165355		"""F-boxes /  ""other"""""	19833	protein-coding gene	gene with protein product		609103	"""F-box only protein 33"""				Standard	NM_203301		Approved	Fbx33	uc001wvk.3	Q7Z6M2	OTTHUMG00000140257	ENST00000298097.7:c.1640A>G	chr14.hg19:g.39868748T>C	ENSP00000298097:p.Glu547Gly	179.0	0.0		125.0	5.0	NM_203301	Q6PIR2|Q86TR2|Q86YE0	Missense_Mutation	SNP	ENST00000298097.7	hg19	CCDS9677.1	.	.	.	.	.	.	.	.	.	.	T	16.84	3.234378	0.58886	.	.	ENSG00000165355	ENST00000298097	T	0.51071	0.72	5.85	5.85	0.93711	.	0.000000	0.85682	D	0.000000	T	0.54967	0.1891	N	0.24115	0.695	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	T	0.53229	-0.8468	9	.	.	.	-16.3324	16.2271	0.82306	0.0:0.0:0.0:1.0	.	547	Q7Z6M2	FBX33_HUMAN	G	547	ENSP00000298097:E547G	.	E	-	2	0	FBXO33	38938499	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.422000	0.80217	2.234000	0.73211	0.460000	0.39030	GAG	.	.		0.403	FBXO33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276769.2		
CDKL1	8814	hgsc.bcm.edu	37	14	50805678	50805678	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:50805678T>C	ENST00000216378.2	-	7	1372	c.728A>G	c.(727-729)gAc>gGc	p.D243G	CDKL1_ENST00000356146.1_5'UTR|CDKL1_ENST00000395834.1_Missense_Mutation_p.D243G	NM_001282236.1	NP_001269165.1	Q00532	CDKL1_HUMAN	cyclin-dependent kinase-like 1 (CDC2-related kinase)	242	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				heart development (GO:0007507)|protein phosphorylation (GO:0006468)|regulation of cell cycle (GO:0051726)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)			endometrium(1)|large_intestine(4)|lung(5)|ovary(1)|stomach(1)	12	all_epithelial(31;0.000746)|Breast(41;0.0102)					ATCTTCAGGGTCTGGAATTTT	0.473																																					p.D243G		Atlas-SNP	.											.	CDKL1	50	.	0			c.A728G						.						207.0	204.0	205.0					14																	50805678		2203	4300	6503	SO:0001583	missense	8814	exon6			TCAGGGTCTGGAA	AF390028	CCDS9699.1, CCDS73637.1	14q21.3	2011-11-04			ENSG00000100490	ENSG00000100490		"""Cyclin-dependent kinases"""	1781	protein-coding gene	gene with protein product		603441				1639063, 7595554	Standard	XM_005268157		Approved	KKIALRE	uc010anu.2	Q00532	OTTHUMG00000140290	ENST00000216378.2:c.728A>G	chr14.hg19:g.50805678T>C	ENSP00000216378:p.Asp243Gly	96.0	0.0		117.0	7.0	NM_004196	Q2M3A4|Q6QUA0|Q8WXQ5	Missense_Mutation	SNP	ENST00000216378.2	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	18.37|18.37	3.608466|3.608466	0.66558|0.66558	.|.	.|.	ENSG00000100490|ENSG00000100490	ENST00000395834;ENST00000216378|ENST00000525911	T;T|.	0.42131|.	0.98;0.98|.	5.23|5.23	5.23|5.23	0.72850|0.72850	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);|.	.|.	.|.	.|.	.|.	T|T	0.52821|0.52821	0.1758|0.1758	N|N	0.25031|0.25031	0.7|0.7	0.80722|0.80722	D|D	1|1	D;B|.	0.63880|.	0.993;0.009|.	P;B|.	0.60789|.	0.879;0.102|.	T|T	0.49615|0.49615	-0.8921|-0.8921	9|5	0.52906|.	T|.	0.07|.	.|.	15.8314|15.8314	0.78757|0.78757	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	914;242|.	Q00532-2;Q00532|.	.;CDKL1_HUMAN|.	G|A	243|24	ENSP00000379176:D243G;ENSP00000216378:D243G|.	ENSP00000216378:D243G|.	D|T	-|-	2|1	0|0	CDKL1|CDKL1	49875428|49875428	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.984000|0.984000	0.73092|0.73092	7.858000|7.858000	0.86971|0.86971	2.279000|2.279000	0.76181|0.76181	0.533000|0.533000	0.62120|0.62120	GAC|ACC	.	.		0.473	CDKL1-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000382103.1		
MAP4K5	11183	hgsc.bcm.edu	37	14	50889884	50889884	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:50889884T>C	ENST00000013125.4	-	31	2726	c.2408A>G	c.(2407-2409)gAg>gGg	p.E803G		NM_006575.4|NM_198794.2	NP_006566.2|NP_942089.1	Q9Y4K4	M4K5_HUMAN	mitogen-activated protein kinase kinase kinase kinase 5	803	CNH. {ECO:0000255|PROSITE- ProRule:PRU00795}.				activation of JUN kinase activity (GO:0007257)|intracellular signal transduction (GO:0035556)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	15	all_epithelial(31;0.000415)|Breast(41;0.0102)					ATCTGAAATCTCCTGGGTAAC	0.308																																					p.E803G		Atlas-SNP	.											.	MAP4K5	48	.	0			c.A2408G						.						50.0	49.0	49.0					14																	50889884		1807	4065	5872	SO:0001583	missense	11183	exon31			GAAATCTCCTGGG	U77129		14q11.2-q21	2011-06-09				ENSG00000012983		"""Mitogen-activated protein kinase cascade / Kinase kinase kinase kinases"""	6867	protein-coding gene	gene with protein product	"""germinal center kinase-related"""	604923				9038372, 8274451	Standard	NM_198794		Approved	KHS1, GCKR, KHS	uc001wyb.3	Q9Y4K4		ENST00000013125.4:c.2408A>G	chr14.hg19:g.50889884T>C	ENSP00000013125:p.Glu803Gly	74.0	0.0		113.0	5.0	NM_006575	Q8IYF6	Missense_Mutation	SNP	ENST00000013125.4	hg19		.	.	.	.	.	.	.	.	.	.	T	26.2	4.718108	0.89205	.	.	ENSG00000012983	ENST00000013125	T	0.05855	3.38	5.64	5.64	0.86602	Citron-like (3);	0.000000	0.85682	D	0.000000	T	0.30854	0.0778	M	0.86740	2.835	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.992;0.996	T	0.12400	-1.0549	10	0.87932	D	0	.	15.8718	0.79127	0.0:0.0:0.0:1.0	.	803;803	B2R928;Q9Y4K4	.;M4K5_HUMAN	G	803	ENSP00000013125:E803G	ENSP00000013125:E803G	E	-	2	0	MAP4K5	49959634	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.624000	0.83124	2.160000	0.67779	0.528000	0.53228	GAG	.	.		0.308	MAP4K5-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000410880.1	NM_006575	
SYNE2	23224	hgsc.bcm.edu	37	14	64460661	64460661	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:64460661A>G	ENST00000344113.4	+	22	2967	c.2755A>G	c.(2755-2757)Agt>Ggt	p.S919G	SYNE2_ENST00000554584.1_Missense_Mutation_p.S919G|SYNE2_ENST00000358025.3_Missense_Mutation_p.S919G|SYNE2_ENST00000357395.3_5'UTR	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	919					centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)			NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		AGAAGAAAAGAGTAGAGATGT	0.348																																					p.S919G		Atlas-SNP	.											.	SYNE2	577	.	0			c.A2755G						.						115.0	111.0	113.0					14																	64460661		1865	4100	5965	SO:0001583	missense	23224	exon22			GAAAAGAGTAGAG	AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"""nuclear envelope spectrin repeat-2"", ""nucleus and actin connecting element"""	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.2755A>G	chr14.hg19:g.64460661A>G	ENSP00000341781:p.Ser919Gly	83.0	0.0		124.0	5.0	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Missense_Mutation	SNP	ENST00000344113.4	hg19	CCDS41963.1	.	.	.	.	.	.	.	.	.	.	A	10.89	1.477194	0.26511	.	.	ENSG00000054654	ENST00000358025;ENST00000344113;ENST00000554584;ENST00000261678	T;T;T	0.59083	0.66;0.66;0.29	5.1	5.1	0.69264	.	0.108697	0.39985	N	0.001216	T	0.67144	0.2862	L	0.53249	1.67	0.80722	D	1	D;D	0.60160	0.978;0.987	P;P	0.59171	0.717;0.853	T	0.70368	-0.4891	10	0.66056	D	0.02	.	13.1187	0.59314	1.0:0.0:0.0:0.0	.	919;919	Q8WXH0;Q8WXH0-2	SYNE2_HUMAN;.	G	919	ENSP00000350719:S919G;ENSP00000341781:S919G;ENSP00000452570:S919G	ENSP00000261678:S919G	S	+	1	0	SYNE2	63530414	1.000000	0.71417	0.981000	0.43875	0.083000	0.17756	2.730000	0.47335	1.921000	0.55644	0.460000	0.39030	AGT	.	.		0.348	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914	
LTBP2	4053	hgsc.bcm.edu	37	14	74976066	74976066	+	Splice_Site	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:74976066T>C	ENST00000261978.4	-	22	3664	c.3278A>G	c.(3277-3279)gAc>gGc	p.D1093G	LTBP2_ENST00000556690.1_Splice_Site_p.D1093G	NM_000428.2	NP_000419.1	Q14767	LTBP2_HUMAN	latent transforming growth factor beta binding protein 2	1093	Cys-rich.|EGF-like 10; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				protein secretion (GO:0009306)|protein targeting (GO:0006605)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)			breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(9)|liver(1)|lung(29)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58				BRCA - Breast invasive adenocarcinoma(234;0.00219)|READ - Rectum adenocarcinoma(1;0.0649)		CTCATCTAGGTCTGCAGACAG	0.667																																					p.D1093G		Atlas-SNP	.											.	LTBP2	158	.	0			c.A3278G						.						57.0	65.0	62.0					14																	74976066		2203	4300	6503	SO:0001630	splice_region_variant	4053	exon22			TCTAGGTCTGCAG		CCDS9831.1	14q24.3	2011-10-20	2001-12-04			ENSG00000119681		"""Latent transforming growth factor, beta binding proteins"""	6715	protein-coding gene	gene with protein product		602091	"""chromosome 14 open reading frame 141"""	LTBP3, C14orf141		7798248	Standard	NM_000428		Approved		uc001xqa.3	Q14767		ENST00000261978.4:c.3278-1A>G	chr14.hg19:g.74976066T>C		112.0	0.0		109.0	5.0	NM_000428	Q99907|Q9NS51	Missense_Mutation	SNP	ENST00000261978.4	hg19	CCDS9831.1	.	.	.	.	.	.	.	.	.	.	T	25.4	4.636580	0.87760	.	.	ENSG00000119681	ENST00000261978;ENST00000556690	D;D	0.99060	-5.38;-5.38	5.31	5.31	0.75309	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);	0.000000	0.42294	D	0.000738	D	0.99149	0.9706	H	0.95982	3.75	0.53005	D	0.999968	B	0.29341	0.242	B	0.40410	0.328	D	0.99856	1.1077	10	0.87932	D	0	.	12.8848	0.58038	0.0:0.0:0.0:1.0	.	1093	Q14767	LTBP2_HUMAN	G	1093	ENSP00000261978:D1093G;ENSP00000451477:D1093G	ENSP00000261978:D1093G	D	-	2	0	LTBP2	74045819	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	4.485000	0.60279	2.234000	0.73211	0.402000	0.26972	GAC	.	.		0.667	LTBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413595.1	NM_000428	Missense_Mutation
MLH3	27030	hgsc.bcm.edu	37	14	75515828	75515828	+	Silent	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:75515828A>G	ENST00000556740.1	-	1	566	c.531T>C	c.(529-531)gcT>gcC	p.A177A	MLH3_ENST00000555671.1_5'Flank|MLH3_ENST00000380968.2_5'UTR|MLH3_ENST00000355774.2_Silent_p.A177A|MLH3_ENST00000238662.7_Silent_p.A177A|MLH3_ENST00000544985.1_5'Flank|MLH3_ENST00000556257.1_Silent_p.A177A			Q9UHC1	MLH3_HUMAN	mutL homolog 3	177					ATP catabolic process (GO:0006200)|female meiosis I (GO:0007144)|male meiosis (GO:0007140)|mismatch repair (GO:0006298)|protein localization (GO:0008104)|reciprocal meiotic recombination (GO:0007131)|synaptonemal complex assembly (GO:0007130)	chiasma (GO:0005712)|male germ cell nucleus (GO:0001673)|mismatch repair complex (GO:0032300)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|centromeric DNA binding (GO:0019237)|chromatin binding (GO:0003682)|mismatched DNA binding (GO:0030983)|satellite DNA binding (GO:0003696)|single-stranded DNA binding (GO:0003697)			breast(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	44				BRCA - Breast invasive adenocarcinoma(234;0.00688)		TGAGTGAGAGAGCTTCTATTC	0.428								Mismatch excision repair (MMR)																													p.A177A		Atlas-SNP	.											.	MLH3	200	.	0			c.T531C						.						75.0	70.0	72.0					14																	75515828		2203	4300	6503	SO:0001819	synonymous_variant	27030	exon2			TGAGAGAGCTTCT	AF195657	CCDS9837.1, CCDS32123.1	14q24.3	2014-09-17	2013-09-12			ENSG00000119684			7128	protein-coding gene	gene with protein product		604395	"""mutL (E. coli) homolog 3"", ""mutL homolog 3 (E. coli)"""			10615123	Standard	XR_245681		Approved		uc001xrd.1	Q9UHC1		ENST00000556740.1:c.531T>C	chr14.hg19:g.75515828A>G		74.0	0.0		62.0	5.0	NM_014381	P49751|Q56DK9|Q9P292|Q9UHC0	Silent	SNP	ENST00000556740.1	hg19	CCDS32123.1																																																																																			.	.		0.428	MLH3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415006.1	NM_014381	
IFT43	112752	hgsc.bcm.edu	37	14	76549846	76549846	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:76549846T>C	ENST00000314067.6	+	9	587	c.553T>C	c.(553-555)Tca>Cca	p.S185P	IFT43_ENST00000238628.6_Missense_Mutation_p.S190P	NM_001102564.1	NP_001096034.1	Q96FT9	IFT43_HUMAN	intraflagellar transport 43	185					cilium morphogenesis (GO:0060271)|intraciliary retrograde transport (GO:0035721)	cytoplasm (GO:0005737)|intraciliary transport particle A (GO:0030991)|microtubule cytoskeleton (GO:0015630)|microtubule organizing center (GO:0005815)				endometrium(1)|large_intestine(3)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	15						TGAGGTGTCCTCAGAGGTCCT	0.582																																					p.S190P		Atlas-SNP	.											.	IFT43	63	.	0			c.T568C						.						81.0	75.0	77.0					14																	76549846		2203	4300	6503	SO:0001583	missense	112752	exon8			GTGTCCTCAGAGG	BC010436	CCDS9847.1, CCDS41973.1, CCDS58330.1	14q24.3	2014-07-03	2014-07-03	2011-06-09				"""Intraflagellar transport homologs"""	29669	protein-coding gene	gene with protein product		614068	"""chromosome 14 open reading frame 179"", ""intraflagellar transport 43 homolog (Chlamydomonas)"""	C14orf179		21378380	Standard	NM_052873		Approved	FLJ32173, MGC16028	uc010asm.1	Q96FT9		ENST00000314067.6:c.553T>C	chr14.hg19:g.76549846T>C	ENSP00000324177:p.Ser185Pro	65.0	0.0		58.0	4.0	NM_052873	B3KPT6|B4DZI9|G3V385|O95418|Q9ULA9	Missense_Mutation	SNP	ENST00000314067.6	hg19	CCDS41973.1	.	.	.	.	.	.	.	.	.	.	T	25.5	4.640458	0.87859	.	.	ENSG00000119650	ENST00000314067;ENST00000238628	T;T	0.52295	0.67;0.67	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	T	0.73024	0.3534	M	0.86420	2.815	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.81914	0.995;0.995	T	0.78745	-0.2084	10	0.87932	D	0	-9.9166	15.87	0.79108	0.0:0.0:0.0:1.0	.	185;190	Q96FT9;Q96FT9-2	IFT43_HUMAN;.	P	185;190	ENSP00000324177:S185P;ENSP00000238628:S190P	ENSP00000238628:S190P	S	+	1	0	IFT43	75619599	1.000000	0.71417	0.997000	0.53966	0.764000	0.43329	7.247000	0.78257	2.145000	0.66743	0.533000	0.62120	TCA	.	.		0.582	IFT43-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_052873	
SEL1L	6400	hgsc.bcm.edu	37	14	81952089	81952089	+	Splice_Site	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:81952089T>C	ENST00000336735.4	-	18	1916	c.1800A>G	c.(1798-1800)agA>agG	p.R600R		NM_005065.5	NP_005056.3	Q9UBV2	SE1L1_HUMAN	sel-1 suppressor of lin-12-like (C. elegans)	600	Interaction with ERLEC1, OS9 and SYVN1.				Notch signaling pathway (GO:0007219)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(4)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)|prostate(2)|urinary_tract(3)	28				BRCA - Breast invasive adenocarcinoma(234;0.0299)		TGCTTGCTTCTCCTACAGGAA	0.373																																					p.R600R		Atlas-SNP	.											.	SEL1L	67	.	0			c.A1800G						.						106.0	106.0	106.0					14																	81952089		2203	4300	6503	SO:0001630	splice_region_variant	6400	exon18			TGCTTCTCCTACA		CCDS9876.1, CCDS58333.1	14q31	2011-03-31	2001-11-28		ENSG00000071537	ENSG00000071537			10717	protein-coding gene	gene with protein product	"""sel-1 suppressor of lin-12-like 1 (C. elegans)"""	602329	"""sel-1 (suppressor of lin-12, C.elegans)-like"""			9417916, 10051412, 16331677	Standard	NM_005065		Approved	IBD2, SEL1L1	uc010tvv.2	Q9UBV2		ENST00000336735.4:c.1799-1A>G	chr14.hg19:g.81952089T>C		121.0	0.0		125.0	5.0	NM_005065	Q6UWT6|Q9P1T9|Q9UHK7	Silent	SNP	ENST00000336735.4	hg19	CCDS9876.1																																																																																			.	.		0.373	SEL1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413325.1	NM_005065	Silent
SEL1L	6400	hgsc.bcm.edu	37	14	81961452	81961452	+	Silent	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:81961452T>C	ENST00000336735.4	-	11	1274	c.1158A>G	c.(1156-1158)ggA>ggG	p.G386G		NM_005065.5	NP_005056.3	Q9UBV2	SE1L1_HUMAN	sel-1 suppressor of lin-12-like (C. elegans)	386	Interaction with ERLEC1, OS9 and SYVN1.				Notch signaling pathway (GO:0007219)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(4)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)|prostate(2)|urinary_tract(3)	28				BRCA - Breast invasive adenocarcinoma(234;0.0299)		CTCCACGCCCTCCGTGCAGGT	0.438																																					p.G386G		Atlas-SNP	.											.	SEL1L	67	.	0			c.A1158G						.						134.0	100.0	111.0					14																	81961452		2203	4300	6503	SO:0001819	synonymous_variant	6400	exon11			ACGCCCTCCGTGC		CCDS9876.1, CCDS58333.1	14q31	2011-03-31	2001-11-28		ENSG00000071537	ENSG00000071537			10717	protein-coding gene	gene with protein product	"""sel-1 suppressor of lin-12-like 1 (C. elegans)"""	602329	"""sel-1 (suppressor of lin-12, C.elegans)-like"""			9417916, 10051412, 16331677	Standard	NM_005065		Approved	IBD2, SEL1L1	uc010tvv.2	Q9UBV2		ENST00000336735.4:c.1158A>G	chr14.hg19:g.81961452T>C		81.0	0.0		90.0	5.0	NM_005065	Q6UWT6|Q9P1T9|Q9UHK7	Silent	SNP	ENST00000336735.4	hg19	CCDS9876.1																																																																																			.	.		0.438	SEL1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413325.1	NM_005065	
MOAP1	64112	hgsc.bcm.edu	37	14	93650222	93650222	+	Silent	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:93650222T>C	ENST00000556883.1	-	2	850	c.366A>G	c.(364-366)agA>agG	p.R122R	RP11-371E8.4_ENST00000557574.1_5'Flank|TMEM251_ENST00000283534.4_5'Flank|MOAP1_ENST00000298894.4_Silent_p.R122R|TMEM251_ENST00000415050.2_5'Flank			Q96BY2	MOAP1_HUMAN	modulator of apoptosis 1	122	BH3-like.				apoptotic signaling pathway (GO:0097190)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|positive regulation of apoptotic process (GO:0043065)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:0001844)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(4)|ovary(1)|skin(2)	13		all_cancers(154;0.00528)|Acute lymphoblastic leukemia(33;0.0497)|all_epithelial(191;0.125)|all_neural(303;0.13)		Epithelial(152;0.178)|all cancers(159;0.2)|COAD - Colon adenocarcinoma(157;0.204)		gtccaagagctctgctcaact	0.493																																					p.R122R		Atlas-SNP	.											.	MOAP1	32	.	0			c.A366G						.						92.0	93.0	93.0					14																	93650222		2203	4300	6503	SO:0001819	synonymous_variant	64112	exon3			AAGAGCTCTGCTC	BC015044	CCDS9908.1	14q32.12	2012-02-09			ENSG00000165943	ENSG00000165943		"""Paraneoplastic Ma antigens"""	16658	protein-coding gene	gene with protein product	"""paraneoplastic Ma antigen family member 4"""	609485				11060313	Standard	NM_022151		Approved	MAP-1, PNMA4	uc001ybj.3	Q96BY2	OTTHUMG00000169184	ENST00000556883.1:c.366A>G	chr14.hg19:g.93650222T>C		98.0	0.0		97.0	6.0	NM_022151	B2RDF6|Q9H833|Q9HAS1	Silent	SNP	ENST00000556883.1	hg19	CCDS9908.1																																																																																			.	.		0.493	MOAP1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412685.1		
IFI27	3429	hgsc.bcm.edu	37	14	94582130	94582130	+	Missense_Mutation	SNP	T	T	C	rs3833507	byFrequency	TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:94582130T>C	ENST00000555744.1	+	4	313	c.125T>C	c.(124-126)gTg>gCg	p.V42A	IFI27_ENST00000444961.1_Splice_Site_p.V45A|IFI27_ENST00000298902.5_Missense_Mutation_p.V42A|IFI27_ENST00000557098.1_5'UTR|IFI27_ENST00000557634.1_Missense_Mutation_p.V32A|IFI27_ENST00000448882.1_Missense_Mutation_p.V45A			P40305	IFI27_HUMAN	interferon, alpha-inducible protein 27	42				V -> VAMA (in Ref. 1; CAA47739). {ECO:0000305}.	activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic signaling pathway (GO:0097190)|cytokine-mediated signaling pathway (GO:0019221)|type I interferon signaling pathway (GO:0060337)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)		p.A43_V44insMAA(1)		breast(1)|lung(3)	4				Epithelial(152;0.112)|all cancers(159;0.187)|COAD - Colon adenocarcinoma(157;0.206)		CCTGCAGTTGTGGCTGTGCCC	0.627																																					p.V42A	GBM(128;797 1667 20895 29868 47129)	Atlas-SNP	.											IFI27,colon,carcinoma,0,16	IFI27	39	.	1	Insertion - In frame(1)	breast(1)	c.T125C						.						14.0	13.0	13.0					14																	94582130		2184	4278	6462	SO:0001583	missense	3429	exon4			CAGTTGTGGCTGT	X67325	CCDS32148.1	14q32.12	2012-10-02			ENSG00000165949	ENSG00000165949			5397	protein-coding gene	gene with protein product		600009				8358738	Standard	NM_005532		Approved	P27, FAM14D	uc021sba.1	P40305	OTTHUMG00000171303	ENST00000555744.1:c.125T>C	chr14.hg19:g.94582130T>C	ENSP00000451956:p.Val42Ala	31.0	1.0		55.0	4.0	NM_005532	Q53YA6|Q6IEC1|Q96BK3	Missense_Mutation	SNP	ENST00000555744.1	hg19	CCDS32148.1	.	.	.	.	.	.	.	.	.	.	T	0.082	-1.181118	0.01633	.	.	ENSG00000165949	ENST00000554448;ENST00000444961;ENST00000448882;ENST00000554800;ENST00000556544;ENST00000298902;ENST00000557634;ENST00000555744	T;T;T;T;T;T;T	0.28255	1.62;1.62;1.62;1.62;1.62;1.62;1.62	3.52	-1.47	0.08772	.	0.951477	0.08752	N	0.898966	T	0.09642	0.0237	N	0.02674	-0.535	0.09310	N	1	B	0.18166	0.026	B	0.19391	0.025	T	0.34925	-0.9809	10	0.02654	T	1	.	7.2043	0.25899	0.0:0.4761:0.0:0.5239	.	42	P40305	IFI27_HUMAN	A	42;45;45;42;42;42;32;42	ENSP00000451370:V42A;ENSP00000413536:V45A;ENSP00000410901:V45A;ENSP00000451875:V42A;ENSP00000298902:V42A;ENSP00000452560:V32A;ENSP00000451956:V42A	ENSP00000298902:V42A	V	+	2	0	IFI27	93651883	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.001000	0.13038	-0.296000	0.08947	-0.400000	0.06385	GTG	.	.		0.627	IFI27-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000412889.1	NM_005532	
PPP2R5C	5527	hgsc.bcm.edu	37	14	102349777	102349777	+	Silent	SNP	G	G	A			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:102349777G>A	ENST00000334743.5	+	5	555	c.507G>A	c.(505-507)gaG>gaA	p.E169E	PPP2R5C_ENST00000445439.3_Silent_p.E169E|PPP2R5C_ENST00000328724.5_Silent_p.E224E|PPP2R5C_ENST00000350249.3_Silent_p.E169E|PPP2R5C_ENST00000422945.2_Silent_p.E200E|PPP2R5C_ENST00000557095.1_Silent_p.E169E	NM_002719.3	NP_002710.2	Q13362	2A5G_HUMAN	protein phosphatase 2, regulatory subunit B', gamma	169					DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|negative regulation of cell proliferation (GO:0008285)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)	chromosome, centromeric region (GO:0000775)|nucleus (GO:0005634)|protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)			breast(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	20						AGCTTTTAGAGCTCTTTGACA	0.418																																					p.E224E		Atlas-SNP	.											.	PPP2R5C	74	.	0			c.G672A						.						90.0	95.0	93.0					14																	102349777		2202	4299	6501	SO:0001819	synonymous_variant	5527	exon7			TTTAGAGCTCTTT	L42375	CCDS9964.1, CCDS9965.1, CCDS45163.1, CCDS53911.1, CCDS53912.1	14q32.31	2010-06-18	2010-04-14		ENSG00000078304	ENSG00000078304		"""Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"""	9311	protein-coding gene	gene with protein product		601645	"""protein phosphatase 2, regulatory subunit B (B56), gamma isoform"", ""protein phosphatase 2, regulatory subunit B', gamma isoform"""			7592815	Standard	NM_002719		Approved	B56G, PR61G	uc001ykk.3	Q13362		ENST00000334743.5:c.507G>A	chr14.hg19:g.102349777G>A		94.0	0.0		91.0	15.0	NM_001161726	B4DYJ8|B5BUA5|F5GWP3|Q14391|Q15060|Q15174|Q6ZN33	Silent	SNP	ENST00000334743.5	hg19	CCDS9964.1																																																																																			.	.		0.418	PPP2R5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414373.2	NM_002719	
DYNC1H1	1778	hgsc.bcm.edu	37	14	102489191	102489191	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:102489191A>G	ENST00000360184.4	+	43	8775	c.8611A>G	c.(8611-8613)Atc>Gtc	p.I2871V		NM_001376.4	NP_001367.2	Q14204	DYHC1_HUMAN	dynein, cytoplasmic 1, heavy chain 1	2871					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|cytoplasmic mRNA processing body assembly (GO:0033962)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic spindle organization (GO:0007052)|stress granule assembly (GO:0034063)|transport (GO:0006810)	centrosome (GO:0005813)|cytoplasmic dynein complex (GO:0005868)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(5)|cervix(1)|endometrium(21)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(28)|lung(60)|ovary(9)|pancreas(1)|prostate(6)|skin(7)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	166						GAGCCGACCCATCTTGTACAG	0.468																																					p.I2871V		Atlas-SNP	.											.	DYNC1H1	395	.	0			c.A8611G						.						227.0	182.0	197.0					14																	102489191		2203	4300	6503	SO:0001583	missense	1778	exon43			CGACCCATCTTGT	AB002323	CCDS9966.1	14q32.31	2006-12-21	2005-11-24	2005-11-24		ENSG00000197102		"""Cytoplasmic dyneins"""	2961	protein-coding gene	gene with protein product		600112	"""dynein, cytoplasmic, heavy polypeptide 1"""	DNECL, DNCL, DNCH1		16260502, 8666668	Standard	NM_001376		Approved	Dnchc1, HL-3, p22, DHC1	uc001yks.2	Q14204		ENST00000360184.4:c.8611A>G	chr14.hg19:g.102489191A>G	ENSP00000348965:p.Ile2871Val	128.0	0.0		125.0	22.0	NM_001376	B0I1R0|Q6DKQ7|Q8WU28|Q92814|Q9Y4G5	Missense_Mutation	SNP	ENST00000360184.4	hg19	CCDS9966.1	.	.	.	.	.	.	.	.	.	.	A	18.15	3.559353	0.65538	.	.	ENSG00000197102	ENST00000360184	T	0.29917	1.55	5.17	5.17	0.71159	.	0.000000	0.85682	D	0.000000	T	0.41511	0.1162	M	0.78344	2.41	0.80722	D	1	P	0.45902	0.868	P	0.45167	0.472	T	0.38972	-0.9636	10	0.34782	T	0.22	.	15.0033	0.71492	1.0:0.0:0.0:0.0	.	2871	Q14204	DYHC1_HUMAN	V	2871	ENSP00000348965:I2871V	ENSP00000348965:I2871V	I	+	1	0	DYNC1H1	101558944	1.000000	0.71417	1.000000	0.80357	0.789000	0.44602	9.209000	0.95087	1.949000	0.56562	0.383000	0.25322	ATC	.	.		0.468	DYNC1H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414574.1	NM_001376	
APOPT1	84334	hgsc.bcm.edu	37	14	104056544	104056544	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:104056544T>C	ENST00000409074.2	+	5	543	c.542T>C	c.(541-543)aTc>aCc	p.I181T	RP11-73M18.2_ENST00000472726.2_Intron|APOPT1_ENST00000477116.1_3'UTR|APOPT1_ENST00000247618.4_Missense_Mutation_p.I168T|APOPT1_ENST00000556253.2_3'UTR	NM_032374.3	NP_115750.2	Q96IL0	APOP1_HUMAN	apoptogenic 1, mitochondrial	181					intrinsic apoptotic signaling pathway (GO:0097193)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)	mitochondrion (GO:0005739)											AATTTTGCCATCACCTTCTTC	0.512																																					p.I181T		Atlas-SNP	.											.	.	.	.	0			c.T542C						.						196.0	194.0	195.0					14																	104056544		2203	4300	6503	SO:0001583	missense	84334	exon5			TTGCCATCACCTT	BC007412	CCDS9983.2	14q32.33	2012-06-28	2012-06-28	2011-09-07	ENSG00000256053	ENSG00000256053			20492	protein-coding gene	gene with protein product	"""apoptogenic protein 1"""		"""chromosome 14 open reading frame 153"", ""apoptogenic 1"""	C14orf153		16782708, 18977203	Standard	NM_032374		Approved	MGC2562, APOP-1		Q96IL0	OTTHUMG00000153929	ENST00000409074.2:c.542T>C	chr14.hg19:g.104056544T>C	ENSP00000386485:p.Ile181Thr	78.0	0.0		83.0	4.0	NM_032374	Q53G28	Missense_Mutation	SNP	ENST00000409074.2	hg19	CCDS9983.2	.	.	.	.	.	.	.	.	.	.	T	18.01	3.528619	0.64860	.	.	ENSG00000256053;ENSG00000256053;ENSG00000256500	ENST00000409074;ENST00000440963;ENST00000247618	T;T;T	0.52983	0.64;0.64;0.64	5.56	5.56	0.83823	.	0.000000	0.85682	D	0.000000	T	0.48223	0.1488	M	0.71206	2.165	0.40554	D	0.981143	B	0.11235	0.004	B	0.14578	0.011	T	0.49173	-0.8967	10	0.51188	T	0.08	.	12.1161	0.53866	0.0:0.0:0.0:1.0	.	181	Q96IL0	APOP1_HUMAN	T	181;93;168	ENSP00000386485:I181T;ENSP00000388067:I93T;ENSP00000247618:I168T	ENSP00000247618:I168T	I	+	2	0	C14orf153;RP11-73M18.2	103126297	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	3.509000	0.53386	2.109000	0.64355	0.533000	0.62120	ATC	.	.		0.512	APOPT1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333060.2	NM_032374	
MTA1	9112	hgsc.bcm.edu	37	14	105916421	105916421	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:105916421C>T	ENST00000331320.7	+	5	482	c.268C>T	c.(268-270)Ccg>Tcg	p.P90S	MTA1_ENST00000405646.1_Missense_Mutation_p.P73S|MTA1_ENST00000406191.1_Missense_Mutation_p.P90S	NM_001203258.1|NM_004689.3	NP_001190187.1|NP_004680.2	Q13330	MTA1_HUMAN	metastasis associated 1	90	BAH. {ECO:0000255|PROSITE- ProRule:PRU00370}.				circadian regulation of gene expression (GO:0032922)|double-strand break repair (GO:0006302)|entrainment of circadian clock by photoperiod (GO:0043153)|locomotor rhythm (GO:0045475)|positive regulation of protein autoubiquitination (GO:1902499)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of gene expression, epigenetic (GO:0040029)|regulation of inflammatory response (GO:0050727)|response to ionizing radiation (GO:0010212)|response to lipopolysaccharide (GO:0032496)|secretory granule organization (GO:0033363)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|intracellular membrane-bounded organelle (GO:0043231)|microtubule (GO:0005874)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|core promoter sequence-specific DNA binding (GO:0001046)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|stomach(1)	14		all_cancers(154;0.0293)|all_epithelial(191;0.128)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.00897)|Epithelial(46;0.026)	Epithelial(152;0.19)		AATGGAGAACCCGGAAATGGT	0.627																																					p.P90S		Atlas-SNP	.											MTA1,NS,carcinoma,0,1	MTA1	61	.	0			c.C268T						.						61.0	66.0	64.0					14																	105916421		2203	4300	6503	SO:0001583	missense	9112	exon5			GAGAACCCGGAAA	U35113	CCDS32169.1, CCDS55954.1	14q32.33	2013-01-25			ENSG00000182979	ENSG00000182979		"""GATA zinc finger domain containing"""	7410	protein-coding gene	gene with protein product		603526				8083195, 7607577	Standard	NM_004689		Approved		uc001yqx.3	Q13330	OTTHUMG00000150362	ENST00000331320.7:c.268C>T	chr14.hg19:g.105916421C>T	ENSP00000333633:p.Pro90Ser	132.0	0.0		169.0	0.0	NM_004689	A5PLK4|Q86SW2|Q8NFI8|Q96GI8	Missense_Mutation	SNP	ENST00000331320.7	hg19	CCDS32169.1	.	.	.	.	.	.	.	.	.	.	C	19.02	3.746070	0.69418	.	.	ENSG00000182979	ENST00000331320;ENST00000406191;ENST00000405646;ENST00000498644	D;D;D;D	0.85702	-2.02;-2.02;-2.02;-2.02	4.14	4.14	0.48551	Bromo adjacent homology (BAH) domain (3);	0.000000	0.85682	U	0.000000	D	0.83367	0.5239	L	0.56396	1.775	0.80722	D	1	P	0.38250	0.624	B	0.39465	0.3	D	0.83910	0.0295	10	0.41790	T	0.15	-11.5496	14.9627	0.71169	0.0:1.0:0.0:0.0	.	90	Q13330	MTA1_HUMAN	S	90;90;73;4	ENSP00000333633:P90S;ENSP00000385702:P90S;ENSP00000384180:P73S;ENSP00000448146:P4S	ENSP00000333633:P90S	P	+	1	0	MTA1	104987466	1.000000	0.71417	0.914000	0.36105	0.674000	0.39518	3.448000	0.52943	1.839000	0.53478	0.306000	0.20318	CCG	.	.		0.627	MTA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000317849.15		
SNURF	8926	hgsc.bcm.edu	37	15	25213117	25213117	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:25213117T>C	ENST00000577949.1	+	3	212	c.149T>C	c.(148-150)gTa>gCa	p.V50A	SNRPN_ENST00000577565.1_5'UTR|SNURF_ENST00000338327.4_Missense_Mutation_p.V50A|SNRPN_ENST00000400098.1_5'UTR|SNRPN_ENST00000553597.1_3'UTR|SNRPN_ENST00000400097.1_5'UTR|SNURF_ENST00000338094.6_Missense_Mutation_p.V50A|SNRPN_ENST00000390687.4_5'UTR|SNRPN_ENST00000346403.6_5'UTR|SNRPN_ENST00000554227.2_5'UTR|SNURF_ENST00000551312.2_Missense_Mutation_p.V50A|SNRPN_ENST00000400100.1_5'UTR			Q9Y675	SNURF_HUMAN	SNRPN upstream reading frame	50						nucleus (GO:0005634)				breast(2)|large_intestine(2)|lung(1)	5		all_cancers(20;1.4e-21)|Breast(32;0.000625)		all cancers(64;3.48e-07)|Epithelial(43;1.83e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0142)		CAGCAGCAAGTACCTGTGGTG	0.428																																					p.V50A		Atlas-SNP	.											.	SNURF	17	.	0			c.T149C						.						142.0	133.0	136.0					15																	25213117		2203	4300	6503	SO:0001583	missense	8926	exon3			AGCAAGTACCTGT		CCDS10016.1	15q11.2	2013-08-27			ENSG00000214265	ENSG00000214265			11171	protein-coding gene	gene with protein product						10318933	Standard	NM_022804		Approved		uc001ywu.3	Q9Y675	OTTHUMG00000129181	ENST00000577949.1:c.149T>C	chr15.hg19:g.25213117T>C	ENSP00000463201:p.Val50Ala	85.0	0.0		86.0	4.0	NM_005678	A6NCW2	Missense_Mutation	SNP	ENST00000577949.1	hg19	CCDS10016.1	.	.	.	.	.	.	.	.	.	.	T	5.100	0.204138	0.09704	.	.	ENSG00000214265	ENST00000338094;ENST00000338327	.	.	.	3.25	0.914	0.19360	.	.	.	.	.	T	0.25827	0.0629	.	.	.	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.18524	-1.0334	7	0.37606	T	0.19	-1.1304	5.0222	0.14367	0.0:0.2608:0.0:0.7392	.	50	Q9Y675	SNURF_HUMAN	A	50	.	ENSP00000336543:V50A	V	+	2	0	SNURF	22764210	0.011000	0.17503	0.135000	0.22099	0.820000	0.46376	-0.238000	0.08977	0.161000	0.19458	-0.376000	0.06991	GTA	.	.		0.428	SNURF-005	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446300.1	NM_005678	
ARHGAP11A	9824	hgsc.bcm.edu	37	15	32928096	32928096	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:32928096A>G	ENST00000361627.3	+	11	2185	c.1463A>G	c.(1462-1464)gAt>gGt	p.D488G	ARHGAP11A_ENST00000565905.1_Missense_Mutation_p.D299G|ARHGAP11A_ENST00000563864.1_Missense_Mutation_p.D460G|ARHGAP11A_ENST00000543522.1_Missense_Mutation_p.D299G|ARHGAP11A_ENST00000567348.1_Missense_Mutation_p.D488G	NM_014783.3	NP_055598.1	Q6P4F7	RHGBA_HUMAN	Rho GTPase activating protein 11A	488					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			breast(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(11)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	31		all_lung(180;1.3e-11)		all cancers(64;3.34e-21)|Epithelial(43;2.64e-15)|GBM - Glioblastoma multiforme(186;5.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.00112)|Lung(196;0.227)		CCAGATGTTGATGAAAAGTTA	0.299																																					p.D488G	Colon(45;757 1134 30003 36652)	Atlas-SNP	.											.	ARHGAP11A	84	.	0			c.A1463G						.						75.0	73.0	73.0					15																	32928096		2201	4298	6499	SO:0001583	missense	9824	exon11			ATGTTGATGAAAA	D87717	CCDS10028.1, CCDS58349.1, CCDS66730.1	15q13.3	2006-09-19			ENSG00000198826	ENSG00000198826		"""Rho GTPase activating proteins"""	15783	protein-coding gene	gene with protein product	"""GAP (1-12)"""	610589				11829490	Standard	NM_199357		Approved	KIAA0013	uc001zgy.1	Q6P4F7	OTTHUMG00000129289	ENST00000361627.3:c.1463A>G	chr15.hg19:g.32928096A>G	ENSP00000355090:p.Asp488Gly	82.0	0.0		119.0	5.0	NM_199357	B4DZN9|Q6PI96|Q9Y3S6	Missense_Mutation	SNP	ENST00000361627.3	hg19	CCDS10028.1	.	.	.	.	.	.	.	.	.	.	.	11.02	1.516057	0.27123	.	.	ENSG00000198826	ENST00000361627;ENST00000543522	T	0.09723	2.95	5.8	-0.261	0.12963	.	0.423937	0.22398	N	0.060596	T	0.08044	0.0201	L	0.41027	1.25	0.26149	N	0.980169	B;B	0.24043	0.001;0.096	B;B	0.22386	0.003;0.039	T	0.35847	-0.9772	10	0.21014	T	0.42	.	10.0965	0.42478	0.5669:0.0:0.4331:0.0	.	488;299	Q6P4F7;B4DZN9	RHGBA_HUMAN;.	G	488;299	ENSP00000355090:D488G	ENSP00000355090:D488G	D	+	2	0	ARHGAP11A	30715388	0.945000	0.32115	0.995000	0.50966	0.993000	0.82548	0.001000	0.13038	-0.064000	0.13043	0.528000	0.53228	GAT	.	.		0.299	ARHGAP11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251417.1	NM_014783	
PHGR1	644844	hgsc.bcm.edu	37	15	40648462	40648462	+	Silent	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:40648462T>C	ENST00000448599.2	+	4	263	c.207T>C	c.(205-207)ccT>ccC	p.P69P	DISP2_ENST00000267889.3_5'Flank	NM_001145643.1	NP_001139115.1	C9JFL3	PHGR1_HUMAN	proline/histidine/glycine-rich 1	69	Gly-rich.																GGCCTCCCCCTGGCCATGGCC	0.682																																					p.P69P		Atlas-SNP	.											.	PHGR1	14	.	0			c.T207C						.						1.0	1.0	1.0					15																	40648462		192	664	856	SO:0001819	synonymous_variant	644844	exon3			TCCCCCTGGCCAT		CCDS45225.1	15q15.1	2009-10-08				ENSG00000233041			37226	protein-coding gene	gene with protein product							Standard	NM_001145643		Approved		uc010uco.2	C9JFL3		ENST00000448599.2:c.207T>C	chr15.hg19:g.40648462T>C		94.0	0.0		119.0	9.0	NM_001145643		Silent	SNP	ENST00000448599.2	hg19	CCDS45225.1																																																																																			.	.		0.682	PHGR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418450.1	NM_001145643	
RTF1	23168	hgsc.bcm.edu	37	15	41768645	41768645	+	Splice_Site	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:41768645T>C	ENST00000389629.4	+	12	1496	c.1484T>C	c.(1483-1485)aTt>aCt	p.I495T		NM_015138.4	NP_055953.3	Q92541	RTF1_HUMAN	Rtf1, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae)	495					DNA-templated transcription, initiation (GO:0006352)|endodermal cell fate commitment (GO:0001711)|histone H3-K4 trimethylation (GO:0080182)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell maintenance (GO:0019827)|Wnt signaling pathway (GO:0016055)	Cdc73/Paf1 complex (GO:0016593)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|single-stranded DNA binding (GO:0003697)			central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(6)|ovary(2)|prostate(1)|skin(1)	18		all_cancers(109;1.79e-19)|all_epithelial(112;8.18e-17)|Lung NSC(122;3.16e-11)|all_lung(180;8.14e-10)|Melanoma(134;0.0179)|Colorectal(260;0.0946)|Ovarian(310;0.143)		OV - Ovarian serous cystadenocarcinoma(18;1.15e-16)|GBM - Glioblastoma multiforme(113;1.81e-06)|BRCA - Breast invasive adenocarcinoma(123;0.119)		CTGGTACAGATTGTAAAAGAG	0.428																																					p.I495T		Atlas-SNP	.											RTF1,NS,carcinoma,0,1	RTF1	76	.	0			c.T1484C						.						117.0	111.0	113.0					15																	41768645		2203	4300	6503	SO:0001630	splice_region_variant	23168	exon12			TACAGATTGTAAA	D87440	CCDS32200.2	15q14	2004-03-03	2005-07-20	2005-07-20	ENSG00000137815	ENSG00000137815			28996	protein-coding gene	gene with protein product		611633	"""KIAA0252"""	KIAA0252		15632063	Standard	NM_015138		Approved		uc001zny.3	Q92541	OTTHUMG00000133744	ENST00000389629.4:c.1483-1T>C	chr15.hg19:g.41768645T>C		45.0	0.0		64.0	3.0	NM_015138	Q96BX6	Missense_Mutation	SNP	ENST00000389629.4	hg19	CCDS32200.2	.	.	.	.	.	.	.	.	.	.	T	22.3	4.265249	0.80358	.	.	ENSG00000137815	ENST00000389629	.	.	.	5.61	5.61	0.85477	.	0.000000	0.85682	D	0.000000	T	0.76004	0.3927	M	0.72894	2.215	0.80722	D	1	P	0.50156	0.932	P	0.61397	0.888	T	0.75314	-0.3361	9	0.37606	T	0.19	-10.4476	15.8085	0.78534	0.0:0.0:0.0:1.0	.	495	Q92541	RTF1_HUMAN	T	495	.	ENSP00000374280:I495T	I	+	2	0	RTF1	39555937	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.825000	0.86693	2.134000	0.65973	0.533000	0.62120	ATT	.	.		0.428	RTF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258111.1	NM_015138	Missense_Mutation
SPTBN5	51332	hgsc.bcm.edu	37	15	42166056	42166056	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:42166056A>G	ENST00000320955.6	-	25	5104	c.4877T>C	c.(4876-4878)gTc>gCc	p.V1626A		NM_016642.2	NP_057726.4	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	1626					actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi organization (GO:0007030)|lysosomal transport (GO:0007041)|protein homooligomerization (GO:0051260)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|photoreceptor connecting cilium (GO:0032391)|photoreceptor disc membrane (GO:0097381)|spectrin (GO:0008091)	actin binding (GO:0003779)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|kinesin binding (GO:0019894)|myosin tail binding (GO:0032029)|protein self-association (GO:0043621)|spectrin binding (GO:0030507)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(6)|lung(18)|ovary(5)|prostate(8)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	62		all_cancers(109;1.84e-17)|all_epithelial(112;1.12e-15)|Lung NSC(122;7.6e-10)|all_lung(180;4.15e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		all cancers(2;4.33e-34)|Epithelial(2;1.72e-25)|OV - Ovarian serous cystadenocarcinoma(18;8.32e-20)|GBM - Glioblastoma multiforme(94;4.69e-07)|Colorectal(2;0.00104)|COAD - Colon adenocarcinoma(120;0.0405)|READ - Rectum adenocarcinoma(92;0.0908)		CTGGAAAGTGACAGCCTGCTG	0.632																																					p.V1591A		Atlas-SNP	.											.	SPTBN5	171	.	0			c.T4772C						.						53.0	57.0	56.0					15																	42166056		2010	4186	6196	SO:0001583	missense	51332	exon25			AAAGTGACAGCCT	AF233523	CCDS61599.1	15q21	2010-08-17			ENSG00000137877	ENSG00000137877			15680	protein-coding gene	gene with protein product	"""beta V spectrin"""	605916				10764729	Standard	NM_016642		Approved	HUSPECV, BSPECV, HUBSPECV	uc001zos.4	Q9NRC6		ENST00000320955.6:c.4877T>C	chr15.hg19:g.42166056A>G	ENSP00000317790:p.Val1626Ala	109.0	0.0		113.0	6.0	NM_016642		Missense_Mutation	SNP	ENST00000320955.6	hg19		.	.	.	.	.	.	.	.	.	.	.	11.47	1.648218	0.29336	.	.	ENSG00000137877	ENST00000320955	T	0.35048	1.33	5.19	-3.13	0.05266	.	0.647525	0.14016	N	0.347115	T	0.17408	0.0418	L	0.35487	1.065	0.09310	N	1	B	0.25048	0.117	B	0.25884	0.064	T	0.31138	-0.9954	10	0.11182	T	0.66	.	1.9549	0.03374	0.4678:0.1253:0.2858:0.1211	.	1626	Q9NRC6	SPTN5_HUMAN	A	1626	ENSP00000317790:V1626A	ENSP00000317790:V1626A	V	-	2	0	SPTBN5	39953348	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	0.924000	0.28777	-0.979000	0.03529	0.529000	0.55759	GTC	.	.		0.632	SPTBN5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000420237.1	NM_016642	
TMEM62	80021	hgsc.bcm.edu	37	15	43446967	43446967	+	Missense_Mutation	SNP	G	G	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:43446967G>C	ENST00000260403.2	+	9	1399	c.1120G>C	c.(1120-1122)Gta>Cta	p.V374L		NM_024956.3	NP_079232.3	Q0P6H9	TMM62_HUMAN	transmembrane protein 62	374						integral component of membrane (GO:0016021)				breast(1)|cervix(1)|endometrium(3)|large_intestine(3)|lung(4)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	18		all_cancers(109;1.16e-10)|all_epithelial(112;2.01e-09)|Lung NSC(122;8.91e-07)|all_lung(180;8.8e-06)|Melanoma(134;0.0728)		GBM - Glioblastoma multiforme(94;4.23e-07)		TCCCATTTTCGTACTGAAGTG	0.373																																					p.V374L		Atlas-SNP	.											.	TMEM62	47	.	0			c.G1120C						.						127.0	110.0	116.0					15																	43446967		2203	4299	6502	SO:0001583	missense	80021	exon9			ATTTTCGTACTGA	BC009981	CCDS32210.1	15q15.2	2014-09-11			ENSG00000137842	ENSG00000137842			26269	protein-coding gene	gene with protein product							Standard	NM_024956		Approved	FLJ23375	uc001zqr.3	Q0P6H9	OTTHUMG00000176485	ENST00000260403.2:c.1120G>C	chr15.hg19:g.43446967G>C	ENSP00000260403:p.Val374Leu	101.0	0.0		152.0	15.0	NM_024956	Q6I9Y5|Q9H5J6	Missense_Mutation	SNP	ENST00000260403.2	hg19	CCDS32210.1	.	.	.	.	.	.	.	.	.	.	G	14.80	2.642270	0.47153	.	.	ENSG00000137842	ENST00000260403	.	.	.	5.67	1.92	0.25849	.	0.486384	0.25130	N	0.032911	T	0.49983	0.1589	M	0.64997	1.995	0.34404	D	0.695626	B	0.26744	0.158	B	0.28465	0.09	T	0.54139	-0.8338	9	0.33940	T	0.23	-0.6828	7.7929	0.29131	0.6476:0.0:0.3524:0.0	.	374	Q0P6H9	TMM62_HUMAN	L	374	.	ENSP00000260403:V374L	V	+	1	0	TMEM62	41234259	1.000000	0.71417	0.996000	0.52242	0.857000	0.48899	3.399000	0.52586	0.499000	0.27970	-0.438000	0.05819	GTA	.	.		0.373	TMEM62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432227.1	NM_024956	
DUOX2	50506	hgsc.bcm.edu	37	15	45386375	45386375	+	Silent	SNP	G	G	A			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:45386375G>A	ENST00000603300.1	-	34	4822	c.4620C>T	c.(4618-4620)caC>caT	p.H1540H	DUOX2_ENST00000389039.6_Silent_p.H1540H	NM_014080.4	NP_054799.4	Q9NRD8	DUOX2_HUMAN	dual oxidase 2	1540					adenohypophysis morphogenesis (GO:0048855)|bone mineralization (GO:0030282)|cuticle development (GO:0042335)|cytokine-mediated signaling pathway (GO:0019221)|fertilization (GO:0009566)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide catabolic process (GO:0042744)|inner ear development (GO:0048839)|multicellular organism growth (GO:0035264)|oxidation-reduction process (GO:0055114)|response to cAMP (GO:0051591)|response to virus (GO:0009615)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|NAD(P)H oxidase activity (GO:0016174)|peroxidase activity (GO:0004601)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(28)|ovary(3)|pancreas(1)|prostate(4)|skin(7)|urinary_tract(1)	63		all_cancers(109;3.79e-11)|all_epithelial(112;2.92e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;1.05e-18)|GBM - Glioblastoma multiforme(94;4.23e-07)|COAD - Colon adenocarcinoma(120;0.0668)|Colorectal(133;0.068)		GGTGCATGAAGTGGGCTCGGT	0.577																																					p.H1540H		Atlas-SNP	.											.	DUOX2	137	.	0			c.C4620T						.						149.0	127.0	134.0					15																	45386375		2198	4298	6496	SO:0001819	synonymous_variant	50506	exon34			CATGAAGTGGGCT	AF181972	CCDS10117.1	15q15.3-q21	2013-01-10			ENSG00000140279	ENSG00000140279		"""EF-hand domain containing"""	13273	protein-coding gene	gene with protein product	"""dual oxidase-like domains 2"", ""nicotinamide adenine dinucleotide phosphate oxidase"", ""flavoprotein NADPH oxidase"", ""NADPH thyroid oxidase 2"", ""NADH/NADPH thyroid oxidase p138-tox"", ""NADPH oxidase/peroxidase DUOX2"""	606759				10601291, 10806195	Standard	NM_014080		Approved	P138-TOX, P138(TOX), THOX2, LNOX2	uc010bea.3	Q9NRD8	OTTHUMG00000131355	ENST00000603300.1:c.4620C>T	chr15.hg19:g.45386375G>A		126.0	0.0		171.0	51.0	NM_014080	A8MQ13|D2XI64|Q9NR02|Q9UHF9	Silent	SNP	ENST00000603300.1	hg19	CCDS10117.1																																																																																			.	.		0.577	DUOX2-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_014080	
MNS1	55329	hgsc.bcm.edu	37	15	56721375	56721375	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:56721375T>C	ENST00000260453.3	-	10	1576	c.1412A>G	c.(1411-1413)gAg>gGg	p.E471G	TEX9_ENST00000537232.1_Intron|MNS1_ENST00000566386.1_5'UTR|TEX9_ENST00000352903.2_Intron	NM_018365.2	NP_060835.1	Q8NEH6	MNS1_HUMAN	meiosis-specific nuclear structural 1	471					cilium organization (GO:0044782)|left/right axis specification (GO:0070986)|meiotic nuclear division (GO:0007126)	axoneme (GO:0005930)|intermediate filament (GO:0005882)|nuclear envelope (GO:0005635)|sperm flagellum (GO:0036126)	identical protein binding (GO:0042802)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(4)|ovary(2)|pancreas(2)|skin(1)|upper_aerodigestive_tract(1)	20				all cancers(107;0.0196)|GBM - Glioblastoma multiforme(80;0.101)		AATATCATCCTCTTTTTTAAA	0.318																																					p.E471G		Atlas-SNP	.											.	MNS1	39	.	0			c.A1412G						.						84.0	81.0	82.0					15																	56721375		2191	4285	6476	SO:0001583	missense	55329	exon10			TCATCCTCTTTTT	AK002084	CCDS10158.1	15q21.3	2013-01-16			ENSG00000138587	ENSG00000138587			29636	protein-coding gene	gene with protein product	"""spermatogenesis associated 40"""	610766				7625268, 8032679	Standard	NM_018365		Approved	FLJ11222, SPATA40	uc002adr.2	Q8NEH6	OTTHUMG00000132034	ENST00000260453.3:c.1412A>G	chr15.hg19:g.56721375T>C	ENSP00000260453:p.Glu471Gly	88.0	0.0		113.0	7.0	NM_018365	Q8IYT6|Q9NUP4	Missense_Mutation	SNP	ENST00000260453.3	hg19	CCDS10158.1	.	.	.	.	.	.	.	.	.	.	T	18.88	3.716836	0.68844	.	.	ENSG00000138587	ENST00000260453	T	0.18016	2.24	6.08	4.97	0.65823	.	0.162086	0.56097	D	0.000031	T	0.20861	0.0502	M	0.65498	2.005	0.52501	D	0.999955	D	0.56746	0.977	B	0.42827	0.399	T	0.01899	-1.1251	10	0.54805	T	0.06	-10.6378	10.9711	0.47441	0.0:0.072:0.0:0.928	.	471	Q8NEH6	MNS1_HUMAN	G	471	ENSP00000260453:E471G	ENSP00000260453:E471G	E	-	2	0	MNS1	54508667	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	2.727000	0.47311	2.333000	0.79357	0.482000	0.46254	GAG	.	.		0.318	MNS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255047.2	NM_018365	
LDHAL6B	92483	hgsc.bcm.edu	37	15	59499975	59499975	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:59499975T>C	ENST00000307144.4	+	1	934	c.836T>C	c.(835-837)gTc>gCc	p.V279A	MYO1E_ENST00000288235.4_Intron	NM_033195.2	NP_149972.1	Q9BYZ2	LDH6B_HUMAN	lactate dehydrogenase A-like 6B	279					cellular carbohydrate metabolic process (GO:0044262)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	L-lactate dehydrogenase activity (GO:0004459)			endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)|stomach(1)	10						TGGAAAAATGTCCACAAAGAA	0.408																																					p.V279A		Atlas-SNP	.											.	LDHAL6B	30	.	0			c.T836C						.						67.0	66.0	66.0					15																	59499975		2191	4290	6481	SO:0001583	missense	92483	exon1			AAAATGTCCACAA	AY009108	CCDS10171.1	15q21.3	2011-01-27	2004-07-27	2004-07-28	ENSG00000171989	ENSG00000171989			21481	protein-coding gene	gene with protein product			"""lactate dehydrogenase A-like 6"""	LDHAL6		15870898	Standard	NM_033195		Approved	LDHL, LDH6B	uc002agb.4	Q9BYZ2	OTTHUMG00000132714	ENST00000307144.4:c.836T>C	chr15.hg19:g.59499975T>C	ENSP00000302393:p.Val279Ala	54.0	0.0		68.0	5.0	NM_033195	Q6DUY4|Q96LI2	Missense_Mutation	SNP	ENST00000307144.4	hg19	CCDS10171.1	.	.	.	.	.	.	.	.	.	.	T	16.41	3.115298	0.56505	.	.	ENSG00000171989	ENST00000307144	T	0.67698	-0.28	1.47	1.47	0.22746	Lactate/malate dehydrogenase, C-terminal (1);Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal (2);	0.206606	0.30575	U	0.009333	T	0.67239	0.2872	M	0.85542	2.76	0.43000	D	0.99451	P	0.39831	0.69	B	0.41619	0.361	T	0.67837	-0.5567	10	0.62326	D	0.03	.	6.659	0.23004	0.0:0.0:0.0:1.0	.	279	Q9BYZ2	LDH6B_HUMAN	A	279	ENSP00000302393:V279A	ENSP00000302393:V279A	V	+	2	0	LDHAL6B	57287267	0.587000	0.26791	0.044000	0.18714	0.689000	0.40095	2.261000	0.43276	0.654000	0.30846	0.254000	0.18369	GTC	.	.		0.408	LDHAL6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256015.1	NM_033195	
CSNK1G1	53944	hgsc.bcm.edu	37	15	64508813	64508813	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:64508813A>G	ENST00000303052.7	-	5	815	c.392T>C	c.(391-393)cTc>cCc	p.L131P	CSNK1G1_ENST00000607537.1_Missense_Mutation_p.L131P|CSNK1G1_ENST00000303032.6_Missense_Mutation_p.L131P|CTD-2116N17.1_ENST00000606793.1_Missense_Mutation_p.L104P	NM_022048.3	NP_071331.2	Q9HCP0	KC1G1_HUMAN	casein kinase 1, gamma 1	131	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|urinary_tract(1)	13						TCGGTCACAGAGGTCAAACAA	0.473																																					p.L131P		Atlas-SNP	.											.	CSNK1G1	56	.	0			c.T392C						.						100.0	82.0	88.0					15																	64508813		2203	4300	6503	SO:0001583	missense	53944	exon5			TCACAGAGGTCAA	AB042562	CCDS10192.2	15q22.1-q22.31	2013-01-17			ENSG00000169118	ENSG00000169118			2454	protein-coding gene	gene with protein product		606274				11124537	Standard	NM_022048		Approved	CK1gamma1	uc002anf.3	Q9HCP0	OTTHUMG00000133019	ENST00000303052.7:c.392T>C	chr15.hg19:g.64508813A>G	ENSP00000305777:p.Leu131Pro	112.0	0.0		85.0	4.0	NM_022048	Q5JPH1|Q96AE9|Q9HCP1	Missense_Mutation	SNP	ENST00000303052.7	hg19	CCDS10192.2	.	.	.	.	.	.	.	.	.	.	A	25.6	4.655024	0.88056	.	.	ENSG00000169118	ENST00000303052;ENST00000447727;ENST00000303032	T;T	0.68624	-0.34;-0.34	5.27	5.27	0.74061	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.171885	0.52532	D	0.000063	D	0.86037	0.5837	M	0.93808	3.46	0.80722	D	1	D;D;D	0.89917	0.999;1.0;0.999	D;D;D	0.80764	0.972;0.994;0.989	D	0.89895	0.4040	10	0.87932	D	0	.	15.4792	0.75511	1.0:0.0:0.0:0.0	.	131;131;131	Q9HCP0-2;Q8IXA3;Q9HCP0	.;.;KC1G1_HUMAN	P	131;87;131	ENSP00000305777:L131P;ENSP00000307753:L131P	ENSP00000307753:L131P	L	-	2	0	CSNK1G1	62295866	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.287000	0.95975	2.120000	0.65058	0.459000	0.35465	CTC	.	.		0.473	CSNK1G1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256605.1	NM_022048	
NOX5	79400	hgsc.bcm.edu	37	15	69339868	69339868	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:69339868T>C	ENST00000388866.3	+	12	1849	c.1808T>C	c.(1807-1809)aTc>aCc	p.I603T	NOX5_ENST00000525163.1_3'UTR|NOX5_ENST00000260364.5_Missense_Mutation_p.I585T|NOX5_ENST00000448182.3_Missense_Mutation_p.I557T|NOX5_ENST00000530406.2_Missense_Mutation_p.I575T|NOX5_ENST00000455873.3_Missense_Mutation_p.I568T	NM_001184779.1|NM_024505.3	NP_001171708.1|NP_078781.3	Q96PH1	NOX5_HUMAN	NADPH oxidase, EF-hand calcium binding domain 5	603					angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|cytokine secretion (GO:0050663)|cytokinesis (GO:0000910)|endothelial cell proliferation (GO:0001935)|oxidation-reduction process (GO:0055114)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|proton transport (GO:0015992)|regulation of fusion of sperm to egg plasma membrane (GO:0043012)|regulation of proton transport (GO:0010155)|superoxide anion generation (GO:0042554)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|flavin adenine dinucleotide binding (GO:0050660)|heme binding (GO:0020037)|hydrogen ion channel activity (GO:0015252)|NADP binding (GO:0050661)|superoxide-generating NADPH oxidase activity (GO:0016175)			breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|liver(2)|lung(18)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	35						CTGCAGAGTATCATGTACAGG	0.597																																					p.I603T		Atlas-SNP	.											.	NOX5	60	.	0			c.T1808C						.						98.0	93.0	95.0					15																	69339868		2200	4298	6498	SO:0001583	missense	79400	exon12			AGAGTATCATGTA	AF317889	CCDS32276.1, CCDS32276.2, CCDS53953.1, CCDS53954.1	15q22.31	2013-01-10			ENSG00000255346	ENSG00000255346		"""EF-hand domain containing"""	14874	protein-coding gene	gene with protein product		606572				11483596	Standard	NM_001184779		Approved	NOX5A, NOX5B	uc002ars.2	Q96PH1	OTTHUMG00000133320	ENST00000388866.3:c.1808T>C	chr15.hg19:g.69339868T>C	ENSP00000373518:p.Ile603Thr	74.0	0.0		79.0	5.0	NM_024505	B2RBJ4|Q08AN2|Q08AN3|Q8TEQ1|Q8TER4|Q96PH2|Q96PJ8|Q96PJ9|Q9H6E0|Q9HAM8	Missense_Mutation	SNP	ENST00000388866.3	hg19	CCDS32276.2	.	.	.	.	.	.	.	.	.	.	T	11.52	1.663214	0.29515	.	.	ENSG00000255346	ENST00000455873;ENST00000448182;ENST00000388866;ENST00000530406	D;D;D	0.95137	-3.62;-3.62;-3.62	3.02	3.02	0.34903	Ferric reductase, NAD binding (1);	0.000000	0.85682	D	0.000000	D	0.97551	0.9198	H	0.94222	3.51	0.49483	D	0.999797	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.81914	0.973;0.995;0.992	D	0.97344	0.9959	10	0.87932	D	0	.	9.9894	0.41860	0.0:0.0:0.0:1.0	.	568;603;575	Q96PH1-6;Q96PH1;Q96PH1-3	.;NOX5_HUMAN;.	T	568;585;603;575	ENSP00000416828:I568T;ENSP00000373518:I603T;ENSP00000432440:I575T	ENSP00000373518:I603T	I	+	2	0	NOX5	67126922	1.000000	0.71417	0.993000	0.49108	0.148000	0.21650	4.693000	0.61753	1.028000	0.39785	0.172000	0.16884	ATC	.	.		0.597	NOX5-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257124.2	NM_024505	
NEO1	4756	hgsc.bcm.edu	37	15	73470686	73470686	+	Silent	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:73470686A>G	ENST00000339362.5	+	8	1656	c.1209A>G	c.(1207-1209)tcA>tcG	p.S403S	NEO1_ENST00000560262.1_Silent_p.S403S|NEO1_ENST00000261908.6_Silent_p.S403S|NEO1_ENST00000558964.1_Silent_p.S403S			Q92859	NEO1_HUMAN	neogenin 1	403	Ig-like C2-type 4.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|iron ion homeostasis (GO:0055072)|muscle cell differentiation (GO:0042692)|myoblast fusion (GO:0007520)|positive regulation of muscle cell differentiation (GO:0051149)|regulation of transcription, DNA-templated (GO:0006355)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(9)|lung(26)|pancreas(2)|prostate(1)|skin(3)|urinary_tract(2)	57						TGGTGAAATCAGATGAAGGGT	0.343																																					p.S403S		Atlas-SNP	.											.	NEO1	102	.	0			c.A1209G						.						96.0	94.0	95.0					15																	73470686		2198	4297	6495	SO:0001819	synonymous_variant	4756	exon7			GAAATCAGATGAA	U61262	CCDS10247.1, CCDS53957.1, CCDS58378.1	15q22.3-q23	2014-06-20	2010-06-24		ENSG00000067141	ENSG00000067141		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	7754	protein-coding gene	gene with protein product	"""immunoglobulin superfamily, DCC subclass, member 2"""	601907	"""neogenin (chicken) homolog 1"""			9121761	Standard	NM_002499		Approved	NGN, HsT17534, IGDCC2, NTN1R2	uc002avm.4	Q92859	OTTHUMG00000133509	ENST00000339362.5:c.1209A>G	chr15.hg19:g.73470686A>G		105.0	0.0		98.0	4.0	NM_001172623	B7ZKM9|B7ZKN0|O00340|Q17RX1	Silent	SNP	ENST00000339362.5	hg19	CCDS10247.1																																																																																			.	.		0.343	NEO1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257472.2	NM_002499	
GOLGA6A	342096	hgsc.bcm.edu	37	15	74364639	74364639	+	Missense_Mutation	SNP	G	G	C	rs200350318		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:74364639G>C	ENST00000290438.3	-	14	1553	c.1513C>G	c.(1513-1515)Caa>Gaa	p.Q505E	RN7SL429P_ENST00000479090.2_RNA	NM_001038640.2	NP_001033729.2	Q9NYA3	GOG6A_HUMAN	golgin A6 family, member A	505						Golgi apparatus (GO:0005794)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|liver(1)|lung(6)|prostate(1)|urinary_tract(1)	16						TCCAGATGTTGTCCTCCATCT	0.632																																					p.Q505E		Atlas-SNP	.											GOLGA6A,NS,carcinoma,0,1	GOLGA6A	28	.	0			c.C1513G						.	C	GLU/GLN	13,2839		0,13,1413	43.0	76.0	64.0		1513	-1.8	0.0	15		64	41,5189		0,41,2574	no	missense	GOLGA6A	NM_001038640.2	29	0,54,3987	CC,CG,GG		0.7839,0.4558,0.6682	benign	505/694	74364639	54,8028	1426	2615	4041	SO:0001583	missense	342096	exon14			GATGTTGTCCTCC	AF263742	CCDS32290.1	15q24.1	2013-05-10	2010-02-12	2009-09-28	ENSG00000159289	ENSG00000159289			13567	protein-coding gene	gene with protein product		610288	"""golgi autoantigen, golgin subfamily a, member 6"", ""golgi autoantigen, golgin subfamily a, 6"", ""golgi autoantigen, golgin subfamily a, 6A"""	GOLGA6		11161787	Standard	NM_001038640		Approved	GLP	uc002axa.1	Q9NYA3	OTTHUMG00000173035	ENST00000290438.3:c.1513C>G	chr15.hg19:g.74364639G>C	ENSP00000290438:p.Gln505Glu	13.0	1.0		58.0	5.0	NM_001038640	A8K959|Q9NYA7	Missense_Mutation	SNP	ENST00000290438.3	hg19	CCDS32290.1	.	.	.	.	.	.	.	.	.	.	C	0	-2.871708	0.00062	0.004558	0.007839	ENSG00000159289	ENST00000290438	T	0.17213	2.29	0.887	-1.77	0.07982	.	.	.	.	.	T	0.02193	0.0068	N	0.00677	-1.265	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.22068	-1.0227	9	0.02654	T	1	.	5.0871	0.14689	0.1703:0.3999:0.4298:0.0	.	505	Q9NYA3	GOG6A_HUMAN	E	505	ENSP00000290438:Q505E	ENSP00000290438:Q505E	Q	-	1	0	GOLGA6A	72151692	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-2.799000	0.00762	-2.200000	0.00747	-2.001000	0.00444	CAA	.	G|0.999;C|0.001		0.632	GOLGA6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421835.1	XM_292357	
CCDC33	80125	hgsc.bcm.edu	37	15	74560701	74560701	+	Missense_Mutation	SNP	G	G	A	rs538969678		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:74560701G>A	ENST00000398814.3	+	5	879	c.448G>A	c.(448-450)Gcc>Acc	p.A150T	CCDC33_ENST00000321288.5_Missense_Mutation_p.A353T	NM_025055.3	NP_079331.3	Q8N5R6	CCD33_HUMAN	coiled-coil domain containing 33	353										breast(2)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(17)|ovary(4)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	39						GTCTGGGAAAGCCGATGAAGC	0.572													G|||	1	0.000199681	0.0	0.0	5008	,	,		15392	0.0		0.0	False		,,,				2504	0.001				p.A150T		Atlas-SNP	.											.	CCDC33	160	.	0			c.G448A						.						49.0	54.0	53.0					15																	74560701		1961	4161	6122	SO:0001583	missense	80125	exon5			GGGAAAGCCGATG	BC025689	CCDS42058.1, CCDS42059.1, CCDS73753.1	15q24.1	2009-08-06				ENSG00000140481			26552	protein-coding gene	gene with protein product	"""cancer/testis antigen 61"""					12477932	Standard	NM_025055		Approved	FLJ32855, CT61	uc002axo.4	Q8N5R6		ENST00000398814.3:c.448G>A	chr15.hg19:g.74560701G>A	ENSP00000381795:p.Ala150Thr	131.0	0.0		160.0	42.0	NM_025055	A8K3U4|A8MPQ6|A8MV61|A8MVU9|B3KQ49|Q8TAX6|Q9H5Q6	Missense_Mutation	SNP	ENST00000398814.3	hg19	CCDS42058.1	.	.	.	.	.	.	.	.	.	.	G	6.961	0.547158	0.13312	.	.	ENSG00000140481	ENST00000321288;ENST00000398814	T;T	0.23552	1.9;2.23	4.17	-3.93	0.04143	.	3.081050	0.01073	N	0.004855	T	0.18676	0.0448	L	0.47716	1.5	0.09310	N	1	B	0.24426	0.103	B	0.19391	0.025	T	0.09552	-1.0669	10	0.27785	T	0.31	.	1.3327	0.02138	0.195:0.3649:0.2146:0.2255	.	150	Q8N5R6-6	.	T	353;150	ENSP00000325012:A353T;ENSP00000381795:A150T	ENSP00000325012:A353T	A	+	1	0	CCDC33	72347754	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.913000	0.04042	-0.555000	0.06142	0.514000	0.50259	GCC	.	.		0.572	CCDC33-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000419491.2	NM_182791	
CLK3	1198	hgsc.bcm.edu	37	15	74921281	74921281	+	Splice_Site	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:74921281A>G	ENST00000395066.3	+	12	2110		c.e12-1		CLK3_ENST00000345005.4_Splice_Site|CLK3_ENST00000352989.5_Splice_Site|CLK3_ENST00000348245.3_Splice_Site	NM_001130028.1	NP_001123500.1	P49761	CLK3_HUMAN	CDC-like kinase 3						protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of RNA splicing (GO:0043484)	cytoplasmic vesicle (GO:0031410)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|prostate(2)|stomach(2)|urinary_tract(1)	15						CTTAATTTTCAGGAAGCAGAA	0.522																																					.	Ovarian(133;694 1754 28950 29027 31859)	Atlas-SNP	.											.	CLK3	78	.	0			c.1206-2A>G						.						50.0	54.0	53.0					15																	74921281		2197	4296	6493	SO:0001630	splice_region_variant	1198	exon12			ATTTTCAGGAAGC	L29220	CCDS10265.1, CCDS45304.1	15q24	2008-05-02			ENSG00000179335	ENSG00000179335		"""CDC-like kinases"""	2071	protein-coding gene	gene with protein product		602990				7990150, 9856501	Standard	NM_003992		Approved	clk3	uc010uln.2	P49761	OTTHUMG00000141320	ENST00000395066.3:c.1650-1A>G	chr15.hg19:g.74921281A>G		68.0	0.0		89.0	5.0	NM_003992	D3DW59|Q53Y48|Q9BRS3|Q9BUJ7	Splice_Site	SNP	ENST00000395066.3	hg19	CCDS45304.1	.	.	.	.	.	.	.	.	.	.	A	18.21	3.572663	0.65765	.	.	ENSG00000179335	ENST00000345005;ENST00000395066;ENST00000454830;ENST00000352989	.	.	.	5.44	5.44	0.79542	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.3135	0.66432	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CLK3	72708334	1.000000	0.71417	0.982000	0.44146	0.930000	0.56654	9.224000	0.95209	2.057000	0.61298	0.459000	0.35465	.	.	.		0.522	CLK3-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000390442.3		Intron
SLC28A1	9154	hgsc.bcm.edu	37	15	85438313	85438313	+	Silent	SNP	C	C	T	rs371921369|rs2277576		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:85438313C>T	ENST00000286749.3	+	5	510	c.420C>T	c.(418-420)ctC>ctT	p.L140L	SLC28A1_ENST00000537624.1_Silent_p.L140L|SLC28A1_ENST00000394573.1_Silent_p.L140L|SLC28A1_ENST00000537703.1_Silent_p.L62L|SLC28A1_ENST00000538177.1_Silent_p.L140L|SLC28A1_ENST00000537216.1_Silent_p.L140L|SLC28A1_ENST00000338602.2_Silent_p.L140L			O00337	S28A1_HUMAN	solute carrier family 28 (concentrative nucleoside transporter), member 1	140			L -> LV (in A). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9124315}.		nucleobase-containing compound metabolic process (GO:0006139)|nucleoside transmembrane transport (GO:1901642)|nucleoside transport (GO:0015858)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	nucleoside binding (GO:0001882)|nucleoside transmembrane transporter activity (GO:0005337)|nucleoside:sodium symporter activity (GO:0005415)	p.L140L(2)		breast(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)	41			BRCA - Breast invasive adenocarcinoma(143;0.0587)		Gemcitabine(DB00441)|Stavudine(DB00649)|Zidovudine(DB00495)	GGAGGTTTCTCAAGCCTCAGG	0.637																																					p.L140L		Atlas-SNP	.											SLC28A1_ENST00000338602,NS,carcinoma,0,1	SLC28A1	118	.	2	Substitution - coding silent(2)	lung(2)	c.C420T						.						45.0	47.0	47.0					15																	85438313		2203	4298	6501	SO:0001819	synonymous_variant	9154	exon6			GTTTCTCAAGCCT	U62967	CCDS10334.1, CCDS10335.1, CCDS73777.1	15q25.3	2013-07-17	2013-07-17		ENSG00000156222	ENSG00000156222		"""Solute carriers"""	11001	protein-coding gene	gene with protein product		606207	"""solute carrier family 28 (sodium-coupled nucleoside transporter), member 1"""			9124315	Standard	NM_004213		Approved	CNT1	uc002blg.3	O00337	OTTHUMG00000148668	ENST00000286749.3:c.420C>T	chr15.hg19:g.85438313C>T		87.0	1.0		90.0	4.0	NM_201651	A0AV42|A8K7I2|O00335|O00336|Q5U5S6|Q5U648|Q9UEZ9	Silent	SNP	ENST00000286749.3	hg19	CCDS10334.1																																																																																			.	.		0.637	SLC28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308998.2		
AGBL1	123624	hgsc.bcm.edu	37	15	87089360	87089360	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:87089360A>G	ENST00000441037.2	+	19	2770	c.2675A>G	c.(2674-2676)tAc>tGc	p.Y892C	AGBL1_ENST00000421325.2_Missense_Mutation_p.Y892C|AGBL1_ENST00000389298.3_Missense_Mutation_p.Y623C	NM_152336.2	NP_689549.2	Q96MI9	CBPC4_HUMAN	ATP/GTP binding protein-like 1	892					C-terminal protein deglutamylation (GO:0035609)|protein side chain deglutamylation (GO:0035610)	cytoplasm (GO:0005737)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			NS(3)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|liver(2)|lung(28)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	62						GAGGTCAACTACAGGGTAAGC	0.428																																					p.Y892C		Atlas-SNP	.											.	AGBL1	151	.	0			c.A2675G						.						72.0	67.0	68.0					15																	87089360		1972	4181	6153	SO:0001583	missense	123624	exon19			TCAACTACAGGGT	AK056872	CCDS58398.1	15q25.3	2014-06-23			ENSG00000166748	ENSG00000166748			26504	protein-coding gene	gene with protein product	"""cytosolic carboxypeptidase 4"""	615496				21074048, 24094747	Standard	NM_152336		Approved	FLJ32310, CCP4	uc002blz.1	Q96MI9	OTTHUMG00000149978	ENST00000441037.2:c.2675A>G	chr15.hg19:g.87089360A>G	ENSP00000413001:p.Tyr892Cys	86.0	0.0		98.0	4.0	NM_152336	A1A4X5|A6NJH6|C9JHL5	Missense_Mutation	SNP	ENST00000441037.2	hg19	CCDS58398.1	.	.	.	.	.	.	.	.	.	.	A	15.04	2.715038	0.48622	.	.	ENSG00000166748	ENST00000441037;ENST00000421325;ENST00000389298	T;T	0.10763	2.84;2.84	5.38	5.38	0.77491	Peptidase M14, carboxypeptidase A (1);	0.000000	0.36167	U	0.002753	T	0.27765	0.0683	L	0.50333	1.59	0.45403	D	0.99838	D	0.89917	1.0	D	0.97110	1.0	T	0.00533	-1.1685	10	0.56958	D	0.05	-12.4782	14.7196	0.69297	1.0:0.0:0.0:0.0	.	892	Q96MI9	CBPC4_HUMAN	C	927;892;623	ENSP00000397173:Y892C;ENSP00000373949:Y623C	ENSP00000373949:Y623C	Y	+	2	0	AGBL1	84890364	1.000000	0.71417	1.000000	0.80357	0.136000	0.21042	8.322000	0.90000	2.264000	0.75181	0.533000	0.62120	TAC	.	.		0.428	AGBL1-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000314929.5	NM_152336	
TM2D3	80213	hgsc.bcm.edu	37	15	102190269	102190269	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:102190269A>G	ENST00000333202.3	-	3	270	c.265T>C	c.(265-267)Tcc>Ccc	p.S89P	RNU6-807P_ENST00000516805.1_RNA|TM2D3_ENST00000561373.1_Missense_Mutation_p.S24P|TM2D3_ENST00000559107.1_Missense_Mutation_p.S89P|TM2D3_ENST00000347970.3_Missense_Mutation_p.S63P|TM2D3_ENST00000428002.2_Missense_Mutation_p.S63P	NM_078474.2	NP_510883.2	Q9BRN9	TM2D3_HUMAN	TM2 domain containing 3	89						integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(2)|lung(6)|ovary(1)	10	Lung NSC(78;0.000991)|all_lung(78;0.00128)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.000268)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			TAGGTACAGGAGAAATTTGTT	0.413																																					p.S89P		Atlas-SNP	.											.	TM2D3	18	.	0			c.T265C						.						117.0	104.0	108.0					15																	102190269		2203	4300	6503	SO:0001583	missense	80213	exon3			TACAGGAGAAATT	AK094955	CCDS10392.1, CCDS10393.1	15q26.3	2014-02-12			ENSG00000184277	ENSG00000184277			24128	protein-coding gene	gene with protein product		610014				11278849	Standard	XM_005254980		Approved	BLP2, FLJ22604	uc002bxi.3	Q9BRN9	OTTHUMG00000149872	ENST00000333202.3:c.265T>C	chr15.hg19:g.102190269A>G	ENSP00000330433:p.Ser89Pro	91.0	0.0		123.0	5.0	NM_078474	B2RDK9|Q9H046|Q9H651	Missense_Mutation	SNP	ENST00000333202.3	hg19	CCDS10393.1	.	.	.	.	.	.	.	.	.	.	A	22.6	4.308257	0.81247	.	.	ENSG00000184277	ENST00000428002;ENST00000347970;ENST00000333202	T;T;T	0.74526	-0.85;-0.85;-0.85	5.53	5.53	0.82687	.	0.115201	0.64402	D	0.000010	D	0.84942	0.5584	M	0.76574	2.34	0.38091	D	0.936973	D;D;D;D	0.89917	0.999;1.0;0.979;0.997	D;D;P;P	0.74023	0.952;0.982;0.865;0.818	D	0.87949	0.2722	10	0.66056	D	0.02	-34.125	13.6005	0.62015	1.0:0.0:0.0:0.0	.	89;63;63;89	B4DKG4;E7EPS7;Q9BRN9-2;Q9BRN9	.;.;.;TM2D3_HUMAN	P	63;63;89	ENSP00000402179:S63P;ENSP00000327584:S63P;ENSP00000330433:S89P	ENSP00000330433:S89P	S	-	1	0	TM2D3	100007792	1.000000	0.71417	0.992000	0.48379	0.958000	0.62258	6.229000	0.72294	2.091000	0.63221	0.533000	0.62120	TCC	.	.		0.413	TM2D3-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000313623.1	NM_078474	
RHBDF1	64285	hgsc.bcm.edu	37	16	109097	109097	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:109097A>G	ENST00000262316.6	-	17	2165	c.2023T>C	c.(2023-2025)Ttc>Ctc	p.F675L		NM_022450.3	NP_071895.3	Q96CC6	RHDF1_HUMAN	rhomboid 5 homolog 1 (Drosophila)	675					cell migration (GO:0016477)|cell proliferation (GO:0008283)|negative regulation of protein secretion (GO:0050709)|protein transport (GO:0015031)|proteolysis (GO:0006508)|regulation of epidermal growth factor receptor signaling pathway (GO:0042058)|regulation of proteasomal protein catabolic process (GO:0061136)|regulation of protein secretion (GO:0050708)	endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(4)|large_intestine(2)|lung(3)|ovary(1)|pancreas(1)|prostate(2)|soft_tissue(1)|upper_aerodigestive_tract(1)	18		all_cancers(16;2.56e-05)|all_epithelial(16;0.000116)|Hepatocellular(780;0.0068)|Lung NSC(18;0.0795)|all_lung(18;0.159)				GTCATCTGGAAGCAGATGGAC	0.612																																					p.F675L		Atlas-SNP	.											.	RHBDF1	54	.	0			c.T2023C						.						37.0	36.0	36.0					16																	109097		2203	4300	6503	SO:0001583	missense	64285	exon17			TCTGGAAGCAGAT	BC014425	CCDS32344.1	16p13.3	2008-02-05	2006-02-22		ENSG00000007384	ENSG00000007384			20561	protein-coding gene	gene with protein product		614403	"""chromosome 16 open reading frame 8"", ""rhomboid family 1 (Drosophila)"""	C16orf8		8318735, 15965977	Standard	NM_022450		Approved	EGFR-RS, FLJ2235, Dist1	uc002cfl.4	Q96CC6	OTTHUMG00000060719	ENST00000262316.6:c.2023T>C	chr16.hg19:g.109097A>G	ENSP00000262316:p.Phe675Leu	77.0	0.0		82.0	4.0	NM_022450	Q04842|Q1W6H2|Q4TT59|Q96S34|Q9H6E1	Missense_Mutation	SNP	ENST00000262316.6	hg19	CCDS32344.1	.	.	.	.	.	.	.	.	.	.	.	27.5	4.837917	0.91117	.	.	ENSG00000007384	ENST00000262316	T	0.13778	2.56	5.65	5.65	0.86999	Peptidase S54, rhomboid domain (1);	0.000000	0.85682	D	0.000000	T	0.25901	0.0631	L	0.42632	1.34	0.80722	D	1	P	0.42123	0.771	P	0.54460	0.753	T	0.00489	-1.1709	10	0.56958	D	0.05	-32.5993	15.069	0.72021	1.0:0.0:0.0:0.0	.	675	Q96CC6	RHDF1_HUMAN	L	675	ENSP00000262316:F675L	ENSP00000262316:F675L	F	-	1	0	RHBDF1	49097	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.502000	0.81614	2.163000	0.67991	0.533000	0.62120	TTC	.	.		0.612	RHBDF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134178.2	NM_022450	
WDR90	197335	hgsc.bcm.edu	37	16	705305	705305	+	Splice_Site	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:705305A>G	ENST00000293879.4	+	15	1556		c.e15-1		LA16c-349E10.1_ENST00000573609.1_RNA|WDR90_ENST00000549091.1_Splice_Site			Q96KV7	WDR90_HUMAN	WD repeat domain 90											endometrium(4)|kidney(3)|large_intestine(2)|lung(22)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	37		Hepatocellular(780;0.0218)				CATTCCTTGCAGGATGGCGTC	0.706																																					.		Atlas-SNP	.											.	WDR90	107	.	0			c.1557-2A>G						.						23.0	32.0	29.0					16																	705305		2191	4285	6476	SO:0001630	splice_region_variant	197335	exon15			CCTTGCAGGATGG	AB067511	CCDS42092.1	16p13.3	2013-01-09			ENSG00000161996	ENSG00000161996		"""WD repeat domain containing"""	26960	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 17"", ""chromosome 16 open reading frame 15"", ""chromosome 16 open reading frame 16"", ""chromosome 16 open reading frame 19"", ""chromosome 16 open reading frame 18"""	C16orf17, C16orf15, C16orf16, C16orf19, C16orf18		11572484, 11157797	Standard	XM_005255160		Approved	FLJ36483, KIAA1924	uc002cii.1	Q96KV7	OTTHUMG00000048040	ENST00000293879.4:c.1557-1A>G	chr16.hg19:g.705305A>G		16.0	0.0		87.0	4.0	NM_145294	Q0VA87|Q0VA88|Q6P048|Q6ZMS1|Q6ZTH1|Q8N202|Q8N221|Q8NBB8|Q96PW4|Q96S18	Splice_Site	SNP	ENST00000293879.4	hg19	CCDS42092.1	.	.	.	.	.	.	.	.	.	.	A	11.31	1.600321	0.28534	.	.	ENSG00000161996	ENST00000549091;ENST00000293879	.	.	.	4.67	4.67	0.58626	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.3099	0.60374	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	WDR90	645306	1.000000	0.71417	0.878000	0.34440	0.069000	0.16628	5.788000	0.69020	1.753000	0.51906	0.459000	0.35465	.	.	.		0.706	WDR90-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404335.1	NM_145294	Intron
MEFV	4210	hgsc.bcm.edu	37	16	3306370	3306370	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:3306370A>G	ENST00000219596.1	-	1	257	c.218T>C	c.(217-219)gTc>gCc	p.V73A	MEFV_ENST00000541159.1_Missense_Mutation_p.V73A|MEFV_ENST00000536379.1_Missense_Mutation_p.V73A|MEFV_ENST00000339854.4_Missense_Mutation_p.V73A	NM_000243.2	NP_000234.1	O15553	MEFV_HUMAN	Mediterranean fever	73	DAPIN. {ECO:0000255|PROSITE- ProRule:PRU00061}.				inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta production (GO:0032691)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of macrophage inflammatory protein 1 alpha production (GO:0071641)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of cysteine-type endopeptidase activity (GO:2001056)	cell projection (GO:0042995)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)	actin binding (GO:0003779)|zinc ion binding (GO:0008270)			NS(2)|biliary_tract(1)|breast(5)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(6)|lung(19)|ovary(3)|prostate(1)|skin(6)	50						GGCCCGCAGGACCTGCAGGGT	0.652																																					p.V73A		Atlas-SNP	.											.	MEFV	170	.	0			c.T218C						.						47.0	48.0	48.0					16																	3306370		2197	4300	6497	SO:0001583	missense	4210	exon1			CGCAGGACCTGCA	AF018080	CCDS10498.1, CCDS55981.1	16p13.3	2014-09-17			ENSG00000103313	ENSG00000103313		"""Tripartite motif containing / Tripartite motif containing"""	6998	protein-coding gene	gene with protein product	"""pyrin"""	608107		MEF		9288094	Standard	NM_000243		Approved	FMF, TRIM20	uc002cun.1	O15553	OTTHUMG00000129324	ENST00000219596.1:c.218T>C	chr16.hg19:g.3306370A>G	ENSP00000219596:p.Val73Ala	90.0	0.0		145.0	6.0	NM_000243	D3DUC0|F5H0Q3|Q3MJ84|Q96PN4|Q96PN5	Missense_Mutation	SNP	ENST00000219596.1	hg19	CCDS10498.1	.	.	.	.	.	.	.	.	.	.	A	19.94	3.919875	0.73098	.	.	ENSG00000103313	ENST00000545159;ENST00000219596;ENST00000339854;ENST00000541159;ENST00000536379;ENST00000534868	T;T;T;T	0.54279	0.58;0.58;0.58;0.58	5.98	5.98	0.97165	Pyrin (2);DEATH-like (2);	0.573434	0.15698	N	0.249041	T	0.67202	0.2868	M	0.64404	1.975	0.23440	N	0.997672	D	0.63046	0.992	P	0.61328	0.887	T	0.62599	-0.6820	10	0.87932	D	0	-17.3031	12.8496	0.57850	1.0:0.0:0.0:0.0	.	73	O15553	MEFV_HUMAN	A	73	ENSP00000219596:V73A;ENSP00000339639:V73A;ENSP00000438711:V73A;ENSP00000445079:V73A	ENSP00000219596:V73A	V	-	2	0	MEFV	3246371	0.985000	0.35326	1.000000	0.80357	0.607000	0.37147	3.228000	0.51270	2.288000	0.76882	0.482000	0.46254	GTC	.	.		0.652	MEFV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251464.1	NM_000243	
KIAA0430	9665	hgsc.bcm.edu	37	16	15705583	15705583	+	Silent	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:15705583T>C	ENST00000396368.3	-	18	3689	c.3483A>G	c.(3481-3483)ggA>ggG	p.G1161G	KIAA0430_ENST00000602337.1_Silent_p.G1158G|KIAA0430_ENST00000551742.1_Silent_p.G1161G|KIAA0430_ENST00000344181.3_Silent_p.G763G|CTB-193M12.1_ENST00000549756.1_RNA|KIAA0430_ENST00000548025.1_Silent_p.G1158G|KIAA0430_ENST00000540441.2_Silent_p.G996G	NM_001184998.1|NM_001184999.1|NM_014647.3	NP_001171927.1|NP_001171928.1|NP_055462.2	Q9Y4F3	MARF1_HUMAN	KIAA0430	1161	HTH OST-type 3. {ECO:0000255|PROSITE- ProRule:PRU00975}.				double-strand break repair (GO:0006302)|female meiotic division (GO:0007143)|negative regulation of phosphatase activity (GO:0010923)|oogenesis (GO:0048477)|regulation of gene expression (GO:0010468)	membrane (GO:0016020)|peroxisome (GO:0005777)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			breast(4)|endometrium(8)|kidney(4)|large_intestine(2)|lung(13)|ovary(3)|prostate(5)|skin(1)	40						TGGAGCCCATTCCAAGAATCT	0.488																																					p.G1161G		Atlas-SNP	.											.	KIAA0430	154	.	0			c.A3483G						.						71.0	70.0	70.0					16																	15705583		1914	4125	6039	SO:0001819	synonymous_variant	9665	exon18			GCCCATTCCAAGA	AB007890	CCDS10562.2, CCDS53990.1, CCDS55991.1	16p13.11	2013-01-11			ENSG00000166783	ENSG00000166783		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	29562	protein-coding gene	gene with protein product	"""limkain b1"", ""protein phosphatase 1, regulatory subunit 34"", ""meiosis arrest female 1"""	614593				9455477, 10493829, 15932519, 22442484, 23090997	Standard	NM_014647		Approved	LKAP, PPP1R34, Marf1	uc010uzw.2	Q9Y4F3	OTTHUMG00000129884	ENST00000396368.3:c.3483A>G	chr16.hg19:g.15705583T>C		78.0	0.0		112.0	5.0	NM_001184998	A8MSK2|B2RNX2|B4DYY9|B7ZMG1|B7ZMG2|F8VV09|Q6P1R6|Q8WYR2|Q9Y4J9	Silent	SNP	ENST00000396368.3	hg19	CCDS10562.2																																																																																			.	.		0.488	KIAA0430-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252131.2	NM_014647	
RBBP6	5930	hgsc.bcm.edu	37	16	24560285	24560285	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:24560285A>G	ENST00000319715.4	+	3	718	c.286A>G	c.(286-288)Atg>Gtg	p.M96V	RBBP6_ENST00000348022.2_Missense_Mutation_p.M96V|RBBP6_ENST00000452655.2_Missense_Mutation_p.M96V|RBBP6_ENST00000381039.3_Missense_Mutation_p.M96V	NM_006910.4	NP_008841.2	Q7Z6E9	RBBP6_HUMAN	retinoblastoma binding protein 6	96					embryonic organ development (GO:0048568)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|somite development (GO:0061053)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(17)|ovary(4)|pancreas(1)|prostate(2)|urinary_tract(1)	46				GBM - Glioblastoma multiforme(48;0.0518)		TGAACCAGCGATGGCAACTAC	0.279																																					p.M96V		Atlas-SNP	.											.	RBBP6	158	.	0			c.A286G						.						101.0	87.0	92.0					16																	24560285		2197	4298	6495	SO:0001583	missense	5930	exon3			CCAGCGATGGCAA		CCDS10621.1, CCDS10622.1, CCDS45444.1	16p12.2	2008-08-04	2001-11-28		ENSG00000122257	ENSG00000122257			9889	protein-coding gene	gene with protein product	"""proliferation potential-related protein"""	600938	"""retinoblastoma-binding protein 6"""			8595913, 16396680	Standard	NM_006910		Approved	P2P-R, PACT, SNAMA	uc002dmh.3	Q7Z6E9	OTTHUMG00000096991	ENST00000319715.4:c.286A>G	chr16.hg19:g.24560285A>G	ENSP00000317872:p.Met96Val	44.0	0.0		59.0	4.0	NM_018703	Q147T5|Q15290|Q6DKH4|Q6P4C2|Q6YNC9|Q7Z6E8|Q8N0V2|Q96PH3|Q9H3I8|Q9H5M5|Q9NPX4	Missense_Mutation	SNP	ENST00000319715.4	hg19	CCDS10621.1	.	.	.	.	.	.	.	.	.	.	A	10.99	1.507309	0.27036	.	.	ENSG00000122257	ENST00000381039;ENST00000452655;ENST00000319715;ENST00000348022	T;T;T;T	0.40476	2.41;1.03;2.67;2.67	5.25	5.25	0.73442	.	0.303560	0.40144	N	0.001171	T	0.30727	0.0774	N	0.19112	0.55	0.37471	D	0.915612	B;B;B;B	0.18610	0.004;0.029;0.017;0.002	B;B;B;B	0.21546	0.002;0.035;0.016;0.003	T	0.16660	-1.0395	10	0.28530	T	0.3	-16.8275	15.4517	0.75279	1.0:0.0:0.0:0.0	.	96;96;96;96	Q7Z6E9-4;Q7Z6E9-2;Q7Z6E9;Q7Z6E9-3	.;.;RBBP6_HUMAN;.	V	96	ENSP00000370427:M96V;ENSP00000390537:M96V;ENSP00000317872:M96V;ENSP00000316291:M96V	ENSP00000317872:M96V	M	+	1	0	RBBP6	24467786	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.099000	0.76981	2.115000	0.64714	0.477000	0.44152	ATG	.	.		0.279	RBBP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214067.2	NM_006910	
TNRC6A	27327	hgsc.bcm.edu	37	16	24826473	24826473	+	Missense_Mutation	SNP	A	A	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:24826473A>C	ENST00000395799.3	+	19	4807	c.4678A>C	c.(4678-4680)Att>Ctt	p.I1560L	CTD-2515A14.1_ENST00000568895.1_RNA|TNRC6A_ENST00000432286.2_Missense_Mutation_p.I38L|TNRC6A_ENST00000315183.7_Missense_Mutation_p.I1511L	NM_014494.2	NP_055309.2	Q8NDV7	TNR6A_HUMAN	trinucleotide repeat containing 6A	1560					cellular response to starvation (GO:0009267)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|micro-ribonucleoprotein complex (GO:0035068)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(13)|kidney(5)|large_intestine(13)|liver(1)|lung(20)|ovary(3)|skin(2)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	64				GBM - Glioblastoma multiforme(48;0.0394)		GTTAGGTGCTATTTCAAGTGG	0.383																																					p.I1560L		Atlas-SNP	.											.	TNRC6A	171	.	0			c.A4678C						.						141.0	133.0	136.0					16																	24826473		2197	4300	6497	SO:0001583	missense	27327	exon19			GGTGCTATTTCAA	U80739	CCDS10624.2	16p11.2	2009-09-22	2004-12-17	2004-12-17	ENSG00000090905	ENSG00000090905		"""Trinucleotide (CAG) repeat containing"""	11969	protein-coding gene	gene with protein product		610739	"""trinucleotide repeat containing 6"""	TNRC6		9225980	Standard	NM_014494		Approved	CAGH26, KIAA1460, GW182	uc002dmm.3	Q8NDV7	OTTHUMG00000096999	ENST00000395799.3:c.4678A>C	chr16.hg19:g.24826473A>C	ENSP00000379144:p.Ile1560Leu	178.0	0.0		212.0	60.0	NM_014494	C9JAR8|O15408|Q658L5|Q6NVB5|Q8NEZ0|Q8TBT8|Q8TCR0|Q9NV59|Q9P268	Missense_Mutation	SNP	ENST00000395799.3	hg19	CCDS10624.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	20.6|20.6	4.010138|4.010138	0.75046|0.75046	.|.	.|.	ENSG00000090905|ENSG00000090905	ENST00000315183;ENST00000395799;ENST00000432286|ENST00000450465	T;T|.	0.13089|.	2.66;2.62|.	5.92|5.92	5.92|5.92	0.95590|0.95590	.|.	0.125092|.	0.64402|.	D|.	0.000005|.	T|T	0.72358|0.72358	0.3450|0.3450	M|M	0.64997|0.64997	1.995|1.995	0.54753|0.54753	D|D	0.999982|0.999982	B;B;B;P|.	0.39480|.	0.194;0.003;0.028;0.675|.	B;B;B;B|.	0.35413|.	0.107;0.01;0.047;0.202|.	T|T	0.71144|0.71144	-0.4678|-0.4678	10|5	0.51188|.	T|.	0.08|.	-12.8497|-12.8497	16.3631|16.3631	0.83280|0.83280	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	227;699;1511;1560|.	B3KSX2;C9JA83;Q8NDV7-6;Q8NDV7|.	.;.;.;TNR6A_HUMAN|.	L|S	1511;1560;38|450	ENSP00000326900:I1511L;ENSP00000379144:I1560L|.	ENSP00000326900:I1511L|.	I|Y	+|+	1|2	0|0	TNRC6A|TNRC6A	24733974|24733974	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.989000|0.989000	0.77384|0.77384	7.975000|7.975000	0.88055|0.88055	2.266000|2.266000	0.75297|0.75297	0.533000|0.533000	0.62120|0.62120	ATT|TAT	.	.		0.383	TNRC6A-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214081.1	NM_020847	
MAZ	4150	hgsc.bcm.edu	37	16	29821464	29821464	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:29821464T>C	ENST00000322945.6	+	5	1511	c.1346T>C	c.(1345-1347)gTa>gCa	p.V449A	AC009133.14_ENST00000563806.1_RNA|AC009133.14_ENST00000569981.1_RNA|PRRT2_ENST00000358758.7_5'Flank|MAZ_ENST00000568282.1_3'UTR|MAZ_ENST00000563402.1_Silent_p.S105S|PRRT2_ENST00000300797.6_5'Flank|AC009133.15_ENST00000566537.1_RNA|MAZ_ENST00000568544.1_Missense_Mutation_p.V50A|MAZ_ENST00000566906.2_Silent_p.S103S|PRRT2_ENST00000567659.1_5'Flank|MAZ_ENST00000545521.1_Missense_Mutation_p.V426A|MAZ_ENST00000562337.1_Missense_Mutation_p.V144A|MAZ_ENST00000219782.6_3'UTR|AC009133.20_ENST00000569039.1_RNA	NM_002383.2	NP_002374.2	P56270	MAZ_HUMAN	MYC-associated zinc finger protein (purine-binding transcription factor)	449	Poly-Ala.				positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|termination of RNA polymerase II transcription (GO:0006369)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			endometrium(3)|lung(4)|ovary(2)|upper_aerodigestive_tract(1)	10						gcggcagcagtagcagcCCCT	0.672																																					p.V449A	Colon(72;875 1167 15364 30899 37091)	Atlas-SNP	.											.,1	MAZ	48	.	0			c.T1346C						.						10.0	15.0	13.0					16																	29821464		1943	4046	5989	SO:0001583	missense	4150	exon5			CAGCAGTAGCAGC	M93339	CCDS42143.1, CCDS42144.1, CCDS61902.1, CCDS61903.1	16p11.2	2013-01-08			ENSG00000103495	ENSG00000103495		"""Zinc fingers, C2H2-type"""	6914	protein-coding gene	gene with protein product		600999				1567856, 1502157	Standard	NM_001276275		Approved	ZF87, Pur-1, Zif87, ZNF801	uc002dtx.4	P56270	OTTHUMG00000132119	ENST00000322945.6:c.1346T>C	chr16.hg19:g.29821464T>C	ENSP00000313362:p.Val449Ala	25.0	0.0		65.0	5.0	NM_002383	A8QJL9|C6G496|G5E927|H3BQD6|Q15703|Q8NFN7|Q99443	Missense_Mutation	SNP	ENST00000322945.6	hg19	CCDS42143.1	.	.	.	.	.	.	.	.	.	.	T	9.414	1.081337	0.20309	.	.	ENSG00000103495	ENST00000545521;ENST00000322945;ENST00000544343	T;T	0.08807	3.11;3.05	3.91	3.91	0.45181	.	.	.	.	.	T	0.12561	0.0305	N	0.14661	0.345	0.80722	D	1	P;D;P	0.61697	0.924;0.99;0.924	P;D;P	0.70935	0.857;0.971;0.857	T	0.08229	-1.0732	9	0.72032	D	0.01	.	9.4274	0.38588	0.0:0.0:0.0:1.0	.	426;224;449	C6G496;F5H7A6;P56270	.;.;MAZ_HUMAN	A	426;449;224	ENSP00000443956:V426A;ENSP00000313362:V449A	ENSP00000313362:V449A	V	+	2	0	MAZ	29728965	0.628000	0.27138	1.000000	0.80357	0.417000	0.31264	1.133000	0.31430	2.008000	0.58898	0.454000	0.30748	GTA	.	.		0.672	MAZ-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000435536.1	NM_002383	
ZNF689	115509	hgsc.bcm.edu	37	16	30615727	30615727	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:30615727T>C	ENST00000287461.3	-	3	1698	c.1361A>G	c.(1360-1362)gAg>gGg	p.E454G	RP11-146F11.5_ENST00000563540.1_RNA|ZNF689_ENST00000566673.1_5'Flank	NM_138447.1	NP_612456.1	Q96CS4	ZN689_HUMAN	zinc finger protein 689	454					regulation of transcription, DNA-templated (GO:0006355)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|prostate(1)|urinary_tract(1)	14			Colorectal(24;0.198)			GAAAGGCTTCTCCCCCGTGTG	0.647																																					p.E454G		Atlas-SNP	.											.	ZNF689	48	.	0			c.A1361G						.						33.0	27.0	29.0					16																	30615727		2197	4300	6497	SO:0001583	missense	115509	exon3			GGCTTCTCCCCCG	BC014000	CCDS10686.1	16p11.2	2013-01-08			ENSG00000156853	ENSG00000156853		"""Zinc fingers, C2H2-type"", ""-"""	25173	protein-coding gene	gene with protein product							Standard	NM_138447		Approved	FLJ90415	uc031qvq.1	Q96CS4	OTTHUMG00000132415	ENST00000287461.3:c.1361A>G	chr16.hg19:g.30615727T>C	ENSP00000287461:p.Glu454Gly	71.0	0.0		168.0	7.0	NM_138447	Q658J5	Missense_Mutation	SNP	ENST00000287461.3	hg19	CCDS10686.1	.	.	.	.	.	.	.	.	.	.	t	15.02	2.708418	0.48517	.	.	ENSG00000156853	ENST00000287461;ENST00000443190	T	0.27557	1.66	4.52	4.52	0.55395	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.49916	D	0.000135	T	0.39860	0.1094	M	0.67625	2.065	0.41007	D	0.984979	P	0.36909	0.573	B	0.43680	0.427	T	0.45011	-0.9290	10	0.87932	D	0	-21.9359	12.5088	0.55995	0.0:0.0:0.0:1.0	.	454	Q96CS4	ZN689_HUMAN	G	454	ENSP00000287461:E454G	ENSP00000287461:E454G	E	-	2	0	ZNF689	30523228	0.586000	0.26782	1.000000	0.80357	0.165000	0.22458	1.714000	0.37961	2.272000	0.75746	0.524000	0.50904	GAG	.	.		0.647	ZNF689-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255552.1	NM_138447	
STX1B	112755	hgsc.bcm.edu	37	16	31012910	31012910	+	Silent	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:31012910A>G	ENST00000215095.5	-	2	276	c.45T>C	c.(43-45)gaT>gaC	p.D15D	STX1B_ENST00000565419.1_Silent_p.D15D	NM_052874.3	NP_443106.1	P61266	STX1B_HUMAN	syntaxin 1B	15					intracellular protein transport (GO:0006886)|neurotransmitter transport (GO:0006836)|regulation of exocytosis (GO:0017157)|regulation of gene expression (GO:0010468)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)			breast(2)|endometrium(1)|large_intestine(5)|lung(5)	13						CCTCTTCATCATCACTGTCTT	0.617																																					p.D15D		Atlas-SNP	.											.	STX1B	26	.	0			c.T45C						.						73.0	63.0	67.0					16																	31012910		2197	4300	6497	SO:0001819	synonymous_variant	112755	exon2			TTCATCATCACTG	AY028792	CCDS10699.1	16p12-p11	2008-02-05	2007-06-20	2007-06-20	ENSG00000099365	ENSG00000099365			18539	protein-coding gene	gene with protein product		601485	"""syntaxin 1B1"", ""syntaxin 1B2"""	STX1B1, STX1B2			Standard	NM_052874		Approved		uc010cad.2	P61266	OTTHUMG00000132391	ENST00000215095.5:c.45T>C	chr16.hg19:g.31012910A>G		72.0	0.0		84.0	4.0	NM_052874	Q15531|Q2VPS2	Silent	SNP	ENST00000215095.5	hg19	CCDS10699.1																																																																																			.	.		0.617	STX1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255521.2		
FUK	197258	hgsc.bcm.edu	37	16	70514950	70514950	+	IGR	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:70514950T>C	ENST00000288078.6	+	0	4081				COG4_ENST00000323786.5_Missense_Mutation_p.D778G	NM_145059.2	NP_659496.2	Q8N0W3	FUK_HUMAN	fucokinase							cytoplasm (GO:0005737)	ATP binding (GO:0005524)|fucokinase activity (GO:0050201)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(11)|ovary(2)|prostate(2)	23		Ovarian(137;0.0694)				ACTGCGGAAGTCTATCCGCAG	0.617																																					p.D778G		Atlas-SNP	.											.	COG4	64	.	0			c.A2333G						.						48.0	49.0	48.0					16																	70514950		2198	4300	6498	SO:0001628	intergenic_variant	25839	exon19			CGGAAGTCTATCC		CCDS10891.2	16q22.1	2008-02-05			ENSG00000157353	ENSG00000157353	2.7.1.52		29500	protein-coding gene	gene with protein product	"""L-fucose kinase"""	608675				12056818	Standard	XM_006721161		Approved	FLJ39408	uc002eyy.3	Q8N0W3	OTTHUMG00000074085		chr16.hg19:g.70514950T>C		67.0	0.0		89.0	5.0	NM_015386	Q5PSM3|Q5XKL6|Q6ZRA0|Q96MT9	Missense_Mutation	SNP	ENST00000288078.6	hg19	CCDS10891.2	.	.	.	.	.	.	.	.	.	.	T	33	5.274405	0.95459	.	.	ENSG00000103051	ENST00000323786;ENST00000338984;ENST00000526700;ENST00000539961	T	0.69561	-0.41	5.97	5.97	0.96955	.	0.000000	0.85682	D	0.000000	D	0.85771	0.5774	M	0.91717	3.235	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;0.998	D	0.88873	0.3334	10	0.87932	D	0	-22.4546	16.4504	0.83984	0.0:0.0:0.0:1.0	.	684;752;774;234	Q8N8L9;Q6PIW8;Q9H9E3;E9PQK0	.;.;COG4_HUMAN;.	G	778;753;234;436	ENSP00000315775:D778G	ENSP00000315775:D778G	D	-	2	0	COG4	69072451	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.755000	0.85180	2.288000	0.76882	0.533000	0.62120	GAC	.	.		0.617	FUK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157291.2	NM_145059	
VAC14	55697	hgsc.bcm.edu	37	16	70820186	70820186	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:70820186A>G	ENST00000261776.5	-	2	447	c.187T>C	c.(187-189)Tct>Cct	p.S63P		NM_018052.3	NP_060522.3	Q08AM6	VAC14_HUMAN	Vac14 homolog (S. cerevisiae)	63					phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|regulation of lipid kinase activity (GO:0043550)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|late endosome membrane (GO:0031902)|PAS complex (GO:0070772)	receptor activity (GO:0004872)			breast(2)|endometrium(2)|kidney(10)|large_intestine(1)|lung(10)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	33		Ovarian(137;0.0699)				GGGTGCTGAGACAGGGCAAAC	0.612																																					p.S63P		Atlas-SNP	.											.	VAC14	65	.	0			c.T187C						.						93.0	95.0	94.0					16																	70820186		2198	4300	6498	SO:0001583	missense	55697	exon2			GCTGAGACAGGGC	AK056433	CCDS10896.1	16q22.1	2010-03-23	2005-02-09		ENSG00000103043	ENSG00000103043			25507	protein-coding gene	gene with protein product		604632	"""Tax1 (human T-cell leukemia virus type I) binding protein 2"""	TAX1BP2		15542851, 12719380	Standard	NM_018052		Approved	FLJ10305, ArPIKfyve	uc002ezm.3	Q08AM6	OTTHUMG00000137583	ENST00000261776.5:c.187T>C	chr16.hg19:g.70820186A>G	ENSP00000261776:p.Ser63Pro	99.0	0.0		94.0	4.0	NM_018052	B3KPJ5|B3KSM8|Q13174|Q6IA12|Q7L4Y1|Q9BW96|Q9H6V6	Missense_Mutation	SNP	ENST00000261776.5	hg19	CCDS10896.1	.	.	.	.	.	.	.	.	.	.	A	31	5.068020	0.93950	.	.	ENSG00000103043	ENST00000261776	.	.	.	5.49	5.49	0.81192	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.84492	0.5484	M	0.89840	3.065	0.80722	D	1	D	0.76494	0.999	D	0.71184	0.972	D	0.87902	0.2691	9	0.72032	D	0.01	-15.7429	15.5895	0.76517	1.0:0.0:0.0:0.0	.	63	Q08AM6	VAC14_HUMAN	P	63	.	ENSP00000261776:S63P	S	-	1	0	VAC14	69377687	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.274000	0.95731	2.085000	0.62840	0.528000	0.53228	TCT	.	.		0.612	VAC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268973.3	NM_018052	
ZFHX3	463	hgsc.bcm.edu	37	16	72828411	72828411	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:72828411T>C	ENST00000268489.5	-	9	8842	c.8170A>G	c.(8170-8172)Act>Gct	p.T2724A	RP5-991G20.4_ENST00000569195.1_RNA|ZFHX3_ENST00000397992.5_Missense_Mutation_p.T1810A	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	2724					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|regulation of neuron differentiation (GO:0045664)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11)	153		Ovarian(137;0.13)				TCAAGAGCAGTCTTGGCTTTG	0.572																																					p.T2724A		Atlas-SNP	.											.	ZFHX3	404	.	0			c.A8170G						.						73.0	63.0	66.0					16																	72828411		2198	4300	6498	SO:0001583	missense	463	exon9			GAGCAGTCTTGGC	D10250	CCDS10908.1, CCDS54035.1	16q22.3	2012-03-09	2007-08-09	2007-08-09	ENSG00000140836	ENSG00000140836		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	777	protein-coding gene	gene with protein product		104155	"""AT-binding transcription factor 1"""	ATBF1		1719379, 7592926	Standard	NM_006885		Approved	ZNF927	uc002fck.3	Q15911	OTTHUMG00000137599	ENST00000268489.5:c.8170A>G	chr16.hg19:g.72828411T>C	ENSP00000268489:p.Thr2724Ala	98.0	0.0		98.0	4.0	NM_006885	D3DWS8|O15101|Q13719	Missense_Mutation	SNP	ENST00000268489.5	hg19	CCDS10908.1	.	.	.	.	.	.	.	.	.	.	T	11.60	1.685672	0.29962	.	.	ENSG00000140836	ENST00000268489;ENST00000397992	T;T	0.27402	1.67;1.67	5.77	5.77	0.91146	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);	0.000000	0.51477	D	0.000089	T	0.49440	0.1557	L	0.47716	1.5	0.80722	D	1	D	0.69078	0.997	D	0.75020	0.985	T	0.46569	-0.9182	10	0.56958	D	0.05	.	16.0858	0.81049	0.0:0.0:0.0:1.0	.	2724	Q15911	ZFHX3_HUMAN	A	2724;1810	ENSP00000268489:T2724A;ENSP00000438926:T1810A	ENSP00000268489:T2724A	T	-	1	0	ZFHX3	71385912	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.221000	0.72243	2.198000	0.70561	0.533000	0.62120	ACT	.	.		0.572	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885	
RFWD3	55159	hgsc.bcm.edu	37	16	74678605	74678605	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:74678605A>G	ENST00000361070.4	-	5	918	c.821T>C	c.(820-822)cTa>cCa	p.L274P	RFWD3_ENST00000571750.1_Missense_Mutation_p.L274P	NM_018124.3	NP_060594.3	Q6PCD5	RFWD3_HUMAN	ring finger and WD repeat domain 3	274					DNA repair (GO:0006281)|mitotic G1 DNA damage checkpoint (GO:0031571)|protein ubiquitination (GO:0016567)|regulation of DNA damage checkpoint (GO:2000001)|response to ionizing radiation (GO:0010212)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|MDM2/MDM4 family protein binding (GO:0097371)|p53 binding (GO:0002039)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(12)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	26						AGCAGAAGGTAGCAGAGGCTC	0.443																																					p.L274P		Atlas-SNP	.											.	RFWD3	49	.	0			c.T821C						.						77.0	74.0	75.0					16																	74678605		2198	4300	6498	SO:0001583	missense	55159	exon5			GAAGGTAGCAGAG	AK001382	CCDS32486.1	16q22.3	2013-01-09						"""WD repeat domain containing"", ""RING-type (C3HC4) zinc fingers"""	25539	protein-coding gene	gene with protein product		614151				21504906	Standard	XM_005256021		Approved	FLJ10520, RNF201	uc002fda.3	Q6PCD5		ENST00000361070.4:c.821T>C	chr16.hg19:g.74678605A>G	ENSP00000354361:p.Leu274Pro	156.0	0.0		194.0	8.0	NM_018124	A8K585|B2RE35|D3DUJ8|Q5XKR3|Q9H9Q3|Q9NVT4	Missense_Mutation	SNP	ENST00000361070.4	hg19	CCDS32486.1	.	.	.	.	.	.	.	.	.	.	A	8.649	0.897741	0.17686	.	.	ENSG00000168411	ENST00000361070	T	0.21191	2.02	5.14	-7.62	0.01294	.	2.609730	0.00953	N	0.002993	T	0.10723	0.0262	N	0.17082	0.46	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.15435	-1.0437	10	0.27785	T	0.31	-8.4184	5.2825	0.15682	0.3366:0.1038:0.4577:0.102	.	274	Q6PCD5	RFWD3_HUMAN	P	274	ENSP00000354361:L274P	ENSP00000354361:L274P	L	-	2	0	RFWD3	73236106	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-0.057000	0.11768	-1.576000	0.01652	-1.527000	0.00925	CTA	.	.		0.443	RFWD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436506.2	NM_018124	
ZNF778	197320	hgsc.bcm.edu	37	16	89293177	89293177	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:89293177A>G	ENST00000433976.2	+	6	729	c.397A>G	c.(397-399)Agc>Ggc	p.S133G	ZNF778_ENST00000306502.6_Missense_Mutation_p.S91G|RP11-46C24.6_ENST00000563182.1_RNA	NM_001201407.1|NM_182531.3	NP_001188336.1|NP_872337.2	Q96MU6	ZN778_HUMAN	zinc finger protein 778	133					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(4)|kidney(1)|large_intestine(4)|lung(11)|prostate(2)|skin(2)	24				BRCA - Breast invasive adenocarcinoma(80;0.0269)		CTCAGGCCTCAGCACACACGT	0.463																																					p.S161G		Atlas-SNP	.											.	ZNF778	67	.	0			c.A481G						.						74.0	77.0	76.0					16																	89293177		2072	4241	6313	SO:0001583	missense	197320	exon7			GGCCTCAGCACAC	AK056437	CCDS45550.1, CCDS73928.1	16q24.3	2014-09-17			ENSG00000170100	ENSG00000170100		"""Zinc fingers, C2H2-type"", ""-"""	26479	protein-coding gene	gene with protein product							Standard	NM_182531		Approved	FLJ31875	uc021tms.1	Q96MU6		ENST00000433976.2:c.397A>G	chr16.hg19:g.89293177A>G	ENSP00000405289:p.Ser133Gly	106.0	0.0		147.0	6.0	NM_001201407	Q08AG0	Missense_Mutation	SNP	ENST00000433976.2	hg19	CCDS45550.1	.	.	.	.	.	.	.	.	.	.	A	9.372	1.070822	0.20147	.	.	ENSG00000170100	ENST00000433976;ENST00000306502	T;T	0.29655	1.56;1.56	1.21	-0.189	0.13260	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);	.	.	.	.	T	0.19525	0.0469	L	0.38175	1.15	0.09310	N	1	P;B	0.35493	0.505;0.208	B;B	0.33960	0.173;0.057	T	0.16305	-1.0407	9	0.30854	T	0.27	.	5.5952	0.17323	0.4044:0.5956:0.0:0.0	.	91;133	Q96MU6-2;Q96MU6	.;ZN778_HUMAN	G	133;91	ENSP00000405289:S133G;ENSP00000305203:S91G	ENSP00000305203:S91G	S	+	1	0	ZNF778	87820678	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	0.008000	0.13197	-0.061000	0.13110	0.378000	0.23410	AGC	.	.		0.463	ZNF778-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430383.1	NM_182531	
FANCA	2175	hgsc.bcm.edu	37	16	89857909	89857909	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:89857909T>C	ENST00000389301.3	-	14	1291	c.1261A>G	c.(1261-1263)Agc>Ggc	p.S421G	FANCA_ENST00000568369.1_Missense_Mutation_p.S421G	NM_000135.2	NP_000126.2	O15360	FANCA_HUMAN	Fanconi anemia, complementation group A	421					DNA repair (GO:0006281)|female gonad development (GO:0008585)|male gonad development (GO:0008584)|male meiosis (GO:0007140)|protein complex assembly (GO:0006461)|regulation of cell proliferation (GO:0042127)	cytoplasm (GO:0005737)|Fanconi anaemia nuclear complex (GO:0043240)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(5)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(3)|skin(2)|urinary_tract(3)	47		Lung NSC(15;8.48e-06)|all_lung(18;1.31e-05)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.028)		AGCTGGCAGCTCTCGAATGCC	0.572			"""D, Mis, N, F, S"""			"""AML, leukemia"""		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.S421G		Atlas-SNP	.	yes	Rec		Fanconi anaemia A	16	16q24.3	2175	"""Fanconi anemia, complementation group A"""		L	.	FANCA	99	.	0			c.A1261G						.						68.0	54.0	58.0					16																	89857909		2198	4300	6498	SO:0001583	missense	2175	exon14	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	GGCAGCTCTCGAA	Z83067	CCDS32515.1, CCDS42221.1, CCDS67099.1	16q24.3	2014-09-17			ENSG00000187741	ENSG00000187741		"""Fanconi anemia, complementation groups"""	3582	protein-coding gene	gene with protein product		607139		FACA, FANCH		7581462, 9382107	Standard	NM_001286167		Approved	FAA, FA-H, FAH	uc002fou.1	O15360		ENST00000389301.3:c.1261A>G	chr16.hg19:g.89857909T>C	ENSP00000373952:p.Ser421Gly	82.0	0.0		99.0	4.0	NM_000135	A5D923|B4DRI7|H3BSR5|O75266|Q6PL10|Q92497|Q96H18|Q9UEA5|Q9UEL8|Q9UEL9|Q9UPK3|Q9Y6M2	Missense_Mutation	SNP	ENST00000389301.3	hg19	CCDS32515.1	.	.	.	.	.	.	.	.	.	.	T	15.44	2.835030	0.50951	.	.	ENSG00000187741	ENST00000389301	D	0.98747	-5.11	5.13	5.13	0.70059	.	0.284959	0.30365	N	0.009785	D	0.98343	0.9450	M	0.73598	2.24	0.80722	D	1	D;D	0.62365	0.991;0.991	P;P	0.51266	0.664;0.664	D	0.98607	1.0661	10	0.62326	D	0.03	-4.3847	14.1777	0.65552	0.0:0.0:0.0:1.0	.	421;421	B4DRI7;O15360	.;FANCA_HUMAN	G	421	ENSP00000373952:S421G	ENSP00000373952:S421G	S	-	1	0	FANCA	88385410	1.000000	0.71417	0.651000	0.29564	0.054000	0.15201	2.685000	0.46959	1.957000	0.56846	0.529000	0.55759	AGC	.	.		0.572	FANCA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000421927.1		
GLOD4	51031	hgsc.bcm.edu	37	17	673366	673366	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:673366T>C	ENST00000301328.5	-	8	730	c.707A>G	c.(706-708)gAg>gGg	p.E236G	GLOD4_ENST00000536578.1_Missense_Mutation_p.E212G|GLOD4_ENST00000301329.6_Missense_Mutation_p.E221G			Q9HC38	GLOD4_HUMAN	glyoxalase domain containing 4	236						extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)				endometrium(1)|large_intestine(1)|prostate(1)	3				UCEC - Uterine corpus endometrioid carcinoma (25;0.022)		CTTCTGGTTCTCCCTTTTCAT	0.532																																					p.E221G		Atlas-SNP	.											.	GLOD4	12	.	0			c.A662G						.						68.0	61.0	63.0					17																	673366		2203	4300	6503	SO:0001583	missense	51031	exon7			TGGTTCTCCCTTT	AF177342	CCDS32520.1	17p13.3	2008-02-05	2007-03-14	2007-03-14		ENSG00000167699			14111	protein-coding gene	gene with protein product			"""chromosome 17 open reading frame 25"""	C17orf25		11642406, 12528892	Standard	NM_016080		Approved	CGI-150, HC71	uc002fru.3	Q9HC38		ENST00000301328.5:c.707A>G	chr17.hg19:g.673366T>C	ENSP00000301328:p.Glu236Gly	124.0	0.0		112.0	5.0	NM_016080	D3DTG9|D3DTH1|Q96B89|Q9H3J8|Q9HC37|Q9NVN1	Missense_Mutation	SNP	ENST00000301328.5	hg19		.	.	.	.	.	.	.	.	.	.	T	16.36	3.102000	0.56183	.	.	ENSG00000167699	ENST00000301329;ENST00000397393;ENST00000301328;ENST00000536578	T;T;T	0.53206	0.63;0.63;0.63	5.79	5.79	0.91817	.	0.092459	0.64402	D	0.000001	T	0.47619	0.1455	L	0.56769	1.78	0.80722	D	1	B;B;B	0.18863	0.031;0.009;0.016	B;B;B	0.24848	0.056;0.012;0.022	T	0.37934	-0.9684	10	0.33940	T	0.23	-16.881	15.3033	0.73972	0.0:0.0:0.0:1.0	.	212;236;221	B7Z403;Q9HC38;Q9HC38-2	.;GLOD4_HUMAN;.	G	221;424;236;212	ENSP00000301329:E221G;ENSP00000301328:E236G;ENSP00000444315:E212G	ENSP00000301328:E236G	E	-	2	0	GLOD4	620116	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.721000	0.84768	2.198000	0.70561	0.533000	0.62120	GAG	.	.		0.532	GLOD4-005	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000437190.1	NM_016080	
CAMTA2	23125	hgsc.bcm.edu	37	17	4883160	4883160	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:4883160T>C	ENST00000348066.3	-	9	1580	c.1457A>G	c.(1456-1458)gAg>gGg	p.E486G	CAMTA2_ENST00000358183.4_Missense_Mutation_p.E486G|CAMTA2_ENST00000571831.1_5'Flank|CAMTA2_ENST00000572543.1_Missense_Mutation_p.E491G|CAMTA2_ENST00000361571.5_Missense_Mutation_p.E485G|CAMTA2_ENST00000414043.3_Missense_Mutation_p.E509G|CAMTA2_ENST00000381311.5_Missense_Mutation_p.E488G	NM_015099.3	NP_055914.2	O94983	CMTA2_HUMAN	calmodulin binding transcription activator 2	486					cardiac muscle hypertrophy in response to stress (GO:0014898)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(5)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	31						AAACAAGGCCTCTCCTCTTCC	0.597																																					p.E509G		Atlas-SNP	.											.	CAMTA2	93	.	0			c.A1526G						.						96.0	96.0	96.0					17																	4883160		2203	4300	6503	SO:0001583	missense	23125	exon9			AAGGCCTCTCCTC	AB020716	CCDS11063.1, CCDS54071.1, CCDS54072.1, CCDS54073.1	17p13.3	2004-09-01			ENSG00000108509	ENSG00000108509			18807	protein-coding gene	gene with protein product		611508				11925432	Standard	NM_015099		Approved	KIAA0909	uc010cku.2	O94983	OTTHUMG00000099417	ENST00000348066.3:c.1457A>G	chr17.hg19:g.4883160T>C	ENSP00000321813:p.Glu486Gly	58.0	0.0		62.0	5.0	NM_001171167	B9EGL0|D3DTL5|E7EWU5|Q7Z6M8|Q8N3V0|Q8NDG4|Q96G17	Missense_Mutation	SNP	ENST00000348066.3	hg19	CCDS11063.1	.	.	.	.	.	.	.	.	.	.	T	16.08	3.022487	0.54683	.	.	ENSG00000108509	ENST00000414043;ENST00000381311;ENST00000361571;ENST00000358183;ENST00000348066	T;T;T;T;T	0.35048	2.55;1.57;1.33;1.58;1.35	5.09	5.09	0.68999	.	0.286088	0.29730	N	0.011354	T	0.44286	0.1286	N	0.24115	0.695	0.28150	N	0.929429	D;D;D;D;B	0.67145	0.993;0.993;0.996;0.993;0.002	D;D;D;D;B	0.75484	0.968;0.968;0.986;0.968;0.005	T	0.33599	-0.9862	10	0.42905	T	0.14	-7.3284	12.8738	0.57980	0.0:0.0:0.0:1.0	.	462;509;488;486;485	B7ZM30;E7EWU5;O94983-3;O94983;O94983-4	.;.;.;CMTA2_HUMAN;.	G	509;488;485;486;486	ENSP00000412886:E509G;ENSP00000370712:E488G;ENSP00000354828:E485G;ENSP00000350910:E486G;ENSP00000321813:E486G	ENSP00000321813:E486G	E	-	2	0	CAMTA2	4823884	0.376000	0.25098	0.938000	0.37757	0.748000	0.42578	1.624000	0.37018	2.144000	0.66660	0.533000	0.62120	GAG	.	.		0.597	CAMTA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216876.1	NM_015099	
ZNF594	84622	hgsc.bcm.edu	37	17	5085336	5085336	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:5085336T>C	ENST00000399604.4	-	1	2356	c.2216A>G	c.(2215-2217)gAg>gGg	p.E739G	ZNF594_ENST00000575779.1_Missense_Mutation_p.E739G			Q96JF6	ZN594_HUMAN	zinc finger protein 594	739					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(3)|lung(10)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	33						GAAGGTTTTCTCACATTCTTC	0.438																																					p.E739G		Atlas-SNP	.											.	ZNF594	89	.	0			c.A2216G						.						198.0	205.0	203.0					17																	5085336		2088	4237	6325	SO:0001583	missense	84622	exon2			GTTTTCTCACATT	AB058774	CCDS42241.1	17p13	2013-01-08			ENSG00000180626	ENSG00000180626		"""Zinc fingers, C2H2-type"""	29392	protein-coding gene	gene with protein product						11347906	Standard	NM_032530		Approved	KIAA1871	uc010cla.1	Q96JF6	OTTHUMG00000132059	ENST00000399604.4:c.2216A>G	chr17.hg19:g.5085336T>C	ENSP00000382513:p.Glu739Gly	98.0	0.0		95.0	5.0	NM_032530	Q6RFS0	Missense_Mutation	SNP	ENST00000399604.4	hg19	CCDS42241.1	.	.	.	.	.	.	.	.	.	.	T	0.035	-1.311791	0.01342	.	.	ENSG00000180626	ENST00000399604	T	0.08984	3.03	1.04	-0.84	0.10755	Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.01489	0.0048	N	0.00380	-1.58	0.22096	N	0.999369	B	0.02656	0.0	B	0.01281	0.0	T	0.43637	-0.9379	9	0.02654	T	1	.	4.4455	0.11595	0.0:0.5034:0.0:0.4966	.	739	Q96JF6	ZN594_HUMAN	G	739	ENSP00000382513:E739G	ENSP00000382513:E739G	E	-	2	0	ZNF594	5026060	0.001000	0.12720	0.025000	0.17156	0.271000	0.26615	0.332000	0.19751	-0.398000	0.07679	0.248000	0.18094	GAG	.	.		0.438	ZNF594-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438996.1	XM_290737	
TP53	7157	hgsc.bcm.edu	37	17	7578460	7578460	+	Missense_Mutation	SNP	A	A	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:7578460A>C	ENST00000269305.4	-	5	659	c.470T>G	c.(469-471)gTc>gGc	p.V157G	TP53_ENST00000359597.4_Missense_Mutation_p.V157G|TP53_ENST00000413465.2_Missense_Mutation_p.V157G|TP53_ENST00000455263.2_Missense_Mutation_p.V157G|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000420246.2_Missense_Mutation_p.V157G|TP53_ENST00000445888.2_Missense_Mutation_p.V157G	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	157	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		V -> A (in sporadic cancers; somatic mutation).|V -> D (in sporadic cancers; somatic mutation).|V -> F (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974}.|V -> G (in sporadic cancers; somatic mutation).|V -> I (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:9419979}.|V -> L (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.V157D(8)|p.0?(8)|p.V157G(7)|p.R156_I162delRVRAMAI(2)|p.T155fs*23(2)|p.V157del(2)|p.V157fs*9(2)|p.P153fs*22(2)|p.V157fs*22(2)|p.V157_C176del20(1)|p.R156_A161delRVRAMA(1)|p.P151_V173del23(1)|p.R156_V157del(1)|p.V157A(1)|p.R156_R158delRVR(1)|p.R156fs*12(1)|p.R156fs*18(1)|p.R156_A161del(1)|p.V157_M160delVRAM(1)|p.D148fs*23(1)|p.V157_R158delVR(1)|p.S149fs*72(1)|p.T155_A161delTRVRAMA(1)|p.G154fs*22(1)|p.R156fs*20(1)|p.V157_I162delVRAMAI(1)|p.V157fs*21(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	CATGGCGCGGACGCGGGTGCC	0.617		111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.V157G	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	TP53_ENST00000545858,NS,carcinoma,0,1	TP53	33396	.	53	Substitution - Missense(16)|Deletion - In frame(14)|Deletion - Frameshift(14)|Whole gene deletion(8)|Complex - frameshift(1)	lung(8)|stomach(6)|oesophagus(6)|breast(5)|ovary(5)|upper_aerodigestive_tract(4)|central_nervous_system(4)|bone(4)|large_intestine(3)|haematopoietic_and_lymphoid_tissue(3)|pancreas(2)|biliary_tract(1)|prostate(1)|liver(1)	c.T470G						.						51.0	52.0	51.0					17																	7578460		2203	4300	6503	SO:0001583	missense	7157	exon5	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	GCGCGGACGCGGG	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"""Li-Fraumeni syndrome"""	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.470T>G	chr17.hg19:g.7578460A>C	ENSP00000269305:p.Val157Gly	145.0	0.0		93.0	37.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	A	17.25	3.342925	0.61073	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315;ENST00000508793	D;D;D;D;D;D;D;D;D	0.99825	-6.97;-6.97;-6.97;-6.97;-6.97;-6.97;-6.97;-6.97;-6.97	5.47	5.47	0.80525	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.216722	0.39210	N	0.001429	D	0.99816	0.9919	M	0.86420	2.815	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.97110	1.0;0.996;0.99;0.988;0.998;0.999;1.0	D	0.96765	0.9564	10	0.87932	D	0	-16.7152	13.8032	0.63214	1.0:0.0:0.0:0.0	.	118;157;157;64;157;157;157	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	G	157;157;157;157;157;157;146;64;25;64;25;157	ENSP00000410739:V157G;ENSP00000352610:V157G;ENSP00000269305:V157G;ENSP00000398846:V157G;ENSP00000391127:V157G;ENSP00000391478:V157G;ENSP00000425104:V25G;ENSP00000423862:V64G;ENSP00000424104:V157G	ENSP00000269305:V157G	V	-	2	0	TP53	7519185	1.000000	0.71417	0.032000	0.17829	0.165000	0.22458	9.287000	0.95975	2.208000	0.71279	0.460000	0.39030	GTC	.	.		0.617	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	
CHD3	1107	hgsc.bcm.edu	37	17	7806316	7806316	+	Silent	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:7806316T>C	ENST00000330494.7	+	22	3582	c.3432T>C	c.(3430-3432)aaT>aaC	p.N1144N	CHD3_ENST00000358181.4_Silent_p.N1144N|CHD3_ENST00000380358.4_Silent_p.N1203N	NM_001005273.2	NP_001005273.1	Q12873	CHD3_HUMAN	chromodomain helicase DNA binding protein 3	1144	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				centrosome organization (GO:0051297)|chromatin assembly or disassembly (GO:0006333)|chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|spindle organization (GO:0007051)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|nucleolus (GO:0005730)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(11)|kidney(6)|large_intestine(13)|liver(2)|lung(14)|ovary(1)|pancreas(1)|prostate(7)|skin(3)|urinary_tract(2)	65		Prostate(122;0.202)				TGGGCATCAATCTGGCCACTG	0.542																																					p.N1203N		Atlas-SNP	.											.	CHD3	169	.	0			c.T3609C						.						97.0	97.0	97.0					17																	7806316		2203	4300	6503	SO:0001819	synonymous_variant	1107	exon22			CATCAATCTGGCC	U08379	CCDS32553.2, CCDS32554.1, CCDS32555.1	17p13	2013-01-28			ENSG00000170004	ENSG00000170004		"""Zinc fingers, PHD-type"""	1918	protein-coding gene	gene with protein product		602120				9326634, 7560064	Standard	NM_001005271		Approved	Mi-2a, ZFH, Mi2-ALPHA	uc002gjd.2	Q12873	OTTHUMG00000150427	ENST00000330494.7:c.3432T>C	chr17.hg19:g.7806316T>C		111.0	0.0		105.0	10.0	NM_001005271	D3DTQ9|E9PG89|Q9Y4I0	Silent	SNP	ENST00000330494.7	hg19	CCDS32554.1																																																																																			.	.		0.542	CHD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318050.1	NM_001005273	
MYH10	4628	hgsc.bcm.edu	37	17	8455401	8455401	+	Silent	SNP	A	A	G	rs200432425		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:8455401A>G	ENST00000269243.4	-	8	990	c.852T>C	c.(850-852)ttT>ttC	p.F284F	MYH10_ENST00000360416.3_Silent_p.F294F|MYH10_ENST00000396239.1_Silent_p.F284F|MYH10_ENST00000379980.4_Silent_p.F300F	NM_005964.3	NP_005955.3	P35580	MYH10_HUMAN	myosin, heavy chain 10, non-muscle	284	Myosin motor.				actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cardiac myofibril assembly (GO:0055003)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|cerebellar Purkinje cell layer development (GO:0021680)|exocytosis (GO:0006887)|fourth ventricle development (GO:0021592)|in utero embryonic development (GO:0001701)|lateral ventricle development (GO:0021670)|mitotic cytokinesis (GO:0000281)|neuromuscular process controlling balance (GO:0050885)|neuron migration (GO:0001764)|nuclear migration (GO:0007097)|plasma membrane repair (GO:0001778)|regulation of cell shape (GO:0008360)|retina development in camera-type eye (GO:0060041)|substrate-dependent cell migration, cell extension (GO:0006930)|third ventricle development (GO:0021678)|ventricular cardiac muscle cell development (GO:0055015)	actomyosin (GO:0042641)|axon (GO:0030424)|cell cortex (GO:0005938)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|midbody (GO:0030496)|myosin complex (GO:0016459)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle (GO:0005819)|stress fiber (GO:0001725)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			breast(5)|endometrium(9)|kidney(2)|large_intestine(16)|lung(9)|ovary(3)|prostate(3)|skin(4)|stomach(1)	52						ACAACTGGTAAAAGATATGAA	0.303																																					p.F294F		Atlas-SNP	.											.	MYH10	148	.	0			c.T882C						.						47.0	48.0	48.0					17																	8455401		2203	4300	6503	SO:0001819	synonymous_variant	4628	exon9			CTGGTAAAAGATA	M69181	CCDS11144.1, CCDS58515.1, CCDS73984.1	17p13	2011-09-27	2006-09-29		ENSG00000133026	ENSG00000133026		"""Myosins / Myosin superfamily : Class II"""	7568	protein-coding gene	gene with protein product		160776	"""myosin, heavy polypeptide 10, non-muscle"""			1860190	Standard	NM_001256012		Approved	NMMHCB	uc002glm.4	P35580	OTTHUMG00000108195	ENST00000269243.4:c.852T>C	chr17.hg19:g.8455401A>G		124.0	0.0		90.0	7.0	NM_001256012	B2RWP9|D3DTS1|F8VTL3|Q12989|Q149N3|Q149N4|Q16087|Q4LE45|Q6PK16|Q9BWG0	Silent	SNP	ENST00000269243.4	hg19	CCDS11144.1																																																																																			.	A|0.999;G|0.001		0.303	MYH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000227001.2		
WDR16	146845	hgsc.bcm.edu	37	17	9545098	9545098	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:9545098T>C	ENST00000352665.5	+	13	1702	c.1633T>C	c.(1633-1635)Tct>Cct	p.S545P	WDR16_ENST00000299764.5_Missense_Mutation_p.S555P|RP11-55L4.2_ENST00000584676.1_RNA|WDR16_ENST00000396219.3_Missense_Mutation_p.S477P	NM_145054.4	NP_659491.4			WD repeat domain 16											NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	31						AGGTTCCCTGTCTGGGTCGAT	0.458																																					p.S545P		Atlas-SNP	.											.	WDR16	67	.	0			c.T1633C						.						119.0	117.0	118.0					17																	9545098		2203	4300	6503	SO:0001583	missense	146845	exon13			TCCCTGTCTGGGT	AB065281	CCDS11149.2, CCDS42262.1	17p13.1	2014-08-01			ENSG00000166596	ENSG00000166596		"""WD repeat domain containing"""	16053	protein-coding gene	gene with protein product	"""WD40-repeat protein upregulated in HCC"""	609804				15967112	Standard	NM_001080556		Approved	WDRPUH, FLJ37528	uc002gly.3	Q8N1V2	OTTHUMG00000150149	ENST00000352665.5:c.1633T>C	chr17.hg19:g.9545098T>C	ENSP00000339449:p.Ser545Pro	112.0	0.0		98.0	5.0	NM_145054		Missense_Mutation	SNP	ENST00000352665.5	hg19	CCDS11149.2	.	.	.	.	.	.	.	.	.	.	T	19.49	3.836856	0.71373	.	.	ENSG00000166596	ENST00000352665;ENST00000396219;ENST00000299764	T;T;T	0.39997	1.05;2.76;2.16	5.59	5.59	0.84812	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.144192	0.64402	D	0.000004	T	0.66771	0.2823	M	0.85299	2.745	0.58432	D	0.999993	D;D;D	0.69078	0.997;0.997;0.983	D;D;P	0.65874	0.939;0.939;0.894	T	0.72711	-0.4211	10	0.66056	D	0.02	-17.9464	14.7694	0.69665	0.0:0.0:0.0:1.0	.	555;477;545	Q8N1V2-2;Q8N1V2-3;Q8N1V2	.;.;WDR16_HUMAN	P	545;477;555	ENSP00000339449:S545P;ENSP00000379521:S477P;ENSP00000299764:S555P	ENSP00000299764:S555P	S	+	1	0	WDR16	9485823	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	2.764000	0.47613	2.140000	0.66376	0.460000	0.39030	TCT	.	.		0.458	WDR16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316569.2	NM_145054	
MYH2	4620	hgsc.bcm.edu	37	17	10427784	10427784	+	Splice_Site	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:10427784T>C	ENST00000245503.5	-	35	5558	c.5174A>G	c.(5173-5175)cAg>cGg	p.Q1725R	RP11-799N11.1_ENST00000581304.1_RNA|CTC-297N7.11_ENST00000587182.2_RNA|MYH2_ENST00000397183.2_Splice_Site_p.Q1725R|MYH2_ENST00000532183.2_Intron|RP11-799N11.1_ENST00000399342.2_RNA	NM_017534.5	NP_060004.3	Q9UKX2	MYH2_HUMAN	myosin, heavy chain 2, skeletal muscle, adult	1725					Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|membrane organization (GO:0061024)|metabolic process (GO:0008152)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|plasma membrane repair (GO:0001778)|response to activity (GO:0014823)	A band (GO:0031672)|actomyosin contractile ring (GO:0005826)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)|protein complex (GO:0043234)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(99)|ovary(6)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(4)	176						GAATCCCACCTGGGTGTGCAG	0.473																																					p.Q1725R		Atlas-SNP	.											.	MYH2	390	.	0			c.A5174G						.						75.0	78.0	77.0					17																	10427784		2203	4300	6503	SO:0001630	splice_region_variant	4620	exon35			CCCACCTGGGTGT		CCDS11156.1	17p13.1	2014-02-04	2006-09-29		ENSG00000125414	ENSG00000125414		"""Myosins / Myosin superfamily : Class II"""	7572	protein-coding gene	gene with protein product		160740	"""myosin, heavy polypeptide 2, skeletal muscle, adult"", ""inclusion body myopathy 3, autosomal dominant"""	IBM3		7545970, 11889243	Standard	NM_001100112		Approved	MYH2A, MYHSA2, MyHC-IIa, MYHas8, MyHC-2A	uc010coi.3	Q9UKX2	OTTHUMG00000130363	ENST00000245503.5:c.5175+1A>G	chr17.hg19:g.10427784T>C		120.0	0.0		120.0	8.0	NM_017534	A0AVL4|Q14322|Q16229|Q567P6|Q86T56	Missense_Mutation	SNP	ENST00000245503.5	hg19	CCDS11156.1	.	.	.	.	.	.	.	.	.	.	T	17.98	3.521326	0.64747	.	.	ENSG00000125414	ENST00000245503;ENST00000397183	T;T	0.79845	-1.31;-1.31	5.42	5.42	0.78866	Myosin tail (1);	0.000000	0.37483	U	0.002063	D	0.87892	0.6292	H	0.95850	3.73	0.58432	D	0.999992	B	0.18013	0.025	B	0.27887	0.084	D	0.87505	0.2436	10	0.72032	D	0.01	.	15.6229	0.76820	0.0:0.0:0.0:1.0	.	1725	Q9UKX2	MYH2_HUMAN	R	1725	ENSP00000245503:Q1725R;ENSP00000380367:Q1725R	ENSP00000245503:Q1725R	Q	-	2	0	MYH2	10368509	1.000000	0.71417	1.000000	0.80357	0.549000	0.35272	7.781000	0.85668	2.279000	0.76181	0.402000	0.26972	CAG	.	.		0.473	MYH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252726.3	NM_017534	Missense_Mutation
RHOT1	55288	hgsc.bcm.edu	37	17	30535190	30535190	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:30535190T>C	ENST00000333942.6	+	18	1840	c.1601T>C	c.(1600-1602)gTt>gCt	p.V534A	RHOT1_ENST00000358365.3_Missense_Mutation_p.V534A|RHOT1_ENST00000354266.3_Missense_Mutation_p.V513A|RHOT1_ENST00000545287.2_Missense_Mutation_p.V534A|RHOT1_ENST00000394692.2_Missense_Mutation_p.V534A|RHOT1_ENST00000583994.1_Missense_Mutation_p.V407A|RHOT1_ENST00000581094.1_Missense_Mutation_p.V534A	NM_018307.3	NP_060777.3	Q8IXI2	MIRO1_HUMAN	ras homolog family member T1	534	Miro 2.				cellular homeostasis (GO:0019725)|mitochondrial outer membrane permeabilization (GO:0097345)|mitochondrion transport along microtubule (GO:0047497)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|integral component of mitochondrial outer membrane (GO:0031307)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			NS(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(10)|ovary(3)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	28		Myeloproliferative disorder(56;0.0255)|Breast(31;0.116)|Ovarian(249;0.182)				CTGCATGAAGTTAAACAAGAA	0.393																																					p.V534A		Atlas-SNP	.											.	RHOT1	69	.	0			c.T1601C						.						117.0	109.0	112.0					17																	30535190		2203	4300	6503	SO:0001583	missense	55288	exon18			ATGAAGTTAAACA	AJ517412	CCDS32610.1, CCDS32611.1, CCDS32612.1, CCDS74030.1, CCDS74031.1	17q11.2-q12	2013-01-10	2012-02-27	2004-03-24		ENSG00000126858		"""EF-hand domain containing"""	21168	protein-coding gene	gene with protein product	"""mitochondrial Rho (MIRO) GTPase 1"""	613888	"""ras homolog gene family, member T1"""	ARHT1		12482879	Standard	NM_001033567		Approved	MIRO-1, FLJ11040	uc002hgw.3	Q8IXI2		ENST00000333942.6:c.1601T>C	chr17.hg19:g.30535190T>C	ENSP00000334724:p.Val534Ala	104.0	0.0		97.0	4.0	NM_001033568	A4FVB6|A6NFV0|B4DG48|J9JIH9|Q6NUR3|Q6P9F8|Q6PJG1|Q6YMW8|Q86UB0|Q8IW28|Q8IXJ7|Q9H067|Q9H9N8|Q9NUZ2	Missense_Mutation	SNP	ENST00000333942.6	hg19	CCDS32612.1	.	.	.	.	.	.	.	.	.	.	T	13.29	2.193786	0.38707	.	.	ENSG00000126858	ENST00000358365;ENST00000354266;ENST00000394692;ENST00000333942	T;T;T	0.19806	2.12;2.12;2.12	5.93	5.93	0.95920	MIRO (1);	0.108387	0.64402	D	0.000007	T	0.18215	0.0437	L	0.28649	0.875	0.80722	D	1	B;B;B;B	0.16603	0.001;0.002;0.018;0.002	B;B;B;B	0.19148	0.004;0.007;0.024;0.011	T	0.04153	-1.0973	10	0.27082	T	0.32	-13.8372	16.3766	0.83401	0.0:0.0:0.0:1.0	.	534;534;534;534	Q8IXI2-2;Q8IXI2;Q8IXI2-5;Q8IXI2-3	.;MIRO1_HUMAN;.;.	A	534	ENSP00000351132:V534A;ENSP00000378184:V534A;ENSP00000334724:V534A	ENSP00000334724:V534A	V	+	2	0	RHOT1	27559303	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	6.231000	0.72307	2.263000	0.75096	0.533000	0.62120	GTT	.	.		0.393	RHOT1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000447097.1	NM_018307	
MYO1D	4642	hgsc.bcm.edu	37	17	30980960	30980960	+	Silent	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:30980960T>C	ENST00000318217.5	-	19	2800	c.2496A>G	c.(2494-2496)ccA>ccG	p.P832P	MYO1D_ENST00000579584.1_Silent_p.P832P|RP11-220C2.1_ENST00000582272.1_RNA|MYO1D_ENST00000394649.4_Silent_p.P744P	NM_015194.1	NP_056009.1	O94832	MYO1D_HUMAN	myosin ID	832	Myosin tail. {ECO:0000255}.				early endosome to recycling endosome transport (GO:0061502)|negative regulation of phosphatase activity (GO:0010923)	axolemma (GO:0030673)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|smooth endoplasmic reticulum (GO:0005790)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)	p.P832P(1)		breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(8)|lung(14)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39			BRCA - Breast invasive adenocarcinoma(9;0.0362)			GAGGTGTATCTGGCTTCTGAA	0.393																																					p.P832P		Atlas-SNP	.											MYO1D,colon,carcinoma,0,1	MYO1D	93	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A2496G						.						87.0	72.0	77.0					17																	30980960		2203	4300	6503	SO:0001819	synonymous_variant	4642	exon19			TGTATCTGGCTTC	AB018270	CCDS32615.1	17q11-q12	2014-06-12				ENSG00000176658		"""Myosins / Myosin superfamily : Class I"""	7598	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 108"""	606539				8884266	Standard	NM_015194		Approved	KIAA0727, myr4, PPP1R108	uc002hho.1	O94832		ENST00000318217.5:c.2496A>G	chr17.hg19:g.30980960T>C		37.0	0.0		43.0	2.0	NM_015194	A6H8V3|Q8NHP9	Silent	SNP	ENST00000318217.5	hg19	CCDS32615.1																																																																																			.	.		0.393	MYO1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447457.1		
MYO1D	4642	hgsc.bcm.edu	37	17	31094666	31094666	+	Silent	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:31094666A>G	ENST00000318217.5	-	7	1123	c.819T>C	c.(817-819)gcT>gcC	p.A273A	MYO1D_ENST00000579584.1_Silent_p.A273A|MYO1D_ENST00000583621.1_Silent_p.A273A|MYO1D_ENST00000394649.4_Silent_p.A185A	NM_015194.1	NP_056009.1	O94832	MYO1D_HUMAN	myosin ID	273	Myosin motor.				early endosome to recycling endosome transport (GO:0061502)|negative regulation of phosphatase activity (GO:0010923)	axolemma (GO:0030673)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|smooth endoplasmic reticulum (GO:0005790)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(8)|lung(14)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39			BRCA - Breast invasive adenocarcinoma(9;0.0362)			AGTGCAGAATAGCAGCCAAAA	0.413																																					p.A273A		Atlas-SNP	.											.	MYO1D	93	.	0			c.T819C						.						121.0	101.0	108.0					17																	31094666		2203	4300	6503	SO:0001819	synonymous_variant	4642	exon7			CAGAATAGCAGCC	AB018270	CCDS32615.1	17q11-q12	2014-06-12				ENSG00000176658		"""Myosins / Myosin superfamily : Class I"""	7598	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 108"""	606539				8884266	Standard	NM_015194		Approved	KIAA0727, myr4, PPP1R108	uc002hho.1	O94832		ENST00000318217.5:c.819T>C	chr17.hg19:g.31094666A>G		56.0	0.0		86.0	5.0	NM_015194	A6H8V3|Q8NHP9	Silent	SNP	ENST00000318217.5	hg19	CCDS32615.1																																																																																			.	.		0.413	MYO1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447457.1		
GAS2L2	246176	hgsc.bcm.edu	37	17	34073357	34073357	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:34073357A>G	ENST00000254466.6	-	6	1186	c.1159T>C	c.(1159-1161)Tca>Cca	p.S387P	GAS2L2_ENST00000587565.1_Missense_Mutation_p.S371P	NM_139285.3	NP_644814.1	Q8NHY3	GA2L2_HUMAN	growth arrest-specific 2 like 2	387					cell cycle arrest (GO:0007050)|microtubule bundle formation (GO:0001578)|negative regulation of microtubule depolymerization (GO:0007026)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	actin filament binding (GO:0051015)|cytoskeletal adaptor activity (GO:0008093)|microtubule binding (GO:0008017)			central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	35		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		TGGGTAGATGAGGACTGGGGG	0.587																																					p.S387P		Atlas-SNP	.											.	GAS2L2	94	.	0			c.T1159C						.						84.0	97.0	93.0					17																	34073357		2203	4300	6503	SO:0001583	missense	246176	exon6			TAGATGAGGACTG	AF508784	CCDS11298.1	17q21	2014-05-06			ENSG00000132139	ENSG00000270765			24846	protein-coding gene	gene with protein product		611398				12584248	Standard	NM_139285		Approved	GAR17	uc002hjv.2	Q8NHY3	OTTHUMG00000188386	ENST00000254466.6:c.1159T>C	chr17.hg19:g.34073357A>G	ENSP00000254466:p.Ser387Pro	73.0	0.0		77.0	4.0	NM_139285	Q8NHY4	Missense_Mutation	SNP	ENST00000254466.6	hg19	CCDS11298.1	.	.	.	.	.	.	.	.	.	.	A	18.55	3.649306	0.67358	.	.	ENSG00000132139	ENST00000254466	T	0.20332	2.08	5.03	5.03	0.67393	.	0.528731	0.15747	N	0.246619	T	0.35038	0.0918	L	0.53249	1.67	0.09310	N	1	D	0.64830	0.994	P	0.58721	0.844	T	0.11767	-1.0574	10	0.33141	T	0.24	-3.1015	12.2752	0.54730	1.0:0.0:0.0:0.0	.	387	Q8NHY3	GA2L2_HUMAN	P	387	ENSP00000254466:S387P	ENSP00000254466:S387P	S	-	1	0	GAS2L2	31097470	0.001000	0.12720	0.000000	0.03702	0.005000	0.04900	1.143000	0.31553	2.118000	0.64928	0.533000	0.62120	TCA	.	.		0.587	GAS2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256497.1	NM_139285	
FBXO47	494188	hgsc.bcm.edu	37	17	37101381	37101381	+	Missense_Mutation	SNP	G	G	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:37101381G>C	ENST00000378079.2	-	7	824	c.625C>G	c.(625-627)Caa>Gaa	p.Q209E		NM_001008777.2	NP_001008777.2	Q5MNV8	FBX47_HUMAN	F-box protein 47	209			Q -> R (in dbSNP:rs9906595). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:15723337}.							NS(1)|breast(1)|endometrium(1)|large_intestine(5)|lung(9)|ovary(1)|prostate(1)|skin(1)	20						TCCAGTTTTTGGGCACTTCCT	0.363																																					p.Q209E		Atlas-SNP	.											.	FBXO47	34	.	0			c.C625G						.						93.0	83.0	86.0					17																	37101381		2203	4300	6503	SO:0001583	missense	494188	exon7			GTTTTTGGGCACT		CCDS32639.1	17q12	2014-08-12			ENSG00000204952	ENSG00000204952		"""F-boxes /  ""other"""""	31969	protein-coding gene	gene with protein product		609498				15723337	Standard	NM_001008777		Approved		uc002hrc.2	Q5MNV8	OTTHUMG00000178945	ENST00000378079.2:c.625C>G	chr17.hg19:g.37101381G>C	ENSP00000367319:p.Gln209Glu	81.0	0.0		100.0	5.0	NM_001008777	B2RTZ4	Missense_Mutation	SNP	ENST00000378079.2	hg19	CCDS32639.1	.	.	.	.	.	.	.	.	.	.	G	8.497	0.863270	0.17250	.	.	ENSG00000204952	ENST00000378079	T	0.69435	-0.4	5.53	0.682	0.17992	.	0.314310	0.34156	N	0.004213	T	0.35364	0.0929	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.28902	-1.0029	10	0.02654	T	1	-0.0407	8.2704	0.31840	0.0778:0.0:0.3612:0.5611	.	209	Q5MNV8	FBX47_HUMAN	E	209	ENSP00000367319:Q209E	ENSP00000367319:Q209E	Q	-	1	0	FBXO47	34354907	0.998000	0.40836	0.801000	0.32222	0.799000	0.45148	0.964000	0.29306	0.662000	0.31006	0.585000	0.79938	CAA	.	.		0.363	FBXO47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444073.1	NM_001008777	
KRT28	162605	hgsc.bcm.edu	37	17	38948685	38948685	+	Silent	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:38948685A>G	ENST00000306658.7	-	8	1454	c.1389T>C	c.(1387-1389)ccT>ccC	p.P463P		NM_181535.3	NP_853513.2			keratin 28											NS(1)|breast(3)|endometrium(1)|kidney(1)|large_intestine(4)|lung(14)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	30		Breast(137;0.000301)				ACAGCTAGAAAGGAACCCTTT	0.338																																					p.P463P	Melanoma(19;789 869 15380 26882 39836)	Atlas-SNP	.											.	KRT28	65	.	0			c.T1389C						.						107.0	99.0	101.0					17																	38948685		2202	4300	6502	SO:0001819	synonymous_variant	162605	exon8			CTAGAAAGGAACC	AK129827	CCDS11376.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000173908	ENSG00000173908		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	30842	protein-coding gene	gene with protein product			"""keratin 25D"""	KRT25D		16831889	Standard	NM_181535		Approved		uc002hvh.1	Q7Z3Y7	OTTHUMG00000133365	ENST00000306658.7:c.1389T>C	chr17.hg19:g.38948685A>G		90.0	0.0		93.0	4.0	NM_181535		Silent	SNP	ENST00000306658.7	hg19	CCDS11376.1																																																																																			.	.		0.338	KRT28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257201.2	NM_181535	
KRT38	8687	hgsc.bcm.edu	37	17	39595478	39595478	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:39595478A>G	ENST00000246646.3	-	3	708	c.709T>C	c.(709-711)Tcc>Ccc	p.S237P		NM_006771.3	NP_006762.3	O76015	KRT38_HUMAN	keratin 38	237	Coil 1B.|Rod.					extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	29		Breast(137;0.000496)				CTCTTGAGGGAGAGCTGCTCC	0.662																																					p.S237P		Atlas-SNP	.											.	KRT38	63	.	0			c.T709C						.						55.0	50.0	52.0					17																	39595478		2203	4300	6503	SO:0001583	missense	8687	exon3			TGAGGGAGAGCTG	Y16794	CCDS11392.1	17q21.2	2013-06-20	2006-07-17	2006-07-17	ENSG00000171360	ENSG00000171360		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6456	protein-coding gene	gene with protein product		604542	"""keratin, hair, acidic, 8"""	KRTHA8		9756910, 16831889	Standard	NM_006771		Approved		uc002hwq.1	O76015	OTTHUMG00000133439	ENST00000246646.3:c.709T>C	chr17.hg19:g.39595478A>G	ENSP00000246646:p.Ser237Pro	97.0	0.0		97.0	4.0	NM_006771	A2RRM5|Q6A164	Missense_Mutation	SNP	ENST00000246646.3	hg19	CCDS11392.1	.	.	.	.	.	.	.	.	.	.	A	12.07	1.826498	0.32329	.	.	ENSG00000171360	ENST00000246646	D	0.88741	-2.42	4.31	0.455	0.16649	Filament (1);	0.877622	0.09568	N	0.784620	D	0.88983	0.6586	L	0.47190	1.495	0.09310	N	1	D	0.57571	0.98	P	0.57468	0.821	T	0.77778	-0.2460	10	0.72032	D	0.01	.	5.4669	0.16648	0.3567:0.2612:0.0:0.3821	.	237	O76015	KRT38_HUMAN	P	237	ENSP00000246646:S237P	ENSP00000246646:S237P	S	-	1	0	KRT38	36849004	0.000000	0.05858	0.660000	0.29694	0.330000	0.28571	0.233000	0.17911	-0.127000	0.11661	-0.636000	0.03981	TCC	.	.		0.662	KRT38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257307.2	NM_006771	
STAT5A	6776	hgsc.bcm.edu	37	17	40456369	40456369	+	Silent	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:40456369T>C	ENST00000345506.4	+	11	1821	c.1179T>C	c.(1177-1179)agT>agC	p.S393S	STAT5A_ENST00000590949.1_Silent_p.S393S|STAT5A_ENST00000588868.1_Silent_p.S393S|STAT5A_ENST00000452307.2_Silent_p.S393S|STAT5A_ENST00000587646.1_5'Flank|STAT5A_ENST00000546010.2_Silent_p.S363S	NM_003152.3	NP_003143.2	P42229	STA5A_HUMAN	signal transducer and activator of transcription 5A	393					2-oxoglutarate metabolic process (GO:0006103)|allantoin metabolic process (GO:0000255)|cellular response to granulocyte macrophage colony-stimulating factor stimulus (GO:0097011)|citrate metabolic process (GO:0006101)|creatine metabolic process (GO:0006600)|creatinine metabolic process (GO:0046449)|development of secondary female sexual characteristics (GO:0046543)|development of secondary male sexual characteristics (GO:0046544)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|fatty acid metabolic process (GO:0006631)|female pregnancy (GO:0007565)|isoleucine metabolic process (GO:0006549)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lactation (GO:0007595)|lipid storage (GO:0019915)|luteinization (GO:0001553)|mammary gland epithelium development (GO:0061180)|natural killer cell differentiation (GO:0001779)|negative regulation of erythrocyte differentiation (GO:0045647)|negative regulation of mast cell apoptotic process (GO:0033026)|oxaloacetate metabolic process (GO:0006107)|peptidyl-tyrosine phosphorylation (GO:0018108)|Peyer's patch development (GO:0048541)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of gamma-delta T cell differentiation (GO:0045588)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of mast cell differentiation (GO:0060376)|positive regulation of mast cell proliferation (GO:0070668)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of natural killer cell differentiation (GO:0032825)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prolactin signaling pathway (GO:0038161)|prostate gland epithelium morphogenesis (GO:0060740)|regulation of cell adhesion (GO:0030155)|regulation of epithelial cell differentiation (GO:0030856)|regulation of multicellular organism growth (GO:0040014)|regulation of steroid metabolic process (GO:0019218)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|succinate metabolic process (GO:0006105)|T cell differentiation in thymus (GO:0033077)|T cell homeostasis (GO:0043029)|taurine metabolic process (GO:0019530)|transcription, DNA-templated (GO:0006351)|valine metabolic process (GO:0006573)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	calcium ion binding (GO:0005509)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			central_nervous_system(1)|kidney(2)|large_intestine(1)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	14		all_cancers(22;1.56e-06)|all_epithelial(22;3.17e-05)|Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.128)		GCGAGTGCAGTGGTGAGATCC	0.642																																					p.S393S		Atlas-SNP	.											.	STAT5A	49	.	0			c.T1179C						.						65.0	56.0	59.0					17																	40456369		2203	4300	6503	SO:0001819	synonymous_variant	6776	exon11			GTGCAGTGGTGAG	U43185	CCDS11424.1, CCDS74066.1, CCDS74067.1	17q11.2	2013-02-14			ENSG00000126561	ENSG00000126561		"""SH2 domain containing"""	11366	protein-coding gene	gene with protein product		601511		STAT5		7719937, 8631883	Standard	NM_003152		Approved	MGF	uc002hzj.2	P42229	OTTHUMG00000150725	ENST00000345506.4:c.1179T>C	chr17.hg19:g.40456369T>C		86.0	0.0		85.0	4.0	NM_003152	Q1KLZ6	Silent	SNP	ENST00000345506.4	hg19	CCDS11424.1																																																																																			.	.		0.642	STAT5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319804.1	NM_003152	
EFCAB13	124989	hgsc.bcm.edu	37	17	45451902	45451902	+	Silent	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:45451902A>G	ENST00000331493.2	+	12	1353	c.942A>G	c.(940-942)ggA>ggG	p.G314G	EFCAB13_ENST00000517484.1_Silent_p.G218G	NM_152347.4	NP_689560.3	Q8IY85	EFC13_HUMAN	EF-hand calcium binding domain 13	314						cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)										GTGTAGCAGGATGCTATCTAA	0.284																																					p.G314G		Atlas-SNP	.											.	.	.	.	0			c.A942G						.						31.0	35.0	34.0					17																	45451902		2189	4260	6449	SO:0001819	synonymous_variant	124989	exon12			AGCAGGATGCTAT	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.942A>G	chr17.hg19:g.45451902A>G		76.0	0.0		92.0	4.0	NM_152347	G3V128|Q49AG9	Silent	SNP	ENST00000331493.2	hg19	CCDS11512.1																																																																																			.	.		0.284	EFCAB13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380147.4	NM_152347	
OR4D1	26689	hgsc.bcm.edu	37	17	56232912	56232912	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:56232912T>C	ENST00000268912.5	+	1	419	c.398T>C	c.(397-399)gTc>gCc	p.V133A		NM_012374.1	NP_036506.1	Q15615	OR4D1_HUMAN	olfactory receptor, family 4, subfamily D, member 1	133					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			kidney(2)|large_intestine(4)|lung(4)|ovary(1)|stomach(1)|urinary_tract(1)	13						CTCCGGTATGTCACCATCATG	0.532																																					p.V133A		Atlas-SNP	.											.	OR4D1	48	.	0			c.T398C						.						74.0	77.0	76.0					17																	56232912		2196	4295	6491	SO:0001583	missense	26689	exon1			GGTATGTCACCAT	X89670	CCDS42365.1	17q22	2012-08-09			ENSG00000141194	ENSG00000141194		"""GPCR / Class A : Olfactory receptors"""	8293	protein-coding gene	gene with protein product				OR4D3		9119360	Standard	NM_012374		Approved	TPCR16	uc010wno.2	Q15615		ENST00000268912.5:c.398T>C	chr17.hg19:g.56232912T>C	ENSP00000365451:p.Val133Ala	89.0	0.0		110.0	7.0	NM_012374	B2RN14|Q8NGB1|Q96R76	Missense_Mutation	SNP	ENST00000268912.5	hg19	CCDS42365.1	.	.	.	.	.	.	.	.	.	.	t	10.31	1.313907	0.23908	.	.	ENSG00000141194	ENST00000268912	T	0.18960	2.18	5.63	4.56	0.56223	GPCR, rhodopsin-like superfamily (1);	0.229124	0.30667	N	0.009135	T	0.11067	0.0270	N	0.13371	0.34	0.21697	N	0.999589	B	0.09022	0.002	B	0.14578	0.011	T	0.28681	-1.0036	10	0.22706	T	0.39	-20.0359	7.2199	0.25981	0.0:0.1716:0.0:0.8284	.	133	Q15615	OR4D1_HUMAN	A	133	ENSP00000365451:V133A	ENSP00000365451:V133A	V	+	2	0	OR4D1	53587911	0.000000	0.05858	0.905000	0.35620	0.888000	0.51559	-0.368000	0.07543	0.966000	0.38159	0.443000	0.29094	GTC	.	.		0.532	OR4D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443364.1		
RAD51C	5889	hgsc.bcm.edu	37	17	56798130	56798130	+	Silent	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:56798130A>G	ENST00000337432.4	+	6	932	c.861A>G	c.(859-861)acA>acG	p.T287T	RAD51C_ENST00000583539.1_Silent_p.T287T	NM_058216.1	NP_478123.1	O43502	RA51C_HUMAN	RAD51 paralog C	287			T -> A (in BROVCA3; dbSNP:rs28363317). {ECO:0000269|PubMed:20400964, ECO:0000269|PubMed:21990120, ECO:0000269|Ref.2}.		blood coagulation (GO:0007596)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|female meiosis sister chromatid cohesion (GO:0007066)|male meiosis I (GO:0007141)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|reciprocal meiotic recombination (GO:0007131)|sister chromatid cohesion (GO:0007062)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|Rad51B-Rad51C-Rad51D-XRCC2 complex (GO:0033063)|Rad51C-XRCC3 complex (GO:0033065)|replication fork (GO:0005657)	ATP binding (GO:0005524)|crossover junction endodeoxyribonuclease activity (GO:0008821)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)			upper_aerodigestive_tract(1)	1	Medulloblastoma(34;0.127)|all_neural(34;0.237)					ATCAGATGACAACAAAGATTG	0.323								Homologous recombination	Hereditary Breast-Ovarian Cancer, non-BRCA1/2																												p.T287T		Atlas-SNP	.											.	RAD51C	39	.	0			c.A861G						.						102.0	105.0	104.0					17																	56798130		2203	4300	6503	SO:0001819	synonymous_variant	5889	exon6	Familial Cancer Database	BRCAX	GATGACAACAAAG	AF029670	CCDS11611.1, CCDS45745.1	17q25.1	2014-09-17	2013-07-02		ENSG00000108384	ENSG00000108384		"""Fanconi anemia, complementation groups"""	9820	protein-coding gene	gene with protein product		602774	"""RAD51 (S. cerevisiae) homolog C"", ""RAD51 homolog C (S. cerevisiae)"""			9469824, 22167183	Standard	NM_058216		Approved	RAD51L2, FANCO	uc002iwu.3	O43502	OTTHUMG00000141292	ENST00000337432.4:c.861A>G	chr17.hg19:g.56798130A>G		60.0	0.0		65.0	4.0	NM_058216	O43503|Q3B783	Silent	SNP	ENST00000337432.4	hg19	CCDS11611.1	.	.	.	.	.	.	.	.	.	.	A	8.905	0.957398	0.18507	.	.	ENSG00000108384	ENST00000413590	.	.	.	5.07	3.91	0.45181	.	.	.	.	.	T	0.59418	0.2192	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.57341	-0.7828	4	.	.	.	-17.848	9.3048	0.37867	0.8192:0.1808:0.0:0.0	.	.	.	.	D	167	.	.	N	+	1	0	RAD51C	54153129	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.373000	0.34272	1.907000	0.55213	0.383000	0.25322	AAC	.	.		0.323	RAD51C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280540.2	NM_058216	
PTRH2	51651	hgsc.bcm.edu	37	17	57774925	57774925	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:57774925T>C	ENST00000470557.2	-	1	3861	c.415A>G	c.(415-417)Act>Gct	p.T139A	PTRH2_ENST00000537860.1_Missense_Mutation_p.T139A|PTRH2_ENST00000579915.1_5'Flank|PTRH2_ENST00000409433.2_Missense_Mutation_p.T140A|PTRH2_ENST00000393038.2_Missense_Mutation_p.T139A			Q9Y3E5	PTH2_HUMAN	peptidyl-tRNA hydrolase 2	139					apoptotic process (GO:0006915)|negative regulation of anoikis (GO:2000811)|negative regulation of gene expression (GO:0010629)|positive regulation of anoikis (GO:2000210)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)	aminoacyl-tRNA hydrolase activity (GO:0004045)			large_intestine(1)	1	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)					AAACTTACAGTCAGTCCCAGC	0.478																																					p.T139A		Atlas-SNP	.											.	PTRH2	8	.	0			c.A415G						.						147.0	138.0	141.0					17																	57774925		2203	4300	6503	SO:0001583	missense	51651	exon2			TTACAGTCAGTCC	AF151905	CCDS11618.1	17q23.2	2014-07-18			ENSG00000141378	ENSG00000141378			24265	protein-coding gene	gene with protein product	"""Bcl-2 inhibitor of transcription"", ""cilia and flagella associated protein 37"""	608625				10810093, 15006356, 14660562	Standard	XM_005257447		Approved	BIT1, CGI-147, PTH2, CFAP37	uc002ixt.3	Q9Y3E5	OTTHUMG00000154532	ENST00000470557.2:c.415A>G	chr17.hg19:g.57774925T>C	ENSP00000464327:p.Thr139Ala	162.0	0.0		210.0	9.0	NM_016077	B3KUY4|Q9NTE5	Missense_Mutation	SNP	ENST00000470557.2	hg19	CCDS11618.1	.	.	.	.	.	.	.	.	.	.	T	11.21	1.572956	0.28092	.	.	ENSG00000141378	ENST00000393038;ENST00000409433;ENST00000537860	.	.	.	5.82	5.82	0.92795	Peptidyl-tRNA hydrolase II domain (2);	0.123586	0.53938	U	0.000042	T	0.45776	0.1359	L	0.31578	0.945	0.47547	D	0.99945	B	0.33288	0.406	B	0.34180	0.177	T	0.38200	-0.9672	9	0.10902	T	0.67	-14.1597	16.1814	0.81903	0.0:0.0:0.0:1.0	.	139	Q9Y3E5	PTH2_HUMAN	A	139;140;139	.	ENSP00000376758:T139A	T	-	1	0	PTRH2	55129707	1.000000	0.71417	1.000000	0.80357	0.729000	0.41735	5.044000	0.64214	2.234000	0.73211	0.533000	0.62120	ACT	.	.		0.478	PTRH2-003	PUTATIVE	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000448482.1	NM_016077	
MRC2	9902	hgsc.bcm.edu	37	17	60743521	60743521	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:60743521A>G	ENST00000303375.5	+	3	989	c.587A>G	c.(586-588)cAg>cGg	p.Q196R		NM_006039.4	NP_006030.2	Q9UBG0	MRC2_HUMAN	mannose receptor, C type 2	196	Fibronectin type-II. {ECO:0000255|PROSITE-ProRule:PRU00479}.				collagen catabolic process (GO:0030574)|endocytosis (GO:0006897)|osteoblast differentiation (GO:0001649)	focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|collagen binding (GO:0005518)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(11)|lung(28)|ovary(2)|prostate(1)|skin(3)	53						TATGACAACCAGTGGTTCCAC	0.637																																					p.Q196R		Atlas-SNP	.											.	MRC2	126	.	0			c.A587G						.						68.0	49.0	56.0					17																	60743521		2203	4300	6503	SO:0001583	missense	9902	exon3			ACAACCAGTGGTT	AB014609	CCDS11634.1	17q23	2011-08-30				ENSG00000011028		"""CD molecules"", ""C-type lectin domain containing"""	16875	protein-coding gene	gene with protein product		612264				9734811, 8702911	Standard	NM_006039		Approved	KIAA0709, ENDO180, CLEC13E, CD280	uc002jad.4	Q9UBG0		ENST00000303375.5:c.587A>G	chr17.hg19:g.60743521A>G	ENSP00000307513:p.Gln196Arg	94.0	0.0		88.0	4.0	NM_006039	A6H8K4|D3DU08|Q7LGE7|Q9Y5P9	Missense_Mutation	SNP	ENST00000303375.5	hg19	CCDS11634.1	.	.	.	.	.	.	.	.	.	.	A	23.5	4.425345	0.83667	.	.	ENSG00000011028	ENST00000303375	T	0.48836	0.8	4.67	4.67	0.58626	Fibronectin, type II, collagen-binding (5);Kringle-like fold (1);	0.000000	0.85682	D	0.000000	T	0.57651	0.2068	L	0.35723	1.085	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	T	0.55879	-0.8071	10	0.36615	T	0.2	-20.6129	14.2837	0.66232	1.0:0.0:0.0:0.0	.	196	Q9UBG0	MRC2_HUMAN	R	196	ENSP00000307513:Q196R	ENSP00000307513:Q196R	Q	+	2	0	MRC2	58097253	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.118000	0.71583	1.967000	0.57214	0.459000	0.35465	CAG	.	.		0.637	MRC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445152.1		
BPTF	2186	hgsc.bcm.edu	37	17	65871699	65871699	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:65871699A>G	ENST00000321892.4	+	5	1953	c.1892A>G	c.(1891-1893)aAc>aGc	p.N631S	BPTF_ENST00000335221.5_Missense_Mutation_p.N631S|BPTF_ENST00000306378.6_Intron|BPTF_ENST00000424123.3_Missense_Mutation_p.N492S			Q12830	BPTF_HUMAN	bromodomain PHD finger transcription factor	631					anterior/posterior pattern specification (GO:0009952)|ATP catabolic process (GO:0006200)|brain development (GO:0007420)|chromatin remodeling (GO:0006338)|embryonic placenta development (GO:0001892)|endoderm development (GO:0007492)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)|NURF complex (GO:0016589)	sequence-specific DNA binding (GO:0043565)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(16)|lung(23)|ovary(3)|pancreas(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	78	all_cancers(12;6e-11)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0984)|LUSC - Lung squamous cell carcinoma(166;0.24)			GATAAAGGTAACTCTGTGTCA	0.443																																					p.N631S		Atlas-SNP	.											.	BPTF	415	.	0			c.A1892G						.						100.0	96.0	97.0					17																	65871699		2203	4300	6503	SO:0001583	missense	2186	exon5			AAGGTAACTCTGT	AY282495	CCDS11673.1	17q24	2013-01-28	2006-12-01	2006-12-01	ENSG00000171634	ENSG00000171634		"""Zinc fingers, PHD-type"""	3581	protein-coding gene	gene with protein product		601819	"""fetal Alzheimer antigen"""	FALZ		8975731, 10662542, 16728976	Standard	NM_182641		Approved	FAC1, NURF301	uc002jgf.3	Q12830	OTTHUMG00000132254	ENST00000321892.4:c.1892A>G	chr17.hg19:g.65871699A>G	ENSP00000315454:p.Asn631Ser	39.0	0.0		52.0	4.0	NM_004459	Q6NX67|Q7Z7D6|Q9UIG2	Missense_Mutation	SNP	ENST00000321892.4	hg19		.	.	.	.	.	.	.	.	.	.	A	12.07	1.829063	0.32329	.	.	ENSG00000171634	ENST00000544491;ENST00000335221;ENST00000321892;ENST00000544778	T;T	0.61510	0.11;0.1	5.04	5.04	0.67666	.	.	.	.	.	T	0.65133	0.2662	L	0.36672	1.1	0.28525	N	0.91287	D;D	0.69078	0.997;0.994	D;D	0.70716	0.97;0.913	T	0.57516	-0.7798	9	0.23302	T	0.38	.	14.0636	0.64815	1.0:0.0:0.0:0.0	.	631;631	Q12830;Q12830-4	BPTF_HUMAN;.	S	536;631;631;492	ENSP00000334351:N631S;ENSP00000315454:N631S	ENSP00000315454:N631S	N	+	2	0	BPTF	63302161	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	3.372000	0.52387	2.204000	0.70986	0.383000	0.25322	AAC	.	.		0.443	BPTF-201	KNOWN	basic	protein_coding	protein_coding		NM_182641, NM_004459	
AMZ2	51321	hgsc.bcm.edu	37	17	66251989	66251989	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:66251989T>C	ENST00000359904.3	+	6	2031	c.899T>C	c.(898-900)gTt>gCt	p.V300A	AMZ2_ENST00000577985.1_Missense_Mutation_p.V300A|AMZ2_ENST00000585050.1_Intron|AMZ2_ENST00000392720.2_Missense_Mutation_p.V300A|AMZ2_ENST00000580753.1_Missense_Mutation_p.V300A|AMZ2_ENST00000577273.1_Intron|AMZ2_ENST00000577866.1_Missense_Mutation_p.V300A|AMZ2_ENST00000359783.4_Missense_Mutation_p.V242A	NM_016627.4	NP_057711.3	Q86W34	AMZ2_HUMAN	archaelysin family metallopeptidase 2	300							metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)	9	all_cancers(12;1.12e-09)		BRCA - Breast invasive adenocarcinoma(8;3.17e-08)|LUSC - Lung squamous cell carcinoma(166;0.24)			CAGTGTGCTGTTGGCTTCAGC	0.478																																					p.V300A		Atlas-SNP	.											.	AMZ2	15	.	0			c.T899C						.						55.0	54.0	55.0					17																	66251989		2203	4300	6503	SO:0001583	missense	51321	exon7			GTGCTGTTGGCTT	CR609550	CCDS11674.1, CCDS32714.1	17q24.2	2010-04-08			ENSG00000196704	ENSG00000196704			28041	protein-coding gene	gene with protein product	"""archaemetzincin-2"""	615169				15972818	Standard	XM_005257436		Approved		uc002jgr.1	Q86W34		ENST00000359904.3:c.899T>C	chr17.hg19:g.66251989T>C	ENSP00000352976:p.Val300Ala	80.0	0.0		86.0	4.0	NM_001033572	A6NLD9|B3KR44|Q5XKF1|Q9NZE2	Missense_Mutation	SNP	ENST00000359904.3	hg19	CCDS11674.1	.	.	.	.	.	.	.	.	.	.	T	13.04	2.117584	0.37339	.	.	ENSG00000196704	ENST00000359904;ENST00000359783;ENST00000392720	T;T;T	0.44482	0.92;0.92;0.92	3.64	3.64	0.41730	.	0.680538	0.12900	N	0.429867	T	0.32164	0.0820	L	0.29908	0.895	0.80722	D	1	B;B	0.23377	0.084;0.012	B;B	0.21708	0.036;0.022	T	0.18023	-1.0350	10	0.54805	T	0.06	-25.5489	10.8589	0.46815	0.0:0.0:0.0:1.0	.	242;300	A6NLD9;Q86W34	.;AMZ2_HUMAN	A	300;242;300	ENSP00000352976:V300A;ENSP00000352831:V242A;ENSP00000376481:V300A	ENSP00000352831:V242A	V	+	2	0	AMZ2	63763584	0.830000	0.29337	0.553000	0.28255	0.603000	0.37013	6.532000	0.73825	1.873000	0.54277	0.383000	0.25322	GTT	.	.		0.478	AMZ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448261.1	NM_016627	
SRP68	6730	hgsc.bcm.edu	37	17	74044023	74044023	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:74044023T>C	ENST00000307877.2	-	10	1267	c.1106A>G	c.(1105-1107)gAg>gGg	p.E369G	SRP68_ENST00000539137.1_Missense_Mutation_p.E331G|SRP68_ENST00000542536.2_5'UTR|SRP68_ENST00000355113.5_Missense_Mutation_p.E268G|SRP68_ENST00000602720.1_Missense_Mutation_p.E30G	NM_014230.3	NP_055045.2	Q9UHB9	SRP68_HUMAN	signal recognition particle 68kDa	369					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|response to drug (GO:0042493)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|nucleolus (GO:0005730)|ribosome (GO:0005840)|signal recognition particle, endoplasmic reticulum targeting (GO:0005786)	7S RNA binding (GO:0008312)|endoplasmic reticulum signal peptide binding (GO:0030942)|poly(A) RNA binding (GO:0044822)|signal recognition particle binding (GO:0005047)			NS(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(5)|lung(4)|ovary(2)|prostate(3)	23						CTTCCCTGGCTCTCCTTCAAG	0.333																																					p.E369G		Atlas-SNP	.											.	SRP68	61	.	0			c.A1106G						.						110.0	108.0	108.0					17																	74044023		2203	4300	6503	SO:0001583	missense	6730	exon10			CCTGGCTCTCCTT	AF195951	CCDS11738.1, CCDS58600.1, CCDS58601.1	17q25.1	2010-04-30	2002-08-29		ENSG00000167881	ENSG00000167881			11302	protein-coding gene	gene with protein product		604858	"""signal recognition particle 68kD"""			10618370	Standard	NM_014230		Approved		uc002jqk.2	Q9UHB9		ENST00000307877.2:c.1106A>G	chr17.hg19:g.74044023T>C	ENSP00000312066:p.Glu369Gly	198.0	0.0		189.0	8.0	NM_014230	B3KUU5|B3KWY7|G3V1U4|Q8NCJ4|Q8WUK2	Missense_Mutation	SNP	ENST00000307877.2	hg19	CCDS11738.1	.	.	.	.	.	.	.	.	.	.	T	13.85	2.359200	0.41801	.	.	ENSG00000167881	ENST00000411758;ENST00000539137;ENST00000542536;ENST00000307877;ENST00000304220;ENST00000355113	.	.	.	6.17	6.17	0.99709	.	0.094899	0.85682	D	0.000000	T	0.39145	0.1067	N	0.12961	0.28	0.80722	D	1	B;B	0.34290	0.447;0.447	B;B	0.33690	0.168;0.109	T	0.37934	-0.9684	9	0.52906	T	0.07	-30.2755	16.0034	0.80327	0.0:0.0:0.0:1.0	.	331;369	G3V1U4;Q9UHB9	.;SRP68_HUMAN	G	109;331;30;369;338;268	.	ENSP00000307756:E338G	E	-	2	0	SRP68	71555618	1.000000	0.71417	0.855000	0.33649	0.158000	0.22134	6.963000	0.76055	2.371000	0.80710	0.533000	0.62120	GAG	.	.		0.333	SRP68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449487.1	NM_014230	
PPP1R27	116729	hgsc.bcm.edu	37	17	79792500	79792500	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:79792500A>G	ENST00000330261.4	-	2	299	c.220T>C	c.(220-222)Tct>Cct	p.S74P	FAM195B_ENST00000572645.1_5'Flank|PPP1R27_ENST00000573182.1_5'Flank|FAM195B_ENST00000538396.1_5'Flank|FAM195B_ENST00000455127.2_5'Flank|FAM195B_ENST00000575061.1_5'Flank|FAM195B_ENST00000573478.1_5'Flank|FAM195B_ENST00000576431.1_5'Flank|PPP1R27_ENST00000570394.1_Missense_Mutation_p.S74P	NM_001007533.3	NP_001007534.1	Q86WC6	PPR27_HUMAN	protein phosphatase 1, regulatory subunit 27	74					negative regulation of phosphatase activity (GO:0010923)		phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)										AGGTTTCCAGAGAGCACGGCT	0.632																																					p.S74P		Atlas-SNP	.											.	.	.	.	0			c.T220C						.						138.0	110.0	119.0					17																	79792500		2203	4300	6503	SO:0001583	missense	116729	exon2			TTCCAGAGAGCAC	AF434846	CCDS32767.1	17q25.3	2013-01-10	2011-10-11	2011-10-11	ENSG00000182676	ENSG00000182676		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Ankyrin repeat domain containing"""	16813	protein-coding gene	gene with protein product			"""dysferlin-interacting protein 1 (toonin)"", ""dysferlin interacting protein 1 (toonin)"", ""dysferlin interacting protein 1"""	DYSFIP1			Standard	NM_001007533		Approved	toonin	uc002kbj.1	Q86WC6		ENST00000330261.4:c.220T>C	chr17.hg19:g.79792500A>G	ENSP00000331065:p.Ser74Pro	122.0	0.0		96.0	4.0	NM_001007533		Missense_Mutation	SNP	ENST00000330261.4	hg19	CCDS32767.1	.	.	.	.	.	.	.	.	.	.	A	20.3	3.968670	0.74131	.	.	ENSG00000182676	ENST00000330261	T	0.67345	-0.26	4.86	3.7	0.42460	.	0.059038	0.64402	D	0.000001	T	0.72153	0.3425	L	0.59967	1.855	0.42293	D	0.992145	D	0.59767	0.986	P	0.60473	0.875	T	0.74272	-0.3719	10	0.72032	D	0.01	.	7.279	0.26300	0.712:0.1465:0.0:0.1415	.	74	Q86WC6	PPR27_HUMAN	P	74	ENSP00000331065:S74P	ENSP00000331065:S74P	S	-	1	0	DYSFIP1	77385789	0.967000	0.33354	0.954000	0.39281	0.809000	0.45718	2.280000	0.43443	1.826000	0.53198	0.459000	0.35465	TCT	.	.		0.632	PPP1R27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439692.1	NM_001007533	
LAMA1	284217	hgsc.bcm.edu	37	18	7034631	7034631	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr18:7034631T>C	ENST00000389658.3	-	14	1991	c.1898A>G	c.(1897-1899)gAg>gGg	p.E633G		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	633	Laminin IV type A 1. {ECO:0000255|PROSITE-ProRule:PRU00458}.				axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				GTTTAGGTACTCTTCATAAGG	0.408																																					p.E633G		Atlas-SNP	.											.	LAMA1	458	.	0			c.A1898G						.						138.0	124.0	129.0					18																	7034631		2203	4300	6503	SO:0001583	missense	284217	exon14			AGGTACTCTTCAT	X58531	CCDS32787.1	18p11.3	2013-03-01			ENSG00000101680	ENSG00000101680		"""Laminins"""	6481	protein-coding gene	gene with protein product		150320		LAMA		2591971	Standard	NM_005559		Approved		uc002knm.3	P25391	OTTHUMG00000133478	ENST00000389658.3:c.1898A>G	chr18.hg19:g.7034631T>C	ENSP00000374309:p.Glu633Gly	114.0	0.0		144.0	6.0	NM_005559		Missense_Mutation	SNP	ENST00000389658.3	hg19	CCDS32787.1	.	.	.	.	.	.	.	.	.	.	T	14.54	2.567018	0.45694	.	.	ENSG00000101680	ENST00000389658	T	0.37058	1.22	5.9	5.9	0.94986	Laminin B type IV (2);Laminin B, subgroup (1);	0.059369	0.64402	D	0.000004	T	0.60314	0.2259	M	0.78456	2.415	0.42300	D	0.992178	D	0.76494	0.999	D	0.72625	0.978	T	0.58713	-0.7588	10	0.25106	T	0.35	.	16.3283	0.82996	0.0:0.0:0.0:1.0	.	633	P25391	LAMA1_HUMAN	G	633	ENSP00000374309:E633G	ENSP00000374309:E633G	E	-	2	0	LAMA1	7024631	1.000000	0.71417	0.997000	0.53966	0.102000	0.19082	5.146000	0.64845	2.257000	0.74773	0.533000	0.62120	GAG	.	.		0.408	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559	
LAMA1	284217	hgsc.bcm.edu	37	18	7044819	7044819	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr18:7044819T>C	ENST00000389658.3	-	7	971	c.878A>G	c.(877-879)gAg>gGg	p.E293G		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	293	Laminin EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00460}.				axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				AGTATTATGCTCACATTGACA	0.448																																					p.E293G		Atlas-SNP	.											.	LAMA1	458	.	0			c.A878G						.						115.0	111.0	112.0					18																	7044819		2203	4300	6503	SO:0001583	missense	284217	exon7			TTATGCTCACATT	X58531	CCDS32787.1	18p11.3	2013-03-01			ENSG00000101680	ENSG00000101680		"""Laminins"""	6481	protein-coding gene	gene with protein product		150320		LAMA		2591971	Standard	NM_005559		Approved		uc002knm.3	P25391	OTTHUMG00000133478	ENST00000389658.3:c.878A>G	chr18.hg19:g.7044819T>C	ENSP00000374309:p.Glu293Gly	120.0	0.0		106.0	5.0	NM_005559		Missense_Mutation	SNP	ENST00000389658.3	hg19	CCDS32787.1	.	.	.	.	.	.	.	.	.	.	T	18.12	3.552286	0.65311	.	.	ENSG00000101680	ENST00000389658	T	0.64085	-0.08	4.97	4.97	0.65823	EGF-like, laminin (4);	0.063251	0.64402	D	0.000011	T	0.80082	0.4558	M	0.82923	2.615	0.53005	D	0.999963	D	0.89917	1.0	D	0.77557	0.99	T	0.83052	-0.0152	10	0.59425	D	0.04	.	14.9339	0.70938	0.0:0.0:0.0:1.0	.	293	P25391	LAMA1_HUMAN	G	293	ENSP00000374309:E293G	ENSP00000374309:E293G	E	-	2	0	LAMA1	7034819	1.000000	0.71417	0.954000	0.39281	0.312000	0.27988	6.223000	0.72257	1.987000	0.57996	0.533000	0.62120	GAG	.	.		0.448	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559	
DSC3	1825	hgsc.bcm.edu	37	18	28611062	28611062	+	Silent	SNP	C	C	T			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr18:28611062C>T	ENST00000360428.4	-	3	311	c.231G>A	c.(229-231)ggG>ggA	p.G77G	DSC3_ENST00000434452.1_Silent_p.G77G	NM_001941.3	NP_001932.2	Q14574	DSC3_HUMAN	desmocollin 3	77					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|in utero embryonic development (GO:0001701)|protein stabilization (GO:0050821)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|desmosome (GO:0030057)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|gamma-catenin binding (GO:0045295)			endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(6)|lung(29)|ovary(2)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	56			OV - Ovarian serous cystadenocarcinoma(10;0.125)			TGTACACTGACCCATCATTTA	0.418																																					p.G77G		Atlas-SNP	.											DSC3_ENST00000434452,right_lower_lobe,carcinoma,0,2	DSC3	225	.	0			c.G231A						.						72.0	64.0	67.0					18																	28611062		2203	4300	6503	SO:0001819	synonymous_variant	1825	exon3			CACTGACCCATCA	X83929	CCDS32810.1	18q12.1	2014-07-30			ENSG00000134762	ENSG00000134762		"""Cadherins / Major cadherins"""	3037	protein-coding gene	gene with protein product		600271		DSC4		7774948, 8486729	Standard	NM_001941		Approved	CDHF3, DSC, DSC1, DSC2	uc002kwj.4	Q14574	OTTHUMG00000179622	ENST00000360428.4:c.231G>A	chr18.hg19:g.28611062C>T		59.0	0.0		78.0	0.0	NM_024423	A6NN35|Q14200|Q9HAZ9	Silent	SNP	ENST00000360428.4	hg19	CCDS32810.1																																																																																			.	.		0.418	DSC3-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447384.1	NM_001941, NM_024423	
PIK3C3	5289	hgsc.bcm.edu	37	18	39542519	39542519	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr18:39542519T>C	ENST00000262039.4	+	3	409	c.323T>C	c.(322-324)cTc>cCc	p.L108P	PIK3C3_ENST00000398870.3_Missense_Mutation_p.L45P|PIK3C3_ENST00000586545.1_Missense_Mutation_p.L108P	NM_002647.2	NP_002638.2	Q8NEB9	PK3C3_HUMAN	phosphatidylinositol 3-kinase, catalytic subunit type 3	108	C2 PI3K-type. {ECO:0000255|PROSITE- ProRule:PRU00880}.				autophagic vacuole assembly (GO:0000045)|cytokinesis (GO:0000910)|early endosome to late endosome transport (GO:0045022)|endosome organization (GO:0007032)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|protein processing (GO:0016485)|regulation of protein secretion (GO:0050708)|response to leucine (GO:0043201)|small molecule metabolic process (GO:0044281)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	axoneme (GO:0005930)|cytosol (GO:0005829)|late endosome (GO:0005770)|membrane (GO:0016020)|midbody (GO:0030496)|phagocytic vesicle (GO:0045335)|phosphatidylinositol 3-kinase complex (GO:0005942)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|protein kinase activity (GO:0004672)			breast(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(10)|liver(1)|lung(25)|ovary(1)|skin(2)|urinary_tract(1)	49						CAAGTGGCCCTCACCATATGG	0.453										TSP Lung(28;0.18)																											p.L108P	NSCLC(37;552 1060 2683 16430 37914)	Atlas-SNP	.											.	PIK3C3	138	.	0			c.T323C						.						105.0	94.0	98.0					18																	39542519		2203	4300	6503	SO:0001583	missense	5289	exon3			TGGCCCTCACCAT	Z46973	CCDS11920.1	18q12.3	2012-07-13	2012-07-13		ENSG00000078142	ENSG00000078142	2.7.1.137		8974	protein-coding gene	gene with protein product		602609	"""phosphoinositide-3-kinase, class 3"""			7628435	Standard	NM_002647		Approved	Vps34	uc002lap.3	Q8NEB9	OTTHUMG00000132593	ENST00000262039.4:c.323T>C	chr18.hg19:g.39542519T>C	ENSP00000262039:p.Leu108Pro	95.0	0.0		124.0	5.0	NM_002647	Q15134	Missense_Mutation	SNP	ENST00000262039.4	hg19	CCDS11920.1	.	.	.	.	.	.	.	.	.	.	T	25.2	4.613515	0.87359	.	.	ENSG00000078142	ENST00000262039;ENST00000398870	T;T	0.81415	-1.49;-1.49	5.88	5.88	0.94601	C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);Phosphoinositide 3-kinase, C2 (2);	0.000000	0.85682	D	0.000000	D	0.89015	0.6595	M	0.79258	2.445	0.80722	D	1	D;D	0.58970	0.972;0.984	P;D	0.65323	0.781;0.934	D	0.89265	0.3600	9	.	.	.	.	16.2898	0.82742	0.0:0.0:0.0:1.0	.	45;108	A8MYT4;Q8NEB9	.;PK3C3_HUMAN	P	108;45	ENSP00000262039:L108P;ENSP00000381845:L45P	.	L	+	2	0	PIK3C3	37796517	1.000000	0.71417	1.000000	0.80357	0.917000	0.54804	7.832000	0.86757	2.250000	0.74265	0.482000	0.46254	CTC	.	.		0.453	PIK3C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255804.1	NM_002647	
LOXHD1	125336	hgsc.bcm.edu	37	18	44181198	44181198	+	Silent	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr18:44181198T>C	ENST00000398722.4	-	1	281	c.282A>G	c.(280-282)agA>agG	p.R94R	LOXHD1_ENST00000441551.2_Silent_p.R372R|LOXHD1_ENST00000536736.1_Silent_p.R372R			Q8IVV2	LOXH1_HUMAN	lipoxygenase homology domains 1	94	PLAT 1. {ECO:0000255|PROSITE- ProRule:PRU00152}.				calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)|sensory perception of sound (GO:0007605)	membrane (GO:0016020)|stereocilium (GO:0032420)	calcium channel activity (GO:0005262)			NS(3)|autonomic_ganglia(1)|breast(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(2)|pancreas(1)|prostate(4)|skin(4)|stomach(1)	36						AGAACCAGCCTCTGTTGACAC	0.552																																					p.R372R		Atlas-SNP	.											.	LOXHD1	367	.	0			c.A1116G						.						39.0	37.0	37.0					18																	44181198		692	1591	2283	SO:0001819	synonymous_variant	125336	exon8			CCAGCCTCTGTTG	AK057232	CCDS45861.1, CCDS45862.1, CCDS54184.1	18q21.1	2009-09-11			ENSG00000167210	ENSG00000167210			26521	protein-coding gene	gene with protein product		613072	"""deafness, autosomal recessive 77"""	DFNB77		19732867	Standard	NM_144612		Approved	FLJ32670, LH2D1	uc010xcw.1	Q8IVV2	OTTHUMG00000132644	ENST00000398722.4:c.282A>G	chr18.hg19:g.44181198T>C		84.0	0.0		82.0	5.0	NM_144612	B7WNN3|B7WNT1|B7WPI9|Q6ZRY7|Q86WW9|Q96DL7	Silent	SNP	ENST00000398722.4	hg19		.	.	.	.	.	.	.	.	.	.	T	10.59	1.392913	0.25118	.	.	ENSG00000167210	ENST00000441551	.	.	.	5.56	0.101	0.14517	.	0.248454	0.41396	D	0.000897	T	0.34600	0.0903	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.06552	-1.0820	6	0.21014	T	0.42	.	0.4714	0.00532	0.323:0.19:0.1168:0.3701	.	.	.	.	G	353	.	ENSP00000387621:R353G	R	-	1	2	LOXHD1	42435196	0.991000	0.36638	0.998000	0.56505	0.994000	0.84299	0.295000	0.19065	0.069000	0.16605	0.459000	0.35465	AGG	.	.		0.552	LOXHD1-201	KNOWN	basic	protein_coding	protein_coding		NM_144612	
SERPINB2	5055	hgsc.bcm.edu	37	18	61569003	61569003	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr18:61569003T>C	ENST00000299502.4	+	6	645	c.565T>C	c.(565-567)Tct>Cct	p.S189P	SERPINB2_ENST00000482254.1_3'UTR|SERPINB2_ENST00000457692.1_Missense_Mutation_p.S189P	NM_002575.2	NP_002566.1	P05120	PAI2_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 2	189					blood coagulation (GO:0007596)|fibrinolysis (GO:0042730)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|central_nervous_system(2)|endometrium(4)|large_intestine(7)|liver(1)|lung(12)|prostate(2)|skin(2)|stomach(1)	32		Esophageal squamous(42;0.131)			Tenecteplase(DB00031)|Urokinase(DB00013)	ACCTGAAGGTTCTGTAGATGG	0.368																																					p.S189P		Atlas-SNP	.											.	SERPINB2	63	.	0			c.T565C						.						113.0	114.0	114.0					18																	61569003		2203	4300	6503	SO:0001583	missense	5055	exon6			GAAGGTTCTGTAG	Y00630	CCDS11989.1	18q21.3	2014-02-18	2005-08-18		ENSG00000197632	ENSG00000197632		"""Serine (or cysteine) peptidase inhibitors"""	8584	protein-coding gene	gene with protein product		173390	"""serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 2"""	PLANH2, PAI2		24172014	Standard	NM_002575		Approved	HsT1201	uc002ljo.3	P05120	OTTHUMG00000060592	ENST00000299502.4:c.565T>C	chr18.hg19:g.61569003T>C	ENSP00000299502:p.Ser189Pro	75.0	0.0		80.0	4.0	NM_002575	Q96E96	Missense_Mutation	SNP	ENST00000299502.4	hg19	CCDS11989.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	15.39|15.39	2.818519|2.818519	0.50633|0.50633	.|.	.|.	ENSG00000242550|ENSG00000197632	ENST00000397996;ENST00000418725|ENST00000299502;ENST00000457692	.|T;T	.|0.13538	.|2.58;2.58	5.9|5.9	3.34|3.34	0.38264|0.38264	.|Serpin domain (3);	.|0.406771	.|0.30210	.|N	.|0.010142	T|T	0.15782|0.15782	0.0380|0.0380	M|M	0.77103|0.77103	2.36|2.36	0.29012|0.29012	N|N	0.886802|0.886802	.|B	.|0.29531	.|0.247	.|B	.|0.29077	.|0.098	T|T	0.18398|0.18398	-1.0338|-1.0338	5|10	.|0.66056	.|D	.|0.02	.|.	4.1622|4.1622	0.10289|0.10289	0.126:0.0702:0.1313:0.6725|0.126:0.0702:0.1313:0.6725	.|.	.|189	.|P05120	.|PAI2_HUMAN	S|P	65|189	.|ENSP00000299502:S189P;ENSP00000401645:S189P	.|ENSP00000299502:S189P	F|S	+|+	2|1	0|0	SERPINB10|SERPINB2	59719983|59719983	0.000000|0.000000	0.05858|0.05858	0.999000|0.999000	0.59377|0.59377	0.578000|0.578000	0.36192|0.36192	-0.303000|-0.303000	0.08210|0.08210	1.036000|1.036000	0.39998|0.39998	0.528000|0.528000	0.53228|0.53228	TTC|TCT	.	.		0.368	SERPINB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134009.1	NM_002575	
GALR1	2587	hgsc.bcm.edu	37	18	74962810	74962810	+	Silent	SNP	G	G	A	rs5375	byFrequency	TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr18:74962810G>A	ENST00000299727.3	+	1	306	c.306G>A	c.(304-306)gtG>gtA	p.V102V		NM_001480.3	NP_001471.2	P47211	GALR1_HUMAN	galanin receptor 1	102					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|digestion (GO:0007586)|negative regulation of adenylate cyclase activity (GO:0007194)|neuropeptide signaling pathway (GO:0007218)|positive regulation of cortisol secretion (GO:0051464)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	galanin receptor activity (GO:0004966)|neuropeptide binding (GO:0042923)|peptide hormone binding (GO:0017046)			breast(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(13)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	24		Prostate(75;0.0865)|Esophageal squamous(42;0.129)|Melanoma(33;0.211)		OV - Ovarian serous cystadenocarcinoma(15;1.03e-06)|BRCA - Breast invasive adenocarcinoma(31;0.104)		CCACCTGGGTGCTGGGCGCCT	0.612																																					p.V102V		Atlas-SNP	.											GALR1,NS,carcinoma,0,1	GALR1	53	.	0			c.G306A						.						129.0	114.0	119.0					18																	74962810		2203	4300	6503	SO:0001819	synonymous_variant	2587	exon1			CTGGGTGCTGGGC	U90658	CCDS12012.1	18q23	2012-08-08			ENSG00000166573	ENSG00000166573		"""GPCR / Class A : Galanin receptors"""	4132	protein-coding gene	gene with protein product		600377		GALNR1, GALNR		7524088	Standard	NM_001480		Approved		uc002lms.4	P47211	OTTHUMG00000132875	ENST00000299727.3:c.306G>A	chr18.hg19:g.74962810G>A		127.0	0.0		181.0	59.0	NM_001480	Q4VBL7	Silent	SNP	ENST00000299727.3	hg19	CCDS12012.1																																																																																			.	G|0.936;T|0.064		0.612	GALR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256362.1		
RBFA	79863	hgsc.bcm.edu	37	18	77796689	77796689	+	Silent	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr18:77796689T>C	ENST00000306735.5	+	2	318	c.180T>C	c.(178-180)agT>agC	p.S60S	TXNL4A_ENST00000585474.1_5'Flank|TXNL4A_ENST00000592957.1_5'Flank|RP11-795F19.5_ENST00000569722.1_Intron|RBFA_ENST00000586847.1_3'UTR|RBFA_ENST00000262197.7_Silent_p.S60S|TXNL4A_ENST00000589926.1_5'Flank	NM_024805.2	NP_079081.2	Q8N0V3	RBFA_HUMAN	ribosome binding factor A (putative)	60					rRNA processing (GO:0006364)	mitochondrion (GO:0005739)				endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|urinary_tract(1)	15						GGTATGAAAGTCCTTCCTTGG	0.378																																					p.S60S		Atlas-SNP	.											.	RBFA	27	.	0			c.T180C						.						122.0	118.0	119.0					18																	77796689		2203	4300	6503	SO:0001819	synonymous_variant	79863	exon2			TGAAAGTCCTTCC	BC014195	CCDS12021.1, CCDS54194.1	18q23	2010-10-21	2010-10-21	2010-10-21	ENSG00000101546	ENSG00000101546			26120	protein-coding gene	gene with protein product			"""chromosome 18 open reading frame 22"""	C18orf22		12477932	Standard	NM_024805		Approved	FLJ21172, HsT169	uc002lns.3	Q8N0V3	OTTHUMG00000132923	ENST00000306735.5:c.180T>C	chr18.hg19:g.77796689T>C		45.0	0.0		68.0	4.0	NM_024805	Q6PF07|Q8WZ65|Q9H776	Silent	SNP	ENST00000306735.5	hg19	CCDS12021.1																																																																																			.	.		0.378	RBFA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256436.2	NM_024805	
MED16	10025	hgsc.bcm.edu	37	19	879947	879947	+	Missense_Mutation	SNP	C	C	T	rs200085016	byFrequency	TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:879947C>T	ENST00000589119.1	-	7	1342	c.1343G>A	c.(1342-1344)aGc>aAc	p.S448N	MED16_ENST00000312090.6_Missense_Mutation_p.S448N|MED16_ENST00000325464.1_Missense_Mutation_p.S448N|MED16_ENST00000606828.1_Intron|MED16_ENST00000269814.4_Missense_Mutation_p.S448N|MED16_ENST00000395808.3_Missense_Mutation_p.S448N			Q9Y2X0	MED16_HUMAN	mediator complex subunit 16	448					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of receptor activity (GO:2000273)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|receptor activity (GO:0004872)|thyroid hormone receptor binding (GO:0046966)|thyroid hormone receptor coactivator activity (GO:0030375)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)	p.S448N(1)		NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(12)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	21		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;6.59e-06)|all_lung(49;9.97e-06)|Breast(49;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)		CTTCCCGTGGCTGTCAATCCC	0.667													T|||	6	0.00119808	0.003	0.0	5008	,	,		14656	0.0		0.0	False		,,,				2504	0.002				p.S448N		Atlas-SNP	.											MED16,NS,carcinoma,0,1	MED16	61	.	1	Substitution - Missense(1)	lung(1)	c.G1343A						.						13.0	12.0	12.0					19																	879947		2156	4256	6412	SO:0001583	missense	10025	exon8			CCGTGGCTGTCAA	AF121228	CCDS12047.1	19p13.3	2013-01-10	2007-07-30	2007-07-30		ENSG00000175221		"""WD repeat domain containing"""	17556	protein-coding gene	gene with protein product		604062	"""thyroid hormone receptor associated protein 5"""	THRAP5		10235266, 10198638	Standard	NM_005481		Approved	DRIP92, TRAP95	uc002lqd.1	Q9Y2X0		ENST00000589119.1:c.1343G>A	chr19.hg19:g.879947C>T	ENSP00000464810:p.Ser448Asn	110.0	0.0		151.0	10.0	NM_005481	Q6PJT2|Q96AD4|Q96I35|Q9Y652	Missense_Mutation	SNP	ENST00000589119.1	hg19	CCDS12047.1	.	.	.	.	.	.	.	.	.	.	T	0.008	-1.912492	0.00508	.	.	ENSG00000175221	ENST00000325464;ENST00000312090;ENST00000395808;ENST00000269814;ENST00000534906;ENST00000537596;ENST00000540679;ENST00000538572;ENST00000424039	T;T;T;T	0.40225	1.04;1.04;1.04;1.04	4.21	3.18	0.36537	WD40 repeat-like-containing domain (1);	0.114163	0.64402	N	0.000019	T	0.18299	0.0439	N	0.12961	0.28	0.21802	N	0.999537	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.04013	0.0;0.0;0.0;0.0;0.001	T	0.30909	-0.9962	10	0.06494	T	0.89	-17.3318	4.2026	0.10473	0.0:0.3061:0.1749:0.519	.	448;448;448;448;448	Q9Y2X0-2;E7ETV0;Q9Y2X0-4;Q9Y2X0-3;Q9Y2X0	.;.;.;.;MED16_HUMAN	N	448;448;448;448;448;304;209;207;448	ENSP00000325612:S448N;ENSP00000308528:S448N;ENSP00000379153:S448N;ENSP00000269814:S448N	ENSP00000269814:S448N	S	-	2	0	MED16	830947	0.999000	0.42202	0.989000	0.46669	0.059000	0.15707	0.492000	0.22435	0.062000	0.16340	-0.442000	0.05670	AGC	.	.		0.667	MED16-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457902.3	NM_005481	
UBXN6	80700	hgsc.bcm.edu	37	19	4453507	4453507	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:4453507A>G	ENST00000301281.6	-	3	384	c.260T>C	c.(259-261)cTt>cCt	p.L87P	CTB-50L17.9_ENST00000592034.1_RNA|UBXN6_ENST00000394765.3_Missense_Mutation_p.L34P	NM_025241.2	NP_079517.1	Q9BZV1	UBXN6_HUMAN	UBX domain protein 6	87						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)				NS(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|skin(1)	12						TTCGGCTTGAAGTTCCTTTCT	0.642																																					p.L87P		Atlas-SNP	.											.	UBXN6	27	.	0			c.T260C						.						52.0	47.0	49.0					19																	4453507		2203	4300	6503	SO:0001583	missense	80700	exon3			GCTTGAAGTTCCT	AF272893	CCDS12129.1, CCDS54201.1	19p13	2008-07-25	2008-07-25	2008-07-25		ENSG00000167671		"""UBX domain containing"""	14928	protein-coding gene	gene with protein product		611946	"""UBX domain-containing 1"", ""UBX domain containing 1"""	UBXD1		11342112	Standard	NM_025241		Approved	UBXDC2	uc002man.2	Q9BZV1		ENST00000301281.6:c.260T>C	chr19.hg19:g.4453507A>G	ENSP00000301281:p.Leu87Pro	73.0	0.0		53.0	4.0	NM_025241	D6W626|Q96AH1|Q96IK9|Q9BZV0	Missense_Mutation	SNP	ENST00000301281.6	hg19	CCDS12129.1	.	.	.	.	.	.	.	.	.	.	A	14.75	2.629811	0.46944	.	.	ENSG00000167671	ENST00000301281;ENST00000394765	T;T	0.53423	0.62;0.62	3.75	2.69	0.31865	.	0.086838	0.47852	D	0.000206	T	0.65133	0.2662	M	0.83012	2.62	0.58432	D	0.999996	D;P	0.89917	1.0;0.884	D;P	0.75020	0.985;0.721	T	0.67894	-0.5552	10	0.87932	D	0	-16.2294	7.2616	0.26207	0.8923:0.0:0.1077:0.0	.	34;87	Q9BZV1-2;Q9BZV1	.;UBXN6_HUMAN	P	87;34	ENSP00000301281:L87P;ENSP00000378246:L34P	ENSP00000301281:L87P	L	-	2	0	UBXN6	4404507	0.999000	0.42202	0.647000	0.29507	0.855000	0.48748	5.517000	0.67061	1.578000	0.49821	0.402000	0.26972	CTT	.	.		0.642	UBXN6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458447.3	NM_025241	
ACER1	125981	hgsc.bcm.edu	37	19	6307247	6307247	+	Silent	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:6307247A>G	ENST00000301452.4	-	5	620	c.543T>C	c.(541-543)gcT>gcC	p.A181A		NM_133492.2	NP_597999.1	Q8TDN7	ACER1_HUMAN	alkaline ceramidase 1	181					cell differentiation (GO:0030154)|cellular response to calcium ion (GO:0071277)|ceramide catabolic process (GO:0046514)|epidermis development (GO:0008544)|keratinocyte differentiation (GO:0030216)|regulation of lipid metabolic process (GO:0019216)|response to alkaline pH (GO:0010446)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingosine biosynthetic process (GO:0046512)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	ceramidase activity (GO:0017040)|dihydroceramidase activity (GO:0071633)			NS(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(4)|pancreas(1)	15						TCAGAGCAACAGCCCATAAAA	0.552																																					p.A181A		Atlas-SNP	.											.	ACER1	38	.	0			c.T543C						.						95.0	91.0	93.0					19																	6307247		2203	4300	6503	SO:0001819	synonymous_variant	125981	exon5			AGCAACAGCCCAT	AF347024	CCDS12161.1	19p13.3	2013-01-25	2008-12-19	2008-12-19	ENSG00000167769	ENSG00000167769	3.5.1.23	"""Alkaline ceramidase"""	18356	protein-coding gene	gene with protein product		613491	"""N-acylsphingosine amidohydrolase (alkaline ceramidase) 3"""	ASAH3		12783875	Standard	NM_133492		Approved		uc002mel.2	Q8TDN7		ENST00000301452.4:c.543T>C	chr19.hg19:g.6307247A>G		64.0	0.0		72.0	4.0	NM_133492		Silent	SNP	ENST00000301452.4	hg19	CCDS12161.1																																																																																			.	.		0.552	ACER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452982.1	NM_133492	
C3	718	hgsc.bcm.edu	37	19	6718129	6718129	+	Silent	SNP	G	G	A			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:6718129G>A	ENST00000245907.6	-	4	572	c.480C>T	c.(478-480)ggC>ggT	p.G160G		NM_000064.2	NP_000055.2	P01024	CO3_HUMAN	complement component 3	160					complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|fatty acid metabolic process (GO:0006631)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of activation of membrane attack complex (GO:0001970)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic cell clearance (GO:2000427)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|positive regulation of glucose transport (GO:0010828)|positive regulation of lipid storage (GO:0010884)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of type IIa hypersensitivity (GO:0001798)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of complement activation (GO:0030449)|regulation of immune response (GO:0050776)|regulation of triglyceride biosynthetic process (GO:0010866)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	C5L2 anaphylatoxin chemotactic receptor binding (GO:0031715)|endopeptidase inhibitor activity (GO:0004866)|receptor binding (GO:0005102)			breast(5)|endometrium(7)|kidney(6)|large_intestine(18)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(5)|skin(7)|upper_aerodigestive_tract(3)	72				GBM - Glioblastoma multiforme(1328;1.36e-05)|Lung(535;0.00661)	Intravenous Immunoglobulin(DB00028)	TGACCGTCCGGCCCACGGGTA	0.622																																					p.G160G		Atlas-SNP	.											.	C3	192	.	0			c.C480T						.						100.0	95.0	96.0					19																	6718129		2203	4300	6503	SO:0001819	synonymous_variant	718	exon4			CGTCCGGCCCACG	J04763	CCDS32883.1	19p13.3-p13.2	2014-09-17			ENSG00000125730	ENSG00000125730	3.4.21.43	"""Complement system"", ""Endogenous ligands"""	1318	protein-coding gene	gene with protein product	"""C3a anaphylatoxin"", ""complement component C3a"", ""complement component C3b"", ""prepro-C3"""	120700					Standard	NM_000064		Approved	CPAMD1, ARMD9, C3a, C3b	uc002mfm.3	P01024	OTTHUMG00000150335	ENST00000245907.6:c.480C>T	chr19.hg19:g.6718129G>A		91.0	0.0		96.0	31.0	NM_000064	A7E236	Silent	SNP	ENST00000245907.6	hg19	CCDS32883.1																																																																																			.	.		0.622	C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317636.2	NM_000064	
XAB2	56949	hgsc.bcm.edu	37	19	7684695	7684695	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:7684695T>C	ENST00000358368.4	-	18	2481	c.2444A>G	c.(2443-2445)aAc>aGc	p.N815S	XAB2_ENST00000534844.1_Missense_Mutation_p.N812S	NM_020196.2	NP_064581.2	Q9HCS7	SYF1_HUMAN	XPA binding protein 2	815					blastocyst development (GO:0001824)|DNA repair (GO:0006281)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|transcription, DNA-templated (GO:0006351)|transcription-coupled nucleotide-excision repair (GO:0006283)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(1)|central_nervous_system(2)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(2)|lung(11)|prostate(1)|skin(2)|urinary_tract(1)	26						CTCCTCGGGGTTGACCTGCTG	0.697								Direct reversal of damage;Nucleotide excision repair (NER)																													p.N815S		Atlas-SNP	.											.	XAB2	69	.	0			c.A2444G						.						118.0	120.0	119.0					19																	7684695		2203	4300	6503	SO:0001583	missense	56949	exon18			TCGGGGTTGACCT	AB026111	CCDS32892.1	19p13.3	2013-08-21				ENSG00000076924			14089	protein-coding gene	gene with protein product	"""SYF1 homolog, RNA splicing factor (S. cerevisiae)"", ""SYF1 pre-mRNA-splicing factor"""	610850				10944529	Standard	NM_020196		Approved	HCNP, HCRN, SYF1, NTC90	uc002mgx.3	Q9HCS7		ENST00000358368.4:c.2444A>G	chr19.hg19:g.7684695T>C	ENSP00000351137:p.Asn815Ser	87.0	0.0		100.0	4.0	NM_020196	Q8TET6|Q96HB0|Q96IW0|Q9NRG6|Q9ULP3	Missense_Mutation	SNP	ENST00000358368.4	hg19	CCDS32892.1	.	.	.	.	.	.	.	.	.	.	T	15.26	2.781387	0.49891	.	.	ENSG00000076924	ENST00000358368;ENST00000534844	T;T	0.31510	1.49;1.49	4.57	3.51	0.40186	.	0.058234	0.64402	D	0.000004	T	0.56659	0.2000	M	0.92367	3.3	0.58432	D	0.999994	D	0.55605	0.972	P	0.58013	0.831	T	0.63305	-0.6667	10	0.87932	D	0	-46.047	10.0458	0.42186	0.0:0.0:0.1702:0.8298	.	815	Q9HCS7	SYF1_HUMAN	S	815;812	ENSP00000351137:N815S;ENSP00000438225:N812S	ENSP00000351137:N815S	N	-	2	0	XAB2	7590695	1.000000	0.71417	0.997000	0.53966	0.629000	0.37895	5.366000	0.66122	0.566000	0.29273	0.254000	0.18369	AAC	.	.		0.697	XAB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000461021.1	NM_020196	
RGL3	57139	hgsc.bcm.edu	37	19	11517507	11517507	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:11517507T>C	ENST00000380456.3	-	6	734	c.671A>G	c.(670-672)gAc>gGc	p.D224G	Y_RNA_ENST00000365487.1_RNA|RGL3_ENST00000393423.3_Missense_Mutation_p.D224G	NM_001035223.2|NM_001161616.1	NP_001030300.2|NP_001155088.1	Q3MIN7	RGL3_HUMAN	ral guanine nucleotide dissociation stimulator-like 3	224					small GTPase mediated signal transduction (GO:0007264)	intracellular (GO:0005622)	Ral guanyl-nucleotide exchange factor activity (GO:0008321)			breast(1)|endometrium(4)|large_intestine(2)|lung(9)|ovary(1)|skin(1)	18						CTCTGAAGAGTCTGGGTCAGA	0.562																																					p.D224G	GBM(174;751 2067 17998 27979 33959)	Atlas-SNP	.											.	RGL3	100	.	0			c.A671G						.						52.0	51.0	51.0					19																	11517507		2203	4299	6502	SO:0001583	missense	57139	exon6			GAAGAGTCTGGGT	BC014426	CCDS32910.1, CCDS54221.1	19p13.2	2008-02-05				ENSG00000205517			30282	protein-coding gene	gene with protein product						10869344	Standard	NM_001035223		Approved	FLJ32585	uc002mro.2	Q3MIN7		ENST00000380456.3:c.671A>G	chr19.hg19:g.11517507T>C	ENSP00000369823:p.Asp224Gly	64.0	0.0		70.0	4.0	NM_001035223	B5ME84|B7ZL22|Q0P6G0	Missense_Mutation	SNP	ENST00000380456.3	hg19	CCDS32910.1	.	.	.	.	.	.	.	.	.	.	T	7.823	0.718103	0.15372	.	.	ENSG00000205517	ENST00000342684;ENST00000393423;ENST00000380456	T;T	0.29142	1.58;1.58	4.25	-6.52	0.01872	Ras guanine nucleotide exchange factor, domain (1);	1.713730	0.03182	N	0.172253	T	0.16300	0.0392	N	0.19112	0.55	0.09310	N	1	B;B	0.13145	0.001;0.007	B;B	0.10450	0.005;0.003	T	0.15263	-1.0443	10	0.49607	T	0.09	.	2.6115	0.04892	0.1318:0.2904:0.4004:0.1774	.	224;224	Q3MIN7;B5ME84	RGL3_HUMAN;.	G	21;224;224	ENSP00000377075:D224G;ENSP00000369823:D224G	ENSP00000344665:D21G	D	-	2	0	RGL3	11378507	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.581000	0.05820	-1.433000	0.01977	-0.435000	0.05868	GAC	.	.		0.562	RGL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421208.3	XM_290867	
RGL3	57139	hgsc.bcm.edu	37	19	11526669	11526669	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:11526669T>C	ENST00000380456.3	-	5	644	c.581A>G	c.(580-582)gAt>gGt	p.D194G	RGL3_ENST00000393423.3_Missense_Mutation_p.D194G	NM_001035223.2|NM_001161616.1	NP_001030300.2|NP_001155088.1	Q3MIN7	RGL3_HUMAN	ral guanine nucleotide dissociation stimulator-like 3	194	N-terminal Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00135}.				small GTPase mediated signal transduction (GO:0007264)	intracellular (GO:0005622)	Ral guanyl-nucleotide exchange factor activity (GO:0008321)			breast(1)|endometrium(4)|large_intestine(2)|lung(9)|ovary(1)|skin(1)	18						CTCCAAAAAATCTTCCAGAAG	0.592																																					p.D194G	GBM(174;751 2067 17998 27979 33959)	Atlas-SNP	.											.	RGL3	100	.	0			c.A581G						.						126.0	140.0	135.0					19																	11526669		2203	4300	6503	SO:0001583	missense	57139	exon5			AAAAAATCTTCCA	BC014426	CCDS32910.1, CCDS54221.1	19p13.2	2008-02-05				ENSG00000205517			30282	protein-coding gene	gene with protein product						10869344	Standard	NM_001035223		Approved	FLJ32585	uc002mro.2	Q3MIN7		ENST00000380456.3:c.581A>G	chr19.hg19:g.11526669T>C	ENSP00000369823:p.Asp194Gly	84.0	0.0		113.0	5.0	NM_001035223	B5ME84|B7ZL22|Q0P6G0	Missense_Mutation	SNP	ENST00000380456.3	hg19	CCDS32910.1	.	.	.	.	.	.	.	.	.	.	T	11.55	1.672144	0.29693	.	.	ENSG00000205517	ENST00000393423;ENST00000380456	T;T	0.28666	1.6;1.6	4.88	1.66	0.24008	Ras guanine nucleotide exchange factor, domain (1);Ras-like guanine nucleotide exchange factor, N-terminal (2);	0.981440	0.08360	N	0.957927	T	0.21674	0.0522	L	0.44542	1.39	0.09310	N	1	B;P	0.35328	0.082;0.495	B;B	0.26517	0.07;0.041	T	0.20405	-1.0276	10	0.54805	T	0.06	.	4.6926	0.12788	0.0:0.2647:0.1571:0.5782	.	194;194	Q3MIN7;B5ME84	RGL3_HUMAN;.	G	194	ENSP00000377075:D194G;ENSP00000369823:D194G	ENSP00000369823:D194G	D	-	2	0	RGL3	11387669	0.000000	0.05858	0.279000	0.24732	0.927000	0.56198	0.349000	0.20055	0.241000	0.21283	0.418000	0.28097	GAT	.	.		0.592	RGL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421208.3	XM_290867	
ZNF44	51710	hgsc.bcm.edu	37	19	12384103	12384103	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:12384103T>C	ENST00000356109.5	-	5	1229	c.1111A>G	c.(1111-1113)Agc>Ggc	p.S371G	ZNF44_ENST00000355684.5_Missense_Mutation_p.S323G	NM_001164276.1	NP_001157748.1	P15621	ZNF44_HUMAN	zinc finger protein 44	371					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			ovary(1)	1		Renal(1328;0.157)		GBM - Glioblastoma multiforme(1328;0.0164)|Lung(535;0.179)		CTTTGAAAGCTTCCAAGATGA	0.413																																					p.S371G		Atlas-SNP	.											.	ZNF44	55	.	0			c.A1111G						.						140.0	142.0	142.0					19																	12384103		2203	4300	6503	SO:0001583	missense	51710	exon5			GAAAGCTTCCAAG	X52338	CCDS45988.1, CCDS54223.1	19p13.2	2013-01-08	2006-05-11		ENSG00000197857	ENSG00000197857		"""Zinc fingers, C2H2-type"", ""-"""	13110	protein-coding gene	gene with protein product		194542	"""zinc finger protein 58"", ""zinc finger protein 44 (KOX 7)"", ""zinc finger protein 55"""	ZNF58, ZNF55		1946370, 1505991	Standard	NM_016264		Approved	KOX7, ZNF504	uc010xmj.2	P15621	OTTHUMG00000156424	ENST00000356109.5:c.1111A>G	chr19.hg19:g.12384103T>C	ENSP00000348419:p.Ser371Gly	62.0	0.0		95.0	4.0	NM_001164276	B4DML9|B9EGJ5|B9ZVM2|P17018|Q9ULZ7	Missense_Mutation	SNP	ENST00000356109.5	hg19	CCDS54223.1	.	.	.	.	.	.	.	.	.	.	T	13.31	2.198311	0.38806	.	.	ENSG00000197857	ENST00000393337;ENST00000356109;ENST00000457673;ENST00000355684	T;T;T	0.16073	2.37;2.37;2.37	0.997	-0.072	0.13741	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.21145	0.0509	L	0.28776	0.89	.	.	.	P;D	0.76494	0.891;0.999	P;D	0.80764	0.783;0.994	T	0.25363	-1.0134	8	0.42905	T	0.14	.	2.1582	0.03818	0.0:0.2424:0.3278:0.4299	.	371;323	P15621;F8W7T7	ZNF44_HUMAN;.	G	371;371;323;323	ENSP00000377008:S371G;ENSP00000348419:S371G;ENSP00000347910:S323G	ENSP00000347910:S323G	S	-	1	0	ZNF44	12245103	0.000000	0.05858	0.001000	0.08648	0.794000	0.44872	-4.679000	0.00199	-0.064000	0.13043	0.254000	0.18369	AGC	.	.		0.413	ZNF44-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000344132.1	NM_016264	
ZNF799	90576	hgsc.bcm.edu	37	19	12502459	12502459	+	Missense_Mutation	SNP	T	T	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:12502459T>G	ENST00000430385.3	-	4	953	c.753A>C	c.(751-753)aaA>aaC	p.K251N	ZNF799_ENST00000419318.1_Missense_Mutation_p.K219N|CTD-3105H18.14_ENST00000435033.1_Intron	NM_001080821.2	NP_001074290.1	Q96GE5	ZN799_HUMAN	zinc finger protein 799	251					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|kidney(2)|large_intestine(4)|lung(4)|ovary(2)|prostate(2)|skin(2)	19						ATTCATACAGTTTCTCCCCAG	0.378																																					p.K251N		Atlas-SNP	.											.	ZNF799	111	.	0			c.A753C						.						78.0	90.0	86.0					19																	12502459		2203	4296	6499	SO:0001583	missense	90576	exon4			ATACAGTTTCTCC	BC009517	CCDS45989.1	19p13.2	2013-01-08			ENSG00000196466	ENSG00000196466		"""Zinc fingers, C2H2-type"", ""-"""	28071	protein-coding gene	gene with protein product			"""zinc finger protein 842"""	ZNF842			Standard	NM_001080821		Approved	HIT-40, MGC71805	uc002mts.4	Q96GE5	OTTHUMG00000156408	ENST00000430385.3:c.753A>C	chr19.hg19:g.12502459T>G	ENSP00000411084:p.Lys251Asn	62.0	0.0		79.0	4.0	NM_001080821		Missense_Mutation	SNP	ENST00000430385.3	hg19	CCDS45989.1	.	.	.	.	.	.	.	.	.	.	T	13.34	2.208657	0.39003	.	.	ENSG00000196466	ENST00000419318;ENST00000430385	T;T	0.26067	1.76;1.76	1.31	-0.963	0.10330	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.41534	0.1163	M	0.73319	2.225	0.26579	N	0.973419	D	0.89917	1.0	D	0.91635	0.999	T	0.27123	-1.0083	9	0.66056	D	0.02	.	3.0181	0.06066	0.0:0.3938:0.265:0.3412	.	251	Q96GE5	ZN799_HUMAN	N	219;251	ENSP00000415278:K219N;ENSP00000411084:K251N	ENSP00000415278:K219N	K	-	3	2	ZNF799	12363459	0.000000	0.05858	0.001000	0.08648	0.117000	0.20001	-1.622000	0.02042	-0.408000	0.07565	0.352000	0.21897	AAA	.	.		0.378	ZNF799-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344099.2	NM_001080821	
OR7A10	390892	hgsc.bcm.edu	37	19	14952035	14952035	+	Missense_Mutation	SNP	A	A	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:14952035A>C	ENST00000248058.1	-	1	654	c.655T>G	c.(655-657)Tct>Gct	p.S219A		NM_001005190.1	NP_001005190.1	O76100	OR7AA_HUMAN	olfactory receptor, family 7, subfamily A, member 10	219						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|stomach(1)	19	Ovarian(108;0.203)					ACTATCTTAGAGTAAGAGTAC	0.468																																					p.S219A		Atlas-SNP	.											.	OR7A10	33	.	0			c.T655G						.						66.0	61.0	63.0					19																	14952035		2203	4300	6503	SO:0001583	missense	390892	exon1			TCTTAGAGTAAGA		CCDS32936.1	19p13.1	2012-08-09						"""GPCR / Class A : Olfactory receptors"""	8356	protein-coding gene	gene with protein product							Standard	NM_001005190		Approved		uc002mzx.1	O76100		ENST00000248058.1:c.655T>G	chr19.hg19:g.14952035A>C	ENSP00000248058:p.Ser219Ala	43.0	0.0		65.0	15.0	NM_001005190	Q6IFP0|Q96R97	Missense_Mutation	SNP	ENST00000248058.1	hg19	CCDS32936.1	.	.	.	.	.	.	.	.	.	.	a	10.12	1.263886	0.23136	.	.	ENSG00000127515	ENST00000248058	T	0.00048	8.82	2.75	0.126	0.14722	GPCR, rhodopsin-like superfamily (1);	0.830271	0.09655	N	0.773210	T	0.00144	0.0004	N	0.25201	0.72	0.09310	N	1	B	0.25486	0.127	B	0.35931	0.214	T	0.09143	-1.0688	10	0.59425	D	0.04	.	5.9723	0.19359	0.3999:0.0:0.0:0.6001	.	219	O76100	OR7AA_HUMAN	A	219	ENSP00000248058:S219A	ENSP00000248058:S219A	S	-	1	0	OR7A10	14813035	0.000000	0.05858	0.010000	0.14722	0.413000	0.31143	-0.733000	0.04898	0.274000	0.22072	0.113000	0.15668	TCT	.	.		0.468	OR7A10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466520.1	NM_001005190	
SLC1A6	6511	hgsc.bcm.edu	37	19	15065025	15065025	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:15065025A>G	ENST00000221742.3	-	7	1293	c.1286T>C	c.(1285-1287)cTc>cCc	p.L429P	SLC1A6_ENST00000600144.1_Missense_Mutation_p.L351P|SLC1A6_ENST00000430939.2_Missense_Mutation_p.L365P	NM_005071.1	NP_005062.1	P48664	EAA4_HUMAN	solute carrier family 1 (high affinity aspartate/glutamate transporter), member 6	429					aspartate transport (GO:0015810)|ion transport (GO:0006811)|L-glutamate transport (GO:0015813)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	L-aspartate transmembrane transporter activity (GO:0015183)|L-glutamate transmembrane transporter activity (GO:0005313)|sodium:dicarboxylate symporter activity (GO:0017153)			breast(1)|central_nervous_system(2)|endometrium(6)|large_intestine(8)|liver(1)|lung(12)|ovary(3)|pancreas(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	42						GGCCTCGTAGAGGGCAGTGCC	0.612																																					p.L429P		Atlas-SNP	.											.	SLC1A6	111	.	0			c.T1286C						.						90.0	80.0	84.0					19																	15065025		2203	4300	6503	SO:0001583	missense	6511	exon7			TCGTAGAGGGCAG		CCDS12321.1, CCDS62578.1	19p13.12	2013-07-15			ENSG00000105143	ENSG00000105143		"""Solute carriers"""	10944	protein-coding gene	gene with protein product		600637				7791878	Standard	NM_005071		Approved	EAAT4	uc002naa.2	P48664	OTTHUMG00000183351	ENST00000221742.3:c.1286T>C	chr19.hg19:g.15065025A>G	ENSP00000221742:p.Leu429Pro	105.0	0.0		115.0	5.0	NM_005071	Q8N753	Missense_Mutation	SNP	ENST00000221742.3	hg19	CCDS12321.1	.	.	.	.	.	.	.	.	.	.	a	21.6	4.180501	0.78677	.	.	ENSG00000105143	ENST00000430939;ENST00000221742	T;T	0.64085	-0.01;-0.08	4.52	4.52	0.55395	Sodium:dicarboxylate symporter, conserved site (1);	0.068216	0.56097	D	0.000023	D	0.84306	0.5443	H	0.96333	3.805	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.997	D	0.88577	0.3134	10	0.87932	D	0	-27.6715	12.1227	0.53900	1.0:0.0:0.0:0.0	.	365;429	E7EV13;P48664	.;EAA4_HUMAN	P	365;429	ENSP00000409386:L365P;ENSP00000221742:L429P	ENSP00000221742:L429P	L	-	2	0	SLC1A6	14926025	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	8.919000	0.92770	2.037000	0.60232	0.446000	0.29264	CTC	.	.		0.612	SLC1A6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466283.1	NM_005071	
CYP4F2	8529	hgsc.bcm.edu	37	19	16008363	16008363	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:16008363A>G	ENST00000221700.6	-	2	154	c.59T>C	c.(58-60)cTg>cCg	p.L20P	CYP4F2_ENST00000011989.7_5'UTR	NM_001082.3	NP_001073.3			cytochrome P450, family 4, subfamily F, polypeptide 2											NS(2)|breast(1)|endometrium(6)|kidney(2)|large_intestine(9)|liver(1)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	46						CAGGAGGAGCAGCCAAGGGGA	0.657																																					p.L20P		Atlas-SNP	.											.	CYP4F2	97	.	0			c.T59C						.						38.0	41.0	40.0					19																	16008363		2203	4300	6503	SO:0001583	missense	8529	exon2			AGGAGCAGCCAAG	U02388	CCDS12336.1	19p13.12	2013-11-11	2003-01-14		ENSG00000186115	ENSG00000186115		"""Cytochrome P450s"""	2645	protein-coding gene	gene with protein product		604426	"""cytochrome P450, subfamily IVF, polypeptide 2"""			8424651, 8026587	Standard	NM_001082		Approved		uc002nbs.1	P78329	OTTHUMG00000185995	ENST00000221700.6:c.59T>C	chr19.hg19:g.16008363A>G	ENSP00000221700:p.Leu20Pro	74.0	0.0		94.0	5.0	NM_001082		Missense_Mutation	SNP	ENST00000221700.6	hg19	CCDS12336.1	.	.	.	.	.	.	.	.	.	.	a	8.377	0.836582	0.16891	.	.	ENSG00000186115	ENST00000221700	D	0.91945	-2.94	2.99	0.675	0.17952	.	2.133910	0.04135	N	0.318526	D	0.89371	0.6696	M	0.63428	1.95	0.45183	D	0.998197	B	0.10296	0.003	B	0.08055	0.003	T	0.75728	-0.3216	10	0.48119	T	0.1	.	3.2861	0.06932	0.6202:0.2404:0.1394:0.0	.	20	P78329	CP4F2_HUMAN	P	20	ENSP00000221700:L20P	ENSP00000221700:L20P	L	-	2	0	CYP4F2	15869363	0.000000	0.05858	0.135000	0.22099	0.048000	0.14542	-0.025000	0.12413	-0.047000	0.13423	-0.533000	0.04299	CTG	.	.		0.657	CYP4F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460372.3	NM_001082	
OCEL1	79629	hgsc.bcm.edu	37	19	17337947	17337947	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:17337947C>T	ENST00000215061.4	+	3	435	c.391C>T	c.(391-393)Cct>Tct	p.P131S	OCEL1_ENST00000597836.1_Missense_Mutation_p.P75S|OCEL1_ENST00000601576.1_3'UTR|OCEL1_ENST00000601529.1_Missense_Mutation_p.P131S	NM_024578.1	NP_078854.1	Q9H607	OCEL1_HUMAN	occludin/ELL domain containing 1	131										central_nervous_system(2)|endometrium(2)|kidney(1)|lung(2)	7						CGCCAAGAAGCCTATTGGAGC	0.597																																					p.P131S		Atlas-SNP	.											.	OCEL1	20	.	0			c.C391T						.						66.0	76.0	72.0					19																	17337947		2203	4300	6503	SO:0001583	missense	79629	exon3			AAGAAGCCTATTG	BC029361	CCDS12351.1	19p13.11	2008-02-05				ENSG00000099330			26221	protein-coding gene	gene with protein product						12477932	Standard	NM_024578		Approved	FLJ22709	uc002nfp.3	Q9H607		ENST00000215061.4:c.391C>T	chr19.hg19:g.17337947C>T	ENSP00000215061:p.Pro131Ser	105.0	0.0		92.0	4.0	NM_024578		Missense_Mutation	SNP	ENST00000215061.4	hg19	CCDS12351.1	.	.	.	.	.	.	.	.	.	.	C	7.427	0.637979	0.14386	.	.	ENSG00000099330	ENST00000215061	T	0.29655	1.56	3.94	-2.51	0.06365	.	1.270950	0.05366	N	0.534623	T	0.13286	0.0322	N	0.08118	0	0.09310	N	1	B	0.17038	0.02	B	0.12837	0.008	T	0.24764	-1.0151	10	0.22706	T	0.39	-0.0364	4.1263	0.10129	0.0:0.3416:0.183:0.4755	.	131	Q9H607	OCEL1_HUMAN	S	131	ENSP00000215061:P131S	ENSP00000215061:P131S	P	+	1	0	OCEL1	17198947	0.000000	0.05858	0.003000	0.11579	0.061000	0.15899	0.014000	0.13333	0.015000	0.14971	-0.339000	0.08088	CCT	.	.		0.597	OCEL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463307.1	NM_024578	
BABAM1	29086	hgsc.bcm.edu	37	19	17389796	17389796	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:17389796A>G	ENST00000359435.4	+	9	1122	c.929A>G	c.(928-930)cAt>cGt	p.H310R	ANKLE1_ENST00000394458.3_5'Flank|ANKLE1_ENST00000433424.2_5'Flank|ANKLE1_ENST00000598347.1_5'Flank|BABAM1_ENST00000447614.2_Missense_Mutation_p.H310R|BABAM1_ENST00000601043.1_Missense_Mutation_p.H310R|ANKLE1_ENST00000594072.1_5'Flank|BABAM1_ENST00000598188.1_Missense_Mutation_p.H310R|CTD-2278I10.6_ENST00000596542.1_Intron|ANKLE1_ENST00000404085.1_5'Flank|BABAM1_ENST00000595632.1_Missense_Mutation_p.H235R	NM_001033549.1	NP_001028721.1	Q9NWV8	BABA1_HUMAN	BRISC and BRCA1 A complex member 1	310					chromatin modification (GO:0016568)|double-strand break repair (GO:0006302)|G2 DNA damage checkpoint (GO:0031572)|positive regulation of DNA repair (GO:0045739)|protein K63-linked deubiquitination (GO:0070536)|response to ionizing radiation (GO:0010212)	BRCA1-A complex (GO:0070531)|BRISC complex (GO:0070552)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)	5						TGCCAGAGCCATGCTTCCTAC	0.577																																					p.H310R		Atlas-SNP	.											.	BABAM1	14	.	0			c.A929G						.						32.0	37.0	36.0					19																	17389796		2048	4199	6247	SO:0001583	missense	29086	exon9			AGAGCCATGCTTC	AK000578	CCDS46012.1, CCDS74310.1	19p13.11	2011-02-21	2011-02-21	2011-01-31	ENSG00000105393	ENSG00000105393			25008	protein-coding gene	gene with protein product	"""Mediator of Rap80 Interactions and Targeting 40 kD"", ""new component of the BRCA1 A complex"""	612766	"""chromosome 19 open reading frame 62"""	C19orf62		11042152	Standard	NM_001288756		Approved	FLJ20571, HSPC142, NBA1, MERIT40	uc002nfv.3	Q9NWV8		ENST00000359435.4:c.929A>G	chr19.hg19:g.17389796A>G	ENSP00000352408:p.His310Arg	95.0	0.0		94.0	4.0	NM_014173	A8MQT0|B4DRY9|B4DVR1|Q6FIA0|Q9P018	Missense_Mutation	SNP	ENST00000359435.4	hg19	CCDS46012.1	.	.	.	.	.	.	.	.	.	.	A	17.16	3.317593	0.60524	.	.	ENSG00000105393	ENST00000359435;ENST00000447614	.	.	.	5.08	5.08	0.68730	.	.	.	.	.	T	0.69160	0.3080	L	0.54323	1.7	0.80722	D	1	D	0.76494	0.999	D	0.78314	0.991	T	0.66854	-0.5818	8	0.32370	T	0.25	-7.3688	12.8452	0.57825	1.0:0.0:0.0:0.0	.	310	Q9NWV8	BABA1_HUMAN	R	310	.	ENSP00000352408:H310R	H	+	2	0	BABAM1	17250796	1.000000	0.71417	0.983000	0.44433	0.427000	0.31564	8.515000	0.90548	2.137000	0.66172	0.533000	0.62120	CAT	.	.		0.577	BABAM1-005	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000463471.1	NM_014173	
GMIP	51291	hgsc.bcm.edu	37	19	19751152	19751152	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:19751152T>C	ENST00000203556.4	-	6	519	c.382A>G	c.(382-384)Agc>Ggc	p.S128G	GMIP_ENST00000587238.1_Missense_Mutation_p.S128G|GMIP_ENST00000445806.2_Missense_Mutation_p.S128G	NM_016573.2	NP_057657.2	Q9P107	GMIP_HUMAN	GEM interacting protein	128					intracellular signal transduction (GO:0035556)|negative regulation of Rho GTPase activity (GO:0034259)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|intracellular (GO:0005622)	metal ion binding (GO:0046872)|Rho GTPase activator activity (GO:0005100)			breast(1)|endometrium(6)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	24						TTCATGGTGCTCTTAGCAAAC	0.612																																					p.S128G		Atlas-SNP	.											.	GMIP	55	.	0			c.A382G						.						69.0	76.0	73.0					19																	19751152		2203	4300	6503	SO:0001583	missense	51291	exon6			TGGTGCTCTTAGC	AF132541	CCDS12408.1, CCDS74318.1	19p13.11	2011-09-07				ENSG00000089639		"""Rho GTPase activating proteins"""	24852	protein-coding gene	gene with protein product		609694				12093360, 16086184	Standard	XM_005259927		Approved	ARHGAP46	uc002nnd.3	Q9P107		ENST00000203556.4:c.382A>G	chr19.hg19:g.19751152T>C	ENSP00000203556:p.Ser128Gly	90.0	0.0		92.0	4.0	NM_016573	A0AVN9|B7ZLZ0	Missense_Mutation	SNP	ENST00000203556.4	hg19	CCDS12408.1	.	.	.	.	.	.	.	.	.	.	T	14.13	2.443194	0.43429	.	.	ENSG00000089639	ENST00000203556;ENST00000445806	T;T	0.43294	0.95;0.95	4.98	4.98	0.66077	.	0.382465	0.22419	N	0.060305	T	0.24198	0.0586	N	0.13327	0.33	0.26813	N	0.968955	B;B;B	0.11235	0.004;0.004;0.001	B;B;B	0.04013	0.001;0.001;0.001	T	0.11494	-1.0585	10	0.09590	T	0.72	-4.2856	12.6474	0.56742	0.0:0.0:0.0:1.0	.	128;128;128	E7ERB7;B7ZLZ0;Q9P107	.;.;GMIP_HUMAN	G	128	ENSP00000203556:S128G;ENSP00000397075:S128G	ENSP00000203556:S128G	S	-	1	0	GMIP	19612152	0.956000	0.32656	0.065000	0.19835	0.742000	0.42306	2.654000	0.46699	1.871000	0.54225	0.459000	0.35465	AGC	.	.		0.612	GMIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460551.1	NM_016573	
ZNF14	7561	hgsc.bcm.edu	37	19	19823792	19823792	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:19823792C>T	ENST00000344099.3	-	4	436	c.298G>A	c.(298-300)Gca>Aca	p.A100T		NM_021030.2	NP_066358.2	P17017	ZNF14_HUMAN	zinc finger protein 14	100					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|cervix(2)|endometrium(1)|large_intestine(9)|lung(8)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	32		Renal(1328;0.0474)				TGTGGTTTTGCTCCAGTAAAA	0.403																																					p.A100T		Atlas-SNP	.											.	ZNF14	89	.	0			c.G298A						.						155.0	141.0	146.0					19																	19823792		2203	4300	6503	SO:0001583	missense	7561	exon4			GTTTTGCTCCAGT	AA286756	CCDS12409.1	19p13.11	2013-01-08	2006-05-10					"""Zinc fingers, C2H2-type"", ""-"""	12924	protein-coding gene	gene with protein product		194556	"""zinc finger protein 14 (KOX 6)"""				Standard	NM_021030		Approved	KOX6, GIOT-4	uc002nnk.1	P17017		ENST00000344099.3:c.298G>A	chr19.hg19:g.19823792C>T	ENSP00000340514:p.Ala100Thr	78.0	0.0		116.0	6.0	NM_021030	B9EGA4|Q9ULZ5	Missense_Mutation	SNP	ENST00000344099.3	hg19	CCDS12409.1	.	.	.	.	.	.	.	.	.	.	C	10.55	1.382501	0.24944	.	.	ENSG00000105708	ENST00000344099	T	0.15017	2.46	1.4	-1.49	0.08718	Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.11580	0.0282	L	0.35542	1.07	0.23076	N	0.998338	B	0.06786	0.001	B	0.08055	0.003	T	0.30357	-0.9981	9	0.66056	D	0.02	.	6.0221	0.19634	0.0:0.6719:0.0:0.3281	.	100	P17017	ZNF14_HUMAN	T	100	ENSP00000340514:A100T	ENSP00000340514:A100T	A	-	1	0	ZNF14	19684792	0.001000	0.12720	0.002000	0.10522	0.048000	0.14542	0.621000	0.24418	-0.253000	0.09514	-0.384000	0.06662	GCA	.	.		0.403	ZNF14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460775.1	NM_021030	
SLC7A9	11136	hgsc.bcm.edu	37	19	33353026	33353026	+	Silent	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:33353026T>C	ENST00000023064.4	-	6	893	c.702A>G	c.(700-702)ggA>ggG	p.G234G	SLC7A9_ENST00000590341.1_Silent_p.G234G|RN7SKP22_ENST00000365097.1_RNA|SLC7A9_ENST00000587772.1_Silent_p.G234G	NM_001126335.1|NM_001243036.1|NM_014270.4	NP_001119807.1|NP_001229965.1|NP_055085.1	P82251	BAT1_HUMAN	solute carrier family 7 (amino acid transporter light chain, bo,+ system), member 9	234					amino acid transport (GO:0006865)|blood coagulation (GO:0007596)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|L-cystine transport (GO:0015811)|leukocyte migration (GO:0050900)|neutral amino acid transport (GO:0015804)|protein complex assembly (GO:0006461)|transmembrane transport (GO:0055085)|transport (GO:0006810)	brush border membrane (GO:0031526)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	amino acid transmembrane transporter activity (GO:0015171)|L-cystine transmembrane transporter activity (GO:0015184)|neutral amino acid transmembrane transporter activity (GO:0015175)|peptide antigen binding (GO:0042605)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(12)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	32	Esophageal squamous(110;0.137)				L-Cystine(DB00138)	CACCTCACCATCCATCATAGG	0.512																																					p.G234G	GBM(181;1335 2108 9644 44178 46689)	Atlas-SNP	.											.	SLC7A9	78	.	0			c.A702G						.						109.0	105.0	107.0					19																	33353026		2203	4300	6503	SO:0001819	synonymous_variant	11136	exon6			TCACCATCCATCA	AF141289	CCDS12425.1	19q13.11	2013-07-19	2013-07-19		ENSG00000021488	ENSG00000021488		"""Solute carriers"""	11067	protein-coding gene	gene with protein product		604144		CSNU3		10471498	Standard	NM_014270		Approved		uc021usa.1	P82251	OTTHUMG00000180287	ENST00000023064.4:c.702A>G	chr19.hg19:g.33353026T>C		70.0	0.0		105.0	6.0	NM_001243036	B2R9A6	Silent	SNP	ENST00000023064.4	hg19	CCDS12425.1																																																																																			.	.		0.512	SLC7A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450585.1		
ZNF599	148103	hgsc.bcm.edu	37	19	35250292	35250292	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:35250292T>C	ENST00000329285.8	-	4	1787	c.1414A>G	c.(1414-1416)Acc>Gcc	p.T472A		NM_001007248.2	NP_001007249.1	Q96NL3	ZN599_HUMAN	zinc finger protein 599	472					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|large_intestine(10)|lung(8)|ovary(1)|pancreas(1)|skin(1)	24	all_lung(56;1.13e-07)|Lung NSC(56;1.81e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.138)			CCACTGTGGGTCCTATTATGT	0.418																																					p.T472A		Atlas-SNP	.											.	ZNF599	72	.	0			c.A1414G						.						95.0	100.0	98.0					19																	35250292		2203	4300	6503	SO:0001583	missense	148103	exon4			TGTGGGTCCTATT	AK055225	CCDS32991.1	19q13.13	2013-01-08				ENSG00000153896		"""Zinc fingers, C2H2-type"", ""-"""	26408	protein-coding gene	gene with protein product							Standard	NM_001007248		Approved	FLJ30663	uc010edn.1	Q96NL3		ENST00000329285.8:c.1414A>G	chr19.hg19:g.35250292T>C	ENSP00000333802:p.Thr472Ala	94.0	0.0		128.0	6.0	NM_001007248	Q569K0|Q5PRG1	Missense_Mutation	SNP	ENST00000329285.8	hg19	CCDS32991.1	.	.	.	.	.	.	.	.	.	.	T	6.943	0.543839	0.13312	.	.	ENSG00000153896	ENST00000392231;ENST00000329285;ENST00000392229	T	0.20332	2.08	2.67	1.65	0.23941	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.15955	0.0384	L	0.39633	1.23	0.48236	D	0.999618	B	0.12630	0.006	B	0.18561	0.022	T	0.06607	-1.0817	9	0.87932	D	0	.	6.1035	0.20061	0.0:0.1358:0.0:0.8642	.	472	Q96NL3	ZN599_HUMAN	A	471;472;246	ENSP00000333802:T472A	ENSP00000333802:T472A	T	-	1	0	ZNF599	39942132	0.000000	0.05858	0.768000	0.31515	0.481000	0.33189	0.297000	0.19101	0.448000	0.26722	-0.353000	0.07706	ACC	.	.		0.418	ZNF599-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460648.2	XM_086046	
LGI4	163175	hgsc.bcm.edu	37	19	35617456	35617456	+	Silent	SNP	C	C	T			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:35617456C>T	ENST00000310123.3	-	8	1536	c.1017G>A	c.(1015-1017)gcG>gcA	p.A339A	LGI4_ENST00000392225.3_Missense_Mutation_p.R365Q|LGI4_ENST00000493050.1_5'UTR	NM_139284.2	NP_644813.1	Q8N135	LGI4_HUMAN	leucine-rich repeat LGI family, member 4	339					adult locomotory behavior (GO:0008344)|glial cell proliferation (GO:0014009)|myelination in peripheral nervous system (GO:0022011)|neuron maturation (GO:0042551)	extracellular space (GO:0005615)				endometrium(1)|large_intestine(1)|lung(4)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10	all_lung(56;7.56e-09)|Lung NSC(56;1.1e-08)|Esophageal squamous(110;0.162)		Epithelial(14;5.54e-20)|OV - Ovarian serous cystadenocarcinoma(14;1.33e-18)|all cancers(14;4.27e-17)|LUSC - Lung squamous cell carcinoma(66;0.0849)			TGGTGCTGCCCGCCTTGGAGG	0.726																																					p.A339A		Atlas-SNP	.											.	LGI4	32	.	0			c.G1017A						.						6.0	7.0	7.0					19																	35617456		2048	4028	6076	SO:0001819	synonymous_variant	163175	exon8			GCTGCCCGCCTTG	AJ487519	CCDS12444.1	19q13.13	2008-07-03			ENSG00000153902	ENSG00000153902			18712	protein-coding gene	gene with protein product		608303				12023020	Standard	NM_139284		Approved		uc002nxx.2	Q8N135	OTTHUMG00000044558	ENST00000310123.3:c.1017G>A	chr19.hg19:g.35617456C>T		2.0	0.0		7.0	6.0	NM_139284	B2RN53|B9EGS7|Q5M8T1	Silent	SNP	ENST00000310123.3	hg19	CCDS12444.1	.	.	.	.	.	.	.	.	.	.	C	12.80	2.047239	0.36085	.	.	ENSG00000153902	ENST00000392225	T	0.64085	-0.08	4.48	-8.96	0.00761	.	.	.	.	.	T	0.51449	0.1675	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.60409	-0.7269	6	0.87932	D	0	.	0.0813	0.00032	0.2884:0.226:0.175:0.3106	.	.	.	.	Q	365	ENSP00000376059:R365Q	ENSP00000376059:R365Q	R	-	2	0	LGI4	40309296	0.000000	0.05858	0.823000	0.32752	0.930000	0.56654	-4.706000	0.00196	-1.885000	0.01118	-1.676000	0.00740	CGG	.	.		0.726	LGI4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103963.1		
ZBTB32	27033	hgsc.bcm.edu	37	19	36205963	36205963	+	Silent	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:36205963T>C	ENST00000392197.2	+	3	753	c.435T>C	c.(433-435)ccT>ccC	p.P145P	KMT2B_ENST00000341701.1_5'Flank|KMT2B_ENST00000222270.7_5'Flank|KMT2B_ENST00000420124.1_5'Flank|KMT2B_ENST00000607650.1_RNA|ZBTB32_ENST00000262630.3_Silent_p.P145P			Q9Y2Y4	ZBT32_HUMAN	zinc finger and BTB domain containing 32	145					DNA repair (GO:0006281)|hemopoiesis (GO:0030097)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of cytokine production (GO:0001817)|T cell proliferation (GO:0042098)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			large_intestine(5)|lung(1)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	14	all_lung(56;2.22e-07)|Lung NSC(56;3.47e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			TGGGGGACCCTGGAGAGAAGC	0.547																																					p.P145P		Atlas-SNP	.											.	ZBTB32	33	.	0			c.T435C						.						41.0	44.0	43.0					19																	36205963		2203	4300	6503	SO:0001819	synonymous_variant	27033	exon2			GGACCCTGGAGAG	AF130255	CCDS12471.1	19q13.1	2013-01-08			ENSG00000011590	ENSG00000011590		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	16763	protein-coding gene	gene with protein product	"""repressor of GATA"""	605859				10572087	Standard	XM_005258739		Approved	TZFP, FAZF, FAXF, Rog, ZNF538	uc002oay.3	Q9Y2Y4	OTTHUMG00000048118	ENST00000392197.2:c.435T>C	chr19.hg19:g.36205963T>C		47.0	0.0		67.0	4.0	NM_014383	Q8WVP2	Silent	SNP	ENST00000392197.2	hg19	CCDS12471.1																																																																																			.	.		0.547	ZBTB32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109491.3	NM_014383	
KMT2B	9757	hgsc.bcm.edu	37	19	36214631	36214631	+	Splice_Site	SNP	C	C	A			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:36214631C>A	ENST00000222270.7	+	8	3058		c.e8-1		KMT2B_ENST00000420124.1_Intron|KMT2B_ENST00000607650.1_RNA	NM_014727.1	NP_055542.1	Q9UMN6	KMT2B_HUMAN	lysine (K)-specific methyltransferase 2B						chromatin-mediated maintenance of transcription (GO:0048096)|gene silencing (GO:0016458)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|oocyte differentiation (GO:0009994)|ovarian follicle development (GO:0001541)|ovulation (GO:0030728)|regulation of histone H3-K4 methylation (GO:0051569)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)										CCTGTTCCCGCAGCCGGACGA	0.627																																					.		Atlas-SNP	.											.	MLL4	229	.	0			c.3059-2C>A						.						11.0	12.0	11.0					19																	36214631		1824	3882	5706	SO:0001630	splice_region_variant	8085	exon8			TTCCCGCAGCCGG	AJ007041	CCDS46055.1	19q13.1	2014-02-18			ENSG00000105663	ENSG00000272333		"""Chromatin-modifying enzymes / K-methyltransferases"""	15840	protein-coding gene	gene with protein product	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila) 4"""	606834				10409430, 10637508	Standard	XM_006723513		Approved	KIAA0304, MLL2, TRX2, HRX2, WBP7, MLL1B, MLL4		Q9UMN6	OTTHUMG00000048119	ENST00000222270.7:c.3059-1C>A	chr19.hg19:g.36214631C>A		35.0	0.0		65.0	4.0	NM_014727	O15022|O95836|Q96GP2|Q96IP3|Q9UK25|Q9Y668|Q9Y669	Splice_Site	SNP	ENST00000222270.7	hg19	CCDS46055.1	.	.	.	.	.	.	.	.	.	.	C	16.79	3.220574	0.58560	.	.	ENSG00000105663	ENST00000222270	.	.	.	5.0	5.0	0.66597	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.6648	0.77221	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	AD000671.1	40906471	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.194000	0.58393	2.757000	0.94681	0.655000	0.94253	.	.	.		0.627	KMT2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014727	Intron
KMT2B	9757	hgsc.bcm.edu	37	19	36214634	36214634	+	Splice_Site	SNP	C	C	G	rs373624638		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:36214634C>G	ENST00000222270.7	+	8	3060	c.3060C>G	c.(3058-3060)ggC>ggG	p.G1020G	KMT2B_ENST00000420124.1_Splice_Site_p.G1020G|KMT2B_ENST00000607650.1_RNA	NM_014727.1	NP_055542.1	Q9UMN6	KMT2B_HUMAN	lysine (K)-specific methyltransferase 2B	1020					chromatin-mediated maintenance of transcription (GO:0048096)|gene silencing (GO:0016458)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|oocyte differentiation (GO:0009994)|ovarian follicle development (GO:0001541)|ovulation (GO:0030728)|regulation of histone H3-K4 methylation (GO:0051569)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)										GTTCCCGCAGCCGGACGATAG	0.637																																					p.G1020G		Atlas-SNP	.											.	MLL4	229	.	0			c.C3060G						.						11.0	12.0	11.0					19																	36214634		1825	3889	5714	SO:0001630	splice_region_variant	8085	exon8			CCGCAGCCGGACG	AJ007041	CCDS46055.1	19q13.1	2014-02-18			ENSG00000105663	ENSG00000272333		"""Chromatin-modifying enzymes / K-methyltransferases"""	15840	protein-coding gene	gene with protein product	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila) 4"""	606834				10409430, 10637508	Standard	XM_006723513		Approved	KIAA0304, MLL2, TRX2, HRX2, WBP7, MLL1B, MLL4		Q9UMN6	OTTHUMG00000048119	ENST00000222270.7:c.3059-1C>G	chr19.hg19:g.36214634C>G		34.0	0.0		67.0	6.0	NM_014727	O15022|O95836|Q96GP2|Q96IP3|Q9UK25|Q9Y668|Q9Y669	Silent	SNP	ENST00000222270.7	hg19	CCDS46055.1																																																																																			.	.		0.637	KMT2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014727	Silent
ARHGAP33	115703	hgsc.bcm.edu	37	19	36273373	36273373	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:36273373A>G	ENST00000007510.4	+	13	1328	c.1184A>G	c.(1183-1185)gAg>gGg	p.E395G	ARHGAP33_ENST00000314737.5_Missense_Mutation_p.E395G|ARHGAP33_ENST00000378944.5_Missense_Mutation_p.E259G			O14559	RHG33_HUMAN	Rho GTPase activating protein 33	395	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				protein transport (GO:0015031)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	phosphatidylinositol binding (GO:0035091)|Rac GTPase activator activity (GO:0030675)			endometrium(7)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	37						TACTTCCGAGAGCTTCCGAAC	0.617																																					p.E395G		Atlas-SNP	.											.	ARHGAP33	102	.	0			c.A1184G						.						82.0	71.0	75.0					19																	36273373		2203	4300	6503	SO:0001583	missense	115703	exon13			TCCGAGAGCTTCC	AY044864	CCDS12477.1, CCDS54254.1	19q13.13	2011-06-29	2010-02-19	2010-02-19		ENSG00000004777		"""Rho GTPase activating proteins"""	23085	protein-coding gene	gene with protein product		614902	"""sorting nexin 26"""	SNX26		12297274, 12461558	Standard	NM_052948		Approved	FLJ39019, TCGAP	uc002obs.2	O14559		ENST00000007510.4:c.1184A>G	chr19.hg19:g.36273373A>G	ENSP00000007510:p.Glu395Gly	70.0	0.0		93.0	4.0	NM_052948	O14552|O14560|Q6ZSP6|Q96CP3|Q9NT23	Missense_Mutation	SNP	ENST00000007510.4	hg19		.	.	.	.	.	.	.	.	.	.	a	19.62	3.862145	0.71949	.	.	ENSG00000004777	ENST00000007510;ENST00000314737;ENST00000378944	T;T;T	0.15017	2.46;2.46;2.46	5.2	5.2	0.72013	.	0.000000	0.85682	D	0.000000	T	0.53254	0.1785	H	0.94345	3.525	0.51767	D	0.999939	D;D	0.89917	0.998;1.0	D;D	0.91635	0.99;0.999	T	0.67432	-0.5672	10	0.87932	D	0	.	14.0423	0.64684	1.0:0.0:0.0:0.0	.	259;395	O14559-10;O14559-11	.;.	G	395;395;259	ENSP00000007510:E395G;ENSP00000320038:E395G;ENSP00000368227:E259G	ENSP00000007510:E395G	E	+	2	0	ARHGAP33	40965213	1.000000	0.71417	1.000000	0.80357	0.388000	0.30384	9.142000	0.94618	1.969000	0.57287	0.375000	0.23000	GAG	.	.		0.617	ARHGAP33-201	KNOWN	basic	protein_coding	protein_coding		NM_052948	
ZFP82	284406	hgsc.bcm.edu	37	19	36883842	36883842	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:36883842A>G	ENST00000392161.3	-	5	1642	c.1400T>C	c.(1399-1401)cTa>cCa	p.L467P	ZFP82_ENST00000392171.1_Missense_Mutation_p.L467P	NM_133466.2	NP_597723.1	Q8N141	ZFP82_HUMAN	ZFP82 zinc finger protein	467					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(7)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						GCTCTGATGTAGAGTAAGTTT	0.383																																					p.L467P		Atlas-SNP	.											.	ZFP82	71	.	0			c.T1400C						.						105.0	101.0	102.0					19																	36883842		2203	4300	6503	SO:0001583	missense	284406	exon5			TGATGTAGAGTAA	AL834267	CCDS12493.1	19q13.13	2013-01-08	2012-11-27	2008-07-01		ENSG00000181007		"""Zinc fingers, C2H2-type"", ""-"""	28682	protein-coding gene	gene with protein product			"""zinc finger protein 545"", ""zinc finger protein 82 homolog (mouse)"", ""zinc finger protein 82"""	ZNF545		11853319	Standard	NM_133466		Approved	MGC45380, KIAA1948	uc002ody.1	Q8N141		ENST00000392161.3:c.1400T>C	chr19.hg19:g.36883842A>G	ENSP00000431265:p.Leu467Pro	96.0	0.0		92.0	4.0	NM_133466	Q8NC63|Q8TF53	Missense_Mutation	SNP	ENST00000392161.3	hg19	CCDS12493.1	.	.	.	.	.	.	.	.	.	.	A	12.39	1.923466	0.33908	.	.	ENSG00000181007	ENST00000392161;ENST00000392171	T;T	0.07444	3.19;3.19	4.2	3.1	0.35709	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.32430	N	0.006102	T	0.11665	0.0284	L	0.33137	0.985	0.24293	N	0.995154	D	0.53619	0.961	P	0.60068	0.868	T	0.08066	-1.0740	10	0.44086	T	0.13	.	4.0395	0.09745	0.6759:0.2134:0.1107:0.0	.	467	Q8N141	ZFP82_HUMAN	P	467	ENSP00000431265:L467P;ENSP00000446080:L467P	ENSP00000431265:L467P	L	-	2	0	ZFP82	41575682	0.000000	0.05858	0.993000	0.49108	0.972000	0.66771	-1.441000	0.02409	1.905000	0.55150	0.482000	0.46254	CTA	.	.		0.383	ZFP82-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109552.2	NM_133466	
CATSPERG	57828	hgsc.bcm.edu	37	19	38828049	38828049	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:38828049A>G	ENST00000409235.3	+	2	290	c.175A>G	c.(175-177)Agt>Ggt	p.S59G	CATSPERG_ENST00000215069.4_Missense_Mutation_p.S75G|CATSPERG_ENST00000410018.1_Missense_Mutation_p.S59G	NM_021185.4	NP_067008.3	Q6ZRH7	CTSRG_HUMAN	catsper channel auxiliary subunit gamma	59					cell differentiation (GO:0030154)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|plasma membrane (GO:0005886)|sperm principal piece (GO:0097228)				breast(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(13)|ovary(1)|pancreas(2)|prostate(6)|skin(3)|stomach(1)|urinary_tract(2)	40						GGTAGGCGAGAGTGGTGTGAG	0.582																																					p.S59G		Atlas-SNP	.											.	CATSPERG	121	.	0			c.A175G						.						221.0	191.0	200.0					19																	38828049		692	1591	2283	SO:0001583	missense	57828	exon2			GGCGAGAGTGGTG	AK128220	CCDS12514.2	19q13.1	2014-05-13	2012-02-22	2009-07-17	ENSG00000099338	ENSG00000099338			25243	protein-coding gene	gene with protein product		613452	"""chromosome 19 open reading frame 15"", ""cation channel, sperm-associated, gamma"""	C19orf15		19516020	Standard	NM_021185		Approved	DKFZp434A1022, FLJ46353	uc002oih.4	Q6ZRH7	OTTHUMG00000153223	ENST00000409235.3:c.175A>G	chr19.hg19:g.38828049A>G	ENSP00000386962:p.Ser59Gly	83.0	0.0		98.0	5.0	NM_021185	A6NEG6|Q659E1	Missense_Mutation	SNP	ENST00000409235.3	hg19	CCDS12514.2	.	.	.	.	.	.	.	.	.	.	a	3.734	-0.054957	0.07362	.	.	ENSG00000099338	ENST00000410018;ENST00000409235;ENST00000409410;ENST00000215069	T;T;T;T	0.34275	1.37;1.37;1.37;1.37	3.09	-1.47	0.08772	.	1.630730	0.03644	N	0.239973	T	0.16214	0.0390	N	0.03608	-0.345	0.09310	N	1	B;B	0.09022	0.001;0.002	B;B	0.11329	0.003;0.006	T	0.18713	-1.0328	10	0.13853	T	0.58	-0.6351	7.3282	0.26567	0.5014:0.0:0.4986:0.0	.	59;59	Q6ZRH7;B8ZZI7	CTSRG_HUMAN;.	G	59;59;59;75	ENSP00000387057:S59G;ENSP00000386962:S59G;ENSP00000386950:S59G;ENSP00000215069:S75G	ENSP00000215069:S75G	S	+	1	0	CATSPERG	43519889	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.622000	0.05553	-0.439000	0.07222	-0.638000	0.03974	AGT	.	.		0.582	CATSPERG-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000330204.1	NM_021185	
ACTN4	81	hgsc.bcm.edu	37	19	39191331	39191331	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:39191331T>C	ENST00000252699.2	+	2	330	c.254T>C	c.(253-255)aTg>aCg	p.M85T	ACTN4_ENST00000424234.2_Missense_Mutation_p.M85T|ACTN4_ENST00000390009.3_Intron	NM_004924.4	NP_004915.2	O43707	ACTN4_HUMAN	actinin, alpha 4	85	Actin-binding.|CH 1. {ECO:0000255|PROSITE- ProRule:PRU00044}.				actin filament bundle assembly (GO:0051017)|blood coagulation (GO:0007596)|negative regulation of cellular component movement (GO:0051271)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of cellular component movement (GO:0051272)|positive regulation of pinocytosis (GO:0048549)|positive regulation of sodium:proton antiporter activity (GO:0032417)|protein localization to tight junction (GO:1902396)|protein transport (GO:0015031)|regulation of apoptotic process (GO:0042981)|response to hypoxia (GO:0001666)|tight junction assembly (GO:0070830)	cell-cell junction (GO:0005911)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|neuron projection (GO:0043005)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|platelet alpha granule lumen (GO:0031093)|protein complex (GO:0043234)|pseudopodium (GO:0031143)|ribonucleoprotein complex (GO:0030529)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|nucleoside binding (GO:0001882)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(12)|ovary(1)|prostate(1)|skin(1)|urinary_tract(3)	30	all_cancers(60;1.57e-05)|Ovarian(47;0.103)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)			CTCAAGCTCATGCTGCTCCTG	0.627																																					p.M85T	Colon(168;199 1940 10254 46213 46384)	Atlas-SNP	.											.	ACTN4	69	.	0			c.T254C						.						115.0	92.0	100.0					19																	39191331		2203	4300	6503	SO:0001583	missense	81	exon2			AGCTCATGCTGCT	D89980	CCDS12518.1	19q13	2013-01-10			ENSG00000130402	ENSG00000130402		"""EF-hand domain containing"""	166	protein-coding gene	gene with protein product		604638	"""focal segmental glomerulosclerosis 1"""	FSGS1		9461087, 10700177	Standard	NM_004924		Approved		uc002oja.2	O43707	OTTHUMG00000137382	ENST00000252699.2:c.254T>C	chr19.hg19:g.39191331T>C	ENSP00000252699:p.Met85Thr	91.0	0.0		122.0	5.0	NM_004924	A4K467|D6PXK4|O76048	Missense_Mutation	SNP	ENST00000252699.2	hg19	CCDS12518.1	.	.	.	.	.	.	.	.	.	.	T	14.37	2.515842	0.44763	.	.	ENSG00000130402	ENST00000252699;ENST00000445727;ENST00000424234	D;D	0.94793	-3.52;-3.52	4.35	4.35	0.52113	Calponin homology domain (5);	0.000000	0.85682	D	0.000000	D	0.93635	0.7967	N	0.12663	0.25	0.40631	D	0.98185	P;P	0.48407	0.91;0.78	D;D	0.76071	0.987;0.986	D	0.94932	0.8083	10	0.87932	D	0	.	12.9372	0.58322	0.0:0.0:0.0:1.0	.	85;85	E7EV83;O43707	.;ACTN4_HUMAN	T	85	ENSP00000252699:M85T;ENSP00000411187:M85T	ENSP00000252699:M85T	M	+	2	0	ACTN4	43883171	1.000000	0.71417	1.000000	0.80357	0.649000	0.38597	7.781000	0.85668	1.964000	0.57103	0.459000	0.35465	ATG	.	.		0.627	ACTN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268091.1		
SHKBP1	92799	hgsc.bcm.edu	37	19	41095066	41095066	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:41095066T>C	ENST00000291842.5	+	15	1620	c.1571T>C	c.(1570-1572)cTc>cCc	p.L524P	SHKBP1_ENST00000600733.1_Missense_Mutation_p.L499P|SHKBP1_ENST00000597649.1_3'UTR	NM_138392.3	NP_612401.2	Q8TBC3	SHKB1_HUMAN	SH3KBP1 binding protein 1	524					protein homooligomerization (GO:0051260)					breast(1)|cervix(1)|endometrium(1)|kidney(4)|large_intestine(5)|lung(10)|ovary(2)|pancreas(1)|skin(3)|urinary_tract(1)	29			Lung(22;0.000114)|LUSC - Lung squamous cell carcinoma(20;0.000384)			TTCGTGCGTCTCTCATCTACT	0.637																																					p.L524P		Atlas-SNP	.											.	SHKBP1	68	.	0			c.T1571C						.						72.0	52.0	59.0					19																	41095066		2203	4300	6503	SO:0001583	missense	92799	exon15			TGCGTCTCTCATC	AF258553	CCDS12560.1	19q13.2	2013-01-10				ENSG00000160410		"""WD repeat domain containing"""	19214	protein-coding gene	gene with protein product						11152963	Standard	NM_138392		Approved	PP203, Sb1	uc002oob.3	Q8TBC3		ENST00000291842.5:c.1571T>C	chr19.hg19:g.41095066T>C	ENSP00000291842:p.Leu524Pro	89.0	0.0		128.0	6.0	NM_138392	Q8N2I6|Q8WY93|Q96IB8	Missense_Mutation	SNP	ENST00000291842.5	hg19	CCDS12560.1	.	.	.	.	.	.	.	.	.	.	T	21.0	4.078549	0.76528	.	.	ENSG00000160410	ENST00000291842;ENST00000446701	T	0.54675	0.56	5.05	5.05	0.67936	WD40 repeat-like-containing domain (1);	0.069879	0.56097	D	0.000028	T	0.72342	0.3448	M	0.77103	2.36	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;0.999;1.0;1.0;0.999	D;D;D;D;D;D	0.91635	0.991;0.988;0.998;0.999;0.998;0.997	T	0.76621	-0.2892	10	0.87932	D	0	-8.6062	13.9039	0.63821	0.0:0.0:0.0:1.0	.	402;304;447;361;524;524	B4DLI0;B4DUW2;B4DUV2;B3KVX8;B2R6W9;Q8TBC3	.;.;.;.;.;SHKB1_HUMAN	P	524;304	ENSP00000291842:L524P	ENSP00000291842:L524P	L	+	2	0	SHKBP1	45786906	0.993000	0.37304	0.180000	0.23079	0.985000	0.73830	7.250000	0.78287	2.129000	0.65627	0.459000	0.35465	CTC	.	.		0.637	SHKBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462613.2	NM_138392	
ADCK4	79934	hgsc.bcm.edu	37	19	41220002	41220002	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:41220002A>G	ENST00000324464.3	-	4	560	c.259T>C	c.(259-261)Tcc>Ccc	p.S87P	ADCK4_ENST00000450541.1_Missense_Mutation_p.S87P|ADCK4_ENST00000243583.6_Missense_Mutation_p.S87P	NM_024876.3	NP_079152.3	Q96D53	ADCK4_HUMAN	aarF domain containing kinase 4	87						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|endometrium(3)|large_intestine(3)|lung(6)|stomach(2)|urinary_tract(1)	17			Lung(22;9.49e-05)|LUSC - Lung squamous cell carcinoma(20;0.000219)			CTGATGCGGGAGGCAGGCACC	0.562																																					p.S87P		Atlas-SNP	.											.	ADCK4	92	.	0			c.T259C						.						89.0	83.0	85.0					19																	41220002		2203	4300	6503	SO:0001583	missense	79934	exon4			TGCGGGAGGCAGG	AK022291	CCDS12562.1, CCDS46081.1	19q13.2	2008-02-05				ENSG00000123815			19041	protein-coding gene	gene with protein product		615567					Standard	NM_024876		Approved	FLJ12229, COQ8	uc002oor.2	Q96D53		ENST00000324464.3:c.259T>C	chr19.hg19:g.41220002A>G	ENSP00000315118:p.Ser87Pro	81.0	0.0		137.0	6.0	NM_001142555	Q8TAJ1|Q9HA52	Missense_Mutation	SNP	ENST00000324464.3	hg19	CCDS12562.1	.	.	.	.	.	.	.	.	.	.	a	23.3	4.398852	0.83120	.	.	ENSG00000123815	ENST00000324464;ENST00000450541;ENST00000243583	T;T;T	0.76968	-1.06;-0.72;-0.72	5.46	5.46	0.80206	.	0.055160	0.64402	D	0.000001	D	0.88020	0.6325	M	0.88310	2.945	0.44388	D	0.997298	D;D	0.69078	0.996;0.997	D;D	0.71870	0.944;0.975	D	0.89413	0.3704	10	0.87932	D	0	-4.8201	8.9137	0.35568	0.834:0.0:0.0:0.166	.	87;87	Q96D53;Q96D53-2	ADCK4_HUMAN;.	P	87	ENSP00000315118:S87P;ENSP00000412839:S87P;ENSP00000243583:S87P	ENSP00000243583:S87P	S	-	1	0	ADCK4	45911842	0.998000	0.40836	1.000000	0.80357	0.995000	0.86356	3.562000	0.53777	2.075000	0.62263	0.454000	0.30748	TCC	.	.		0.562	ADCK4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462731.1	NM_024876	
MEGF8	1954	hgsc.bcm.edu	37	19	42840481	42840481	+	Silent	SNP	C	C	T			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:42840481C>T	ENST00000251268.6	+	6	1227	c.1227C>T	c.(1225-1227)caC>caT	p.H409H	MEGF8_ENST00000334370.4_Silent_p.H409H	NM_001271938.1	NP_001258867.1	Q7Z7M0	MEGF8_HUMAN	multiple EGF-like-domains 8	409					BMP signaling pathway (GO:0030509)|cell migration involved in gastrulation (GO:0042074)|craniofacial suture morphogenesis (GO:0097094)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of heart left/right asymmetry (GO:0061371)|embryonic heart tube left/right pattern formation (GO:0060971)|embryonic heart tube morphogenesis (GO:0003143)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal system morphogenesis (GO:0048704)|epiboly involved in gastrulation with mouth forming second (GO:0055113)|fasciculation of sensory neuron axon (GO:0097155)|left/right pattern formation (GO:0060972)|limb morphogenesis (GO:0035108)|positive regulation of axon extension involved in axon guidance (GO:0048842)|regulation of gene expression (GO:0010468)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|receptor activity (GO:0004872)			breast(2)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	50		Prostate(69;0.00682)				ATGGTGGACACCGGCCCTCCA	0.637																																					p.H409H		Atlas-SNP	.											.	MEGF8	358	.	0			c.C1227T						.						23.0	25.0	24.0					19																	42840481		2072	4184	6256	SO:0001819	synonymous_variant	1954	exon6			TGGACACCGGCCC	AB011541	CCDS12604.2, CCDS62693.1	19q13.2	2011-11-24	2006-03-31	2006-03-31	ENSG00000105429	ENSG00000105429			3233	protein-coding gene	gene with protein product	"""HBV pre s2 binding protein 1"""	604267	"""EGF-like-domain, multiple 4"", ""chromosome 19 open reading frame 49"""	EGFL4, C19orf49		9693030	Standard	NM_001410		Approved	SBP1, FLJ22365	uc002otm.5	Q7Z7M0	OTTHUMG00000150342	ENST00000251268.6:c.1227C>T	chr19.hg19:g.42840481C>T		43.0	0.0		53.0	4.0	NM_001271938	A8KAY0|O75097	Silent	SNP	ENST00000251268.6	hg19																																																																																				.	.		0.637	MEGF8-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000463854.1	NM_001410	
ZNF221	7638	hgsc.bcm.edu	37	19	44471324	44471324	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:44471324G>A	ENST00000251269.5	+	6	1998	c.1670G>A	c.(1669-1671)gGg>gAg	p.G557E	ZNF221_ENST00000592350.1_Missense_Mutation_p.G557E|ZNF221_ENST00000587682.1_Missense_Mutation_p.G557E	NM_013359.2	NP_037491	Q9UK13	ZN221_HUMAN	zinc finger protein 221	557			G -> R (in dbSNP:rs366111). {ECO:0000269|PubMed:12743021, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.5}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.G557V(1)		central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(11)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	30		Prostate(69;0.0352)				AGGGTCCACGGGGGAGAGCGA	0.453																																					p.G557E		Atlas-SNP	.											.,1	ZNF221	59	.	1	Substitution - Missense(1)	lung(1)	c.G1670A						.						86.0	84.0	85.0					19																	44471324		2203	4300	6503	SO:0001583	missense	7638	exon6			TCCACGGGGGAGA	AF187987	CCDS12633.1	19q13.31	2013-01-08				ENSG00000159905		"""Zinc fingers, C2H2-type"", ""-"""	13014	protein-coding gene	gene with protein product							Standard	NM_013359		Approved		uc002oxx.2	Q9UK13		ENST00000251269.5:c.1670G>A	chr19.hg19:g.44471324G>A	ENSP00000251269:p.Gly557Glu	64.0	0.0		86.0	0.0	NM_013359	B2RAI6|Q2M2H2|Q9P1U8	Missense_Mutation	SNP	ENST00000251269.5	hg19	CCDS12633.1	.	.	.	.	.	.	.	.	.	.	g	15.07	2.725374	0.48833	.	.	ENSG00000159905	ENST00000251269	T	0.17054	2.3	2.77	0.498	0.16908	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.07593	0.0191	N	0.04508	-0.205	0.09310	N	0.999994	B	0.02656	0.0	B	0.04013	0.001	T	0.31916	-0.9926	9	0.87932	D	0	.	6.751	0.23487	0.0:0.6588:0.2182:0.123	.	557	Q9UK13	ZN221_HUMAN	E	557	ENSP00000251269:G557E	ENSP00000251269:G557E	G	+	2	0	ZNF221	49163164	0.011000	0.17503	0.260000	0.24451	0.883000	0.51084	0.266000	0.18534	0.463000	0.27118	0.456000	0.33151	GGG	.	.		0.453	ZNF221-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460068.1		
ZNF227	7770	hgsc.bcm.edu	37	19	44739699	44739699	+	Silent	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:44739699A>G	ENST00000313040.7	+	6	1321	c.1116A>G	c.(1114-1116)agA>agG	p.R372R	ZNF227_ENST00000589005.1_Silent_p.R321R|ZNF227_ENST00000391961.2_Silent_p.R321R	NM_182490.1	NP_872296.1	Q86WZ6	ZN227_HUMAN	zinc finger protein 227	372					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(12)|ovary(2)|stomach(1)|urinary_tract(1)	24		Prostate(69;0.0435)				GCCATCAGAGAGTCCACACTG	0.428																																					p.R372R		Atlas-SNP	.											.	ZNF227	62	.	0			c.A1116G						.						75.0	84.0	81.0					19																	44739699		2203	4300	6503	SO:0001819	synonymous_variant	7770	exon6			TCAGAGAGTCCAC	AK092253	CCDS12636.1, CCDS74388.1	19q13.32	2013-01-08						"""Zinc fingers, C2H2-type"", ""-"""	13020	protein-coding gene	gene with protein product							Standard	XM_005259232		Approved		uc002oyu.3	Q86WZ6		ENST00000313040.7:c.1116A>G	chr19.hg19:g.44739699A>G		41.0	0.0		32.0	4.0	NM_182490	B3KRU7|B7Z5P9	Silent	SNP	ENST00000313040.7	hg19	CCDS12636.1																																																																																			.	.		0.428	ZNF227-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460720.1	NM_182490	
ZC3H4	23211	hgsc.bcm.edu	37	19	47570722	47570722	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:47570722T>C	ENST00000253048.5	-	15	2840	c.2803A>G	c.(2803-2805)Aag>Gag	p.K935E	ZC3H4_ENST00000594019.1_Intron	NM_015168.1	NP_055983.1	Q9UPT8	ZC3H4_HUMAN	zinc finger CCCH-type containing 4	935							metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(13)|ovary(4)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)	41		all_cancers(25;3.3e-08)|all_epithelial(76;2.28e-06)|all_lung(116;7.86e-06)|Lung NSC(112;2.31e-05)|all_neural(266;0.026)|Ovarian(192;0.0392)|Breast(70;0.0889)		OV - Ovarian serous cystadenocarcinoma(262;5.76e-05)|all cancers(93;7.69e-05)|Epithelial(262;0.00354)|GBM - Glioblastoma multiforme(486;0.0372)		TTCACGGCCTTCTCCCGCAGG	0.672																																					p.K935E		Atlas-SNP	.											.	ZC3H4	96	.	0			c.A2803G						.						67.0	79.0	75.0					19																	47570722		1986	4139	6125	SO:0001583	missense	23211	exon15			CGGCCTTCTCCCG	AB028987	CCDS42582.1	19q13.33	2012-07-05	2007-10-18	2007-10-18		ENSG00000130749		"""Zinc fingers, CCCH-type domain containing"""	17808	protein-coding gene	gene with protein product			"""chromosome 19 open reading frame 7"""	C19orf7			Standard	NM_015168		Approved	KIAA1064	uc002pga.4	Q9UPT8		ENST00000253048.5:c.2803A>G	chr19.hg19:g.47570722T>C	ENSP00000253048:p.Lys935Glu	79.0	0.0		95.0	4.0	NM_015168	Q9Y420	Missense_Mutation	SNP	ENST00000253048.5	hg19	CCDS42582.1	.	.	.	.	.	.	.	.	.	.	T	16.40	3.112675	0.56398	.	.	ENSG00000130749	ENST00000253048	T	0.34859	1.34	5.17	5.17	0.71159	.	0.129536	0.50627	D	0.000105	T	0.56906	0.2017	M	0.64404	1.975	0.49483	D	0.999791	D	0.71674	0.998	D	0.77004	0.989	T	0.60429	-0.7265	10	0.72032	D	0.01	.	14.2891	0.66265	0.0:0.0:0.0:1.0	.	935	Q9UPT8	ZC3H4_HUMAN	E	935	ENSP00000253048:K935E	ENSP00000253048:K935E	K	-	1	0	ZC3H4	52262562	1.000000	0.71417	1.000000	0.80357	0.345000	0.29048	3.675000	0.54605	2.078000	0.62432	0.460000	0.39030	AAG	.	.		0.672	ZC3H4-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466667.1		
NR1H2	7376	hgsc.bcm.edu	37	19	50881820	50881820	+	Missense_Mutation	SNP	A	A	C	rs397738863|rs78398331|rs55652650	byFrequency	TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:50881820A>C	ENST00000253727.5	+	6	749	c.514A>C	c.(514-516)Aaa>Caa	p.K172Q	NR1H2_ENST00000598168.1_Missense_Mutation_p.K172Q|NR1H2_ENST00000542413.1_5'UTR|NR1H2_ENST00000593926.1_Missense_Mutation_p.K172Q|NR1H2_ENST00000599105.1_Missense_Mutation_p.K172Q|NR1H2_ENST00000411902.2_Missense_Mutation_p.K75Q	NM_007121.5	NP_009052	P55055	NR1H2_HUMAN	nuclear receptor subfamily 1, group H, member 2	172					cellular lipid metabolic process (GO:0044255)|gene expression (GO:0010467)|negative regulation of cholesterol storage (GO:0010887)|negative regulation of interferon-gamma-mediated signaling pathway (GO:0060336)|negative regulation of lipid transport (GO:0032369)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|negative regulation of pinocytosis (GO:0048550)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of cholesterol transport (GO:0032376)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of lipoprotein lipase activity (GO:0051006)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of triglyceride biosynthetic process (GO:0010867)|regulation of cholesterol homeostasis (GO:2000188)|retinoic acid receptor signaling pathway (GO:0048384)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	apolipoprotein A-I receptor binding (GO:0034191)|ATPase binding (GO:0051117)|DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific transcription regulatory region DNA binding RNA polymerase II transcription factor recruiting transcription factor activity (GO:0001133)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(1)|lung(3)|upper_aerodigestive_tract(2)	8		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00757)|GBM - Glioblastoma multiforme(134;0.0186)		GAAGATTCGGAAACAGCAGCA	0.637																																					p.K172Q		Atlas-SNP	.											.,1	NR1H2	47	.	0			c.A514C						.						36.0	45.0	42.0					19																	50881820		2126	4246	6372	SO:0001583	missense	7376	exon6			ATTCGGAAACAGC	U14534	CCDS42593.1, CCDS58673.1	19q13.3	2013-01-16				ENSG00000131408		"""Nuclear hormone receptors"""	7965	protein-coding gene	gene with protein product	"""liver X receptor-beta"""	600380	"""ubiquitously-expressed nuclear receptor"""	UNR		7782080, 7971966	Standard	NM_007121		Approved	NER, NER-I, RIP15, LXR-b	uc010enw.4	P55055		ENST00000253727.5:c.514A>C	chr19.hg19:g.50881820A>C	ENSP00000253727:p.Lys172Gln	85.0	2.0		92.0	4.0	NM_007121	A8K490|B4DNM6|E7EWA6|Q12970|Q5I0Y1	Missense_Mutation	SNP	ENST00000253727.5	hg19	CCDS42593.1	.	.	.	.	.	.	.	.	.	.	A	16.32	3.090515	0.55968	.	.	ENSG00000131408	ENST00000253727;ENST00000411902;ENST00000376942	D;D	0.92545	-3.05;-3.06	4.44	3.39	0.38822	Nuclear hormone receptor, ligand-binding (2);	0.390877	0.22454	N	0.059841	D	0.93103	0.7804	L	0.42245	1.32	0.80722	D	1	D;B;D	0.76494	0.999;0.416;0.984	D;B;P	0.72982	0.979;0.063;0.889	D	0.91856	0.5495	10	0.54805	T	0.06	.	10.3348	0.43844	0.8342:0.1658:0.0:0.0	.	172;75;172	P55055;E7EWA6;F1D8P7	NR1H2_HUMAN;.;.	Q	172;75;172	ENSP00000253727:K172Q;ENSP00000396151:K75Q	ENSP00000253727:K172Q	K	+	1	0	NR1H2	55573632	1.000000	0.71417	0.848000	0.33437	0.651000	0.38670	3.746000	0.55127	0.814000	0.34374	0.459000	0.35465	AAA	.	.		0.637	NR1H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464724.2		
SIGLEC12	89858	hgsc.bcm.edu	37	19	52004796	52004797	+	Missense_Mutation	DNP	GA	GA	TG			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G|A	G|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:52004796_52004797GA>TG	ENST00000291707.3	-	1	246_247	c.191_192TC>CA	c.(190-192)tTC>tCA	p.F64S	SIGLEC12_ENST00000598614.1_5'Flank	NM_053003.2	NP_443729.1	Q96PQ1	SIG12_HUMAN	sialic acid binding Ig-like lectin 12 (gene/pseudogene)	64	Ig-like V-type 1.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			NS(2)|biliary_tract(1)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(8)|liver(1)|lung(23)|ovary(4)|prostate(2)|skin(8)|stomach(3)|upper_aerodigestive_tract(2)	61		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.00161)|OV - Ovarian serous cystadenocarcinoma(262;0.0102)		CCCCTGCCCGGAACCAGTAGCC	0.599																																					p.F64L|p.F64S		Atlas-SNP	.											.	SIGLEC12	243	.	0			c.C192A|c.T191C						.																																			SO:0001583	missense	89858	exon1			TGCCCGGAACCAG|GCCCGGAACCAGT	AF282256	CCDS12833.1, CCDS59416.1	19q13.41	2013-01-29	2011-06-29	2004-10-20	ENSG00000254521	ENSG00000254521		"""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15482	protein-coding gene	gene with protein product		606094	"""SIGLEC-like 1"", ""sialic acid binding Ig-like lectin 12"""	SIGLECL1		11409877, 11328818, 21555517	Standard	NM_053003		Approved	SLG, S2V, Siglec-XII, Siglec-12, Siglec-L1	uc002pwx.1	Q96PQ1	OTTHUMG00000165524	ENST00000291707.3:c.191_192delinsTG	chr19.hg19:g.52004796_52004797delinsTG	ENSP00000291707:p.Phe64Ser	112.0|114.0	0.0		155.0	14.0|9.0	NM_053003	Q8IYH7	Missense_Mutation	SNP	ENST00000291707.3	hg19	CCDS12833.1																																																																																			.	.		0.599	SIGLEC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384641.2	NM_053003	
ZNF665	79788	hgsc.bcm.edu	37	19	53686151	53686151	+	Intron	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:53686151T>C	ENST00000600412.1	-	1	63				ZNF665_ENST00000598440.1_5'UTR|ZNF665_ENST00000396424.3_Start_Codon_SNP_p.M1V			Q9H7R5	ZN665_HUMAN	zinc finger protein 665						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|kidney(2)|large_intestine(10)|lung(16)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	35				GBM - Glioblastoma multiforme(134;0.0196)		GGAAGAGCCATCCCTGACTCC	0.448																																					p.M1V		Atlas-SNP	.											.	ZNF665	136	.	0			c.A1G						.						166.0	130.0	142.0					19																	53686151		2203	4300	6503	SO:0001627	intron_variant	79788	exon2			GAGCCATCCCTGA		CCDS46169.1	19q13.42	2013-01-08				ENSG00000197497		"""Zinc fingers, C2H2-type"", ""-"""	25885	protein-coding gene	gene with protein product							Standard	NM_024733		Approved	FLJ14345	uc010eqm.1	Q9H7R5		ENST00000600412.1:c.52+10413A>G	chr19.hg19:g.53686151T>C		16.0	0.0		50.0	4.0	NM_024733	A8K5T8	Missense_Mutation	SNP	ENST00000600412.1	hg19		.	.	.	.	.	.	.	.	.	.	T	11.08	1.532935	0.27387	.	.	ENSG00000197497	ENST00000396424	T	0.00792	5.69	2.37	1.33	0.21861	.	.	.	.	.	T	0.00666	0.0022	.	.	.	0.80722	D	1	P	0.36171	0.541	B	0.31337	0.128	T	0.69098	-0.5235	8	0.62326	D	0.03	.	3.5461	0.07829	0.0:0.2023:0.0:0.7977	.	1	Q9H7R5-2	.	V	1	ENSP00000379702:M1V	ENSP00000379702:M1V	M	-	1	0	ZNF665	58377963	0.352000	0.24895	0.303000	0.25071	0.072000	0.16883	1.070000	0.30653	1.078000	0.41014	0.459000	0.35465	ATG	.	.		0.448	ZNF665-002	PUTATIVE	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000464179.1	NM_024733	
ZNF677	342926	hgsc.bcm.edu	37	19	53740870	53740870	+	Silent	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:53740870A>G	ENST00000598513.1	-	5	1260	c.1110T>C	c.(1108-1110)acT>acC	p.T370T	ZNF677_ENST00000333952.4_Silent_p.T370T	NM_182609.2	NP_872415.1	Q86XU0	ZN677_HUMAN	zinc finger protein 677	370					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(13)|lung(6)|ovary(1)|pancreas(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				GBM - Glioblastoma multiforme(134;0.00352)		GTTTCTCTCCAGTATGAATTC	0.403																																					p.T370T		Atlas-SNP	.											.	ZNF677	94	.	0			c.T1110C						.						79.0	74.0	76.0					19																	53740870		2203	4300	6503	SO:0001819	synonymous_variant	342926	exon5			CTCTCCAGTATGA	BC050038	CCDS12861.1	19q13.42	2013-01-08				ENSG00000197928		"""Zinc fingers, C2H2-type"", ""-"""	28730	protein-coding gene	gene with protein product	"""hypothetical protein MGC48625"""					12477932	Standard	NM_182609		Approved	MGC48625	uc002qbg.1	Q86XU0		ENST00000598513.1:c.1110T>C	chr19.hg19:g.53740870A>G		72.0	0.0		112.0	5.0	NM_182609		Silent	SNP	ENST00000598513.1	hg19	CCDS12861.1																																																																																			.	.		0.403	ZNF677-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464189.1	NM_182609	
ZNF667	63934	hgsc.bcm.edu	37	19	56953864	56953864	+	Missense_Mutation	SNP	G	G	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:56953864G>C	ENST00000504904.3	-	7	1219	c.500C>G	c.(499-501)aCa>aGa	p.T167R	ZNF667_ENST00000591790.1_3'UTR|ZNF667_ENST00000342634.3_Missense_Mutation_p.T295R|ZNF667_ENST00000292069.6_Missense_Mutation_p.T167R			Q5HYK9	ZN667_HUMAN	zinc finger protein 667	167					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(18)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)	38		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0615)		CTTCTCTCCTGTATGAATGTT	0.378																																					p.T167R		Atlas-SNP	.											ZNF667,caecum,carcinoma,0,1	ZNF667	95	.	0			c.C500G						.						83.0	87.0	85.0					19																	56953864		2203	4300	6503	SO:0001583	missense	63934	exon5			TCTCCTGTATGAA		CCDS12944.1	19q13.43	2013-01-08				ENSG00000198046		"""Zinc fingers, C2H2-type"", ""-"""	28854	protein-coding gene	gene with protein product		611024					Standard	NM_022103		Approved	FLJ14011	uc002qnd.3	Q5HYK9		ENST00000504904.3:c.500C>G	chr19.hg19:g.56953864G>C	ENSP00000439402:p.Thr167Arg	112.0	0.0		164.0	0.0	NM_022103	B2RMS6|B9EK36|Q6B093|Q9H807	Missense_Mutation	SNP	ENST00000504904.3	hg19	CCDS12944.1	.	.	.	.	.	.	.	.	.	.	G	8.465	0.856145	0.17106	.	.	ENSG00000198046	ENST00000342634;ENST00000504904;ENST00000292069;ENST00000360227	T;T;T	0.25749	1.78;1.78;1.78	4.86	2.68	0.31781	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.308196	0.23591	N	0.046547	T	0.37237	0.0996	L	0.60067	1.865	0.09310	N	1	D;P	0.58620	0.983;0.942	P;P	0.57101	0.813;0.725	T	0.08973	-1.0696	10	0.87932	D	0	-0.7584	9.5492	0.39299	0.1798:0.0:0.8202:0.0	.	295;167	E7EPS0;Q5HYK9	.;ZN667_HUMAN	R	295;167;167;41	ENSP00000344699:T295R;ENSP00000439402:T167R;ENSP00000292069:T167R	ENSP00000292069:T167R	T	-	2	0	ZNF667	61645676	0.003000	0.15002	0.006000	0.13384	0.004000	0.04260	1.077000	0.30741	1.275000	0.44379	-0.237000	0.12165	ACA	.	.		0.378	ZNF667-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458394.1	NM_022103	
ZFP28	140612	hgsc.bcm.edu	37	19	57066048	57066048	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:57066048C>T	ENST00000301318.3	+	8	1965	c.1894C>T	c.(1894-1896)Ctt>Ttt	p.L632F	AC007228.11_ENST00000596587.1_RNA	NM_020828.1	NP_065879.1	Q8NHY6	ZFP28_HUMAN	ZFP28 zinc finger protein	632					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|kidney(1)|large_intestine(14)|lung(6)|ovary(1)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	35		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0302)		CAGTTCTCAGCTTGCCACTCA	0.453																																					p.L632F	Ovarian(124;554 1662 19430 21141 52494)	Atlas-SNP	.											.	ZFP28	99	.	0			c.C1894T						.						89.0	96.0	93.0					19																	57066048		2203	4300	6503	SO:0001583	missense	140612	exon8			TCTCAGCTTGCCA		CCDS12946.1	19q13.43	2013-01-08	2012-11-27			ENSG00000196867		"""Zinc fingers, C2H2-type"", ""-"""	17801	protein-coding gene	gene with protein product			"""zinc finger protein 28 homolog (mouse)"""				Standard	NM_020828		Approved	KIAA1431, mkr5	uc002qnj.3	Q8NHY6		ENST00000301318.3:c.1894C>T	chr19.hg19:g.57066048C>T	ENSP00000301318:p.Leu632Phe	80.0	0.0		96.0	4.0	NM_020828	A0JNV6|K7ES88|Q8NHU8|Q9BY30|Q9P2B6	Missense_Mutation	SNP	ENST00000301318.3	hg19	CCDS12946.1	.	.	.	.	.	.	.	.	.	.	C	16.67	3.188855	0.57909	.	.	ENSG00000196867	ENST00000301318	T	0.52057	0.68	4.23	4.23	0.50019	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.40302	N	0.001133	T	0.70745	0.3259	M	0.82193	2.58	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.76610	-0.2896	10	0.72032	D	0.01	.	15.8942	0.79323	0.0:1.0:0.0:0.0	.	632	Q8NHY6	ZFP28_HUMAN	F	632	ENSP00000301318:L632F	ENSP00000301318:L632F	L	+	1	0	ZFP28	61757860	0.245000	0.23899	1.000000	0.80357	0.995000	0.86356	1.319000	0.33655	2.357000	0.79964	0.555000	0.69702	CTT	.	.		0.453	ZFP28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458409.1	NM_020828	
ZNF134	7693	hgsc.bcm.edu	37	19	58132374	58132374	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:58132374T>C	ENST00000396161.5	+	3	1197	c.887T>C	c.(886-888)gTc>gCc	p.V296A		NM_003435.3	NP_003426.3	P52741	ZN134_HUMAN	zinc finger protein 134	296					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(3)|prostate(1)	11		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0265)		TGTGGGAAAGTCTTCAGACAC	0.398																																					p.V296A		Atlas-SNP	.											.	ZNF134	34	.	0			c.T887C						.						111.0	114.0	113.0					19																	58132374		2200	4299	6499	SO:0001583	missense	7693	exon3			GGAAAGTCTTCAG	U09412	CCDS42638.1	19q13.4	2013-01-08	2006-06-13			ENSG00000213762		"""Zinc fingers, C2H2-type"""	12918	protein-coding gene	gene with protein product		604076	"""zinc finger protein 134 (clone pHZ-15)"""			7557990	Standard	NM_003435		Approved	pHZ-15	uc002qpn.2	P52741		ENST00000396161.5:c.887T>C	chr19.hg19:g.58132374T>C	ENSP00000379464:p.Val296Ala	72.0	0.0		85.0	4.0	NM_003435	Q9Y4B2	Missense_Mutation	SNP	ENST00000396161.5	hg19	CCDS42638.1	.	.	.	.	.	.	.	.	.	.	T	3.925	-0.017305	0.07681	.	.	ENSG00000213762	ENST00000418193;ENST00000541849;ENST00000396161	T	0.00949	5.51	4.45	-0.858	0.10689	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00384	0.0012	N	0.01152	-0.98	0.19775	N	0.999959	B	0.18013	0.025	B	0.15052	0.012	T	0.43410	-0.9393	9	0.02654	T	1	.	6.4658	0.21981	0.0:0.4523:0.2503:0.2974	.	296	P52741	ZN134_HUMAN	A	363;216;296	ENSP00000379464:V296A	ENSP00000379464:V296A	V	+	2	0	ZNF134	62824186	0.000000	0.05858	0.660000	0.29694	0.888000	0.51559	-0.618000	0.05578	-0.080000	0.12685	0.459000	0.35465	GTC	.	.		0.398	ZNF134-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466808.1	NM_003435	
ZNF8	7554	hgsc.bcm.edu	37	19	58797546	58797546	+	Silent	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:58797546A>G	ENST00000196548.5	+	3	395	c.264A>G	c.(262-264)agA>agG	p.R88R	CTD-3138B18.4_ENST00000600029.1_3'UTR|AC010642.1_ENST00000591325.1_3'UTR|ZNF8_ENST00000608843.1_Silent_p.R88R			P17098	ZNF8_HUMAN	zinc finger protein 8	88	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				BMP signaling pathway (GO:0030509)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(12)|ovary(1)|skin(1)	19		all_cancers(17;6.46e-05)|Lung NSC(17;0.0233)|all_neural(62;0.0381)|all_epithelial(17;0.0427)|all_lung(17;0.057)|Ovarian(87;0.17)|Colorectal(82;0.227)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.00619)		TGGCTGAGAGAGGAACCACCC	0.572																																					p.R88R		Atlas-SNP	.											.	ZNF8	60	.	0			c.A264G						.						54.0	47.0	50.0					19																	58797546		2203	4300	6503	SO:0001819	synonymous_variant	7554	exon3			TGAGAGAGGAACC	M29581	CCDS12974.1	19q13.43	2013-01-08	2006-05-09					"""Zinc fingers, C2H2-type"", ""-"""	13154	protein-coding gene	gene with protein product		194532	"""zinc finger protein 8 (clone HF.18)"""			2106481	Standard	NM_021089		Approved	HF.18, Zfp128	uc002qry.1	P17098		ENST00000196548.5:c.264A>G	chr19.hg19:g.58797546A>G		85.0	0.0		87.0	4.0	NM_021089	Q6PI99	Silent	SNP	ENST00000196548.5	hg19	CCDS12974.1																																																																																			.	.		0.572	ZNF8-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000459135.1	NM_021089	
ZNF132	7691	hgsc.bcm.edu	37	19	58945615	58945615	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:58945615T>C	ENST00000254166.3	-	3	1596	c.1196A>G	c.(1195-1197)cAg>cGg	p.Q399R		NM_003433.3	NP_003424.3	P52740	ZN132_HUMAN	zinc finger protein 132	399					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(1)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	19		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0171)|Lung(386;0.182)		AGGTCTTACCTGTGTGTGAAC	0.468																																					p.Q399R		Atlas-SNP	.											.	ZNF132	56	.	0			c.A1196G						.						100.0	94.0	96.0					19																	58945615		2203	4300	6503	SO:0001583	missense	7691	exon3			CTTACCTGTGTGT	U09411	CCDS12980.1	19q13.4	2013-01-08	2006-06-13			ENSG00000131849		"""Zinc fingers, C2H2-type"", ""-"""	12916	protein-coding gene	gene with protein product		604074	"""zinc finger protein 132 (clone pHZ-12)"""			7557990	Standard	NM_003433		Approved	pHZ-12	uc002qst.4	P52740		ENST00000254166.3:c.1196A>G	chr19.hg19:g.58945615T>C	ENSP00000254166:p.Gln399Arg	43.0	0.0		70.0	4.0	NM_003433	Q32MI9	Missense_Mutation	SNP	ENST00000254166.3	hg19	CCDS12980.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	10.63|10.63	1.404504|1.404504	0.25378|0.25378	.|.	.|.	ENSG00000131849|ENSG00000131849	ENST00000391695|ENST00000254166	.|T	.|0.18338	.|2.22	3.78|3.78	-1.83|-1.83	0.07833|0.07833	.|Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.|.	.|.	.|.	.|.	.|T	.|0.06781	.|0.0173	N|N	0.03917|0.03917	-0.325|-0.325	0.09310|0.09310	N|N	1|1	.|B	.|0.16166	.|0.016	.|B	.|0.13407	.|0.009	.|T	.|0.34104	.|-0.9842	.|9	.|0.87932	.|D	.|0	.|.	5.9234|5.9234	0.19094|0.19094	0.0:0.5743:0.199:0.2266|0.0:0.5743:0.199:0.2266	.|.	.|399	.|P52740	.|ZN132_HUMAN	.|R	-1|399	.|ENSP00000254166:Q399R	.|ENSP00000254166:Q399R	.|Q	-|-	.|2	.|0	ZNF132|ZNF132	63637427|63637427	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.912000|0.912000	0.54170|0.54170	-0.469000|-0.469000	0.06648|0.06648	-0.269000|-0.269000	0.09298|0.09298	0.533000|0.533000	0.62120|0.62120	.|CAG	.	.		0.468	ZNF132-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467035.1	NM_003433	
HSPA12B	116835	hgsc.bcm.edu	37	20	3723057	3723057	+	Splice_Site	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr20:3723057T>C	ENST00000254963.2	+	4	411		c.e4+2		HSPA12B_ENST00000542646.1_Intron	NM_001197327.1|NM_052970.4	NP_001184256.1|NP_443202.3	Q96MM6	HS12B_HUMAN	heat shock 70kD protein 12B								ATP binding (GO:0005524)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|skin(1)	14						CATGATGAGGTGAGGTCGGCT	0.577																																					.		Atlas-SNP	.											.	HSPA12B	43	.	0			c.266+2T>C						.						51.0	48.0	49.0					20																	3723057		2203	4300	6503	SO:0001630	splice_region_variant	116835	exon4			ATGAGGTGAGGTC	AK056712	CCDS13061.1	20p13	2011-09-02	2003-04-10	2003-04-10	ENSG00000132622	ENSG00000132622		"""Heat shock proteins / HSP70"""	16193	protein-coding gene	gene with protein product		610702	"""chromosome 20 open reading frame 60"""	C20orf60		12552099	Standard	NM_052970		Approved	dJ1009E24.2	uc002wjd.3	Q96MM6	OTTHUMG00000031755	ENST00000254963.2:c.266+2T>C	chr20.hg19:g.3723057T>C		62.0	0.0		84.0	4.0	NM_001197327	D3DVX7|Q2TAK3|Q9BR52	Splice_Site	SNP	ENST00000254963.2	hg19	CCDS13061.1	.	.	.	.	.	.	.	.	.	.	T	15.46	2.840376	0.51057	.	.	ENSG00000132622	ENST00000254963;ENST00000399701	.	.	.	4.73	4.73	0.59995	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.5017	0.55960	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	HSPA12B	3671057	1.000000	0.71417	0.993000	0.49108	0.617000	0.37484	5.934000	0.70138	2.122000	0.65172	0.533000	0.62120	.	.	.		0.577	HSPA12B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077756.2	NM_052970	Intron
PROKR2	128674	hgsc.bcm.edu	37	20	5283258	5283258	+	Missense_Mutation	SNP	T	T	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr20:5283258T>G	ENST00000217270.3	-	2	582	c.583A>C	c.(583-585)Acg>Ccg	p.T195P	PROKR2_ENST00000546004.1_Missense_Mutation_p.T195P	NM_144773.2	NP_658986.1	Q8NFJ6	PKR2_HUMAN	prokineticin receptor 2	195					circadian rhythm (GO:0007623)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neuropeptide Y receptor activity (GO:0004983)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(3)|lung(22)|ovary(5)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)	53						AAGAGGACCGTTTCTGTTGCA	0.488										HNSCC(71;0.22)																											p.T195P		Atlas-SNP	.											.	PROKR2	90	.	0			c.A583C						.						145.0	145.0	145.0					20																	5283258		2203	4300	6503	SO:0001583	missense	128674	exon2			GGACCGTTTCTGT	AL121755	CCDS13089.1	20p12.3	2012-08-08	2006-02-15	2006-02-15	ENSG00000101292	ENSG00000101292		"""GPCR / Class A : Prokineticin receptors"""	15836	protein-coding gene	gene with protein product		607123	"""G protein-coupled receptor 73-like 1"", ""Kallmann syndrome 3 (autosomal dominant)"""	GPR73L1, KAL3		11886876, 17054399	Standard	NM_144773		Approved	GPR73b, PKR2, GPRg2, dJ680N4.3	uc010zqw.2	Q8NFJ6	OTTHUMG00000031800	ENST00000217270.3:c.583A>C	chr20.hg19:g.5283258T>G	ENSP00000217270:p.Thr195Pro	145.0	0.0		173.0	7.0	NM_144773	A5JUU1|Q2M3C0|Q5TDY1|Q9NTT0	Missense_Mutation	SNP	ENST00000217270.3	hg19	CCDS13089.1	.	.	.	.	.	.	.	.	.	.	T	16.00	2.999718	0.54147	.	.	ENSG00000101292	ENST00000546004;ENST00000217270	T;T	0.72835	-0.69;-0.69	5.31	4.21	0.49690	GPCR, rhodopsin-like superfamily (1);	0.144071	0.64402	D	0.000006	T	0.66954	0.2842	L	0.55481	1.735	0.45502	D	0.99846	P	0.48016	0.904	P	0.48738	0.588	T	0.63363	-0.6654	10	0.33141	T	0.24	.	4.8238	0.13405	0.1643:0.0886:0.0:0.7471	.	195	Q8NFJ6	PKR2_HUMAN	P	195	ENSP00000440790:T195P;ENSP00000217270:T195P	ENSP00000217270:T195P	T	-	1	0	PROKR2	5231258	1.000000	0.71417	0.368000	0.25939	0.913000	0.54294	5.692000	0.68256	0.869000	0.35703	0.533000	0.62120	ACG	.	.		0.488	PROKR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077854.1	NM_144773	
KIF16B	55614	hgsc.bcm.edu	37	20	16351274	16351274	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr20:16351274T>C	ENST00000354981.2	-	22	3612	c.3455A>G	c.(3454-3456)gAg>gGg	p.E1152G	KIF16B_ENST00000378003.2_Missense_Mutation_p.E378G|KIF16B_ENST00000355755.3_Missense_Mutation_p.E1152G|KIF16B_ENST00000408042.1_Missense_Mutation_p.E1152G	NM_001199865.1|NM_024704.4	NP_001186794.1|NP_078980.3	Q96L93	KI16B_HUMAN	kinesin family member 16B	1152					ATP catabolic process (GO:0006200)|early endosome to late endosome transport (GO:0045022)|endoderm development (GO:0007492)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|formation of primary germ layer (GO:0001704)|Golgi to endosome transport (GO:0006895)|microtubule-based movement (GO:0007018)|receptor catabolic process (GO:0032801)|regulation of receptor recycling (GO:0001919)	early endosome (GO:0005769)|endosome (GO:0005768)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|plus-end-directed microtubule motor activity (GO:0008574)			NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(6)|large_intestine(15)|lung(24)|ovary(1)|prostate(15)|skin(3)|upper_aerodigestive_tract(2)	74						GTGAAGTTTCTCATTATCCTG	0.368																																					p.E1152G		Atlas-SNP	.											.	KIF16B	305	.	0			c.A3455G						.						104.0	99.0	101.0					20																	16351274		2202	4300	6502	SO:0001583	missense	55614	exon22			AGTTTCTCATTAT	AK000142	CCDS13122.1, CCDS56178.1	20p11.23	2008-03-03	2008-03-03	2008-03-03	ENSG00000089177	ENSG00000089177		"""Kinesins"""	15869	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 23"""	C20orf23		16084724, 16782399	Standard	NM_024704		Approved	FLJ20135, dJ971B4.1, SNX23	uc010gci.2	Q96L93	OTTHUMG00000031927	ENST00000354981.2:c.3455A>G	chr20.hg19:g.16351274T>C	ENSP00000347076:p.Glu1152Gly	42.0	0.0		72.0	4.0	NM_001199866	A6NKJ9|A7E2A8|B1AKG3|B1AKT7|C9JDN5|C9JI52|C9JSM8|C9JWJ7|Q2TBF5|Q5HYC0|Q5HYK1|Q5JWW3|Q5TFK5|Q86VL9|Q86YS5|Q8IYU0|Q9BQJ8|Q9BQM0|Q9BQM1|Q9BQM5|Q9H5U0|Q9HCI2|Q9NXN9	Missense_Mutation	SNP	ENST00000354981.2	hg19	CCDS13122.1	.	.	.	.	.	.	.	.	.	.	T	26.7	4.766397	0.90020	.	.	ENSG00000089177	ENST00000354981;ENST00000355755;ENST00000377997;ENST00000378003;ENST00000408042	T;T;T;T	0.77098	-0.72;-1.07;2.17;-0.79	5.76	5.76	0.90799	.	0.051713	0.85682	D	0.000000	D	0.83487	0.5265	L	0.55481	1.735	0.40287	D	0.978464	D;D;D	0.69078	0.978;0.997;0.995	P;P;P	0.59825	0.773;0.864;0.735	D	0.84314	0.0512	10	0.46703	T	0.11	.	16.0643	0.80861	0.0:0.0:0.0:1.0	.	1152;1152;1152	Q96L93-2;Q96L93-6;Q96L93	.;.;KI16B_HUMAN	G	1152;1152;996;378;1152	ENSP00000347076:E1152G;ENSP00000347995:E1152G;ENSP00000367242:E378G;ENSP00000384164:E1152G	ENSP00000347076:E1152G	E	-	2	0	KIF16B	16299274	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.825000	0.69286	2.202000	0.70862	0.450000	0.29827	GAG	.	.		0.368	KIF16B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078104.2	NM_017683	
ZNF341	84905	hgsc.bcm.edu	37	20	32346565	32346565	+	Silent	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr20:32346565T>C	ENST00000375200.1	+	7	1346	c.981T>C	c.(979-981)tgT>tgC	p.C327C	ZNF341_ENST00000342427.2_Silent_p.C320C	NM_001282933.1	NP_001269862.1	Q9BYN7	ZN341_HUMAN	zinc finger protein 341	327					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(3)|lung(8)|ovary(2)|prostate(3)|skin(1)|urinary_tract(3)	31						GCTCATACTGTGACAAGTCAT	0.557																																					p.C320C		Atlas-SNP	.											.	ZNF341	73	.	0			c.T960C						.						96.0	73.0	81.0					20																	32346565		2203	4300	6503	SO:0001819	synonymous_variant	84905	exon7			ATACTGTGACAAG	AK027550	CCDS13227.1, CCDS74719.1	20q11.22	2013-01-08			ENSG00000131061	ENSG00000131061		"""Zinc fingers, C2H2-type"""	15992	protein-coding gene	gene with protein product							Standard	NM_001282933		Approved	dJ553F4.3	uc002wzx.3	Q9BYN7	OTTHUMG00000032275	ENST00000375200.1:c.981T>C	chr20.hg19:g.32346565T>C		68.0	0.0		89.0	4.0	NM_032819	A2RUF4|B2RXE5|B7ZM09|Q5JXM8|Q96ST5	Silent	SNP	ENST00000375200.1	hg19																																																																																				.	.		0.557	ZNF341-201	KNOWN	basic	protein_coding	protein_coding			
KIAA1755	85449	hgsc.bcm.edu	37	20	36842112	36842112	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr20:36842112T>C	ENST00000279024.4	-	14	3206	c.2935A>G	c.(2935-2937)Atg>Gtg	p.M979V		NM_001029864.1	NP_001025035.1	Q5JYT7	K1755_HUMAN	KIAA1755	979										breast(2)|endometrium(3)|kidney(1)|large_intestine(5)|lung(31)|ovary(5)|pancreas(2)|skin(4)|stomach(1)	54		Myeloproliferative disorder(115;0.00874)				AGCTGGGCCATCAGGTCCTGA	0.607																																					p.M979V		Atlas-SNP	.											.	KIAA1755	145	.	0			c.A2935G						.						18.0	16.0	17.0					20																	36842112		2202	4300	6502	SO:0001583	missense	85449	exon14			GGGCCATCAGGTC	AB051542	CCDS33467.1	20q11.23	2007-12-07			ENSG00000149633	ENSG00000149633			29372	protein-coding gene	gene with protein product						11214970	Standard	NM_001029864		Approved	RP5-1054A22.3	uc002xhy.1	Q5JYT7	OTTHUMG00000032436	ENST00000279024.4:c.2935A>G	chr20.hg19:g.36842112T>C	ENSP00000279024:p.Met979Val	65.0	0.0		100.0	4.0	NM_001029864	Q9C0A8	Missense_Mutation	SNP	ENST00000279024.4	hg19	CCDS33467.1	.	.	.	.	.	.	.	.	.	.	T	5.990	0.366597	0.11352	.	.	ENSG00000149633	ENST00000279024	T	0.04603	3.59	5.14	-2.67	0.06059	.	0.360778	0.23926	N	0.043189	T	0.04318	0.0119	L	0.50919	1.6	0.09310	N	0.999994	B	0.02656	0.0	B	0.04013	0.001	T	0.30446	-0.9978	10	0.48119	T	0.1	.	6.4846	0.22081	0.0:0.4782:0.1678:0.354	.	979	Q5JYT7	K1755_HUMAN	V	979	ENSP00000279024:M979V	ENSP00000279024:M979V	M	-	1	0	KIAA1755	36275526	0.769000	0.28531	0.126000	0.21872	0.993000	0.82548	-0.119000	0.10676	-0.368000	0.08040	0.459000	0.35465	ATG	.	.		0.607	KIAA1755-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079144.3	NM_001029864	
LBP	3929	hgsc.bcm.edu	37	20	36989407	36989407	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr20:36989407T>C	ENST00000217407.2	+	6	799	c.638T>C	c.(637-639)cTc>cCc	p.L213P		NM_004139.3	NP_004130.2	P18428	LBP_HUMAN	lipopolysaccharide binding protein	213					acute-phase response (GO:0006953)|cellular defense response (GO:0006968)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to lipoteichoic acid (GO:0071223)|defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|detection of molecule of bacterial origin (GO:0032490)|innate immune response (GO:0045087)|leukocyte chemotaxis involved in inflammatory response (GO:0002232)|lipopolysaccharide transport (GO:0015920)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|macrophage activation involved in immune response (GO:0002281)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of tumor necrosis factor production (GO:0032720)|opsonization (GO:0008228)|positive regulation of chemokine production (GO:0032722)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of macrophage activation (GO:0043032)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of respiratory burst involved in inflammatory response (GO:0060265)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|positive regulation of tumor necrosis factor production (GO:0032760)|response to lipopolysaccharide (GO:0032496)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	lipopolysaccharide binding (GO:0001530)|lipoteichoic acid binding (GO:0070891)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(16)|ovary(2)|prostate(1)|urinary_tract(1)	28		Myeloproliferative disorder(115;0.00878)				CAGCCTTATCTCCAAACTCTG	0.418																																					p.L213P		Atlas-SNP	.											.	LBP	60	.	0			c.T638C						.						170.0	167.0	168.0					20																	36989407		2203	4300	6503	SO:0001583	missense	3929	exon6			CTTATCTCCAAAC		CCDS13304.1	20q11.23	2011-08-16	2001-11-28		ENSG00000129988	ENSG00000129988		"""BPI fold containing"""	6517	protein-coding gene	gene with protein product	"""BPI fold containing family D, member 2"""	151990	"""lipopolysaccharide-binding protein"""			8432532	Standard	NM_004139		Approved	BPIFD2	uc002xic.2	P18428	OTTHUMG00000032447	ENST00000217407.2:c.638T>C	chr20.hg19:g.36989407T>C	ENSP00000217407:p.Leu213Pro	95.0	0.0		131.0	6.0	NM_004139	B2R938|O43438|Q92672|Q9H403|Q9UD66	Missense_Mutation	SNP	ENST00000217407.2	hg19	CCDS13304.1	.	.	.	.	.	.	.	.	.	.	T	19.37	3.815307	0.70912	.	.	ENSG00000129988	ENST00000217407;ENST00000538599	T	0.14766	2.48	5.28	5.28	0.74379	Lipid-binding serum glycoprotein, N-terminal (1);Bactericidal permeability-increasing protein, alpha/beta domain (1);	0.000000	0.64402	D	0.000011	T	0.43433	0.1247	M	0.88450	2.955	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.50980	-0.8763	10	0.87932	D	0	-35.8502	13.2224	0.59896	0.0:0.0:0.0:1.0	.	213	P18428	LBP_HUMAN	P	213	ENSP00000217407:L213P	ENSP00000217407:L213P	L	+	2	0	LBP	36422821	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	4.379000	0.59575	2.225000	0.72522	0.533000	0.62120	CTC	.	.		0.418	LBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079174.2	NM_004139	
TMPRSS15	5651	hgsc.bcm.edu	37	21	19770597	19770597	+	Silent	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr21:19770597T>C	ENST00000284885.3	-	2	228	c.195A>G	c.(193-195)acA>acG	p.T65T		NM_002772.2	NP_002763	P98073	ENTK_HUMAN	transmembrane protease, serine 15	65	SEA. {ECO:0000255|PROSITE- ProRule:PRU00188}.		T -> I (in dbSNP:rs35987974).			brush border (GO:0005903)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(7)|large_intestine(19)|lung(36)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	85						TAACTCCGGATGTTATTTTAA	0.378																																					p.T65T		Atlas-SNP	.											.	TMPRSS15	189	.	0			c.A195G						.						79.0	81.0	80.0					21																	19770597		2203	4300	6503	SO:0001819	synonymous_variant	5651	exon2			TCCGGATGTTATT		CCDS13571.1	21q21	2010-12-09	2010-04-21	2010-04-21	ENSG00000154646	ENSG00000154646		"""Serine peptidases / Transmembrane"""	9490	protein-coding gene	gene with protein product	"""proenterokinase"", ""enteropeptidase"""	606635	"""protease, serine, 7 (enterokinase)"""	PRSS7		8052624	Standard	NM_002772		Approved	ENTK, MGC133046	uc002ykw.3	P98073	OTTHUMG00000074518	ENST00000284885.3:c.195A>G	chr21.hg19:g.19770597T>C		44.0	0.0		71.0	23.0	NM_002772	Q2NKL7	Silent	SNP	ENST00000284885.3	hg19	CCDS13571.1																																																																																			.	.		0.378	TMPRSS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000158231.2	NM_002772	
HUNK	30811	hgsc.bcm.edu	37	21	33312481	33312481	+	Silent	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr21:33312481T>C	ENST00000270112.2	+	3	919	c.559T>C	c.(559-561)Ttg>Ctg	p.L187L		NM_014586.1	NP_055401.1	P57058	HUNK_HUMAN	hormonally up-regulated Neu-associated kinase	187	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(15)|ovary(1)|skin(2)|stomach(1)	30						TTTCAGAGACTTGAAGATAGA	0.303																																					p.L187L		Atlas-SNP	.											.	HUNK	74	.	0			c.T559C						.						122.0	119.0	120.0					21																	33312481		2201	4298	6499	SO:0001819	synonymous_variant	30811	exon3			AGAGACTTGAAGA	AJ271722	CCDS13610.1	21q22.1	2008-06-05	2008-06-05		ENSG00000142149	ENSG00000142149			13326	protein-coding gene	gene with protein product		606532	"""hormonally upregulated Neu-associated kinase"""			10662544, 10830953	Standard	NM_014586		Approved		uc002yph.3	P57058	OTTHUMG00000085019	ENST00000270112.2:c.559T>C	chr21.hg19:g.33312481T>C		57.0	0.0		50.0	4.0	NM_014586		Silent	SNP	ENST00000270112.2	hg19	CCDS13610.1																																																																																			.	.		0.303	HUNK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000192782.1	NM_014586	
URB1	9875	hgsc.bcm.edu	37	21	33688875	33688875	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr21:33688875T>C	ENST00000382751.3	-	38	6651	c.6536A>G	c.(6535-6537)cAg>cGg	p.Q2179R		NM_014825.2	NP_055640.2	O60287	NPA1P_HUMAN	URB1 ribosome biogenesis 1 homolog (S. cerevisiae)	2179						nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(9)|kidney(3)|skin(1)|stomach(1)	19						AGCCACCAGCTGCAGCATGAC	0.632																																					p.Q2179R		Atlas-SNP	.											.	URB1	176	.	0			c.A6536G						.						21.0	28.0	26.0					21																	33688875		692	1591	2283	SO:0001583	missense	9875	exon38			ACCAGCTGCAGCA	AB011111	CCDS46645.1	21q22.11	2006-11-28	2006-11-28	2006-11-28	ENSG00000142207	ENSG00000142207			17344	protein-coding gene	gene with protein product	nucleolar preribosomal-associated protein 1	608865	"""chromosome 21 open reading frame 108"""	C21orf108		9628581	Standard	NM_014825		Approved	KIAA0539, NPA1	uc002ypn.2	O60287	OTTHUMG00000064919	ENST00000382751.3:c.6536A>G	chr21.hg19:g.33688875T>C	ENSP00000372199:p.Gln2179Arg	69.0	0.0		84.0	4.0	NM_014825	D3DSE5|Q96NX1|Q9NYQ1	Missense_Mutation	SNP	ENST00000382751.3	hg19	CCDS46645.1	.	.	.	.	.	.	.	.	.	.	T	9.408	1.079808	0.20309	.	.	ENSG00000142207	ENST00000382751	T	0.29142	1.58	5.31	-1.09	0.09904	.	0.528560	0.23000	N	0.053087	T	0.12646	0.0307	N	0.15975	0.35	0.29813	N	0.831477	B	0.06786	0.001	B	0.04013	0.001	T	0.26849	-1.0091	10	0.14656	T	0.56	-6.7455	6.04	0.19728	0.0:0.2645:0.1259:0.6097	.	2179	O60287	NPA1P_HUMAN	R	2179	ENSP00000372199:Q2179R	ENSP00000372199:Q2179R	Q	-	2	0	URB1	32610746	0.597000	0.26874	0.900000	0.35374	0.956000	0.61745	0.049000	0.14099	-0.194000	0.10399	0.454000	0.30748	CAG	.	.		0.632	URB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139400.2		
GART	2618	hgsc.bcm.edu	37	21	34882122	34882122	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr21:34882122T>C	ENST00000381831.3	-	18	2683	c.2420A>G	c.(2419-2421)aAg>aGg	p.K807R	GART_ENST00000543717.1_Missense_Mutation_p.K359R|GART_ENST00000381839.3_Missense_Mutation_p.K807R|GART_ENST00000381815.4_Missense_Mutation_p.K807R	NM_001136005.1	NP_001129477.1	P22102	PUR2_HUMAN	phosphoribosylglycinamide formyltransferase, phosphoribosylglycinamide synthetase, phosphoribosylaminoimidazole synthetase	807	AIRS.				'de novo' IMP biosynthetic process (GO:0006189)|brainstem development (GO:0003360)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|glycine metabolic process (GO:0006544)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase biosynthetic process (GO:0009113)|purine nucleobase metabolic process (GO:0006144)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|response to inorganic substance (GO:0010035)|response to organic substance (GO:0010033)|small molecule metabolic process (GO:0044281)|tetrahydrofolate biosynthetic process (GO:0046654)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)|phosphoribosylamine-glycine ligase activity (GO:0004637)|phosphoribosylformylglycinamidine cyclo-ligase activity (GO:0004641)|phosphoribosylglycinamide formyltransferase activity (GO:0004644)	p.K807fs*7(2)		NS(2)|breast(1)|endometrium(3)|large_intestine(3)|lung(13)|ovary(3)|prostate(5)|urinary_tract(1)	31					Pemetrexed(DB00642)	CACTCTGGCCTTTTTTTTTTC	0.448																																					p.K807R		Atlas-SNP	.											.,5	GART	81	.	2	Deletion - Frameshift(2)	ovary(2)	c.A2420G						.						66.0	70.0	68.0					21																	34882122		2203	4300	6503	SO:0001583	missense	2618	exon18			CTGGCCTTTTTTT	M32082	CCDS13627.1, CCDS13628.1	21q22.11	2012-10-02			ENSG00000159131	ENSG00000159131	2.1.2.2, 6.3.3.1, 6.3.4.13		4163	protein-coding gene	gene with protein product		138440		PRGS, PGFT		2050105	Standard	NM_001136005		Approved		uc002yrx.3	P22102	OTTHUMG00000065628	ENST00000381831.3:c.2420A>G	chr21.hg19:g.34882122T>C	ENSP00000371253:p.Lys807Arg	62.0	1.0		69.0	3.0	NM_001136005	A8K945|A8KA32|D3DSF3|D3DSF4|O14659|Q52M77	Missense_Mutation	SNP	ENST00000381831.3	hg19	CCDS13627.1	.	.	.	.	.	.	.	.	.	.	T	8.259	0.810646	0.16537	.	.	ENSG00000159131	ENST00000414353;ENST00000381815;ENST00000381831;ENST00000381839;ENST00000543717	T;T;T;T	0.46063	1.46;1.46;1.46;0.88	5.52	1.39	0.22231	.	0.269064	0.42420	N	0.000720	T	0.19927	0.0479	N	0.08118	0	0.42171	D	0.991646	B	0.09022	0.002	B	0.12156	0.007	T	0.05699	-1.0869	10	0.20046	T	0.44	-12.4071	9.947	0.41616	0.0:0.2362:0.0:0.7638	.	807	P22102	PUR2_HUMAN	R	71;807;807;807;359	ENSP00000371236:K807R;ENSP00000371253:K807R;ENSP00000371261:K807R;ENSP00000443579:K359R	ENSP00000371236:K807R	K	-	2	0	GART	33803992	1.000000	0.71417	0.803000	0.32268	0.561000	0.35649	1.563000	0.36364	0.393000	0.25203	0.482000	0.46254	AAG	.	.		0.448	GART-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140626.3	NM_000819	
RRP1	8568	hgsc.bcm.edu	37	21	45222190	45222190	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr21:45222190T>C	ENST00000497547.1	+	12	1162	c.1045T>C	c.(1045-1047)Tgc>Cgc	p.C349R	RRP1_ENST00000471909.1_3'UTR	NM_003683.5	NP_003674.1	P05386	RLA1_HUMAN	ribosomal RNA processing 1	0					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)	RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			central_nervous_system(1)|kidney(1)|lung(4)|stomach(2)	8				COAD - Colon adenocarcinoma(84;0.00753)|Colorectal(79;0.0157)|STAD - Stomach adenocarcinoma(101;0.171)		AGAGAAGGCCTGCAGGCGCCT	0.587																																					p.C349R		Atlas-SNP	.											.	RRP1	23	.	0			c.T1045C						.						77.0	87.0	84.0					21																	45222190		1900	4120	6020	SO:0001583	missense	8568	exon12			AAGGCCTGCAGGC	U79775	CCDS42951.1	21q22.3	2013-07-02	2013-07-02		ENSG00000160214	ENSG00000160214			18785	protein-coding gene	gene with protein product	"""DNA segment on chromosome 21 (unique) 2056 expressed sequence"", ""Nnp1 homolog, nucleolar protein (Drosophila)"""	610653	"""ribosomal RNA processing 1 homolog (S. cerevisiae)"""			10830953, 10341208	Standard	NM_003683		Approved	NNP-1, Nop52, NOP52, RRP1A, D21S2056E	uc002zds.2	P56182	OTTHUMG00000086884	ENST00000497547.1:c.1045T>C	chr21.hg19:g.45222190T>C	ENSP00000417464:p.Cys349Arg	90.0	0.0		77.0	4.0	NM_003683	A6NIB2	Missense_Mutation	SNP	ENST00000497547.1	hg19	CCDS42951.1	.	.	.	.	.	.	.	.	.	.	T	8.391	0.839676	0.16891	.	.	ENSG00000160214	ENST00000497547;ENST00000400387	T	0.00940	5.52	3.23	3.23	0.37069	.	0.652897	0.15680	N	0.249974	T	0.01156	0.0038	N	0.22421	0.69	0.09310	N	0.999997	P;D;B	0.56521	0.697;0.976;0.396	B;P;B	0.47528	0.201;0.549;0.059	T	0.56631	-0.7947	10	0.87932	D	0	.	8.2511	0.31717	0.0:0.0:0.0:1.0	.	349;216;349	B4DZM3;Q96J73;P56182	.;.;RRP1_HUMAN	R	349	ENSP00000417464:C349R	ENSP00000383237:C349R	C	+	1	0	RRP1	44046618	0.178000	0.23122	0.005000	0.12908	0.070000	0.16714	2.964000	0.49192	1.735000	0.51646	0.459000	0.35465	TGC	.	.		0.587	RRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195680.1	NM_003683	
PCBP3	54039	hgsc.bcm.edu	37	21	47320946	47320946	+	Nonsense_Mutation	SNP	C	C	A			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr21:47320946C>A	ENST00000400314.1	+	7	596	c.258C>A	c.(256-258)tgC>tgA	p.C86*	PCBP3_ENST00000400310.1_Nonsense_Mutation_p.C86*|PCBP3_ENST00000400309.1_Nonsense_Mutation_p.C86*|PCBP3_ENST00000400304.1_Nonsense_Mutation_p.C54*|PCBP3_ENST00000400308.1_Nonsense_Mutation_p.C86*|PCBP3_ENST00000449640.1_Nonsense_Mutation_p.C86*			P57721	PCBP3_HUMAN	poly(rC) binding protein 3	86	KH 1. {ECO:0000255|PROSITE- ProRule:PRU00117}.				mRNA metabolic process (GO:0016071)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			biliary_tract(1)|endometrium(3)|large_intestine(2)|lung(7)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	17	all_hematologic(128;0.24)			Colorectal(79;0.0411)|READ - Rectum adenocarcinoma(84;0.0649)		AGGGAAACTGCCCAGAGAGGA	0.557																																					p.C86X		Atlas-SNP	.											.	PCBP3	82	.	0			c.C258A						.						99.0	111.0	107.0					21																	47320946		2007	4160	6167	SO:0001587	stop_gained	54039	exon5			AAACTGCCCAGAG	AF176329	CCDS42974.2, CCDS46652.1	21q22.3	2013-07-16	2001-11-28		ENSG00000183570	ENSG00000183570			8651	protein-coding gene	gene with protein product		608502	"""poly(rC)-binding protein 3"""			10936052	Standard	NM_020528		Approved		uc002zhq.2	P57721	OTTHUMG00000090399	ENST00000400314.1:c.258C>A	chr21.hg19:g.47320946C>A	ENSP00000383168:p.Cys86*	93.0	0.0		89.0	12.0	NM_001130141	A8MPS2|A8MQ26|B7WNN9|B7WPC1|Q8N9K6|Q96EP6	Nonsense_Mutation	SNP	ENST00000400314.1	hg19	CCDS42974.2	.	.	.	.	.	.	.	.	.	.	C	39	7.893716	0.98548	.	.	ENSG00000183570	ENST00000400314;ENST00000400310;ENST00000400309;ENST00000400308;ENST00000449640;ENST00000346743;ENST00000400305;ENST00000400304	.	.	.	4.86	2.07	0.26955	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.6788	9.6505	0.39895	0.0:0.6423:0.0:0.3577	.	.	.	.	X	86;86;86;86;86;86;62;54	.	ENSP00000330225:C86X	C	+	3	2	PCBP3	46145374	0.884000	0.30299	1.000000	0.80357	0.992000	0.81027	-0.039000	0.12124	0.230000	0.21059	-0.136000	0.14681	TGC	.	.		0.557	PCBP3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206808.2		
MICAL3	57553	hgsc.bcm.edu	37	22	18310443	18310443	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr22:18310443T>C	ENST00000441493.2	-	22	3512	c.3160A>G	c.(3160-3162)Atg>Gtg	p.M1054V		NM_015241.2	NP_056056.2	Q7RTP6	MICA3_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 3	1054	Glu-rich.				actin filament depolymerization (GO:0030042)|cytoskeleton organization (GO:0007010)|exocytosis (GO:0006887)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	actin binding (GO:0003779)|FAD binding (GO:0071949)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	4		all_epithelial(15;0.198)		Lung(27;0.0427)		GCCGGCGCCATCCTCTCTTCC	0.647																																					p.M1054V		Atlas-SNP	.											.	MICAL3	53	.	0			c.A3160G						.						20.0	24.0	22.0					22																	18310443		1995	4152	6147	SO:0001583	missense	57553	exon22			GCGCCATCCTCTC	AB037785	CCDS46659.1, CCDS46660.1, CCDS46661.1	22q11.21	2013-03-26	2013-03-26		ENSG00000243156	ENSG00000243156			24694	protein-coding gene	gene with protein product		608882				12110185	Standard	NM_015241		Approved	KIAA0819	uc002zng.4	Q7RTP6	OTTHUMG00000150067	ENST00000441493.2:c.3160A>G	chr22.hg19:g.18310443T>C	ENSP00000416015:p.Met1054Val	86.0	0.0		60.0	5.0	NM_015241	B2RXJ5|E9PEF0|O94909|Q5U4P4|Q6ICK4|Q96DF2|Q9P2I3	Missense_Mutation	SNP	ENST00000441493.2	hg19	CCDS46659.1	.	.	.	.	.	.	.	.	.	.	T	3.985	-0.005707	0.07773	.	.	ENSG00000093100	ENST00000441493	T	0.61980	0.06	4.95	1.63	0.23807	.	.	.	.	.	T	0.50154	0.1599	L	0.42245	1.32	0.09310	N	0.999992	B	0.02656	0.0	B	0.01281	0.0	T	0.34601	-0.9822	9	0.29301	T	0.29	.	8.5145	0.33237	0.0:0.3186:0.0:0.6814	.	1054	Q7RTP6	MICA3_HUMAN	V	1054	ENSP00000416015:M1054V	ENSP00000416015:M1054V	M	-	1	0	XXbac-B461K10.4	16690443	0.004000	0.15560	0.006000	0.13384	0.554000	0.35429	0.207000	0.17395	0.039000	0.15632	0.448000	0.29417	ATG	.	.		0.647	MICAL3-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447351.1		
CLTCL1	8218	hgsc.bcm.edu	37	22	19189001	19189001	+	Nonsense_Mutation	SNP	C	C	A	rs374660081		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr22:19189001C>A	ENST00000263200.10	-	23	3676	c.3604G>T	c.(3604-3606)Gga>Tga	p.G1202*	CLTCL1_ENST00000353891.5_Nonsense_Mutation_p.G1202*|CLTCL1_ENST00000442042.2_5'UTR|CLTCL1_ENST00000427926.1_Intron	NM_007098.3	NP_009029.3	P53675	CLH2_HUMAN	clathrin, heavy chain-like 1	1202	Heavy chain arm.|Proximal segment.				anatomical structure morphogenesis (GO:0009653)|intracellular protein transport (GO:0006886)|mitotic nuclear division (GO:0007067)|positive regulation of glucose import (GO:0046326)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)	clathrin coat of coated pit (GO:0030132)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|coated vesicle (GO:0030135)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|spindle (GO:0005819)|trans-Golgi network (GO:0005802)	signal transducer activity (GO:0004871)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(2)|endometrium(9)|kidney(3)|large_intestine(11)|lung(9)|ovary(5)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49	Colorectal(54;0.0993)					CAGCGGTCTCCAACTACGGAT	0.483			T	?	ALCL																																p.G1202X		Atlas-SNP	.		Dom	yes		22	22q11.21	8218	"""clathrin, heavy polypeptide-like 1"""		L	.	CLTCL1	115	.	0			c.G3604T						.						73.0	77.0	76.0					22																	19189001		1951	4165	6116	SO:0001587	stop_gained	8218	exon23			GGTCTCCAACTAC		CCDS46662.1, CCDS54497.1, CCDS46662.2, CCDS54497.2	22q11.2	2008-06-10	2006-09-29		ENSG00000070371	ENSG00000070371			2093	protein-coding gene	gene with protein product		601273	"""clathrin, heavy polypeptide-like 1"""	CLTCL		8844170, 15133132	Standard	NM_007098		Approved	CLTD, CLH22, CHC22	uc021wle.1	P53675	OTTHUMG00000150109	ENST00000263200.10:c.3604G>T	chr22.hg19:g.19189001C>A	ENSP00000445677:p.Gly1202*	85.0	0.0		102.0	7.0	NM_001835	B7Z7U5|Q14017|Q15808|Q15809	Nonsense_Mutation	SNP	ENST00000263200.10	hg19	CCDS46662.1	.	.	.	.	.	.	.	.	.	.	C	39	7.894032	0.98548	.	.	ENSG00000070371	ENST00000353891;ENST00000263200	.	.	.	3.33	3.33	0.38152	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	14.834	0.70169	0.0:1.0:0.0:0.0	.	.	.	.	X	1202	.	ENSP00000445677:G1202X	G	-	1	0	CLTCL1	17569001	1.000000	0.71417	0.981000	0.43875	0.267000	0.26476	6.846000	0.75399	1.668000	0.50843	0.491000	0.48974	GGA	.	.		0.483	CLTCL1-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316397.5	NM_007098	
ZDHHC8	29801	hgsc.bcm.edu	37	22	20131139	20131139	+	Silent	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr22:20131139T>C	ENST00000334554.7	+	10	2127	c.1986T>C	c.(1984-1986)agT>agC	p.S662S	ZDHHC8_ENST00000405930.3_Silent_p.S662S|ZDHHC8_ENST00000320602.7_Silent_p.S570S	NM_013373.3	NP_037505.1	Q9ULC8	ZDHC8_HUMAN	zinc finger, DHHC-type containing 8	662					locomotory behavior (GO:0007626)|protein palmitoylation (GO:0018345)	cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(3)|endometrium(1)|kidney(3)|large_intestine(1)|lung(8)|ovary(1)|prostate(1)	20	Colorectal(54;0.0993)					GGCCCAGCAGTGGCTCACACA	0.711																																					p.S662S		Atlas-SNP	.											.	ZDHHC8	77	.	0			c.T1986C						.						15.0	17.0	17.0					22																	20131139		2187	4292	6479	SO:0001819	synonymous_variant	29801	exon10			CAGCAGTGGCTCA	AB033118	CCDS13776.1, CCDS54502.1	22q11.21	2009-10-06		2003-02-28	ENSG00000099904	ENSG00000099904		"""Zinc fingers, DHHC-type"""	18474	protein-coding gene	gene with protein product		608784				10574462, 15184899	Standard	NM_013373		Approved	ZNF378, KIAA1292	uc002zrr.2	Q9ULC8	OTTHUMG00000150499	ENST00000334554.7:c.1986T>C	chr22.hg19:g.20131139T>C		13.0	0.0		88.0	4.0	NM_001185024	Q2TGE9|Q6ICL1|Q6ZNF5|Q7Z6L9	Silent	SNP	ENST00000334554.7	hg19	CCDS13776.1																																																																																			.	.		0.711	ZDHHC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318564.1	NM_013373	
NIPSNAP1	8508	hgsc.bcm.edu	37	22	29957568	29957568	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr22:29957568T>C	ENST00000216121.7	-	6	760	c.506A>G	c.(505-507)gAg>gGg	p.E169G		NM_001202502.1|NM_003634.3	NP_001189431.1|NP_003625.2	Q9BPW8	NIPS1_HUMAN	nipsnap homolog 1 (C. elegans)	169					sensory perception of pain (GO:0019233)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|synaptic membrane (GO:0097060)	neurotransmitter binding (GO:0042165)	p.?(1)		large_intestine(2)|lung(2)|skin(1)	5						GAAGCTGAACTCGAGGAGCAG	0.577																																					p.E169G		Atlas-SNP	.											.	NIPSNAP1	17	.	1	Unknown(1)	lung(1)	c.A506G						.						98.0	94.0	96.0					22																	29957568		2203	4300	6503	SO:0001583	missense	8508	exon6			CTGAACTCGAGGA	AJ001258	CCDS13860.1	22q12	2013-09-12	2001-11-28		ENSG00000184117	ENSG00000184117			7827	protein-coding gene	gene with protein product	"""4-nitrophenylphosphatase domain and non-neuronal SNAP25-like 1"""	603249	"""NIPSNAP, C. elegans, homolog 1"""			9661659	Standard	NM_003634		Approved		uc003afx.4	Q9BPW8	OTTHUMG00000151294	ENST00000216121.7:c.506A>G	chr22.hg19:g.29957568T>C	ENSP00000216121:p.Glu169Gly	72.0	0.0		75.0	5.0	NM_003634	B2RAY3|O43800	Missense_Mutation	SNP	ENST00000216121.7	hg19	CCDS13860.1	.	.	.	.	.	.	.	.	.	.	T	23.6	4.430142	0.83776	.	.	ENSG00000184117	ENST00000216121;ENST00000437094	T;T	0.70516	0.92;-0.49	4.83	4.83	0.62350	Dimeric alpha-beta barrel (1);	0.000000	0.85682	D	0.000000	T	0.80358	0.4608	M	0.85542	2.76	0.80722	D	1	P;P	0.47409	0.82;0.895	P;P	0.50860	0.652;0.468	D	0.83783	0.0226	10	0.56958	D	0.05	-23.3612	14.8543	0.70323	0.0:0.0:0.0:1.0	.	149;169	B4DQI7;Q9BPW8	.;NIPS1_HUMAN	G	169;34	ENSP00000216121:E169G;ENSP00000403448:E34G	ENSP00000216121:E169G	E	-	2	0	NIPSNAP1	28287568	1.000000	0.71417	0.992000	0.48379	0.885000	0.51271	7.596000	0.82721	2.165000	0.68154	0.379000	0.24179	GAG	.	.		0.577	NIPSNAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322117.1		
SYN3	8224	hgsc.bcm.edu	37	22	32914045	32914045	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr22:32914045G>A	ENST00000358763.2	-	13	1837	c.1595C>T	c.(1594-1596)cCc>cTc	p.P532L	SYN3_ENST00000332840.5_Missense_Mutation_p.P532L|SYN3_ENST00000467095.1_5'UTR	NM_001135774.1	NP_001129246.1	O14994	SYN3_HUMAN	synapsin III	532	E.				neurotransmitter secretion (GO:0007269)|regulation of synaptic transmission, GABAergic (GO:0032228)	cell junction (GO:0030054)|synaptic vesicle (GO:0008021)|synaptic vesicle membrane (GO:0030672)	ATP binding (GO:0005524)|catalytic activity (GO:0003824)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(15)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	33						ATGCGGATGGGGTGGTGCTGG	0.592																																					p.P532L		Atlas-SNP	.											.	SYN3	77	.	0			c.C1595T						.						71.0	80.0	77.0					22																	32914045		2203	4300	6503	SO:0001583	missense	8224	exon12			GGATGGGGTGGTG	AF046873	CCDS13908.1	22q12.3	2008-05-14			ENSG00000185666	ENSG00000185666			11496	protein-coding gene	gene with protein product		602705				9539796	Standard	NM_003490		Approved		uc003amx.3	O14994	OTTHUMG00000031004	ENST00000358763.2:c.1595C>T	chr22.hg19:g.32914045G>A	ENSP00000351614:p.Pro532Leu	87.0	0.0		90.0	4.0	NM_003490	B1B1F9	Missense_Mutation	SNP	ENST00000358763.2	hg19	CCDS13908.1	.	.	.	.	.	.	.	.	.	.	G	19.53	3.844091	0.71488	.	.	ENSG00000185666	ENST00000358763;ENST00000332840;ENST00000445154	T;T	0.35421	1.31;1.31	5.97	5.97	0.96955	.	0.207650	0.42172	N	0.000756	T	0.57533	0.2060	L	0.55990	1.75	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.66084	0.941;0.941	T	0.55379	-0.8150	10	0.72032	D	0.01	-8.266	20.428	0.99075	0.0:0.0:1.0:0.0	.	531;532	Q17R54;O14994	.;SYN3_HUMAN	L	532;532;138	ENSP00000351614:P532L;ENSP00000330219:P532L	ENSP00000330219:P532L	P	-	2	0	SYN3	31244045	1.000000	0.71417	0.924000	0.36721	0.276000	0.26787	5.335000	0.65929	2.837000	0.97791	0.655000	0.94253	CCC	.	.		0.592	SYN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075892.4		
ST13	6767	hgsc.bcm.edu	37	22	41244327	41244327	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr22:41244327T>C	ENST00000216218.3	-	3	696	c.215A>G	c.(214-216)gAc>gGc	p.D72G		NM_003932.3	NP_003923.2	P50502	F10A1_HUMAN	suppression of tumorigenicity 13 (colon carcinoma) (Hsp70 interacting protein)	72					chaperone cofactor-dependent protein refolding (GO:0070389)|negative regulation of protein refolding (GO:0061084)|protein folding (GO:0006457)|protein homooligomerization (GO:0051260)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	dATP binding (GO:0032564)|protein binding, bridging (GO:0030674)			cervix(1)|large_intestine(1)|lung(3)|skin(1)	6						TGATGGTTCGTCTGCCTTTAA	0.353																																					p.D72G		Atlas-SNP	.											.	ST13	16	.	0			c.A215G						.						102.0	85.0	91.0					22																	41244327		2203	4300	6503	SO:0001583	missense	6767	exon3			GGTTCGTCTGCCT		CCDS14006.1	22q13.2	2013-01-10	2001-11-29		ENSG00000100380	ENSG00000100380		"""Tetratricopeptide (TTC) repeat domain containing"""	11343	protein-coding gene	gene with protein product	"""progesterone receptor-associated p48 protein"""	606796	"""suppression of tumorigenicity 13 (colon carcinoma) (Hsp70-interacting protein)"""			9925927, 8721986	Standard	NM_003932		Approved	SNC6, HSPABP1, HIP, P48, FAM10A1	uc003aze.3	P50502	OTTHUMG00000151201	ENST00000216218.3:c.215A>G	chr22.hg19:g.41244327T>C	ENSP00000216218:p.Asp72Gly	74.0	0.0		76.0	4.0	NM_003932	O14999|Q2TU77	Missense_Mutation	SNP	ENST00000216218.3	hg19	CCDS14006.1	.	.	.	.	.	.	.	.	.	.	T	14.95	2.688006	0.48097	.	.	ENSG00000100380	ENST00000216218;ENST00000542699;ENST00000401032;ENST00000411695	T;T	0.49720	2.07;0.77	5.74	5.74	0.90152	.	0.864536	0.10555	N	0.660944	T	0.53222	0.1783	M	0.76838	2.35	0.28390	N	0.919121	B;B	0.14805	0.011;0.011	B;B	0.17979	0.02;0.011	T	0.50939	-0.8768	10	0.56958	D	0.05	.	12.4232	0.55532	0.0:0.0:0.0:1.0	.	62;72	B4E0U6;P50502	.;F10A1_HUMAN	G	72;72;72;35	ENSP00000216218:D72G;ENSP00000392067:D35G	ENSP00000216218:D72G	D	-	2	0	ST13	39574273	0.987000	0.35691	0.921000	0.36526	0.784000	0.44337	2.496000	0.45346	2.193000	0.70182	0.402000	0.26972	GAC	.	.		0.353	ST13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321759.1	NM_003932	
GTSE1	51512	hgsc.bcm.edu	37	22	46725998	46725998	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr22:46725998A>G	ENST00000454366.1	+	12	2403	c.2191A>G	c.(2191-2193)Aac>Gac	p.N731D		NM_016426.6	NP_057510	Q9NYZ3	GTSE1_HUMAN	G-2 and S-phase expressed 1	712					DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|microtubule-based process (GO:0007017)	cytoplasmic microtubule (GO:0005881)|membrane (GO:0016020)				NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(3)	27		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00462)		TGACAAGGAGAACGTGGATTC	0.532																																					p.N731D	GBM(153;542 1915 12487 29016 50495)	Atlas-SNP	.											.	GTSE1	100	.	0			c.A2191G						.						106.0	83.0	91.0					22																	46725998		2203	4300	6503	SO:0001583	missense	51512	exon12			AAGGAGAACGTGG	AF223408	CCDS14074.2	22q13.2-q13.3	2008-06-10			ENSG00000075218	ENSG00000075218			13698	protein-coding gene	gene with protein product		607477				10974554, 10984615, 12750368	Standard	NM_016426		Approved	GTSE-1, B99	uc011aqy.2	Q9NYZ3	OTTHUMG00000150486	ENST00000454366.1:c.2191A>G	chr22.hg19:g.46725998A>G	ENSP00000415430:p.Asn731Asp	77.0	0.0		90.0	4.0	NM_016426	B0QYM3|Q20WK2|Q53GX5|Q5R3I6|Q6DHX4|Q9BRE0|Q9UGZ9|Q9Y557	Missense_Mutation	SNP	ENST00000454366.1	hg19	CCDS14074.2	.	.	.	.	.	.	.	.	.	.	A	16.79	3.220206	0.58560	.	.	ENSG00000075218	ENST00000454366;ENST00000361934	T	0.20069	2.1	5.39	5.39	0.77823	.	0.048570	0.85682	D	0.000000	T	0.47303	0.1438	M	0.79475	2.455	0.51482	D	0.999925	D	0.89917	1.0	D	0.70935	0.971	T	0.51756	-0.8665	10	0.87932	D	0	-39.8752	14.3849	0.66938	1.0:0.0:0.0:0.0	.	712	Q9NYZ3	GTSE1_HUMAN	D	731;691	ENSP00000415430:N731D	ENSP00000354634:N691D	N	+	1	0	GTSE1	45104662	1.000000	0.71417	0.863000	0.33907	0.151000	0.21798	5.620000	0.67736	2.027000	0.59764	0.374000	0.22700	AAC	.	.		0.532	GTSE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318360.2	NM_016426	
CELSR1	9620	hgsc.bcm.edu	37	22	46776815	46776815	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr22:46776815T>C	ENST00000262738.3	-	22	7125	c.7126A>G	c.(7126-7128)Agc>Ggc	p.S2376G		NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	2376					anterior/posterior pattern specification (GO:0009952)|apical protein localization (GO:0045176)|central nervous system development (GO:0007417)|establishment of body hair planar orientation (GO:0048105)|establishment of planar polarity (GO:0001736)|establishment of planar polarity of embryonic epithelium (GO:0042249)|G-protein coupled receptor signaling pathway (GO:0007186)|hair follicle development (GO:0001942)|homophilic cell adhesion (GO:0007156)|inner ear morphogenesis (GO:0042472)|lateral sprouting involved in lung morphogenesis (GO:0060490)|locomotory behavior (GO:0007626)|neural tube closure (GO:0001843)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|orthogonal dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060488)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|planar dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060489)|protein localization involved in establishment of planar polarity (GO:0090251)|regulation of actin cytoskeleton organization (GO:0032956)|Rho protein signal transduction (GO:0007266)|wound healing (GO:0042060)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)|protein dimerization activity (GO:0046983)|transmembrane signaling receptor activity (GO:0004888)	p.S2376C(1)		breast(8)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(13)|lung(27)|ovary(2)|pancreas(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(3)	95		Ovarian(80;0.00142)|Breast(42;0.00296)|all_neural(38;0.0416)|Colorectal(5;0.0766)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00643)|BRCA - Breast invasive adenocarcinoma(115;0.171)		ACCAGCGTGCTCACCATCGGG	0.617																																					p.S2376G		Atlas-SNP	.											CELSR1,NS,carcinoma,0,1	CELSR1	242	.	1	Substitution - Missense(1)	breast(1)	c.A7126G						.						39.0	40.0	40.0					22																	46776815		2203	4300	6503	SO:0001583	missense	9620	exon22			GCGTGCTCACCAT	AF231024	CCDS14076.1	22q13.31	2014-08-08	2013-02-18		ENSG00000075275	ENSG00000075275		"""Cadherins / Major cadherins"", ""-"", ""GPCR / Class B : Orphans"""	1850	protein-coding gene	gene with protein product	"""flamingo homolog 2 (Drosophila)"""	604523	"""cadherin, EGF LAG seven-pass G-type receptor 1, flamingo (Drosophila) homolog"""			9339365	Standard	XM_006724383		Approved	ME2, HFMI2, FMI2, CDHF9	uc003bhw.1	Q9NYQ6	OTTHUMG00000150423	ENST00000262738.3:c.7126A>G	chr22.hg19:g.46776815T>C	ENSP00000262738:p.Ser2376Gly	70.0	1.0		72.0	3.0	NM_014246	O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Missense_Mutation	SNP	ENST00000262738.3	hg19	CCDS14076.1	.	.	.	.	.	.	.	.	.	.	T	19.42	3.824348	0.71143	.	.	ENSG00000075275	ENST00000262738	T	0.11712	2.75	4.28	4.28	0.50868	Domain of unknown function DUF3497 (1);	0.122517	0.52532	U	0.000077	T	0.31857	0.0810	M	0.81497	2.545	0.80722	D	1	D;D	0.65815	0.995;0.971	D;P	0.63957	0.92;0.868	T	0.14448	-1.0472	10	0.87932	D	0	.	13.091	0.59167	0.0:0.0:0.0:1.0	.	697;2376	B7Z7U7;Q9NYQ6	.;CELR1_HUMAN	G	2376	ENSP00000262738:S2376G	ENSP00000262738:S2376G	S	-	1	0	CELSR1	45155479	1.000000	0.71417	0.950000	0.38849	0.335000	0.28730	7.363000	0.79516	1.592000	0.50018	0.260000	0.18958	AGC	.	.		0.617	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318037.1	NM_014246	
TLR8	51311	hgsc.bcm.edu	37	X	12938331	12938331	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:12938331T>C	ENST00000218032.6	+	2	1259	c.1172T>C	c.(1171-1173)aTg>aCg	p.M391T	TLR8_ENST00000311912.5_Missense_Mutation_p.M409T	NM_138636.4	NP_619542.1	Q9NR97	TLR8_HUMAN	toll-like receptor 8	391					cellular response to mechanical stimulus (GO:0071260)|defense response to virus (GO:0051607)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|immunoglobulin mediated immune response (GO:0016064)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of innate immune response (GO:0045089)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|regulation of cytokine secretion (GO:0050707)|response to virus (GO:0009615)|toll-like receptor 8 signaling pathway (GO:0034158)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	endolysosome membrane (GO:0036020)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|drug binding (GO:0008144)|receptor activity (GO:0004872)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)			breast(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(21)|ovary(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	50					Imiquimod(DB00724)	CAGCCCCTGATGCAGCTTCCA	0.348																																					p.M391T		Atlas-SNP	.											.	TLR8	134	.	0			c.T1172C						.						77.0	80.0	79.0					X																	12938331		2200	4299	6499	SO:0001583	missense	51311	exon2			CCCTGATGCAGCT	AF246971	CCDS14152.1, CCDS14153.1	Xp22	2009-11-23			ENSG00000101916	ENSG00000101916		"""CD molecules"""	15632	protein-coding gene	gene with protein product		300366				11022119	Standard	NM_138636		Approved	CD288	uc004cve.3	Q9NR97	OTTHUMG00000021145	ENST00000218032.6:c.1172T>C	chrX.hg19:g.12938331T>C	ENSP00000218032:p.Met391Thr	42.0	0.0		79.0	4.0	NM_138636	B3Y654|D1CS70|D1CS76|Q495P4|Q6UXL6|Q9NYG9	Missense_Mutation	SNP	ENST00000218032.6	hg19	CCDS14152.1	.	.	.	.	.	.	.	.	.	.	T	0.010	-1.752097	0.00663	.	.	ENSG00000101916	ENST00000218032;ENST00000311912	T;T	0.00892	5.57;5.57	5.57	-1.24	0.09435	.	0.820841	0.10242	N	0.698262	T	0.00608	0.0020	N	0.16166	0.38	0.09310	N	1	B;B	0.10296	0.003;0.003	B;B	0.06405	0.002;0.002	T	0.45411	-0.9263	10	0.22706	T	0.39	.	3.8548	0.08971	0.1213:0.0747:0.3998:0.4042	.	391;409	Q9NR97;D1CS70	TLR8_HUMAN;.	T	391;409	ENSP00000218032:M391T;ENSP00000312082:M409T	ENSP00000218032:M391T	M	+	2	0	TLR8	12848252	0.000000	0.05858	0.000000	0.03702	0.055000	0.15305	-0.193000	0.09573	-0.242000	0.09667	0.486000	0.48141	ATG	.	.		0.348	TLR8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055784.2	NM_016610	
FANCB	2187	hgsc.bcm.edu	37	X	14863048	14863048	+	Silent	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:14863048T>C	ENST00000324138.3	-	7	2010	c.1857A>G	c.(1855-1857)agA>agG	p.R619R	FANCB_ENST00000398334.1_Silent_p.R619R	NM_152633.2	NP_689846.1	Q8NB91	FANCB_HUMAN	Fanconi anemia, complementation group B	619					DNA repair (GO:0006281)	Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)				NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(9)|skin(1)|upper_aerodigestive_tract(1)	24	Hepatocellular(33;0.183)					TTAAAAAAACTCTGCCACACA	0.338								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.R619R		Atlas-SNP	.											.	FANCB	78	.	0			c.A1857G						.						138.0	142.0	141.0					X																	14863048		2203	4300	6503	SO:0001819	synonymous_variant	2187	exon7	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	AAAAACTCTGCCA	AK091383	CCDS14161.1	Xp22.2	2014-09-17			ENSG00000181544	ENSG00000181544		"""Fanconi anemia, complementation groups"""	3583	protein-coding gene	gene with protein product		300515				9382107, 15502827	Standard	NM_152633		Approved	FAB, FLJ34064, FAAP95	uc004cwh.1	Q8NB91	OTTHUMG00000021168	ENST00000324138.3:c.1857A>G	chrX.hg19:g.14863048T>C		60.0	0.0		88.0	4.0	NM_152633	B2RMZ4|Q7Z2U2|Q86XG1	Silent	SNP	ENST00000324138.3	hg19	CCDS14161.1																																																																																			.	.		0.338	FANCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055835.1	NM_152633	
PHKA2	5256	hgsc.bcm.edu	37	X	18949832	18949832	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:18949832T>C	ENST00000379942.4	-	12	1837	c.1172A>G	c.(1171-1173)gAc>gGc	p.D391G		NM_000292.2	NP_000283.1	P46019	KPB2_HUMAN	phosphorylase kinase, alpha 2 (liver)	391					carbohydrate metabolic process (GO:0005975)|cellular protein modification process (GO:0006464)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphorylase kinase complex (GO:0005964)|plasma membrane (GO:0005886)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|phosphorylase kinase activity (GO:0004689)			NS(1)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(12)|lung(23)|ovary(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	61	Hepatocellular(33;0.183)					AGGAACTCGGTCTACTGTGTG	0.498											OREG0019698	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D391G		Atlas-SNP	.											.	PHKA2	122	.	0			c.A1172G						.						239.0	191.0	207.0					X																	18949832		2203	4300	6503	SO:0001583	missense	5256	exon12			ACTCGGTCTACTG		CCDS14190.1	Xp22.2-p22.1	2009-07-10			ENSG00000044446	ENSG00000044446	2.7.11.19		8926	protein-coding gene	gene with protein product		300798		PHK, PYK		2387090	Standard	NM_000292		Approved		uc004cyv.4	P46019	OTTHUMG00000021222	ENST00000379942.4:c.1172A>G	chrX.hg19:g.18949832T>C	ENSP00000369274:p.Asp391Gly	89.0	0.0	729	88.0	4.0	NM_000292	A8K1T1|Q6LAJ5|Q7Z6W0|Q96CR3|Q9UDA1	Missense_Mutation	SNP	ENST00000379942.4	hg19	CCDS14190.1	.	.	.	.	.	.	.	.	.	.	t	23.4	4.413831	0.83449	.	.	ENSG00000044446	ENST00000379942	D	0.91237	-2.81	5.28	5.28	0.74379	Six-hairpin glycosidase-like (1);Glycoside hydrolase 15-related (1);	0.088152	0.85682	D	0.000000	D	0.89567	0.6752	L	0.61036	1.89	0.80722	D	1	B	0.24721	0.11	B	0.29077	0.098	D	0.87324	0.2320	10	0.48119	T	0.1	-24.7587	14.4937	0.67670	0.0:0.0:0.0:1.0	.	391	P46019	KPB2_HUMAN	G	391	ENSP00000369274:D391G	ENSP00000369274:D391G	D	-	2	0	PHKA2	18859753	1.000000	0.71417	1.000000	0.80357	0.805000	0.45488	7.991000	0.88244	1.870000	0.54199	0.478000	0.44815	GAC	.	.		0.498	PHKA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055960.1	NM_000292	
DDX53	168400	hgsc.bcm.edu	37	X	23018954	23018954	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:23018954A>G	ENST00000327968.5	+	1	868	c.780A>G	c.(778-780)atA>atG	p.I260M	RP11-40F8.2_ENST00000455399.1_lincRNA	NM_182699.3	NP_874358.2	Q86TM3	DDX53_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 53	260	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.					nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|RNA binding (GO:0003723)			breast(2)|endometrium(5)|kidney(4)|large_intestine(3)|lung(15)|ovary(1)|prostate(1)|skin(2)|urinary_tract(2)	35						TACAAGGAATAGATCTTATAG	0.393																																					p.I260M		Atlas-SNP	.											.	DDX53	76	.	0			c.A780G						.						72.0	69.0	70.0					X																	23018954		2203	4300	6503	SO:0001583	missense	168400	exon1			AGGAATAGATCTT	AY039237	CCDS35214.1	Xp22.13	2009-03-25			ENSG00000184735	ENSG00000184735		"""DEAD-boxes"""	20083	protein-coding gene	gene with protein product	"""cancer associated gene"", ""cancer/testis antigen 26"""						Standard	NM_182699		Approved	CAGE, CT26	uc004daj.3	Q86TM3	OTTHUMG00000021248	ENST00000327968.5:c.780A>G	chrX.hg19:g.23018954A>G	ENSP00000368667:p.Ile260Met	58.0	0.0		100.0	4.0	NM_182699	Q0D2N2|Q6NVV4	Missense_Mutation	SNP	ENST00000327968.5	hg19	CCDS35214.1	.	.	.	.	.	.	.	.	.	.	A	7.824	0.718360	0.15372	.	.	ENSG00000184735	ENST00000327968	T	0.14640	2.49	4.07	-1.57	0.08506	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.552762	0.18269	N	0.146369	T	0.05593	0.0147	N	0.05124	-0.11	0.30013	N	0.815048	B	0.31769	0.339	B	0.37267	0.245	T	0.23619	-1.0183	10	0.42905	T	0.14	1.9321	2.9999	0.06010	0.3189:0.0:0.2216:0.4595	.	260	Q86TM3	DDX53_HUMAN	M	260	ENSP00000368667:I260M	ENSP00000368667:I260M	I	+	3	3	DDX53	22928875	0.997000	0.39634	0.915000	0.36163	0.417000	0.31264	0.348000	0.20031	-0.148000	0.11234	0.486000	0.48141	ATA	.	.		0.393	DDX53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056043.1	NM_182699	
PTCHD1	139411	hgsc.bcm.edu	37	X	23411607	23411607	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:23411607A>G	ENST00000379361.4	+	3	2832	c.1972A>G	c.(1972-1974)Aga>Gga	p.R658G		NM_173495.2	NP_775766.2	Q96NR3	PTHD1_HUMAN	patched domain containing 1	658					cognition (GO:0050890)|smoothened signaling pathway (GO:0007224)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hedgehog receptor activity (GO:0008158)			NS(1)|breast(4)|endometrium(3)|kidney(3)|large_intestine(9)|lung(14)|ovary(4)|skin(2)|urinary_tract(2)	42						GGAAACAAACAGAGAAGAACT	0.423																																					p.R658G		Atlas-SNP	.											.	PTCHD1	213	.	0			c.A1972G						.						70.0	66.0	67.0					X																	23411607		2203	4300	6503	SO:0001583	missense	139411	exon3			ACAAACAGAGAAG	AK054858	CCDS35215.2	Xp22.13	2008-02-05			ENSG00000165186	ENSG00000165186			26392	protein-coding gene	gene with protein product		300828					Standard	NM_173495		Approved	FLJ30296	uc004dal.4	Q96NR3	OTTHUMG00000021251	ENST00000379361.4:c.1972A>G	chrX.hg19:g.23411607A>G	ENSP00000368666:p.Arg658Gly	54.0	0.0		86.0	4.0	NM_173495	B4DQH0|Q0IJ60|Q6P6B8	Missense_Mutation	SNP	ENST00000379361.4	hg19	CCDS35215.2	.	.	.	.	.	.	.	.	.	.	A	14.76	2.632079	0.46944	.	.	ENSG00000165186	ENST00000379361	D	0.85339	-1.97	5.48	4.24	0.50183	.	0.051778	0.85682	D	0.000000	T	0.79155	0.4398	L	0.46157	1.445	0.38785	D	0.954854	B	0.22346	0.068	B	0.24006	0.05	T	0.75007	-0.3469	10	0.23302	T	0.38	-9.8247	10.9957	0.47573	0.6293:0.3707:0.0:0.0	.	658	Q96NR3	PTHD1_HUMAN	G	658	ENSP00000368666:R658G	ENSP00000368666:R658G	R	+	1	2	PTCHD1	23321528	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	4.306000	0.59117	1.816000	0.52996	0.486000	0.48141	AGA	.	.		0.423	PTCHD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056047.2	NM_173495	
SYTL5	94122	hgsc.bcm.edu	37	X	37981401	37981401	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:37981401T>C	ENST00000357972.5	+	15	2320	c.1774T>C	c.(1774-1776)Ttc>Ctc	p.F592L	SYTL5_ENST00000297875.2_Missense_Mutation_p.F592L|TM4SF2_ENST00000465127.1_Intron|SYTL5_ENST00000456733.2_Missense_Mutation_p.F614L			Q8TDW5	SYTL5_HUMAN	synaptotagmin-like 5	592	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)	membrane (GO:0016020)	metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(9)|lung(23)|prostate(1)|skin(2)|urinary_tract(1)	44						ACTAGAAGTGTTCATCAAAGA	0.408																																					p.F614L		Atlas-SNP	.											.	SYTL5	72	.	0			c.T1840C						.						111.0	96.0	101.0					X																	37981401		2202	4300	6502	SO:0001583	missense	94122	exon15			GAAGTGTTCATCA		CCDS14244.1, CCDS55399.1	Xp21.1	2008-02-05			ENSG00000147041	ENSG00000147041			15589	protein-coding gene	gene with protein product	"""exophilin 9"""						Standard	NM_138780		Approved		uc004ddx.3	Q8TDW5	OTTHUMG00000033176	ENST00000357972.5:c.1774T>C	chrX.hg19:g.37981401T>C	ENSP00000350657:p.Phe592Leu	80.0	0.0		97.0	4.0	NM_001163334	A2RRF2	Missense_Mutation	SNP	ENST00000357972.5	hg19	CCDS14244.1	.	.	.	.	.	.	.	.	.	.	T	3.540	-0.093825	0.07053	.	.	ENSG00000147041	ENST00000297875;ENST00000357972;ENST00000456733	T;T;T	0.68624	-0.34;-0.34;-0.34	5.44	0.0938	0.14478	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.307265	0.36703	N	0.002455	T	0.28200	0.0696	N	0.01761	-0.735	0.20489	N	0.999893	B;B	0.02656	0.0;0.0	B;B	0.09377	0.004;0.001	T	0.22034	-1.0228	10	0.07990	T	0.79	-13.4634	4.011	0.09623	0.1189:0.4331:0.1206:0.3274	.	614;592	A2RRF2;Q8TDW5	.;SYTL5_HUMAN	L	592;592;614	ENSP00000297875:F592L;ENSP00000350657:F592L;ENSP00000395220:F614L	ENSP00000297875:F592L	F	+	1	0	SYTL5	37866345	0.117000	0.22190	0.773000	0.31616	0.992000	0.81027	0.239000	0.18023	-0.353000	0.08224	0.486000	0.48141	TTC	.	.		0.408	SYTL5-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080883.1	NM_138780	
RBM3	5935	hgsc.bcm.edu	37	X	48434040	48434040	+	Silent	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:48434040A>G	ENST00000376759.3	+	3	258	c.195A>G	c.(193-195)agA>agG	p.R65R	RBM3_ENST00000466764.1_3'UTR|RBM3_ENST00000376755.1_Silent_p.R65R|RBM3_ENST00000430348.2_5'UTR|AC115618.1_ENST00000376775.2_5'Flank|RBM3_ENST00000354480.2_5'Flank	NM_006743.4	NP_006734.1	P98179	RBM3_HUMAN	RNA binding motif (RNP1, RRM) protein 3	65	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				positive regulation of translation (GO:0045727)|production of miRNAs involved in gene silencing by miRNA (GO:0035196)|regulation of translation (GO:0006417)|response to cold (GO:0009409)|RNA processing (GO:0006396)|translation (GO:0006412)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|ribosomal large subunit binding (GO:0043023)|RNA binding (GO:0003723)			endometrium(1)|large_intestine(1)|lung(1)|ovary(1)	4						TTGCCATGAGAGCCATGAACG	0.552																																					p.R65R		Atlas-SNP	.											.	RBM3	20	.	0			c.A195G						.						65.0	55.0	59.0					X																	48434040		2203	4300	6503	SO:0001819	synonymous_variant	5935	exon3			CATGAGAGCCATG	BC006825	CCDS14301.1	Xp11.2	2014-05-19	2004-04-23		ENSG00000102317	ENSG00000102317		"""RNA binding motif (RRM) containing"""	9900	protein-coding gene	gene with protein product		300027	"""RNA binding motif protein 3"""			8634703	Standard	NM_006743		Approved	IS1-RNPL	uc004dkf.2	P98179	OTTHUMG00000024121	ENST00000376759.3:c.195A>G	chrX.hg19:g.48434040A>G		92.0	0.0		99.0	4.0	NM_006743		Silent	SNP	ENST00000376759.3	hg19	CCDS14301.1																																																																																			.	.		0.552	RBM3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060755.1	NM_006743	
SHROOM4	57477	hgsc.bcm.edu	37	X	50351077	50351077	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:50351077T>C	ENST00000289292.7	-	6	3348	c.3065A>G	c.(3064-3066)gAc>gGc	p.D1022G	SHROOM4_ENST00000376020.2_Missense_Mutation_p.D1022G|SHROOM4_ENST00000460112.3_Missense_Mutation_p.D906G			Q9ULL8	SHRM4_HUMAN	shroom family member 4	1022					actin cytoskeleton organization (GO:0030036)|actin filament organization (GO:0007015)|brain development (GO:0007420)|cognition (GO:0050890)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|myosin II complex (GO:0016460)|stress fiber (GO:0001725)	actin filament binding (GO:0051015)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(5)|large_intestine(6)|liver(1)|lung(20)|ovary(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	52	Ovarian(276;0.236)					TCCAAGGAGGTCAAGAGAAGA	0.502																																					p.D1022G		Atlas-SNP	.											.	SHROOM4	171	.	0			c.A3065G						.						55.0	50.0	51.0					X																	50351077		2203	4300	6503	SO:0001583	missense	57477	exon6			AGGAGGTCAAGAG	AB033028	CCDS35277.1	Xp11.22	2008-02-05			ENSG00000158352	ENSG00000158352			29215	protein-coding gene	gene with protein product		300579				10574462, 16615870	Standard	NR_027121		Approved	KIAA1202	uc004dpe.2	Q9ULL8	OTTHUMG00000021521	ENST00000289292.7:c.3065A>G	chrX.hg19:g.50351077T>C	ENSP00000289292:p.Asp1022Gly	119.0	0.0		186.0	9.0	NM_020717	A7E2X9|D6RFW0|Q96LA0	Missense_Mutation	SNP	ENST00000289292.7	hg19	CCDS35277.1	.	.	.	.	.	.	.	.	.	.	T	15.37	2.812003	0.50527	.	.	ENSG00000158352	ENST00000289292;ENST00000376020;ENST00000460112	T;T;T	0.18810	2.61;2.61;2.19	5.78	5.78	0.91487	.	0.213352	0.40640	N	0.001058	T	0.35068	0.0919	L	0.34521	1.04	0.45580	D	0.998525	D	0.89917	1.0	D	0.80764	0.994	T	0.11767	-1.0574	10	0.87932	D	0	.	12.8679	0.57949	0.0:0.0:0.0:1.0	.	1022	Q9ULL8	SHRM4_HUMAN	G	1022;1022;906	ENSP00000289292:D1022G;ENSP00000365188:D1022G;ENSP00000421450:D906G	ENSP00000289292:D1022G	D	-	2	0	SHROOM4	50367817	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.453000	0.52978	1.946000	0.56461	0.486000	0.48141	GAC	.	.		0.502	SHROOM4-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056564.4	NM_020717	
CENPI	2491	hgsc.bcm.edu	37	X	100357276	100357276	+	Silent	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:100357276T>C	ENST00000372927.1	+	3	517	c.240T>C	c.(238-240)gcT>gcC	p.A80A	CENPI_ENST00000372926.1_Silent_p.A80A|CENPI_ENST00000218507.5_Silent_p.A80A|CENPI_ENST00000423383.1_Silent_p.A80A	NM_006733.2	NP_006724.2	Q92674	CENPI_HUMAN	centromere protein I	80					CENP-A containing nucleosome assembly (GO:0034080)|mitotic cell cycle (GO:0000278)|nucleosome assembly (GO:0006334)|sex differentiation (GO:0007548)	cytosol (GO:0005829)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)				breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(19)|prostate(1)|skin(2)	30						CCATTAAAGCTTCACAGAATA	0.303																																					p.A80A		Atlas-SNP	.											.	CENPI	70	.	0			c.T240C						.						86.0	90.0	89.0					X																	100357276		2203	4299	6502	SO:0001819	synonymous_variant	2491	exon3			TAAAGCTTCACAG	X97249	CCDS14479.1	Xq22.1	2013-11-05	2006-06-15	2006-06-15	ENSG00000102384	ENSG00000102384			3968	protein-coding gene	gene with protein product		300065	"""FSH primary response (LRPR1, rat) homolog 1"", ""FSH primary response (LRPR1 homolog, rat) 1"""	FSHPRH1		16622420	Standard	NM_006733		Approved	LRPR1, CENP-I, Mis6	uc004egx.3	Q92674	OTTHUMG00000022018	ENST00000372927.1:c.240T>C	chrX.hg19:g.100357276T>C		73.0	0.0		84.0	4.0	NM_006733	Q5JWZ9|Q96ED0	Silent	SNP	ENST00000372927.1	hg19	CCDS14479.1																																																																																			.	.		0.303	CENPI-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057519.1	NM_006733	
TCEAL6	158931	hgsc.bcm.edu	37	X	101395773	101395773	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:101395773G>T	ENST00000372774.3	-	3	780	c.531C>A	c.(529-531)gaC>gaA	p.D177E	TCEAL6_ENST00000372773.1_Missense_Mutation_p.D177E	NM_001006938.2	NP_001006939.2	Q6IPX3	TCAL6_HUMAN	transcription elongation factor A (SII)-like 6	0					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	14						ACACCCCGTTGTCCCCTTGGG	0.502																																					p.D177E		Atlas-SNP	.											.	TCEAL6	27	.	0			c.C531A						.						22.0	21.0	21.0					X																	101395773		2197	4275	6472	SO:0001583	missense	158931	exon3			CCCGTTGTCCCCT	BC071675	CCDS43978.1	Xq22.1	2014-03-21			ENSG00000204071	ENSG00000204071			24553	protein-coding gene	gene with protein product						16221301	Standard	NM_001006938		Approved	WEX2	uc004eiq.3	Q6IPX3	OTTHUMG00000022050	ENST00000372774.3:c.531C>A	chrX.hg19:g.101395773G>T	ENSP00000361860:p.Asp177Glu	68.0	0.0		141.0	10.0	NM_001006938	Q5H9J8	Missense_Mutation	SNP	ENST00000372774.3	hg19	CCDS43978.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	0.032|0.032	-1.327438|-1.327438	0.01309|0.01309	.|.	.|.	ENSG00000204071|ENSG00000204071	ENST00000372774;ENST00000372773|ENST00000536102	T;T|.	0.21191|.	2.02;2.02|.	2.82|2.82	2.82|2.82	0.32997|0.32997	.|.	0.272209|.	0.20313|.	N|.	0.094788|.	T|T	0.20455|0.20455	0.0492|0.0492	N|N	0.24115|0.24115	0.695|0.695	0.09310|0.09310	N|N	1|1	B|.	0.16396|.	0.017|.	B|.	0.13407|.	0.009|.	T|T	0.20638|0.20638	-1.0269|-1.0269	10|6	0.22706|0.06236	T|T	0.39|0.91	.|.	8.3639|8.3639	0.32374|0.32374	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	177|.	Q6IPX3-2|.	.|.	E|K	177|177	ENSP00000361860:D177E;ENSP00000361859:D177E|.	ENSP00000361859:D177E|ENSP00000437364:Q177K	D|Q	-|-	3|1	2|0	TCEAL6|TCEAL6	101282429|101282429	0.014000|0.014000	0.17966|0.17966	0.012000|0.012000	0.15200|0.15200	0.864000|0.864000	0.49448|0.49448	2.835000|2.835000	0.48175|0.48175	1.692000|1.692000	0.51112|0.51112	0.468000|0.468000	0.43344|0.43344	GAC|CAA	.	.		0.502	TCEAL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057609.1	NM_001006938	
TCEAL6	158931	hgsc.bcm.edu	37	X	101395778	101395778	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:101395778C>T	ENST00000372774.3	-	3	775	c.526G>A	c.(526-528)Ggg>Agg	p.G176R	TCEAL6_ENST00000372773.1_Missense_Mutation_p.G176R	NM_001006938.2	NP_001006939.2	Q6IPX3	TCAL6_HUMAN	transcription elongation factor A (SII)-like 6	0					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	14						CCGTTGTCCCCTTGGGCGAAT	0.502																																					p.G176R		Atlas-SNP	.											.	TCEAL6	27	.	0			c.G526A						.						13.0	13.0	13.0					X																	101395778		2197	4251	6448	SO:0001583	missense	158931	exon3			TGTCCCCTTGGGC	BC071675	CCDS43978.1	Xq22.1	2014-03-21			ENSG00000204071	ENSG00000204071			24553	protein-coding gene	gene with protein product						16221301	Standard	NM_001006938		Approved	WEX2	uc004eiq.3	Q6IPX3	OTTHUMG00000022050	ENST00000372774.3:c.526G>A	chrX.hg19:g.101395778C>T	ENSP00000361860:p.Gly176Arg	65.0	0.0		138.0	18.0	NM_001006938	Q5H9J8	Missense_Mutation	SNP	ENST00000372774.3	hg19	CCDS43978.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	9.605|9.605	1.129729|1.129729	0.21041|0.21041	.|.	.|.	ENSG00000204071|ENSG00000204071	ENST00000372774;ENST00000372773|ENST00000536102	T;T|.	0.40225|.	1.04;1.04|.	2.82|2.82	2.82|2.82	0.32997|0.32997	.|.	0.000000|.	0.39341|.	N|.	0.001392|.	T|T	0.27832|0.27832	0.0685|0.0685	L|L	0.32530|0.32530	0.975|0.975	0.09310|0.09310	N|N	1|1	D|.	0.57257|.	0.979|.	P|.	0.56563|.	0.801|.	T|T	0.22243|0.22243	-1.0222|-1.0222	10|6	0.54805|0.06365	T|T	0.06|0.9	.|.	8.3639|8.3639	0.32374|0.32374	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	176|.	Q6IPX3-2|.	.|.	R|K	176|175	ENSP00000361860:G176R;ENSP00000361859:G176R|.	ENSP00000361859:G176R|ENSP00000437364:R175K	G|R	-|-	1|2	0|0	TCEAL6|TCEAL6	101282434|101282434	0.007000|0.007000	0.16637|0.16637	0.089000|0.089000	0.20774|0.20774	0.743000|0.743000	0.42351|0.42351	1.059000|1.059000	0.30517|0.30517	1.692000|1.692000	0.51112|0.51112	0.468000|0.468000	0.43344|0.43344	GGG|AGG	.	.		0.502	TCEAL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057609.1	NM_001006938	
GRIA3	2892	hgsc.bcm.edu	37	X	122336600	122336600	+	Intron	SNP	T	T	G	rs11452643		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:122336600T>G	ENST00000371251.1	+	2	320				GRIA3_ENST00000479118.1_Intron|GRIA3_ENST00000371264.3_Silent_p.G127G|GRIA3_ENST00000541091.1_Intron|GRIA3_ENST00000371266.1_Silent_p.G127G|GRIA3_ENST00000371256.5_Intron|GRIA3_ENST00000542149.1_Intron|GRIA3_ENST00000264357.5_Intron			P42263	GRIA3_HUMAN	glutamate receptor, ionotropic, AMPA 3						glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)			breast(2)|central_nervous_system(1)|endometrium(8)|kidney(3)|large_intestine(8)|lung(25)|ovary(3)|pancreas(2)|skin(2)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)	57					Lithium(DB01356)	GTTCACCAGGTGGGCCCGCCA	0.512																																					p.G127G		Atlas-SNP	.											.	GRIA3	386	.	0			c.T381G						.																																			SO:0001627	intron_variant	2892	exon3			ACCAGGTGGGCCC	U10301	CCDS14604.1, CCDS14605.1, CCDS76017.1	Xq25	2012-08-29	2012-02-03		ENSG00000125675	ENSG00000125675		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4573	protein-coding gene	gene with protein product		305915	"""glutamate receptor, ionotrophic, AMPA 3"""	GLUR3		1319477, 10644433	Standard	NM_007325		Approved	GluA3, GLURC, MRX94	uc004etr.4	P42263	OTTHUMG00000022685	ENST00000371251.1:c.268+16758T>G	chrX.hg19:g.122336600T>G		58.0	0.0		64.0	5.0	NM_001256743	D3DTF1|Q4VXD5|Q4VXD6|Q9HDA0|Q9HDA1|Q9HDA2|Q9P0H1	Silent	SNP	ENST00000371251.1	hg19	CCDS14604.1																																																																																			.	.		0.512	GRIA3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058854.1	NM_000828	
GRIA3	2892	hgsc.bcm.edu	37	X	122336608	122336608	+	Intron	SNP	C	C	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:122336608C>G	ENST00000371251.1	+	2	320				GRIA3_ENST00000479118.1_Intron|GRIA3_ENST00000371264.3_Missense_Mutation_p.A130G|GRIA3_ENST00000541091.1_Intron|GRIA3_ENST00000371266.1_Missense_Mutation_p.A130G|GRIA3_ENST00000371256.5_Intron|GRIA3_ENST00000542149.1_Intron|GRIA3_ENST00000264357.5_Intron			P42263	GRIA3_HUMAN	glutamate receptor, ionotropic, AMPA 3						glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)			breast(2)|central_nervous_system(1)|endometrium(8)|kidney(3)|large_intestine(8)|lung(25)|ovary(3)|pancreas(2)|skin(2)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)	57					Lithium(DB01356)	GGTGGGCCCGCCAAAACTGGG	0.502																																					p.A130G		Atlas-SNP	.											.	GRIA3	386	.	0			c.C389G						.																																			SO:0001627	intron_variant	2892	exon3			GGCCCGCCAAAAC	U10301	CCDS14604.1, CCDS14605.1, CCDS76017.1	Xq25	2012-08-29	2012-02-03		ENSG00000125675	ENSG00000125675		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4573	protein-coding gene	gene with protein product		305915	"""glutamate receptor, ionotrophic, AMPA 3"""	GLUR3		1319477, 10644433	Standard	NM_007325		Approved	GluA3, GLURC, MRX94	uc004etr.4	P42263	OTTHUMG00000022685	ENST00000371251.1:c.268+16766C>G	chrX.hg19:g.122336608C>G		52.0	0.0		52.0	5.0	NM_001256743	D3DTF1|Q4VXD5|Q4VXD6|Q9HDA0|Q9HDA1|Q9HDA2|Q9P0H1	Missense_Mutation	SNP	ENST00000371251.1	hg19	CCDS14604.1	.	.	.	.	.	.	.	.	.	.	C	14.15	2.450610	0.43531	.	.	ENSG00000125675	ENST00000371266;ENST00000371264	.	.	.	4.06	1.29	0.21616	.	.	.	.	.	T	0.28134	0.0694	.	.	.	0.09310	N	1	B	0.06786	0.001	B	0.09377	0.004	T	0.28138	-1.0053	7	0.87932	D	0	.	3.503	0.07680	0.0:0.5445:0.2109:0.2445	.	130	Q4TT43	.	G	130	.	ENSP00000360311:A130G	A	+	2	0	GRIA3	122164289	0.000000	0.05858	0.000000	0.03702	0.033000	0.12548	-0.326000	0.07965	0.146000	0.19002	0.538000	0.68166	GCC	.	.		0.502	GRIA3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058854.1	NM_000828	
STAG2	10735	hgsc.bcm.edu	37	X	123217394	123217394	+	Silent	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:123217394A>G	ENST00000371160.1	+	29	3338	c.3048A>G	c.(3046-3048)agA>agG	p.R1016R	STAG2_ENST00000218089.9_Silent_p.R1016R|STAG2_ENST00000371157.3_Silent_p.R1016R|STAG2_ENST00000469481.1_Intron|STAG2_ENST00000371144.3_Silent_p.R1016R|STAG2_ENST00000371145.3_Silent_p.R1016R|STAG2_ENST00000354548.5_Silent_p.R947R	NM_001282418.1	NP_001269347.1	Q8N3U4	STAG2_HUMAN	stromal antigen 2	1016					meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of DNA endoreduplication (GO:0032876)|sister chromatid cohesion (GO:0007062)|stem cell maintenance (GO:0019827)	actin cytoskeleton (GO:0015629)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chromatin binding (GO:0003682)			breast(5)|central_nervous_system(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(9)|lung(21)|ovary(5)|prostate(2)|skin(5)|urinary_tract(4)	78						AAGACAAAAGAACAGTGTATG	0.358																																					p.R1016R		Atlas-SNP	.											.	STAG2	309	.	0			c.A3048G						.						78.0	75.0	76.0					X																	123217394		2203	4299	6502	SO:0001819	synonymous_variant	10735	exon29			CAAAAGAACAGTG	Z75331	CCDS14607.1, CCDS43990.1	Xq25	2014-09-17			ENSG00000101972	ENSG00000101972			11355	protein-coding gene	gene with protein product		300826				9305759	Standard	NM_001042750		Approved	SA-2, SCC3B	uc004eua.3	Q8N3U4	OTTHUMG00000022725	ENST00000371160.1:c.3048A>G	chrX.hg19:g.123217394A>G		51.0	0.0		73.0	4.0	NM_001042749	B1AMT5|D3DTF5|O00540|Q5JTI6|Q68DE9|Q9H1N8	Silent	SNP	ENST00000371160.1	hg19	CCDS14607.1																																																																																			.	.		0.358	STAG2-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000156159.2	NM_006603	
AIFM1	9131	hgsc.bcm.edu	37	X	129290533	129290533	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:129290533T>C	ENST00000287295.3	-	2	381	c.151A>G	c.(151-153)Aca>Gca	p.T51A	AIFM1_ENST00000346424.2_Intron|AIFM1_ENST00000319908.3_Intron|AIFM1_ENST00000535724.1_Intron	NM_001130847.3|NM_004208.3	NP_001124319.1|NP_004199.1	O95831	AIFM1_HUMAN	apoptosis-inducing factor, mitochondrion-associated, 1	51					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|cell redox homeostasis (GO:0045454)|chromosome condensation (GO:0030261)|DNA catabolic process (GO:0006308)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|mitochondrial respiratory chain complex I assembly (GO:0032981)|neuron apoptotic process (GO:0051402)|neuron differentiation (GO:0030182)|positive regulation of apoptotic process (GO:0043065)|regulation of apoptotic DNA fragmentation (GO:1902510)	cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	DNA binding (GO:0003677)|electron carrier activity (GO:0009055)|FAD binding (GO:0071949)|NAD(P)H oxidase activity (GO:0016174)|oxidoreductase activity, acting on NAD(P)H (GO:0016651)			central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(4)|liver(2)|lung(8)|ovary(4)|prostate(2)|urinary_tract(1)	30					Flavin adenine dinucleotide(DB03147)	ATTTGTCTTGTCATCTGGAGT	0.393																																					p.T51A		Atlas-SNP	.											.	AIFM1	75	.	0			c.A151G						.						217.0	187.0	197.0					X																	129290533		2203	4300	6503	SO:0001583	missense	9131	exon2			GTCTTGTCATCTG	AF100928	CCDS14618.1, CCDS14619.1, CCDS48167.1	Xq26.1	2014-01-30	2006-11-16	2006-11-16	ENSG00000156709	ENSG00000156709			8768	protein-coding gene	gene with protein product		300169	"""programmed cell death 8 (apoptosis-inducing factor)"", ""neuropathy, axonal, motor-sensory with deafness and mental retardation (Cowchock syndrome)"""	PDCD8, NAMSD		9989411, 23217327	Standard	NM_004208		Approved	AIF, CMTX4	uc004evg.3	O95831	OTTHUMG00000022392	ENST00000287295.3:c.151A>G	chrX.hg19:g.129290533T>C	ENSP00000287295:p.Thr51Ala	87.0	0.0		72.0	4.0	NM_001130847	A4QPB4|B1ALN1|B2RB08|D3DTE9|Q1L6K4|Q1L6K6|Q2QKE4|Q5JUZ7|Q6I9X6|Q9Y3I3|Q9Y3I4	Missense_Mutation	SNP	ENST00000287295.3	hg19	CCDS14618.1	.	.	.	.	.	.	.	.	.	.	T	9.404	1.078720	0.20227	.	.	ENSG00000156709	ENST00000287295	T	0.20200	2.09	5.49	1.86	0.25419	.	0.395064	0.30771	N	0.008908	T	0.09247	0.0228	N	0.10874	0.06	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.23440	-1.0188	10	0.21540	T	0.41	-4.1489	7.3059	0.26447	0.0:0.2604:0.0:0.7396	.	51;51	Q1L6K6;O95831	.;AIFM1_HUMAN	A	51	ENSP00000287295:T51A	ENSP00000287295:T51A	T	-	1	0	AIFM1	129118214	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.179000	0.31993	0.242000	0.21303	0.437000	0.28790	ACA	.	.		0.393	AIFM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058247.2		
ABCD1	215	hgsc.bcm.edu	37	X	153009116	153009116	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:153009116A>G	ENST00000218104.3	+	10	2564	c.2165A>G	c.(2164-2166)gAg>gGg	p.E722G	U52111.14_ENST00000434284.1_RNA	NM_000033.3	NP_000024.2	P33897	ABCD1_HUMAN	ATP-binding cassette, sub-family D (ALD), member 1	722					alpha-linolenic acid metabolic process (GO:0036109)|ATP catabolic process (GO:0006200)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|linoleic acid metabolic process (GO:0043651)|long-chain fatty acid catabolic process (GO:0042758)|peroxisomal long-chain fatty acid import (GO:0015910)|peroxisomal membrane transport (GO:0015919)|peroxisome organization (GO:0007031)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|unsaturated fatty acid metabolic process (GO:0033559)|very long-chain fatty acid catabolic process (GO:0042760)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|integral component of peroxisomal membrane (GO:0005779)|membrane (GO:0016020)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|peroxisomal fatty-acyl-CoA transporter activity (GO:0005325)|protein homodimerization activity (GO:0042803)|transporter activity (GO:0005215)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(6)|urinary_tract(2)	18	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					ATCCTGGGCGAGGCCGTGGCC	0.721																																					p.E722G		Atlas-SNP	.											.	ABCD1	59	.	0			c.A2165G						.						6.0	6.0	6.0					X																	153009116		2130	4176	6306	SO:0001583	missense	215	exon10			TGGGCGAGGCCGT	Z21876	CCDS14728.1	Xq28	2012-03-14			ENSG00000101986	ENSG00000101986		"""ATP binding cassette transporters / subfamily D"""	61	protein-coding gene	gene with protein product		300371		ALD		8441467, 6795626	Standard	NM_000033		Approved	AMN, ALDP, adrenoleukodystrophy	uc004fif.2	P33897	OTTHUMG00000024215	ENST00000218104.3:c.2165A>G	chrX.hg19:g.153009116A>G	ENSP00000218104:p.Glu722Gly	24.0	0.0		63.0	4.0	NM_000033	Q6GTZ2	Missense_Mutation	SNP	ENST00000218104.3	hg19	CCDS14728.1	.	.	.	.	.	.	.	.	.	.	A	21.0	4.088547	0.76756	.	.	ENSG00000101986	ENST00000218104	D	0.94793	-3.52	4.65	4.65	0.58169	.	0.443226	0.17631	N	0.167383	D	0.95765	0.8622	M	0.85710	2.77	0.80722	D	1	P	0.44044	0.825	P	0.48524	0.58	D	0.95633	0.8691	10	0.66056	D	0.02	-16.8889	12.2981	0.54859	1.0:0.0:0.0:0.0	.	722	P33897	ABCD1_HUMAN	G	722	ENSP00000218104:E722G	ENSP00000218104:E722G	E	+	2	0	ABCD1	152662310	0.999000	0.42202	0.814000	0.32528	0.456000	0.32438	4.668000	0.61568	1.537000	0.49254	0.425000	0.28330	GAG	.	.		0.721	ABCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061041.1	NM_000033	
PDZD4	57595	hgsc.bcm.edu	37	X	153070036	153070036	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:153070036A>G	ENST00000164640.4	-	8	1273	c.1082T>C	c.(1081-1083)cTg>cCg	p.L361P	PDZD4_ENST00000544474.1_Missense_Mutation_p.L252P|PDZD4_ENST00000475140.1_5'Flank|PDZD4_ENST00000393758.2_Missense_Mutation_p.L286P	NM_032512.2	NP_115901.2	Q76G19	PDZD4_HUMAN	PDZ domain containing 4	361						cytoplasm (GO:0005737)				breast(3)|cervix(1)|endometrium(5)|lung(13)|skin(1)	23	all_lung(58;3.39e-06)|all_hematologic(71;4.25e-06)|Lung NSC(58;4.7e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					CTTGATCTCCAGGAGCTCACG	0.667																																					p.L361P		Atlas-SNP	.											.	PDZD4	67	.	0			c.T1082C						.						47.0	41.0	43.0					X																	153070036		2203	4300	6503	SO:0001583	missense	57595	exon8			ATCTCCAGGAGCT	AK091444	CCDS14732.1	Xq28	2008-02-05		2006-01-24	ENSG00000067840	ENSG00000067840			21167	protein-coding gene	gene with protein product		300634		PDZK4		10819331, 15077175	Standard	NM_032512		Approved	KIAA1444, LU1, FLJ34125, PDZRN4L	uc004fiz.1	Q76G19	OTTHUMG00000024209	ENST00000164640.4:c.1082T>C	chrX.hg19:g.153070036A>G	ENSP00000164640:p.Leu361Pro	84.0	0.0		106.0	5.0	NM_032512	B3KXB1|B7ZKY3|Q8NB75|Q9BUH9|Q9P284	Missense_Mutation	SNP	ENST00000164640.4	hg19	CCDS14732.1	.	.	.	.	.	.	.	.	.	.	A	15.81	2.944624	0.53079	.	.	ENSG00000067840	ENST00000164640;ENST00000393758;ENST00000537633;ENST00000544474	T;T;T	0.19394	2.15;2.17;2.4	5.15	5.15	0.70609	.	0.000000	0.64402	D	0.000001	T	0.44350	0.1289	M	0.67397	2.05	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;0.998;0.999;1.0	T	0.42599	-0.9442	10	0.87932	D	0	-18.6317	13.0044	0.58696	1.0:0.0:0.0:0.0	.	252;367;361;286;265	B7ZKY3;Q17RL8;Q76G19;D3DWW0;B3KVR9	.;.;PDZD4_HUMAN;.;.	P	361;286;265;252	ENSP00000164640:L361P;ENSP00000377355:L286P;ENSP00000442033:L252P	ENSP00000164640:L361P	L	-	2	0	PDZD4	152723230	1.000000	0.71417	0.998000	0.56505	0.463000	0.32649	9.332000	0.96446	1.711000	0.51337	0.430000	0.28490	CTG	.	.		0.667	PDZD4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061013.3	NM_032512	
MT-ND6	4541	hgsc.bcm.edu	37	M	14645	14645	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrM:14645A>G	ENST00000361681.2	-	1	28	c.29T>C	c.(28-30)gTg>gCg	p.V10A	MT-TS2_ENST00000387449.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TP_ENST00000387461.2_RNA|MT-TH_ENST00000387441.1_RNA|MT-CYB_ENST00000361789.2_5'Flank|MT-TE_ENST00000387459.1_RNA|MT-TT_ENST00000387460.2_RNA			P03923	NU6M_HUMAN	mitochondrially encoded NADH dehydrogenase 6	10					cellular metabolic process (GO:0044237)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|respiratory chain (GO:0070469)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(1)|endometrium(10)|kidney(17)|urinary_tract(1)	29						TTACTAAACCCACACTCAACA	0.408																																					p.V10A		Atlas-SNP	.											.	.	.	.	0			c.T29C						.																																			SO:0001583	missense	0	exon1			AAACCCACACTCA			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198695	ENSG00000198695	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7462	protein-coding gene	gene with protein product	"""complex I ND6 subunit"", ""NADH-ubiquinone oxidoreductase chain 6"""	516006	"""NADH dehydrogenase 6"""	MTND6			Standard			Approved	NAD6, ND6		P03923		ENST00000361681.2:c.29T>C	chrM.hg19:g.14645A>G	ENSP00000354665:p.Val10Ala	46.0	0.0		72.0	4.0	ENST00000361681	Q34774|Q8HG30	Missense_Mutation	SNP	ENST00000361681.2	hg19																																																																																				.	.		0.408	MT-ND6-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024037	
MT-CYB	4519	hgsc.bcm.edu	37	M	15591	15591	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrM:15591G>T	ENST00000361789.2	+	1	845	c.845G>T	c.(844-846)cGa>cTa	p.R282L	MT-ND6_ENST00000361681.2_5'Flank|MT-TP_ENST00000387461.2_RNA|MT-TE_ENST00000387459.1_RNA|MT-TT_ENST00000387460.2_RNA			P00156	CYB_HUMAN	mitochondrially encoded cytochrome b	282					cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|mitochondrial electron transport, ubiquinol to cytochrome c (GO:0006122)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex III (GO:0005750)|mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|ubiquinol-cytochrome-c reductase activity (GO:0008121)			breast(6)|endometrium(25)|kidney(33)|prostate(1)	65						CACAATTCTCCGATCCGTCCC	0.478											OREG0007583	type=REGULATORY REGION|TFbs=ESR1|Dataset=Estrogen Receptor Alpha Binding Sites|EvidenceSubtype=Chromatin immunoprecipitation with tag sequencing (ChIP-TS)																									p.R282L		Atlas-SNP	.											.	.	.	.	0			c.G845T						.																																			SO:0001583	missense	0	exon1			TTCTCCGATCCGT			mitochondria	2012-11-16	2005-02-15	2005-02-16	ENSG00000198727	ENSG00000198727		"""Cytochrome b genes"", ""Mitochondrial respiratory chain complex / Complex III"""	7427	protein-coding gene	gene with protein product		516020	"""cytochrome b"""	MTCYB			Standard			Approved	COB, CYTB, UQCR3		P00156		ENST00000361789.2:c.845G>T	chrM.hg19:g.15591G>T	ENSP00000354554:p.Arg282Leu	15.0	0.0	585	15.0	7.0	ENST00000361789	Q34786|Q8HBR6|Q8HNQ0|Q8HNQ1|Q8HNQ9|Q8HNR4|Q8HNR7|Q8W7V8|Q8WCV9|Q8WCY2|Q8WCY7|Q8WCY8|Q9B1A6|Q9B1B6|Q9B1B8|Q9B1D4|Q9B1X6|Q9B2V0|Q9B2V8|Q9B2W0|Q9B2W3|Q9B2W8|Q9B2X1|Q9B2X7|Q9B2X9|Q9B2Y3|Q9B2Z0|Q9B2Z4|Q9T6H6|Q9T9Y0|Q9TEH4	Missense_Mutation	SNP	ENST00000361789.2	hg19																																																																																				.	.		0.478	MT-CYB-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024038	
PTPN20A	653129	hgsc.bcm.edu	37	10	46568210	46568210	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:46568210delT	ENST00000374339.3	-	7	689	c.613delA	c.(613-615)agcfs	p.S205fs	PTPN20A_ENST00000506080.1_Frame_Shift_Del_p.S177fs|PTPN20A_ENST00000502705.1_Intron|PTPN20A_ENST00000437863.1_Frame_Shift_Del_p.S177fs|PTPN20A_ENST00000395721.2_Frame_Shift_Del_p.S124fs|PTPN20A_ENST00000508602.1_Intron|PTPN20A_ENST00000503851.1_Intron|PTPN20A_ENST00000509599.1_Intron|PTPN20A_ENST00000509774.1_Intron|PTPN20A_ENST00000511769.1_Frame_Shift_Del_p.S196fs|PTPN20A_ENST00000374218.2_Frame_Shift_Del_p.S124fs|PTPN20A_ENST00000505814.1_Frame_Shift_Del_p.S124fs|PTPN20A_ENST00000513156.1_Intron|PTPN20A_ENST00000395722.3_Intron|PTPN20A_ENST00000395725.3_Intron|PTPN20A_ENST00000374346.3_Intron|PTPN20A_ENST00000509900.1_Intron|PTPN20A_ENST00000513266.1_Intron|PTPN20A_ENST00000502254.1_Intron|PTPN20A_ENST00000374340.3_5'UTR|PTPN20A_ENST00000395727.2_Frame_Shift_Del_p.S13fs|PTPN20A_ENST00000374342.2_Intron			Q4JDL3	PTN20_HUMAN	protein tyrosine phosphatase, non-receptor type 20A	205	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.					cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)								Kidney(211;0.201)		TAGTCCTTGCTTTTTCCAAGA	0.393																																					p.S205fs		Atlas-INDEL	.											.	.	.	.	0			c.614delG						.																																			SO:0001589	frameshift_variant	653129	exon7			.			10q11.22	2011-06-09			ENSG00000204179	ENSG00000204179		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	23422	protein-coding gene	gene with protein product	"""cancer/testis antigen 126"""						Standard			Approved	bA142I17.1, CT126		Q4JDL3	OTTHUMG00000018094	ENST00000374339.3:c.613delA	chr10.hg19:g.46568210delT	ENSP00000363459:p.Ser205fs	194.0	0.0		181.0	12.0	NM_001042389	A6NNH8|B7ZKV3|Q4JDG6|Q4JDK1|Q4JDK5|Q4JDK6|Q4JDK8|Q4JDK9|Q4JDL0|Q4JDL1|Q4JDL4|Q4JDL5|Q4JDL6|Q4JDL7|Q4JDL8|Q5RJ33|Q5T1G3	Frame_Shift_Del	DEL	ENST00000374339.3	hg19	CCDS31190.1																																																																																			.	.		0.393	PTPN20A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000358639.1		
ZNF562	54811	hgsc.bcm.edu	37	19	9767254	9767254	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:9767254delA	ENST00000448622.1	-	5	479	c.317delT	c.(316-318)ttgfs	p.L106fs	ZNF562_ENST00000590155.1_Frame_Shift_Del_p.L106fs|ZNF562_ENST00000537617.1_5'UTR|ZNF562_ENST00000453372.2_Frame_Shift_Del_p.L106fs|ZNF562_ENST00000541032.1_Frame_Shift_Del_p.L69fs|ZNF562_ENST00000453792.2_Frame_Shift_Del_p.L37fs|ZNF562_ENST00000293648.4_Frame_Shift_Del_p.L34fs|ZNF562_ENST00000587392.1_Intron	NM_001130031.1|NM_001130032.1	NP_001123503.1|NP_001123504.1	Q6V9R5	ZN562_HUMAN	zinc finger protein 562	106	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(7)|prostate(1)|skin(1)|urinary_tract(1)	17						TTGATTCTTCAAAAAACCCTG	0.373																																					p.L106fs		Atlas-INDEL	.											.	ZNF562	72	.	0			c.318delG						.						145.0	142.0	143.0					19																	9767254		2203	4300	6503	SO:0001589	frameshift_variant	54811	exon5			.	AK000086	CCDS12217.1, CCDS45956.1, CCDS74280.1	19p13.2	2013-09-20			ENSG00000171466	ENSG00000171466		"""Zinc fingers, C2H2-type"", ""-"""	25950	protein-coding gene	gene with protein product							Standard	NM_001130031		Approved	FLJ20079	uc010xks.2	Q6V9R5	OTTHUMG00000180205	ENST00000448622.1:c.317delT	chr19.hg19:g.9767254delA	ENSP00000411784:p.Leu106fs	169.0	0.0		165.0	11.0	NM_001130032	Q32MN2|Q9NXS5	Frame_Shift_Del	DEL	ENST00000448622.1	hg19	CCDS45956.1																																																																																			.	.		0.373	ZNF562-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000450239.1	NM_017656	
ASB18	401036	hgsc.bcm.edu	37	2	237103580	237103580	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:237103580delG	ENST00000409749.3	-	6	1335	c.1336delC	c.(1336-1338)ctgfs	p.L447fs	AC079135.1_ENST00000483218.1_RNA|AC079135.1_ENST00000415226.1_RNA|ASB18_ENST00000330842.6_Frame_Shift_Del_p.L418fs	NM_212556.2	NP_997721.2	Q6ZVZ8	ASB18_HUMAN	ankyrin repeat and SOCS box containing 18	447	SOCS box. {ECO:0000255|PROSITE- ProRule:PRU00194}.				intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)					large_intestine(1)|lung(3)|ovary(1)|prostate(1)	6		all_hematologic(139;0.00615)|Renal(207;0.00963)|Breast(86;0.0126)|Acute lymphoblastic leukemia(138;0.0815)		Epithelial(121;2.04e-26)|OV - Ovarian serous cystadenocarcinoma(60;1.47e-11)|BRCA - Breast invasive adenocarcinoma(100;2.88e-05)|Lung(119;0.000383)|LUSC - Lung squamous cell carcinoma(224;0.00644)|GBM - Glioblastoma multiforme(43;0.244)		AAGGGTAACAGGGGGATGAGG	0.542																																					p.L446fs		Atlas-INDEL	.											.	ASB18	34	.	0			c.1337delT						.						63.0	73.0	70.0					2																	237103580		2063	4217	6280	SO:0001589	frameshift_variant	401036	exon6			.	AK123854	CCDS46548.1	2q37.2	2013-01-10	2011-01-25		ENSG00000182177	ENSG00000182177		"""Ankyrin repeat domain containing"""	19770	protein-coding gene	gene with protein product			"""ankyrin repeat and SOCS box-containing 18"""			12076535	Standard	NM_212556		Approved		uc010znh.2	Q6ZVZ8	OTTHUMG00000153086	ENST00000409749.3:c.1336delC	chr2.hg19:g.237103580delG	ENSP00000386532:p.Leu447fs	130.0	0.0		138.0	10.0	NM_212556	B6ZDL7	Frame_Shift_Del	DEL	ENST00000409749.3	hg19	CCDS46548.1																																																																																			.	.		0.542	ASB18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329436.1	NM_212556	
GRIA3	2892	hgsc.bcm.edu	37	X	122528895	122528895	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:122528895delA	ENST00000371251.1	+	6	879	c.827delA	c.(826-828)gaafs	p.E276fs	GRIA3_ENST00000541091.1_Frame_Shift_Del_p.E260fs|GRIA3_ENST00000371256.5_Frame_Shift_Del_p.E276fs|GRIA3_ENST00000542149.1_Frame_Shift_Del_p.E276fs|GRIA3_ENST00000264357.5_Frame_Shift_Del_p.E276fs			P42263	GRIA3_HUMAN	glutamate receptor, ionotropic, AMPA 3	276					glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)			breast(2)|central_nervous_system(1)|endometrium(8)|kidney(3)|large_intestine(8)|lung(25)|ovary(3)|pancreas(2)|skin(2)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)	57					Lithium(DB01356)	GTCAACAATGAAAACCCTATG	0.443																																					p.E276fs		Atlas-INDEL	.											.	GRIA3	386	.	0			c.826delG						.						132.0	122.0	126.0					X																	122528895		2203	4300	6503	SO:0001589	frameshift_variant	2892	exon6			.	U10301	CCDS14604.1, CCDS14605.1, CCDS76017.1	Xq25	2012-08-29	2012-02-03		ENSG00000125675	ENSG00000125675		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4573	protein-coding gene	gene with protein product		305915	"""glutamate receptor, ionotrophic, AMPA 3"""	GLUR3		1319477, 10644433	Standard	NM_007325		Approved	GluA3, GLURC, MRX94	uc004etr.4	P42263	OTTHUMG00000022685	ENST00000371251.1:c.827delA	chrX.hg19:g.122528895delA	ENSP00000360297:p.Glu276fs	144.0	0.0		185.0	12.0	NM_000828	D3DTF1|Q4VXD5|Q4VXD6|Q9HDA0|Q9HDA1|Q9HDA2|Q9P0H1	Frame_Shift_Del	DEL	ENST00000371251.1	hg19	CCDS14604.1																																																																																			.	.		0.443	GRIA3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058854.1	NM_000828	
USP28	57646	hgsc.bcm.edu	37	11	113704215	113704215	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:113704215delT	ENST00000003302.4	-	7	754	c.686delA	c.(685-687)aatfs	p.N229fs	USP28_ENST00000542033.1_5'UTR|USP28_ENST00000545540.1_Frame_Shift_Del_p.N104fs|USP28_ENST00000537706.1_Frame_Shift_Del_p.N229fs|USP28_ENST00000260188.5_Frame_Shift_Del_p.N229fs	NM_020886.2	NP_065937.1	Q96RU2	UBP28_HUMAN	ubiquitin specific peptidase 28	229	USP.				cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|protein deubiquitination (GO:0016579)|response to ionizing radiation (GO:0010212)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(4)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(12)|lung(24)|ovary(1)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	59		all_cancers(61;3.74e-18)|all_epithelial(67;3.75e-11)|Melanoma(852;1.46e-05)|all_hematologic(158;4.65e-05)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|Prostate(24;0.0153)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;3.93e-06)|Epithelial(105;0.000122)|all cancers(92;0.00104)		AAATTTTCTATTTGATCCCAT	0.383																																					p.N229fs	Melanoma(4;162 555 7664)|GBM(79;500 2010 17506)|Esophageal Squamous(9;463 924 15765)	Atlas-INDEL	.											.	USP28	135	.	0			c.687delT						.						109.0	110.0	110.0					11																	113704215		2201	4296	6497	SO:0001589	frameshift_variant	57646	exon7			.	AB040948	CCDS31680.1, CCDS73394.1	11q23	2008-04-11	2005-08-08		ENSG00000048028	ENSG00000048028		"""Ubiquitin-specific peptidases"""	12625	protein-coding gene	gene with protein product		610748	"""ubiquitin specific protease 28"""			12838346, 11597335	Standard	XM_005271630		Approved	KIAA1515	uc001poh.3	Q96RU2	OTTHUMG00000168205	ENST00000003302.4:c.686delA	chr11.hg19:g.113704215delT	ENSP00000003302:p.Asn229fs	133.0	0.0		148.0	10.0	NM_020886	B0YJC0|B0YJC1|Q9P213	Frame_Shift_Del	DEL	ENST00000003302.4	hg19	CCDS31680.1																																																																																			.	.		0.383	USP28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398789.1		
SETBP1	26040	hgsc.bcm.edu	37	18	42456590	42456590	+	Intron	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr18:42456590delA	ENST00000282030.5	+	3	836				SETBP1_ENST00000426838.4_Frame_Shift_Del_p.K202fs	NM_015559.2	NP_056374.2	Q9Y6X0	SETBP_HUMAN	SET binding protein 1							nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|breast(2)|endometrium(9)|kidney(9)|large_intestine(20)|lung(47)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	104				Colorectal(1;0.0622)|COAD - Colon adenocarcinoma(74;0.201)		CATCCCATTCAAAAAGCAATT	0.493									Schinzel-Giedion syndrome																												p.F200fs		Atlas-INDEL	.											.	SETBP1	577	.	0			c.600delC						.						103.0	100.0	101.0					18																	42456590		692	1591	2283	SO:0001627	intron_variant	26040	exon4	Familial Cancer Database	SGC, Schinzel-Giedion Midface Retraction syndrome	.	AB022660	CCDS11923.2, CCDS45859.1	18q21.1	2008-08-01			ENSG00000152217	ENSG00000152217			15573	protein-coding gene	gene with protein product		611060				11231286	Standard	NM_015559		Approved	SEB, KIAA0437	uc010dni.3	Q9Y6X0	OTTHUMG00000132613	ENST00000282030.5:c.540+7342A>-	chr18.hg19:g.42456590delA		164.0	0.0		173.0	11.0	NM_001130110	A6H8W5|Q6P6C3|Q9UEF3	Frame_Shift_Del	DEL	ENST00000282030.5	hg19	CCDS11923.2																																																																																			.	.		0.493	SETBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255854.4	NM_001130110	
MORN1	79906	hgsc.bcm.edu	37	1	2268183	2268183	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:2268183delG	ENST00000378531.3	-	11	1316	c.1143delC	c.(1141-1143)cccfs	p.P381fs	MORN1_ENST00000606372.1_5'UTR	NM_024848.1	NP_079124.1	Q5T089	MORN1_HUMAN	MORN repeat containing 1	381										breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(1)|liver(1)|lung(1)|ovary(2)	9	all_cancers(77;0.000194)|all_epithelial(69;9.96e-05)|all_lung(157;0.016)|Lung NSC(156;0.0376)|Ovarian(185;0.0634)	all_epithelial(116;3.3e-15)|all_lung(118;1.15e-06)|Lung NSC(185;6.26e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Medulloblastoma(700;0.151)|Lung SC(97;0.217)		Epithelial(90;2.21e-37)|OV - Ovarian serous cystadenocarcinoma(86;5.01e-23)|GBM - Glioblastoma multiforme(42;2.8e-08)|Colorectal(212;5.97e-05)|COAD - Colon adenocarcinoma(227;0.000241)|Kidney(185;0.00137)|BRCA - Breast invasive adenocarcinoma(365;0.00488)|STAD - Stomach adenocarcinoma(132;0.00665)|KIRC - Kidney renal clear cell carcinoma(229;0.0203)|Lung(427;0.212)		GGAACAGGAAGGGGTGGTACC	0.677																																					p.F382fs		Atlas-INDEL	.											.	MORN1	38	.	0			c.1144delT						.						23.0	25.0	24.0					1																	2268183		2201	4296	6497	SO:0001589	frameshift_variant	79906	exon11			.	AK024003	CCDS40.1, CCDS72688.1	1p36.33-p36.32	2008-02-05			ENSG00000116151	ENSG00000116151			25852	protein-coding gene	gene with protein product						12477932	Standard	XM_005244798		Approved	FLJ13941	uc001ajb.1	Q5T089	OTTHUMG00000001402	ENST00000378531.3:c.1143delC	chr1.hg19:g.2268183delG	ENSP00000367792:p.Pro381fs	142.0	0.0		151.0	11.0	NM_024848	A6NKZ6|Q8WW30|Q9H852	Frame_Shift_Del	DEL	ENST00000378531.3	hg19	CCDS40.1																																																																																			.	.		0.677	MORN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000004055.1	NM_024848	
ISG20L2	81875	hgsc.bcm.edu	37	1	156697122	156697122	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:156697122delT	ENST00000313146.6	-	1	1105	c.323delA	c.(322-324)aagfs	p.K108fs	RRNAD1_ENST00000368218.4_5'Flank|RRNAD1_ENST00000524343.1_5'Flank|ISG20L2_ENST00000368219.1_Frame_Shift_Del_p.K108fs|RRNAD1_ENST00000368216.4_5'Flank|ISG20L2_ENST00000472824.2_5'Flank	NM_030980.1	NP_112242.1	Q9H9L3	I20L2_HUMAN	interferon stimulated exonuclease gene 20kDa-like 2	108					ribosome biogenesis (GO:0042254)	nucleus (GO:0005634)	exonuclease activity (GO:0004527)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(6)|ovary(1)|skin(1)	16	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					AGAATCAGCCTTTTTTGAAGG	0.517											OREG0013885	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.K108fs		Atlas-INDEL	.											.	ISG20L2	43	.	0			c.324delG						.						71.0	73.0	72.0					1																	156697122		2203	4300	6503	SO:0001589	frameshift_variant	81875	exon1			.	AK095697	CCDS1153.1	1q23.1	2013-10-11			ENSG00000143319	ENSG00000143319			25745	protein-coding gene	gene with protein product		611930				18065403	Standard	NM_030980		Approved	FLJ12671	uc001fps.1	Q9H9L3	OTTHUMG00000041301	ENST00000313146.6:c.323delA	chr1.hg19:g.156697122delT	ENSP00000323424:p.Lys108fs	89.0	0.0	1780	180.0	13.0	NM_030980	D3DVC6|Q64KA2	Frame_Shift_Del	DEL	ENST00000313146.6	hg19	CCDS1153.1																																																																																			.	.		0.517	ISG20L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098969.1	NM_030980	
EXOC2	55770	hgsc.bcm.edu	37	6	556513	556513	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:556513delC	ENST00000230449.4	-	18	2038	c.1903delG	c.(1903-1905)gttfs	p.V635fs	EXOC2_ENST00000448181.3_Frame_Shift_Del_p.V230fs	NM_018303.5	NP_060773.3	Q96KP1	EXOC2_HUMAN	exocyst complex component 2	635					cellular protein metabolic process (GO:0044267)|exocytosis (GO:0006887)|Golgi to plasma membrane transport (GO:0006893)|membrane organization (GO:0061024)|protein transport (GO:0015031)	exocyst (GO:0000145)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|liver(1)|lung(16)|ovary(4)|pancreas(1)|prostate(2)	46	Ovarian(93;0.0733)	Breast(5;0.0014)|all_lung(73;0.0697)|all_hematologic(90;0.0897)		OV - Ovarian serous cystadenocarcinoma(45;0.0507)|BRCA - Breast invasive adenocarcinoma(62;0.14)		CACTCCAGAACCCCCTTCAGT	0.478																																					p.V635fs		Atlas-INDEL	.											.	EXOC2	81	.	0			c.1904delT						.						75.0	68.0	70.0					6																	556513		2203	4300	6503	SO:0001589	frameshift_variant	55770	exon18			.	AJ420556	CCDS34327.1	6p25.3	2013-01-22	2005-11-01	2005-11-01	ENSG00000112685	ENSG00000112685			24968	protein-coding gene	gene with protein product		615329	"""SEC5-like 1 (S. cerevisiae)"""	SEC5L1		12575951, 12459492	Standard	NM_018303		Approved	FLJ11026, Sec5p	uc003mtd.4	Q96KP1	OTTHUMG00000137437	ENST00000230449.4:c.1903delG	chr6.hg19:g.556513delC	ENSP00000230449:p.Val635fs	180.0	0.0		243.0	15.0	NM_018303	B2RBE6|Q5JPC8|Q96AN6|Q9NUZ8|Q9UJM7	Frame_Shift_Del	DEL	ENST00000230449.4	hg19	CCDS34327.1																																																																																			.	.		0.478	EXOC2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039627.1	NM_018303	
ACSS3	79611	hgsc.bcm.edu	37	12	81647384	81647384	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:81647384delA	ENST00000548058.1	+	15	2840	c.1930delA	c.(1930-1932)aaafs	p.K644fs	ACSS3_ENST00000261206.3_Frame_Shift_Del_p.K643fs|ACSS3_ENST00000548324.1_Frame_Shift_Del_p.K326fs			Q9H6R3	ACSS3_HUMAN	acyl-CoA synthetase short-chain family member 3	644						mitochondrion (GO:0005739)	acetate-CoA ligase activity (GO:0003987)|ATP binding (GO:0005524)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(5)|kidney(2)|large_intestine(7)|liver(3)|lung(20)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)	51						ACAGCTACCCAAAACCAGATC	0.418																																					p.P643fs		Atlas-INDEL	.											.	ACSS3	118	.	0			c.1929delC						.						96.0	97.0	96.0					12																	81647384		2203	4300	6503	SO:0001589	frameshift_variant	79611	exon15			.		CCDS9022.1	12q21.31	2014-08-08			ENSG00000111058	ENSG00000111058		"""Acyl-CoA synthetase family"""	24723	protein-coding gene	gene with protein product		614356				17762044	Standard	NM_024560		Approved	FLJ21963	uc001szl.1	Q9H6R3	OTTHUMG00000170179	ENST00000548058.1:c.1930delA	chr12.hg19:g.81647384delA	ENSP00000449535:p.Lys644fs	93.0	0.0		108.0	10.0	NM_024560	Q8NC66	Frame_Shift_Del	DEL	ENST00000548058.1	hg19	CCDS9022.1																																																																																			.	.		0.418	ACSS3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000407794.1	NM_024560	
PCDHAC1	56135	hgsc.bcm.edu	37	5	140306876	140306876	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:140306876delC	ENST00000253807.2	+	1	399	c.399delC	c.(397-399)atcfs	p.I133fs	PCDHA3_ENST00000522353.2_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA12_ENST00000398631.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA13_ENST00000289272.2_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA13_ENST00000409494.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHAC1_ENST00000409700.3_Frame_Shift_Del_p.I133fs|PCDHA6_ENST00000527624.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA6_ENST00000529310.1_Intron	NM_018898.3	NP_061721.2	Q9H158	PCDC1_HUMAN	protocadherin alpha subfamily C, 1	133	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|breast(3)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(13)|liver(2)|lung(13)|ovary(3)|prostate(2)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(4)	65			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGCTGCACATCCCCGAGTTCC	0.587																																					p.I133fs		Atlas-INDEL	.											.	PCDHAC1	141	.	0			c.398delT						.						65.0	62.0	63.0					5																	140306876		2203	4300	6503	SO:0001589	frameshift_variant	56135	exon1			.	AF152473	CCDS4241.1	5q31	2010-11-26			ENSG00000248383	ENSG00000248383		"""Cadherins / Protocadherins : Clustered"""	8676	other	complex locus constituent	"""PCDH-ALPHA-C1"""	606320				10380929	Standard	NM_018898		Approved			Q9H158	OTTHUMG00000129603	ENST00000253807.2:c.399delC	chr5.hg19:g.140306876delC	ENSP00000253807:p.Ile133fs	145.0	0.0		180.0	11.0	NM_031882	Q9Y5F5|Q9Y5I5	Frame_Shift_Del	DEL	ENST00000253807.2	hg19	CCDS4241.1																																																																																			.	.		0.587	PCDHAC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251798.1	NM_018898	
CNOT6L	246175	hgsc.bcm.edu	37	4	78697453	78697453	+	Frame_Shift_Del	DEL	T	T	-	rs200743940		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:78697453delT	ENST00000504123.1	-	2	229	c.99delA	c.(97-99)aaafs	p.K33fs	CNOT6L_ENST00000264903.4_Frame_Shift_Del_p.K33fs|CNOT6L_ENST00000506166.1_5'UTR			Q96LI5	CNO6L_HUMAN	CCR4-NOT transcription complex, subunit 6-like	33	Required for interaction with CNOT1, CNOT3 and CNOT7.				gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA destabilization (GO:0061157)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytoplasmic mRNA processing body assembly (GO:0010606)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|transcription, DNA-templated (GO:0006351)	CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A)-specific ribonuclease activity (GO:0004535)			kidney(1)|large_intestine(1)|lung(6)|urinary_tract(1)	9						CCCAGTGAGATTTTTTCCCAT	0.373																																					p.S34fs		Atlas-INDEL	.											.	CNOT6L	57	.	0			c.100delT						.						125.0	120.0	121.0					4																	78697453		1812	4081	5893	SO:0001589	frameshift_variant	246175	exon2			.	AL133112	CCDS68731.1	4q13.3	2014-06-17				ENSG00000138767			18042	protein-coding gene	gene with protein product							Standard	NM_144571		Approved	DKFZp434K098, Ccr4b	uc003hks.3	Q96LI5		ENST00000504123.1:c.99delA	chr4.hg19:g.78697453delT	ENSP00000424896:p.Lys33fs	123.0	0.0		128.0	11.0	NM_144571	Q9UF92	Frame_Shift_Del	DEL	ENST00000504123.1	hg19																																																																																				.	.		0.373	CNOT6L-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000362515.1		
ANKAR	150709	hgsc.bcm.edu	37	2	190611122	190611122	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:190611122delA	ENST00000520309.1	+	23	4162	c.4074delA	c.(4072-4074)agafs	p.R1358fs	ANKAR_ENST00000281412.6_3'UTR|ANKAR_ENST00000438402.2_3'UTR|ANKAR_ENST00000313581.4_Frame_Shift_Del_p.R1358fs|ANKAR_ENST00000431575.2_Frame_Shift_Del_p.R1287fs	NM_144708.3	NP_653309.3	Q7Z5J8	ANKAR_HUMAN	ankyrin and armadillo repeat containing	1358						integral component of membrane (GO:0016021)				breast(3)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|liver(2)|lung(16)|ovary(2)|pancreas(1)|skin(1)|urinary_tract(2)	46			OV - Ovarian serous cystadenocarcinoma(117;0.00156)|Epithelial(96;0.0256)|all cancers(119;0.0744)			AGCACCGAAGAAAATTAAAAC	0.348																																					p.R1358fs		Atlas-INDEL	.											.	ANKAR	184	.	0			c.4073delG						.						95.0	107.0	103.0					2																	190611122		2202	4298	6500	SO:0001589	frameshift_variant	150709	exon23			.	AJ549812	CCDS33351.1, CCDS33351.2	2q32.2	2013-02-14			ENSG00000151687	ENSG00000151687		"""Ankyrin repeat domain containing"", ""Armadillo repeat containing"""	26350	protein-coding gene	gene with protein product		609803				15110750	Standard	NM_144708		Approved	FLJ25415	uc002uqw.2	Q7Z5J8	OTTHUMG00000154398	ENST00000520309.1:c.4074delA	chr2.hg19:g.190611122delA	ENSP00000427882:p.Arg1358fs	147.0	0.0		158.0	10.0	NM_144708	Q3ZCS6|Q4G0M2|Q6ZU02	Frame_Shift_Del	DEL	ENST00000520309.1	hg19	CCDS33351.2																																																																																			.	.		0.348	ANKAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335045.3	NM_144708	
GCM2	9247	hgsc.bcm.edu	37	6	10876681	10876681	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:10876681delA	ENST00000379491.4	-	3	600	c.453delT	c.(451-453)tttfs	p.F151fs	RP11-637O19.3_ENST00000480294.1_Intron|SYCP2L_ENST00000543878.1_Intron	NM_004752.3	NP_004743.1	O75603	GCM2_HUMAN	glial cells missing homolog 2 (Drosophila)	151					cell differentiation (GO:0030154)|cellular calcium ion homeostasis (GO:0006874)|cellular phosphate ion homeostasis (GO:0030643)|cellular response to organic substance (GO:0071310)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|parathyroid gland development (GO:0060017)|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 (GO:0043565)			NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)	30	Breast(50;0.0838)|Ovarian(93;0.107)	all_hematologic(90;0.135)				GACCTACCTGAAAAAAGATCG	0.502																																					p.Q152fs		Atlas-INDEL	.											.	GCM2	81	.	0			c.454delC						.						88.0	76.0	80.0					6																	10876681		2203	4300	6503	SO:0001589	frameshift_variant	9247	exon3			.	AF079550	CCDS4517.1	6p24.2	2008-08-29	2001-11-28	2002-09-27	ENSG00000124827	ENSG00000124827			4198	protein-coding gene	gene with protein product		603716	"""glial cells missing (Drosophila) homolog b"""	GCMB		9928992	Standard	NM_004752		Approved	hGCMb	uc003mzn.4	O75603	OTTHUMG00000014249	ENST00000379491.4:c.453delT	chr6.hg19:g.10876681delA	ENSP00000368805:p.Phe151fs	98.0	0.0		177.0	14.0	NM_004752	D3GDV6|Q5THN5	Frame_Shift_Del	DEL	ENST00000379491.4	hg19	CCDS4517.1																																																																																			.	.		0.502	GCM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039844.1		
PIF1	80119	hgsc.bcm.edu	37	15	65108937	65108937	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:65108937delA	ENST00000268043.4	-	12	1796	c.1702delT	c.(1702-1704)tctfs	p.S568fs	PIF1_ENST00000333425.6_Frame_Shift_Del_p.S568fs|PIF1_ENST00000559239.1_Frame_Shift_Del_p.S568fs					PIF1 5'-to-3' DNA helicase											kidney(1)|lung(1)	2						CGGCCCAGAGAAATCTCCACA	0.612																																					p.S568fs		Atlas-INDEL	.											PIF1_ENST00000268043,NS,carcinoma,0,1	PIF1	43	.	0			c.1703delC						.						42.0	38.0	40.0					15																	65108937		2200	4295	6495	SO:0001589	frameshift_variant	80119	exon12			.	AK026345	CCDS10195.2, CCDS66797.1	15q22.1	2013-05-13	2013-05-13	2006-11-24	ENSG00000140451	ENSG00000140451	3.6.4.12		26220	protein-coding gene	gene with protein product		610953	"""chromosome 15 open reading frame 20"", ""PIF1 5'-to-3' DNA helicase homolog (S. cerevisiae)"""	C15orf20		10926538, 16522649	Standard	NM_025049		Approved	FLJ22692	uc002ant.2	Q9H611	OTTHUMG00000132974	ENST00000268043.4:c.1702delT	chr15.hg19:g.65108937delA	ENSP00000268043:p.Ser568fs	180.0	0.0		209.0	13.0	NM_025049		Frame_Shift_Del	DEL	ENST00000268043.4	hg19	CCDS10195.2																																																																																			.	.		0.612	PIF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256533.1	NM_025049	
HNRNPUL1	11100	hgsc.bcm.edu	37	19	41811722	41811722	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:41811722delC	ENST00000392006.3	+	14	2577	c.2404delC	c.(2404-2406)cccfs	p.P803fs	HNRNPUL1_ENST00000595018.1_Frame_Shift_Del_p.P703fs|HNRNPUL1_ENST00000593587.1_Frame_Shift_Del_p.P703fs|HNRNPUL1_ENST00000352456.3_Frame_Shift_Del_p.P713fs|HNRNPUL1_ENST00000378215.4_Frame_Shift_Del_p.P699fs|HNRNPUL1_ENST00000602130.1_Intron|HNRNPUL1_ENST00000263367.3_Frame_Shift_Del_p.P714fs	NM_007040.3	NP_008971.2	Q9BUJ2	HNRL1_HUMAN	heterogeneous nuclear ribonucleoprotein U-like 1	803	Necessary for interaction with TP53.|Pro-rich.|Tyr-rich.				gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|regulation of transcription, DNA-templated (GO:0006355)|response to virus (GO:0009615)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(8)|prostate(1)|skin(1)|urinary_tract(1)	29						CCCACCGCCACCCCCCACTGC	0.637																																					p.P801fs		Atlas-INDEL	.											.	HNRNPUL1	73	.	0			c.2403delA						.						36.0	38.0	37.0					19																	41811722		2202	4299	6501	SO:0001589	frameshift_variant	11100	exon14			.	AJ007509	CCDS12576.1, CCDS12577.1	19q13.2	2013-06-12		2008-04-18	ENSG00000105323	ENSG00000105323			17011	protein-coding gene	gene with protein product	"""E1B 55kDa associated protein 5"""	605800		HNRPUL1		9733834, 12489984	Standard	XM_005258459		Approved	E1B-AP5, E1BAP5, FLJ12944	uc002oqb.4	Q9BUJ2	OTTHUMG00000182740	ENST00000392006.3:c.2404delC	chr19.hg19:g.41811722delC	ENSP00000375863:p.Pro803fs	98.0	0.0		112.0	10.0	NM_007040	B3KMW7|O76022|Q6ZSZ0|Q7L8P4|Q8N6Z4|Q96G37|Q9HAL3|Q9UG75	Frame_Shift_Del	DEL	ENST00000392006.3	hg19	CCDS12576.1																																																																																			.	.		0.637	HNRNPUL1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463406.1	NM_144732, NM_007040	
HELLS	3070	hgsc.bcm.edu	37	10	96348094	96348094	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:96348094delT	ENST00000348459.5	+	13	1540	c.1435delT	c.(1435-1437)tttfs	p.F479fs	HELLS_ENST00000394036.1_3'UTR|HELLS_ENST00000394045.1_Frame_Shift_Del_p.F381fs|RP11-119K6.6_ENST00000432120.1_RNA|HELLS_ENST00000239026.6_3'UTR|HELLS_ENST00000371332.4_Frame_Shift_Del_p.F525fs	NM_018063.3	NP_060533.2			helicase, lymphoid-specific											endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(4)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	22		Colorectal(252;0.0429)		all cancers(201;2.13e-05)		GCAGGAGATCTTTTATACAGC	0.368																																					p.I478fs		Atlas-INDEL	.											.	HELLS	63	.	0			c.1434delC						.						109.0	106.0	107.0					10																	96348094		2203	4300	6503	SO:0001589	frameshift_variant	3070	exon13			.	AF155827	CCDS7434.1, CCDS73162.1, CCDS73163.1, CCDS73164.1, CCDS73165.1	10q24.2	2008-08-01			ENSG00000119969	ENSG00000119969			4861	protein-coding gene	gene with protein product	"""SWI/SNF2-related, matrix-associated, actin-dependent regulator of chromatin, subfamily A, member 6"", ""proliferation-associated SNF2-like protein"""	603946				9878251, 10910076	Standard	NM_018063		Approved	PASG, SMARCA6, LSH, Nbla10143	uc001kjt.3	Q9NRZ9	OTTHUMG00000018793	ENST00000348459.5:c.1435delT	chr10.hg19:g.96348094delT	ENSP00000239027:p.Phe479fs	135.0	0.0		130.0	10.0	NM_018063		Frame_Shift_Del	DEL	ENST00000348459.5	hg19	CCDS7434.1																																																																																			.	.		0.368	HELLS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049475.1	NM_018063	
ANKRD20A1	84210	hgsc.bcm.edu	37	9	67934789	67934789	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:67934789delA	ENST00000377477.2	+	4	671	c.559delA	c.(559-561)aaafs	p.K189fs	RNU6-368P_ENST00000391117.1_RNA	NM_032250.3	NP_115626.2	Q5TYW2	A20A1_HUMAN	ankyrin repeat domain 20 family, member A1	189						plasma membrane (GO:0005886)				kidney(1)|large_intestine(4)|lung(5)|urinary_tract(1)	11						ATTTTTATTGAAAAAGAAAGC	0.313																																					p.L186fs		Atlas-INDEL	.											.	ANKRD20A1	16	.	0			c.558delG						.						1.0	1.0	1.0					9																	67934789		284	618	902	SO:0001589	frameshift_variant	84210	exon4			.	AL136793	CCDS6620.1	9p12	2014-04-16	2005-08-23	2005-08-23	ENSG00000196774	ENSG00000260691		"""Ankyrin repeat domain containing"""	23665	protein-coding gene	gene with protein product			"""ankyrin repeat domain 20A"""	ANKRD20A			Standard	NM_032250		Approved	DKFZp434A171		Q5TYW2	OTTHUMG00000188594	ENST00000377477.2:c.559delA	chr9.hg19:g.67934789delA	ENSP00000366697:p.Lys189fs	198.0	0.0		193.0	12.0	NM_032250	Q9H0H6	Frame_Shift_Del	DEL	ENST00000377477.2	hg19	CCDS6620.1																																																																																			.	.		0.313	ANKRD20A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083800.1		
EGFR	1956	hgsc.bcm.edu	37	7	55220290	55220290	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:55220290delC	ENST00000275493.2	+	6	857	c.680delC	c.(679-681)tccfs	p.S227fs	EGFR_ENST00000420316.2_Frame_Shift_Del_p.S227fs|EGFR_ENST00000442591.1_Frame_Shift_Del_p.S227fs|EGFR_ENST00000455089.1_Frame_Shift_Del_p.S182fs|EGFR_ENST00000344576.2_Frame_Shift_Del_p.S227fs|EGFR_ENST00000342916.3_Frame_Shift_Del_p.S227fs|EGFR_ENST00000454757.2_Frame_Shift_Del_p.S174fs	NM_005228.3	NP_005219.2	P00533	EGFR_HUMAN	epidermal growth factor receptor	227			Missing (variant EGFR vIII; found in a lung cancer sample; somatic mutation; induces lung cancer when exogenously expressed). {ECO:0000269|PubMed:16672372}.		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)	CGTGGCAAGTCCCCCAGTGAC	0.612		8	"""A, O, Mis"""		"""glioma, NSCLC"""	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)																											p.S227fs		Atlas-INDEL	.	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.679delT						.						72.0	82.0	78.0					7																	55220290		2203	4299	6502	SO:0001589	frameshift_variant	1956	exon6	Familial Cancer Database	incl. Hereditary Lung cancer, Hereditary Non-Small Cell Lung cancer	.		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.680delC	chr7.hg19:g.55220290delC	ENSP00000275493:p.Ser227fs	157.0	0.0		180.0	11.0	NM_005228	O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	Frame_Shift_Del	DEL	ENST00000275493.2	hg19	CCDS5514.1																																																																																			.	.		0.612	EGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251456.2	NM_005228	
SAMD11	148398	hgsc.bcm.edu	37	1	874450	874450	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:874450delC	ENST00000342066.3	+	6	544	c.461delC	c.(460-462)tccfs	p.S154fs		NM_152486.2	NP_689699	Q96NU1	SAM11_HUMAN	sterile alpha motif domain containing 11	154					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00459)|Epithelial(90;1.74e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.93e-23)|Colorectal(212;0.000159)|COAD - Colon adenocarcinoma(227;0.000193)|BRCA - Breast invasive adenocarcinoma(365;0.000472)|Kidney(185;0.0023)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0342)|Lung(427;0.199)		CTGGGCCGCTCCCCCCGTATC	0.622																																					p.S154fs		Atlas-INDEL	.											.	SAMD11	34	.	0			c.460delT						.						38.0	35.0	36.0					1																	874450		2201	4300	6501	SO:0001589	frameshift_variant	148398	exon6			.	BC024295	CCDS2.2	1p36.33	2013-01-10			ENSG00000187634	ENSG00000187634		"""Sterile alpha motif (SAM) domain containing"""	28706	protein-coding gene	gene with protein product						12477932	Standard	NM_152486		Approved	MGC45873	uc001abw.1	Q96NU1	OTTHUMG00000040719	ENST00000342066.3:c.461delC	chr1.hg19:g.874450delC	ENSP00000342313:p.Ser154fs	157.0	0.0		176.0	12.0	NM_152486	A2AA76|I7FV78|I7FV81|I7G0Z6|Q5SV96|Q5SV99|Q5SVA0|Q8N195|Q8TB59	Frame_Shift_Del	DEL	ENST00000342066.3	hg19	CCDS2.2																																																																																			.	.		0.622	SAMD11-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276866.2	NM_152486	
IDI2	91734	hgsc.bcm.edu	37	10	1065633	1065633	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:1065633delT	ENST00000277517.1	-	5	572	c.508delA	c.(508-510)agcfs	p.S170fs	GTPBP4_ENST00000360803.4_3'UTR|IDI2-AS1_ENST00000536039.1_RNA|IDI2-AS1_ENST00000434470.1_RNA|IDI2-AS1_ENST00000428780.2_RNA|IDI2-AS1_ENST00000437374.1_RNA|IDI2-AS1_ENST00000420381.1_RNA	NM_033261.2	NP_150286.1	Q9BXS1	IDI2_HUMAN	isopentenyl-diphosphate delta isomerase 2	170	Nudix hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00794}.				cholesterol biosynthetic process (GO:0006695)|dimethylallyl diphosphate biosynthetic process (GO:0050992)|isopentenyl diphosphate metabolic process (GO:0046490)|isoprenoid biosynthetic process (GO:0008299)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|peroxisome (GO:0005777)	hydrolase activity (GO:0016787)|isopentenyl-diphosphate delta-isomerase activity (GO:0004452)|metal ion binding (GO:0046872)			kidney(1)|large_intestine(3)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	9		Colorectal(49;0.235)	OV - Ovarian serous cystadenocarcinoma(33;0.143)	Epithelial(11;0.067)|OV - Ovarian serous cystadenocarcinoma(14;0.169)|all cancers(11;0.192)		TAGAGGATGCTTTTCGTTTCA	0.522																																					p.S170fs		Atlas-INDEL	.											.	IDI2	20	.	0			c.509delG						.						99.0	89.0	92.0					10																	1065633		2203	4300	6503	SO:0001589	frameshift_variant	91734	exon5			.	AF271725	CCDS7055.1	10p15.3	2003-11-19			ENSG00000148377	ENSG00000148377			23487	protein-coding gene	gene with protein product		615389				12477932	Standard	NM_033261		Approved	IPPI2	uc001ifv.1	Q9BXS1	OTTHUMG00000017537	ENST00000277517.1:c.508delA	chr10.hg19:g.1065633delT	ENSP00000277517:p.Ser170fs	180.0	0.0		183.0	11.0	NM_033261		Frame_Shift_Del	DEL	ENST00000277517.1	hg19	CCDS7055.1																																																																																			.	.		0.522	IDI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046411.1	NM_033261	
TMEFF2	23671	hgsc.bcm.edu	37	2	192818525	192818525	+	Frame_Shift_Del	DEL	T	T	-	rs200174014		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:192818525delT	ENST00000272771.5	-	9	2092	c.908delA	c.(907-909)aagfs	p.K303fs	AC098617.1_ENST00000424116.2_RNA|AC098617.1_ENST00000428980.2_RNA|TMEFF2_ENST00000392314.1_Frame_Shift_Del_p.K303fs	NM_016192.2	NP_057276.2	Q9UIK5	TEFF2_HUMAN	transmembrane protein with EGF-like and two follistatin-like domains 2	303	Required for shedding.					extracellular region (GO:0005576)|integral component of membrane (GO:0016021)				breast(2)|cervix(1)|kidney(2)|large_intestine(4)|liver(1)|lung(12)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27			OV - Ovarian serous cystadenocarcinoma(117;0.0835)			ACTGTAGTCCTTTTTTTCACA	0.398																																					p.K303fs	Pancreas(50;1277 1381 28487 47072)	Atlas-INDEL	.											.	TMEFF2	54	.	0			c.909delG						.			2,4264		1,0,2132	111.0	97.0	102.0			4.1	1.0	2		103	0,8254		0,0,4127	no	frameshift	TMEFF2	NM_016192.2		1,0,6259	A1A1,A1R,RR		0.0,0.0469,0.016			192818525	2,12518	2203	4300	6503	SO:0001589	frameshift_variant	23671	exon9			.	AB017269	CCDS2314.1	2q32.3	2010-05-04			ENSG00000144339	ENSG00000144339			11867	protein-coding gene	gene with protein product	"""transmembrane protein TENB2"", ""tomoregulin"", ""cancer/testis antigen family 120, member 2"""	605734				10903839	Standard	NM_016192		Approved	TENB2, HPP1, TR, TPEF, CT120.2	uc002utc.3	Q9UIK5	OTTHUMG00000132723	ENST00000272771.5:c.908delA	chr2.hg19:g.192818525delT	ENSP00000272771:p.Lys303fs	113.0	0.0		138.0	11.0	NM_016192	Q2FA44|Q4ZFW4|Q53H90|Q53RE1|Q8N2R5|Q9NR15|Q9NSS5|Q9P2Y9|Q9UK65	Frame_Shift_Del	DEL	ENST00000272771.5	hg19	CCDS2314.1																																																																																			.	.		0.398	TMEFF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256065.2	NM_016192	
UNC13C	440279	hgsc.bcm.edu	37	15	54626040	54626040	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:54626040delT	ENST00000260323.11	+	15	4570	c.4570delT	c.(4570-4572)tttfs	p.F1525fs	UNC13C_ENST00000537900.1_Frame_Shift_Del_p.F1523fs|UNC13C_ENST00000545554.1_Frame_Shift_Del_p.F1525fs	NM_001080534.1	NP_001074003.1	Q8NB66	UN13C_HUMAN	unc-13 homolog C (C. elegans)	1525					exocytosis (GO:0006887)|intracellular signal transduction (GO:0035556)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)			breast(3)|endometrium(5)|kidney(5)|large_intestine(20)|lung(70)|ovary(6)|pancreas(2)|prostate(2)|upper_aerodigestive_tract(4)|urinary_tract(4)	121				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)		AAGTATCACCTTTTTTAGGAT	0.368																																					p.T1523fs		Atlas-INDEL	.											.	UNC13C	674	.	0			c.4569delC						.						137.0	125.0	129.0					15																	54626040		1853	4078	5931	SO:0001589	frameshift_variant	440279	exon14			.	AK091491	CCDS45264.1	15q21.3	2012-10-02			ENSG00000137766	ENSG00000137766			23149	protein-coding gene	gene with protein product		614568					Standard	NM_001080534		Approved	Munc13-3, DKFZp547H074	uc021smr.1	Q8NB66	OTTHUMG00000172542	ENST00000260323.11:c.4570delT	chr15.hg19:g.54626040delT	ENSP00000260323:p.Phe1525fs	113.0	0.0		165.0	11.0	NM_001080534	Q0P613|Q8ND48|Q96NP3	Frame_Shift_Del	DEL	ENST00000260323.11	hg19	CCDS45264.1																																																																																			.	.		0.368	UNC13C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419028.3	NM_173166	
TACR2	6865	hgsc.bcm.edu	37	10	71164684	71164684	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:71164684delG	ENST00000373306.4	-	5	1638	c.1095delC	c.(1093-1095)cccfs	p.P365fs	TACR2_ENST00000373307.1_Frame_Shift_Del_p.P153fs	NM_001057.2	NP_001048.2	P21452	NK2R_HUMAN	tachykinin receptor 2	365					excretion (GO:0007588)|intestine smooth muscle contraction (GO:0014827)|muscle contraction (GO:0006936)|negative regulation of luteinizing hormone secretion (GO:0033685)|operant conditioning (GO:0035106)|positive regulation of acetylcholine secretion, neurotransmission (GO:0014057)|positive regulation of uterine smooth muscle contraction (GO:0070474)|positive regulation of vascular permeability (GO:0043117)|prolactin secretion (GO:0070459)|tachykinin receptor signaling pathway (GO:0007217)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	substance K receptor activity (GO:0016497)|tachykinin receptor activity (GO:0004995)			endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	11						TAGCCTCGGAGGGGGCTGTGT	0.562																																					p.S366fs		Atlas-INDEL	.											.	TACR2	37	.	0			c.1096delT						.						83.0	81.0	82.0					10																	71164684		2203	4300	6503	SO:0001589	frameshift_variant	6865	exon5			.		CCDS7293.1	10q22.1	2012-09-20			ENSG00000075073	ENSG00000075073		"""GPCR / Class A : Tachykinin receptors"""	11527	protein-coding gene	gene with protein product		162321		TAC2R, NKNAR			Standard	NM_001057		Approved	SKR, NK2R	uc001jpn.2	P21452	OTTHUMG00000018377	ENST00000373306.4:c.1095delC	chr10.hg19:g.71164684delG	ENSP00000362403:p.Pro365fs	132.0	0.0		165.0	10.0	NM_001057	A8K7I1|Q4QRI5|Q8NGQ8|Q9UDE6|Q9UDE7	Frame_Shift_Del	DEL	ENST00000373306.4	hg19	CCDS7293.1																																																																																			.	.		0.562	TACR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048411.1		
KCNH5	27133	hgsc.bcm.edu	37	14	63174303	63174303	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:63174303delG	ENST00000322893.7	-	11	3158	c.2890delC	c.(2890-2892)cagfs	p.Q964fs	KCNH5_ENST00000420622.2_3'UTR	NM_139318.3	NP_647479.2	Q8NCM2	KCNH5_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 5	964					potassium ion transmembrane transport (GO:0071805)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(33)|ovary(5)|prostate(2)|skin(17)|upper_aerodigestive_tract(4)|urinary_tract(2)	99				OV - Ovarian serous cystadenocarcinoma(108;0.00958)|BRCA - Breast invasive adenocarcinoma(234;0.168)		CATGGTATCTGGGGGGGTACT	0.393																																					p.Q964fs		Atlas-INDEL	.											KCNH5,NS,carcinoma,-1,1	KCNH5	320	.	0			c.2891delA						.						110.0	126.0	120.0					14																	63174303		2203	4300	6503	SO:0001589	frameshift_variant	27133	exon11			.	U69185	CCDS9756.1, CCDS45122.1	14q23.1	2012-07-05			ENSG00000140015	ENSG00000140015		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6254	protein-coding gene	gene with protein product		605716				9738473, 16382104	Standard	NM_139318		Approved	Kv10.2, H-EAG2, eag2	uc001xfx.3	Q8NCM2	OTTHUMG00000029041	ENST00000322893.7:c.2890delC	chr14.hg19:g.63174303delG	ENSP00000321427:p.Gln964fs	147.0	0.0		159.0	11.0	NM_139318	C9JP98	Frame_Shift_Del	DEL	ENST00000322893.7	hg19	CCDS9756.1																																																																																			.	.		0.393	KCNH5-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411747.1	NM_139318	
KIF24	347240	hgsc.bcm.edu	37	9	34306393	34306393	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:34306393delT	ENST00000402558.2	-	2	694	c.670delA	c.(670-672)atcfs	p.I224fs	KIF24_ENST00000379166.2_Frame_Shift_Del_p.I224fs|KIF24_ENST00000379174.3_Frame_Shift_Del_p.I224fs|KIF24_ENST00000345050.2_Frame_Shift_Del_p.I224fs			Q5T7B8	KIF24_HUMAN	kinesin family member 24	224	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|cilium assembly (GO:0042384)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)	centriole (GO:0005814)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|protein complex (GO:0043234)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|endometrium(5)|large_intestine(4)|liver(1)|lung(13)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	32			LUSC - Lung squamous cell carcinoma(29;0.0107)			CAAACTCTGATTTTCTCCATC	0.363																																					p.I224fs		Atlas-INDEL	.											.	KIF24	64	.	0			c.671delT						.						182.0	172.0	175.0					9																	34306393		1818	4082	5900	SO:0001589	frameshift_variant	347240	exon3			.	AK001795	CCDS6551.2	9p13.3	2013-01-10			ENSG00000186638	ENSG00000186638		"""Kinesins"", ""Sterile alpha motif (SAM) domain containing"""	19916	protein-coding gene	gene with protein product		613747	"""chromosome 9 open reading frame 48"""	C9orf48		12477932	Standard	NM_194313		Approved	bA571F15.4, FLJ10933, FLJ43884	uc003zua.4	Q5T7B8	OTTHUMG00000019810	ENST00000402558.2:c.670delA	chr9.hg19:g.34306393delT	ENSP00000384433:p.Ile224fs	192.0	0.0		207.0	13.0	NM_194313	Q2TB93|Q5T7B5|Q5T7B7|Q6ZU97|Q6ZUZ2|Q86XZ0|Q9NV43	Frame_Shift_Del	DEL	ENST00000402558.2	hg19	CCDS6551.2																																																																																			.	.		0.363	KIF24-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052150.5		
ZC3H7A	29066	hgsc.bcm.edu	37	16	11868316	11868316	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:11868316delA	ENST00000396516.2	-	8	876	c.679delT	c.(679-681)tctfs	p.S227fs	ZC3H7A_ENST00000355758.4_Frame_Shift_Del_p.S227fs|ZC3H7A_ENST00000575170.1_5'Flank			Q8IWR0	Z3H7A_HUMAN	zinc finger CCCH-type containing 7A	227						nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(3)|kidney(5)|large_intestine(2)|liver(1)|lung(3)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|urinary_tract(2)	25						ACTTCATGAGAAAAACTGGGT	0.448																																					p.S227fs		Atlas-INDEL	.											.	ZC3H7A	72	.	0			c.680delC						.						87.0	86.0	86.0					16																	11868316		2197	4300	6497	SO:0001589	frameshift_variant	29066	exon9			.	AF161540	CCDS10550.1	16p13-p12	2013-01-11	2005-06-02	2005-06-08	ENSG00000122299	ENSG00000122299		"""Zinc fingers, CCCH-type domain containing"", ""Tetratricopeptide (TTC) repeat domain containing"""	30959	protein-coding gene	gene with protein product			"""zinc finger CCCH-type domain containing 7"", ""zinc finger CCCH-type containing 7"""	ZC3HDC7, ZC3H7		11042152	Standard	NM_014153		Approved	HSPC055, FLJ20318	uc002dbl.3	Q8IWR0	OTTHUMG00000129825	ENST00000396516.2:c.679delT	chr16.hg19:g.11868316delA	ENSP00000379773:p.Ser227fs	84.0	0.0		112.0	11.0	NM_014153	D3DUG5|Q9NPE9	Frame_Shift_Del	DEL	ENST00000396516.2	hg19	CCDS10550.1																																																																																			.	.		0.448	ZC3H7A-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437066.1	NM_014153	
MMRN1	22915	hgsc.bcm.edu	37	4	90816715	90816715	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:90816715delA	ENST00000394980.1	+	2	912	c.593delA	c.(592-594)caafs	p.Q198fs	MMRN1_ENST00000264790.2_Frame_Shift_Del_p.Q198fs|MMRN1_ENST00000394981.1_Frame_Shift_Del_p.Q164fs			Q13201	MMRN1_HUMAN	multimerin 1	198					blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|platelet alpha granule lumen (GO:0031093)				breast(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(12)|liver(2)|lung(34)|ovary(5)|prostate(1)|skin(6)|stomach(1)|urinary_tract(2)	72		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;6.96e-05)		ACTGACTACCAAAAATCAAAT	0.443																																					p.Q198fs		Atlas-INDEL	.											.	MMRN1	174	.	0			c.592delC						.						32.0	33.0	33.0					4																	90816715		2203	4300	6503	SO:0001589	frameshift_variant	22915	exon1			.	U27109	CCDS3635.1	4q22	2008-02-05	2004-03-02	2004-03-02	ENSG00000138722	ENSG00000138722		"""EMI domain containing"""	7178	protein-coding gene	gene with protein product	"""glycoprotein Ia*"""	601456	"""multimerin"""	MMRN		7629143, 10828608	Standard	NM_007351		Approved	ECM, EMILIN4, GPIa*	uc003hst.3	Q13201	OTTHUMG00000130947	ENST00000394980.1:c.593delA	chr4.hg19:g.90816715delA	ENSP00000378431:p.Gln198fs	73.0	0.0		76.0	11.0	NM_007351	Q4W5L1|Q6P3T8|Q6ZUL9	Frame_Shift_Del	DEL	ENST00000394980.1	hg19	CCDS3635.1																																																																																			.	.		0.443	MMRN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253546.2	NM_007351	
ZNF630	57232	hgsc.bcm.edu	37	X	47919479	47919479	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:47919479delT	ENST00000409324.3	-	5	578	c.352delA	c.(352-354)atcfs	p.I118fs	ZNF630-AS1_ENST00000436124.1_RNA|ZNF630_ENST00000276054.4_5'UTR|ZNF630_ENST00000442455.3_Frame_Shift_Del_p.I104fs	NM_001037735.2	NP_001032824.2	Q2M218	ZN630_HUMAN	zinc finger protein 630	118					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|large_intestine(6)|lung(11)|ovary(1)	19						ATATGCCAGATTTTTAAAACA	0.373																																					p.I118fs		Atlas-INDEL	.											.	ZNF630	71	.	0			c.353delT						.						49.0	41.0	44.0					X																	47919479		2193	4284	6477	SO:0001589	frameshift_variant	57232	exon5			.	AK000580	CCDS35237.2, CCDS75971.1	Xp11.3-p11.1	2013-01-08			ENSG00000221994	ENSG00000221994		"""Zinc fingers, C2H2-type"", ""-"""	28855	protein-coding gene	gene with protein product		300819					Standard	NM_001037735		Approved	BC037316, dJ54B20.2, FLJ20573, MGC138344	uc004div.4	Q2M218	OTTHUMG00000021463	ENST00000409324.3:c.352delA	chrX.hg19:g.47919479delT	ENSP00000386393:p.Ile118fs	126.0	0.0		176.0	11.0	NM_001037735	F8WAG4|Q5H8Z5	Frame_Shift_Del	DEL	ENST00000409324.3	hg19	CCDS35237.2																																																																																			.	.		0.373	ZNF630-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327254.1	NM_001037735	
NEK11	79858	hgsc.bcm.edu	37	3	130887702	130887702	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:130887702delA	ENST00000510769.1	+	9	1143	c.890delA	c.(889-891)gaafs	p.E297fs	NEK11_ENST00000510688.1_Frame_Shift_Del_p.E402fs|NEK11_ENST00000356918.4_Frame_Shift_Del_p.E402fs|NEK11_ENST00000511262.1_Frame_Shift_Del_p.E402fs|NEK11_ENST00000508196.1_Frame_Shift_Del_p.E402fs|NEK11_ENST00000383366.4_Frame_Shift_Del_p.E402fs|NEK11_ENST00000507910.1_Frame_Shift_Del_p.E402fs|NEK11_ENST00000412440.2_Intron|NEK11_ENST00000429253.2_Frame_Shift_Del_p.E402fs					NIMA-related kinase 11											breast(2)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(8)|lung(14)|stomach(1)|urinary_tract(2)	33						GGAATGGAAGAAAAGGAGGAG	0.428																																					p.E402fs		Atlas-INDEL	.											.	NEK11	76	.	0			c.1204delG						.						68.0	65.0	66.0					3																	130887702		2203	4300	6503	SO:0001589	frameshift_variant	79858	exon13			.	AK027148	CCDS3069.1, CCDS46915.1, CCDS54639.1	3q22.1	2012-11-15	2012-11-15		ENSG00000114670	ENSG00000114670			18593	protein-coding gene	gene with protein product		609779	"""NIMA (never in mitosis gene a)- related kinase 11"""				Standard	NM_024800		Approved	FLJ23495	uc003eny.3	Q8NG66	OTTHUMG00000159654	ENST00000510769.1:c.890delA	chr3.hg19:g.130887702delA	ENSP00000421549:p.Glu297fs	101.0	0.0		160.0	10.0	NM_024800		Frame_Shift_Del	DEL	ENST00000510769.1	hg19																																																																																				.	.		0.428	NEK11-005	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000356757.1	NM_024800	
DGCR8	54487	hgsc.bcm.edu	37	22	20094164	20094164	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr22:20094164delA	ENST00000351989.3	+	11	2368	c.1939delA	c.(1939-1941)aaafs	p.K647fs	DGCR8_ENST00000407755.1_Frame_Shift_Del_p.K614fs|DGCR8_ENST00000383024.2_Frame_Shift_Del_p.K614fs	NM_022720.6	NP_073557.3	Q8WYQ5	DGCR8_HUMAN	DGCR8 microprocessor complex subunit	647	DRBM 2. {ECO:0000255|PROSITE- ProRule:PRU00266}.|Necessary for heme-binding and pri-miRNA processing.|Necessary for interaction with DROSHA.				gene expression (GO:0010467)|primary miRNA processing (GO:0031053)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)			NS(2)|breast(1)|endometrium(5)|large_intestine(5)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	22	Colorectal(54;0.0993)					GGTTCCTGGGAAAAACCAGAA	0.557																																					p.G646fs		Atlas-INDEL	.											.	DGCR8	53	.	0			c.1938delG						.						137.0	129.0	132.0					22																	20094164		2203	4300	6503	SO:0001589	frameshift_variant	54487	exon11			.	AF165527, AB050770	CCDS13773.1, CCDS54501.1	22q11.2	2013-05-02	2013-05-02		ENSG00000128191	ENSG00000128191			2847	protein-coding gene	gene with protein product		609030	"""chromosome 22 open reading frame 12"", ""DiGeorge syndrome critical region gene 8"""	C22orf12		21454614	Standard	NM_001190326		Approved	DGCRK6, Gy1, pasha	uc002zri.3	Q8WYQ5	OTTHUMG00000150503	ENST00000351989.3:c.1939delA	chr22.hg19:g.20094164delA	ENSP00000263209:p.Lys647fs	195.0	0.0		230.0	14.0	NM_022720	B2R8G1|Q6DCB2|Q6MZE9|Q6Y2L0|Q96G39|Q96GP8|Q9H6L8|Q9H6T7|Q9NRW2	Frame_Shift_Del	DEL	ENST00000351989.3	hg19	CCDS13773.1																																																																																			.	.		0.557	DGCR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318654.1		
BAI2	576	hgsc.bcm.edu	37	1	32196841	32196841	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:32196841delC	ENST00000373658.3	-	29	4281	c.3940delG	c.(3940-3942)gagfs	p.E1314fs	BAI2_ENST00000257070.4_Frame_Shift_Del_p.E1281fs|BAI2_ENST00000440175.2_Frame_Shift_Del_p.E923fs|BAI2_ENST00000398538.1_Frame_Shift_Del_p.E1302fs|BAI2_ENST00000373655.2_Frame_Shift_Del_p.E1314fs|BAI2_ENST00000398556.3_Frame_Shift_Del_p.E1229fs|BAI2_ENST00000465256.1_5'UTR|BAI2_ENST00000527361.1_Frame_Shift_Del_p.E1281fs|BAI2_ENST00000398542.1_Frame_Shift_Del_p.E1214fs|BAI2_ENST00000398547.1_Frame_Shift_Del_p.E1247fs	NM_001703.2	NP_001694.2	O60241	BAI2_HUMAN	brain-specific angiogenesis inhibitor 2	1314					G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|neuropeptide signaling pathway (GO:0007218)|peripheral nervous system development (GO:0007422)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(5)|central_nervous_system(2)|endometrium(1)|large_intestine(7)|liver(2)|lung(24)|ovary(7)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	55		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0606)|all_neural(195;0.0837)|Breast(348;0.174)		STAD - Stomach adenocarcinoma(196;0.0557)		GGCGGAGGCTCCCCCAGCCCT	0.677																																					p.E1314fs		Atlas-INDEL	.											.	BAI2	128	.	0			c.3941delA						.						23.0	21.0	22.0					1																	32196841		2199	4298	6497	SO:0001589	frameshift_variant	576	exon29			.	AB005298	CCDS72746.1, CCDS72747.1	1p35	2014-08-08			ENSG00000121753	ENSG00000121753		"""-"", ""GPCR / Class B : Orphans"""	944	protein-coding gene	gene with protein product		602683				9533023	Standard	XM_006710783		Approved		uc001btn.3	O60241	OTTHUMG00000003885	ENST00000373658.3:c.3940delG	chr1.hg19:g.32196841delC	ENSP00000362762:p.Glu1314fs	182.0	0.0		178.0	12.0	NM_001703	B9EGK9|Q5T6K0|Q8NGW8|Q96GZ9	Frame_Shift_Del	DEL	ENST00000373658.3	hg19	CCDS346.2																																																																																			.	.		0.677	BAI2-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000381838.1	NM_001703	
DCAF8L1	139425	hgsc.bcm.edu	37	X	27997984	27997984	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:27997984delG	ENST00000441525.1	-	1	1582	c.1468delC	c.(1468-1470)cacfs	p.H490fs		NM_001017930.1	NP_001017930.1	A6NGE4	DC8L1_HUMAN	DDB1 and CUL4 associated factor 8-like 1	490										NS(1)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(24)|ovary(3)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	56						AGGTAAGGGTGGGGTTCAAGA	0.498																																					p.H490fs		Atlas-INDEL	.											.	DCAF8L1	121	.	0			c.1469delA						.						76.0	69.0	72.0					X																	27997984		2202	4300	6502	SO:0001589	frameshift_variant	139425	exon1			.		CCDS35222.1	Xp22.11	2013-01-09	2009-07-17	2009-07-17	ENSG00000226372	ENSG00000226372		"""WD repeat domain containing"""	31810	protein-coding gene	gene with protein product			"""WD repeat domain 42B"""	WDR42B			Standard	NM_001017930		Approved		uc004dbx.1	A6NGE4	OTTHUMG00000021312	ENST00000441525.1:c.1468delC	chrX.hg19:g.27997984delG	ENSP00000405222:p.His490fs	141.0	0.0		166.0	10.0	NM_001017930	B3KXX1	Frame_Shift_Del	DEL	ENST00000441525.1	hg19	CCDS35222.1																																																																																			.	.		0.498	DCAF8L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056150.2	XM_066690	
DFNA5	1687	hgsc.bcm.edu	37	7	24738821	24738821	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:24738821delG	ENST00000342947.3	-	10	1740	c.1315delC	c.(1315-1317)ctgfs	p.L439fs	DFNA5_ENST00000419307.1_Frame_Shift_Del_p.L275fs|DFNA5_ENST00000409970.1_Frame_Shift_Del_p.L275fs|DFNA5_ENST00000545231.1_Frame_Shift_Del_p.L275fs|DFNA5_ENST00000409775.3_Frame_Shift_Del_p.L439fs	NM_004403.2	NP_004394.1	O60443	DFNA5_HUMAN	deafness, autosomal dominant 5	439					apoptotic process (GO:0006915)|inner ear receptor cell differentiation (GO:0060113)|negative regulation of cell proliferation (GO:0008285)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|prostate(3)|stomach(1)	19						GTATCTTTCAGGGGAGTCAAG	0.418																																					p.L439fs	GBM(78;184 1250 20134 20900 23600)	Atlas-INDEL	.											.	DFNA5	51	.	0			c.1316delT						.						69.0	64.0	66.0					7																	24738821		2203	4300	6503	SO:0001589	frameshift_variant	1687	exon10			.	AF007790	CCDS5389.1, CCDS47563.1	7p15	2011-07-01			ENSG00000105928	ENSG00000105928			2810	protein-coding gene	gene with protein product		608798				8589696, 9450185	Standard	NM_004403		Approved	ICERE-1	uc010kus.1	O60443	OTTHUMG00000023237	ENST00000342947.3:c.1315delC	chr7.hg19:g.24738821delG	ENSP00000339587:p.Leu439fs	227.0	0.0		306.0	22.0	NM_001127453	A4D156|B2RAX9|B3KT05|O14590|Q08AQ8|Q9UBV3	Frame_Shift_Del	DEL	ENST00000342947.3	hg19	CCDS5389.1																																																																																			.	.		0.418	DFNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214060.2	NM_004403	
DTNBP1	84062	hgsc.bcm.edu	37	6	15615504	15615504	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:15615504delT	ENST00000344537.5	-	6	654	c.482delA	c.(481-483)aatfs	p.N161fs	DTNBP1_ENST00000355917.3_Frame_Shift_Del_p.N161fs|DTNBP1_ENST00000338950.5_Frame_Shift_Del_p.N161fs	NM_032122.4	NP_115498.2	Q96EV8	DTBP1_HUMAN	dystrobrevin binding protein 1	161					actin cytoskeleton reorganization (GO:0031532)|anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|blood coagulation (GO:0007596)|melanosome organization (GO:0032438)|membrane organization (GO:0061024)|neuron projection development (GO:0031175)|neuron projection morphogenesis (GO:0048812)|platelet dense granule organization (GO:0060155)|positive regulation of gene expression (GO:0010628)|positive regulation of neurotransmitter secretion (GO:0001956)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of dopamine receptor signaling pathway (GO:0060159)|regulation of dopamine secretion (GO:0014059)	axon (GO:0030424)|BLOC-1 complex (GO:0031083)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|growth cone (GO:0030426)|neuron projection (GO:0043005)|nucleus (GO:0005634)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)|synaptic vesicle membrane (GO:0030672)				cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(5)|ovary(1)|skin(2)	14	Breast(50;0.0289)|Ovarian(93;0.103)	all_hematologic(90;0.0895)	Epithelial(50;0.211)			TCACCTCTTATTTTTCTTGTA	0.393									Hermansky-Pudlak syndrome																												p.N161fs		Atlas-INDEL	.											.	DTNBP1	56	.	0			c.483delT						.						168.0	160.0	163.0					6																	15615504		2203	4300	6503	SO:0001589	frameshift_variant	84062	exon6	Familial Cancer Database	HPS, HPS1-8	.	AF394226	CCDS4534.1, CCDS4535.1, CCDS75404.1, CCDS75405.1	6p22.3	2013-09-27			ENSG00000047579	ENSG00000047579		"""Biogenesis of lysosomal organelles complex-1 subunits"""	17328	protein-coding gene	gene with protein product	"""dysbindin-1"", ""biogenesis of lysosomal organelles complex-1, subunit 8"""	607145				11316798	Standard	NM_032122		Approved	Dysbindin, My031, HPS7, DBND, BLOC1S8	uc003nbm.3	Q96EV8	OTTHUMG00000014295	ENST00000344537.5:c.482delA	chr6.hg19:g.15615504delT	ENSP00000341680:p.Asn161fs	161.0	0.0		251.0	18.0	NM_183040	A8K3V3|Q5THY3|Q5THY4|Q96NV2|Q9H0U2|Q9H3J5	Frame_Shift_Del	DEL	ENST00000344537.5	hg19	CCDS4534.1																																																																																			.	.		0.393	DTNBP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000039933.2	NM_032122	
TAF1	6872	hgsc.bcm.edu	37	X	70597472	70597472	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:70597472delT	ENST00000373790.4	+	6	782	c.731delT	c.(730-732)cttfs	p.L244fs	TAF1_ENST00000276072.3_Frame_Shift_Del_p.L265fs|TAF1_ENST00000423759.1_Frame_Shift_Del_p.L265fs|TAF1_ENST00000449580.1_Frame_Shift_Del_p.L244fs	NM_004606.3|NM_138923.2	NP_004597.2|NP_620278.1	P21675	TAF1_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa	244	Protein kinase 1.				cellular response to DNA damage stimulus (GO:0006974)|DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|histone acetylation (GO:0016573)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|protein autophosphorylation (GO:0046777)|regulation of transcription involved in G2/M transition of mitotic cell cycle (GO:0000117)|RNA polymerase II transcriptional preinitiation complex assembly (GO:0051123)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	ATP binding (GO:0005524)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein serine/threonine kinase activity (GO:0004674)|sequence-specific DNA binding (GO:0043565)|TBP-class protein binding (GO:0017025)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			breast(13)|central_nervous_system(6)|cervix(1)|endometrium(25)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(16)|lung(34)|ovary(9)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	124	Renal(35;0.156)	all_lung(315;0.000321)				TTTCTACGTCTTTTTGGACCA	0.473																																					p.L265fs		Atlas-INDEL	.											.	TAF1	439	.	0			c.793delC						.						128.0	98.0	108.0					X																	70597472		2203	4300	6503	SO:0001589	frameshift_variant	6872	exon6			.		CCDS14412.1, CCDS35325.1, CCDS69783.1	Xq13.1	2011-07-01	2002-08-29	2001-12-07	ENSG00000147133	ENSG00000147133		"""Chromatin-modifying enzymes / K-acetyltransferases"""	11535	protein-coding gene	gene with protein product		313650	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, A, 250kD"", ""dystonia 3 (with Parkinsonism)"""	TAF2A, BA2R, CCG1, CCGS, DYT3		3556424, 12928496, 17952504	Standard	XM_005262295		Approved	NSCL2, TAFII250, KAT4, DYT3/TAF1	uc004dzt.4	P21675	OTTHUMG00000022723	ENST00000373790.4:c.731delT	chrX.hg19:g.70597472delT	ENSP00000362895:p.Leu244fs	113.0	0.0		159.0	10.0	NM_004606	A5CVC8|A5CVC9|A5CVD0|A5CVD1|B1Q2X3|Q59FZ3|Q6IUZ1|Q70Q86|Q70Q87|Q70T00|Q70T01|Q70T02|Q70T03	Frame_Shift_Del	DEL	ENST00000373790.4	hg19	CCDS35325.1																																																																																			.	.		0.473	TAF1-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058995.2	NM_004606	
HS3ST4	9951	hgsc.bcm.edu	37	16	25704315	25704315	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:25704315delG	ENST00000331351.5	+	1	969	c.577delG	c.(577-579)gggfs	p.G193fs		NM_006040.2	NP_006031.2	Q9Y661	HS3S4_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 4	193					heparan sulfate proteoglycan metabolic process (GO:0030201)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity (GO:0008467)			breast(2)|endometrium(3)|large_intestine(1)|lung(9)	15				GBM - Glioblastoma multiforme(48;0.0988)		CCCCGACTATGGGGAGAAGAA	0.701																																					p.Y192X		Atlas-INDEL	.											.	HS3ST4	120	.	0			c.576delT						.						11.0	17.0	15.0					16																	25704315		1966	4115	6081	SO:0001589	frameshift_variant	9951	exon1			.	AF105378	CCDS53995.1	16p11.2	2008-03-12			ENSG00000182601	ENSG00000182601	2.8.2.23	"""Sulfotransferases, membrane-bound"""	5200	protein-coding gene	gene with protein product		604059				9988767	Standard	NM_006040		Approved	3OST4	uc002dof.3	Q9Y661	OTTHUMG00000059978	ENST00000331351.5:c.577delG	chr16.hg19:g.25704315delG	ENSP00000330606:p.Gly193fs	94.0	0.0		146.0	10.0	NM_006040	Q5QI42|Q8NDC2	Frame_Shift_Del	DEL	ENST00000331351.5	hg19	CCDS53995.1																																																																																			.	.		0.701	HS3ST4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133286.2	NM_006040	
LONP2	83752	hgsc.bcm.edu	37	16	48295434	48295434	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:48295434delA	ENST00000285737.4	+	5	916	c.823delA	c.(823-825)aaafs	p.K276fs	LONP2_ENST00000535754.1_Frame_Shift_Del_p.K232fs	NM_031490.2	NP_113678.2			lon peptidase 2, peroxisomal											breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31						CATGCTAGAGAAAAAAATACG	0.343																																					p.E274fs		Atlas-INDEL	.											.	LONP2	63	.	0			c.822delG						.						132.0	131.0	131.0					16																	48295434		2200	4300	6500	SO:0001589	frameshift_variant	83752	exon5			.	AJ548761	CCDS10734.1, CCDS73880.1	16q12.1	2010-04-21			ENSG00000102910	ENSG00000102910		"""ATPases / AAA-type"""	20598	protein-coding gene	gene with protein product						14561759	Standard	XM_005256191		Approved	MGC4840, LONP, LONPL	uc002efi.1	Q86WA8	OTTHUMG00000133144	ENST00000285737.4:c.823delA	chr16.hg19:g.48295434delA	ENSP00000285737:p.Lys276fs	127.0	0.0		171.0	11.0	NM_031490		Frame_Shift_Del	DEL	ENST00000285737.4	hg19	CCDS10734.1																																																																																			.	.		0.343	LONP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256839.2	NM_031490	
TPBG	7162	hgsc.bcm.edu	37	6	83075723	83075723	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:83075723delC	ENST00000369750.3	+	2	1662	c.1045delC	c.(1045-1047)cccfs	p.P350fs	TPBG_ENST00000535040.1_Frame_Shift_Del_p.P350fs|TPBG_ENST00000543496.1_Frame_Shift_Del_p.P350fs			Q13641	TPBG_HUMAN	trophoblast glycoprotein	350					cell adhesion (GO:0007155)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)				central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(6)|ovary(2)|prostate(1)|skin(1)|stomach(1)	15		all_cancers(76;0.000805)|Acute lymphoblastic leukemia(125;3.85e-06)|all_hematologic(105;0.0017)|all_epithelial(107;0.0897)		BRCA - Breast invasive adenocarcinoma(397;0.107)		CCCGATTCTTCCCCCATCCCT	0.498																																					p.L348fs		Atlas-INDEL	.											.	TPBG	37	.	0			c.1044delT						.						107.0	100.0	102.0					6																	83075723		2203	4300	6503	SO:0001589	frameshift_variant	7162	exon2			.	AJ012159	CCDS4995.1	6q14-q15	2008-07-29			ENSG00000146242	ENSG00000146242			12004	protein-coding gene	gene with protein product		190920				8132670	Standard	NM_006670		Approved	5T4-AG, 5T4	uc003pjo.3	Q13641	OTTHUMG00000015103	ENST00000369750.3:c.1045delC	chr6.hg19:g.83075723delC	ENSP00000358765:p.Pro350fs	138.0	0.0		156.0	10.0	NM_001166392	A8K555	Frame_Shift_Del	DEL	ENST00000369750.3	hg19	CCDS4995.1																																																																																			.	.		0.498	TPBG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041340.1		
SH3KBP1	30011	hgsc.bcm.edu	37	X	19663542	19663542	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:19663542delT	ENST00000397821.3	-	7	1068	c.778delA	c.(778-780)acafs	p.T260fs	SH3KBP1_ENST00000379698.4_Frame_Shift_Del_p.T223fs|SH3KBP1_ENST00000379716.1_Frame_Shift_Del_p.T22fs|SH3KBP1_ENST00000379697.3_Frame_Shift_Del_p.T304fs|SH3KBP1_ENST00000541422.1_5'UTR|SH3KBP1_ENST00000477102.1_5'UTR	NM_031892.2	NP_114098.1	Q96B97	SH3K1_HUMAN	SH3-domain kinase binding protein 1	260					apoptotic process (GO:0006915)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|cytoskeleton organization (GO:0007010)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|regulation of cell shape (GO:0008360)	cell-cell junction (GO:0005911)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)				breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(8)|skin(4)	29						TCCATTTCTGTTTTTGATGAG	0.348																																					p.T260fs		Atlas-INDEL	.											.	SH3KBP1	96	.	0			c.779delC						.						246.0	217.0	227.0					X																	19663542		2203	4300	6503	SO:0001589	frameshift_variant	30011	exon7			.	AF230904	CCDS14193.1, CCDS35213.1, CCDS55383.1	Xp22.1-p21.3	2008-02-05			ENSG00000147010	ENSG00000147010			13867	protein-coding gene	gene with protein product		300374				8889549, 7566098	Standard	NM_031892		Approved	CIN85	uc004czm.3	Q96B97	OTTHUMG00000021227	ENST00000397821.3:c.778delA	chrX.hg19:g.19663542delT	ENSP00000380921:p.Thr260fs	89.0	0.0		160.0	10.0	NM_031892	B7Z1D5|Q5JPT4|Q5JPT5|Q8IWX6|Q8IX98|Q96RN4|Q9NYR0	Frame_Shift_Del	DEL	ENST00000397821.3	hg19	CCDS14193.1																																																																																			.	.		0.348	SH3KBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055992.1	NM_031892	
PTPRM	5797	hgsc.bcm.edu	37	18	8248169	8248169	+	Intron	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr18:8248169delT	ENST00000332175.8	+	16	3564				PTPRM_ENST00000400060.4_Frame_Shift_Del_p.I850fs|PTPRM_ENST00000444013.1_Intron|PTPRM_ENST00000580170.1_Frame_Shift_Del_p.I850fs|PTPRM_ENST00000400053.4_Intron	NM_002845.3	NP_002836.3	P28827	PTPRM_HUMAN	protein tyrosine phosphatase, receptor type, M						homophilic cell adhesion (GO:0007156)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|neuron projection development (GO:0031175)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of vasodilation (GO:0045909)|protein dephosphorylation (GO:0006470)|response to drug (GO:0042493)|retina layer formation (GO:0010842)|retinal ganglion cell axon guidance (GO:0031290)|signal transduction (GO:0007165)	cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|perinuclear region of cytoplasm (GO:0048471)	cadherin binding (GO:0045296)|identical protein binding (GO:0042802)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(3)|central_nervous_system(1)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(32)|lung(25)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	90		Colorectal(10;0.234)				CCAACTGCAATTTTAGGTGAG	0.388																																					p.I850fs		Atlas-INDEL	.											.	PTPRM	185	.	0			c.2548delA						.						277.0	275.0	275.0					18																	8248169		2114	4235	6349	SO:0001627	intron_variant	5797	exon17			.	X58288	CCDS11840.1, CCDS58613.1	18p11.2	2013-02-11			ENSG00000173482	ENSG00000173482		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	9675	protein-coding gene	gene with protein product		176888		PTPRL1		1655529, 8404049	Standard	NM_002845		Approved	RPTPU, hR-PTPu	uc010dkv.3	P28827	OTTHUMG00000131575	ENST00000332175.8:c.2527+252T>-	chr18.hg19:g.8248169delT		189.0	0.0		202.0	14.0	NM_001105244	A7MBN1|D3DUH8|J3QL11	Frame_Shift_Del	DEL	ENST00000332175.8	hg19	CCDS11840.1																																																																																			.	.		0.388	PTPRM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254456.1		
PIAS2	9063	hgsc.bcm.edu	37	18	44444168	44444168	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr18:44444168delA	ENST00000585916.1	-	3	542	c.543delT	c.(541-543)tttfs	p.F181fs	PIAS2_ENST00000545673.1_5'UTR|PIAS2_ENST00000324794.7_Frame_Shift_Del_p.F181fs	NM_004671.3	NP_004662.2	O75928	PIAS2_HUMAN	protein inhibitor of activated STAT, 2	181	PINIT. {ECO:0000255|PROSITE- ProRule:PRU00799}.				androgen receptor signaling pathway (GO:0030521)|negative regulation of androgen receptor signaling pathway (GO:0060766)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein sumoylation (GO:0016925)|regulation of osteoblast differentiation (GO:0045667)|transcription, DNA-templated (GO:0006351)	nuclear body (GO:0016604)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|DNA binding (GO:0003677)|SUMO ligase activity (GO:0019789)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(8)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	22						GTGTCAAAGCAAAAATAAAAA	0.313																																					p.A182fs		Atlas-INDEL	.											.	PIAS2	85	.	0			c.544delG						.						53.0	58.0	56.0					18																	44444168		2202	4300	6502	SO:0001589	frameshift_variant	9063	exon3			.	AF077953	CCDS32824.1, CCDS32825.1	18q12.1-q12.3	2011-10-11				ENSG00000078043		"""Zinc fingers, MIZ-type"""	17311	protein-coding gene	gene with protein product	"""zinc finger, MIZ-type containing 4"""	603567				9724754, 9256341	Standard	NM_004671		Approved	PIASX-BETA, miz, PIASX-ALPHA, ZMIZ4	uc002lck.3	O75928		ENST00000585916.1:c.543delT	chr18.hg19:g.44444168delA	ENSP00000465676:p.Phe181fs	118.0	0.0		167.0	13.0	NM_173206	O75927|Q96BT5|Q96KE3	Frame_Shift_Del	DEL	ENST00000585916.1	hg19	CCDS32824.1																																																																																			.	.		0.313	PIAS2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445656.2	NM_004671	
AGFG1	3267	hgsc.bcm.edu	37	2	228418462	228418462	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:228418462delC	ENST00000310078.8	+	12	1840	c.1580delC	c.(1579-1581)accfs	p.T527fs	AGFG1_ENST00000373671.3_Frame_Shift_Del_p.T487fs|AGFG1_ENST00000409171.1_Frame_Shift_Del_p.T525fs|AGFG1_ENST00000409315.1_Frame_Shift_Del_p.T506fs|AGFG1_ENST00000409979.2_Frame_Shift_Del_p.T549fs	NM_001135188.1|NM_001135189.1|NM_004504.4	NP_001128660.1|NP_001128661.1|NP_004495.2	P52594	AGFG1_HUMAN	ArfGAP with FG repeats 1	527					cell differentiation (GO:0030154)|mRNA export from nucleus (GO:0006406)|multicellular organismal development (GO:0007275)|regulation of ARF GTPase activity (GO:0032312)|spermatogenesis (GO:0007283)	cytoplasmic vesicle (GO:0031410)|intracellular membrane-bounded organelle (GO:0043231)|nuclear pore (GO:0005643)	ARF GTPase activator activity (GO:0008060)|DNA binding (GO:0003677)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|large_intestine(5)|liver(2)|lung(2)|ovary(1)|prostate(1)|skin(4)|stomach(1)	18						CCAGTAGTAACCCCTTTTGGT	0.333																																					p.T549fs		Atlas-INDEL	.											.	AGFG1	80	.	0			c.1645delA						.						104.0	110.0	108.0					2																	228418462		2203	4300	6503	SO:0001589	frameshift_variant	3267	exon13			.		CCDS2467.1, CCDS46533.1, CCDS46534.1, CCDS46535.1	2q36	2009-11-30	2008-09-22	2008-09-22	ENSG00000173744	ENSG00000173744		"""ADP-ribosylation factor GTPase activating proteins"""	5175	protein-coding gene	gene with protein product		600862	"""HIV-1 Rev binding protein"""	HRB		7637788	Standard	NM_004504		Approved	RIP, RAB	uc002vpd.2	P52594	OTTHUMG00000133186	ENST00000310078.8:c.1580delC	chr2.hg19:g.228418462delC	ENSP00000312059:p.Thr527fs	108.0	0.0		182.0	12.0	NM_001135187	B3KUL1|E9PHX7|Q15277|Q4VAS0|Q4VAS1|Q4VAS3|Q53QT8|Q53R11	Frame_Shift_Del	DEL	ENST00000310078.8	hg19	CCDS2467.1																																																																																			.	.		0.333	AGFG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256895.2	NM_004504	
TBC1D8B	54885	hgsc.bcm.edu	37	X	106096825	106096825	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:106096825delA	ENST00000357242.5	+	13	2372	c.2198delA	c.(2197-2199)gaafs	p.E733fs	TBC1D8B_ENST00000276175.3_Frame_Shift_Del_p.E727fs	NM_017752.2	NP_060222.2	Q0IIM8	TBC8B_HUMAN	TBC1 domain family, member 8B (with GRAM domain)	733							calcium ion binding (GO:0005509)|Rab GTPase activator activity (GO:0005097)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(6)|liver(4)|lung(15)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	47						GTGAGTGATGAAAAAACCAGT	0.308																																					p.E733fs		Atlas-INDEL	.											.	TBC1D8B	181	.	0			c.2197delG						.						116.0	112.0	114.0					X																	106096825		2203	4300	6503	SO:0001589	frameshift_variant	54885	exon13			.	AK123957	CCDS14522.1, CCDS14523.1	Xq22.3	2013-01-10			ENSG00000133138	ENSG00000133138		"""EF-hand domain containing"""	24715	protein-coding gene	gene with protein product						8889548	Standard	NM_017752		Approved	FLJ20298, RP11-321G1.1	uc004emo.3	Q0IIM8	OTTHUMG00000022152	ENST00000357242.5:c.2198delA	chrX.hg19:g.106096825delA	ENSP00000349781:p.Glu733fs	141.0	0.0		201.0	13.0	NM_017752	B9A6K5|B9A6K6|Q5JRB7|Q6ZVX5|Q9NXE3	Frame_Shift_Del	DEL	ENST00000357242.5	hg19	CCDS14522.1																																																																																			.	.		0.308	TBC1D8B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057807.2	NM_017752	
CIDEC	63924	hgsc.bcm.edu	37	3	9911858	9911858	+	Frame_Shift_Del	DEL	G	G	-	rs145091411		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:9911858delG	ENST00000336832.2	-	4	495	c.356delC	c.(355-357)ccafs	p.P119fs	CIDEC_ENST00000423850.1_Frame_Shift_Del_p.P45fs|CIDEC_ENST00000455015.1_Frame_Shift_Del_p.P45fs|CIDEC_ENST00000443115.1_Intron|CIDEC_ENST00000383817.1_Intron|CIDEC_ENST00000430427.1_Frame_Shift_Del_p.P129fs	NM_001199552.1|NM_001199623.1|NM_022094.3	NP_001186481.1|NP_001186552.1|NP_071377.2	Q96AQ7	CIDEC_HUMAN	cell death-inducing DFFA-like effector c	119					apoptotic process (GO:0006915)|execution phase of apoptosis (GO:0097194)|lipid particle organization (GO:0034389)|regulation of apoptotic process (GO:0042981)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|lipid particle (GO:0005811)|nucleus (GO:0005634)		p.P119Q(1)		breast(2)|central_nervous_system(1)|endometrium(1)|lung(2)|ovary(1)|skin(1)	8	Medulloblastoma(99;0.227)					CTGTTCTGATGGGGGCTGCCA	0.532																																					p.P132fs		Atlas-INDEL	.											.	CIDEC	22	.	1	Substitution - Missense(1)	lung(1)	c.396delA						.						64.0	67.0	66.0					3																	9911858		2203	4300	6503	SO:0001589	frameshift_variant	63924	exon4			.		CCDS2587.1, CCDS56239.1, CCDS74897.1	3p25	2004-07-26			ENSG00000187288	ENSG00000187288			24229	protein-coding gene	gene with protein product		612120				12429024	Standard	NM_001199623		Approved	CIDE-3, FLJ20871, Fsp27	uc021wsw.1	Q96AQ7	OTTHUMG00000128522	ENST00000336832.2:c.356delC	chr3.hg19:g.9911858delG	ENSP00000338642:p.Pro119fs	92.0	0.0		131.0	13.0	NM_001199623	C9JMN7|Q67DW9|Q9GZY9	Frame_Shift_Del	DEL	ENST00000336832.2	hg19	CCDS2587.1																																																																																			.	.		0.532	CIDEC-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000250334.1	NM_022094	
MAP3K13	9175	hgsc.bcm.edu	37	3	185165720	185165720	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:185165720delA	ENST00000265026.3	+	5	1329	c.995delA	c.(994-996)gaafs	p.E332fs	MAP3K13_ENST00000446828.1_Frame_Shift_Del_p.E125fs|MAP3K13_ENST00000535426.1_Frame_Shift_Del_p.E188fs|MAP3K13_ENST00000424227.1_Frame_Shift_Del_p.E332fs|MAP3K13_ENST00000443863.1_Frame_Shift_Del_p.E188fs	NM_004721.4	NP_004712.1			mitogen-activated protein kinase kinase kinase 13											NS(1)|biliary_tract(1)|breast(3)|endometrium(3)|kidney(1)|large_intestine(13)|lung(22)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	54	all_cancers(143;7.21e-11)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;1.93e-20)			CCTGTCTCTGAAAAAGTTGAT	0.468																																					p.E332fs		Atlas-INDEL	.											.	MAP3K13	209	.	0			c.994delG						.						58.0	55.0	56.0					3																	185165720		2203	4300	6503	SO:0001589	frameshift_variant	9175	exon6			.	BC031677	CCDS3270.1, CCDS56298.1	3q27	2011-06-09			ENSG00000073803	ENSG00000073803		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6852	protein-coding gene	gene with protein product	"""leucine zipper-bearing kinase"""	604915				9353328	Standard	NM_004721		Approved	LZK, MEKK13	uc003fpi.3	O43283	OTTHUMG00000156673	ENST00000265026.3:c.995delA	chr3.hg19:g.185165720delA	ENSP00000265026:p.Glu332fs	150.0	0.0		163.0	12.0	NM_001242314		Frame_Shift_Del	DEL	ENST00000265026.3	hg19	CCDS3270.1																																																																																			.	.		0.468	MAP3K13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345268.1	NM_004721	
MADD	8567	hgsc.bcm.edu	37	11	47315481	47315481	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:47315481delA	ENST00000311027.5	+	22	3628	c.3463delA	c.(3463-3465)aaafs	p.K1156fs	MADD_ENST00000395336.3_Frame_Shift_Del_p.K1156fs|MADD_ENST00000405573.2_5'UTR|MADD_ENST00000395344.3_Frame_Shift_Del_p.K1075fs|MADD_ENST00000349238.3_Frame_Shift_Del_p.K1138fs|MADD_ENST00000342922.4_Frame_Shift_Del_p.K1118fs|MADD_ENST00000406482.1_Frame_Shift_Del_p.K1075fs|MADD_ENST00000402799.1_Frame_Shift_Del_p.K1075fs|MADD_ENST00000402192.2_Frame_Shift_Del_p.K1118fs|MADD_ENST00000407859.3_Frame_Shift_Del_p.K1095fs	NM_003682.3	NP_003673.3			MAP-kinase activating death domain											breast(7)|central_nervous_system(2)|endometrium(9)|kidney(3)|large_intestine(19)|lung(26)|ovary(6)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	84				Lung(87;0.182)		GACAGAGGAGAAAAAGTCCCA	0.483																																					p.E1154fs		Atlas-INDEL	.											.	MADD	172	.	0			c.3462delG						.						158.0	143.0	148.0					11																	47315481		2201	4298	6499	SO:0001589	frameshift_variant	8567	exon22			.	AB002356	CCDS7930.1, CCDS7931.1, CCDS7932.1, CCDS41642.1, CCDS44586.1, CCDS44587.1, CCDS44588.1, CCDS44589.1, CCDS44590.1	11p11.2	2012-10-04			ENSG00000110514	ENSG00000110514		"""DENN/MADD domain containing"""	6766	protein-coding gene	gene with protein product		603584				9115275, 9796103	Standard	NM_130476		Approved	DENN, KIAA0358, RAB3GEP	uc001ner.1	Q8WXG6	OTTHUMG00000150350	ENST00000311027.5:c.3463delA	chr11.hg19:g.47315481delA	ENSP00000310933:p.Lys1156fs	110.0	0.0		150.0	12.0	NM_130475		Frame_Shift_Del	DEL	ENST00000311027.5	hg19	CCDS7930.1																																																																																			.	.		0.483	MADD-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317746.1		
RNASEL	6041	hgsc.bcm.edu	37	1	182555572	182555572	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:182555572delA	ENST00000367559.3	-	2	623	c.370delT	c.(370-372)tatfs	p.Y124fs	RNASEL_ENST00000539397.1_Frame_Shift_Del_p.Y124fs|RNASEL_ENST00000444138.1_Frame_Shift_Del_p.Y124fs	NM_021133.3	NP_066956.1	Q05823	RN5A_HUMAN	ribonuclease L (2',5'-oligoisoadenylate synthetase-dependent)	124					cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|mRNA processing (GO:0006397)|negative regulation of viral genome replication (GO:0045071)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|rRNA processing (GO:0006364)|type I interferon signaling pathway (GO:0060337)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nuclear matrix (GO:0016363)	ATP binding (GO:0005524)|endoribonuclease activity (GO:0004521)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|RNA binding (GO:0003723)|rRNA binding (GO:0019843)			NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(9)|ovary(4)|prostate(1)|stomach(1)|urinary_tract(1)	27						GTGAAGCCATAAAAATCACAC	0.463																																					p.Y124fs		Atlas-INDEL	.											.	RNASEL	83	.	0			c.371delA						.						46.0	47.0	47.0					1																	182555572		2203	4300	6503	SO:0001589	frameshift_variant	6041	exon2			.	L10381	CCDS1347.1	1q25	2013-01-10			ENSG00000135828	ENSG00000135828	3.1.26.-	"""Ankyrin repeat domain containing"""	10050	protein-coding gene	gene with protein product		180435	"""prostate cancer 1"""	RNS4, PRCA1		7514564	Standard	NM_021133		Approved		uc009wxz.2	Q05823	OTTHUMG00000035213	ENST00000367559.3:c.370delT	chr1.hg19:g.182555572delA	ENSP00000356530:p.Tyr124fs	74.0	0.0		150.0	10.0	NM_021133	Q5W0L2|Q6AI46	Frame_Shift_Del	DEL	ENST00000367559.3	hg19	CCDS1347.1																																																																																			.	.		0.463	RNASEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085189.1	NM_021133	
SETDB1	9869	hgsc.bcm.edu	37	1	150933041	150933041	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:150933041delA	ENST00000271640.5	+	16	2693	c.2503delA	c.(2503-2505)aaafs	p.K835fs	SETDB1_ENST00000368969.4_Frame_Shift_Del_p.K835fs|SETDB1_ENST00000459773.1_3'UTR	NM_001145415.1|NM_012432.3	NP_001138887.1|NP_036564.3	Q15047	SETB1_HUMAN	SET domain, bifurcated 1	835	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				bone development (GO:0060348)|histone H3-K9 trimethylation (GO:0036124)|inner cell mass cell proliferation (GO:0001833)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			NS(1)|large_intestine(5)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	12	all_lung(15;9e-35)|Lung NSC(24;3.45e-31)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.108)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|BRCA - Breast invasive adenocarcinoma(12;0.0152)|LUSC - Lung squamous cell carcinoma(543;0.211)			ATTCTCAGGCAAAATCCTGAC	0.388																																					p.G834fs		Atlas-INDEL	.											.	SETDB1	204	.	0			c.2502delC						.						66.0	66.0	66.0					1																	150933041		2203	4300	6503	SO:0001589	frameshift_variant	9869	exon16			.	D31891	CCDS972.1, CCDS44217.1, CCDS58026.1	1q21	2013-01-23			ENSG00000143379	ENSG00000143379		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Tudor domain containing"""	10761	protein-coding gene	gene with protein product	"""tudor domain containing 21"""	604396				10343109	Standard	NM_001145415		Approved	KG1T, KIAA0067, ESET, KMT1E, TDRD21	uc001evu.2	Q15047	OTTHUMG00000035003	ENST00000271640.5:c.2503delA	chr1.hg19:g.150933041delA	ENSP00000271640:p.Lys835fs	79.0	0.0		154.0	10.0	NM_012432	A6NEW2|Q5SZD8|Q5SZD9|Q5SZE0|Q5SZE7|Q96GM9	Frame_Shift_Del	DEL	ENST00000271640.5	hg19	CCDS44217.1																																																																																			.	.		0.388	SETDB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000084717.2		
SCN7A	6332	hgsc.bcm.edu	37	2	167288989	167288989	+	Frame_Shift_Del	DEL	T	T	-	rs146072866	byFrequency	TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:167288989delT	ENST00000409855.1	-	15	2557	c.2431delA	c.(2431-2433)agcfs	p.S812fs		NM_002976.3	NP_002967.2	Q01118	SCN7A_HUMAN	sodium channel, voltage-gated, type VII, alpha subunit	812					membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|neuronal action potential (GO:0019228)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	glial cell projection (GO:0097386)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(30)|prostate(4)|soft_tissue(1)|urinary_tract(1)	44					Valproic Acid(DB00313)	GTGCCACTGCTTTTTTCCTTA	0.388																																					p.S811fs		Atlas-INDEL	.											.	SCN7A	410	.	0			c.2432delG						.						242.0	228.0	233.0					2																	167288989		1834	4091	5925	SO:0001589	frameshift_variant	6332	exon15			.	M91556	CCDS46442.1	2q21-q23	2012-03-05	2012-02-28	2002-06-14	ENSG00000136546	ENSG00000136546		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10594	protein-coding gene	gene with protein product		182392	"""sodium channel, voltage-gated, type VI, alpha"", ""sodium channel, voltage-gated, type VII, alpha"""	SCN6A		10198179	Standard	NM_002976		Approved	Nav2.1, Nav2.2, NaG	uc002udu.2	Q01118	OTTHUMG00000154078	ENST00000409855.1:c.2431delA	chr2.hg19:g.167288989delT	ENSP00000386796:p.Ser812fs	151.0	0.0		192.0	14.0	NM_002976		Frame_Shift_Del	DEL	ENST00000409855.1	hg19	CCDS46442.1																																																																																			.	.		0.388	SCN7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333745.1		
SLC17A1	6568	hgsc.bcm.edu	37	6	25813132	25813132	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:25813132delA	ENST00000244527.4	-	8	939	c.824delT	c.(823-825)ttcfs	p.F275fs	SLC17A1_ENST00000476801.1_Frame_Shift_Del_p.F275fs|SLC17A1_ENST00000468082.1_Intron|SLC17A1_ENST00000427328.1_Intron	NM_005074.3	NP_005065.2	Q14916	NPT1_HUMAN	solute carrier family 17 (organic anion transporter), member 1	275					ion transport (GO:0006811)|phosphate ion transport (GO:0006817)|sodium ion transport (GO:0006814)|sodium-dependent phosphate transport (GO:0044341)|transmembrane transport (GO:0055085)|urate metabolic process (GO:0046415)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium-dependent phosphate transmembrane transporter activity (GO:0015321)|symporter activity (GO:0015293)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(14)|ovary(3)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	36						ATGTGACCAGAAAAACGTAAA	0.358																																					p.F275fs		Atlas-INDEL	.											.	SLC17A1	71	.	0			c.825delC						.						70.0	70.0	70.0					6																	25813132		2203	4300	6503	SO:0001589	frameshift_variant	6568	exon8			.		CCDS4565.1	6p22.2	2013-07-18	2013-07-18		ENSG00000124568	ENSG00000124568		"""Solute carriers"""	10929	protein-coding gene	gene with protein product		182308	"""solute carrier family 17 (sodium phosphate), member 1"""	NPT1		8288239	Standard	NM_005074		Approved	NAPI-1	uc003nfh.4	Q14916	OTTHUMG00000016297	ENST00000244527.4:c.824delT	chr6.hg19:g.25813132delA	ENSP00000244527:p.Phe275fs	104.0	0.0		160.0	10.0	NM_005074	A8K418|O60761|Q13783|Q3MIP5|Q5MJP8|Q5TB83|Q96KL8	Frame_Shift_Del	DEL	ENST00000244527.4	hg19	CCDS4565.1																																																																																			.	.		0.358	SLC17A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043647.2		
PER3	8863	hgsc.bcm.edu	37	1	7895908	7895908	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:7895908delA	ENST00000361923.2	+	19	3449	c.3274delA	c.(3274-3276)aaafs	p.K1093fs	PER3_ENST00000377532.3_Frame_Shift_Del_p.K1102fs	NM_016831.1	NP_058515.1	P56645	PER3_HUMAN	period circadian clock 3	1093					circadian regulation of gene expression (GO:0032922)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of circadian sleep/wake cycle, sleep (GO:0045187)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)			breast(4)|central_nervous_system(3)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	39	Ovarian(185;0.0634)|all_lung(157;0.178)	all_epithelial(116;9.35e-21)|all_lung(118;7.57e-07)|Lung NSC(185;4.52e-06)|Renal(390;0.000147)|Breast(487;0.00086)|Colorectal(325;0.000959)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|all cancers(8;8.58e-70)|GBM - Glioblastoma multiforme(8;1.81e-35)|Colorectal(212;2.06e-07)|COAD - Colon adenocarcinoma(227;1.92e-05)|Kidney(185;7.18e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000472)|STAD - Stomach adenocarcinoma(132;0.00118)|KIRC - Kidney renal clear cell carcinoma(229;0.00122)|READ - Rectum adenocarcinoma(331;0.0649)		GGACGTACAGAAAAAAGAAAC	0.433																																					p.Q1091fs		Atlas-INDEL	.											.	PER3	95	.	0			c.3273delG						.						94.0	89.0	91.0					1																	7895908		2203	4300	6503	SO:0001589	frameshift_variant	8863	exon19			.	BC026102	CCDS89.1, CCDS72695.1	1p36.23	2012-12-13	2012-12-13		ENSG00000049246	ENSG00000049246			8847	protein-coding gene	gene with protein product		603427	"""period (Drosophila) homolog 3"", ""period homolog 3 (Drosophila)"""			9427249	Standard	XM_005263520		Approved		uc001aoo.3	P56645	OTTHUMG00000001216	ENST00000361923.2:c.3274delA	chr1.hg19:g.7895908delA	ENSP00000355031:p.Lys1093fs	167.0	0.0		222.0	15.0	NM_016831	Q5H8X4|Q5H8X5|Q969K6|Q96S77|Q96S78|Q9C0J3|Q9NSP9|Q9UGU8	Frame_Shift_Del	DEL	ENST00000361923.2	hg19	CCDS89.1																																																																																			.	.		0.433	PER3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000003607.1	NM_016831	
PSMD3	5709	hgsc.bcm.edu	37	17	38137367	38137367	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:38137367delG	ENST00000264639.4	+	1	318	c.144delG	c.(142-144)acgfs	p.T48fs	PSMD3_ENST00000541736.1_Intron	NM_002809.3	NP_002800.2	O43242	PSMD3_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 3	48					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of protein catabolic process (GO:0042176)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)	enzyme regulator activity (GO:0030234)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	26	Colorectal(19;0.000442)					GCGGGTCGACGGGGGAGGCAG	0.711											OREG0024385	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.T48fs	Ovarian(186;531 2051 6385 19668 48409)	Atlas-INDEL	.											.	PSMD3	56	.	0			c.143delC						.						10.0	18.0	15.0					17																	38137367		1961	3796	5757	SO:0001589	frameshift_variant	5709	exon1			.	D67025	CCDS11356.1	17q21.2	2010-07-23			ENSG00000108344	ENSG00000108344		"""Proteasome (prosome, macropain) subunits"""	9560	protein-coding gene	gene with protein product			"""tissue specific transplantation antigen 2"""	TSTA2		9017604	Standard	NM_002809		Approved	S3, P58, Rpn3	uc002htn.2	O43242	OTTHUMG00000133251	ENST00000264639.4:c.144delG	chr17.hg19:g.38137367delG	ENSP00000264639:p.Thr48fs	119.0	0.0	875	175.0	12.0	NM_002809	B3KMW9|B4DT72|Q96EI2|Q9BQA4	Frame_Shift_Del	DEL	ENST00000264639.4	hg19	CCDS11356.1																																																																																			.	.		0.711	PSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257018.1	NM_002809	
MTRF1	9617	hgsc.bcm.edu	37	13	41800662	41800662	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr13:41800662delT	ENST00000379480.4	-	8	1131	c.1031delA	c.(1030-1032)aatfs	p.N344fs	MTRF1_ENST00000430347.2_Frame_Shift_Del_p.N357fs|MTRF1_ENST00000379477.1_Frame_Shift_Del_p.N344fs	NM_004294.2	NP_004285.2	O75570	RF1M_HUMAN	mitochondrial translational release factor 1	344					regulation of translational termination (GO:0006449)	mitochondrion (GO:0005739)	translation release factor activity (GO:0003747)|translation release factor activity, codon specific (GO:0016149)			breast(1)|endometrium(4)|large_intestine(3)|lung(6)	14		Lung NSC(96;4.52e-06)|Breast(139;0.00123)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)|Ovarian(182;0.125)		OV - Ovarian serous cystadenocarcinoma(117;4.24e-10)|all cancers(112;2.05e-09)|Epithelial(112;2.48e-09)|GBM - Glioblastoma multiforme(144;0.00115)|BRCA - Breast invasive adenocarcinoma(63;0.0721)|KIRC - Kidney renal clear cell carcinoma(186;0.248)		TATTTCTTTATTTTTTATCTG	0.383																																					p.N344fs		Atlas-INDEL	.											.	MTRF1	24	.	0			c.1032delT						.						164.0	158.0	160.0					13																	41800662		2203	4300	6503	SO:0001589	frameshift_variant	9617	exon8			.	AF072934	CCDS9378.1	13q14.1-q14.3	2008-07-18			ENSG00000120662	ENSG00000120662			7469	protein-coding gene	gene with protein product	"""mitochontrial peptide chain release factor 1"""	604601				9838146, 10773675	Standard	NM_004294		Approved	RF1, MTTRF1, MGC47721	uc001uxy.3	O75570	OTTHUMG00000016790	ENST00000379480.4:c.1031delA	chr13.hg19:g.41800662delT	ENSP00000368793:p.Asn344fs	151.0	0.0		219.0	14.0	NM_004294	B4DG01|Q5T6Y5|Q8IUQ6	Frame_Shift_Del	DEL	ENST00000379480.4	hg19	CCDS9378.1																																																																																			.	.		0.383	MTRF1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044666.3	NM_004294	
PTPRJ	5795	hgsc.bcm.edu	37	11	48149344	48149344	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:48149344delT	ENST00000418331.2	+	7	1458	c.1106delT	c.(1105-1107)gttfs	p.V369fs	PTPRJ_ENST00000440289.2_Frame_Shift_Del_p.V369fs	NM_002843.3	NP_002834.3	Q12913	PTPRJ_HUMAN	protein tyrosine phosphatase, receptor type, J	369	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				contact inhibition (GO:0060242)|heart development (GO:0007507)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of platelet-derived growth factor receptor signaling pathway (GO:0010642)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of T cell receptor signaling pathway (GO:0050860)|negative regulation of vascular permeability (GO:0043116)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive chemotaxis (GO:0050918)|positive regulation of cell adhesion (GO:0045785)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of cell adhesion (GO:0030155)|vasculogenesis (GO:0001570)	cell projection (GO:0042995)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|delta-catenin binding (GO:0070097)|gamma-catenin binding (GO:0045295)|mitogen-activated protein kinase binding (GO:0051019)|phosphatase activity (GO:0016791)|platelet-derived growth factor receptor binding (GO:0005161)|protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)			breast(3)|endometrium(7)|kidney(7)|large_intestine(5)|lung(15)|ovary(1)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	52						GCTATTCAGGTTTTTGACGTC	0.493																																					p.V369fs		Atlas-INDEL	.											.	PTPRJ	225	.	0			c.1105delG						.						94.0	85.0	88.0					11																	48149344		2201	4298	6499	SO:0001589	frameshift_variant	5795	exon7			.	U10886	CCDS7945.1, CCDS44596.1	11p11.2	2013-02-11			ENSG00000149177	ENSG00000149177		"""CD molecules"", ""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9673	protein-coding gene	gene with protein product		600925				7937872, 7994032	Standard	NM_001098503		Approved	DEP1, HPTPeta, CD148	uc001ngp.4	Q12913	OTTHUMG00000166573	ENST00000418331.2:c.1106delT	chr11.hg19:g.48149344delT	ENSP00000400010:p.Val369fs	71.0	0.0		104.0	10.0	NM_001098503	Q15255|Q6P4H4|Q8NHM2|Q9UDA9	Frame_Shift_Del	DEL	ENST00000418331.2	hg19	CCDS7945.1																																																																																			.	.		0.493	PTPRJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390525.1		
SEC22C	9117	hgsc.bcm.edu	37	3	42599114	42599114	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:42599114delG	ENST00000264454.3	-	5	744	c.601delC	c.(601-603)ctgfs	p.L201fs	SEC22C_ENST00000536332.1_Frame_Shift_Del_p.L131fs|SEC22C_ENST00000273156.7_Frame_Shift_Del_p.L201fs|SEC22C_ENST00000417572.1_Frame_Shift_Del_p.L201fs|SEC22C_ENST00000423701.2_Frame_Shift_Del_p.L201fs			Q9BRL7	SC22C_HUMAN	SEC22 vesicle trafficking protein homolog C (S. cerevisiae)	201					ER to Golgi vesicle-mediated transport (GO:0006888)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(2)	3				KIRC - Kidney renal clear cell carcinoma(284;0.222)		ATGAGATTCAGGGCAGCACAC	0.383																																					p.L201fs		Atlas-INDEL	.											.	SEC22C	27	.	0			c.602delT						.						106.0	109.0	108.0					3																	42599114		2203	4300	6503	SO:0001589	frameshift_variant	9117	exon5			.	AF039568	CCDS2699.1, CCDS2700.1, CCDS56246.1	3p24.3-p22.1	2006-04-25	2006-04-25	2006-04-25	ENSG00000093183	ENSG00000093183			16828	protein-coding gene	gene with protein product		604028	"""SEC22 vesicle trafficking protein-like 3 (S. cerevisiae)"""	SEC22L3		9501016, 11001058	Standard	NM_004206		Approved	MGC13261, MGC5373	uc003clj.3	Q9BRL7	OTTHUMG00000131797	ENST00000264454.3:c.601delC	chr3.hg19:g.42599114delG	ENSP00000264454:p.Leu201fs	180.0	0.0		164.0	11.0	NM_004206	O95152|Q68CX3|Q6UW18	Frame_Shift_Del	DEL	ENST00000264454.3	hg19	CCDS2700.1																																																																																			.	.		0.383	SEC22C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254734.1	NM_004206	
SLCO4A1	28231	hgsc.bcm.edu	37	20	61303147	61303147	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr20:61303147delC	ENST00000370507.1	+	11	2167	c.2071delC	c.(2071-2073)cccfs	p.P691fs	SLCO4A1_ENST00000217159.1_Frame_Shift_Del_p.P691fs			Q96BD0	SO4A1_HUMAN	solute carrier organic anion transporter family, member 4A1	691					sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			endometrium(6)|kidney(2)|large_intestine(1)|lung(7)|ovary(3)|prostate(2)	21	Breast(26;3.65e-08)		BRCA - Breast invasive adenocarcinoma(19;2.33e-06)		Benzylpenicillin(DB01053)|Conjugated Estrogens(DB00286)|Dextrothyroxine(DB00509)|Digoxin(DB00390)|Dinoprostone(DB00917)|Estradiol(DB00783)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)	CTTATACAAGCCCCTGTCGGA	0.612																																					p.K690fs	Pancreas(168;741 2006 10379 40139 45334)	Atlas-INDEL	.											.	SLCO4A1	65	.	0			c.2070delG						.						88.0	87.0	87.0					20																	61303147		2203	4300	6503	SO:0001589	frameshift_variant	28231	exon12			.	AB031051	CCDS13501.1	20q13.1	2013-05-22	2003-11-25	2003-11-26	ENSG00000101187	ENSG00000101187		"""Solute carriers"""	10953	protein-coding gene	gene with protein product		612436	"""solute carrier family 21 (organic anion transporter), member 12"""	SLC21A12		10873595	Standard	NM_016354		Approved	OATP-E, OATP4A1	uc002ydb.1	Q96BD0	OTTHUMG00000032923	ENST00000370507.1:c.2071delC	chr20.hg19:g.61303147delC	ENSP00000359538:p.Pro691fs	134.0	0.0		182.0	11.0	NM_016354	Q9H4T7|Q9H4T8|Q9H8P2|Q9NWX8|Q9UI35|Q9UIG7	Frame_Shift_Del	DEL	ENST00000370507.1	hg19	CCDS13501.1																																																																																			.	.		0.612	SLCO4A1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080048.2	NM_016354	
MUC5B	727897	hgsc.bcm.edu	37	11	1278487	1278487	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:1278487delG	ENST00000529681.1	+	40	16313	c.16255delG	c.(16255-16257)gggfs	p.G5419fs	MUC5B_ENST00000447027.1_Frame_Shift_Del_p.G5422fs	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	5419	VWFC 2. {ECO:0000255|PROSITE- ProRule:PRU00220}.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		GGGACCCGATGGGTTTCCTAA	0.632																																					p.D5418fs		Atlas-INDEL	.											.	MUC5B	473	.	0			c.16254delT						.						96.0	104.0	102.0					11																	1278487		2025	4175	6200	SO:0001589	frameshift_variant	727897	exon40			.	U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"""Mucins"""	7516	protein-coding gene	gene with protein product		600770	"""mucin 5, subtype B, tracheobronchial"""	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.16255delG	chr11.hg19:g.1278487delG	ENSP00000436812:p.Gly5419fs	191.0	0.0		208.0	13.0	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Frame_Shift_Del	DEL	ENST00000529681.1	hg19	CCDS44515.2																																																																																			.	.		0.632	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
THNSL1	79896	hgsc.bcm.edu	37	10	25314273	25314273	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:25314273delT	ENST00000524413.1	+	3	2468	c.2121delT	c.(2119-2121)gctfs	p.A707fs	THNSL1_ENST00000376356.4_Frame_Shift_Del_p.A707fs			Q8IYQ7	THNS1_HUMAN	threonine synthase-like 1 (S. cerevisiae)	707						cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				NS(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(5)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	28					L-Threonine(DB00156)	TGCATGAGGCTTTATTAGAGA	0.398																																					p.A707fs		Atlas-INDEL	.											.	THNSL1	70	.	0			c.2120delC						.						84.0	82.0	83.0					10																	25314273		2203	4300	6503	SO:0001589	frameshift_variant	79896	exon3			.	AK025655	CCDS7147.1	10p12.31	2008-02-05	2007-06-20		ENSG00000185875	ENSG00000185875			26160	protein-coding gene	gene with protein product		611260	"""threonine synthase-like 1 (bacterial)"""			12477932	Standard	NM_024838		Approved	FLJ22002	uc001isi.4	Q8IYQ7	OTTHUMG00000017828	ENST00000524413.1:c.2121delT	chr10.hg19:g.25314273delT	ENSP00000434887:p.Ala707fs	118.0	0.0		241.0	15.0	NM_024838	B3KWL1|D3DRV3|Q5VV21	Frame_Shift_Del	DEL	ENST00000524413.1	hg19	CCDS7147.1																																																																																			.	.		0.398	THNSL1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394913.1	NM_024838	
OXCT1	5019	hgsc.bcm.edu	37	5	41862804	41862804	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:41862804delA	ENST00000196371.5	-	2	287	c.127delT	c.(127-129)tatfs	p.Y43fs		NM_000436.3	NP_000427.1	P55809	SCOT1_HUMAN	3-oxoacid CoA transferase 1	43					adipose tissue development (GO:0060612)|brain development (GO:0007420)|cellular ketone body metabolic process (GO:0046950)|cellular lipid metabolic process (GO:0044255)|cellular response to acid chemical (GO:0071229)|cellular response to glucose stimulus (GO:0071333)|heart development (GO:0007507)|ketone body catabolic process (GO:0046952)|ketone catabolic process (GO:0042182)|positive regulation of insulin secretion (GO:0032024)|response to activity (GO:0014823)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to hormone (GO:0009725)|response to nutrient (GO:0007584)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	3-oxoacid CoA-transferase activity (GO:0008260)|protein homodimerization activity (GO:0042803)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(1)|skin(2)	28					Succinic acid(DB00139)	GGATCTGTATAAAACTTGGTA	0.373																																					p.Y43fs		Atlas-INDEL	.											.	OXCT1	54	.	0			c.128delA						.						128.0	114.0	119.0					5																	41862804		2203	4300	6503	SO:0001589	frameshift_variant	5019	exon2			.	U62961	CCDS3937.1	5p13	2008-02-05		2004-05-12	ENSG00000083720	ENSG00000083720			8527	protein-coding gene	gene with protein product		601424	"""3-oxoacid CoA transferase"""	OXCT		8751852	Standard	NM_000436		Approved	SCOT	uc003jmn.3	P55809	OTTHUMG00000094783	ENST00000196371.5:c.127delT	chr5.hg19:g.41862804delA	ENSP00000196371:p.Tyr43fs	172.0	0.0		185.0	13.0	NM_000436	B2R5V2|B7Z528	Frame_Shift_Del	DEL	ENST00000196371.5	hg19	CCDS3937.1																																																																																			.	.		0.373	OXCT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211594.2	NM_000436	
CHD8	57680	hgsc.bcm.edu	37	14	21876929	21876929	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:21876929delT	ENST00000557364.1	-	12	2683	c.2420delA	c.(2419-2421)aacfs	p.N807fs	CHD8_ENST00000430710.3_Frame_Shift_Del_p.N528fs|CHD8_ENST00000555962.1_Intron|CHD8_ENST00000399982.2_Frame_Shift_Del_p.N807fs			Q9HCK8	CHD8_HUMAN	chromodomain helicase DNA binding protein 8	807					ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|canonical Wnt signaling pathway (GO:0060070)|DNA duplex unwinding (GO:0032508)|in utero embryonic development (GO:0001701)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of Wnt signaling pathway (GO:0030178)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	MLL1 complex (GO:0071339)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|beta-catenin binding (GO:0008013)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA-dependent ATPase activity (GO:0008094)|histone binding (GO:0042393)|methylated histone binding (GO:0035064)|p53 binding (GO:0002039)			NS(2)|breast(1)|central_nervous_system(1)|cervix(4)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(33)|ovary(6)|prostate(7)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	85	all_cancers(95;0.00121)		Epithelial(56;2.55e-06)|all cancers(55;1.73e-05)	GBM - Glioblastoma multiforme(265;0.00424)		CTGGTTTCTGTTTTTATATTC	0.388																																					p.N807fs		Atlas-INDEL	.											.	CHD8	339	.	0			c.2421delC						.						87.0	75.0	79.0					14																	21876929		1807	4075	5882	SO:0001589	frameshift_variant	57680	exon11			.	AB046784	CCDS45081.1, CCDS53885.1	14q11.2	2008-02-05	2004-06-22	2004-06-23		ENSG00000100888			20153	protein-coding gene	gene with protein product		610528	"""helicase with SNF2 domain 1"""	HELSNF1		10997877	Standard	NM_020920		Approved	KIAA1564, DUPLIN	uc001war.2	Q9HCK8		ENST00000557364.1:c.2420delA	chr14.hg19:g.21876929delT	ENSP00000451601:p.Asn807fs	117.0	0.0		164.0	11.0	NM_001170629	Q4G0D8|Q68DQ0|Q6DKH9|Q6P440|Q6ZNL7|Q8N3Z9|Q8NCY4|Q8TBR9|Q96F26	Frame_Shift_Del	DEL	ENST00000557364.1	hg19	CCDS53885.1																																																																																			.	.		0.388	CHD8-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410436.1	NM_020920	
ZCCHC7	84186	hgsc.bcm.edu	37	9	37349430	37349430	+	Frame_Shift_Del	DEL	A	A	-	rs555354129		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:37349430delA	ENST00000336755.5	+	7	1170	c.1064delA	c.(1063-1065)caafs	p.Q355fs	ZCCHC7_ENST00000534928.1_Frame_Shift_Del_p.Q65fs|ZCCHC7_ENST00000461038.1_3'UTR	NM_032226.2	NP_115602.2	Q8N3Z6	ZCHC7_HUMAN	zinc finger, CCHC domain containing 7	355						cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(2)|lung(14)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	30				GBM - Glioblastoma multiforme(29;0.0137)		CACTGCGCGCAAAAAGGCCAT	0.438																																					p.Q355fs		Atlas-INDEL	.											.	ZCCHC7	56	.	0			c.1063delC						.						154.0	124.0	134.0					9																	37349430		2203	4300	6503	SO:0001589	frameshift_variant	84186	exon7			.	AK026264	CCDS6608.2	9p13.1	2008-05-02			ENSG00000147905	ENSG00000147905		"""Zinc fingers, CCHC domain containing"""	26209	protein-coding gene	gene with protein product							Standard	NM_032226		Approved	FLJ22611, AIR1	uc003zzq.3	Q8N3Z6	OTTHUMG00000019915	ENST00000336755.5:c.1064delA	chr9.hg19:g.37349430delA	ENSP00000337839:p.Gln355fs	113.0	0.0		147.0	11.0	NM_032226	B2RCI4|D3DRQ0|Q5T0Q8|Q5T0Q9|Q5T0R0|Q8N2M1|Q8N4J2|Q8TBK8|Q9H648|Q9P0F0	Frame_Shift_Del	DEL	ENST00000336755.5	hg19	CCDS6608.2																																																																																			.	.		0.438	ZCCHC7-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052453.2	NM_032226	
LENG8	114823	hgsc.bcm.edu	37	19	54967951	54967951	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:54967951delC	ENST00000326764.5	+	11	2061	c.1582delC	c.(1582-1584)cccfs	p.P528fs	LENG8_ENST00000376514.2_Intron	NM_052925.2	NP_443157.1	Q96PV6	LENG8_HUMAN	leukocyte receptor cluster (LRC) member 8	491										breast(1)|central_nervous_system(3)|endometrium(3)|kidney(1)|large_intestine(6)|lung(9)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	30	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.139)		GCGCCTCGAGCCCCTGGTGCT	0.667																																					p.E527fs		Atlas-INDEL	.											.	LENG8	73	.	0			c.1581delG						.						28.0	27.0	27.0					19																	54967951		2202	4298	6500	SO:0001589	frameshift_variant	114823	exon11			.	AF211975	CCDS12894.1	19q13.4	2008-02-05			ENSG00000167615	ENSG00000167615			15500	protein-coding gene	gene with protein product						10941842	Standard	XM_005278248		Approved	KIAA1932, MGC40108, pp13842	uc002qfw.2	Q96PV6	OTTHUMG00000065548	ENST00000326764.5:c.1582delC	chr19.hg19:g.54967951delC	ENSP00000318374:p.Pro528fs	73.0	0.0		127.0	10.0	NM_052925	B0VJY9|Q8IZ27|Q8NCX6	Frame_Shift_Del	DEL	ENST00000326764.5	hg19	CCDS12894.1																																																																																			.	.		0.667	LENG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140523.2	NM_052925	
KCNT2	343450	hgsc.bcm.edu	37	1	196227429	196227429	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:196227429delT	ENST00000294725.9	-	26	4021	c.3106delA	c.(3106-3108)atafs	p.I1036fs	KCNT2_ENST00000367431.4_Frame_Shift_Del_p.I970fs|KCNT2_ENST00000367433.5_Frame_Shift_Del_p.I1012fs|KCNT2_ENST00000498426.1_5'UTR|KCNT2_ENST00000451324.2_3'UTR|KCNT2_ENST00000609185.1_Frame_Shift_Del_p.I969fs			Q6UVM3	KCNT2_HUMAN	potassium channel, subfamily T, member 2	1036					potassium ion transmembrane transport (GO:0071805)	voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|calcium-activated potassium channel activity (GO:0015269)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(16)|lung(43)|ovary(5)|pancreas(1)|prostate(1)|skin(11)|stomach(2)|upper_aerodigestive_tract(1)	97						TGCTGGGTTATTTTTTCAGCT	0.473																																					p.I1036fs		Atlas-Indel,Pindel	.											.	KCNT2	243	.	0			c.3107delT						.						113.0	108.0	110.0					1																	196227429		2203	4300	6503	SO:0001589	frameshift_variant	343450	exon26			.	BX647852, AY359444, AK127807	CCDS1384.1, CCDS72994.1, CCDS72995.1	1q31.3	2012-07-05			ENSG00000162687	ENSG00000162687		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, calcium-activated"""	18866	protein-coding gene	gene with protein product	"""sodium and chloride activated ATP sensitive potassium channel"""	610044				16382103	Standard	NM_198503		Approved	KCa4.2, SLICK, SLO2.1	uc001gtd.1	Q6UVM3	OTTHUMG00000035611	ENST00000294725.9:c.3106delA	chr1.hg19:g.196227429delT	ENSP00000294725:p.Ile1036fs	229.0	0.0		346.0	22.0	NM_198503	Q3SY59|Q5VTN1|Q6ZMT3	Frame_Shift_Del	DEL	ENST00000294725.9	hg19	CCDS1384.1																																																																																			.	.		0.473	KCNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086418.2	NM_198503	
CELA2A	63036	hgsc.bcm.edu	37	1	15783592	15783592	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:15783592delG	ENST00000359621.4	+	2	77	c.52delG	c.(52-54)gggfs	p.G18fs	CELA2A_ENST00000497590.1_3'UTR	NM_033440.2	NP_254275.1	P08217	CEL2A_HUMAN	chymotrypsin-like elastase family, member 2A	18						extracellular region (GO:0005576)|keratohyalin granule (GO:0036457)	serine hydrolase activity (GO:0017171)|serine-type endopeptidase activity (GO:0004252)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(7)|ovary(2)|prostate(1)	16						CCTCAGTTGTGGGGACCCCAC	0.542																																					p.C17fs		Atlas-INDEL	.											.	CELA2A	32	.	0			c.51delT						.						90.0	85.0	87.0					1																	15783592		2203	4300	6503	SO:0001589	frameshift_variant	63036	exon2			.		CCDS157.1	1p36.21	2009-07-09			ENSG00000142615	ENSG00000142615	3.4.21.71		24609	protein-coding gene	gene with protein product	"""elastase 2A"""	609443				3646943, 2834346	Standard	NM_033440		Approved	ELA2A	uc001awk.3	P08217	OTTHUMG00000002258	ENST00000359621.4:c.52delG	chr1.hg19:g.15783592delG	ENSP00000352639:p.Gly18fs	207.0	0.0		238.0	15.0	NM_033440	B2R5I4|Q14243	Frame_Shift_Del	DEL	ENST00000359621.4	hg19	CCDS157.1																																																																																			.	.		0.542	CELA2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006445.1	NM_033440	
RBMXL3	139804	hgsc.bcm.edu	37	X	114426075	114426075	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:114426075delG	ENST00000424776.3	+	1	2113	c.2071delG	c.(2071-2073)gggfs	p.G692fs	LRCH2_ENST00000538422.1_Intron|LRCH2_ENST00000317135.8_Intron	NM_001145346.1	NP_001138818.1	Q8N7X1	RMXL3_HUMAN	RNA binding motif protein, X-linked-like 3	692	Gly-rich.						nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			endometrium(13)|kidney(2)|skin(1)	16						TGCCTACAGTGGGGGCCACGA	0.657																																					p.S690fs		Atlas-INDEL	.											.	RBMXL3	83	.	0			c.2070delT						.						47.0	50.0	49.0					X																	114426075		692	1591	2283	SO:0001589	frameshift_variant	139804	exon1			.	AK097568	CCDS55478.1	Xq23	2013-02-12	2009-03-24	2009-03-24	ENSG00000175718	ENSG00000175718		"""RNA binding motif (RRM) containing"""	26859	protein-coding gene	gene with protein product			"""chromosome X open reading frame 55"""	CXorf55			Standard	NM_001145346		Approved	FLJ40249	uc011mte.1	Q8N7X1	OTTHUMG00000022230	ENST00000424776.3:c.2071delG	chrX.hg19:g.114426075delG	ENSP00000417451:p.Gly692fs	148.0	0.0		174.0	12.0	NM_001145346	B4DXC0	Frame_Shift_Del	DEL	ENST00000424776.3	hg19	CCDS55478.1																																																																																			.	.		0.657	RBMXL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057968.3	NM_001145346	
SNRK	54861	hgsc.bcm.edu	37	3	43389468	43389468	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:43389468delC	ENST00000296088.7	+	7	2021	c.1717delC	c.(1717-1719)cccfs	p.P574fs	SNRK_ENST00000437827.1_Frame_Shift_Del_p.P368fs|RP11-188P20.3_ENST00000607513.1_RNA|SNRK_ENST00000454177.1_Frame_Shift_Del_p.P574fs|SNRK_ENST00000429705.2_Frame_Shift_Del_p.P574fs|SNRK-AS1_ENST00000422681.1_RNA	NM_017719.4	NP_060189.3			SNF related kinase											breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|liver(2)|lung(3)|ovary(5)|prostate(1)|skin(2)|stomach(1)	27				KIRC - Kidney renal clear cell carcinoma(284;0.0636)|Kidney(284;0.0792)		CAGCGAGGGGCCCCCTGGCAG	0.627																																					p.G572fs		Atlas-INDEL	.											.	SNRK	118	.	0			c.1716delG						.						28.0	34.0	32.0					3																	43389468		1911	4105	6016	SO:0001589	frameshift_variant	54861	exon6			.	D43636	CCDS43075.1	3p22.1	2005-08-09			ENSG00000163788	ENSG00000163788			30598	protein-coding gene	gene with protein product		612760				8654423, 7788527	Standard	NM_017719		Approved	FLJ20224, HSNFRK, KIAA0096	uc003cmt.4	Q9NRH2	OTTHUMG00000156491	ENST00000296088.7:c.1717delC	chr3.hg19:g.43389468delC	ENSP00000296088:p.Pro574fs	129.0	0.0		153.0	10.0	NM_001100594		Frame_Shift_Del	DEL	ENST00000296088.7	hg19	CCDS43075.1																																																																																			.	.		0.627	SNRK-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344325.1	NM_017719	
TFDP3	51270	hgsc.bcm.edu	37	X	132351743	132351743	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:132351743delT	ENST00000310125.4	-	1	633	c.545delA	c.(544-546)aagfs	p.K183fs		NM_016521.2	NP_057605.3	Q5H9I0	TFDP3_HUMAN	transcription factor Dp family, member 3	183	Involved in negatively regulating E2F activity.				cellular response to DNA damage stimulus (GO:0006974)|G1/S transition of mitotic cell cycle (GO:0000082)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|kidney(4)|large_intestine(1)|lung(8)|ovary(1)|prostate(2)	19	Acute lymphoblastic leukemia(192;0.000127)					CTTGATCTTCTTTTTCTCCCT	0.448																																					p.K182fs		Atlas-INDEL	.											.	TFDP3	92	.	0			c.546delG						.						101.0	90.0	94.0					X																	132351743		2203	4300	6503	SO:0001589	frameshift_variant	51270	exon1			.	AF219119	CCDS14636.2	Xq26.2	2009-03-25			ENSG00000183434	ENSG00000183434			24603	protein-coding gene	gene with protein product	"""E2F-like protein"", ""cancer/testis antigen 30"""	300772				12097419	Standard	NM_016521		Approved	HCA661, E2F-like, CT30	uc004exb.1	Q5H9I0	OTTHUMG00000022433	ENST00000310125.4:c.545delA	chrX.hg19:g.132351743delT	ENSP00000385461:p.Lys183fs	64.0	0.0		95.0	10.0	NM_016521	Q6DK49|Q9NZ54	Frame_Shift_Del	DEL	ENST00000310125.4	hg19	CCDS14636.2																																																																																			.	.		0.448	TFDP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058337.1	NM_016521	
NID2	22795	hgsc.bcm.edu	37	14	52505655	52505655	+	Frame_Shift_Del	DEL	A	A	-	rs150250347		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:52505655delA	ENST00000216286.5	-	9	2066	c.2067delT	c.(2065-2067)tttfs	p.F689fs	NID2_ENST00000541773.1_Frame_Shift_Del_p.F636fs	NM_007361.3	NP_031387.3	Q14112	NID2_HUMAN	nidogen 2 (osteonidogen)	689	Nidogen G2 beta-barrel. {ECO:0000255|PROSITE-ProRule:PRU00348}.				basement membrane organization (GO:0071711)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|cell surface (GO:0009986)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)			NS(1)|breast(5)|endometrium(9)|kidney(4)|large_intestine(11)|liver(1)|lung(40)|ovary(2)|pancreas(2)|prostate(2)|skin(3)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	87	Breast(41;0.0639)|all_epithelial(31;0.123)					TGATTGCACCAAAAGTCAGAG	0.473																																					p.G690fs		Atlas-INDEL	.											.	NID2	201	.	0			c.2068delG						.						113.0	107.0	109.0					14																	52505655		2203	4300	6503	SO:0001589	frameshift_variant	22795	exon9			.	AB009799	CCDS9706.1	14q22.1	2008-05-14			ENSG00000087303	ENSG00000087303			13389	protein-coding gene	gene with protein product		605399				9733643	Standard	NM_007361		Approved		uc001wzo.3	Q14112	OTTHUMG00000140298	ENST00000216286.5:c.2067delT	chr14.hg19:g.52505655delA	ENSP00000216286:p.Phe689fs	123.0	0.0		155.0	11.0	NM_007361	A8K6I7|B4DU19|O43710	Frame_Shift_Del	DEL	ENST00000216286.5	hg19	CCDS9706.1																																																																																			.	.		0.473	NID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276888.1		
SAMD3	154075	hgsc.bcm.edu	37	6	130467230	130467230	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:130467230delA	ENST00000368134.2	-	12	1728	c.1120delT	c.(1120-1122)tcafs	p.S374fs	RP11-73O6.3_ENST00000609978.1_RNA|SAMD3_ENST00000437477.2_Frame_Shift_Del_p.S374fs|SAMD3_ENST00000457563.2_Frame_Shift_Del_p.S398fs|SAMD3_ENST00000439090.2_Frame_Shift_Del_p.S374fs	NM_001258275.1	NP_001245204.1	Q8N6K7	SAMD3_HUMAN	sterile alpha motif domain containing 3	374										breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(3)|lung(15)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	29				GBM - Glioblastoma multiforme(226;0.00594)|OV - Ovarian serous cystadenocarcinoma(155;0.128)		TCCACCACTGAAAAAGAAGTC	0.318																																					p.S374X		Atlas-INDEL	.											.	SAMD3	98	.	0			c.1121delC						.						98.0	101.0	100.0					6																	130467230		2202	4293	6495	SO:0001589	frameshift_variant	154075	exon10			.	AK091351	CCDS34539.1, CCDS64525.1	6q23.1	2013-01-10			ENSG00000164483	ENSG00000164483		"""Sterile alpha motif (SAM) domain containing"""	21574	protein-coding gene	gene with protein product							Standard	NM_001017373		Approved	bA73O6.2, FLJ34032	uc031spp.1	Q8N6K7	OTTHUMG00000015556	ENST00000368134.2:c.1120delT	chr6.hg19:g.130467230delA	ENSP00000357116:p.Ser374fs	80.0	0.0		97.0	10.0	NM_001017373	B4DY20|E1P576|J3KQK4|Q4VXD8|Q8NAY1|Q8NB96	Frame_Shift_Del	DEL	ENST00000368134.2	hg19	CCDS34539.1																																																																																			.	.		0.318	SAMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042197.3	NM_152552	
RERE	473	hgsc.bcm.edu	37	1	8421412	8421412	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:8421412delG	ENST00000337907.3	-	19	2789	c.2155delC	c.(2155-2157)cagfs	p.Q719fs	RERE_ENST00000476556.1_Frame_Shift_Del_p.Q165fs|RERE_ENST00000400908.2_Frame_Shift_Del_p.Q719fs|RERE_ENST00000377464.1_Frame_Shift_Del_p.Q451fs|RERE_ENST00000400907.2_Intron	NM_012102.3	NP_036234.3	Q9P2R6	RERE_HUMAN	arginine-glutamic acid dipeptide (RE) repeats	719					chromatin remodeling (GO:0006338)|multicellular organismal development (GO:0007275)|NLS-bearing protein import into nucleus (GO:0006607)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|poly-glutamine tract binding (GO:0008267)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|liver(1)|lung(16)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	49	Ovarian(185;0.0661)	all_epithelial(116;1.17e-21)|all_lung(118;1.4e-06)|Lung NSC(185;3.06e-06)|Renal(390;0.000147)|Breast(348;0.000206)|Colorectal(325;0.00187)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;9.64e-67)|GBM - Glioblastoma multiforme(8;9.89e-33)|Colorectal(212;1.45e-07)|COAD - Colon adenocarcinoma(227;3.42e-05)|Kidney(185;6e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000533)|KIRC - Kidney renal clear cell carcinoma(229;0.00106)|STAD - Stomach adenocarcinoma(132;0.00118)|READ - Rectum adenocarcinoma(331;0.0419)|Lung(427;0.195)		TCATTGTCCTGGGGGCTGGGG	0.632																																					p.Q719fs		Atlas-INDEL	.											.	RERE	129	.	0			c.2156delA						.						92.0	88.0	90.0					1																	8421412		2203	4300	6503	SO:0001589	frameshift_variant	473	exon19			.	AF016005	CCDS95.1, CCDS41243.1	1p36.23	2013-01-25			ENSG00000142599	ENSG00000142599		"""GATA zinc finger domain containing"""	9965	protein-coding gene	gene with protein product		605226		ATN1L		10814707, 10729226	Standard	NM_012102		Approved	KIAA0458, ARP, ARG, DNB1	uc001apf.3	Q9P2R6	OTTHUMG00000001765	ENST00000337907.3:c.2155delC	chr1.hg19:g.8421412delG	ENSP00000338629:p.Gln719fs	124.0	0.0		136.0	10.0	NM_012102	O43393|O75046|O75359|Q5VXL9|Q6P6B9|Q9Y2W4	Frame_Shift_Del	DEL	ENST00000337907.3	hg19	CCDS95.1																																																																																			.	.		0.632	RERE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004916.1		
FARP2	9855	hgsc.bcm.edu	37	2	242373660	242373660	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:242373660delT	ENST00000264042.3	+	10	1125	c.955delT	c.(955-957)tttfs	p.F320fs	FARP2_ENST00000373287.4_Frame_Shift_Del_p.F320fs|FARP2_ENST00000545004.1_Frame_Shift_Del_p.F320fs	NM_014808.2	NP_055623.1	O94887	FARP2_HUMAN	FERM, RhoGEF and pleckstrin domain protein 2	320	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				actin cytoskeleton reorganization (GO:0031532)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|neuron remodeling (GO:0016322)|osteoclast differentiation (GO:0030316)|podosome assembly (GO:0071800)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|Rac protein signal transduction (GO:0016601)|regulation of integrin activation (GO:0033623)|regulation of Rac GTPase activity (GO:0032314)|semaphorin-plexin signaling pathway (GO:0071526)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)	Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(18)|ovary(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	43		all_cancers(19;4.88e-34)|all_epithelial(40;4.81e-14)|Breast(86;0.000141)|Renal(207;0.0143)|all_lung(227;0.0344)|Lung NSC(271;0.0886)|Ovarian(221;0.0905)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;1.81e-33)|all cancers(36;1.61e-30)|OV - Ovarian serous cystadenocarcinoma(60;6.83e-15)|Kidney(56;1.19e-08)|KIRC - Kidney renal clear cell carcinoma(57;8.98e-08)|BRCA - Breast invasive adenocarcinoma(100;1.49e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00125)|Colorectal(34;0.0199)|COAD - Colon adenocarcinoma(134;0.121)		GTATCACACCTTTTTTAGACT	0.453																																					p.T318fs		Atlas-INDEL	.											.	FARP2	92	.	0			c.954delC						.						140.0	144.0	142.0					2																	242373660		2203	4300	6503	SO:0001589	frameshift_variant	9855	exon10			.	AB018336	CCDS33424.1, CCDS63197.1	2q37.3	2013-01-10			ENSG00000006607	ENSG00000006607		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	16460	protein-coding gene	gene with protein product						9872452, 12351724	Standard	NM_001282984		Approved	KIAA0793, FIR, PLEKHC3, FRG	uc002wbi.2	O94887	OTTHUMG00000151574	ENST00000264042.3:c.955delT	chr2.hg19:g.242373660delT	ENSP00000264042:p.Phe320fs	126.0	0.0		159.0	12.0	NM_014808	B7Z6J8|F5GZ84|Q53QM5|Q8WU27|Q9UFE7	Frame_Shift_Del	DEL	ENST00000264042.3	hg19	CCDS33424.1																																																																																			.	.		0.453	FARP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323153.1		
TTLL4	9654	hgsc.bcm.edu	37	2	219602445	219602445	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:219602445delA	ENST00000392102.1	+	3	386	c.46delA	c.(46-48)aaafs	p.K16fs	TTLL4_ENST00000258398.4_Frame_Shift_Del_p.K16fs|TTLL4_ENST00000457313.1_Intron|TTLL4_ENST00000442769.1_Frame_Shift_Del_p.K16fs	NM_014640.4	NP_055455.3	Q14679	TTLL4_HUMAN	tubulin tyrosine ligase-like family, member 4	16					protein polyglutamylation (GO:0018095)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	ligase activity (GO:0016874)|tubulin binding (GO:0015631)			endometrium(3)|kidney(1)|large_intestine(6)|lung(21)|ovary(3)|skin(3)|upper_aerodigestive_tract(2)	39		Renal(207;0.0915)		Epithelial(149;5.03e-07)|all cancers(144;0.000106)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.0101)		CCTCCGCCAGAAAAACAGCTT	0.587																																					p.Q15fs	GBM(172;1818 2053 15407 20943 49753)	Atlas-INDEL	.											.	TTLL4	96	.	0			c.45delG						.						58.0	58.0	58.0					2																	219602445		2203	4300	6503	SO:0001589	frameshift_variant	9654	exon3			.		CCDS2422.1	2p24.3-p24.1	2013-02-14			ENSG00000135912	ENSG00000135912		"""Tubulin tyrosine ligase-like family"""	28976	protein-coding gene	gene with protein product						11054573	Standard	NM_014640		Approved	KIAA0173	uc002viy.3	Q14679	OTTHUMG00000133081	ENST00000392102.1:c.46delA	chr2.hg19:g.219602445delA	ENSP00000375951:p.Lys16fs	123.0	0.0		170.0	11.0	NM_014640	A8K6V5|Q8WW29	Frame_Shift_Del	DEL	ENST00000392102.1	hg19	CCDS2422.1																																																																																			.	.		0.587	TTLL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256726.1	NM_014640	
DDX42	11325	hgsc.bcm.edu	37	17	61877936	61877936	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:61877936delA	ENST00000578681.1	+	7	1181	c.580delA	c.(580-582)aaafs	p.K195fs	DDX42_ENST00000583590.1_Frame_Shift_Del_p.K195fs|DDX42_ENST00000457800.2_Frame_Shift_Del_p.K195fs|DDX42_ENST00000389924.2_Frame_Shift_Del_p.K195fs|DDX42_ENST00000359353.5_Frame_Shift_Del_p.K76fs	NM_007372.2	NP_031398.2	Q86XP3	DDX42_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 42	195					protein localization (GO:0008104)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(12)|kidney(3)|large_intestine(6)|lung(12)|ovary(2)|prostate(2)|skin(3)	46						TGCACCTACCAAAAAAATCAT	0.403																																					p.T193fs		Atlas-INDEL	.											.	DDX42	86	.	0			c.579delC						.						239.0	198.0	212.0					17																	61877936		2203	4300	6503	SO:0001589	frameshift_variant	11325	exon6			.	BC015505	CCDS32704.1	17q23	2014-02-14	2013-05-13			ENSG00000198231		"""DEAD-boxes"""	18676	protein-coding gene	gene with protein product	"""splicing factor 3b, subunit 8"""	613369	"""DEAD (Asp-Glu-Ala-Asp) box polypeptide 42"""			10727850, 16397294	Standard	NM_007372		Approved	RNAHP, RHELP, SF3b125, SF3B8	uc002jbv.3	Q86XP3		ENST00000578681.1:c.580delA	chr17.hg19:g.61877936delA	ENSP00000464050:p.Lys195fs	135.0	0.0		191.0	15.0	NM_203499	A6NML1|A8KA43|O75619|Q68G51|Q96BK1|Q96HR7|Q9Y3V8	Frame_Shift_Del	DEL	ENST00000578681.1	hg19	CCDS32704.1																																																																																			.	.		0.403	DDX42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444368.1	NM_007372	
HTR2C	3358	hgsc.bcm.edu	37	X	114141772	114141772	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:114141772delA	ENST00000276198.1	+	6	1899	c.1171delA	c.(1171-1173)aaafs	p.K392fs	HTR2C_ENST00000371951.1_Frame_Shift_Del_p.K392fs|HTR2C_ENST00000371950.3_3'UTR	NM_000868.2	NP_000859.1	P28335	5HT2C_HUMAN	5-hydroxytryptamine (serotonin) receptor 2C, G protein-coupled	392					behavioral fear response (GO:0001662)|cellular calcium ion homeostasis (GO:0006874)|cGMP biosynthetic process (GO:0006182)|feeding behavior (GO:0007631)|locomotory behavior (GO:0007626)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|phospholipase C-activating serotonin receptor signaling pathway (GO:0007208)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phosphatidylinositol biosynthetic process (GO:0010513)|regulation of appetite (GO:0032098)|regulation of corticotropin-releasing hormone secretion (GO:0043397)|regulation of neurological system process (GO:0031644)|release of sequestered calcium ion into cytosol (GO:0051209)|response to drug (GO:0042493)|serotonin receptor signaling pathway (GO:0007210)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	1-(4-iodo-2,5-dimethoxyphenyl)propan-2-amine binding (GO:0071886)|drug binding (GO:0008144)|Gq/11-coupled serotonin receptor activity (GO:0001587)|serotonin binding (GO:0051378)|serotonin receptor activity (GO:0004993)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(15)|ovary(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	50					Agomelatine(DB06594)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Clomipramine(DB01242)|Clozapine(DB00363)|Cyproheptadine(DB00434)|Desipramine(DB01151)|Dexfenfluramine(DB01191)|Doxepin(DB01142)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Imipramine(DB00458)|Ketamine(DB01221)|Lisuride(DB00589)|Lorcaserin(DB04871)|Loxapine(DB00408)|Maprotiline(DB00934)|Methotrimeprazine(DB01403)|Methysergide(DB00247)|Mianserin(DB06148)|Minaprine(DB00805)|Mirtazapine(DB00370)|Nefazodone(DB01149)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Paliperidone(DB01267)|Pergolide(DB01186)|Pramipexole(DB00413)|Promazine(DB00420)|Propiomazine(DB00777)|Quetiapine(DB01224)|Risperidone(DB00734)|Ropinirole(DB00268)|Sertindole(DB06144)|Tramadol(DB00193)|Trazodone(DB00656)|Trimipramine(DB00726)|Yohimbine(DB01392)|Ziprasidone(DB00246)	TAAGGTAGAGAAAAAGCCTCC	0.428																																					p.E390fs		Atlas-INDEL	.											.	HTR2C	117	.	0			c.1170delG						.						84.0	84.0	84.0					X																	114141772		2203	4300	6503	SO:0001589	frameshift_variant	3358	exon6			.		CCDS14564.1, CCDS59174.1	Xq23	2013-12-19	2012-02-03		ENSG00000147246	ENSG00000147246		"""5-HT (serotonin) receptors"", ""GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"""	5295	protein-coding gene	gene with protein product		312861	"""5-hydroxytryptamine (serotonin) receptor 2C"""	HTR1C		7895773	Standard	NM_000868		Approved	5-HT2C, 5HTR2C	uc004epu.1	P28335	OTTHUMG00000022226	ENST00000276198.1:c.1171delA	chrX.hg19:g.114141772delA	ENSP00000276198:p.Lys392fs	131.0	0.0		166.0	11.0	NM_000868	B1AMW4|Q5VUF8|Q9NP28	Frame_Shift_Del	DEL	ENST00000276198.1	hg19	CCDS14564.1																																																																																			.	.		0.428	HTR2C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057962.1	NM_000868	
SLFN11	91607	hgsc.bcm.edu	37	17	33680769	33680769	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:33680769delC	ENST00000394566.1	-	6	1780	c.1508delG	c.(1507-1509)ggcfs	p.G503fs	SLFN11_ENST00000308377.4_Frame_Shift_Del_p.G503fs	NM_001104587.1|NM_001104588.1|NM_001104589.1|NM_001104590.1	NP_001098057.1|NP_001098058.1|NP_001098059.1|NP_001098060.1	Q7Z7L1	SLN11_HUMAN	schlafen family member 11	503					defense response to virus (GO:0051607)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|tRNA binding (GO:0000049)			autonomic_ganglia(1)|breast(1)|kidney(3)|large_intestine(14)|lung(17)|ovary(1)|prostate(4)|skin(2)|stomach(5)|upper_aerodigestive_tract(2)	50		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		CCCGGTGTAGCCCCCCATGTT	0.577																																					p.G503fs		Atlas-INDEL	.											.	SLFN11	112	.	0			c.1509delC						.						8.0	7.0	7.0					17																	33680769		2087	4116	6203	SO:0001589	frameshift_variant	91607	exon4			.	AK074184	CCDS11294.1	17q12	2006-04-05			ENSG00000172716	ENSG00000172716			26633	protein-coding gene	gene with protein product		614953				12477932	Standard	NM_001104587		Approved	FLJ34922	uc010ctr.3	Q7Z7L1	OTTHUMG00000132948	ENST00000394566.1:c.1508delG	chr17.hg19:g.33680769delC	ENSP00000378067:p.Gly503fs	366.0	0.0		338.0	21.0	NM_152270	E1P643|Q8N3S8|Q8N762|Q8TEE0	Frame_Shift_Del	DEL	ENST00000394566.1	hg19	CCDS11294.1																																																																																			.	.		0.577	SLFN11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256480.1	NM_152270	
SVEP1	79987	hgsc.bcm.edu	37	9	113132231	113132231	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:113132231delA	ENST00000401783.2	-	47	11002	c.10666delT	c.(10666-10668)tctfs	p.S3557fs	SVEP1_ENST00000374469.1_Frame_Shift_Del_p.S3534fs|SVEP1_ENST00000297826.5_Frame_Shift_Del_p.S1483fs|RNU6-1039P_ENST00000383931.1_RNA	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	3557	EGF-like 9. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)			NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(2)|endometrium(19)|kidney(8)|large_intestine(24)|lung(58)|ovary(7)|prostate(7)|skin(1)|stomach(4)|upper_aerodigestive_tract(5)|urinary_tract(4)	147						GTCCAAGAAGAAAGACAGTGA	0.368																																					p.S3556fs		Atlas-INDEL	.											.	SVEP1	326	.	0			c.10667delC						.						90.0	83.0	85.0					9																	113132231		1858	4098	5956	SO:0001589	frameshift_variant	79987	exon47			.	AK027870		9q31-q32	2008-02-05	2005-03-15	2005-03-17	ENSG00000165124	ENSG00000165124			15985	protein-coding gene	gene with protein product		611691	"""chromosome 9 open reading frame 13"""	C9orf13			Standard	NM_153366		Approved	bA427L11.3, POLYDOM, FLJ13529	uc010mtz.3	Q4LDE5	OTTHUMG00000020482	ENST00000401783.2:c.10666delT	chr9.hg19:g.113132231delA	ENSP00000384917:p.Ser3557fs	125.0	0.0		121.0	10.0	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Frame_Shift_Del	DEL	ENST00000401783.2	hg19	CCDS48004.1																																																																																			.	.		0.368	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
DCBLD2	131566	hgsc.bcm.edu	37	3	98544174	98544174	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:98544174delA	ENST00000326840.6	-	4	970	c.608delT	c.(607-609)ttgfs	p.L203fs	DCBLD2_ENST00000469648.1_5'UTR|DCBLD2_ENST00000326857.9_Frame_Shift_Del_p.L203fs	NM_080927.3	NP_563615.3	Q96PD2	DCBD2_HUMAN	discoidin, CUB and LCCL domain containing 2	203	LCCL. {ECO:0000255|PROSITE- ProRule:PRU00123}.				cell adhesion (GO:0007155)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of cell growth (GO:0030308)|wound healing (GO:0042060)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)				breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|prostate(1)|stomach(2)	25						CTCAGGTTCCAAAAAATTGGA	0.279																																					p.L203fs		Atlas-INDEL	.											.	DCBLD2	62	.	0			c.609delG						.						33.0	30.0	31.0					3																	98544174		1792	4061	5853	SO:0001589	frameshift_variant	131566	exon4			.		CCDS46878.1	3q12.2	2006-04-12			ENSG00000057019	ENSG00000057019			24627	protein-coding gene	gene with protein product		608698				11447234	Standard	NM_080927		Approved	CLCP1, ESDN	uc003dtd.3	Q96PD2	OTTHUMG00000151985	ENST00000326840.6:c.608delT	chr3.hg19:g.98544174delA	ENSP00000321573:p.Leu203fs	100.0	0.0		134.0	10.0	NM_080927	B7WNL1|D3DN41|Q8N6M4|Q8TDX2	Frame_Shift_Del	DEL	ENST00000326840.6	hg19	CCDS46878.1																																																																																			.	.		0.279	DCBLD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324675.2	NM_080927	
ADAMTSL3	57188	hgsc.bcm.edu	37	15	84592778	84592778	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:84592778delC	ENST00000286744.5	+	17	2334	c.2110delC	c.(2110-2112)cccfs	p.P705fs	ADAMTSL3_ENST00000567476.1_Frame_Shift_Del_p.P705fs	NM_207517.2	NP_997400.2	P82987	ATL3_HUMAN	ADAMTS-like 3	705	TSP type-1 5. {ECO:0000255|PROSITE- ProRule:PRU00210}.					proteinaceous extracellular matrix (GO:0005578)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(2)|breast(7)|central_nervous_system(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(24)|lung(51)|ovary(7)|pancreas(2)|prostate(2)|skin(8)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	130			BRCA - Breast invasive adenocarcinoma(143;0.211)			AGAGCCCTGTCCCCCCAGGTA	0.547																																					p.C703fs		Atlas-INDEL	.											ADAMTSL3,mouth,carcinoma,0,1	ADAMTSL3	290	.	0			c.2109delT						.						101.0	70.0	81.0					15																	84592778		2203	4300	6503	SO:0001589	frameshift_variant	57188	exon17			.	AF237652	CCDS10326.1, CCDS73773.1	15q25.2	2013-01-29			ENSG00000156218	ENSG00000156218		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	14633	protein-coding gene	gene with protein product		609199				9628581, 10574462	Standard	NM_207517		Approved	KIAA1233, punctin-2	uc002bjz.4	P82987	OTTHUMG00000147363	ENST00000286744.5:c.2110delC	chr15.hg19:g.84592778delC	ENSP00000286744:p.Pro705fs	156.0	0.0		172.0	11.0	NM_207517	A1A566|A1A567|Q9ULI7	Frame_Shift_Del	DEL	ENST00000286744.5	hg19	CCDS10326.1																																																																																			.	.		0.547	ADAMTSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304007.2	NM_207517	
PDE2A	5138	hgsc.bcm.edu	37	11	72342169	72342169	+	Intron	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:72342169delG	ENST00000334456.5	-	2	390				PDE2A_ENST00000540345.1_Intron|PDE2A_ENST00000418754.2_Intron|PDE2A_ENST00000376450.3_Intron|PDE2A_ENST00000540380.1_Intron|PDE2A_ENST00000444035.2_Intron|PDE2A_ENST00000544570.1_Intron	NM_002599.4	NP_002590.1	O00408	PDE2A_HUMAN	phosphodiesterase 2A, cGMP-stimulated						blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cAMP catabolic process (GO:0006198)|cAMP-mediated signaling (GO:0019933)|cellular response to cGMP (GO:0071321)|cellular response to drug (GO:0035690)|cellular response to granulocyte macrophage colony-stimulating factor stimulus (GO:0097011)|cellular response to macrophage colony-stimulating factor stimulus (GO:0036006)|cellular response to mechanical stimulus (GO:0071260)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cGMP catabolic process (GO:0046069)|cGMP-mediated signaling (GO:0019934)|establishment of endothelial barrier (GO:0061028)|metabolic process (GO:0008152)|monocyte differentiation (GO:0030224)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of protein import into nucleus, translocation (GO:0033159)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of vascular permeability (GO:0043116)|positive regulation of inflammatory response (GO:0050729)|positive regulation of vascular permeability (GO:0043117)|protein targeting to mitochondrion (GO:0006626)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|mitochondrial matrix (GO:0005759)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	calcium channel activity (GO:0005262)|cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|cGMP-stimulated cyclic-nucleotide phosphodiesterase activity (GO:0004118)|cyclic-nucleotide phosphodiesterase activity (GO:0004112)|drug binding (GO:0008144)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|TPR domain binding (GO:0030911)			breast(2)|endometrium(1)|kidney(3)|large_intestine(2)|lung(21)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	36			BRCA - Breast invasive adenocarcinoma(5;3.55e-05)		Caffeine(DB00201)|Tofisopam(DB08811)	TCCTTTGCAAGGGGGTCCAGG	0.652																																					p.L12fs		Atlas-INDEL	.											.	PDE2A	156	.	0			c.35delT						.																																			SO:0001627	intron_variant	5138	exon2			.	U67733	CCDS8216.1, CCDS44670.1, CCDS53678.1, CCDS73345.1	11q13.1-q14.1	2008-05-14			ENSG00000186642	ENSG00000186642	3.1.4.17	"""Phosphodiesterases"""	8777	protein-coding gene	gene with protein product		602658				9210593	Standard	NM_002599		Approved		uc010rrc.2	O00408	OTTHUMG00000102045	ENST00000334456.5:c.144+11128C>-	chr11.hg19:g.72342169delG		83.0	0.0		133.0	10.0	NM_001243784	B2R646|B3KRV5|E9PGI1|F6W5Z0|Q5J791|Q5J792|Q5J793|Q6ZMR1	Frame_Shift_Del	DEL	ENST00000334456.5	hg19	CCDS8216.1																																																																																			.	.		0.652	PDE2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219839.2	NM_002599	
ERG	2078	hgsc.bcm.edu	37	21	39755389	39755389	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr21:39755389delC	ENST00000417133.2	-	12	1582	c.1397delG	c.(1396-1398)ggtfs	p.G466fs	ERG_ENST00000398905.1_Frame_Shift_Del_p.G435fs|ERG_ENST00000398919.2_Frame_Shift_Del_p.G466fs|ERG_ENST00000398910.1_Frame_Shift_Del_p.G443fs|ERG_ENST00000453032.2_Frame_Shift_Del_p.G367fs|ERG_ENST00000288319.7_Frame_Shift_Del_p.G459fs|ERG_ENST00000398907.1_Frame_Shift_Del_p.G436fs|ERG_ENST00000398911.1_Frame_Shift_Del_p.G442fs|ERG_ENST00000442448.1_Frame_Shift_Del_p.G442fs|ERG_ENST00000398897.1_Frame_Shift_Del_p.G343fs	NM_001136154.1|NM_001243432.1	NP_001129626.1|NP_001230361.1	Q12809	KCNH2_HUMAN	v-ets avian erythroblastosis virus E26 oncogene homolog	0					cardiac muscle contraction (GO:0060048)|cellular response to drug (GO:0035690)|membrane depolarization during action potential (GO:0086010)|membrane repolarization during action potential (GO:0086011)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|negative regulation of potassium ion export (GO:1902303)|negative regulation of potassium ion transmembrane transport (GO:1901380)|positive regulation of potassium ion transmembrane transport (GO:1901381)|potassium ion export (GO:0071435)|potassium ion homeostasis (GO:0055075)|potassium ion transmembrane transport (GO:0071805)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of heart rate by hormone (GO:0003064)|regulation of membrane potential (GO:0042391)|regulation of membrane repolarization (GO:0060306)|regulation of potassium ion transmembrane transport (GO:1901379)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|synaptic transmission (GO:0007268)|ventricular cardiac muscle cell action potential (GO:0086005)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|identical protein binding (GO:0042802)|inward rectifier potassium channel activity (GO:0005242)|phosphorelay sensor kinase activity (GO:0000155)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization (GO:1902282)		EWSR1/ERG(178)|NDRG1/ERG(5)|TMPRSS2/ERG(3582)|FUS/ERG(167)|SLC45A3/ERG(50)	lung(2)|ovary(1)|skin(1)	4		Prostate(19;3.6e-06)			Alfuzosin(DB00346)|Amiodarone(DB01118)|Amsacrine(DB00276)|Astemizole(DB00637)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Cisapride(DB00604)|Dofetilide(DB00204)|Doxazosin(DB00590)|Doxepin(DB01142)|Dronedarone(DB04855)|Halofantrine(DB01218)|Ibutilide(DB00308)|Imipramine(DB00458)|Miconazole(DB01110)|Pimozide(DB01100)|Prazosin(DB00457)|Propafenone(DB01182)|Quinidine(DB00908)|Sertindole(DB06144)|Sotalol(DB00489)|Terazosin(DB01162)|Thioridazine(DB00679)|Verapamil(DB00661)	GGGGTATATACCCCCAGTTGG	0.537			T	"""EWSR1, TMPRSS2, ELF4, FUS, HERPUD1, NDRG1"""	"""Ewing sarcoma, prostate, AML"""																																p.G466fs	Esophageal Squamous(130;336 1700 3010 3083 40589)	Atlas-INDEL	.		Dom	yes		21	21q22.3	2078	v-ets erythroblastosis virus E26 oncogene like (avian)		"""M, E, L"""	.	ERG	78	.	0			c.1398delT						.						34.0	35.0	35.0					21																	39755389		2203	4300	6503	SO:0001589	frameshift_variant	2078	exon12			.		CCDS13657.1, CCDS13658.1, CCDS46648.1, CCDS46649.1, CCDS58789.1	21q22.3	2013-07-09	2013-07-09		ENSG00000157554	ENSG00000157554			3446	protein-coding gene	gene with protein product	"""v-ets avian erythroblastosis virus E26 oncogene related"", ""transcriptional regulator ERG (transforming protein ERG)"", ""v-ets erythroblastosis virus E26 oncogene like"", ""TMPRSS2-ERG prostate cancer specific"""	165080	"""v-ets avian erythroblastosis virus E26 oncogene related"""			3274086	Standard	NM_001136154		Approved	erg-3, p55	uc002yxa.3	P11308	OTTHUMG00000090767	ENST00000417133.2:c.1397delG	chr21.hg19:g.39755389delC	ENSP00000414150:p.Gly466fs	131.0	0.0		150.0	10.0	NM_001136154	A5H1P7|C4PFH9|D3DX04|O75418|O75680|Q708S9|Q9BT72|Q9BUT7|Q9H3P0	Frame_Shift_Del	DEL	ENST00000417133.2	hg19	CCDS46648.1																																																																																			.	.		0.537	ERG-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207532.2	NM_182918	
GGCT	79017	hgsc.bcm.edu	37	7	30540183	30540183	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:30540183delT	ENST00000275428.4	-	2	390	c.256delA	c.(256-258)atgfs	p.M86fs	GGCT_ENST00000409390.1_Frame_Shift_Del_p.M86fs|GGCT_ENST00000409144.1_Intron|GGCT_ENST00000598361.1_Start_Codon_Del|GGCT_ENST00000005374.6_Frame_Shift_Del_p.M86fs|GGCT_ENST00000409436.1_Frame_Shift_Del_p.M86fs	NM_024051.3	NP_076956.1	O75223	GGCT_HUMAN	gamma-glutamylcyclotransferase	86					glutathione biosynthetic process (GO:0006750)|glutathione derivative biosynthetic process (GO:1901687)|release of cytochrome c from mitochondria (GO:0001836)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	gamma-glutamylcyclotransferase activity (GO:0003839)|protein homodimerization activity (GO:0042803)			endometrium(2)|kidney(1)|large_intestine(2)|lung(3)	8						CTTTTGTTCATTTTCCATACT	0.388																																					p.M86fs		Atlas-INDEL	.											.	GGCT	17	.	0			c.257delT						.						158.0	148.0	151.0					7																	30540183		2202	4300	6502	SO:0001589	frameshift_variant	79017	exon2			.	BC019243	CCDS5428.1, CCDS56474.1, CCDS56475.1, CCDS56476.1	7p15-p14	2010-04-23	2010-04-23	2008-08-04	ENSG00000006625	ENSG00000006625	2.3.2.4		21705	protein-coding gene	gene with protein product		137170	"""chromosome 7 open reading frame 24"""	C7orf24, GCTG		17932939, 18515354	Standard	NM_024051		Approved	MGC3077, CRF21, Ggc	uc003tba.3	O75223	OTTHUMG00000128593	ENST00000275428.4:c.256delA	chr7.hg19:g.30540183delT	ENSP00000275428:p.Met86fs	98.0	0.0		133.0	10.0	NM_024051	B2RDN0|B8ZZN4|B8ZZR8|Q9BS37	Frame_Shift_Del	DEL	ENST00000275428.4	hg19	CCDS5428.1																																																																																			.	.		0.388	GGCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250447.2	NM_024051	
PBX4	80714	hgsc.bcm.edu	37	19	19681606	19681606	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:19681606delG	ENST00000251203.9	-	3	516	c.230delC	c.(229-231)cctfs	p.P77fs		NM_025245.2	NP_079521.1	Q9BYU1	PBX4_HUMAN	pre-B-cell leukemia homeobox 4	77					positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)|XY body (GO:0001741)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			large_intestine(1)|lung(4)|ovary(1)|prostate(3)	9						CTGGGCGTCAGGGGGATCTTC	0.552																																					p.P77fs		Atlas-INDEL	.											.	PBX4	34	.	0			c.231delT						.						67.0	69.0	69.0					19																	19681606		2203	4300	6503	SO:0001589	frameshift_variant	80714	exon3			.	AJ300182	CCDS12406.1	19p13.11	2014-09-11	2007-01-30		ENSG00000105717			"""Homeoboxes / TALE class"""	13403	protein-coding gene	gene with protein product		608127	"""pre-B-cell leukemia transcription factor 4"""				Standard	NM_025245		Approved		uc002nmy.3	Q9BYU1	OTTHUMG00000172310	ENST00000251203.9:c.230delC	chr19.hg19:g.19681606delG	ENSP00000251203:p.Pro77fs	96.0	0.0		133.0	10.0	NM_025245	A5D8Y0|B3KUK9	Frame_Shift_Del	DEL	ENST00000251203.9	hg19	CCDS12406.1																																																																																			.	.		0.552	PBX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417784.6		
CELSR2	1952	hgsc.bcm.edu	37	1	109810210	109810210	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:109810210delC	ENST00000271332.3	+	16	6115	c.6054delC	c.(6052-6054)ctcfs	p.L2018fs		NM_001408.2	NP_001399.1	Q9HCU4	CELR2_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 2	2018					cerebrospinal fluid secretion (GO:0033326)|cilium assembly (GO:0042384)|cilium movement (GO:0003341)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|neural plate anterior/posterior regionalization (GO:0021999)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|regulation of cell-cell adhesion (GO:0022407)|regulation of protein localization (GO:0032880)|regulation of transcription, DNA-templated (GO:0006355)|ventricular system development (GO:0021591)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(27)|ovary(5)|prostate(1)|skin(3)|urinary_tract(2)	82		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244)		Colorectal(144;0.0296)|Lung(183;0.067)|COAD - Colon adenocarcinoma(174;0.114)|Epithelial(280;0.193)|all cancers(265;0.219)		GGGGGTGGCTCCCCCCAAACC	0.587																																					p.L2018fs	NSCLC(158;1285 2011 34800 34852 42084)	Atlas-INDEL	.											.	CELSR2	228	.	0			c.6053delT						.						105.0	103.0	104.0					1																	109810210		2203	4300	6503	SO:0001589	frameshift_variant	1952	exon16			.	D87469	CCDS796.1	1p13.3	2014-08-08	2013-02-18		ENSG00000143126	ENSG00000143126		"""Cadherins / Major cadherins"", ""-"", ""GPCR / Class B : Orphans"""	3231	protein-coding gene	gene with protein product		604265	"""cadherin, EGF LAG seven-pass G-type receptor 2, flamingo (Drosophila) homolog"""	EGFL2		9693030, 10907856	Standard	NM_001408		Approved	KIAA0279, MEGF3, Flamingo1, CDHF10	uc001dxa.4	Q9HCU4	OTTHUMG00000012003	ENST00000271332.3:c.6054delC	chr1.hg19:g.109810210delC	ENSP00000271332:p.Leu2018fs	157.0	0.0		145.0	11.0	NM_001408	Q5T2Y7|Q92566	Frame_Shift_Del	DEL	ENST00000271332.3	hg19	CCDS796.1																																																																																			.	.		0.587	CELSR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033200.1	NM_001408	
CLASP1	23332	hgsc.bcm.edu	37	2	122182819	122182819	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:122182819delC	ENST00000263710.4	-	22	2497	c.2108delG	c.(2107-2109)ggcfs	p.G703fs	CLASP1_ENST00000455322.2_Frame_Shift_Del_p.G703fs|CLASP1_ENST00000409078.3_Frame_Shift_Del_p.G703fs|CLASP1_ENST00000545861.1_Frame_Shift_Del_p.G479fs|CLASP1_ENST00000397587.3_Frame_Shift_Del_p.G711fs|CLASP1_ENST00000541859.1_Frame_Shift_Del_p.G472fs|CLASP1_ENST00000541377.1_Frame_Shift_Del_p.G710fs	NM_015282.2	NP_056097.1	Q7Z460	CLAP1_HUMAN	cytoplasmic linker associated protein 1	703	Interaction with microtubules, MAPRE1 and MAPRE3.|Ser-rich.				axon guidance (GO:0007411)|cell division (GO:0051301)|establishment of spindle orientation (GO:0051294)|establishment or maintenance of cell polarity (GO:0007163)|exit from mitosis (GO:0010458)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule anchoring (GO:0034453)|microtubule bundle formation (GO:0001578)|microtubule cytoskeleton organization (GO:0000226)|microtubule nucleation (GO:0007020)|microtubule organizing center organization (GO:0031023)|mitotic cell cycle (GO:0000278)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of microtubule polymerization or depolymerization (GO:0031111)	cell cortex (GO:0005938)|centrosomal corona (GO:0031592)|centrosome (GO:0005813)|cortical microtubule cytoskeleton (GO:0030981)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|membrane (GO:0016020)|spindle microtubule (GO:0005876)	kinetochore binding (GO:0043515)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)			NS(2)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(4)|large_intestine(8)|lung(19)|ovary(1)|prostate(1)	47	Renal(3;0.0496)					TCGTGAGGAGCCCCCAGTAAG	0.498																																					p.G711fs		Atlas-INDEL	.											.	CLASP1	135	.	0			c.2133delC						.						88.0	86.0	87.0					2																	122182819		1837	4085	5922	SO:0001589	frameshift_variant	23332	exon23			.	AB014522		2q14.2-q14.3	2013-01-18			ENSG00000074054	ENSG00000074054			17088	protein-coding gene	gene with protein product	"""multiple asters 1"""	605852				9734811, 10899121, 16914514	Standard	NM_015282		Approved	KIAA0622, MAST1	uc002tnc.3	Q7Z460	OTTHUMG00000153331	ENST00000263710.4:c.2108delG	chr2.hg19:g.122182819delC	ENSP00000263710:p.Gly703fs	104.0	0.0		144.0	10.0	NM_001142273	B7ZLX3|O75118|Q2KHQ9|Q5H9P0|Q8N5B8|Q9BQT5	Frame_Shift_Del	DEL	ENST00000263710.4	hg19																																																																																				.	.		0.498	CLASP1-201	KNOWN	basic	protein_coding	protein_coding		NM_015282	
MED14	9282	hgsc.bcm.edu	37	X	40562784	40562784	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:40562784delG	ENST00000324817.1	-	11	1441	c.1323delC	c.(1321-1323)cccfs	p.P441fs		NM_004229.3	NP_004220.2	O60244	MED14_HUMAN	mediator complex subunit 14	441	Interaction with STAT2.				androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			NS(2)|breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(7)|lung(8)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						GCTCCAAGATGGGAACAACAA	0.343																																					p.I442fs		Atlas-INDEL	.											.	MED14	108	.	0			c.1324delA						.						52.0	46.0	48.0					X																	40562784		2203	4300	6503	SO:0001589	frameshift_variant	9282	exon11			.	AB006651	CCDS14254.1	Xp11.4	2008-05-14	2007-07-30	2007-07-30	ENSG00000180182	ENSG00000180182			2370	protein-coding gene	gene with protein product		300182	"""cofactor required for Sp1 transcriptional activation, subunit 2, 150kDa"""	CXorf4, CRSP2		9989412, 9598311	Standard	NM_004229		Approved	EXLM1, CRSP150, TRAP170, RGR1, CSRP	uc004dex.4	O60244	OTTHUMG00000024107	ENST00000324817.1:c.1323delC	chrX.hg19:g.40562784delG	ENSP00000323720:p.Pro441fs	132.0	0.0		199.0	14.0	NM_004229	Q4KMR7|Q9UNB3	Frame_Shift_Del	DEL	ENST00000324817.1	hg19	CCDS14254.1																																																																																			.	.		0.343	MED14-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060692.1	NM_004229	
MAP7D3	79649	hgsc.bcm.edu	37	X	135323367	135323367	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:135323367delT	ENST00000316077.9	-	5	707	c.487delA	c.(487-489)agafs	p.R163fs	MAP7D3_ENST00000370661.1_Frame_Shift_Del_p.R163fs|MAP7D3_ENST00000370663.5_Frame_Shift_Del_p.R145fs	NM_024597.3	NP_078873.2	Q8IWC1	MA7D3_HUMAN	MAP7 domain containing 3	163					microtubule cytoskeleton organization (GO:0000226)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|microtubule (GO:0005874)|nucleus (GO:0005634)				central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(21)|ovary(2)|prostate(1)|skin(1)	44	Acute lymphoblastic leukemia(192;0.000127)					CATGACCATCTTTTTTGCTGA	0.328																																					p.R163fs		Atlas-INDEL	.											.	MAP7D3	102	.	0			c.488delG						.						63.0	57.0	59.0					X																	135323367		1846	4102	5948	SO:0001589	frameshift_variant	79649	exon5			.	AL832120	CCDS44004.1, CCDS55508.1, CCDS55509.1	Xq26.3	2014-08-13			ENSG00000129680	ENSG00000129680			25742	protein-coding gene	gene with protein product		300930				24927501	Standard	NM_001173516		Approved	FLJ12649	uc004ezt.3	Q8IWC1	OTTHUMG00000022507	ENST00000316077.9:c.487delA	chrX.hg19:g.135323367delT	ENSP00000318086:p.Arg163fs	146.0	0.0		157.0	10.0	NM_024597	A2A2J0|A6NCZ7|A6NHR4|B4DWD2|H7BY77|Q5JXI5|Q5JXI6|Q6P2S1|Q9H9M8	Frame_Shift_Del	DEL	ENST00000316077.9	hg19	CCDS44004.1																																																																																			.	.		0.328	MAP7D3-001	PUTATIVE	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058487.2		
PADI3	51702	hgsc.bcm.edu	37	1	17593227	17593227	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:17593227delG	ENST00000375460.3	+	5	462	c.422delG	c.(421-423)tggfs	p.W141fs		NM_016233.2	NP_057317.2	Q9ULW8	PADI3_HUMAN	peptidyl arginine deiminase, type III	141					protein citrullination (GO:0018101)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|protein-arginine deiminase activity (GO:0004668)			breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|liver(2)|lung(10)|ovary(2)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000337)|Lung NSC(340;0.000419)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00488)|BRCA - Breast invasive adenocarcinoma(304;1.17e-05)|COAD - Colon adenocarcinoma(227;1.18e-05)|Kidney(64;0.000186)|KIRC - Kidney renal clear cell carcinoma(64;0.00272)|STAD - Stomach adenocarcinoma(196;0.00656)|READ - Rectum adenocarcinoma(331;0.0655)|Lung(427;0.189)	L-Citrulline(DB00155)	CAGTGGGTCTGGGGGCCCAGT	0.587																																					p.W141fs		Atlas-INDEL	.											.	PADI3	81	.	0			c.421delT						.						118.0	104.0	109.0					1																	17593227		2203	4300	6503	SO:0001589	frameshift_variant	51702	exon5			.	AB026831	CCDS179.1	1p36.13	2008-02-05			ENSG00000142619	ENSG00000142619	3.5.3.15	"""Peptidyl arginine deiminases"""	18337	protein-coding gene	gene with protein product		606755				11069618	Standard	NM_016233		Approved	PDI3	uc001bai.3	Q9ULW8	OTTHUMG00000002373	ENST00000375460.3:c.422delG	chr1.hg19:g.17593227delG	ENSP00000364609:p.Trp141fs	151.0	0.0		184.0	12.0	NM_016233	Q58EY7|Q70SX5	Frame_Shift_Del	DEL	ENST00000375460.3	hg19	CCDS179.1																																																																																			.	.		0.587	PADI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006805.1		
RNF123	63891	hgsc.bcm.edu	37	3	49740924	49740924	+	Frame_Shift_Del	DEL	G	G	-	rs138522949	byFrequency	TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:49740924delG	ENST00000327697.6	+	21	1959	c.1815delG	c.(1813-1815)ctgfs	p.L605fs	RNF123_ENST00000432042.1_Frame_Shift_Del_p.L459fs	NM_022064.3	NP_071347.2	Q5XPI4	RN123_HUMAN	ring finger protein 123	605					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38				BRCA - Breast invasive adenocarcinoma(193;4.71e-05)|Kidney(197;0.00227)|KIRC - Kidney renal clear cell carcinoma(197;0.00255)		TGCAGCGCCTGGGGGGCCTCC	0.632											OREG0015571	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L605fs		Atlas-INDEL	.											.	RNF123	100	.	0			c.1814delT						.						38.0	38.0	38.0					3																	49740924		2203	4300	6503	SO:0001589	frameshift_variant	63891	exon21			.	AK022627	CCDS33758.1	3p24.3	2008-02-05			ENSG00000164068	ENSG00000164068		"""RING-type (C3HC4) zinc fingers"""	21148	protein-coding gene	gene with protein product		614472					Standard	NM_022064		Approved	FLJ12565	uc003cxh.4	Q5XPI4	OTTHUMG00000156891	ENST00000327697.6:c.1815delG	chr3.hg19:g.49740924delG	ENSP00000328287:p.Leu605fs	208.0	0.0	964	241.0	20.0	NM_022064	A1L4Q3|A6NLS5|Q5I022|Q6PFW4|Q71RH0|Q8IW18|Q9H0M8|Q9H5L8|Q9H9T2	Frame_Shift_Del	DEL	ENST00000327697.6	hg19	CCDS33758.1																																																																																			.	.		0.632	RNF123-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346475.2	NM_022064	
NWD1	284434	hgsc.bcm.edu	37	19	16908642	16908642	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:16908642delT	ENST00000552788.1	+	14	3404	c.3404delT	c.(3403-3405)gttfs	p.V1135fs	NWD1_ENST00000549814.1_Frame_Shift_Del_p.V1135fs|NWD1_ENST00000523826.1_Frame_Shift_Del_p.V929fs|NWD1_ENST00000339803.6_Frame_Shift_Del_p.V1000fs|NWD1_ENST00000379808.3_Frame_Shift_Del_p.V1135fs|NWD1_ENST00000524140.2_Frame_Shift_Del_p.V1135fs			Q149M9	NWD1_HUMAN	NACHT and WD repeat domain containing 1	1135							ATP binding (GO:0005524)			NS(3)|breast(2)|cervix(1)|endometrium(8)|large_intestine(17)|lung(18)|ovary(2)|pancreas(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						GAGACGGCTGTTTTTGGTACT	0.552																																					p.V1135fs		Atlas-INDEL	.											.	NWD1	303	.	0			c.3403delG						.						301.0	275.0	284.0					19																	16908642		2203	4300	6503	SO:0001589	frameshift_variant	284434	exon16			.	BX648940	CCDS32945.1, CCDS32945.2	19p13.11	2013-01-09				ENSG00000188039		"""WD repeat domain containing"""	27619	protein-coding gene	gene with protein product							Standard	NM_001007525		Approved		uc002neu.4	Q149M9		ENST00000552788.1:c.3404delT	chr19.hg19:g.16908642delT	ENSP00000447224:p.Val1135fs	153.0	0.0		162.0	15.0	NM_001007525	C9J021|Q68CT3	Frame_Shift_Del	DEL	ENST00000552788.1	hg19																																																																																				.	.		0.552	NWD1-005	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000403569.1	NM_001007525	
HKDC1	80201	hgsc.bcm.edu	37	10	71017124	71017124	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:71017124delG	ENST00000354624.5	+	14	2107	c.1974delG	c.(1972-1974)gtgfs	p.V658fs	HKDC1_ENST00000395086.2_Frame_Shift_Del_p.V658fs	NM_025130.3	NP_079406	Q2TB90	HKDC1_HUMAN	hexokinase domain containing 1	658	Hexokinase type-1 2.				carbohydrate phosphorylation (GO:0046835)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glycolytic process (GO:0006096)|hexose metabolic process (GO:0019318)	cytosol (GO:0005829)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|mannokinase activity (GO:0019158)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(11)|ovary(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	34						ATGATACAGTGGGGACCATGA	0.438																																					p.V658fs		Atlas-INDEL	.											.	HKDC1	98	.	0			c.1973delT						.						249.0	210.0	223.0					10																	71017124		2203	4300	6503	SO:0001589	frameshift_variant	80201	exon14			.		CCDS7288.1	10q22.1	2006-10-24			ENSG00000156510	ENSG00000156510			23302	protein-coding gene	gene with protein product						12477932	Standard	NM_025130		Approved	FLJ37767, FLJ22761	uc001jpf.4	Q2TB90	OTTHUMG00000018371	ENST00000354624.5:c.1974delG	chr10.hg19:g.71017124delG	ENSP00000346643:p.Val658fs	149.0	0.0		183.0	12.0	NM_025130	B5MDN9|Q2TB91|Q5VTC7|Q7Z373|Q8WU37|Q96EH2|Q9H5Y9	Frame_Shift_Del	DEL	ENST00000354624.5	hg19	CCDS7288.1																																																																																			.	.		0.438	HKDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048389.1	NM_025130	
FST	10468	hgsc.bcm.edu	37	5	52779494	52779494	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:52779494delA	ENST00000256759.3	+	3	821	c.438delA	c.(436-438)ctafs	p.L146fs	FST_ENST00000396947.3_Frame_Shift_Del_p.L146fs	NM_013409.2	NP_037541.1	P19883	FST_HUMAN	follistatin	146	Kazal-like 1. {ECO:0000255|PROSITE- ProRule:PRU00798}.				BMP signaling pathway (GO:0030509)|female gonad development (GO:0008585)|gamete generation (GO:0007276)|hair follicle morphogenesis (GO:0031069)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinocyte proliferation (GO:0043616)|negative regulation of activin receptor signaling pathway (GO:0032926)|negative regulation of cell differentiation (GO:0045596)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|odontogenesis of dentin-containing tooth (GO:0042475)|pattern specification process (GO:0007389)|positive regulation of hair follicle development (GO:0051798)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|nucleus (GO:0005634)	activin binding (GO:0048185)|signal transducer activity (GO:0004871)			breast(1)|endometrium(1)|large_intestine(4)|lung(7)|prostate(1)|urinary_tract(1)	15		Ovarian(174;1.78e-06)|Lung NSC(810;3.55e-06)|Breast(144;4.08e-05)				GTGCACTCCTAAAGGCAAGAT	0.542																																					p.L146fs		Atlas-INDEL	.											.	FST	42	.	0			c.437delT						.						70.0	65.0	67.0					5																	52779494		2203	4300	6503	SO:0001589	frameshift_variant	10468	exon3			.	M19481	CCDS3959.1, CCDS43315.1	5q11.2	2008-02-05			ENSG00000134363	ENSG00000134363			3971	protein-coding gene	gene with protein product		136470				10411917, 3380788	Standard	NM_006350		Approved	FS	uc003jpd.3	P19883	OTTHUMG00000131183	ENST00000256759.3:c.438delA	chr5.hg19:g.52779494delA	ENSP00000256759:p.Leu146fs	136.0	0.0		213.0	15.0	NM_006350	B5BU94|Q9BTH0	Frame_Shift_Del	DEL	ENST00000256759.3	hg19	CCDS3959.1																																																																																			.	.		0.542	FST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253906.1	NM_013409	
ATP8A1	10396	hgsc.bcm.edu	37	4	42588395	42588395	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:42588395delA	ENST00000381668.5	-	9	924	c.693delT	c.(691-693)tttfs	p.F231fs	ATP8A1_ENST00000264449.10_Frame_Shift_Del_p.F231fs	NM_006095.2	NP_006086.1	Q9Y2Q0	AT8A1_HUMAN	ATPase, aminophospholipid transporter (APLT), class I, type 8A, member 1	231					cation transmembrane transport (GO:0098655)|ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|transmembrane transport (GO:0055085)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(18)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	51					Phosphatidylserine(DB00144)	TGTTTCCAACAAAATCGTAGA	0.393																																					p.V232fs		Atlas-INDEL	.											.	ATP8A1	206	.	0			c.694delG						.						125.0	118.0	120.0					4																	42588395		2203	4300	6503	SO:0001589	frameshift_variant	10396	exon9			.	AF067820	CCDS3466.1, CCDS47049.1	4p13	2010-04-20	2007-09-19		ENSG00000124406	ENSG00000124406		"""ATPases / P-type"""	13531	protein-coding gene	gene with protein product		609542	"""ATPase, aminophospholipid transporter (APLT), Class I, type 8A, member 1"""			10198212, 9548971	Standard	NM_006095		Approved	ATPIA	uc003gwr.2	Q9Y2Q0	OTTHUMG00000099403	ENST00000381668.5:c.693delT	chr4.hg19:g.42588395delA	ENSP00000371084:p.Phe231fs	182.0	0.0		179.0	11.0	NM_006095	Q32M35|Q32M36|Q4W5J7|Q4W5P2	Frame_Shift_Del	DEL	ENST00000381668.5	hg19	CCDS3466.1																																																																																			.	.		0.393	ATP8A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216861.2	NM_006095	
SUPT20HL2	170067	hgsc.bcm.edu	37	X	24330071	24330071	+	IGR	DEL	G	G	-	rs147318848		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:24330071delG								AC096509.1 (25277 upstream) : AC004552.1 (36854 downstream)																							CTCCCTTCCCGGATACTGAAG	0.547																																					p.G455fs		Atlas-INDEL	.											.	.	.	.	0			c.1363delG						.						83.0	78.0	79.0					X																	24330071		1529	3560	5089	SO:0001628	intergenic_variant	170067	exon1			.																													chrX.hg19:g.24330071delG		91.0	0.0		112.0	12.0	NM_001136233		Frame_Shift_Del	DEL		hg19																																																																																				.	.	0	0.547								
LAMA2	3908	hgsc.bcm.edu	37	6	129826417	129826417	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:129826417delA	ENST00000421865.2	+	61	8669	c.8620delA	c.(8620-8622)aaafs	p.K2875fs		NM_000426.3|NM_001079823.1	NP_000417|NP_001073291.1	P24043	LAMA2_HUMAN	laminin, alpha 2	2875	Laminin G-like 4. {ECO:0000255|PROSITE- ProRule:PRU00122}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|myelination in peripheral nervous system (GO:0022011)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|sarcolemma (GO:0042383)	structural molecule activity (GO:0005198)			NS(2)|biliary_tract(2)|breast(10)|central_nervous_system(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(35)|lung(84)|ovary(10)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(2)	194				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)		CATCAGTCCCAAAAAAGCCGA	0.403																																					p.P2873fs		Atlas-INDEL	.											.,1	LAMA2	481	.	0			c.8619delC						.						91.0	93.0	93.0					6																	129826417		2203	4300	6503	SO:0001589	frameshift_variant	3908	exon61			.	Z26653	CCDS5138.1	6q22-q23	2014-09-17	2008-08-01		ENSG00000196569	ENSG00000196569		"""Laminins"""	6482	protein-coding gene	gene with protein product	"""merosin"", ""congenital muscular dystrophy"""	156225		LAMM		2185464, 8294519	Standard	NM_000426		Approved		uc003qbn.3	P24043	OTTHUMG00000015545	ENST00000421865.2:c.8620delA	chr6.hg19:g.129826417delA	ENSP00000400365:p.Lys2875fs	187.0	0.0		173.0	13.0	NM_000426	Q14736|Q5VUM2|Q93022	Frame_Shift_Del	DEL	ENST00000421865.2	hg19	CCDS5138.1																																																																																			.	.		0.403	LAMA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042180.1		
TRAK1	22906	hgsc.bcm.edu	37	3	42166974	42166974	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:42166974delC	ENST00000327628.5	+	2	554	c.154delC	c.(154-156)cccfs	p.P52fs	TRAK1_ENST00000487159.1_3'UTR	NM_001042646.2	NP_001036111.1	Q9UPV9	TRAK1_HUMAN	trafficking protein, kinesin binding 1	52	HAP1 N-terminal.				endosome to lysosome transport (GO:0008333)|protein O-linked glycosylation (GO:0006493)|protein targeting (GO:0006605)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(8)|lung(6)|ovary(1)|upper_aerodigestive_tract(2)	22						GGAGCAGCTGCCCCATTATAA	0.488																																					p.L51fs	GBM(44;195 884 22595 31865 41850)	Atlas-INDEL	.											.	TRAK1	188	.	0			c.153delG						.						92.0	89.0	90.0					3																	42166974		1952	4161	6113	SO:0001589	frameshift_variant	22906	exon2			.		CCDS2695.1, CCDS43072.1, CCDS58826.1, CCDS74922.1	3p22.1	2012-03-05			ENSG00000182606	ENSG00000182606			29947	protein-coding gene	gene with protein product	"""OGT(O Glc NAc transferase) interacting protein 106 KDa"", ""O-linked N-acetylglucosamine transferase interacting protein 106"", ""milton homolog 1 (Drosophila)"""	608112				10470851, 12435728, 16380713, 20230862	Standard	NM_014965		Approved	OIP106, KIAA1042, MILT1	uc003cky.4	Q9UPV9	OTTHUMG00000131795	ENST00000327628.5:c.154delC	chr3.hg19:g.42166974delC	ENSP00000328998:p.Pro52fs	111.0	0.0		159.0	10.0	NM_001042646	E9PDS2|J3KNT7|Q63HR0|Q659B5|Q96B69	Frame_Shift_Del	DEL	ENST00000327628.5	hg19	CCDS43072.1																																																																																			.	.		0.488	TRAK1-004	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343413.1	NM_014965	
LY86	9450	hgsc.bcm.edu	37	6	6588976	6588976	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:6588976delT	ENST00000379953.2	+	2	361	c.9delT	c.(7-9)ggtfs	p.G3fs	LY86-AS1_ENST00000429345.1_RNA|LY86-AS1_ENST00000435641.1_RNA|LY86-AS1_ENST00000447858.1_RNA|LY86_ENST00000230568.4_Frame_Shift_Del_p.G3fs			O95711	LY86_HUMAN	lymphocyte antigen 86	3					apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|humoral immune response (GO:0006959)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of lipopolysaccharide-mediated signaling pathway (GO:0031666)	extracellular region (GO:0005576)|plasma membrane (GO:0005886)				large_intestine(2)|lung(6)	8	Ovarian(93;0.0377)					CCATGAAGGGTTTCACAGCCA	0.542																																					p.G3fs		Atlas-INDEL	.											.	LY86	18	.	0			c.8delG						.						82.0	80.0	80.0					6																	6588976		2203	4300	6503	SO:0001589	frameshift_variant	9450	exon1			.	AF057178	CCDS4498.1	6p24.3	2010-07-08			ENSG00000112799	ENSG00000112799			16837	protein-coding gene	gene with protein product		605241				9763566	Standard	NM_004271		Approved	MD-1, dJ80N2.1	uc003mwy.1	O95711	OTTHUMG00000014190	ENST00000379953.2:c.9delT	chr6.hg19:g.6588976delT	ENSP00000369286:p.Gly3fs	55.0	0.0		135.0	10.0	NM_004271	Q9UQC4	Frame_Shift_Del	DEL	ENST00000379953.2	hg19	CCDS4498.1																																																																																			.	.		0.542	LY86-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039762.2		
PRH1	5554	hgsc.bcm.edu	37	12	11035175	11035175	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:11035175delG	ENST00000428168.2	-	3	260	c.223delC	c.(223-225)caafs	p.Q76fs	PRR4_ENST00000536668.1_5'UTR	NM_006250.3	NP_006241.2	P02810	PRPC_HUMAN	proline-rich protein HaeIII subfamily 1	76						extracellular space (GO:0005615)				endometrium(1)|kidney(1)|lung(2)|upper_aerodigestive_tract(1)	5				BRCA - Breast invasive adenocarcinoma(232;0.245)		CCTCCTTGTTGGGGTGGTCCC	0.602																																					p.Q75fs		Atlas-INDEL	.											.	PRH1	17	.	0			c.224delA						.						153.0	131.0	138.0					12																	11035175		2203	4300	6503	SO:0001589	frameshift_variant	5554	exon3			.			12p13.2	2013-05-10			ENSG00000231887	ENSG00000231887			9366	protein-coding gene	gene with protein product		168730				3009472	Standard	NM_001291314		Approved	Pa	uc021qvf.1	P02810		ENST00000428168.2:c.223delC	chr12.hg19:g.11035175delG	ENSP00000412436:p.Gln76fs	220.0	0.0		214.0	14.0	NM_006250	A2VCM0|A3KN66|A5D902|B2RMW2|Q4VBP2|Q53XA2|Q6P2F6	Frame_Shift_Del	DEL	ENST00000428168.2	hg19																																																																																				.	.		0.602	PRH1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_006250	
RERE	473	hgsc.bcm.edu	37	1	8418658	8418658	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:8418658delC	ENST00000337907.3	-	21	4571	c.3937delG	c.(3937-3939)gagfs	p.E1313fs	RERE_ENST00000476556.1_Frame_Shift_Del_p.E759fs|RERE_ENST00000400908.2_Frame_Shift_Del_p.E1313fs|RERE_ENST00000377464.1_Frame_Shift_Del_p.E1045fs|RERE_ENST00000400907.2_Intron	NM_012102.3	NP_036234.3	Q9P2R6	RERE_HUMAN	arginine-glutamic acid dipeptide (RE) repeats	1313	Arg/Glu-rich (mixed charge).				chromatin remodeling (GO:0006338)|multicellular organismal development (GO:0007275)|NLS-bearing protein import into nucleus (GO:0006607)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|poly-glutamine tract binding (GO:0008267)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|liver(1)|lung(16)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	49	Ovarian(185;0.0661)	all_epithelial(116;1.17e-21)|all_lung(118;1.4e-06)|Lung NSC(185;3.06e-06)|Renal(390;0.000147)|Breast(348;0.000206)|Colorectal(325;0.00187)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;9.64e-67)|GBM - Glioblastoma multiforme(8;9.89e-33)|Colorectal(212;1.45e-07)|COAD - Colon adenocarcinoma(227;3.42e-05)|Kidney(185;6e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000533)|KIRC - Kidney renal clear cell carcinoma(229;0.00106)|STAD - Stomach adenocarcinoma(132;0.00118)|READ - Rectum adenocarcinoma(331;0.0419)|Lung(427;0.195)		TCTCGGATCTCCCGCTCTCGG	0.697																																					p.E1313fs		Atlas-INDEL	.											.	RERE	129	.	0			c.3938delA						.						20.0	25.0	24.0					1																	8418658		2189	4292	6481	SO:0001589	frameshift_variant	473	exon21			.	AF016005	CCDS95.1, CCDS41243.1	1p36.23	2013-01-25			ENSG00000142599	ENSG00000142599		"""GATA zinc finger domain containing"""	9965	protein-coding gene	gene with protein product		605226		ATN1L		10814707, 10729226	Standard	NM_012102		Approved	KIAA0458, ARP, ARG, DNB1	uc001apf.3	Q9P2R6	OTTHUMG00000001765	ENST00000337907.3:c.3937delG	chr1.hg19:g.8418658delC	ENSP00000338629:p.Glu1313fs	105.0	0.0		131.0	11.0	NM_012102	O43393|O75046|O75359|Q5VXL9|Q6P6B9|Q9Y2W4	Frame_Shift_Del	DEL	ENST00000337907.3	hg19	CCDS95.1																																																																																			.	.		0.697	RERE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004916.1		
NFATC1	4772	hgsc.bcm.edu	37	18	77193695	77193695	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr18:77193695delG	ENST00000427363.2	+	3	1343	c.1343delG	c.(1342-1344)cggfs	p.R448fs	NFATC1_ENST00000591814.1_Frame_Shift_Del_p.R448fs|NFATC1_ENST00000587635.1_Frame_Shift_Del_p.R448fs|NFATC1_ENST00000318065.5_Frame_Shift_Del_p.R435fs|NFATC1_ENST00000253506.5_Frame_Shift_Del_p.R448fs|NFATC1_ENST00000542384.1_Frame_Shift_Del_p.R448fs|NFATC1_ENST00000397790.2_5'UTR|NFATC1_ENST00000545796.1_5'UTR|NFATC1_ENST00000586434.1_Frame_Shift_Del_p.R435fs|NFATC1_ENST00000592223.1_Frame_Shift_Del_p.R435fs|NFATC1_ENST00000329101.4_Frame_Shift_Del_p.R435fs			O95644	NFAC1_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 1	448	RHD. {ECO:0000255|PROSITE- ProRule:PRU00265}.				calcium ion transport (GO:0006816)|epithelial to mesenchymal transition (GO:0001837)|Fc-epsilon receptor signaling pathway (GO:0038095)|G1/S transition of mitotic cell cycle (GO:0000082)|heart development (GO:0007507)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|osteoclast differentiation (GO:0030316)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	FK506 binding (GO:0005528)|mitogen-activated protein kinase p38 binding (GO:0048273)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(2)|breast(1)|endometrium(7)|kidney(1)|large_intestine(4)|lung(17)|ovary(2)|prostate(4)|skin(1)|soft_tissue(1)	40		Esophageal squamous(42;0.0157)|Melanoma(33;0.144)		OV - Ovarian serous cystadenocarcinoma(15;3.73e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0257)	Pseudoephedrine(DB00852)	GAGGGCAGCCGGGGGGCCGTG	0.642																																					p.R448fs	GBM(151;1210 2593 28719 45011)	Atlas-INDEL	.											.	NFATC1	105	.	0			c.1342delC						.						52.0	57.0	56.0					18																	77193695		2202	4297	6499	SO:0001589	frameshift_variant	4772	exon3			.	U08015	CCDS12015.1, CCDS12016.1, CCDS32850.1, CCDS59326.1, CCDS59327.1, CCDS62467.1, CCDS62468.1, CCDS62469.1, CCDS62470.1, CCDS62471.1	18q23	2009-11-24			ENSG00000131196	ENSG00000131196		"""Nuclear factor of activated T-cells"""	7775	protein-coding gene	gene with protein product		600489				8202141	Standard	NM_001278669		Approved	NF-ATC, NFATc, NFAT2	uc002lnf.3	O95644	OTTHUMG00000132897	ENST00000427363.2:c.1343delG	chr18.hg19:g.77193695delG	ENSP00000389377:p.Arg448fs	99.0	0.0		155.0	10.0	NM_006162	B5B2M4|B5B2M5|B5B2M6|B5B2M7|B5B2M8|B5B2M9|B5B2N1|Q12865|Q15793|Q2M1S3	Frame_Shift_Del	DEL	ENST00000427363.2	hg19																																																																																				.	.		0.642	NFATC1-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000450507.1	NM_172390	
COPS6	10980	hgsc.bcm.edu	37	7	99687281	99687281	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:99687281delG	ENST00000303904.3	+	3	283	c.246delG	c.(244-246)gagfs	p.E82fs	COPS6_ENST00000418625.1_Frame_Shift_Del_p.E81fs	NM_006833.4	NP_006824.2	Q7L5N1	CSN6_HUMAN	COP9 signalosome subunit 6	82	MPN.				cullin deneddylation (GO:0010388)|viral process (GO:0016032)	COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)				breast(1)|endometrium(3)|large_intestine(4)|lung(2)|prostate(1)|stomach(1)	12	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)		STAD - Stomach adenocarcinoma(171;0.129)			GAAATATCGAGGTGATGAACT	0.468																																					p.E82fs		Atlas-INDEL	.											.	COPS6	31	.	0			c.245delA						.						147.0	133.0	138.0					7																	99687281		2203	4300	6503	SO:0001589	frameshift_variant	10980	exon3			.	BC002520	CCDS5682.1	7q22.1	2013-03-14	2013-03-14		ENSG00000168090	ENSG00000168090			21749	protein-coding gene	gene with protein product	"""COP9 subunit 6 (MOV34 homolog, 34 kD)"""	614729	"""COP9 constitutive photomorphogenic homolog subunit 6 (Arabidopsis)"""			12477932	Standard	NM_006833		Approved	MOV34-34KD, CSN6	uc003usu.3	Q7L5N1	OTTHUMG00000154632	ENST00000303904.3:c.246delG	chr7.hg19:g.99687281delG	ENSP00000304102:p.Glu82fs	199.0	0.0		199.0	12.0	NM_006833	A4D2A3|O15387	Frame_Shift_Del	DEL	ENST00000303904.3	hg19	CCDS5682.1																																																																																			.	.		0.468	COPS6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000336412.3	NM_006833	
MAP3K1	4214	hgsc.bcm.edu	37	5	56170970	56170970	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:56170970delG	ENST00000399503.3	+	10	1798	c.1798delG	c.(1798-1800)gggfs	p.G600fs		NM_005921.1	NP_005912.1	Q13233	M3K1_HUMAN	mitogen-activated protein kinase kinase kinase 1, E3 ubiquitin protein ligase	600					activation of MAPKK activity (GO:0000186)|apoptotic mitochondrial changes (GO:0008637)|cellular response to mechanical stimulus (GO:0071260)|epithelial cell morphogenesis (GO:0003382)|eyelid development in camera-type eye (GO:0061029)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of actin filament polymerization (GO:0030838)|protein phosphorylation (GO:0006468)|regulation of cell migration (GO:0030334)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	cytosol (GO:0005829)	ATP binding (GO:0005524)|JUN kinase kinase activity (GO:0008545)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|zinc ion binding (GO:0008270)			NS(1)|breast(19)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(11)|ovary(1)|skin(3)|urinary_tract(1)	57		Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223)		OV - Ovarian serous cystadenocarcinoma(10;6.08e-40)		GTTGGCAAATGGGGAGAGCAC	0.562																																					p.N599fs		Atlas-INDEL	.											.	MAP3K1	355	.	0			c.1797delT						.						81.0	82.0	81.0					5																	56170970		1923	4124	6047	SO:0001589	frameshift_variant	4214	exon10			.	U29671, AF042838	CCDS43318.1	5q11.2	2012-02-23	2012-02-23		ENSG00000095015	ENSG00000095015		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6848	protein-coding gene	gene with protein product		600982	"""mitogen-activated protein kinase kinase kinase 1"""	MEKK1		8597633	Standard	NM_005921		Approved	MEKK, MAPKKK1	uc003jqw.4	Q13233	OTTHUMG00000059486	ENST00000399503.3:c.1798delG	chr5.hg19:g.56170970delG	ENSP00000382423:p.Gly600fs	197.0	0.0		193.0	14.0	NM_005921		Frame_Shift_Del	DEL	ENST00000399503.3	hg19	CCDS43318.1																																																																																			.	.		0.562	MAP3K1-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000132309.2	XM_042066	
UNK	85451	hgsc.bcm.edu	37	17	73818612	73818612	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:73818612delC	ENST00000589666.1	+	14	2002	c.1892delC	c.(1891-1893)tccfs	p.S631fs	RP11-552F3.4_ENST00000586808.1_RNA|UNK_ENST00000293218.3_Frame_Shift_Del_p.S707fs	NM_001080419.2	NP_001073888.2	Q9C0B0	UNK_HUMAN	unkempt family zinc finger	631							poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.S631C(1)|p.S707C(1)		cervix(3)|endometrium(8)|kidney(2)|large_intestine(5)|lung(3)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	25			all cancers(21;2.61e-06)|Epithelial(20;7.39e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|LUSC - Lung squamous cell carcinoma(166;0.154)			GGAAGCTTCTCCCCGGGCACT	0.617																																					p.S631fs		Atlas-INDEL	.											.	UNK	87	.	2	Substitution - Missense(2)	lung(2)	c.1891delT						.						93.0	101.0	99.0					17																	73818612		1944	4137	6081	SO:0001589	frameshift_variant	85451	exon14			.	AB051540	CCDS45778.1, CCDS45778.2	17q25.3	2013-10-17	2013-10-17	2007-02-06		ENSG00000132478		"""Zinc fingers, CCCH-type domain containing"""	29369	protein-coding gene	gene with protein product			"""zinc finger CCCH-type domain containing 5"", ""zinc finger CCCH-type containing 5"", ""unkempt homolog (Drosophila)"""	ZC3HDC5, ZC3H5		11214970	Standard	NM_001080419		Approved	KIAA1753	uc021udd.2	Q9C0B0		ENST00000589666.1:c.1892delC	chr17.hg19:g.73818612delC	ENSP00000464893:p.Ser631fs	127.0	0.0		152.0	10.0	NM_001080419		Frame_Shift_Del	DEL	ENST00000589666.1	hg19	CCDS45778.2																																																																																			.	.		0.617	UNK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448835.1	NM_001080419	
ALS2CL	259173	hgsc.bcm.edu	37	3	46724741	46724741	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:46724741delC	ENST00000318962.4	-	10	1071	c.988delG	c.(988-990)gctfs	p.A330fs	ALS2CL_ENST00000415953.1_Frame_Shift_Del_p.A330fs	NM_147129.3	NP_667340.2	Q60I27	AL2CL_HUMAN	ALS2 C-terminal like	330					endosome organization (GO:0007032)|protein localization (GO:0008104)	cytoplasmic membrane-bounded vesicle (GO:0016023)	GTPase activator activity (GO:0005096)|identical protein binding (GO:0042802)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(1)|lung(7)|skin(3)|stomach(2)	29				BRCA - Breast invasive adenocarcinoma(193;0.000726)|KIRC - Kidney renal clear cell carcinoma(197;0.0171)|Kidney(197;0.0202)		TCCAGGCCAGCCCCCAGCACG	0.667																																					p.A330fs		Atlas-INDEL	.											.	ALS2CL	78	.	0			c.989delC						.						17.0	21.0	20.0					3																	46724741		2203	4300	6503	SO:0001589	frameshift_variant	259173	exon10			.	AK074118	CCDS2743.1, CCDS43080.1	3p21.31	2008-01-30			ENSG00000178038	ENSG00000178038			20605	protein-coding gene	gene with protein product		612402				15388334, 8889548, 17239822	Standard	NM_147129		Approved	FLJ36525, RN49018, DKFZp686I0110	uc003cqb.2	Q60I27	OTTHUMG00000128673	ENST00000318962.4:c.988delG	chr3.hg19:g.46724741delC	ENSP00000313670:p.Ala330fs	114.0	0.0		144.0	10.0	NM_001190707	Q32MA1|Q6AI56|Q6ZNC5|Q6ZNC7|Q6ZTL4|Q86YD2|Q8N9U1|Q8NAL7	Frame_Shift_Del	DEL	ENST00000318962.4	hg19	CCDS2743.1																																																																																			.	.		0.667	ALS2CL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250567.3	NM_147129	
SLC2A2	6514	hgsc.bcm.edu	37	3	170716076	170716076	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:170716076delA	ENST00000314251.3	-	10	1359	c.1280delT	c.(1279-1281)ttcfs	p.F427fs	SLC2A2_ENST00000382808.4_Frame_Shift_Del_p.F308fs	NM_000340.1	NP_000331.1	P11168	GTR2_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 2	427					carbohydrate metabolic process (GO:0005975)|endocrine pancreas development (GO:0031018)|energy reserve metabolic process (GO:0006112)|glucose transport (GO:0015758)|hexose transmembrane transport (GO:0035428)|hexose transport (GO:0008645)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	brush border (GO:0005903)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	D-glucose transmembrane transporter activity (GO:0055056)|dehydroascorbic acid transporter activity (GO:0033300)|glucose transmembrane transporter activity (GO:0005355)|hexose transmembrane transporter activity (GO:0015149)	p.F427S(1)		central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24	all_cancers(22;1.41e-19)|all_lung(20;1.59e-15)|Lung NSC(18;7.08e-15)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;1.1e-14)|Lung(28;2.99e-14)		Streptozocin(DB00428)	TCCTTGACTGAAAAACTCAGC	0.473																																					p.F427fs		Atlas-INDEL	.											.	SLC2A2	71	.	1	Substitution - Missense(1)	lung(1)	c.1281delC						.						80.0	80.0	80.0					3																	170716076		2203	4300	6503	SO:0001589	frameshift_variant	6514	exon10			.	J03810	CCDS3215.1	3q26.2-q27	2013-05-22			ENSG00000163581	ENSG00000163581		"""Solute carriers"""	11006	protein-coding gene	gene with protein product		138160		GLUT2		1852621	Standard	NM_000340		Approved		uc003fhe.1	P11168	OTTHUMG00000158997	ENST00000314251.3:c.1280delT	chr3.hg19:g.170716076delA	ENSP00000323568:p.Phe427fs	156.0	0.0		174.0	11.0	NM_000340	A8K481|B2R936|B7Z547|F8W8V8|Q9UCW9	Frame_Shift_Del	DEL	ENST00000314251.3	hg19	CCDS3215.1																																																																																			.	.		0.473	SLC2A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352834.1	NM_000340	
SOX15	6665	hgsc.bcm.edu	37	17	7492683	7492683	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:7492683delC	ENST00000250055.2	-	1	805	c.312delG	c.(310-312)cggfs	p.R104fs	SOX15_ENST00000538513.2_Frame_Shift_Del_p.R104fs|MPDU1_ENST00000423172.2_Intron|FXR2_ENST00000573057.1_5'Flank|SOX15_ENST00000570788.1_Frame_Shift_Del_p.R104fs	NM_006942.1	NP_008873.1	O60248	SOX15_HUMAN	SRY (sex determining region Y)-box 15	104					cell differentiation (GO:0030154)|chromatin organization (GO:0006325)|male gonad development (GO:0008584)|myoblast development (GO:0048627)|negative regulation of striated muscle tissue development (GO:0045843)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of G0 to G1 transition (GO:0070318)|positive regulation of myoblast proliferation (GO:2000288)|positive regulation of satellite cell activation involved in skeletal muscle regeneration (GO:0014718)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|skeletal muscle tissue regeneration (GO:0043403)	cytoplasm (GO:0005737)|nuclear transcription factor complex (GO:0044798)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|prostate(1)	2						GGGCGCGGAGCCGCTTGGCCT	0.682											OREG0024139	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L105fs		Atlas-INDEL	.											.	SOX15	10	.	0			c.313delC						.						23.0	26.0	25.0					17																	7492683		2202	4298	6500	SO:0001589	frameshift_variant	6665	exon1			.	AJ006222	CCDS32549.1	17p13.1	2014-08-12	2002-07-22	2002-07-26	ENSG00000129194	ENSG00000129194		"""SRY (sex determining region Y)-boxes"""	11196	protein-coding gene	gene with protein product		601297	"""SRY (sex determining region Y)-box 20"""	SOX20		8978787, 9730625	Standard	NM_006942		Approved	SOX27, SOX26	uc002ghz.1	O60248	OTTHUMG00000178146	ENST00000250055.2:c.312delG	chr17.hg19:g.7492683delC	ENSP00000355354:p.Arg104fs	126.0	0.0	642	158.0	11.0	NM_006942	B4DWU7|D3DTQ0|P35717|Q9Y6W7	Frame_Shift_Del	DEL	ENST00000250055.2	hg19	CCDS32549.1																																																																																			.	.		0.682	SOX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440757.1	NM_006942	
OTOA	146183	hgsc.bcm.edu	37	16	21742178	21742178	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:21742178delC	ENST00000286149.4	+	20	2271	c.2270delC	c.(2269-2271)gccfs	p.A757fs	OTOA_ENST00000388956.4_Frame_Shift_Del_p.A664fs|OTOA_ENST00000388958.3_Frame_Shift_Del_p.A743fs|OTOA_ENST00000388957.3_Frame_Shift_Del_p.A419fs			Q7RTW8	OTOAN_HUMAN	otoancorin	757					cell-matrix adhesion (GO:0007160)|sensory perception of sound (GO:0007605)|transmission of nerve impulse (GO:0019226)	anchored component of membrane (GO:0031225)|apical plasma membrane (GO:0016324)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|liver(2)|lung(23)|ovary(1)|prostate(1)|skin(5)|stomach(1)	46				GBM - Glioblastoma multiforme(48;0.0414)		CACTGGACAGCCGAGACCACG	0.448																																					p.A743fs		Atlas-INDEL	.											.	OTOA	144	.	0			c.2227delG						.						102.0	81.0	88.0					16																	21742178		2195	4271	6466	SO:0001589	frameshift_variant	146183	exon20			.	AK057335	CCDS10600.2, CCDS32403.1, CCDS53994.1	16p12.2	2009-08-18	2002-07-05		ENSG00000155719	ENSG00000155719			16378	protein-coding gene	gene with protein product	"""cancer/testis antigen 108"""	607038	"""deafness, autosomal recessive 22"""	DFNB22		11972037, 19088187	Standard	NM_170664		Approved	CT108	uc002djh.3	Q7RTW8	OTTHUMG00000090721	ENST00000286149.4:c.2270delC	chr16.hg19:g.21742178delC	ENSP00000286149:p.Ala757fs	154.0	0.0		153.0	10.0	NM_144672	A1L3A8|A2VDI0|B3KWU3|E9PF51|Q8NA86|Q96M76	Frame_Shift_Del	DEL	ENST00000286149.4	hg19																																																																																				.	.		0.448	OTOA-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000430021.1		
SCML1	6322	hgsc.bcm.edu	37	X	17763578	17763578	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:17763578delA	ENST00000380041.3	+	3	364	c.36delA	c.(34-36)atafs	p.I12fs	SCML1_ENST00000380043.3_Intron|SCML1_ENST00000398080.1_Intron|SCML1_ENST00000380045.3_Intron	NM_001037540.1	NP_001032629.1	Q9UN30	SCML1_HUMAN	sex comb on midleg-like 1 (Drosophila)	12					anatomical structure morphogenesis (GO:0009653)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|endometrium(2)|kidney(2)|large_intestine(2)|ovary(1)	10	Hepatocellular(33;0.183)					TTCCTCAGATAAAAACAAGAA	0.303																																					p.I12fs		Atlas-INDEL	.											.	SCML1	55	.	0			c.35delT						.						65.0	58.0	60.0					X																	17763578		2198	4295	6493	SO:0001589	frameshift_variant	6322	exon3			.		CCDS14182.2, CCDS35210.1, CCDS35211.1	Xp22	2013-01-10	2001-11-28		ENSG00000047634	ENSG00000047634		"""Sterile alpha motif (SAM) domain containing"""	10580	protein-coding gene	gene with protein product		300227	"""sex comb on midleg (Drosophila)-like 1"""			9570953	Standard	XM_005274578		Approved		uc004cyc.3	Q9UN30	OTTHUMG00000021206	ENST00000380041.3:c.36delA	chrX.hg19:g.17763578delA	ENSP00000369380:p.Ile12fs	138.0	0.0		152.0	12.0	NM_001037540	B0FZN6|B2RA08|Q5H968|Q5H969	Frame_Shift_Del	DEL	ENST00000380041.3	hg19	CCDS35210.1																																																																																			.	.		0.303	SCML1-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060495.5	NM_006746	
ATR	545	hgsc.bcm.edu	37	3	142178110	142178110	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:142178110delA	ENST00000350721.4	-	43	7429	c.7308delT	c.(7306-7308)tttfs	p.F2436fs	ATR_ENST00000383101.3_Frame_Shift_Del_p.F2372fs	NM_001184.3	NP_001175.2	Q13535	ATR_HUMAN	ATR serine/threonine kinase	2436	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|multicellular organismal development (GO:0007275)|negative regulation of DNA replication (GO:0008156)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|protein autophosphorylation (GO:0046777)|regulation of protein binding (GO:0043393)|replicative senescence (GO:0090399)|response to drug (GO:0042493)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|PML body (GO:0016605)|XY body (GO:0001741)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|MutLalpha complex binding (GO:0032405)|MutSalpha complex binding (GO:0032407)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(10)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|liver(2)|lung(45)|ovary(3)|skin(10)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(4)	122						ACCACTCATGAAAAATAGGAG	0.363								Other conserved DNA damage response genes																													p.H2437fs		Atlas-INDEL	.											.	ATR	285	.	0			c.7309delC						.						68.0	69.0	69.0					3																	142178110		2203	4300	6503	SO:0001589	frameshift_variant	545	exon43			.	U76308	CCDS3124.1	3q23	2014-06-17	2014-06-17		ENSG00000175054	ENSG00000175054			882	protein-coding gene	gene with protein product	"""MEC1, mitosis entry checkpoint 1, homolog (S. cerevisiae)"""	601215	"""ataxia telangiectasia and Rad3 related"""			8978690, 8610130	Standard	NM_001184		Approved	FRP1, SCKL, SCKL1, MEC1	uc003eux.4	Q13535	OTTHUMG00000159234	ENST00000350721.4:c.7308delT	chr3.hg19:g.142178110delA	ENSP00000343741:p.Phe2436fs	112.0	0.0		139.0	10.0	NM_001184	Q59HB2|Q7KYL3|Q93051|Q9BXK4	Frame_Shift_Del	DEL	ENST00000350721.4	hg19	CCDS3124.1																																																																																			.	.		0.363	ATR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353995.2	NM_001184	
GALNT4	8693	hgsc.bcm.edu	37	12	89918093	89918093	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:89918093delC	ENST00000529983.2	-	1	490	c.234delG	c.(232-234)gggfs	p.G78fs	GALNT4_ENST00000413530.1_Intron|RP11-734K2.4_ENST00000605233.1_RNA|POC1B_ENST00000541909.1_Intron|POC1B-GALNT4_ENST00000547474.1_Intron|POC1B_ENST00000393179.4_Intron|POC1B_ENST00000313546.3_Intron|POC1B-GALNT4_ENST00000548729.1_Frame_Shift_Del_p.G75fs|POC1B_ENST00000549504.1_Intron|POC1B_ENST00000549035.1_Intron	NM_003774.4	NP_003765.2	Q8N4A0	GALT4_HUMAN	polypeptide N-acetylgalactosaminyltransferase 4	78					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			endometrium(4)|kidney(2)|lung(5)|prostate(2)|upper_aerodigestive_tract(1)	14						TGCTGGCTTTCCCCCACTCCC	0.498											OREG0022018	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.K79fs		Atlas-INDEL	.											.	GALNT4	38	.	0			c.235delA						.						123.0	126.0	125.0					12																	89918093		1911	4116	6027	SO:0001589	frameshift_variant	8693	exon1			.	Y08564	CCDS53817.1	12q21.33	2014-03-13	2014-03-13		ENSG00000257594	ENSG00000257594	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	4126	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 4"""	603565	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 4 (GalNAc-T4)"""			9804815	Standard	NM_003774		Approved	GalNAc-T4	uc001tbd.3	Q8N4A0	OTTHUMG00000166292	ENST00000529983.2:c.234delG	chr12.hg19:g.89918093delC	ENSP00000436604:p.Gly78fs	144.0	0.0	1271	161.0	10.0	NM_003774	B2R775|B4DMX6|O00208	Frame_Shift_Del	DEL	ENST00000529983.2	hg19	CCDS53817.1																																																																																			.	.		0.498	GALNT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388973.2	NM_003774	
POU5F2	134187	hgsc.bcm.edu	37	5	93076558	93076558	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:93076558delG	ENST00000510627.4	-	1	785	c.712delC	c.(712-714)cagfs	p.Q239fs	FAM172A_ENST00000509163.1_Intron|RP11-185E12.2_ENST00000606528.1_RNA|FAM172A_ENST00000505869.1_Intron|FAM172A_ENST00000509739.1_Intron|FAM172A_ENST00000395965.3_Intron|POU5F2_ENST00000606183.1_5'UTR	NM_153216.1	NP_694948.1	Q8N7G0	PO5F2_HUMAN	POU domain class 5, transcription factor 2	239					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)						all_cancers(142;3.87e-05)|all_epithelial(76;4.59e-07)|all_lung(232;0.0126)|Lung NSC(167;0.0155)|Ovarian(174;0.0218)|Prostate(281;0.173)|Colorectal(57;0.19)		UCEC - Uterine corpus endometrioid carcinoma (5;0.0415)|all cancers(79;2.03e-19)		CTGATTTGCTGGGGTGTGGGC	0.552																																					p.Q238fs		Atlas-INDEL	.											.	POU5F2	10	.	0			c.713delA						.						52.0	52.0	52.0					5																	93076558		1995	4178	6173	SO:0001589	frameshift_variant	134187	exon1			.		CCDS59489.1	5q15	2011-06-20				ENSG00000248483		"""Homeoboxes / POU class"""	26367	protein-coding gene	gene with protein product						7908264	Standard	NM_153216		Approved	SPRM-1, FLJ25680	uc003kkl.1	Q8N7G0		ENST00000510627.4:c.712delC	chr5.hg19:g.93076558delG	ENSP00000464890:p.Gln239fs	201.0	0.0		221.0	14.0	NM_153216	Q15169|Q6MZL7|Q8N748	Frame_Shift_Del	DEL	ENST00000510627.4	hg19	CCDS59489.1																																																																																			.	.		0.552	POU5F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369873.5	NM_153216	
LRFN4	78999	hgsc.bcm.edu	37	11	66627324	66627324	+	Frame_Shift_Del	DEL	G	G	-	rs142190580		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:66627324delG	ENST00000309602.4	+	2	1809	c.1566delG	c.(1564-1566)gtgfs	p.V522fs	LRFN4_ENST00000393952.3_Intron|PC_ENST00000393955.2_Intron|PC_ENST00000393958.2_Intron|PC_ENST00000393960.1_Intron	NM_024036.4	NP_076941.2	Q6PJG9	LRFN4_HUMAN	leucine rich repeat and fibronectin type III domain containing 4	522						integral component of membrane (GO:0016021)				breast(1)|lung(1)|prostate(1)	3						CCGTGGCCGTGGGGGGTGTGC	0.716																																					p.V522fs		Atlas-INDEL	.											.	LRFN4	25	.	0			c.1565delT						.						28.0	22.0	24.0					11																	66627324		2187	4280	6467	SO:0001589	frameshift_variant	78999	exon2			.	BC007718	CCDS8153.1	11q13.1	2013-02-11				ENSG00000173621		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	28456	protein-coding gene	gene with protein product	"""fibronectin type III, immunoglobulin and leucine rich repeat domains 6"""	612810				16495444, 16828986	Standard	NM_024036		Approved	MGC3103, SALM3., FIGLER6	uc001ojr.3	Q6PJG9		ENST00000309602.4:c.1566delG	chr11.hg19:g.66627324delG	ENSP00000312535:p.Val522fs	67.0	0.0		124.0	11.0	NM_024036	Q4VBZ3|Q59GV4|Q8N644|Q9BWJ0	Frame_Shift_Del	DEL	ENST00000309602.4	hg19	CCDS8153.1																																																																																			.	.		0.716	LRFN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393127.1	NM_024036	
CCDC80	151887	hgsc.bcm.edu	37	3	112335650	112335650	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:112335650delA	ENST00000206423.3	-	5	3181	c.2228delT	c.(2227-2229)ttcfs	p.F743fs	CCDC80_ENST00000439685.2_Frame_Shift_Del_p.F743fs	NM_199511.1|NM_199512.1	NP_955805.1|NP_955806.1	Q76M96	CCD80_HUMAN	coiled-coil domain containing 80	743					extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	basement membrane (GO:0005604)|interstitial matrix (GO:0005614)	heparin binding (GO:0008201)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|liver(1)|lung(21)|ovary(3)|pancreas(2)|prostate(4)	51						TCGGGACTGGAAAGTATCGAT	0.393																																					p.F743fs		Atlas-INDEL	.											.	CCDC80	100	.	0			c.2229delC						.						181.0	162.0	168.0					3																	112335650		2203	4300	6503	SO:0001589	frameshift_variant	151887	exon5			.	AY333429	CCDS2968.1	3q13.2	2010-12-24			ENSG00000091986	ENSG00000091986			30649	protein-coding gene	gene with protein product	"""steroid sensitive gene 1"""	608298				15325258, 18178152	Standard	XM_005247135		Approved	URB, SSG1, DRO1	uc003dzf.3	Q76M96	OTTHUMG00000159265	ENST00000206423.3:c.2228delT	chr3.hg19:g.112335650delA	ENSP00000206423:p.Phe743fs	119.0	0.0		158.0	11.0	NM_199512	D3DN67|Q5PR20|Q6GPG9|Q8IVT6|Q8NBV1|Q8NHY8	Frame_Shift_Del	DEL	ENST00000206423.3	hg19	CCDS2968.1																																																																																			.	.		0.393	CCDC80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354219.1	NM_199511	
UFL1	23376	hgsc.bcm.edu	37	6	96990799	96990799	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:96990799delG	ENST00000369278.4	+	12	1375	c.1309delG	c.(1309-1311)gggfs	p.G438fs		NM_015323.4	NP_056138.1	O94874	UFL1_HUMAN	UFM1-specific ligase 1	438					negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein ubiquitination (GO:0031397)|osteoblast differentiation (GO:0001649)|protein ufmylation (GO:0071569)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|response to endoplasmic reticulum stress (GO:0034976)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleus (GO:0005634)	UFM1 conjugating enzyme activity (GO:0071568)										AGGAGGAGGTGGGGGCAATGC	0.373																																					p.G436fs		Atlas-INDEL	.											.	.	.	.	0			c.1308delT						.						54.0	56.0	55.0					6																	96990799		2203	4300	6503	SO:0001589	frameshift_variant	23376	exon12			.	BC036379	CCDS5034.1	6q16.3	2011-08-18	2011-08-18	2011-08-18	ENSG00000014123	ENSG00000014123			23039	protein-coding gene	gene with protein product	"""novel LZAP-binding protein"", ""Regulator of CDK5RAP3 and DDRGK1"""	613372	"""KIAA0776"""	KIAA0776		20018847, 20164180, 20228063, 20531390	Standard	NM_015323		Approved	NLBP, Maxer, RCAD	uc003por.3	O94874	OTTHUMG00000015238	ENST00000369278.4:c.1309delG	chr6.hg19:g.96990799delG	ENSP00000358283:p.Gly438fs	223.0	0.0		232.0	14.0	NM_015323	A0PJ53|B4DJ57|C0H5X5|Q8N765|Q9NTQ0	Frame_Shift_Del	DEL	ENST00000369278.4	hg19	CCDS5034.1																																																																																			.	.		0.373	UFL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041557.1	NM_015323	
PARG	8505	hgsc.bcm.edu	37	10	51077558	51077558	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:51077558delT	ENST00000402038.3	-	6	576	c.577delA	c.(577-579)acgfs	p.T193fs		NM_003631.2	NP_003622.2	Q86W56	PARG_HUMAN	poly (ADP-ribose) glycohydrolase	678	A-domain.				carbohydrate metabolic process (GO:0005975)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	poly(ADP-ribose) glycohydrolase activity (GO:0004649)			endometrium(5)|kidney(2)|lung(1)|ovary(2)	10				Epithelial(53;0.213)		CAGAAGAGCGTTTTAAGTTTC	0.338																																					p.T678fs		Atlas-INDEL	.											.	PARG	46	.	0			c.2033delC						.						41.0	36.0	38.0					10																	51077558		692	1588	2280	SO:0001589	frameshift_variant	8505	exon10			.	AF005043	CCDS73130.1	10q11.23	2012-04-20			ENSG00000227345	ENSG00000227345	3.2.1.143		8605	protein-coding gene	gene with protein product		603501				9115250, 10449915	Standard	NM_003631		Approved		uc001jif.3	Q86W56	OTTHUMG00000018201	ENST00000402038.3:c.577delA	chr10.hg19:g.51077558delT	ENSP00000384408:p.Thr193fs	179.0	0.0		212.0	13.0	NM_003631	A5YBK3|B2RC24|B4DIU5|B4DYR4|I6RUV3|Q6E4P6|Q6E4P7|Q7Z742|Q9Y4W7	Frame_Shift_Del	DEL	ENST00000402038.3	hg19																																																																																				.	.		0.338	PARG-001	KNOWN	mRNA_start_NF|cds_start_NF|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000048011.2	NM_003631	
CDH20	28316	hgsc.bcm.edu	37	18	59167713	59167713	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr18:59167713delT	ENST00000262717.4	+	4	1037	c.639delT	c.(637-639)tatfs	p.Y213fs	CDH20_ENST00000536675.2_Frame_Shift_Del_p.Y213fs|CDH20_ENST00000538374.1_Frame_Shift_Del_p.Y213fs			Q9HBT6	CAD20_HUMAN	cadherin 20, type 2	213	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(33)|ovary(1)|pancreas(1)|skin(3)	61		Colorectal(73;0.186)				GCCAGCCATATTTTTCTGTGG	0.488																																					p.Y213fs		Atlas-INDEL	.											.	CDH20	117	.	0			c.638delA						.						144.0	140.0	141.0					18																	59167713		2203	4300	6503	SO:0001589	frameshift_variant	28316	exon3			.	AF217289	CCDS11977.1	18q21.33	2010-01-26			ENSG00000101542	ENSG00000101542		"""Cadherins / Major cadherins"""	1760	protein-coding gene	gene with protein product		605807				10995570	Standard	NM_031891		Approved	CDH7L3, Cdh7	uc010dps.1	Q9HBT6	OTTHUMG00000132768	ENST00000262717.4:c.639delT	chr18.hg19:g.59167713delT	ENSP00000262717:p.Tyr213fs	106.0	0.0		163.0	11.0	NM_031891	Q495S3	Frame_Shift_Del	DEL	ENST00000262717.4	hg19	CCDS11977.1																																																																																			.	.		0.488	CDH20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256141.2	NM_031891	
PRRT4	401399	hgsc.bcm.edu	37	7	127999861	127999861	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:127999861delC	ENST00000446477.2	-	3	498	c.185delG	c.(184-186)ggafs	p.G62fs	PRRT4_ENST00000435512.1_Frame_Shift_Del_p.G62fs|PRRT4_ENST00000535159.1_Frame_Shift_Del_p.G62fs|PRRT4_ENST00000489835.2_Frame_Shift_Del_p.G62fs	NM_001174164.1	NP_001167635.1	C9JH25	PRRT4_HUMAN	proline-rich transmembrane protein 4	62						integral component of membrane (GO:0016021)				endometrium(4)|prostate(1)	5						AGCAGCAGGTCCCCGAAGATG	0.602																																					p.G62fs		Atlas-INDEL	.											.	PRRT4	31	.	0			c.186delA						.						31.0	36.0	34.0					7																	127999861		692	1591	2283	SO:0001589	frameshift_variant	401399	exon3			.	BC063892	CCDS47698.1, CCDS47698.2, CCDS55160.1	7q32.1	2011-10-10			ENSG00000224940	ENSG00000224940		"""Proline-rich transmembrane proteins"""	37280	protein-coding gene	gene with protein product							Standard	NM_001114726		Approved		uc022aky.1	C9JH25	OTTHUMG00000157714	ENST00000446477.2:c.185delG	chr7.hg19:g.127999861delC	ENSP00000415026:p.Gly62fs	158.0	0.0		182.0	11.0	NM_001174164	A4D0Z9|C9JVW7	Frame_Shift_Del	DEL	ENST00000446477.2	hg19	CCDS55160.1																																																																																			.	.		0.602	PRRT4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001114726	
PODNL1	79883	hgsc.bcm.edu	37	19	14044198	14044198	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:14044198delG	ENST00000339560.5	-	8	1132	c.859delC	c.(859-861)cggfs	p.R287fs	PODNL1_ENST00000254320.3_Frame_Shift_Del_p.R205fs|PODNL1_ENST00000538371.2_Frame_Shift_Del_p.R285fs|PODNL1_ENST00000538517.2_Frame_Shift_Del_p.R196fs	NM_024825.3	NP_079101.3	Q6PEZ8	PONL1_HUMAN	podocan-like 1	287	Leu-rich.					proteinaceous extracellular matrix (GO:0005578)				central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(2)|skin(1)	8			OV - Ovarian serous cystadenocarcinoma(19;5.26e-23)			GCCAGGGTCCGGGGCAGGCCG	0.652																																					p.R287fs		Atlas-INDEL	.											.	PODNL1	27	.	0			c.860delG						.						16.0	21.0	20.0					19																	14044198		2194	4288	6482	SO:0001589	frameshift_variant	79883	exon8			.	AK027100	CCDS12300.1, CCDS54225.1, CCDS54226.1	19p13.12	2008-02-05							26275	protein-coding gene	gene with protein product						12477932	Standard	NM_024825		Approved	FLJ23447, SLRR5B	uc010xnj.2	Q6PEZ8		ENST00000339560.5:c.859delC	chr19.hg19:g.14044198delG	ENSP00000345175:p.Arg287fs	158.0	0.0		168.0	12.0	NM_024825	B7Z564|Q9H5G9	Frame_Shift_Del	DEL	ENST00000339560.5	hg19	CCDS12300.1																																																																																			.	.		0.652	PODNL1-003	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457967.1	NM_024825	
PRRC2C	23215	hgsc.bcm.edu	37	1	171483721	171483721	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:171483721delC	ENST00000338920.4	+	4	568	c.331delC	c.(331-333)cccfs	p.P112fs	PRRC2C_ENST00000367742.3_Frame_Shift_Del_p.P114fs|PRRC2C_ENST00000476522.1_3'UTR|PRRC2C_ENST00000392078.3_Frame_Shift_Del_p.P114fs|PRRC2C_ENST00000426496.2_Frame_Shift_Del_p.P112fs	NM_015172.3	NP_055987.2	Q9Y520	PRC2C_HUMAN	proline-rich coiled-coil 2C	112					hematopoietic progenitor cell differentiation (GO:0002244)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)										GGTTGCAGCTCCCCCAGAAGT	0.453																																					p.A110fs		Atlas-INDEL	.											.	.	.	.	0			c.330delT						.						56.0	44.0	48.0					1																	171483721		2193	4277	6470	SO:0001589	frameshift_variant	23215	exon4			.	AL096857	CCDS1296.2	1q24.3	2012-07-18	2010-12-09	2010-12-09	ENSG00000117523	ENSG00000117523			24903	protein-coding gene	gene with protein product			"""BAT2 domain containing 1"", ""HLA-B associated transcript 2-like 2"""	BAT2D1, BAT2L2		10470851, 12443540	Standard	NM_015172		Approved	KIAA1096, XTP2	uc010pmg.2	Q9Y520	OTTHUMG00000034665	ENST00000338920.4:c.331delC	chr1.hg19:g.171483721delC	ENSP00000343629:p.Pro112fs	157.0	0.0		312.0	21.0	NM_015172	Q05DM8|Q49A39|Q6PD54|Q9H2N2|Q9HA05|Q9NSM8|Q9NXL3|Q9UF29|Q9UPQ6	Frame_Shift_Del	DEL	ENST00000338920.4	hg19	CCDS1296.2																																																																																			.	.		0.453	PRRC2C-010	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000314826.4	NM_015172	
BACE1	23621	hgsc.bcm.edu	37	11	117186306	117186306	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:117186306delC	ENST00000313005.6	-	1	666	c.206delG	c.(205-207)ggcfs	p.G69fs	BACE1_ENST00000514464.1_5'UTR|BACE1_ENST00000528053.1_Frame_Shift_Del_p.G69fs|BACE1_ENST00000445823.2_Frame_Shift_Del_p.G69fs|AP000892.4_ENST00000504906.1_RNA|BACE1_ENST00000428381.2_Frame_Shift_Del_p.G69fs|BACE1_ENST00000513780.1_Frame_Shift_Del_p.G69fs	NM_012104.4|NM_138971.3|NM_138972.3|NM_138973.3	NP_036236|NP_620427.1|NP_620428.1|NP_620429.1	P56817	BACE1_HUMAN	beta-site APP-cleaving enzyme 1	69					beta-amyloid metabolic process (GO:0050435)|membrane protein ectodomain proteolysis (GO:0006509)|proteolysis (GO:0006508)	axon (GO:0030424)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|multivesicular body (GO:0005771)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	aspartic-type endopeptidase activity (GO:0004190)|beta-amyloid binding (GO:0001540)|beta-aspartyl-peptidase activity (GO:0008798)|enzyme binding (GO:0019899)			breast(2)|endometrium(4)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)|prostate(1)	19	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.69e-05)|Epithelial(105;0.000563)|all cancers(92;0.0032)		CCCCGACTTGCCCCTCAGGTT	0.706																																					p.G69fs		Atlas-INDEL	.											.	BACE1	33	.	0			c.207delC						.						49.0	47.0	48.0					11																	117186306		2201	4296	6497	SO:0001589	frameshift_variant	23621	exon1			.	AF190725	CCDS8383.1, CCDS44739.1, CCDS44740.1, CCDS44741.1, CCDS55787.1, CCDS55786.1	11q23-q24	2011-07-27	2004-04-02	2004-04-02	ENSG00000186318	ENSG00000186318			933	protein-coding gene	gene with protein product		604252	"""beta-site APP-cleaving enzyme"""	BACE		10531052	Standard	NM_012104		Approved		uc001pqz.3	P56817	OTTHUMG00000160636	ENST00000313005.6:c.206delG	chr11.hg19:g.117186306delC	ENSP00000318585:p.Gly69fs	140.0	0.0		166.0	12.0	NM_138972	A0M8W7|B0YIU9|E9PE65|H7BXJ9|Q9BYB9|Q9BYC0|Q9BYC1|Q9UJT5|Q9ULS1	Frame_Shift_Del	DEL	ENST00000313005.6	hg19	CCDS8383.1																																																																																			.	.		0.706	BACE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361505.1		
GTF2I	2969	hgsc.bcm.edu	37	7	74163404	74163404	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:74163404delA	ENST00000324896.4	+	25	2602	c.2213delA	c.(2212-2214)gaafs	p.E738fs	GTF2I_ENST00000416070.1_Frame_Shift_Del_p.E697fs|GTF2I_ENST00000353920.4_Frame_Shift_Del_p.E718fs|GTF2I_ENST00000438130.2_3'UTR|GTF2I_ENST00000346152.4_Frame_Shift_Del_p.E717fs	NM_032999.2	NP_127492.1	P78347	GTF2I_HUMAN	general transcription factor IIi	738					negative regulation of angiogenesis (GO:0016525)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(7)|kidney(1)|large_intestine(1)|lung(5)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	19						CAGAAAGTTGAAAATCTCTTC	0.403																																					p.E738fs		Atlas-INDEL	.											.	GTF2I	40	.	0			c.2212delG						.						1.0	1.0	1.0					7																	74163404		25	63	88	SO:0001589	frameshift_variant	2969	exon25			.	U77948	CCDS5573.1, CCDS5574.1, CCDS5575.1, CCDS47614.1, CCDS64680.1	7q11.23	2011-05-25	2009-07-23			ENSG00000263001		"""General transcription factors"""	4659	protein-coding gene	gene with protein product		601679	"""general transcription factor II, i"""	WBSCR6		9334314, 9012831	Standard	NM_032999		Approved	TFII-I, BAP-135, SPIN, BTKAP1, DIWS, IB291	uc003uau.3	P78347		ENST00000324896.4:c.2213delA	chr7.hg19:g.74163404delA	ENSP00000322542:p.Glu738fs	106.0	0.0		177.0	11.0	NM_032999	O14743|O15359|O43546|O43588|O43589|Q75M85|Q75M86|Q75M87|Q75M88|Q86U51|Q9BSZ4	Frame_Shift_Del	DEL	ENST00000324896.4	hg19	CCDS5573.1																																																																																			.	.		0.403	GTF2I-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252708.1	NM_032999	
IQCG	84223	hgsc.bcm.edu	37	3	197659165	197659165	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:197659165delA	ENST00000265239.6	-	6	948	c.524delT	c.(523-525)ttcfs	p.F175fs	IQCG_ENST00000455191.1_Frame_Shift_Del_p.F175fs|IQCG_ENST00000453254.1_Frame_Shift_Del_p.F175fs	NM_032263.3	NP_115639.1	Q9H095	IQCG_HUMAN	IQ motif containing G	175						extracellular vesicular exosome (GO:0070062)				autonomic_ganglia(1)|breast(2)|cervix(1)|kidney(1)|large_intestine(3)|lung(10)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)		Epithelial(36;7.19e-24)|all cancers(36;3.34e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07)	GBM - Glioblastoma multiforme(93;0.149)		CACATCGCTGAAAAACTGCCT	0.433																																					p.F175fs		Atlas-INDEL	.											.	IQCG	44	.	0			c.525delC						.						96.0	90.0	93.0					3																	197659165		2203	4300	6503	SO:0001589	frameshift_variant	84223	exon6			.	AL136889	CCDS3331.1	3q29	2014-07-18			ENSG00000114473	ENSG00000114473			25251	protein-coding gene	gene with protein product	"""dynein regulatory complex subunit 9"""	612477				11230166, 23427265, 24362311	Standard	NM_032263		Approved	DKFZp434B227, DRC9, CFAP122	uc003fyo.3	Q9H095	OTTHUMG00000155408	ENST00000265239.6:c.524delT	chr3.hg19:g.197659165delA	ENSP00000265239:p.Phe175fs	113.0	0.0		160.0	11.0	NM_032263	Q9BST2|Q9HAG8	Frame_Shift_Del	DEL	ENST00000265239.6	hg19	CCDS3331.1																																																																																			.	.		0.433	IQCG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339730.1	NM_032263	
SF3A1	10291	hgsc.bcm.edu	37	22	30733103	30733103	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr22:30733103delG	ENST00000215793.8	-	13	2172	c.2018delC	c.(2017-2019)ccafs	p.P675fs	SF3A1_ENST00000439242.1_Frame_Shift_Del_p.P610fs	NM_005877.4	NP_005868.1	Q15459	SF3A1_HUMAN	splicing factor 3a, subunit 1, 120kDa	675	Poly-Pro.				gene expression (GO:0010467)|mRNA 3'-splice site recognition (GO:0000389)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U2-type spliceosomal complex (GO:0005684)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(9)|ovary(4)|pancreas(1)|prostate(1)|urinary_tract(1)	29						CATGGGAGGTGGGGGATGCAC	0.567																																					p.P673fs		Atlas-INDEL	.											.	SF3A1	61	.	0			c.2019delA						.						61.0	60.0	61.0					22																	30733103		2203	4300	6503	SO:0001589	frameshift_variant	10291	exon13			.	X85237	CCDS13875.1	22q12.2	2014-09-17	2002-08-29		ENSG00000099995	ENSG00000099995			10765	protein-coding gene	gene with protein product		605595	"""splicing factor 3a, subunit 1, 120kD"""			7489498	Standard	NM_005877		Approved	SF3a120, SAP114, PRPF21, Prp21	uc003ahl.3	Q15459	OTTHUMG00000151005	ENST00000215793.8:c.2018delC	chr22.hg19:g.30733103delG	ENSP00000215793:p.Pro675fs	113.0	0.0		166.0	10.0	NM_005877	E9PAW1	Frame_Shift_Del	DEL	ENST00000215793.8	hg19	CCDS13875.1																																																																																			.	.		0.567	SF3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320916.2	NM_005877	
RRH	10692	hgsc.bcm.edu	37	4	110758642	110758642	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:110758642delC	ENST00000317735.4	+	5	635	c.601delC	c.(601-603)cccfs	p.P201fs		NM_006583.2	NP_006574.1	O14718	OPSX_HUMAN	retinal pigment epithelium-derived rhodopsin homolog	201					G-protein coupled receptor signaling pathway (GO:0007186)|phototransduction (GO:0007602)|protein-chromophore linkage (GO:0018298)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)|photoreceptor activity (GO:0009881)			endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|pancreas(1)	12		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00109)		TTTTATTGTGCCCTTGACAGT	0.393																																					p.V200fs		Atlas-INDEL	.											.	RRH	24	.	0			c.600delG						.						182.0	154.0	163.0					4																	110758642		2203	4300	6503	SO:0001589	frameshift_variant	10692	exon5			.	AF012270	CCDS3687.1	4q25	2012-08-08			ENSG00000180245	ENSG00000180245		"""GPCR / Class A : Opsin receptors"""	10450	protein-coding gene	gene with protein product	"""peropsin"""	605224				9275222	Standard	NM_006583		Approved	peropsin	uc003hzv.3	O14718	OTTHUMG00000132045	ENST00000317735.4:c.601delC	chr4.hg19:g.110758642delC	ENSP00000314992:p.Pro201fs	198.0	0.0		173.0	11.0	NM_006583	A1A4V2|Q7RTS4	Frame_Shift_Del	DEL	ENST00000317735.4	hg19	CCDS3687.1																																																																																			.	.		0.393	RRH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255066.1	NM_006583	
UGGT1	56886	hgsc.bcm.edu	37	2	128900693	128900693	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:128900693delA	ENST00000259253.6	+	17	1792	c.1745delA	c.(1744-1746)gaafs	p.E582fs	UGGT1_ENST00000375990.3_Frame_Shift_Del_p.E558fs	NM_020120.3	NP_064505.1	Q9NYU2	UGGG1_HUMAN	UDP-glucose glycoprotein glucosyltransferase 1	582					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)	UDP-glucose:glycoprotein glucosyltransferase activity (GO:0003980)|unfolded protein binding (GO:0051082)			NS(1)|breast(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(14)|lung(20)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	63						AGGACTGGAGAAAAAGTGAAA	0.348																																					p.E582fs		Atlas-INDEL	.											.	UGGT1	126	.	0			c.1744delG						.						131.0	127.0	128.0					2																	128900693		2203	4300	6503	SO:0001589	frameshift_variant	56886	exon17			.	AF227905	CCDS2154.1	2q14.3	2009-07-23	2009-07-23	2009-07-23	ENSG00000136731	ENSG00000136731			15663	protein-coding gene	gene with protein product		605897	"""UDP-glucose ceramide glucosyltransferase-like 1"""	UGCGL1		10694380	Standard	NM_020120		Approved	HUGT1	uc002tps.3	Q9NYU2	OTTHUMG00000131570	ENST00000259253.6:c.1745delA	chr2.hg19:g.128900693delA	ENSP00000259253:p.Glu582fs	80.0	0.0		129.0	10.0	NM_020120	Q53QP2|Q53SL3|Q8IW30|Q9H8I4	Frame_Shift_Del	DEL	ENST00000259253.6	hg19	CCDS2154.1																																																																																			.	.		0.348	UGGT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254435.2	NM_020120	
NEMF	9147	hgsc.bcm.edu	37	14	50295460	50295460	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:50295460delT	ENST00000298310.5	-	14	1747	c.1298delA	c.(1297-1299)aatfs	p.N433fs	NEMF_ENST00000556925.1_5'UTR|NEMF_ENST00000546046.1_Frame_Shift_Del_p.N433fs|NEMF_ENST00000545773.1_Frame_Shift_Del_p.N391fs			O60524	NEMF_HUMAN	nuclear export mediator factor	433					nuclear export (GO:0051168)	nucleus (GO:0005634)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(13)|liver(1)|lung(9)|prostate(1)|skin(1)|urinary_tract(1)	36						TTCAGTTTCATTTTTCTCAAC	0.343																																					p.N433fs		Atlas-INDEL	.											.	NEMF	79	.	0			c.1299delT						.						79.0	76.0	77.0					14																	50295460		2203	4300	6503	SO:0001589	frameshift_variant	9147	exon14			.	AF039687	CCDS9694.1	14q21.3	2012-11-19	2011-01-31	2011-01-31	ENSG00000165525	ENSG00000165525			10663	protein-coding gene	gene with protein product		608378	"""serologically defined colon cancer antigen 1"""	SDCCAG1		9610721, 10575219	Standard	XR_429334		Approved	NY-CO-1, FLJ10051	uc001wxc.3	O60524	OTTHUMG00000170857	ENST00000298310.5:c.1298delA	chr14.hg19:g.50295460delT	ENSP00000298310:p.Asn433fs	135.0	0.0		148.0	10.0	NM_004713	A0JLQ3|B3KSK1|B4DDL3|B4DHA9|B4E3F3|Q32Q66|Q8WW70|Q9NWG1	Frame_Shift_Del	DEL	ENST00000298310.5	hg19	CCDS9694.1																																																																																			.	.		0.343	NEMF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410798.1	NM_004713	
PPWD1	23398	hgsc.bcm.edu	37	5	64865782	64865782	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:64865782delT	ENST00000261308.5	+	4	550	c.478delT	c.(478-480)tttfs	p.F160fs	PPWD1_ENST00000538977.1_Frame_Shift_Del_p.F4fs|PPWD1_ENST00000535264.1_Frame_Shift_Del_p.F130fs	NM_015342.3	NP_056157.1	Q96BP3	PPWD1_HUMAN	peptidylprolyl isomerase domain and WD repeat containing 1	160					mRNA splicing, via spliceosome (GO:0000398)|protein folding (GO:0006457)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)	19		Lung NSC(167;7.21e-05)|Prostate(74;0.0174)|Ovarian(174;0.186)		Lung(70;0.00451)		AATGAAGGTGTTTGATGTAGT	0.313																																					p.V159fs		Atlas-INDEL	.											.	PPWD1	47	.	0			c.477delG						.						134.0	132.0	133.0					5																	64865782		2203	4300	6503	SO:0001589	frameshift_variant	23398	exon4			.	AK025679	CCDS3985.1, CCDS64161.1, CCDS64162.1	5q12.3	2013-01-09			ENSG00000113593	ENSG00000113593		"""WD repeat domain containing"""	28954	protein-coding gene	gene with protein product						7584044	Standard	NM_015342		Approved	KIAA0073	uc003jtv.5	Q96BP3	OTTHUMG00000131226	ENST00000261308.5:c.478delT	chr5.hg19:g.64865782delT	ENSP00000261308:p.Phe160fs	110.0	0.0		164.0	10.0	NM_015342	B4DWR9|Q15002|Q7KZ89	Frame_Shift_Del	DEL	ENST00000261308.5	hg19	CCDS3985.1																																																																																			.	.		0.313	PPWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253970.2	NM_015342	
GPX7	2882	hgsc.bcm.edu	37	1	53074002	53074002	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:53074002delG	ENST00000361314.4	+	3	507	c.469delG	c.(469-471)gggfs	p.G157fs		NM_015696.4	NP_056511.2	Q96SL4	GPX7_HUMAN	glutathione peroxidase 7	157					response to oxidative stress (GO:0006979)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	glutathione peroxidase activity (GO:0004602)|peroxidase activity (GO:0004601)			breast(1)|kidney(1)|lung(4)|upper_aerodigestive_tract(1)	7					Glutathione(DB00143)	AAAGGTGGTAGGGGCTTGGGA	0.537																																					p.V156fs		Atlas-INDEL	.											.	GPX7	16	.	0			c.468delA						.						122.0	116.0	118.0					1																	53074002		2203	4300	6503	SO:0001589	frameshift_variant	2882	exon3			.	AF091092	CCDS569.1	1p32	2008-02-05			ENSG00000116157	ENSG00000116157			4559	protein-coding gene	gene with protein product		615784				15294905	Standard	NM_015696		Approved	FLJ14777, GPX6, NPGPx	uc001cue.3	Q96SL4	OTTHUMG00000008322	ENST00000361314.4:c.469delG	chr1.hg19:g.53074002delG	ENSP00000354677:p.Gly157fs	77.0	0.0		103.0	10.0	NM_015696	O95337|Q5T501	Frame_Shift_Del	DEL	ENST00000361314.4	hg19	CCDS569.1																																																																																			.	.		0.537	GPX7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022913.1	NM_015696	
BUB1	699	hgsc.bcm.edu	37	2	111406915	111406915	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:111406915delA	ENST00000302759.6	-	19	2361	c.2243delT	c.(2242-2244)ttcfs	p.F748fs	BUB1_ENST00000535254.1_Frame_Shift_Del_p.F728fs|BUB1_ENST00000409311.1_Frame_Shift_Del_p.F748fs	NM_004336.3	NP_004327.1	O43683	BUB1_HUMAN	BUB1 mitotic checkpoint serine/threonine kinase	748					apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|regulation of chromosome segregation (GO:0051983)|regulation of sister chromatid cohesion (GO:0007063)|spindle assembly checkpoint (GO:0071173)|viral process (GO:0016032)	condensed chromosome kinetochore (GO:0000777)|condensed nuclear chromosome, centromeric region (GO:0000780)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|endometrium(8)|kidney(4)|large_intestine(9)|lung(18)|ovary(1)|prostate(1)|stomach(1)	45		Ovarian(717;0.0822)		BRCA - Breast invasive adenocarcinoma(221;0.0556)		TAAAAGTTTGAAAATCAGCTT	0.353																																					p.F748fs		Atlas-INDEL	.											.	BUB1	91	.	0			c.2244delC						.						93.0	97.0	95.0					2																	111406915		2203	4300	6503	SO:0001589	frameshift_variant	699	exon19			.	AF046078	CCDS33273.1, CCDS62984.1, CCDS62985.1	2q13	2013-01-17	2013-01-17		ENSG00000169679	ENSG00000169679			1148	protein-coding gene	gene with protein product		602452	"""budding uninhibited by benzimidazoles 1 (yeast homolog)"", ""budding uninhibited by benzimidazoles 1 homolog (yeast)"""	BUB1L			Standard	NM_004336		Approved	hBUB1, BUB1A	uc002tgc.3	O43683	OTTHUMG00000153638	ENST00000302759.6:c.2243delT	chr2.hg19:g.111406915delA	ENSP00000302530:p.Phe748fs	163.0	0.0		238.0	16.0	NM_004336	E9PC26|F5GXI5|O43430|O43643|O60626|Q53QE4	Frame_Shift_Del	DEL	ENST00000302759.6	hg19	CCDS33273.1																																																																																			.	.		0.353	BUB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331925.1	NM_004336	
TBC1D20	128637	hgsc.bcm.edu	37	20	428697	428697	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr20:428697delT	ENST00000354200.4	-	2	239	c.92delA	c.(91-93)aagfs	p.K32fs	Y_RNA_ENST00000384070.1_RNA	NM_144628.2	NP_653229.1	Q96BZ9	TBC20_HUMAN	TBC1 domain family, member 20	32					acrosome assembly (GO:0001675)|cargo loading into COPII-coated vesicle (GO:0090110)|ER to Golgi vesicle-mediated transport (GO:0006888)|Golgi organization (GO:0007030)|lens fiber cell morphogenesis (GO:0070309)|lipid particle organization (GO:0034389)|positive regulation of ER to Golgi vesicle-mediated transport (GO:1902953)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)|seminiferous tubule development (GO:0072520)|virion assembly (GO:0019068)	endoplasmic reticulum membrane (GO:0005789)|integral component of Golgi membrane (GO:0030173)|nuclear membrane (GO:0031965)	Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	12		all_epithelial(17;0.228)|Breast(17;0.231)				TGCCACTTTCTTTTTCCTTTT	0.478																																					p.K31fs		Atlas-INDEL	.											.	TBC1D20	34	.	0			c.93delG						.						169.0	130.0	143.0					20																	428697		2203	4300	6503	SO:0001589	frameshift_variant	128637	exon2			.	AK055573	CCDS13002.1	20p13	2013-07-10	2005-01-05	2005-01-05	ENSG00000125875	ENSG00000125875			16133	protein-coding gene	gene with protein product		611663	"""chromosome 20 open reading frame 140"""	C20orf140		17901050	Standard	XM_005260661		Approved	dJ852M4.2	uc002wds.3	Q96BZ9	OTTHUMG00000031637	ENST00000354200.4:c.92delA	chr20.hg19:g.428697delT	ENSP00000346139:p.Lys32fs	125.0	0.0		166.0	11.0	NM_144628	A8K6I3|B9A6M1|Q5JWQ7|Q6ZSY8|Q96NE1|Q9BYM7|Q9H140	Frame_Shift_Del	DEL	ENST00000354200.4	hg19	CCDS13002.1																																																																																			.	.		0.478	TBC1D20-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251397.2	NM_144628	
ACVR2B	93	hgsc.bcm.edu	37	3	38519754	38519754	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:38519754delC	ENST00000352511.4	+	4	965	c.493delC	c.(493-495)cccfs	p.P166fs		NM_001106.3	NP_001097.2	Q13705	AVR2B_HUMAN	activin A receptor, type IIB	166					activation of protein kinase activity (GO:0032147)|activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|blood vessel remodeling (GO:0001974)|BMP signaling pathway (GO:0030509)|determination of left/right symmetry (GO:0007368)|embryonic foregut morphogenesis (GO:0048617)|gastrulation with mouth forming second (GO:0001702)|heart development (GO:0007507)|insulin secretion (GO:0030073)|kidney development (GO:0001822)|lung development (GO:0030324)|lymphangiogenesis (GO:0001946)|lymphatic endothelial cell differentiation (GO:0060836)|mesoderm development (GO:0007498)|odontogenesis of dentin-containing tooth (GO:0042475)|organ growth (GO:0035265)|palate development (GO:0060021)|pancreas development (GO:0031016)|positive regulation of activin receptor signaling pathway (GO:0032927)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|post-embryonic development (GO:0009791)|regulation of transcription, DNA-templated (GO:0006355)|response to glucose (GO:0009749)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction (GO:0007165)|skeletal system morphogenesis (GO:0048705)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)|venous blood vessel development (GO:0060841)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta-activated receptor activity (GO:0005024)			lung(1)	1	Medulloblastoma(35;0.163)			KIRC - Kidney renal clear cell carcinoma(284;0.0565)|Kidney(284;0.071)		GCATCGCAAGCCCCCCTACGG	0.617																																					p.K164fs		Atlas-INDEL	.											.	ACVR2B	88	.	0			c.492delG						.						68.0	67.0	67.0					3																	38519754		2203	4300	6503	SO:0001589	frameshift_variant	93	exon4			.	X77533	CCDS2679.1	3p22	2006-11-06			ENSG00000114739	ENSG00000114739			174	protein-coding gene	gene with protein product		602730				8161782, 9621519	Standard	NM_001106		Approved	ActR-IIB	uc003cif.3	Q13705	OTTHUMG00000131291	ENST00000352511.4:c.493delC	chr3.hg19:g.38519754delC	ENSP00000340361:p.Pro166fs	100.0	0.0		146.0	12.0	NM_001106	Q4VAV0	Frame_Shift_Del	DEL	ENST00000352511.4	hg19	CCDS2679.1																																																																																			.	.		0.617	ACVR2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254059.3	NM_001106	
TMTC4	84899	hgsc.bcm.edu	37	13	101278382	101278382	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr13:101278382delT	ENST00000376234.3	-	12	1661	c.1472delA	c.(1471-1473)aacfs	p.N491fs	TMTC4_ENST00000462211.1_5'UTR|TMTC4_ENST00000328767.5_Frame_Shift_Del_p.N380fs|TMTC4_ENST00000342624.5_Frame_Shift_Del_p.N510fs	NM_001079669.1	NP_001073137.1	Q5T4D3	TMTC4_HUMAN	transmembrane and tetratricopeptide repeat containing 4	491						integral component of membrane (GO:0016021)				breast(3)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(14)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	34	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					ATCAGCCAGGTTTTTGCCAAT	0.463																																					p.N510fs		Atlas-INDEL	.											.	TMTC4	103	.	0			c.1530delC						.						123.0	116.0	118.0					13																	101278382		2203	4300	6503	SO:0001589	frameshift_variant	84899	exon13			.		CCDS9497.2, CCDS41904.1, CCDS66575.1	13q32.3	2013-01-10	2006-01-06		ENSG00000125247	ENSG00000125247		"""Tetratricopeptide (TTC) repeat domain containing"""	25904	protein-coding gene	gene with protein product							Standard	XM_005254082		Approved	FLJ14624, FLJ22153	uc001vot.3	Q5T4D3	OTTHUMG00000017289	ENST00000376234.3:c.1472delA	chr13.hg19:g.101278382delT	ENSP00000365408:p.Asn491fs	264.0	0.0		320.0	23.0	NM_032813	A6NLI7|B7Z666|Q5T4D4|Q5T4D5|Q5T4D6|Q8WV63|Q96SU8	Frame_Shift_Del	DEL	ENST00000376234.3	hg19	CCDS41904.1																																																																																			.	.		0.463	TMTC4-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045649.2	NM_032813	
DEPDC1B	55789	hgsc.bcm.edu	37	5	59893603	59893603	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:59893603delT	ENST00000265036.5	-	11	1634	c.1567delA	c.(1567-1569)agafs	p.R523fs	DEPDC1B_ENST00000453022.2_Frame_Shift_Del_p.R461fs|DEPDC1B_ENST00000545085.1_Frame_Shift_Del_p.R434fs	NM_018369.2	NP_060839.2	Q8WUY9	DEP1B_HUMAN	DEP domain containing 1B	523					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(6)|ovary(1)|pancreas(2)|skin(2)	17		Lung NSC(810;0.000214)|Prostate(74;0.0147)|Breast(144;0.0991)|Ovarian(174;0.17)				CTTCTAGTTCTTTGAAATGGT	0.423																																					p.R523fs		Atlas-INDEL	.											.	DEPDC1B	56	.	0			c.1568delG						.						192.0	184.0	187.0					5																	59893603		2203	4300	6503	SO:0001589	frameshift_variant	55789	exon11			.	AF303178	CCDS3977.1, CCDS47214.1	5q12	2008-02-05			ENSG00000035499	ENSG00000035499			24902	protein-coding gene	gene with protein product	"""breast cancer cell 3"""					12477932	Standard	NM_001145208		Approved	XTP1, BRCC3	uc003jsh.3	Q8WUY9	OTTHUMG00000097083	ENST00000265036.5:c.1567delA	chr5.hg19:g.59893603delT	ENSP00000265036:p.Arg523fs	108.0	0.0		164.0	11.0	NM_018369	A8K3R9|B4DUT4|Q86WJ3|Q8IZY6|Q9NUN3|Q9NW57	Frame_Shift_Del	DEL	ENST00000265036.5	hg19	CCDS3977.1																																																																																			.	.		0.423	DEPDC1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214207.1	NM_018369	
DOT1L	84444	hgsc.bcm.edu	37	19	2191141	2191141	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:2191141delC	ENST00000398665.3	+	5	431	c.395delC	c.(394-396)tccfs	p.S132fs		NM_032482.2	NP_115871.1	Q8TEK3	DOT1L_HUMAN	DOT1-like histone H3K79 methyltransferase	132	DOT1. {ECO:0000255|PROSITE- ProRule:PRU00902}.				histone lysine methylation (GO:0034968)|regulation of JAK-STAT cascade (GO:0046425)|regulation of transcription regulatory region DNA binding (GO:2000677)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription factor binding (GO:0008134)			NS(1)|breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(3)|lung(14)|ovary(2)|pancreas(2)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(9)	42		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)		GAGCCCTTCTCCCCCGAGGTG	0.597																																					p.S132fs		Atlas-INDEL	.											.	DOT1L	205	.	0			c.394delT						.						95.0	105.0	102.0					19																	2191141		2088	4218	6306	SO:0001589	frameshift_variant	84444	exon5			.	AF509504	CCDS42460.1	19p13.3	2013-05-21	2013-05-21		ENSG00000104885	ENSG00000104885	2.1.1.43	"""Chromatin-modifying enzymes / K-methyltransferases"""	24948	protein-coding gene	gene with protein product	"""histone methyltransferase DOT1L"""	607375	"""DOT1-like, histone H3 methyltransferase (S. cerevisiae)"""			11347906, 12123582	Standard	NM_032482		Approved	KIAA1814, DOT1, KMT4	uc002lvb.4	Q8TEK3	OTTHUMG00000150431	ENST00000398665.3:c.395delC	chr19.hg19:g.2191141delC	ENSP00000381657:p.Ser132fs	157.0	0.0		159.0	10.0	NM_032482	O60379|Q96JL1	Frame_Shift_Del	DEL	ENST00000398665.3	hg19	CCDS42460.1																																																																																			.	.		0.597	DOT1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318066.1	NM_032482	
GPATCH1	55094	hgsc.bcm.edu	37	19	33605287	33605287	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:33605287delA	ENST00000170564.2	+	15	2472	c.2158delA	c.(2158-2160)aaafs	p.K720fs		NM_018025.2	NP_060495.2	Q9BRR8	GPTC1_HUMAN	G patch domain containing 1	720					mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)	nucleic acid binding (GO:0003676)			breast(4)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(15)|prostate(4)|skin(4)	40	Esophageal squamous(110;0.137)					CTTAGTAAACAAAGAGGAAGA	0.433																																					p.N719fs	Pancreas(67;88 1713 4567 18227)	Atlas-INDEL	.											.	GPATCH1	79	.	0			c.2157delC						.						72.0	78.0	76.0					19																	33605287		2203	4300	6503	SO:0001589	frameshift_variant	55094	exon15			.	AF434677	CCDS12428.1	19q13.12	2013-01-28		2006-12-13		ENSG00000076650		"""G patch domain containing"""	24658	protein-coding gene	gene with protein product	"""evolutionarily conserved G patch domain containing"""			GPATC1		12477932	Standard	NM_018025		Approved	ECGP, FLJ10206, FLJ38686	uc002nug.1	Q9BRR8		ENST00000170564.2:c.2158delA	chr19.hg19:g.33605287delA	ENSP00000170564:p.Lys720fs	126.0	0.0		157.0	10.0	NM_018025	Q8IZV6|Q8N3B7|Q9NW94	Frame_Shift_Del	DEL	ENST00000170564.2	hg19	CCDS12428.1																																																																																			.	.		0.433	GPATCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450834.1	NM_018025	
PCDHB12	56124	hgsc.bcm.edu	37	5	140590838	140590838	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:140590838delC	ENST00000239450.2	+	1	2548	c.2359delC	c.(2359-2361)cccfs	p.P788fs	PCDHB13_ENST00000341948.4_5'Flank|PCDHB12_ENST00000541609.1_Frame_Shift_Del_p.P451fs	NM_018932.3	NP_061755.1	Q9Y5F1	PCDBC_HUMAN	protocadherin beta 12	788					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|endometrium(10)|large_intestine(17)|lung(38)|ovary(3)|pancreas(1)|prostate(2)|skin(7)|stomach(1)	83			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CGAAGAAAATCCCCCATTTCA	0.378																																					p.N786fs		Atlas-INDEL	.											.	PCDHB12	179	.	0			c.2358delT						.						55.0	57.0	56.0					5																	140590838		2202	4300	6502	SO:0001589	frameshift_variant	56124	exon1			.	AF152491	CCDS4254.1	5q31	2010-01-26			ENSG00000120328	ENSG00000120328		"""Cadherins / Protocadherins : Clustered"""	8683	other	protocadherin		606338				10380929	Standard	NM_018932		Approved	PCDH-BETA12	uc003liz.3	Q9Y5F1	OTTHUMG00000129620	ENST00000239450.2:c.2359delC	chr5.hg19:g.140590838delC	ENSP00000239450:p.Pro788fs	138.0	0.0		194.0	12.0	NM_018932	B4DDU1	Frame_Shift_Del	DEL	ENST00000239450.2	hg19	CCDS4254.1																																																																																			.	.		0.378	PCDHB12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251815.2	NM_018932	
FOSL2	2355	hgsc.bcm.edu	37	2	28635091	28635091	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:28635091delG	ENST00000264716.4	+	4	1620	c.757delG	c.(757-759)gggfs	p.G254fs	FOSL2_ENST00000545753.1_Frame_Shift_Del_p.G215fs|FOSL2_ENST00000379619.1_Frame_Shift_Del_p.G246fs	NM_005253.3	NP_005244.1	P15408	FOSL2_HUMAN	FOS-like antigen 2	254					cell death (GO:0008219)|cellular response to hormone stimulus (GO:0032870)|female pregnancy (GO:0007565)|positive regulation of fibroblast proliferation (GO:0048146)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to cAMP (GO:0051591)|response to corticosterone (GO:0051412)|response to drug (GO:0042493)|response to mechanical stimulus (GO:0009612)|response to morphine (GO:0043278)|response to progesterone (GO:0032570)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(1)|large_intestine(3)|lung(1)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	14	Acute lymphoblastic leukemia(172;0.155)					CAGCATTGCTGGGGGCTTCTA	0.632																																					p.A252fs		Atlas-INDEL	.											.	FOSL2	39	.	0			c.756delT						.						44.0	40.0	41.0					2																	28635091		2203	4300	6503	SO:0001589	frameshift_variant	2355	exon4			.		CCDS1766.1	2p23.3	2013-01-10			ENSG00000075426	ENSG00000075426		"""basic leucine zipper proteins"""	3798	protein-coding gene	gene with protein product		601575					Standard	NM_005253		Approved	FRA2, FLJ23306	uc002rma.3	P15408	OTTHUMG00000097832	ENST00000264716.4:c.757delG	chr2.hg19:g.28635091delG	ENSP00000264716:p.Gly254fs	93.0	0.0		137.0	11.0	NM_005253	B2RD58|B3KP27|B4DYV4|Q6FG46	Frame_Shift_Del	DEL	ENST00000264716.4	hg19	CCDS1766.1																																																																																			.	.		0.632	FOSL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215116.2	NM_005253	
RTCB	51493	hgsc.bcm.edu	37	22	32784009	32784009	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr22:32784009delT	ENST00000216038.5	-	12	1586	c.1488delA	c.(1486-1488)aaafs	p.K496fs	RTCB_ENST00000451746.2_3'UTR|RP1-149A16.17_ENST00000444848.1_lincRNA	NM_014306.4	NP_055121.1			RNA 2',3'-cyclic phosphate and 5'-OH ligase																		TTGGTCTCAGTTTAATGGCTT	0.468																																					p.L497X		Atlas-INDEL	.											.	C22orf28	43	.	0			c.1489delC						.						210.0	173.0	186.0					22																	32784009		2203	4300	6503	SO:0001589	frameshift_variant	51493	exon12			.	BC016707	CCDS13905.1	22q12.3	2013-05-22	2013-05-22	2013-05-22	ENSG00000100220	ENSG00000100220	6.5.1.3		26935	protein-coding gene	gene with protein product	"""focal adhesion-associated protein"""	613901	"""chromosome 22 open reading frame 28"""	C22orf28		11042152, 21209330, 21311021	Standard	NM_014306		Approved	HSPC117, FAAP		Q9Y3I0	OTTHUMG00000030300	ENST00000216038.5:c.1488delA	chr22.hg19:g.32784009delT	ENSP00000216038:p.Lys496fs	191.0	0.0		198.0	12.0	NM_014306		Frame_Shift_Del	DEL	ENST00000216038.5	hg19	CCDS13905.1																																																																																			.	.		0.468	RTCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075188.3	NM_014306	
STPG1	90529	hgsc.bcm.edu	37	1	24696176	24696176	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:24696176delT	ENST00000374409.1	-	7	979	c.725delA	c.(724-726)aagfs	p.K242fs	STPG1_ENST00000468303.1_5'UTR|STPG1_ENST00000003583.8_Frame_Shift_Del_p.K195fs|STPG1_ENST00000440416.1_Frame_Shift_Del_p.K195fs|STPG1_ENST00000337248.4_Frame_Shift_Del_p.K242fs	NM_001199012.1	NP_001185941.1	Q5TH74	STPG1_HUMAN	sperm-tail PG-rich repeat containing 1	242					apoptotic process (GO:0006915)	cytoplasm (GO:0005737)|nucleus (GO:0005634)											GAAAAGAGTCTTTTTTGGAAC	0.438																																					p.K242fs		Atlas-INDEL	.											.	.	.	.	0			c.726delG						.						117.0	117.0	117.0					1																	24696176		2203	4300	6503	SO:0001589	frameshift_variant	90529	exon7			.	BC047705	CCDS253.1, CCDS55581.1	1p36.11	2012-10-31	2012-07-30	2012-07-30	ENSG00000001460	ENSG00000001460			28070	protein-coding gene	gene with protein product	"""O6-methylguanine-induced apoptosis 2"""	615826	"""chromosome 1 open reading frame 201"""	C1orf201		23028632	Standard	NM_001199012		Approved	FLJ33340, MAPO2	uc001bjc.3	Q5TH74	OTTHUMG00000003297	ENST00000374409.1:c.725delA	chr1.hg19:g.24696176delT	ENSP00000363530:p.Lys242fs	107.0	0.0		157.0	10.0	NM_001199012	Q49AP0|Q6P3R4|Q86VU9|Q8WVQ3	Frame_Shift_Del	DEL	ENST00000374409.1	hg19	CCDS55581.1																																																																																			.	.		0.438	STPG1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009172.1	NM_178122	
SDC3	9672	hgsc.bcm.edu	37	1	31351530	31351530	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:31351530delC	ENST00000339394.6	-	2	370	c.196delG	c.(196-198)gatfs	p.D68fs	SDC3_ENST00000471567.1_5'UTR|SDC3_ENST00000336798.7_5'UTR	NM_014654.3	NP_055469.3	O75056	SDC3_HUMAN	syndecan 3	68					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(5)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Myeloproliferative disorder(586;0.0393)|Colorectal(325;0.0466)|all_neural(195;0.0966)|Ovarian(437;0.127)|Medulloblastoma(700;0.151)		STAD - Stomach adenocarcinoma(196;0.0197)|READ - Rectum adenocarcinoma(331;0.0649)		GAGTCATCATCCCCAGAGCCC	0.632																																					p.D66fs		Atlas-INDEL	.											.	SDC3	45	.	0			c.197delA						.						134.0	119.0	124.0					1																	31351530		2203	4300	6503	SO:0001589	frameshift_variant	9672	exon2			.	AF248634	CCDS30661.1	1p35.2	2013-09-19	2007-02-15		ENSG00000162512	ENSG00000162512		"""Proteoglycans / Cell Surface : Syndecans"""	10660	protein-coding gene	gene with protein product	"""syndecan proteoglycan 3"""	186357	"""syndecan 3 (N-syndecan)"""			1556152, 11527150	Standard	NM_014654		Approved	N-syndecan, SYND3	uc001bse.2	O75056	OTTHUMG00000043646	ENST00000339394.6:c.196delG	chr1.hg19:g.31351530delC	ENSP00000344468:p.Asp68fs	141.0	0.0		161.0	10.0	NM_014654	Q5T1Z6|Q5T1Z7|Q96CT3|Q96PR8	Frame_Shift_Del	DEL	ENST00000339394.6	hg19	CCDS30661.1																																																																																			.	.		0.632	SDC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102017.1	NM_014654	
APOA2	336	hgsc.bcm.edu	37	1	161192790	161192790	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:161192790delA	ENST00000367990.3	-	3	160	c.103delT	c.(103-105)tctfs	p.S35fs	APOA2_ENST00000470459.2_Frame_Shift_Del_p.S35fs|APOA2_ENST00000464492.1_Frame_Shift_Del_p.S68fs|APOA2_ENST00000491350.1_Intron|APOA2_ENST00000468465.1_Intron|APOA2_ENST00000463812.1_5'UTR	NM_001643.1	NP_001634.1	P02652	APOA2_HUMAN	apolipoprotein A-II	35	O-glycosylated at one site.				acute inflammatory response (GO:0002526)|cellular lipid metabolic process (GO:0044255)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|diacylglycerol catabolic process (GO:0046340)|high-density lipoprotein particle assembly (GO:0034380)|high-density lipoprotein particle clearance (GO:0034384)|high-density lipoprotein particle remodeling (GO:0034375)|lipoprotein metabolic process (GO:0042157)|low-density lipoprotein particle remodeling (GO:0034374)|negative regulation of cholesterol import (GO:0060621)|negative regulation of cholesterol transport (GO:0032375)|negative regulation of cholesterol transporter activity (GO:0060695)|negative regulation of cytokine secretion involved in immune response (GO:0002740)|negative regulation of lipase activity (GO:0060192)|negative regulation of lipid catabolic process (GO:0050995)|negative regulation of very-low-density lipoprotein particle remodeling (GO:0010903)|organ regeneration (GO:0031100)|peptidyl-methionine modification (GO:0018206)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid catabolic process (GO:0009395)|phospholipid efflux (GO:0033700)|phototransduction, visible light (GO:0007603)|positive regulation of catalytic activity (GO:0043085)|positive regulation of cholesterol esterification (GO:0010873)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|positive regulation of lipid catabolic process (GO:0050996)|protein folding (GO:0006457)|protein oxidation (GO:0018158)|regulation of intestinal cholesterol absorption (GO:0030300)|regulation of protein stability (GO:0031647)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to glucocorticoid (GO:0051384)|response to glucose (GO:0009749)|retinoid metabolic process (GO:0001523)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)|triglyceride metabolic process (GO:0006641)|triglyceride-rich lipoprotein particle remodeling (GO:0034370)|viral process (GO:0016032)	blood microparticle (GO:0072562)|chylomicron (GO:0042627)|cytosol (GO:0005829)|early endosome (GO:0005769)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)|spherical high-density lipoprotein particle (GO:0034366)|very-low-density lipoprotein particle (GO:0034361)	apolipoprotein receptor binding (GO:0034190)|cholesterol binding (GO:0015485)|cholesterol transporter activity (GO:0017127)|high-density lipoprotein particle binding (GO:0008035)|high-density lipoprotein particle receptor binding (GO:0070653)|lipase inhibitor activity (GO:0055102)|lipid binding (GO:0008289)|lipid transporter activity (GO:0005319)|phosphatidylcholine binding (GO:0031210)|phosphatidylcholine-sterol O-acyltransferase activator activity (GO:0060228)|phospholipid binding (GO:0005543)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			endometrium(1)|large_intestine(1)|lung(2)|skin(2)	6	all_cancers(52;1.86e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00376)			AAGTACTGAGAAACCAGGCTC	0.542																																					p.S35fs		Atlas-INDEL	.											.	APOA2	12	.	0			c.104delC						.						124.0	116.0	119.0					1																	161192790		2203	4300	6503	SO:0001589	frameshift_variant	336	exon3			.		CCDS1226.1	1q23.3	2013-01-24			ENSG00000158874	ENSG00000158874		"""Apolipoproteins"""	601	protein-coding gene	gene with protein product		107670				2415515	Standard	NM_001643		Approved		uc001fzc.1	P02652	OTTHUMG00000034346	ENST00000367990.3:c.103delT	chr1.hg19:g.161192790delA	ENSP00000356969:p.Ser35fs	89.0	0.0		161.0	10.0	NM_001643	B2R524	Frame_Shift_Del	DEL	ENST00000367990.3	hg19	CCDS1226.1																																																																																			.	.		0.542	APOA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083037.1	NM_001643	
ANKRD12	23253	hgsc.bcm.edu	37	18	9279637	9279637	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr18:9279637delT	ENST00000262126.4	+	12	6238	c.5998delT	c.(5998-6000)ttafs	p.L2000fs	ANKRD12_ENST00000383440.2_Frame_Shift_Del_p.L1977fs|ANKRD12_ENST00000400020.3_Frame_Shift_Del_p.L1977fs|snoU13_ENST00000459594.1_RNA	NM_015208.4	NP_056023.3	Q6UB98	ANR12_HUMAN	ankyrin repeat domain 12	2000						cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|breast(3)|central_nervous_system(2)|endometrium(8)|kidney(2)|large_intestine(20)|lung(18)|ovary(3)|pancreas(1)|prostate(4)|skin(1)|urinary_tract(2)	65						ATTTGACAAATTAAAGGTATG	0.333																																					p.K1999fs		Atlas-INDEL	.											.	ANKRD12	167	.	0			c.5997delA						.						94.0	101.0	99.0					18																	9279637		2203	4299	6502	SO:0001589	frameshift_variant	23253	exon12			.	AY373757	CCDS11843.1, CCDS42411.1	18p11.22	2013-01-10			ENSG00000101745	ENSG00000101745		"""Ankyrin repeat domain containing"""	29135	protein-coding gene	gene with protein product		610616				10048485	Standard	NM_001204056		Approved	KIAA0874, FLJ20053, GAC-1	uc002knv.3	Q6UB98	OTTHUMG00000131595	ENST00000262126.4:c.5998delT	chr18.hg19:g.9279637delT	ENSP00000262126:p.Leu2000fs	145.0	0.0		180.0	12.0	NM_015208	O94951|Q658K1|Q6QMF7|Q9H231|Q9H784	Frame_Shift_Del	DEL	ENST00000262126.4	hg19	CCDS11843.1																																																																																			.	.		0.333	ANKRD12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254478.2	NM_015208	
KLHL14	57565	hgsc.bcm.edu	37	18	30349862	30349862	+	Frame_Shift_Del	DEL	G	G	-	rs147661052		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr18:30349862delG	ENST00000359358.4	-	2	1131	c.693delC	c.(691-693)cccfs	p.P231fs	AC012123.1_ENST00000426194.1_Frame_Shift_Del_p.T30fs|KLHL14_ENST00000358095.4_Frame_Shift_Del_p.P231fs	NM_020805.1	NP_065856.1	Q9P2G3	KLH14_HUMAN	kelch-like family member 14	231	BACK.					endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)				breast(3)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(20)|ovary(2)	31						CCGACTCCACGGGGGGCGGCA	0.642																																					p.V232fs		Atlas-INDEL	.											.	KLHL14	92	.	0			c.694delG						.						45.0	38.0	40.0					18																	30349862		2203	4300	6503	SO:0001589	frameshift_variant	57565	exon2			.	AB037805	CCDS32813.1	18q12.1	2013-10-15	2013-01-30		ENSG00000197705	ENSG00000197705		"""Kelch-like"", ""BTB/POZ domain containing"""	29266	protein-coding gene	gene with protein product	"""printor"""	613772	"""kelch-like 14 (Drosophila)"""			10718198, 19535332	Standard	NM_020805		Approved	KIAA1384	uc002kxm.1	Q9P2G3	OTTHUMG00000179819	ENST00000359358.4:c.693delC	chr18.hg19:g.30349862delG	ENSP00000352314:p.Pro231fs	159.0	0.0		191.0	12.0	NM_020805	A6NNW1|B4DHA0|Q8WU41	Frame_Shift_Del	DEL	ENST00000359358.4	hg19	CCDS32813.1																																																																																			.	.		0.642	KLHL14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448376.1		
ATR	545	hgsc.bcm.edu	37	3	142281476	142281476	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:142281476delA	ENST00000350721.4	-	4	889	c.768delT	c.(766-768)tttfs	p.F256fs	ATR_ENST00000383101.3_Frame_Shift_Del_p.F256fs	NM_001184.3	NP_001175.2	Q13535	ATR_HUMAN	ATR serine/threonine kinase	256					cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|multicellular organismal development (GO:0007275)|negative regulation of DNA replication (GO:0008156)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|protein autophosphorylation (GO:0046777)|regulation of protein binding (GO:0043393)|replicative senescence (GO:0090399)|response to drug (GO:0042493)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|PML body (GO:0016605)|XY body (GO:0001741)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|MutLalpha complex binding (GO:0032405)|MutSalpha complex binding (GO:0032407)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(10)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|liver(2)|lung(45)|ovary(3)|skin(10)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(4)	122						CTCCAAGCTGAAAAAGTTCTG	0.373								Other conserved DNA damage response genes																													p.Q257fs		Atlas-INDEL	.											.	ATR	285	.	0			c.769delC						.						61.0	63.0	62.0					3																	142281476		2203	4300	6503	SO:0001589	frameshift_variant	545	exon4			.	U76308	CCDS3124.1	3q23	2014-06-17	2014-06-17		ENSG00000175054	ENSG00000175054			882	protein-coding gene	gene with protein product	"""MEC1, mitosis entry checkpoint 1, homolog (S. cerevisiae)"""	601215	"""ataxia telangiectasia and Rad3 related"""			8978690, 8610130	Standard	NM_001184		Approved	FRP1, SCKL, SCKL1, MEC1	uc003eux.4	Q13535	OTTHUMG00000159234	ENST00000350721.4:c.768delT	chr3.hg19:g.142281476delA	ENSP00000343741:p.Phe256fs	128.0	0.0		170.0	11.0	NM_001184	Q59HB2|Q7KYL3|Q93051|Q9BXK4	Frame_Shift_Del	DEL	ENST00000350721.4	hg19	CCDS3124.1																																																																																			.	.		0.373	ATR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353995.2	NM_001184	
OSBP	5007	hgsc.bcm.edu	37	11	59345771	59345771	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:59345771delT	ENST00000263847.1	-	12	2390	c.1911delA	c.(1909-1911)aaafs	p.K637fs		NM_002556.2	NP_002547.1	P22059	OSBP1_HUMAN	oxysterol binding protein	637					lipid transport (GO:0006869)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	oxysterol binding (GO:0008142)			NS(2)|breast(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	26		all_epithelial(135;0.000236)		BRCA - Breast invasive adenocarcinoma(625;0.00607)|LUSC - Lung squamous cell carcinoma(625;0.207)		CAAAGTGGACTTTTCCTGATG	0.488																																					p.V638fs		Atlas-INDEL	.											.	OSBP	57	.	0			c.1912delG						.						158.0	142.0	148.0					11																	59345771		2201	4295	6496	SO:0001589	frameshift_variant	5007	exon12			.	AF185696	CCDS7974.1	11q12-q13	2013-01-10			ENSG00000110048	ENSG00000110048		"""Oxysterol binding proteins"", ""Pleckstrin homology (PH) domain containing"""	8503	protein-coding gene	gene with protein product		167040					Standard	NM_002556		Approved	OSBP1	uc001noc.1	P22059	OTTHUMG00000167422	ENST00000263847.1:c.1911delA	chr11.hg19:g.59345771delT	ENSP00000263847:p.Lys637fs	212.0	0.0		235.0	15.0	NM_002556	Q6P524	Frame_Shift_Del	DEL	ENST00000263847.1	hg19	CCDS7974.1																																																																																			.	.		0.488	OSBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394555.1		
PDE7A	5150	hgsc.bcm.edu	37	8	66753692	66753692	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr8:66753692delG	ENST00000401827.3	-	1	495	c.52delC	c.(52-54)cagfs	p.Q18fs	CTD-2532N20.1_ENST00000607622.1_lincRNA|PDE7A_ENST00000396642.3_Frame_Shift_Del_p.Q18fs	NM_001242318.2	NP_001229247.1	Q13946	PDE7A_HUMAN	phosphodiesterase 7A	18					cAMP catabolic process (GO:0006198)|signal transduction (GO:0007165)	cytosol (GO:0005829)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|metal ion binding (GO:0046872)			large_intestine(5)|lung(3)|stomach(1)|urinary_tract(1)	10			Epithelial(68;0.0509)|BRCA - Breast invasive adenocarcinoma(89;0.111)|all cancers(69;0.168)|OV - Ovarian serous cystadenocarcinoma(28;0.238)		Caffeine(DB00201)|Dyphylline(DB00651)|Ketotifen(DB00920)	AGGACGTGCTGGGGGACCGGC	0.706																																					p.Q18fs		Atlas-INDEL	.											.	PDE7A	78	.	0			c.53delA						.						13.0	19.0	17.0					8																	66753692		1957	4152	6109	SO:0001589	frameshift_variant	5150	exon1			.	L12052	CCDS34901.1, CCDS56538.1	8q13	2008-03-18				ENSG00000205268	3.1.4.17	"""Phosphodiesterases"""	8791	protein-coding gene	gene with protein product		171885				8389765, 9521885	Standard	NM_001242318		Approved	HCP1	uc003xvq.3	Q13946		ENST00000401827.3:c.52delC	chr8.hg19:g.66753692delG	ENSP00000385632:p.Gln18fs	111.0	0.0		232.0	14.0	NM_001242318	A0AVH6|A8K436|A8K9G5|O15380|Q96T72	Frame_Shift_Del	DEL	ENST00000401827.3	hg19	CCDS56538.1																																																																																			.	.		0.706	PDE7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378905.1		
KIF21B	23046	hgsc.bcm.edu	37	1	200944033	200944033	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:200944033delG	ENST00000422435.2	-	34	4939	c.4623delC	c.(4621-4623)cccfs	p.P1541fs	KIF21B_ENST00000461742.2_Frame_Shift_Del_p.P1541fs|KIF21B_ENST00000360529.5_Frame_Shift_Del_p.P1528fs|KIF21B_ENST00000332129.2_Frame_Shift_Del_p.P1528fs	NM_001252100.1	NP_001239029.1	O75037	KI21B_HUMAN	kinesin family member 21B	1541					ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(4)|large_intestine(8)|liver(1)|lung(27)|ovary(3)|pancreas(1)|prostate(5)|skin(8)|stomach(2)|urinary_tract(2)	83						TGTGCGCATTGGGGATTTGCT	0.642																																					p.N1542fs		Atlas-INDEL	.											.	KIF21B	208	.	0			c.4624delA						.						68.0	71.0	70.0					1																	200944033		2203	4300	6503	SO:0001589	frameshift_variant	23046	exon34			.	BC031927	CCDS30965.1, CCDS58054.1, CCDS58055.1, CCDS58056.1	1q32.1	2013-01-10			ENSG00000116852	ENSG00000116852		"""Kinesins"", ""WD repeat domain containing"""	29442	protein-coding gene	gene with protein product		608322				9455484	Standard	NM_001252100		Approved	DKFZP434J212, KIAA0449	uc001gvs.2	O75037	OTTHUMG00000035787	ENST00000422435.2:c.4623delC	chr1.hg19:g.200944033delG	ENSP00000411831:p.Pro1541fs	110.0	0.0		164.0	10.0	NM_001252102	B2RP62|B7ZMI0|Q5T4J3	Frame_Shift_Del	DEL	ENST00000422435.2	hg19	CCDS58056.1																																																																																			.	.		0.642	KIF21B-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382635.1	XM_371332	
ZNF214	7761	hgsc.bcm.edu	37	11	7022374	7022374	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:7022374delT	ENST00000278314.4	-	3	855	c.540delA	c.(538-540)aaafs	p.K180fs	ZNF214_ENST00000536068.1_Frame_Shift_Del_p.K180fs|ZNF214_ENST00000531083.1_5'Flank	NM_013249.2	NP_037381.2	Q9UL59	ZN214_HUMAN	zinc finger protein 214	180					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(10)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	29				Epithelial(150;3.87e-08)|BRCA - Breast invasive adenocarcinoma(625;0.081)		GCTTCTGTTCTTTTTCCATGG	0.438																																					p.E181fs	Ovarian(22;251 657 736 21522 46864)	Atlas-INDEL	.											.	ZNF214	65	.	0			c.541delG						.						110.0	111.0	111.0					11																	7022374		2200	4294	6494	SO:0001589	frameshift_variant	7761	exon3			.	AF056617	CCDS31418.1	11p15.4	2013-01-08				ENSG00000149050		"""Zinc fingers, C2H2-type"", ""-"""	13006	protein-coding gene	gene with protein product		605015					Standard	NM_013249		Approved		uc001mfa.2	Q9UL59		ENST00000278314.4:c.540delA	chr11.hg19:g.7022374delT	ENSP00000278314:p.Lys180fs	83.0	0.0		134.0	10.0	NM_013249	B2R8Q1	Frame_Shift_Del	DEL	ENST00000278314.4	hg19	CCDS31418.1																																																																																			.	.		0.438	ZNF214-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385349.1		
HIST1H2AM	8336	hgsc.bcm.edu	37	6	27860701	27860701	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:27860701delT	ENST00000359611.2	-	1	262	c.227delA	c.(226-228)aagfs	p.K76fs	HIST1H3J_ENST00000479986.1_5'UTR|HIST1H2BO_ENST00000303806.4_5'Flank|HIST1H3J_ENST00000359303.2_5'Flank	NM_003514.2	NP_003505.1	P0C0S8	H2A1_HUMAN	histone cluster 1, H2am	76						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)			endometrium(3)|kidney(2)|large_intestine(1)|lung(6)|ovary(2)	14						GATGCGGGTCTTTTTGTTGTC	0.642																																					p.K76fs		Atlas-INDEL	.											HIST1H2AM,NS,carcinoma,0,1	HIST1H2AM	27	.	0			c.228delG						.						102.0	107.0	105.0					6																	27860701		2203	4300	6503	SO:0001589	frameshift_variant	8336	exon1			.	X57138	CCDS4639.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000233224	ENSG00000278677		"""Histones / Replication-dependent"""	4735	protein-coding gene	gene with protein product		602796	"""H2A histone family, member N"", ""histone 1, H2am"""	H2AFN		1768865, 9439656, 12408966	Standard	NM_003514		Approved	H2A/n, H2A.1	uc003nkb.1	P0C0S8	OTTHUMG00000014494	ENST00000359611.2:c.227delA	chr6.hg19:g.27860701delT	ENSP00000352627:p.Lys76fs	200.0	0.0		414.0	26.0	NM_003514	P02261|Q2M1R2|Q76PA6	Frame_Shift_Del	DEL	ENST00000359611.2	hg19	CCDS4639.1																																																																																			.	.		0.642	HIST1H2AM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040162.1	NM_003514	
HECTD1	25831	hgsc.bcm.edu	37	14	31617938	31617938	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:31617938delT	ENST00000399332.1	-	15	2973	c.2485delA	c.(2485-2487)acafs	p.T829fs	HECTD1_ENST00000553700.1_Frame_Shift_Del_p.T829fs	NM_015382.2	NP_056197.2	Q9ULT8	HECD1_HUMAN	HECT domain containing E3 ubiquitin protein ligase 1	829					neural tube closure (GO:0001843)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|metal ion binding (GO:0046872)|ubiquitin-protein transferase activity (GO:0004842)			breast(10)|endometrium(7)|kidney(5)|large_intestine(12)|lung(23)|ovary(4)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	70	Hepatocellular(127;0.0877)|Breast(36;0.176)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.111)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00617)		TTTTGCTTTGTTTTTTCTAAC	0.333																																					p.T829fs		Atlas-INDEL	.											.	HECTD1	159	.	0			c.2486delC						.						107.0	94.0	98.0					14																	31617938		1803	4068	5871	SO:0001589	frameshift_variant	25831	exon15			.	AB032957	CCDS41939.1	14q12	2013-01-10	2012-02-23		ENSG00000092148	ENSG00000092148		"""Ankyrin repeat domain containing"""	20157	protein-coding gene	gene with protein product			"""HECT domain containing 1"""			10574461	Standard	XM_005267502		Approved	KIAA1131	uc001wrc.1	Q9ULT8	OTTHUMG00000170670	ENST00000399332.1:c.2485delA	chr14.hg19:g.31617938delT	ENSP00000382269:p.Thr829fs	131.0	0.0		142.0	10.0	NM_015382	D3DS86|Q6P445|Q86VJ1|Q96F34|Q9UFZ7	Frame_Shift_Del	DEL	ENST00000399332.1	hg19	CCDS41939.1																																																																																			.	.		0.333	HECTD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409942.1		
MINK1	50488	hgsc.bcm.edu	37	17	4794826	4794826	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:4794826delC	ENST00000355280.6	+	16	2012	c.1816delC	c.(1816-1818)cccfs	p.P606fs	MINK1_ENST00000453408.3_Frame_Shift_Del_p.P586fs|MINK1_ENST00000347992.7_Frame_Shift_Del_p.P606fs	NM_001024937.3|NM_015716.4|NM_153827.4	NP_001020108.1|NP_056531.1|NP_722549.2			misshapen-like kinase 1											central_nervous_system(2)|large_intestine(1)|lung(1)|skin(1)|stomach(1)	6						GCAGGACCAGCCCACCCGAAA	0.677																																					p.Q605fs		Atlas-INDEL	.											.	MINK1	110	.	0			c.1815delG						.						39.0	52.0	48.0					17																	4794826		2083	4211	6294	SO:0001589	frameshift_variant	50488	exon16			.	AY775058	CCDS45588.1, CCDS45589.1, CCDS45590.1	17p13.2	2011-04-14	2010-06-24		ENSG00000141503	ENSG00000141503			17565	protein-coding gene	gene with protein product	"""misshapen/NIK-related kinase"""	609426	"""misshapen-like kinase 1 (zebrafish)"""			10708748, 12087176	Standard	NM_015716		Approved	B55, MINK, ZC3, MAP4K6, YSK2	uc010vsl.2	Q8N4C8		ENST00000355280.6:c.1816delC	chr17.hg19:g.4794826delC	ENSP00000347427:p.Pro606fs	176.0	0.0		153.0	10.0	NM_170663		Frame_Shift_Del	DEL	ENST00000355280.6	hg19	CCDS45588.1																																																																																			.	.		0.677	MINK1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439801.1	NM_015716	
RELA	5970	hgsc.bcm.edu	37	11	65422151	65422151	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:65422151delC	ENST00000406246.3	-	11	1615	c.1354delG	c.(1354-1356)gccfs	p.A452fs	RELA_ENST00000525693.1_3'UTR|RELA_ENST00000308639.9_Frame_Shift_Del_p.A449fs	NM_001243984.1|NM_001243985.1|NM_021975.3	NP_001230913.1|NP_001230914.1|NP_068810.3	Q04206	TF65_HUMAN	v-rel avian reticuloendotheliosis viral oncogene homolog A	452	Activation domain.				acetaldehyde metabolic process (GO:0006117)|aging (GO:0007568)|cellular defense response (GO:0006968)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to interleukin-1 (GO:0071347)|cellular response to interleukin-6 (GO:0071354)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to nicotine (GO:0071316)|cellular response to peptide hormone stimulus (GO:0071375)|cellular response to tumor necrosis factor (GO:0071356)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|Fc-epsilon receptor signaling pathway (GO:0038095)|hair follicle development (GO:0001942)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|liver development (GO:0001889)|membrane protein intracellular domain proteolysis (GO:0031293)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070431)|organ morphogenesis (GO:0009887)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|positive regulation of miRNA metabolic process (GO:2000630)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of Schwann cell differentiation (GO:0014040)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|regulation of inflammatory response (GO:0050727)|response to amino acid (GO:0043200)|response to cAMP (GO:0051591)|response to cobalamin (GO:0033590)|response to drug (GO:0042493)|response to insulin (GO:0032868)|response to interleukin-1 (GO:0070555)|response to mechanical stimulus (GO:0009612)|response to morphine (GO:0043278)|response to muramyl dipeptide (GO:0032495)|response to organic substance (GO:0010033)|response to progesterone (GO:0032570)|response to UV-B (GO:0010224)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|NF-kappaB binding (GO:0051059)|phosphate ion binding (GO:0042301)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|repressing transcription factor binding (GO:0070491)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(11)|ovary(1)|urinary_tract(1)	19						ccaagcaaggcccccaggtct	0.617																																					p.A452fs		Atlas-INDEL	.											.	RELA	44	.	0			c.1355delC						.						37.0	37.0	37.0					11																	65422151		2201	4297	6498	SO:0001589	frameshift_variant	5970	exon11			.	Z22951	CCDS31609.1, CCDS44651.1, CCDS73322.1	11q13	2013-07-09	2013-07-09		ENSG00000173039	ENSG00000173039			9955	protein-coding gene	gene with protein product		164014	"""nuclear factor of kappa light polypeptide gene enhancer in B-cells 3"""	NFKB3		2001591	Standard	NM_021975		Approved	p65	uc001ofg.3	Q04206	OTTHUMG00000166566	ENST00000406246.3:c.1354delG	chr11.hg19:g.65422151delC	ENSP00000384273:p.Ala452fs	84.0	0.0		119.0	10.0	NM_021975	Q6GTV1|Q6SLK1	Frame_Shift_Del	DEL	ENST00000406246.3	hg19	CCDS31609.1																																																																																			.	.		0.617	RELA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390457.2	NM_021975	
ITM2C	81618	hgsc.bcm.edu	37	2	231741644	231741644	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:231741644delC	ENST00000326427.6	+	4	649	c.523delC	c.(523-525)cccfs	p.P176fs	ITM2C_ENST00000492029.1_3'UTR|ITM2C_ENST00000326407.6_Intron|ITM2C_ENST00000335005.6_Frame_Shift_Del_p.P129fs|ITM2C_ENST00000409704.2_Frame_Shift_Del_p.P114fs	NM_030926.4	NP_112188.1	Q9NQX7	ITM2C_HUMAN	integral membrane protein 2C	176	BRICHOS. {ECO:0000255|PROSITE- ProRule:PRU00255}.				negative regulation of neuron projection development (GO:0010977)|neuron differentiation (GO:0030182)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|beta-amyloid binding (GO:0001540)	p.P176fs*9(1)		cervix(2)|lung(1)|ovary(1)|skin(1)	5		Renal(207;0.0112)|all_lung(227;0.0741)|all_hematologic(139;0.0748)|Acute lymphoblastic leukemia(138;0.167)|Lung NSC(271;0.204)		Epithelial(121;8.47e-12)|all cancers(144;3.44e-09)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.0142)		CATTGTGCTGCCCCCTCGCAA	0.582																																					p.L174fs		Atlas-INDEL	.											.	ITM2C	17	.	1	Deletion - Frameshift(1)	lung(1)	c.522delG						.						152.0	141.0	144.0					2																	231741644		2203	4300	6503	SO:0001589	frameshift_variant	81618	exon4			.	AF038953	CCDS2479.1, CCDS33395.1, CCDS33396.1, CCDS74665.1	2q37	2012-10-10			ENSG00000135916	ENSG00000135916		"""BRICHOS domain containing"""	6175	protein-coding gene	gene with protein product	"""BRICHOS domain containing 2C"""	609554				9653160	Standard	NM_030926		Approved	BRI3, E25, hRPC.1050_D_4, ITM3, BRICD2C	uc002vqz.3	Q9NQX7	OTTHUMG00000133219	ENST00000326427.6:c.523delC	chr2.hg19:g.231741644delC	ENSP00000322730:p.Pro176fs	124.0	0.0		178.0	11.0	NM_030926	B3KPG4|Q4G0A8|Q53H84|Q6IAE7|Q86VK5|Q8N288|Q8TAW0|Q9BUP8	Frame_Shift_Del	DEL	ENST00000326427.6	hg19	CCDS2479.1																																																																																			.	.		0.582	ITM2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256954.2	NM_030926	
GUSB	2990	hgsc.bcm.edu	37	7	65444761	65444761	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:65444761delG	ENST00000304895.4	-	3	664	c.534delC	c.(532-534)cccfs	p.P178fs	GUSB_ENST00000345660.6_Frame_Shift_Del_p.P178fs|GUSB_ENST00000476486.1_Intron|GUSB_ENST00000421103.1_Intron	NM_000181.3	NP_000172.2	P08236	BGLR_HUMAN	glucuronidase, beta	178					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)	beta-glucuronidase activity (GO:0004566)	p.T179fs*13(1)		breast(1)|cervix(2)|kidney(2)|large_intestine(4)|lung(10)|skin(1)	20						GCAGGGTGGTGGGGGTGAGTG	0.627																																					p.T179fs		Atlas-INDEL	.											.,1	GUSB	52	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.535delA						.						180.0	181.0	181.0					7																	65444761		2203	4300	6503	SO:0001589	frameshift_variant	2990	exon3			.	M15182	CCDS5530.1, CCDS64665.1	7q11.21	2012-10-02			ENSG00000169919	ENSG00000169919	3.2.1.31		4696	protein-coding gene	gene with protein product		611499				3468507	Standard	NM_000181		Approved		uc003tun.3	P08236	OTTHUMG00000023735	ENST00000304895.4:c.534delC	chr7.hg19:g.65444761delG	ENSP00000302728:p.Pro178fs	80.0	0.0		121.0	10.0	NM_000181	B4E1F6|E9PCV0|Q549U0|Q96CL9	Frame_Shift_Del	DEL	ENST00000304895.4	hg19	CCDS5530.1																																																																																			.	.		0.627	GUSB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251637.3	NM_000181	
EFCAB13	124989	hgsc.bcm.edu	37	17	45468832	45468832	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:45468832delA	ENST00000331493.2	+	15	2023	c.1612delA	c.(1612-1614)aaafs	p.K538fs	EFCAB13_ENST00000517484.1_Frame_Shift_Del_p.K442fs	NM_152347.4	NP_689560.3	Q8IY85	EFC13_HUMAN	EF-hand calcium binding domain 13	538	EF-hand 2.					cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)										AGCCATTGATAAAATTAAAGA	0.279																																					p.D537fs		Atlas-INDEL	.											.	.	.	.	0			c.1611delT						.						47.0	51.0	49.0					17																	45468832		2203	4299	6502	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.1612delA	chr17.hg19:g.45468832delA	ENSP00000332111:p.Lys538fs	134.0	0.0		161.0	10.0	NM_152347	G3V128|Q49AG9	Frame_Shift_Del	DEL	ENST00000331493.2	hg19	CCDS11512.1																																																																																			.	.		0.279	EFCAB13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380147.4	NM_152347	
PDGFA	5154	hgsc.bcm.edu	37	7	540104	540104	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:540104delT	ENST00000354513.5	-	6	1005	c.613delA	c.(613-615)agafs	p.R205fs	PDGFA_ENST00000402802.3_Intron	NM_002607.5	NP_002598.4	P04085	PDGFA_HUMAN	platelet-derived growth factor alpha polypeptide	205					actin cytoskeleton organization (GO:0030036)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cell activation (GO:0001775)|cell projection assembly (GO:0030031)|cell-cell signaling (GO:0007267)|embryo development (GO:0009790)|epidermal growth factor receptor signaling pathway (GO:0007173)|extracellular matrix organization (GO:0030198)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hair follicle development (GO:0001942)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|lung alveolus development (GO:0048286)|negative chemotaxis (GO:0050919)|negative regulation of phosphatidylinositol biosynthetic process (GO:0010512)|negative regulation of platelet activation (GO:0010544)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA replication (GO:0045740)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway (GO:0035793)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein autophosphorylation (GO:0031954)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of branching involved in salivary gland morphogenesis by epithelial-mesenchymal signaling (GO:0060683)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|regulation of smooth muscle cell migration (GO:0014910)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to hypoxia (GO:0001666)|response to inorganic substance (GO:0010035)|response to retinoic acid (GO:0032526)|response to wounding (GO:0009611)|skin development (GO:0043588)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	cell surface (GO:0009986)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi membrane (GO:0000139)|microvillus (GO:0005902)|platelet alpha granule lumen (GO:0031093)	collagen binding (GO:0005518)|growth factor activity (GO:0008083)|platelet-derived growth factor binding (GO:0048407)|platelet-derived growth factor receptor binding (GO:0005161)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	16		Ovarian(82;0.0112)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|Epithelial(4;1.1e-17)|OV - Ovarian serous cystadenocarcinoma(56;1.7e-17)|all cancers(6;4.89e-15)		AACCTTTTTCTTTTCCGTTTT	0.557																																					p.R205fs		Atlas-INDEL	.											.	PDGFA	34	.	0			c.614delG						.						226.0	176.0	193.0					7																	540104		2203	4296	6499	SO:0001589	frameshift_variant	5154	exon6			.		CCDS34578.1, CCDS47524.1	7p22	2008-07-18			ENSG00000197461	ENSG00000197461			8799	protein-coding gene	gene with protein product	"""PDGF A-chain"", ""platelet-derived growth factor alpha chain"""	173430				1505216, 2536956	Standard	NM_002607		Approved	PDGF1, PDGF-A	uc003sir.3	P04085	OTTHUMG00000151412	ENST00000354513.5:c.613delA	chr7.hg19:g.540104delT	ENSP00000346508:p.Arg205fs	133.0	0.0		165.0	11.0	NM_002607	B5BU73	Frame_Shift_Del	DEL	ENST00000354513.5	hg19	CCDS34578.1																																																																																			.	.		0.557	PDGFA-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000322534.1		
ECM1	1893	hgsc.bcm.edu	37	1	150484838	150484838	+	Frame_Shift_Del	DEL	C	C	-	rs202156901		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:150484838delC	ENST00000369047.4	+	8	1219	c.1094delC	c.(1093-1095)accfs	p.T365fs	ECM1_ENST00000470432.1_3'UTR|ECM1_ENST00000346569.6_Frame_Shift_Del_p.T240fs|ECM1_ENST00000369049.4_Frame_Shift_Del_p.T392fs	NM_004425.3	NP_004416.2	Q16610	ECM1_HUMAN	extracellular matrix protein 1	365	2 X approximate repeats.				angiogenesis (GO:0001525)|biomineral tissue development (GO:0031214)|inflammatory response (GO:0006954)|negative regulation of bone mineralization (GO:0030502)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|negative regulation of peptidase activity (GO:0010466)|ossification (GO:0001503)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of T cell migration (GO:2000404)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of type 2 immune response (GO:0002828)|signal transduction (GO:0007165)	extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	enzyme binding (GO:0019899)|laminin binding (GO:0043236)|protease binding (GO:0002020)|protein C-terminus binding (GO:0008022)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(1)|lung(7)|ovary(2)|prostate(3)|urinary_tract(1)	22	all_cancers(9;3.13e-53)|all_epithelial(9;3.74e-43)|all_lung(15;2.43e-34)|Lung NSC(24;8.86e-31)|Breast(34;0.000326)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0757)|all cancers(9;1.29e-21)|BRCA - Breast invasive adenocarcinoma(12;0.000734)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206)			TGGGAGGATACCCTTGACAAA	0.567																																					p.T392fs	Melanoma(156;1696 2560 11093 19685)	Atlas-INDEL	.											.	ECM1	96	.	0			c.1174delA						.						88.0	77.0	81.0					1																	150484838		2203	4300	6503	SO:0001589	frameshift_variant	1893	exon8			.	U68186	CCDS953.1, CCDS954.1, CCDS55632.1	1q21	2008-02-05			ENSG00000143369	ENSG00000143369			3153	protein-coding gene	gene with protein product		602201				9367673, 9501329	Standard	NM_004425		Approved		uc001eus.3	Q16610	OTTHUMG00000012806	ENST00000369047.4:c.1094delC	chr1.hg19:g.150484838delC	ENSP00000358043:p.Thr365fs	99.0	0.0		226.0	14.0	NM_001202858	A8K8S0|B4DW49|B4DY60|O43266|Q5T5G4|Q5T5G5|Q5T5G6|Q8IZ60	Frame_Shift_Del	DEL	ENST00000369047.4	hg19	CCDS953.1																																																																																			.	.		0.567	ECM1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000035832.2	NM_004425	
AASS	10157	hgsc.bcm.edu	37	7	121758669	121758669	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:121758669delA	ENST00000393376.1	-	4	583	c.488delT	c.(487-489)ttafs	p.L163fs	AASS_ENST00000417368.2_Frame_Shift_Del_p.L163fs|AASS_ENST00000473553.1_Intron			Q9UDR5	AASS_HUMAN	aminoadipate-semialdehyde synthase	163	Lysine-ketoglutarate reductase.				cellular nitrogen compound metabolic process (GO:0034641)|L-lysine catabolic process to acetyl-CoA via saccharopine (GO:0033512)|lysine catabolic process (GO:0006554)|protein tetramerization (GO:0051262)|small molecule metabolic process (GO:0044281)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	saccharopine dehydrogenase (NAD+, L-glutamate-forming) activity (GO:0047131)|saccharopine dehydrogenase (NADP+, L-lysine-forming) activity (GO:0047130)			autonomic_ganglia(1)|breast(2)|endometrium(3)|kidney(6)|large_intestine(12)|lung(27)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	54						CATTCCATGTAAAATGTTGAT	0.373																																					p.L163fs		Atlas-INDEL	.											.	AASS	123	.	0			c.489delA						.						78.0	71.0	74.0					7																	121758669		2203	4300	6503	SO:0001589	frameshift_variant	10157	exon5			.	AF229180	CCDS5783.1	7q31.3	2010-12-14			ENSG00000008311	ENSG00000008311			17366	protein-coding gene	gene with protein product		605113				10775527	Standard	NM_005763		Approved	LORSDH, LKRSDH	uc003vkb.3	Q9UDR5	OTTHUMG00000157058	ENST00000393376.1:c.488delT	chr7.hg19:g.121758669delA	ENSP00000377040:p.Leu163fs	167.0	0.0		203.0	14.0	NM_005763	O95462	Frame_Shift_Del	DEL	ENST00000393376.1	hg19	CCDS5783.1																																																																																			.	.		0.373	AASS-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347300.1	NM_005763	
SAMD7	344658	hgsc.bcm.edu	37	3	169644580	169644580	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:169644580delG	ENST00000428432.2	+	6	919	c.530delG	c.(529-531)tggfs	p.W177fs	SAMD7_ENST00000335556.3_Frame_Shift_Del_p.W177fs	NM_182610.2	NP_872416.1	Q7Z3H4	SAMD7_HUMAN	sterile alpha motif domain containing 7	177										NS(1)|biliary_tract(1)|breast(1)|kidney(1)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	31	all_cancers(22;1.55e-22)|all_epithelial(15;2.41e-27)|all_lung(20;3.52e-17)|Lung NSC(18;1.44e-16)|Ovarian(172;0.000337)|Breast(254;0.169)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.0106)			GAGGAGAGCTGGGGGCAGAGA	0.493																																					p.W177fs		Atlas-INDEL	.											.	SAMD7	69	.	0			c.529delT						.						62.0	65.0	64.0					3																	169644580		2203	4300	6503	SO:0001589	frameshift_variant	344658	exon6			.	BX537903	CCDS3209.1	3q26.31	2013-01-10			ENSG00000187033	ENSG00000187033		"""Sterile alpha motif (SAM) domain containing"""	25394	protein-coding gene	gene with protein product							Standard	NM_182610		Approved	DKFZp686E1583	uc003fgd.3	Q7Z3H4	OTTHUMG00000158730	ENST00000428432.2:c.530delG	chr3.hg19:g.169644580delG	ENSP00000391299:p.Trp177fs	140.0	0.0		169.0	12.0	NM_182610		Frame_Shift_Del	DEL	ENST00000428432.2	hg19	CCDS3209.1																																																																																			.	.		0.493	SAMD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351959.1	NM_182610	
CHD5	26038	hgsc.bcm.edu	37	1	6202277	6202277	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:6202277delC	ENST00000262450.3	-	15	2446	c.2347delG	c.(2347-2349)gacfs	p.D783fs	CHD5_ENST00000378021.1_5'UTR	NM_015557.2	NP_056372.1	O00258	WRB_HUMAN	chromodomain helicase DNA binding protein 5	0					tail-anchored membrane protein insertion into ER membrane (GO:0071816)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(3)|central_nervous_system(3)|liver(1)|lung(1)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	16	Ovarian(185;0.0634)	all_cancers(23;5.36e-32)|all_epithelial(116;2.32e-17)|all_neural(13;3.68e-06)|all_lung(118;3.94e-06)|all_hematologic(16;2.39e-05)|Lung NSC(185;5.33e-05)|Acute lymphoblastic leukemia(12;0.000372)|Glioma(11;0.00127)|Renal(390;0.00188)|Colorectal(325;0.00342)|Breast(487;0.00373)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.15)		Epithelial(90;3.08e-37)|GBM - Glioblastoma multiforme(13;1.36e-31)|OV - Ovarian serous cystadenocarcinoma(86;7.7e-19)|Colorectal(212;9.97e-08)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(185;6.16e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00109)|BRCA - Breast invasive adenocarcinoma(365;0.0012)|STAD - Stomach adenocarcinoma(132;0.00346)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.193)		CTCTCCTTGTCCCCCGTGTAG	0.582																																					p.D783fs		Atlas-INDEL	.											.	CHD5	267	.	0			c.2348delA						.						126.0	119.0	121.0					1																	6202277		2203	4300	6503	SO:0001589	frameshift_variant	26038	exon15			.	AF425231	CCDS57.1	1p36.3	2013-01-28			ENSG00000116254	ENSG00000116254		"""Zinc fingers, PHD-type"""	16816	protein-coding gene	gene with protein product		610771				11889561, 12592387	Standard	NM_015557		Approved		uc001amb.2	Q8TDI0	OTTHUMG00000000952	ENST00000262450.3:c.2347delG	chr1.hg19:g.6202277delC	ENSP00000262450:p.Asp783fs	148.0	0.0		158.0	10.0	NM_015557	A8KAP8|A8MQ44|D3DSH9|O60740	Frame_Shift_Del	DEL	ENST00000262450.3	hg19	CCDS57.1																																																																																			.	.		0.582	CHD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002823.2	NM_015557	
ARAP1	116985	hgsc.bcm.edu	37	11	72437746	72437746	+	Frame_Shift_Del	DEL	G	G	-	rs372690916	byFrequency	TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:72437746delG	ENST00000393609.3	-	3	630	c.428delC	c.(427-429)ccgfs	p.P143fs	ARAP1_ENST00000455638.2_Frame_Shift_Del_p.P143fs|ARAP1_ENST00000359373.5_Frame_Shift_Del_p.P143fs	NM_001040118.2	NP_001035207.1	Q96P48	ARAP1_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1	143					actin filament reorganization involved in cell cycle (GO:0030037)|negative regulation of stress fiber assembly (GO:0051497)|positive regulation of Cdc42 GTPase activity (GO:0043089)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of receptor recycling (GO:0001921)|regulation of ARF GTPase activity (GO:0032312)|regulation of cell shape (GO:0008360)|regulation of cellular component movement (GO:0051270)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270)			cervix(2)|endometrium(2)|large_intestine(10)|lung(8)|ovary(1)|skin(3)|urinary_tract(1)	27						AGCAGGCAGCGGGGGCAGCAC	0.721																																					p.P143fs	Ovarian(102;1198 1520 13195 17913 37529)	Atlas-INDEL	.											.	ARAP1	168	.	0			c.429delG						.						4.0	6.0	5.0					11																	72437746		1930	4038	5968	SO:0001589	frameshift_variant	116985	exon3			.	AF411983	CCDS8217.2, CCDS41687.1, CCDS44671.1	11q13.3	2013-01-11	2008-09-22	2008-09-22	ENSG00000186635	ENSG00000186635		"""ADP-ribosylation factor GTPase activating proteins"", ""Sterile alpha motif (SAM) domain containing"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	16925	protein-coding gene	gene with protein product		606646	"""centaurin, delta 2"""	CENTD2			Standard	NM_001040118		Approved		uc001osu.3	Q96P48	OTTHUMG00000157102	ENST00000393609.3:c.428delC	chr11.hg19:g.72437746delG	ENSP00000377233:p.Pro143fs	86.0	0.0		135.0	11.0	NM_001040118	A3KLL7|B2RTS2|O94879|Q4LDD5|Q59FI7|Q6PHS3|Q8WU51|Q96HP6|Q96L71	Frame_Shift_Del	DEL	ENST00000393609.3	hg19	CCDS41687.1																																																																																			.	.		0.721	ARAP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347428.1	NM_001040118	
COL6A1	1291	hgsc.bcm.edu	37	21	47418082	47418082	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr21:47418082delC	ENST00000361866.3	+	23	1686	c.1572delC	c.(1570-1572)ttcfs	p.F524fs		NM_001848.2	NP_001839.2	P12109	CO6A1_HUMAN	collagen, type VI, alpha 1	524	Triple-helical region.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|osteoblast differentiation (GO:0001649)|protein heterotrimerization (GO:0070208)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|protein complex (GO:0043234)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)	platelet-derived growth factor binding (GO:0048407)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(18)|ovary(1)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	33	all_hematologic(128;0.24)			Colorectal(79;0.0265)|READ - Rectum adenocarcinoma(84;0.0649)		TCCCCGGCTTCCCCGTAAGTG	0.682																																					p.F524fs		Atlas-INDEL	.											.	COL6A1	101	.	0			c.1571delT						.						23.0	29.0	27.0					21																	47418082		2197	4296	6493	SO:0001589	frameshift_variant	1291	exon23			.	M20776	CCDS13727.1	21q22.3	2014-09-17			ENSG00000142156	ENSG00000142156		"""Collagens"""	2211	protein-coding gene	gene with protein product		120220					Standard	XM_006723964		Approved		uc002zhu.1	P12109	OTTHUMG00000090440	ENST00000361866.3:c.1572delC	chr21.hg19:g.47418082delC	ENSP00000355180:p.Phe524fs	89.0	0.0		140.0	10.0	NM_001848	O00117|O00118|Q14040|Q14041|Q16258|Q7Z645|Q9BSA8	Frame_Shift_Del	DEL	ENST00000361866.3	hg19	CCDS13727.1																																																																																			.	.		0.682	COL6A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206877.1	NM_001848	
EP300	2033	hgsc.bcm.edu	37	22	41574679	41574679	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr22:41574679delC	ENST00000263253.7	+	31	8183	c.6964delC	c.(6964-6966)cccfs	p.P2323fs	RP1-85F18.6_ENST00000415054.1_RNA|RP1-85F18.5_ENST00000420537.1_RNA	NM_001429.3	NP_001420.2	Q09472	EP300_HUMAN	E1A binding protein p300	2323					apoptotic process (GO:0006915)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|circadian rhythm (GO:0007623)|G2/M transition of mitotic cell cycle (GO:0000086)|heart development (GO:0007507)|histone H2B acetylation (GO:0043969)|histone H4 acetylation (GO:0043967)|innate immune response (GO:0045087)|internal peptidyl-lysine acetylation (GO:0018393)|internal protein amino acid acetylation (GO:0006475)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|lung development (GO:0030324)|mitotic cell cycle (GO:0000278)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of protein binding (GO:0032092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of cell cycle (GO:0051726)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|regulation of tubulin deacetylation (GO:0090043)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|skeletal muscle tissue development (GO:0007519)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|activating transcription factor binding (GO:0033613)|androgen receptor binding (GO:0050681)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0004468)|nuclear hormone receptor binding (GO:0035257)|pre-mRNA intronic binding (GO:0097157)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transferase activity, transferring acyl groups (GO:0016746)|zinc ion binding (GO:0008270)			NS(2)|breast(11)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(31)|kidney(5)|large_intestine(31)|liver(2)|lung(33)|ovary(2)|pancreas(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(16)	171						ACAGTCCCAGCCCCCCCACTC	0.612			"""T,  N, F, Mis, O"""	"""MLL, RUNXBP2"""	"""colorectal, breast, pancreatic, AML, ALL, DLBCL"""				Rubinstein-Taybi syndrome																												p.Q2321fs		Atlas-INDEL	.		Rec	yes		22	22q13	2033	300 kd E1A-Binding protein gene		"""L, E"""	.	EP300	367	.	0			c.6963delG						.						87.0	91.0	90.0					22																	41574679		2203	4300	6503	SO:0001589	frameshift_variant	2033	exon31	Familial Cancer Database	Broad Thumb-Hallux syndrome	.	U01877	CCDS14010.1	22q13.2	2011-07-01			ENSG00000100393	ENSG00000100393		"""Chromatin-modifying enzymes / K-acetyltransferases"""	3373	protein-coding gene	gene with protein product	"""histone acetyltransferase p300"""	602700				7523245	Standard	NM_001429		Approved	p300, KAT3B	uc003azl.4	Q09472	OTTHUMG00000150937	ENST00000263253.7:c.6964delC	chr22.hg19:g.41574679delC	ENSP00000263253:p.Pro2323fs	116.0	0.0		154.0	11.0	NM_001429	B1AKC2	Frame_Shift_Del	DEL	ENST00000263253.7	hg19	CCDS14010.1																																																																																			.	.		0.612	EP300-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320600.1	NM_001429	
SF3B4	10262	hgsc.bcm.edu	37	1	149895562	149895562	+	Frame_Shift_Del	DEL	G	G	-	rs387907187		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:149895562delG	ENST00000271628.8	-	6	1731	c.1147delC	c.(1147-1149)catfs	p.H383fs		NM_005850.4	NP_005841.1	Q15427	SF3B4_HUMAN	splicing factor 3b, subunit 4, 49kDa	383					gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	nucleoplasm (GO:0005654)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.H383fs*>43(1)|p.H383fs*>42(1)		endometrium(2)|large_intestine(4)|lung(7)|ovary(2)|prostate(1)|skin(1)	17	Breast(34;0.0009)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.221)|STAD - Stomach adenocarcinoma(528;0.247)			GTGTATCCATGGGGGGGCATC	0.622																																					p.H383fs		Atlas-INDEL	.											.,1	SF3B4	37	.	2	Deletion - Frameshift(1)|Insertion - Frameshift(1)	large_intestine(2)	c.1148delA						.						19.0	23.0	21.0					1																	149895562		2203	4297	6500	SO:0001589	frameshift_variant	10262	exon6			.	L35013	CCDS72900.1	1q21.2	2013-02-12	2002-08-29		ENSG00000143368	ENSG00000143368		"""RNA binding motif (RRM) containing"""	10771	protein-coding gene	gene with protein product		605593	"""splicing factor 3b, subunit 4, 49kD"""			7958871	Standard	NM_005850		Approved	SAP49, SF3b49, Hsh49	uc001etk.2	Q15427	OTTHUMG00000012208	ENST00000271628.8:c.1147delC	chr1.hg19:g.149895562delG	ENSP00000271628:p.His383fs	86.0	0.0		180.0	11.0	NM_005850	Q5SZ63	Frame_Shift_Del	DEL	ENST00000271628.8	hg19	CCDS941.1																																																																																			.	.		0.622	SF3B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033753.1	NM_005850	
MTHFSD	64779	hgsc.bcm.edu	37	16	86565823	86565823	+	Frame_Shift_Del	DEL	C	C	-	rs142996375	byFrequency	TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:86565823delC	ENST00000360900.6	-	8	971	c.946delG	c.(946-948)gacfs	p.D316fs	MTHFSD_ENST00000381214.5_Frame_Shift_Del_p.D316fs|MTHFSD_ENST00000543303.2_Frame_Shift_Del_p.D315fs|MTHFSD_ENST00000322911.6_Frame_Shift_Del_p.D315fs|MTHFSD_ENST00000546093.1_Frame_Shift_Del_p.D153fs	NM_001159380.1	NP_001152852.1	Q2M296	MTHSD_HUMAN	methenyltetrahydrofolate synthetase domain containing	316	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.						nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(1)|large_intestine(3)|lung(6)|skin(1)	11						ACACGGGCGTCCCCGGGGAGG	0.677																																					p.D316fs		Atlas-INDEL	.											.	MTHFSD	52	.	0			c.947delA						.						11.0	14.0	13.0					16																	86565823		1873	4094	5967	SO:0001589	frameshift_variant	64779	exon8			.	AK023060	CCDS54047.1, CCDS54048.1, CCDS58490.1	16q24.1	2013-02-12				ENSG00000103248		"""RNA binding motif (RRM) containing"""	25778	protein-coding gene	gene with protein product						12477932	Standard	NM_022764		Approved	FLJ12998	uc010vor.2	Q2M296		ENST00000360900.6:c.946delG	chr16.hg19:g.86565823delC	ENSP00000354152:p.Asp316fs	106.0	0.0		159.0	11.0	NM_001159377	A8MQ77|B7ZLC0|B7ZLC2|D3DUM9|E9PAM1|Q9H878|Q9H954	Frame_Shift_Del	DEL	ENST00000360900.6	hg19	CCDS54047.1																																																																																			.	.		0.677	MTHFSD-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000432182.1	NM_022764	
KLHDC4	54758	hgsc.bcm.edu	37	16	87788891	87788891	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:87788891delA	ENST00000270583.5	-	4	336	c.278delT	c.(277-279)ttgfs	p.L93fs	KLHDC4_ENST00000353170.5_Frame_Shift_Del_p.L36fs|KLHDC4_ENST00000347925.5_Frame_Shift_Del_p.L93fs	NM_017566.3	NP_060036.2	Q8TBB5	KLDC4_HUMAN	kelch domain containing 4	93										breast(2)|endometrium(3)|lung(10)|pancreas(2)|prostate(1)|skin(1)|urinary_tract(2)	21				BRCA - Breast invasive adenocarcinoma(80;0.0283)		CTCGTTATACAAAAAAGTCTA	0.453																																					p.L93fs		Atlas-INDEL	.											.	KLHDC4	45	.	0			c.279delG						.						134.0	128.0	130.0					16																	87788891		2198	4300	6498	SO:0001589	frameshift_variant	54758	exon4			.	AK001742	CCDS10963.1, CCDS54050.1, CCDS54051.1	16q24	2008-02-05			ENSG00000104731	ENSG00000104731			25272	protein-coding gene	gene with protein product							Standard	NM_001184854		Approved	DKFZp434G0522	uc002fki.3	Q8TBB5	OTTHUMG00000137657	ENST00000270583.5:c.278delT	chr16.hg19:g.87788891delA	ENSP00000270583:p.Leu93fs	152.0	0.0		166.0	11.0	NM_001184856	D3DUN3|D3DUN4|D3DUN5|Q96F29|Q9BVN3	Frame_Shift_Del	DEL	ENST00000270583.5	hg19	CCDS10963.1																																																																																			.	.		0.453	KLHDC4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000269109.2	NM_017566	
MYO7B	4648	hgsc.bcm.edu	37	2	128384760	128384760	+	Splice_Site	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:128384760delC	ENST00000409816.2	+	31	4289	c.4257delC	c.(4255-4257)ggc>gg	p.G1419fs	MYO7B_ENST00000409090.1_Splice_Site_p.G272fs|RP11-286H15.1_ENST00000609697.1_RNA|MYO7B_ENST00000389524.4_Splice_Site_p.G1419fs|MYO7B_ENST00000428314.1_Splice_Site_p.G1419fs			Q6PIF6	MYO7B_HUMAN	myosin VIIB	1419	FERM 1. {ECO:0000255|PROSITE- ProRule:PRU00084}.					extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(46)|ovary(3)|pancreas(1)|prostate(3)|urinary_tract(1)	75	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0753)		CCTGGCCAGGCCCCCGCCTGC	0.612																																					p.G1419fs		Atlas-INDEL	.											.	MYO7B	359	.	0			c.4256delG						.						22.0	24.0	23.0					2																	128384760		1968	4142	6110	SO:0001630	splice_region_variant	4648	exon32			.		CCDS46405.1	2q21.1	2011-09-27			ENSG00000169994	ENSG00000169994		"""Myosins / Myosin superfamily : Class VII"""	7607	protein-coding gene	gene with protein product		606541				8022818, 8884266	Standard	NM_001080527		Approved		uc002top.3	Q6PIF6	OTTHUMG00000153419	ENST00000409816.2:c.4256-1C>-	chr2.hg19:g.128384760delC		131.0	0.0		156.0	10.0	NM_001080527	Q14786|Q8TEE1	Frame_Shift_Del	DEL	ENST00000409816.2	hg19	CCDS46405.1																																																																																			.	.		0.612	MYO7B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000331124.3	XM_291001	Frame_Shift_Del
SLC35A4	113829	hgsc.bcm.edu	37	5	139946770	139946770	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:139946770delG	ENST00000514199.1	+	2	1702	c.16delG	c.(16-18)gggfs	p.G7fs	APBB3_ENST00000412920.3_5'Flank|APBB3_ENST00000507279.1_Intron|APBB3_ENST00000356738.2_5'Flank|SLC35A4_ENST00000508770.1_3'UTR|APBB3_ENST00000358580.5_5'Flank|APBB3_ENST00000354402.5_5'Flank|SLC35A4_ENST00000323146.3_Frame_Shift_Del_p.G7fs|APBB3_ENST00000511201.2_5'Flank|APBB3_ENST00000357560.4_5'Flank|APBB3_ENST00000508496.2_5'Flank			Q96G79	S35A4_HUMAN	solute carrier family 35, member A4	7						Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	sugar:proton symporter activity (GO:0005351)			endometrium(4)|kidney(2)|large_intestine(3)|lung(4)	13			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGTAGAGGATGGGGGTATGCC	0.602																																					p.D5fs		Atlas-INDEL	.											.	SLC35A4	25	.	0			c.15delT						.						74.0	78.0	77.0					5																	139946770		2203	4300	6503	SO:0001589	frameshift_variant	113829	exon3			.	AJ420598	CCDS4231.1	5q31.3	2013-05-22			ENSG00000176087	ENSG00000176087		"""Solute carriers"""	20753	protein-coding gene	gene with protein product							Standard	NM_080670		Approved		uc003lgg.1	Q96G79	OTTHUMG00000129495	ENST00000514199.1:c.16delG	chr5.hg19:g.139946770delG	ENSP00000424566:p.Gly7fs	120.0	0.0		159.0	12.0	NM_080670	A8K013	Frame_Shift_Del	DEL	ENST00000514199.1	hg19	CCDS4231.1																																																																																			.	.		0.602	SLC35A4-004	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372815.1	NM_080670	
LRRC2	79442	hgsc.bcm.edu	37	3	46580564	46580564	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:46580564delT	ENST00000395905.3	-	4	853	c.461delA	c.(460-462)aacfs	p.N154fs	LRRC2_ENST00000296144.3_Frame_Shift_Del_p.N154fs	NM_024512.4	NP_078788.2	Q9BYS8	LRRC2_HUMAN	leucine rich repeat containing 2	154										breast(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)	17		Ovarian(412;0.0563)		OV - Ovarian serous cystadenocarcinoma(275;6.37e-05)|BRCA - Breast invasive adenocarcinoma(193;0.00133)|KIRC - Kidney renal clear cell carcinoma(197;0.0214)|Kidney(197;0.0254)		TGAGATTTGGTTTTTTGGCAG	0.438																																					p.N154fs		Atlas-INDEL	.											.	LRRC2	37	.	0			c.462delC						.						148.0	133.0	138.0					3																	46580564		2203	4300	6503	SO:0001589	frameshift_variant	79442	exon4			.	AJ308569	CCDS2741.1	3p21.3	2014-07-30	2003-11-19		ENSG00000163827	ENSG00000163827			14676	protein-coding gene	gene with protein product		607180	"""leucine-rich repeat-containing 2"""			11896456	Standard	NM_024512		Approved		uc010hji.3	Q9BYS8	OTTHUMG00000133479	ENST00000395905.3:c.461delA	chr3.hg19:g.46580564delT	ENSP00000379241:p.Asn154fs	118.0	0.0		162.0	10.0	NM_024512	B2RDQ7|Q96LT5	Frame_Shift_Del	DEL	ENST00000395905.3	hg19	CCDS2741.1																																																																																			.	.		0.438	LRRC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257375.2		
TMX3	54495	hgsc.bcm.edu	37	18	66367677	66367677	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr18:66367677delT	ENST00000299608.2	-	6	673	c.357delA	c.(355-357)aaafs	p.K119fs	TMX3_ENST00000443099.2_Intron|TMX3_ENST00000562706.1_Frame_Shift_Del_p.K119fs	NM_019022.3	NP_061895.3	Q96JJ7	TMX3_HUMAN	thioredoxin-related transmembrane protein 3	119	Thioredoxin. {ECO:0000255|PROSITE- ProRule:PRU00691}.				cell redox homeostasis (GO:0045454)|protein folding (GO:0006457)|response to endoplasmic reticulum stress (GO:0034976)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	protein disulfide isomerase activity (GO:0003756)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)|skin(1)|urinary_tract(1)	17						TAATATCATCTTTTGTTCGTG	0.249																																					p.D120fs		Atlas-INDEL	.											.	TMX3	44	.	0			c.358delG						.						90.0	96.0	94.0					18																	66367677		2203	4287	6490	SO:0001589	frameshift_variant	54495	exon6			.	BX647846	CCDS32840.1	18q22	2011-10-19	2009-02-23	2009-02-23		ENSG00000166479		"""Protein disulfide isomerases"""	24718	protein-coding gene	gene with protein product	"""protein disulfide isomerase family A, member 13"""		"""thioredoxin domain containing 10"""	TXNDC10		15623505	Standard	NM_019022		Approved	FLJ20793, KIAA1830, PDIA13	uc002lkf.3	Q96JJ7		ENST00000299608.2:c.357delA	chr18.hg19:g.66367677delT	ENSP00000299608:p.Lys119fs	130.0	0.0		187.0	12.0	NM_019022	B3KV75|Q52LT7|Q8N5J0|Q9NWJ9	Frame_Shift_Del	DEL	ENST00000299608.2	hg19	CCDS32840.1																																																																																			.	.		0.249	TMX3-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420155.1	NM_019022	
KIAA1468	57614	hgsc.bcm.edu	37	18	59936142	59936142	+	Frame_Shift_Del	DEL	C	C	-	rs17645999	byFrequency	TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr18:59936142delC	ENST00000398130.2	+	20	2953	c.2721delC	c.(2719-2721)gtcfs	p.V907fs	KIAA1468_ENST00000256858.6_Frame_Shift_Del_p.V907fs	NM_020854.3	NP_065905.2	Q9P260	K1468_HUMAN	KIAA1468	907										autonomic_ganglia(1)|breast(4)|endometrium(4)|kidney(4)|large_intestine(7)|lung(20)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	47		Colorectal(73;0.186)				AAGCTACAGTCCCCATTTATG	0.303																																					p.V907fs		Atlas-INDEL	.											.	KIAA1468	93	.	0			c.2720delT						.						49.0	49.0	49.0					18																	59936142		2203	4299	6502	SO:0001589	frameshift_variant	57614	exon20			.	BC011992	CCDS11979.2	18q21.33	2005-11-03			ENSG00000134444	ENSG00000134444			29289	protein-coding gene	gene with protein product						11973628	Standard	NM_020854		Approved	HsT885, HsT3308, FLJ33841	uc002lil.3	Q9P260	OTTHUMG00000132780	ENST00000398130.2:c.2721delC	chr18.hg19:g.59936142delC	ENSP00000381198:p.Val907fs	170.0	0.0		211.0	18.0	NM_020854		Frame_Shift_Del	DEL	ENST00000398130.2	hg19	CCDS11979.2																																																																																			.	.		0.303	KIAA1468-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256187.1	NM_020854	
SEMA3C	10512	hgsc.bcm.edu	37	7	80447658	80447658	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:80447658delA	ENST00000265361.3	-	5	965	c.404delT	c.(403-405)ttcfs	p.F135fs	SEMA3C_ENST00000536800.1_Intron|SEMA3C_ENST00000419255.2_Frame_Shift_Del_p.F135fs|SEMA3C_ENST00000544525.1_Frame_Shift_Del_p.F153fs	NM_006379.3	NP_006370.1	Q99985	SEM3C_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C	135	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|blood vessel remodeling (GO:0001974)|cardiac right ventricle morphogenesis (GO:0003215)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|immune response (GO:0006955)|limb bud formation (GO:0060174)|neural crest cell migration (GO:0001755)|neural tube development (GO:0021915)|outflow tract morphogenesis (GO:0003151)|post-embryonic development (GO:0009791)|pulmonary myocardium development (GO:0003350)|response to drug (GO:0042493)|somitogenesis (GO:0001756)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	receptor activity (GO:0004872)			NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	34						GACAGGACTGAAAGCGCCACT	0.388																																					p.F135fs		Atlas-INDEL	.											.	SEMA3C	106	.	0			c.405delC						.						88.0	79.0	82.0					7																	80447658		2203	4300	6503	SO:0001589	frameshift_variant	10512	exon5			.	AB000220	CCDS5596.1	7q21-q31	2013-01-11			ENSG00000075223	ENSG00000075223		"""Semaphorins"", ""Immunoglobulin superfamily / I-set domain containing"""	10725	protein-coding gene	gene with protein product		602645		SEMAE		7748561, 9168980	Standard	NM_006379		Approved	SemE	uc003uhj.3	Q99985	OTTHUMG00000023447	ENST00000265361.3:c.404delT	chr7.hg19:g.80447658delA	ENSP00000265361:p.Phe135fs	162.0	0.0		167.0	11.0	NM_006379	B4DRL8	Frame_Shift_Del	DEL	ENST00000265361.3	hg19	CCDS5596.1																																																																																			.	.		0.388	SEMA3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253279.1	NM_006379	
SAAL1	113174	hgsc.bcm.edu	37	11	18111818	18111818	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:18111818delA	ENST00000524803.1	-	6	542	c.493delT	c.(493-495)tccfs	p.S165fs	SAAL1_ENST00000300013.4_Frame_Shift_Del_p.S165fs|SAAL1_ENST00000529318.1_Frame_Shift_Del_p.S165fs|SAAL1_ENST00000533851.1_5'UTR			Q96ER3	SAAL1_HUMAN	serum amyloid A-like 1	165										breast(2)|large_intestine(5)|lung(8)	15						TCTGCCTGGGAAAGGCAAGTA	0.343																																					p.S165fs		Atlas-INDEL	.											.	SAAL1	34	.	0			c.494delC						.						52.0	48.0	49.0					11																	18111818		2200	4293	6493	SO:0001589	frameshift_variant	113174	exon6			.	AK123457	CCDS31439.1	11p15.1	2005-10-28			ENSG00000166788	ENSG00000166788			25158	protein-coding gene	gene with protein product							Standard	NM_138421		Approved	FLJ41463	uc001mnq.3	Q96ER3	OTTHUMG00000166428	ENST00000524803.1:c.493delT	chr11.hg19:g.18111818delA	ENSP00000432487:p.Ser165fs	101.0	0.0		133.0	10.0	NM_138421	A6NH05	Frame_Shift_Del	DEL	ENST00000524803.1	hg19	CCDS31439.1																																																																																			.	.		0.343	SAAL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000389728.1	NM_138421	
ADAM22	53616	hgsc.bcm.edu	37	7	87808298	87808298	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:87808298delT	ENST00000265727.7	+	27	2428	c.2349delT	c.(2347-2349)tctfs	p.S783fs	ADAM22_ENST00000315984.7_Intron|ADAM22_ENST00000398204.4_Intron|ADAM22_ENST00000398209.3_Intron|ADAM22_ENST00000398201.4_Frame_Shift_Del_p.S783fs			Q9P0K1	ADA22_HUMAN	ADAM metallopeptidase domain 22	783					adult locomotory behavior (GO:0008344)|cell adhesion (GO:0007155)|central nervous system development (GO:0007417)|myelination in peripheral nervous system (GO:0022011)|negative regulation of cell adhesion (GO:0007162)	integral component of membrane (GO:0016021)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(7)|kidney(4)|large_intestine(7)|liver(2)|lung(20)|ovary(6)|prostate(4)|skin(3)	53	Esophageal squamous(14;0.00202)		STAD - Stomach adenocarcinoma(171;0.215)			ATGGTGACTCTTTTTATAGCG	0.413																																					p.S783fs		Atlas-INDEL	.											.	ADAM22	280	.	0			c.2348delC						.						115.0	123.0	121.0					7																	87808298		2186	4292	6478	SO:0001589	frameshift_variant	53616	exon27			.	AB009671	CCDS43608.1, CCDS43609.1, CCDS43610.1, CCDS47637.1	7q21	2008-07-18	2005-08-18		ENSG00000008277	ENSG00000008277		"""ADAM metallopeptidase domain containing"""	201	protein-coding gene	gene with protein product	"""metalloproteinase-like, disintegrin-like, and cysteine-rich protein 2"""	603709	"""a disintegrin and metalloproteinase domain 22"""			9693107, 10524237	Standard	NM_021723		Approved	MDC2	uc003ujn.3	Q9P0K1	OTTHUMG00000137417	ENST00000265727.7:c.2349delT	chr7.hg19:g.87808298delT	ENSP00000265727:p.Ser783fs	188.0	0.0		240.0	16.0	NM_021723	O75075|O75076|Q9P0K2|Q9UIA1|Q9UKK2	Frame_Shift_Del	DEL	ENST00000265727.7	hg19	CCDS47637.1																																																																																			.	.		0.413	ADAM22-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268370.2	NM_021723	
AP1G2	8906	hgsc.bcm.edu	37	14	24032654	24032654	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:24032654delC	ENST00000308724.5	-	13	2100	c.1345delG	c.(1345-1347)gccfs	p.A449fs	RP11-66N24.4_ENST00000553985.1_RNA|AP1G2_ENST00000556277.1_5'Flank|RP11-66N24.3_ENST00000555968.1_RNA|AP1G2_ENST00000397120.3_Frame_Shift_Del_p.A449fs	NM_003917.2	NP_003908.1	O75843	AP1G2_HUMAN	adaptor-related protein complex 1, gamma 2 subunit	449					intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)|viral process (GO:0016032)	AP-1 adaptor complex (GO:0030121)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|Golgi-associated vesicle (GO:0005798)|membrane (GO:0016020)|transport vesicle (GO:0030133)	protein transporter activity (GO:0008565)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(10)|lung(4)|ovary(1)|pancreas(1)|stomach(1)	28	all_cancers(95;0.000251)			GBM - Glioblastoma multiforme(265;0.00672)		AGCTCCTGGGCCCCCCCAATC	0.612											OREG0022605	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A449fs		Atlas-INDEL	.											.,1	AP1G2	75	.	0			c.1346delC						.						65.0	53.0	57.0					14																	24032654		2203	4300	6503	SO:0001589	frameshift_variant	8906	exon14			.	AB015318	CCDS9602.1	14q11.2	2008-07-03			ENSG00000213983	ENSG00000213983			556	protein-coding gene	gene with protein product		603534				9733768, 9762922	Standard	XM_005268167		Approved	G2AD	uc001wkl.2	O75843	OTTHUMG00000028760	ENST00000308724.5:c.1345delG	chr14.hg19:g.24032654delC	ENSP00000312442:p.Ala449fs	166.0	0.0	768	151.0	11.0	NM_003917	D3DS51|O75504	Frame_Shift_Del	DEL	ENST00000308724.5	hg19	CCDS9602.1																																																																																			.	.		0.612	AP1G2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071812.4	NM_003917	
NPAS1	4861	hgsc.bcm.edu	37	19	47546077	47546077	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:47546077delG	ENST00000602212.1	+	11	1447	c.1227delG	c.(1225-1227)gagfs	p.E409fs	NPAS1_ENST00000602189.1_Frame_Shift_Del_p.E234fs|NPAS1_ENST00000449844.2_Frame_Shift_Del_p.E409fs|NPAS1_ENST00000439365.2_Frame_Shift_Del_p.G218fs			Q99742	NPAS1_HUMAN	neuronal PAS domain protein 1	409					central nervous system development (GO:0007417)|maternal behavior (GO:0042711)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|startle response (GO:0001964)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			endometrium(2)|kidney(1)|large_intestine(2)|lung(1)	6		all_cancers(25;4.31e-08)|all_epithelial(76;2.96e-06)|all_lung(116;7.86e-06)|Lung NSC(112;2.31e-05)|all_neural(266;0.026)|Ovarian(192;0.0392)|Breast(70;0.102)		all cancers(93;6.02e-05)|OV - Ovarian serous cystadenocarcinoma(262;7.35e-05)|Epithelial(262;0.00389)|GBM - Glioblastoma multiforme(486;0.0252)		GCCAAGCCGAGGGTGGCCAAA	0.632																																					p.E409fs		Atlas-INDEL	.											.	NPAS1	32	.	0			c.1226delA						.						58.0	43.0	48.0					19																	47546077		2203	4300	6503	SO:0001589	frameshift_variant	4861	exon10			.	U77968	CCDS12694.1	19q13.2-q13.3	2013-05-21				ENSG00000130751		"""Basic helix-loop-helix proteins"""	7894	protein-coding gene	gene with protein product	"""neuronal PAS1"", ""member of PAS superfamily 5"""	603346				9012850, 9079689	Standard	NM_002517		Approved	MOP5, PASD5, bHLHe11	uc002pfy.3	Q99742		ENST00000602212.1:c.1227delG	chr19.hg19:g.47546077delG	ENSP00000469142:p.Glu409fs	180.0	0.0		201.0	13.0	NM_002517	B4DR69|Q99632|Q9BY83	Frame_Shift_Del	DEL	ENST00000602212.1	hg19	CCDS12694.1																																																																																			.	.		0.632	NPAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466658.1	NM_002517	
CPLX2	10814	hgsc.bcm.edu	37	5	175305939	175305939	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:175305939delG	ENST00000359546.4	+	4	703	c.60delG	c.(58-60)ctgfs	p.L20fs	CPLX2_ENST00000515094.1_Frame_Shift_Del_p.L20fs|CPLX2_ENST00000393745.3_Frame_Shift_Del_p.L20fs|CPLX2_ENST00000512824.1_Frame_Shift_Del_p.L20fs	NM_001008220.1|NM_006650.3	NP_001008221.1|NP_006641.1	Q6PUV4	CPLX2_HUMAN	complexin 2	20					cell differentiation (GO:0030154)|mast cell degranulation (GO:0043303)|nervous system development (GO:0007399)|positive regulation of synaptic plasticity (GO:0031915)|regulation of exocytosis (GO:0017157)|synaptic vesicle exocytosis (GO:0016079)|vesicle docking involved in exocytosis (GO:0006904)	dendrite (GO:0030425)|mast cell granule (GO:0042629)|neuronal cell body (GO:0043025)|synapse (GO:0045202)|synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex (GO:0070033)|synaptobrevin 2-SNAP-25-syntaxin-3-complexin complex (GO:0070554)				endometrium(3)|kidney(2)|lung(3)|ovary(2)	10	all_cancers(89;0.004)|Renal(175;0.000269)|Lung NSC(126;0.00441)|all_lung(126;0.00747)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|all_hematologic(541;0.214)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			GGAAGATGCTggggggagagg	0.682																																					p.L20fs		Atlas-INDEL	.											.	CPLX2	42	.	0			c.59delT						.						18.0	18.0	18.0					5																	175305939		2203	4300	6503	SO:0001589	frameshift_variant	10814	exon4			.	U35100	CCDS4396.1	5q35.2	2008-05-23			ENSG00000145920	ENSG00000145920			2310	protein-coding gene	gene with protein product		605033				7553862, 16162394	Standard	XM_005265798		Approved	CPX-2, DKFZp547D155	uc003mdf.1	Q6PUV4	OTTHUMG00000130665	ENST00000359546.4:c.60delG	chr5.hg19:g.175305939delG	ENSP00000352544:p.Leu20fs	162.0	0.0		194.0	13.0	NM_006650	B2RAG2|O09056|Q13329|Q28184|Q52M15|Q64386	Frame_Shift_Del	DEL	ENST00000359546.4	hg19	CCDS4396.1																																																																																			.	.		0.682	CPLX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253157.2		
MYLK2	85366	hgsc.bcm.edu	37	20	30419520	30419520	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr20:30419520delC	ENST00000375994.2	+	10	1712	c.1439delC	c.(1438-1440)tccfs	p.S480fs	MYLK2_ENST00000468730.1_3'UTR|MYLK2_ENST00000375985.4_Frame_Shift_Del_p.S480fs			Q9H1R3	MYLK2_HUMAN	myosin light chain kinase 2	480	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cardiac muscle contraction (GO:0060048)|cardiac muscle tissue morphogenesis (GO:0055008)|neuromuscular synaptic transmission (GO:0007274)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of gene expression (GO:0010628)|protein autophosphorylation (GO:0046777)|regulation of muscle filament sliding (GO:0032971)|skeletal muscle cell differentiation (GO:0035914)|skeletal muscle satellite cell differentiation (GO:0014816)|striated muscle contraction (GO:0006941)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|myosin light chain kinase activity (GO:0004687)			NS(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	33			Colorectal(19;0.00306)|COAD - Colon adenocarcinoma(19;0.0347)			AGCGGCCTCTCCCCCTTCCTG	0.572																																					p.S480fs		Atlas-INDEL	.											.	MYLK2	76	.	0			c.1438delT						.						109.0	93.0	99.0					20																	30419520		2203	4300	6503	SO:0001589	frameshift_variant	85366	exon11			.	AF325549	CCDS13191.1	20q13.31	2014-09-17	2008-01-23		ENSG00000101306	ENSG00000101306	2.7.11.18		16243	protein-coding gene	gene with protein product	"""skeletal muscle myosin light chain kinase"""	606566	"""myosin light chain kinase 2, skeletal muscle"""				Standard	NM_033118		Approved	skMLCK, KMLC, MLCK2	uc002wwq.2	Q9H1R3	OTTHUMG00000032194	ENST00000375994.2:c.1439delC	chr20.hg19:g.30419520delC	ENSP00000365162:p.Ser480fs	89.0	0.0		145.0	11.0	NM_033118	Q569L1|Q96I84	Frame_Shift_Del	DEL	ENST00000375994.2	hg19	CCDS13191.1																																																																																			.	.		0.572	MYLK2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078583.2	NM_033118	
WDR89	112840	hgsc.bcm.edu	37	14	64066253	64066253	+	Frame_Shift_Del	DEL	T	T	-	rs376382796|rs148702795		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:64066253delT	ENST00000394942.2	-	2	496	c.408delA	c.(406-408)aaafs	p.K136fs	WDR89_ENST00000267522.3_Frame_Shift_Del_p.K136fs|CTD-2302E22.2_ENST00000553983.1_lincRNA	NM_001008726.2|NM_001258272.1|NM_080666.3	NP_001008726.1|NP_001245201.1|NP_542397.1	Q96FK6	WDR89_HUMAN	WD repeat domain 89	136										endometrium(1)|kidney(1)|large_intestine(3)|liver(1)|lung(7)|upper_aerodigestive_tract(1)	14				OV - Ovarian serous cystadenocarcinoma(108;0.00543)|all cancers(60;0.0181)|BRCA - Breast invasive adenocarcinoma(234;0.101)		CATCATCAACTTTTTCTGTAC	0.338																																					p.V137fs		Atlas-INDEL	.											.	WDR89	22	.	0			c.409delG						.						70.0	67.0	68.0					14																	64066253		2203	4300	6503	SO:0001589	frameshift_variant	112840	exon3			.	AF115513	CCDS9759.1	14q23.2	2013-01-09		2006-07-07	ENSG00000140006	ENSG00000140006		"""WD repeat domain containing"""	20489	protein-coding gene	gene with protein product				C14orf150			Standard	NM_080666		Approved	MGC9907	uc001xgi.4	Q96FK6	OTTHUMG00000140340	ENST00000394942.2:c.408delA	chr14.hg19:g.64066253delT	ENSP00000378399:p.Lys136fs	153.0	0.0		150.0	10.0	NM_080666		Frame_Shift_Del	DEL	ENST00000394942.2	hg19	CCDS9759.1																																																																																			.	.		0.338	WDR89-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411879.2	NM_080666	
RGS7	6000	hgsc.bcm.edu	37	1	241262025	241262025	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:241262025delT	ENST00000407727.1	-	2	115	c.116delA	c.(115-117)aatfs	p.N39fs	RGS7_ENST00000401882.1_Frame_Shift_Del_p.N39fs|RGS7_ENST00000366563.1_Frame_Shift_Del_p.N39fs|RGS7_ENST00000348120.2_Frame_Shift_Del_p.N39fs|RGS7_ENST00000366562.4_Frame_Shift_Del_p.N39fs|RGS7_ENST00000366564.1_Frame_Shift_Del_p.N39fs|RGS7_ENST00000366565.1_Frame_Shift_Del_p.N39fs|RGS7_ENST00000331110.7_Frame_Shift_Del_p.N13fs|RGS7_ENST00000446183.2_De_novo_Start_OutOfFrame			P49802	RGS7_HUMAN	regulator of G-protein signaling 7	39	DEP. {ECO:0000255|PROSITE- ProRule:PRU00066}.				G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite terminus (GO:0044292)|heterotrimeric G-protein complex (GO:0005834)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein beta-subunit binding (GO:0031681)|GTPase activator activity (GO:0005096)|signal transducer activity (GO:0004871)			breast(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(51)|ovary(4)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	76		all_cancers(173;0.0131)	OV - Ovarian serous cystadenocarcinoma(106;0.027)			AGGAATTCCATTTTTTTCATC	0.353																																					p.N39fs		Atlas-INDEL	.											.	RGS7	308	.	0			c.117delT						.						184.0	162.0	170.0					1																	241262025		2203	4300	6503	SO:0001589	frameshift_variant	6000	exon3			.	BC022009	CCDS31071.1, CCDS60457.1, CCDS60458.1, CCDS60459.1	1q43	2008-02-05	2007-08-14		ENSG00000182901	ENSG00000182901		"""Regulators of G-protein signaling"""	10003	protein-coding gene	gene with protein product		602517	"""regulator of G-protein signalling 7"""			8548815	Standard	XM_005273218		Approved		uc001hyv.2	P49802	OTTHUMG00000040107	ENST00000407727.1:c.116delA	chr1.hg19:g.241262025delT	ENSP00000384428:p.Asn39fs	52.0	0.0		107.0	11.0	NM_002924	Q5T3H4|Q8TD66|Q8TD67|Q8WW09|Q9UNU7|Q9Y6B9	Frame_Shift_Del	DEL	ENST00000407727.1	hg19																																																																																				.	.		0.353	RGS7-204	KNOWN	basic	protein_coding	protein_coding		NM_002924	
CNGB1	1258	hgsc.bcm.edu	37	16	57949179	57949179	+	Frame_Shift_Del	DEL	G	G	-	rs572146377		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:57949179delG	ENST00000251102.8	-	23	2338	c.2278delC	c.(2278-2280)ctcfs	p.L761fs	CNGB1_ENST00000564448.1_Frame_Shift_Del_p.L755fs	NM_001297.4	NP_001288.3	Q14028	CNGB1_HUMAN	cyclic nucleotide gated channel beta 1	761					cation transport (GO:0006812)|cytosolic calcium ion homeostasis (GO:0051480)|detection of light stimulus involved in visual perception (GO:0050908)|phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|protein heterotetramerization (GO:0051290)|regulation of membrane potential (GO:0042391)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina homeostasis (GO:0001895)|rhodopsin mediated signaling pathway (GO:0016056)|sensory perception of smell (GO:0007608)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|intracellular cyclic nucleotide activated cation channel complex (GO:0017071)|plasma membrane (GO:0005886)|terminal bouton (GO:0043195)|transmembrane transporter complex (GO:1902495)	cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|ligand-gated ion channel activity (GO:0015276)|voltage-gated potassium channel activity (GO:0005249)			breast(7)|cervix(2)|endometrium(4)|kidney(2)|large_intestine(11)|liver(1)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	54						AGGCGGAGGAGGGGGTTCACA	0.577																																					p.L760fs	Colon(156;1293 1853 16336 28962 38659)	Atlas-INDEL	.											.	CNGB1	105	.	0			c.2279delT						.						45.0	48.0	47.0					16																	57949179		1936	4128	6064	SO:0001589	frameshift_variant	1258	exon23			.	AF042498	CCDS42169.1, CCDS45495.1, CCDS67042.1	16q13	2013-02-14			ENSG00000070729	ENSG00000070729		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	2151	protein-coding gene	gene with protein product	"""glutamic acid-rich protein"""	600724		CNCG2, CNCG3L		8766832, 7590744, 16382102	Standard	NM_001297		Approved	RCNC2, RCNCb, GARP, GAR1, CNGB1B, RP45	uc002emt.2	Q14028	OTTHUMG00000154810	ENST00000251102.8:c.2278delC	chr16.hg19:g.57949179delG	ENSP00000251102:p.Leu761fs	134.0	0.0		133.0	10.0	NM_001297	H3BN09|O43636|Q13059|Q14029|Q9UMG2	Frame_Shift_Del	DEL	ENST00000251102.8	hg19	CCDS42169.1																																																																																			.	.		0.577	CNGB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337167.2	NM_001297	
VPS13D	55187	hgsc.bcm.edu	37	1	12339690	12339690	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:12339690delT	ENST00000358136.3	+	20	4715	c.4585delT	c.(4585-4587)tttfs	p.F1529fs	VPS13D_ENST00000356315.4_Frame_Shift_Del_p.F1529fs	NM_015378.2	NP_056193.2			vacuolar protein sorting 13 homolog D (S. cerevisiae)											NS(1)|breast(6)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(28)|lung(44)|ovary(5)|pancreas(1)|prostate(8)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(4)	130	Ovarian(185;0.249)	Lung NSC(185;4.08e-05)|all_lung(284;4.55e-05)|Renal(390;0.000147)|Colorectal(325;0.00058)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0327)|Colorectal(212;4.63e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000289)|COAD - Colon adenocarcinoma(227;0.000801)|Kidney(185;0.00216)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0476)|Lung(427;0.209)		TGAAGGAAAATTTGTCAATCC	0.328																																					p.K1528fs		Atlas-INDEL	.											.	VPS13D	316	.	0			c.4584delA						.						65.0	65.0	65.0					1																	12339690		2203	4300	6503	SO:0001589	frameshift_variant	55187	exon20			.	AJ608774	CCDS30588.1, CCDS30589.1	1p36.21	2008-02-05	2006-04-04		ENSG00000048707	ENSG00000048707			23595	protein-coding gene	gene with protein product		608877	"""vacuolar protein sorting 13D (yeast)"""				Standard	NM_015378		Approved	FLJ10619, KIAA0453	uc001atv.3	Q5THJ4	OTTHUMG00000013155	ENST00000358136.3:c.4585delT	chr1.hg19:g.12339690delT	ENSP00000350854:p.Phe1529fs	163.0	0.0		166.0	12.0	NM_015378		Frame_Shift_Del	DEL	ENST00000358136.3	hg19	CCDS30588.1																																																																																			.	.		0.328	VPS13D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000036897.2	NM_015378	
TMPRSS7	344805	hgsc.bcm.edu	37	3	111780666	111780666	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:111780666delT	ENST00000452346.2	+	11	1346	c.1343delT	c.(1342-1344)attfs	p.I448fs	TMPRSS7_ENST00000419127.1_Frame_Shift_Del_p.I322fs			Q7RTY8	TMPS7_HUMAN	transmembrane protease, serine 7	448	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.				proteolysis (GO:0006508)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			breast(2)|endometrium(6)|kidney(2)|large_intestine(4)|lung(11)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	34						CATCAGACAATTTTTCGAGTG	0.488																																					p.I322fs		Atlas-INDEL	.											.	TMPRSS7	126	.	0			c.964delA						.						128.0	128.0	128.0					3																	111780666		1929	4133	6062	SO:0001589	frameshift_variant	344805	exon9			.	BN000125	CCDS43129.2	3q13.2	2010-04-13	2004-03-16		ENSG00000176040	ENSG00000176040		"""Serine peptidases / Transmembrane"""	30846	protein-coding gene	gene with protein product			"""type II transmembrane serine protease 7"""			12838346	Standard	NM_001042575		Approved		uc010hqb.2	Q7RTY8	OTTHUMG00000157148	ENST00000452346.2:c.1343delT	chr3.hg19:g.111780666delT	ENSP00000398236:p.Ile448fs	139.0	0.0		172.0	12.0	NM_001042575	C9J8P7|E9PAS3|Q17RH4	Frame_Shift_Del	DEL	ENST00000452346.2	hg19																																																																																				.	.		0.488	TMPRSS7-003	NOVEL	NAGNAG_splice_site|not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000347592.2	XM_293599	
GPR119	139760	hgsc.bcm.edu	37	X	129518461	129518461	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:129518461delT	ENST00000276218.2	-	1	1050	c.961delA	c.(961-963)agtfs	p.S322fs		NM_178471.2	NP_848566.1	Q8TDV5	GP119_HUMAN	G protein-coupled receptor 119	322					insulin secretion (GO:0030073)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)|phosphatidylcholine binding (GO:0031210)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(1)|ovary(3)|prostate(1)	11						TGACAGGAACTTTCCCTGGGC	0.537																																					p.S321fs		Atlas-INDEL	.											.	GPR119	34	.	0			c.962delG						.						99.0	90.0	93.0					X																	129518461		2203	4300	6503	SO:0001589	frameshift_variant	139760	exon1			.	AY288416	CCDS14625.1	Xq26.1	2014-01-30			ENSG00000147262	ENSG00000147262		"""GPCR / Class A : Orphans"""	19060	protein-coding gene	gene with protein product		300513				12044878, 14623098	Standard	NM_178471		Approved	hGPCR2, GPCR2	uc011muv.2	Q8TDV5	OTTHUMG00000022397	ENST00000276218.2:c.961delA	chrX.hg19:g.129518461delT	ENSP00000276218:p.Ser322fs	78.0	0.0		127.0	10.0	NM_178471	Q495H7|Q4VBN3	Frame_Shift_Del	DEL	ENST00000276218.2	hg19	CCDS14625.1																																																																																			.	.		0.537	GPR119-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058270.1	NM_178471	
XDH	7498	hgsc.bcm.edu	37	2	31571774	31571774	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:31571774delA	ENST00000379416.3	-	27	3090	c.3042delT	c.(3040-3042)tttfs	p.F1014fs		NM_000379.3	NP_000370.2	P47989	XDH_HUMAN	xanthine dehydrogenase	1014					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|lactation (GO:0007595)|negative regulation of endothelial cell differentiation (GO:0045602)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of gene expression (GO:0010629)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|negative regulation of vasculogenesis (GO:2001213)|nucleobase-containing small molecule metabolic process (GO:0055086)|positive regulation of p38MAPK cascade (GO:1900745)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide catabolic process (GO:0006195)|small molecule metabolic process (GO:0044281)|xanthine catabolic process (GO:0009115)	cytosol (GO:0005829)|extracellular space (GO:0005615)|peroxisome (GO:0005777)	2 iron, 2 sulfur cluster binding (GO:0051537)|electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|iron ion binding (GO:0005506)|molybdopterin cofactor binding (GO:0043546)|protein homodimerization activity (GO:0042803)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)|xanthine dehydrogenase activity (GO:0004854)|xanthine oxidase activity (GO:0004855)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(31)|ovary(1)|pancreas(1)|prostate(3)|skin(9)|urinary_tract(1)	74	Acute lymphoblastic leukemia(172;0.155)				Aldesleukin(DB00041)|Allopurinol(DB00437)|Azathioprine(DB00993)|Carboplatin(DB00958)|Carvedilol(DB01136)|Chlorphenesin(DB00856)|Cisplatin(DB00515)|Daunorubicin(DB00694)|Deferoxamine(DB00746)|Doxorubicin(DB00997)|Flavin adenine dinucleotide(DB03147)|L-Carnitine(DB00583)|Menadione(DB00170)|Mercaptopurine(DB01033)|Nitrofural(DB00336)|Procarbazine(DB01168)|Pyrazinamide(DB00339)|Spermine(DB00127)|Trifluoperazine(DB00831)	CCTGATTCAGAAAAGGAACTG	0.383																																					p.L1015X	Colon(66;682 1445 30109 40147)	Atlas-INDEL	.											.	XDH	191	.	0			c.3043delC						.						95.0	94.0	94.0					2																	31571774		2203	4300	6503	SO:0001589	frameshift_variant	7498	exon27			.	D11456	CCDS1775.1	2p23.1	2009-07-10	2003-03-20		ENSG00000158125	ENSG00000158125	1.17.1.4		12805	protein-coding gene	gene with protein product		607633	"""xanthene dehydrogenase"""			8224915	Standard	NM_000379		Approved	XOR, XO	uc002rnv.1	P47989	OTTHUMG00000099385	ENST00000379416.3:c.3042delT	chr2.hg19:g.31571774delA	ENSP00000368727:p.Phe1014fs	90.0	0.0		173.0	11.0	NM_000379	Q16681|Q16712|Q4PJ16	Frame_Shift_Del	DEL	ENST00000379416.3	hg19	CCDS1775.1																																																																																			.	.		0.383	XDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216840.1	NM_000379	
ATXN1	6310	hgsc.bcm.edu	37	6	16327684	16327684	+	Frame_Shift_Del	DEL	G	G	-	rs202200269	byFrequency	TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:16327684delG	ENST00000244769.4	-	8	1794	c.858delC	c.(856-858)cccfs	p.P286fs	ATXN1_ENST00000436367.1_Frame_Shift_Del_p.P286fs	NM_000332.3	NP_000323.2	P54253	ATX1_HUMAN	ataxin 1	286					adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|nuclear export (GO:0051168)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear inclusion body (GO:0042405)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|poly(G) binding (GO:0034046)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|protein self-association (GO:0043621)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(11)|lung(12)|prostate(2)|skin(7)|upper_aerodigestive_tract(2)	44	Breast(50;0.063)|Ovarian(93;0.0733)	all_hematologic(90;0.000682)|Ovarian(999;0.00973)				CGACCTGGGAGGGGGGCCCCA	0.682																																					p.S287fs		Atlas-INDEL	.											.	ATXN1	117	.	0			c.859delT						.						31.0	34.0	33.0					6																	16327684		2203	4300	6503	SO:0001589	frameshift_variant	6310	exon7			.	X79204	CCDS34342.1	6p23	2014-09-17	2004-08-12	2004-08-13	ENSG00000124788	ENSG00000124788		"""Ataxins"""	10548	protein-coding gene	gene with protein product		601556	"""spinocerebellar ataxia 1 (olivopontocerebellar ataxia 1, autosomal dominant, ataxin 1)"""	SCA1		1582256	Standard	NM_000332		Approved	D6S504E, ATX1	uc010jpi.3	P54253	OTTHUMG00000014303	ENST00000244769.4:c.858delC	chr6.hg19:g.16327684delG	ENSP00000244769:p.Pro286fs	181.0	0.0		334.0	21.0	NM_001128164	Q17S02|Q9UJG2|Q9Y4J1	Frame_Shift_Del	DEL	ENST00000244769.4	hg19	CCDS34342.1																																																																																			.	.		0.682	ATXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039943.3	NM_000332	
TTC38	55020	hgsc.bcm.edu	37	22	46671215	46671215	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr22:46671215delA	ENST00000381031.3	+	5	512	c.436delA	c.(436-438)aaafs	p.K146fs	TTC38_ENST00000445282.2_Intron	NM_017931.2	NP_060401	Q5R3I4	TTC38_HUMAN	tetratricopeptide repeat domain 38	146						extracellular vesicular exosome (GO:0070062)				endometrium(4)|large_intestine(3)|lung(4)|ovary(1)	12						GTTGGCCCTGAAATTTTCCCA	0.473																																					p.L145fs		Atlas-INDEL	.											TTC38,NS,carcinoma,0,1	TTC38	40	.	0			c.435delG						.						111.0	107.0	108.0					22																	46671215		1857	4105	5962	SO:0001589	frameshift_variant	55020	exon5			.		CCDS43030.1	22q13	2013-01-11			ENSG00000075234	ENSG00000075234		"""Tetratricopeptide (TTC) repeat domain containing"""	26082	protein-coding gene	gene with protein product							Standard	NM_017931		Approved	FLJ20699	uc003bhi.3	Q5R3I4	OTTHUMG00000150494	ENST00000381031.3:c.436delA	chr22.hg19:g.46671215delA	ENSP00000370419:p.Lys146fs	116.0	0.0		162.0	10.0	NM_017931	Q8WV27|Q9NWP8	Frame_Shift_Del	DEL	ENST00000381031.3	hg19	CCDS43030.1																																																																																			.	.		0.473	TTC38-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000318469.1	NM_017931	
UIMC1	51720	hgsc.bcm.edu	37	5	176409596	176409596	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:176409596delT	ENST00000377227.4	-	2	153	c.21delA	c.(19-21)aaafs	p.K7fs	UIMC1_ENST00000506128.1_Frame_Shift_Del_p.K7fs|UIMC1_ENST00000511320.1_Frame_Shift_Del_p.K7fs|UIMC1_ENST00000377219.2_Frame_Shift_Del_p.K7fs			Q96RL1	UIMC1_HUMAN	ubiquitin interaction motif containing 1	7	Necessary for transcriptional repression.				double-strand break repair (GO:0006302)|G2 DNA damage checkpoint (GO:0031572)|histone H2A K63-linked deubiquitination (GO:0070537)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of DNA repair (GO:0045739)|response to ionizing radiation (GO:0010212)|transcription, DNA-templated (GO:0006351)	BRCA1-A complex (GO:0070531)|nucleus (GO:0005634)	histone binding (GO:0042393)|K63-linked polyubiquitin binding (GO:0070530)			NS(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(5)|ovary(4)|pancreas(1)|prostate(1)|skin(1)	21	all_cancers(89;7.96e-05)|Renal(175;0.000269)|Lung NSC(126;0.00476)|all_lung(126;0.00806)	Medulloblastoma(196;0.0145)|all_neural(177;0.0325)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CTTCTTTAACTTTTTTCTTTC	0.358																																					p.V8fs		Atlas-INDEL	.											.	UIMC1	55	.	0			c.22delG						.						103.0	99.0	100.0					5																	176409596		2203	4300	6503	SO:0001589	frameshift_variant	51720	exon2			.	AF349313	CCDS4408.1	5q35.2	2008-02-05			ENSG00000087206	ENSG00000087206			30298	protein-coding gene	gene with protein product	"""receptor associated protein 80"""	609433				12080054	Standard	NM_001199297		Approved	RAP80	uc021yin.1	Q96RL1	OTTHUMG00000130852	ENST00000377227.4:c.21delA	chr5.hg19:g.176409596delT	ENSP00000366434:p.Lys7fs	168.0	0.0		236.0	15.0	NM_016290	A8MSA1|B3KMZ1|B4E3N2|Q5XKQ1|Q7Z3W7|Q8N5B9|Q9BZR1|Q9BZR5|Q9UHX7	Frame_Shift_Del	DEL	ENST00000377227.4	hg19	CCDS4408.1																																																																																			.	.		0.358	UIMC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253422.1	NM_016290	
UBE2C	11065	hgsc.bcm.edu	37	20	44444540	44444540	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr20:44444540delA	ENST00000356455.4	+	5	589	c.469delA	c.(469-471)aaafs	p.K157fs	UBE2C_ENST00000405520.1_Frame_Shift_Del_p.K118fs|UBE2C_ENST00000243893.6_3'UTR|UBE2C_ENST00000372568.4_Frame_Shift_Del_p.K118fs|UBE2C_ENST00000335046.3_Frame_Shift_Del_p.K139fs|UBE2C_ENST00000352551.5_Frame_Shift_Del_p.K128fs|UBE2C_ENST00000496085.1_3'UTR	NM_007019.2	NP_008950.1	O00762	UBE2C_HUMAN	ubiquitin-conjugating enzyme E2C	157					activation of anaphase-promoting complex activity (GO:0051488)|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cyclin catabolic process (GO:0008054)|exit from mitosis (GO:0010458)|free ubiquitin chain polymerization (GO:0010994)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of exit from mitosis (GO:0031536)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|protein K48-linked ubiquitination (GO:0070936)|protein ubiquitination (GO:0016567)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|ubiquitin-dependent protein catabolic process (GO:0006511)	anaphase-promoting complex (GO:0005680)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|ubiquitin-protein transferase activity (GO:0004842)			large_intestine(2)|lung(2)|skin(1)	5		Myeloproliferative disorder(115;0.0122)				CGAGCTCTGGAAAAACCCCAC	0.557																																					p.W156X		Atlas-INDEL	.											.	UBE2C	31	.	0			c.468delG						.						127.0	122.0	124.0					20																	44444540		2203	4300	6503	SO:0001589	frameshift_variant	11065	exon5			.	U73379	CCDS13370.1, CCDS13371.1, CCDS13372.1, CCDS13374.1, CCDS74733.1, CCDS74734.1	20q13.12	2007-02-05			ENSG00000175063	ENSG00000175063		"""Ubiquitin-conjugating enzymes E2"""	15937	protein-coding gene	gene with protein product		605574				9122200	Standard	NM_007019		Approved	UBCH10	uc002xpm.3	O00762	OTTHUMG00000033038	ENST00000356455.4:c.469delA	chr20.hg19:g.44444540delA	ENSP00000348838:p.Lys157fs	82.0	0.0		105.0	10.0	NM_007019	A6NP33|E1P5N7|G3XAB7	Frame_Shift_Del	DEL	ENST00000356455.4	hg19	CCDS13370.1																																																																																			.	.		0.557	UBE2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080309.2	NM_007019	
COPB2	9276	hgsc.bcm.edu	37	3	139096994	139096994	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:139096994delT	ENST00000333188.5	-	5	574	c.393delA	c.(391-393)aaafs	p.K131fs	COPB2_ENST00000510491.1_5'Flank|COPB2_ENST00000507777.1_Frame_Shift_Del_p.K102fs	NM_004766.2	NP_004757.1	P35606	COPB2_HUMAN	coatomer protein complex, subunit beta 2 (beta prime)	131					COPI coating of Golgi vesicle (GO:0048205)|intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	COPI vesicle coat (GO:0030126)|cytosol (GO:0005829)	structural molecule activity (GO:0005198)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(4)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	24						AGCAAGACCATTTTTTATCCC	0.383																																					p.W132fs		Atlas-INDEL	.											.	COPB2	80	.	0			c.394delT						.						239.0	224.0	229.0					3																	139096994		2203	4300	6503	SO:0001589	frameshift_variant	9276	exon5			.	BC000326	CCDS3108.1	3q23	2013-01-10			ENSG00000184432	ENSG00000184432		"""WD repeat domain containing"""	2232	protein-coding gene	gene with protein product		606990				9858824	Standard	NM_004766		Approved	beta'-COP, betaprime-COP	uc003etf.4	P35606	OTTHUMG00000159959	ENST00000333188.5:c.393delA	chr3.hg19:g.139096994delT	ENSP00000329419:p.Lys131fs	111.0	0.0		128.0	10.0	NM_004766	B4DZI8	Frame_Shift_Del	DEL	ENST00000333188.5	hg19	CCDS3108.1																																																																																			.	.		0.383	COPB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358495.2	NM_004766	
ATP10D	57205	hgsc.bcm.edu	37	4	47574996	47574996	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:47574996delT	ENST00000273859.3	+	18	3617	c.3348delT	c.(3346-3348)tatfs	p.Y1116fs		NM_020453.3	NP_065186.3	Q9P241	AT10D_HUMAN	ATPase, class V, type 10D	1116					cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(2)|endometrium(5)|kidney(5)|large_intestine(14)|liver(2)|lung(26)|ovary(2)|pancreas(1)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1)	66						TGATTCTCTATTTTTTCTATA	0.438																																					p.Y1116fs		Atlas-INDEL	.											.	ATP10D	168	.	0			c.3347delA						.						209.0	202.0	204.0					4																	47574996		2203	4300	6503	SO:0001589	frameshift_variant	57205	exon18			.	AB040920	CCDS3476.1	4p12	2010-04-20	2007-09-19		ENSG00000145246	ENSG00000145246		"""ATPases / P-type"""	13549	protein-coding gene	gene with protein product			"""ATPase, Class V, type 10D"""			12532265	Standard	NM_020453		Approved	ATPVD, KIAA1487	uc003gxk.1	Q9P241	OTTHUMG00000160784	ENST00000273859.3:c.3348delT	chr4.hg19:g.47574996delT	ENSP00000273859:p.Tyr1116fs	159.0	0.0		206.0	14.0	NM_020453	A2RRC8|D6REN2|Q8NC70|Q96SR3	Frame_Shift_Del	DEL	ENST00000273859.3	hg19	CCDS3476.1																																																																																			.	.		0.438	ATP10D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216900.1	NM_020453	
LTF	4057	hgsc.bcm.edu	37	3	46479553	46479553	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:46479553delT	ENST00000231751.4	-	16	2271	c.1976delA	c.(1975-1977)aacfs	p.N659fs	LTF_ENST00000426532.2_Frame_Shift_Del_p.N615fs|LTF_ENST00000493056.1_5'UTR|LTF_ENST00000417439.1_Frame_Shift_Del_p.N657fs	NM_002343.3	NP_002334.2	P02788	TRFL_HUMAN	lactotransferrin	659	Transferrin-like 2. {ECO:0000255|PROSITE- ProRule:PRU00741}.				antibacterial humoral response (GO:0019731)|antifungal humoral response (GO:0019732)|bone morphogenesis (GO:0060349)|humoral immune response (GO:0006959)|innate immune response in mucosa (GO:0002227)|interaction with host (GO:0051701)|iron assimilation by chelation and transport (GO:0033214)|iron ion transport (GO:0006826)|negative regulation of apoptotic process (GO:0043066)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)|negative regulation of osteoclast development (GO:2001205)|negative regulation of single-species biofilm formation in or on host organism (GO:1900229)|negative regulation of tumor necrosis factor (ligand) superfamily member 11 production (GO:2000308)|ossification (GO:0001503)|phagosome maturation (GO:0090382)|positive regulation of bone mineralization involved in bone maturation (GO:1900159)|positive regulation of chondrocyte proliferation (GO:1902732)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|regulation of cytokine production (GO:0001817)|regulation of tumor necrosis factor production (GO:0032680)|response to host immune response (GO:0052572)|retina homeostasis (GO:0001895)|transcription, DNA-templated (GO:0006351)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|phagocytic vesicle lumen (GO:0097013)|secretory granule (GO:0030141)|specific granule (GO:0042581)	DNA binding (GO:0003677)|ferric iron binding (GO:0008199)|heparin binding (GO:0008201)|iron ion binding (GO:0005506)|protein serine/threonine kinase activator activity (GO:0043539)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(5)|lung(13)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	40				all cancers(1;7.55e-14)|GBM - Glioblastoma multiforme(1;2.1e-09)|Epithelial(1;9.25e-07)|Colorectal(1;3.81e-05)|BRCA - Breast invasive adenocarcinoma(193;0.00129)|COAD - Colon adenocarcinoma(1;0.00308)|KIRC - Kidney renal clear cell carcinoma(197;0.0205)|Kidney(197;0.0242)|OV - Ovarian serous cystadenocarcinoma(275;0.089)		GAACAGAAGGTTTTTGGTTTC	0.433																																					p.N659fs		Atlas-INDEL	.											.	LTF	98	.	0			c.1977delC						.						162.0	163.0	163.0					3																	46479553		2203	4300	6503	SO:0001589	frameshift_variant	4057	exon16			.		CCDS33747.1, CCDS56251.1	3p21.31	2012-10-02			ENSG00000012223	ENSG00000012223			6720	protein-coding gene	gene with protein product		150210				17476971, 3356163	Standard	NM_001199149		Approved	HLF2	uc003cpq.3	P02788	OTTHUMG00000156325	ENST00000231751.4:c.1976delA	chr3.hg19:g.46479553delT	ENSP00000231751:p.Asn659fs	136.0	0.0		193.0	12.0	NM_002343	A8K9U8|B2MV13|B7Z4X2|E7EQH5|O00756|Q16780|Q16785|Q16786|Q16789|Q5DSM0|Q8IU92|Q8IZH6|Q8TCD2|Q96KZ4|Q96KZ5|Q9H1Z3|Q9UCY5	Frame_Shift_Del	DEL	ENST00000231751.4	hg19	CCDS33747.1																																																																																			.	.		0.433	LTF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000343951.2	NM_002343	
LRRC36	55282	hgsc.bcm.edu	37	16	67381385	67381385	+	Intron	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:67381385delT	ENST00000329956.6	+	4	410				LRRC36_ENST00000563189.1_Frame_Shift_Del_p.F6fs|LRRC36_ENST00000435835.3_Frame_Shift_Del_p.F6fs|LRRC36_ENST00000541146.1_5'UTR|LRRC36_ENST00000563303.1_Intron|LRRC36_ENST00000290940.7_5'UTR	NM_018296.5	NP_060766.5	Q1X8D7	LRC36_HUMAN	leucine rich repeat containing 36											endometrium(4)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	24		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0669)|Epithelial(162;0.161)		CAGACCACGGTTTTTGCCTCC	0.408																																					p.R5fs		Atlas-INDEL	.											.	LRRC36	68	.	0			c.15delG						.						98.0	95.0	96.0					16																	67381385		2198	4300	6498	SO:0001627	intron_variant	55282	exon1			.	BC026156	CCDS32467.1, CCDS58474.1	16q22.1	2008-02-05				ENSG00000159708			25615	protein-coding gene	gene with protein product						12477932	Standard	NM_001161575		Approved	FLJ11004	uc002esv.3	Q1X8D7		ENST00000329956.6:c.392-13T>-	chr16.hg19:g.67381385delT		125.0	0.0		152.0	10.0	NM_001161575	A4FTV6|A6NDE9|A8K8E6|Q7Z5K5	Frame_Shift_Del	DEL	ENST00000329956.6	hg19	CCDS32467.1																																																																																			.	.		0.408	LRRC36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421770.1	NM_018296	
GPR180	160897	hgsc.bcm.edu	37	13	95278272	95278272	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr13:95278272delT	ENST00000376958.4	+	8	1164	c.1139delT	c.(1138-1140)attfs	p.I380fs		NM_180989.5	NP_851320.1	Q86V85	GP180_HUMAN	G protein-coupled receptor 180	380					G-protein coupled receptor signaling pathway (GO:0007186)|response to pheromone (GO:0019236)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(1)|kidney(1)|large_intestine(3)|lung(4)|urinary_tract(1)	10	all_neural(89;0.0684)|Medulloblastoma(90;0.163)					ATTTCTGTCATTTTTAGCGAC	0.318																																					p.I380fs		Atlas-INDEL	.											.	GPR180	24	.	0			c.1138delA						.						145.0	126.0	133.0					13																	95278272		2203	4300	6503	SO:0001589	frameshift_variant	160897	exon8			.	AF339823	CCDS9472.1	13q32.1	2006-04-05			ENSG00000152749	ENSG00000152749			28899	protein-coding gene	gene with protein product	"""intimal thickness related receptor"""	607787				12538434	Standard	NM_180989		Approved	ITR	uc001vly.3	Q86V85	OTTHUMG00000017207	ENST00000376958.4:c.1139delT	chr13.hg19:g.95278272delT	ENSP00000366157:p.Ile380fs	78.0	0.0		160.0	12.0	NM_180989	A8K1D5	Frame_Shift_Del	DEL	ENST00000376958.4	hg19	CCDS9472.1																																																																																			.	.		0.318	GPR180-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045465.3	NM_180989	
GPATCH8	23131	hgsc.bcm.edu	37	17	42478249	42478249	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:42478249delG	ENST00000591680.1	-	8	1226	c.1196delC	c.(1195-1197)ccafs	p.P399fs	GPATCH8_ENST00000434000.1_Frame_Shift_Del_p.P321fs	NM_001002909.2	NP_001002909.1	Q9UKJ3	GPTC8_HUMAN	G patch domain containing 8	399							metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			breast(4)|endometrium(7)|kidney(6)|large_intestine(4)|liver(2)|lung(21)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	50		Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.206)		GCAGTGTGCTGGGGGGATGTA	0.438											OREG0024461	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P399fs		Atlas-INDEL	.											.	GPATCH8	114	.	0			c.1197delA						.						110.0	110.0	110.0					17																	42478249		2203	4300	6503	SO:0001589	frameshift_variant	23131	exon8			.	AB011125	CCDS32666.1	17q21.31	2013-01-28	2006-08-22	2006-12-13	ENSG00000186566	ENSG00000186566		"""G patch domain containing"""	29066	protein-coding gene	gene with protein product		614396	"""KIAA0553"""	KIAA0553, GPATC8		9628581	Standard	NM_001002909		Approved		uc002igw.2	Q9UKJ3	OTTHUMG00000181818	ENST00000591680.1:c.1196delC	chr17.hg19:g.42478249delG	ENSP00000467556:p.Pro399fs	110.0	0.0	909	122.0	10.0	NM_001002909	B9EGP9|O60300|Q8TB99	Frame_Shift_Del	DEL	ENST00000591680.1	hg19	CCDS32666.1																																																																																			.	.		0.438	GPATCH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457797.1	NM_001002909	
SLCO1B3	28234	hgsc.bcm.edu	37	12	21032426	21032426	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:21032426delA	ENST00000381545.3	+	11	1411	c.1192delA	c.(1192-1194)aaafs	p.K399fs	LST3_ENST00000540229.1_Frame_Shift_Del_p.K399fs|SLCO1B3_ENST00000553473.1_Frame_Shift_Del_p.K399fs|SLCO1B3_ENST00000261196.2_Frame_Shift_Del_p.K399fs|LST3_ENST00000381541.3_Intron|SLCO1B7_ENST00000554957.1_Intron	NM_019844.3	NP_062818.1	Q9NPD5	SO1B3_HUMAN	solute carrier organic anion transporter family, member 1B3	399					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	organic anion transmembrane transporter activity (GO:0008514)			breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(23)|ovary(2)|prostate(2)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(2)	63	Esophageal squamous(101;0.149)				Atorvastatin(DB01076)|Cabazitaxel(DB06772)|Caspofungin(DB00520)|Conjugated Estrogens(DB00286)|Dabrafenib(DB08912)|Digoxin(DB00390)|Docetaxel(DB01248)|Estradiol(DB00783)|Fexofenadine(DB00950)|Fluvastatin(DB01095)|Gadoxetate(DB08884)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)|Methotrexate(DB00563)|Mycophenolate mofetil(DB00688)|Olmesartan(DB00275)|Ouabain(DB01092)|Paclitaxel(DB01229)|Pioglitazone(DB01132)|Pitavastatin(DB08860)|Pravastatin(DB00175)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Rosuvastatin(DB01098)|Valsartan(DB00177)	ATTTATCATTAAAAAATTCAA	0.294																																					p.I397fs		Atlas-INDEL	.											.	SLCO1B3	151	.	0			c.1191delT						.						65.0	66.0	66.0					12																	21032426		2203	4300	6503	SO:0001589	frameshift_variant	28234	exon11			.		CCDS8684.1	12p12	2013-05-22	2003-11-25	2003-11-26		ENSG00000111700		"""Solute carriers"""	10961	protein-coding gene	gene with protein product		605495	"""solute carrier family 21 (organic anion transporter), member 8"""	SLC21A8			Standard	NM_019844		Approved	OATP8, OATP1B3	uc001rel.4	Q9NPD5	OTTHUMG00000169011	ENST00000381545.3:c.1192delA	chr12.hg19:g.21032426delA	ENSP00000370956:p.Lys399fs	139.0	0.0		134.0	17.0	NM_019844	E7EMT8|Q5JAR4	Frame_Shift_Del	DEL	ENST00000381545.3	hg19	CCDS8684.1																																																																																			.	.		0.294	SLCO1B3-001	KNOWN	upstream_ATG|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000401936.1	NM_019844	
ANK2	287	hgsc.bcm.edu	37	4	114278579	114278579	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:114278579delT	ENST00000357077.4	+	38	8858	c.8805delT	c.(8803-8805)tctfs	p.S2935fs	ANK2_ENST00000264366.6_Frame_Shift_Del_p.S2902fs|ANK2_ENST00000506722.1_Intron|ANK2_ENST00000509550.1_Intron|ANK2_ENST00000510275.2_Intron|ANK2_ENST00000394537.3_Intron	NM_001148.4	NP_001139.3	Q01484	ANK2_HUMAN	ankyrin 2, neuronal	2935					atrial cardiac muscle cell action potential (GO:0086014)|atrial cardiac muscle cell to AV node cell communication (GO:0086066)|atrial septum development (GO:0003283)|axon guidance (GO:0007411)|cardiac muscle contraction (GO:0060048)|cellular calcium ion homeostasis (GO:0006874)|cellular protein localization (GO:0034613)|membrane depolarization during SA node cell action potential (GO:0086046)|paranodal junction assembly (GO:0030913)|positive regulation of calcium ion transmembrane transporter activity (GO:1901021)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cation channel activity (GO:2001259)|positive regulation of gene expression (GO:0010628)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein localization to cell surface (GO:0034394)|protein localization to endoplasmic reticulum (GO:0070972)|protein localization to M-band (GO:0036309)|protein localization to organelle (GO:0033365)|protein localization to plasma membrane (GO:0072659)|protein localization to T-tubule (GO:0036371)|protein stabilization (GO:0050821)|protein targeting to plasma membrane (GO:0072661)|regulation of calcium ion transmembrane transporter activity (GO:1901019)|regulation of calcium ion transport (GO:0051924)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of protein stability (GO:0031647)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to methylmercury (GO:0051597)|SA node cell action potential (GO:0086015)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|T-tubule organization (GO:0033292)|ventricular cardiac muscle cell action potential (GO:0086005)	A band (GO:0031672)|basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intracellular (GO:0005622)|M band (GO:0031430)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|potassium channel regulator activity (GO:0015459)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(54)|liver(2)|lung(112)|ovary(8)|pancreas(1)|prostate(7)|skin(11)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(10)	248		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)		CTTCCCAATCTTTTTTCTCTA	0.398																																					p.S2935fs		Atlas-INDEL	.											.	ANK2	576	.	0			c.8804delC						.						170.0	178.0	175.0					4																	114278579		2203	4300	6503	SO:0001589	frameshift_variant	287	exon38			.	M37123	CCDS3702.1, CCDS43261.1, CCDS54796.1	4q25-q26	2014-09-17	2003-03-12		ENSG00000145362	ENSG00000145362		"""Ankyrin repeat domain containing"""	493	protein-coding gene	gene with protein product		106410	"""long (electrocardiographic) QT syndrome 4"""	LQT4		7485162, 12571597	Standard	NM_001148		Approved		uc003ibe.4	Q01484	OTTHUMG00000132912	ENST00000357077.4:c.8805delT	chr4.hg19:g.114278579delT	ENSP00000349588:p.Ser2935fs	130.0	0.0		166.0	10.0	NM_001148	Q01485|Q08AC7|Q08AC8|Q7Z3L5	Frame_Shift_Del	DEL	ENST00000357077.4	hg19	CCDS3702.1																																																																																			.	.		0.398	ANK2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256422.2	NM_001148	
PDE4D	5144	hgsc.bcm.edu	37	5	58271490	58271490	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:58271490delT	ENST00000340635.6	-	14	2182	c.2007delA	c.(2005-2007)aaafs	p.K669fs	PDE4D_ENST00000503258.1_Frame_Shift_Del_p.K539fs|PDE4D_ENST00000360047.5_Frame_Shift_Del_p.K533fs|PDE4D_ENST00000546160.1_Frame_Shift_Del_p.K608fs|PDE4D_ENST00000317118.8_Frame_Shift_Del_p.K378fs|PDE4D_ENST00000507116.1_Frame_Shift_Del_p.K605fs|PDE4D_ENST00000405755.2_Frame_Shift_Del_p.K547fs|PDE4D_ENST00000358923.6_Frame_Shift_Del_p.K367fs|PDE4D_ENST00000502484.2_Frame_Shift_Del_p.K608fs	NM_001104631.1	NP_001098101.1	Q08499	PDE4D_HUMAN	phosphodiesterase 4D, cAMP-specific	669					adrenergic receptor signaling pathway (GO:0071875)|adrenergic receptor signaling pathway involved in positive regulation of heart rate (GO:0086024)|aging (GO:0007568)|cAMP catabolic process (GO:0006198)|cAMP-mediated signaling (GO:0019933)|cellular response to cAMP (GO:0071320)|cellular response to epinephrine stimulus (GO:0071872)|cellular response to lipopolysaccharide (GO:0071222)|establishment of endothelial barrier (GO:0061028)|multicellular organism growth (GO:0035264)|negative regulation of heart contraction (GO:0045822)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of relaxation of cardiac muscle (GO:1901898)|neutrophil chemotaxis (GO:0030593)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of interleukin-5 production (GO:0032754)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901844)|regulation of heart rate (GO:0002027)|regulation of receptor activity (GO:0010469)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|smooth muscle contraction (GO:0006939)|T cell receptor signaling pathway (GO:0050852)	calcium channel complex (GO:0034704)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|ATPase binding (GO:0051117)|beta-2 adrenergic receptor binding (GO:0031698)|cAMP binding (GO:0030552)|drug binding (GO:0008144)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|metal ion binding (GO:0046872)|scaffold protein binding (GO:0097110)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(8)|pancreas(1)	15		all_cancers(5;6.5e-58)|all_epithelial(5;1.75e-57)|all_lung(5;6.84e-18)|Lung NSC(5;1.29e-17)|Melanoma(5;0.00168)|Prostate(74;0.00234)|Colorectal(97;0.00629)|Ovarian(174;0.00832)|Breast(144;0.00996)|all_hematologic(6;0.0344)|Hepatocellular(6;0.0742)|Esophageal squamous(6;0.0954)		Epithelial(2;2.6e-55)|all cancers(2;2.66e-49)|OV - Ovarian serous cystadenocarcinoma(10;1.48e-39)|Colorectal(2;8.29e-08)|Lung(2;4.47e-07)|STAD - Stomach adenocarcinoma(2;1.11e-05)|COAD - Colon adenocarcinoma(2;0.00012)|LUSC - Lung squamous cell carcinoma(2;0.000775)|LUAD - Lung adenocarcinoma(3;0.0173)|READ - Rectum adenocarcinoma(2;0.0276)	Adenosine monophosphate(DB00131)|Caffeine(DB00201)|Dyphylline(DB00651)|Ibudilast(DB05266)|Iloprost(DB01088)|Ketotifen(DB00920)|Roflumilast(DB01656)	TTACCTGTGATTTTTCCACGG	0.438																																					p.S670fs		Atlas-INDEL	.											.	PDE4D	345	.	0			c.2008delT						.						81.0	85.0	84.0					5																	58271490		2147	4290	6437	SO:0001589	frameshift_variant	5144	exon14			.		CCDS47213.1, CCDS54858.1, CCDS54859.1, CCDS56369.1, CCDS56370.1, CCDS56371.1, CCDS56372.1, CCDS56373.1	5q12	2010-06-24	2010-06-24				3.1.4.17	"""Phosphodiesterases"""	8783	protein-coding gene	gene with protein product	"""phosphodiesterase E3 dunce homolog (Drosophila)"""	600129	"""phosphodiesterase 4D, cAMP-specific (dunce (Drosophila)-homolog phosphodiesterase E3)"""	DPDE3			Standard	NM_006203		Approved		uc003jsa.2	Q08499		ENST00000340635.6:c.2007delA	chr5.hg19:g.58271490delT	ENSP00000345502:p.Lys669fs	142.0	0.0		180.0	11.0	NM_001104631	O43433|Q13549|Q13550|Q13551|Q7Z2L8|Q8IV84|Q8IVA9|Q8IVD2|Q8IVD3|Q96HL4|Q9HCX7	Frame_Shift_Del	DEL	ENST00000340635.6	hg19	CCDS47213.1																																																																																			.	.		0.438	PDE4D-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367940.3		
HOXB2	3212	hgsc.bcm.edu	37	17	46620942	46620942	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:46620942delC	ENST00000330070.4	-	2	1726	c.559delG	c.(559-561)gtcfs	p.V187fs	HOXB-AS1_ENST00000435312.1_RNA|HOXB-AS1_ENST00000504972.3_RNA|HOXB-AS1_ENST00000508688.1_RNA|HOXB2_ENST00000504772.3_5'Flank	NM_002145.3	NP_002136.1	P14652	HXB2_HUMAN	homeobox B2	187					anterior/posterior pattern specification (GO:0009952)|blood circulation (GO:0008015)|dorsal/ventral pattern formation (GO:0009953)|embryonic skeletal system morphogenesis (GO:0048704)|facial nerve structural organization (GO:0021612)|morphogenesis of an epithelial sheet (GO:0002011)|multicellular organismal development (GO:0007275)|neural nucleus development (GO:0048857)|rhombomere 3 development (GO:0021569)|rhombomere 4 development (GO:0021570)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|prostate(1)|skin(1)	11						CAGACTTTGACCTGCCTTTCG	0.627																																					p.V187fs		Atlas-INDEL	.											.	HOXB2	23	.	0			c.560delT						.						54.0	59.0	57.0					17																	46620942		2193	4294	6487	SO:0001589	frameshift_variant	3212	exon2			.		CCDS11527.1	17q21.32	2012-02-22	2005-12-22		ENSG00000173917	ENSG00000173917		"""Homeoboxes / ANTP class : HOXL subclass"""	5113	protein-coding gene	gene with protein product		142967	"""homeo box B2"""	HOX2, HOX2H		1973146, 1358459	Standard	XM_005257276		Approved		uc002inm.3	P14652	OTTHUMG00000159930	ENST00000330070.4:c.559delG	chr17.hg19:g.46620942delC	ENSP00000331741:p.Val187fs	218.0	0.0		181.0	11.0	NM_002145	P10913|P17485	Frame_Shift_Del	DEL	ENST00000330070.4	hg19	CCDS11527.1																																																																																			.	.		0.627	HOXB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358384.2		
PCCB	5096	hgsc.bcm.edu	37	3	135979364	135979364	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:135979364delA	ENST00000251654.4	+	4	486	c.416delA	c.(415-417)caafs	p.Q139fs	PCCB_ENST00000474833.1_Intron|PCCB_ENST00000490504.1_Intron|PCCB_ENST00000478469.1_Frame_Shift_Del_p.Q139fs|PCCB_ENST00000469217.1_Frame_Shift_Del_p.Q159fs|PCCB_ENST00000468777.1_Frame_Shift_Del_p.Q170fs|PCCB_ENST00000471595.1_Frame_Shift_Del_p.Q139fs|PCCB_ENST00000466072.1_Frame_Shift_Del_p.Q139fs|PCCB_ENST00000483687.1_Intron|PCCB_ENST00000462637.1_Frame_Shift_Del_p.Q116fs|PCCB_ENST00000482086.1_Intron	NM_000532.4	NP_000523.2	P05166	PCCB_HUMAN	propionyl CoA carboxylase, beta polypeptide	139	Carboxyltransferase.				biotin metabolic process (GO:0006768)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|short-chain fatty acid catabolic process (GO:0019626)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|propionyl-CoA carboxylase activity (GO:0004658)			breast(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(10)|ovary(1)|urinary_tract(1)	25					Biotin(DB00121)|L-Valine(DB00161)	GCACATGCCCAAAAGATCTGC	0.373																																					p.Q159fs		Atlas-INDEL	.											.	PCCB	52	.	0			c.475delC						.						130.0	118.0	122.0					3																	135979364		2203	4300	6503	SO:0001589	frameshift_variant	5096	exon5			.		CCDS3089.1, CCDS54643.1	3q21-q22	2010-07-01	2010-04-30		ENSG00000114054	ENSG00000114054	6.4.1.3		8654	protein-coding gene	gene with protein product		232050	"""propionyl Coenzyme A carboxylase, beta polypeptide"""			2895916	Standard	NM_000532		Approved		uc003eqy.2	P05166	OTTHUMG00000159792	ENST00000251654.4:c.416delA	chr3.hg19:g.135979364delA	ENSP00000251654:p.Gln139fs	122.0	0.0		152.0	10.0	NM_001178014	B7Z2Z4|Q16813|Q96CX0	Frame_Shift_Del	DEL	ENST00000251654.4	hg19	CCDS3089.1																																																																																			.	.		0.373	PCCB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000357335.1		
PAPSS1	9061	hgsc.bcm.edu	37	4	108615045	108615045	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:108615045delT	ENST00000265174.4	-	3	565	c.293delA	c.(292-294)aatfs	p.N98fs	PAPSS1_ENST00000511304.1_Intron	NM_005443.4	NP_005434.4	O43252	PAPS1_HUMAN	3'-phosphoadenosine 5'-phosphosulfate synthase 1	98					3'-phosphoadenosine 5'-phosphosulfate biosynthetic process (GO:0050428)|3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)|sulfate assimilation (GO:0000103)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	adenylylsulfate kinase activity (GO:0004020)|ATP binding (GO:0005524)|nucleotidyltransferase activity (GO:0016779)|sulfate adenylyltransferase (ATP) activity (GO:0004781)			NS(1)|endometrium(2)|kidney(5)|large_intestine(2)|lung(5)|ovary(1)	16		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;5.49e-05)		AAAGCCAAGATTTTTATTGAG	0.443																																					p.N98fs		Atlas-INDEL	.											.	PAPSS1	57	.	0			c.294delT						.						140.0	125.0	130.0					4																	108615045		2203	4300	6503	SO:0001589	frameshift_variant	9061	exon3			.	Y10387	CCDS3676.1	4q24	2012-07-13			ENSG00000138801	ENSG00000138801	2.7.7.4, 2.7.1.25		8603	protein-coding gene	gene with protein product		603262				9576487, 9771708	Standard	NM_005443		Approved	ATPSK1, PAPSS	uc003hyk.3	O43252	OTTHUMG00000131210	ENST00000265174.4:c.293delA	chr4.hg19:g.108615045delT	ENSP00000265174:p.Asn98fs	102.0	0.0		107.0	11.0	NM_005443	O43841|O75332|Q96FB1|Q96TF4|Q9P1P9|Q9UE98	Frame_Shift_Del	DEL	ENST00000265174.4	hg19	CCDS3676.1																																																																																			.	.		0.443	PAPSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253946.2		
FAM135A	57579	hgsc.bcm.edu	37	6	71191751	71191751	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:71191751delT	ENST00000418814.2	+	10	1331	c.717delT	c.(715-717)cgtfs	p.R239fs	FAM135A_ENST00000361499.3_Frame_Shift_Del_p.R239fs|FAM135A_ENST00000505769.1_Frame_Shift_Del_p.R239fs|FAM135A_ENST00000505868.1_Frame_Shift_Del_p.R239fs|FAM135A_ENST00000457062.2_Frame_Shift_Del_p.R196fs|FAM135A_ENST00000370479.3_Frame_Shift_Del_p.R196fs	NM_001105531.2|NM_001162529.1	NP_001099001.1|NP_001156001.1	Q9P2D6	F135A_HUMAN	family with sequence similarity 135, member A	239										breast(2)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(12)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	38						ATGCGTATCGTTTTCATTATA	0.388																																					p.R239fs		Atlas-INDEL	.											.	FAM135A	181	.	0			c.716delG						.						210.0	180.0	190.0					6																	71191751		2203	4300	6503	SO:0001589	frameshift_variant	57579	exon8			.	AK000183	CCDS34481.1, CCDS47448.1, CCDS55028.1	6q13	2008-10-30	2007-05-11	2007-05-11	ENSG00000082269	ENSG00000082269			21084	protein-coding gene	gene with protein product			"""KIAA1411"""	KIAA1411		10718198	Standard	NM_001105531		Approved	FLJ20176	uc003pfj.3	Q9P2D6	OTTHUMG00000014991	ENST00000418814.2:c.717delT	chr6.hg19:g.71191751delT	ENSP00000410768:p.Arg239fs	142.0	0.0		154.0	10.0	NM_001162529	A2RRQ5|Q3C0H3|Q5JXK0|Q5JXK1|Q68DW0|Q6P081|Q9H0F2|Q9NU48|Q9NUQ5|Q9NXL5	Frame_Shift_Del	DEL	ENST00000418814.2	hg19	CCDS55028.1																																																																																			.	.		0.388	FAM135A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041137.2	NM_020819	
THSD7A	221981	hgsc.bcm.edu	37	7	11632925	11632925	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:11632925delT	ENST00000423059.4	-	3	1478	c.1227delA	c.(1225-1227)aaafs	p.K409fs		NM_015204.2	NP_056019.1	Q9UPZ6	THS7A_HUMAN	thrombospondin, type I, domain containing 7A	409	TSP type-1 3. {ECO:0000255|PROSITE- ProRule:PRU00210}.				angiogenesis (GO:0001525)|cell differentiation (GO:0030154)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(5)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(7)|lung(68)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(11)	113				UCEC - Uterine corpus endometrioid carcinoma (126;0.163)		AACAGGGTTCTTTTTCTTCAA	0.478										HNSCC(18;0.044)																											p.E410fs		Atlas-INDEL	.											THSD7A,colon,carcinoma,0,1	THSD7A	219	.	0			c.1228delG						.						88.0	85.0	86.0					7																	11632925		1910	4133	6043	SO:0001589	frameshift_variant	221981	exon3			.		CCDS47543.1	7p21.3	2006-10-16			ENSG00000005108	ENSG00000005108			22207	protein-coding gene	gene with protein product		612249					Standard	NM_015204		Approved	KIAA0960	uc021zzn.1	Q9UPZ6	OTTHUMG00000152346	ENST00000423059.4:c.1227delA	chr7.hg19:g.11632925delT	ENSP00000406482:p.Lys409fs	96.0	0.0		124.0	10.0	NM_015204		Frame_Shift_Del	DEL	ENST00000423059.4	hg19	CCDS47543.1																																																																																			.	.		0.478	THSD7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325944.4	XM_928187.2	
DDX52	11056	hgsc.bcm.edu	37	17	35988606	35988606	+	Splice_Site	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:35988606delA	ENST00000349699.2	-	6	901	c.858delT	c.(856-858)ttt>tt	p.F286fs	DDX52_ENST00000394367.3_Splice_Site_p.F178fs	NM_007010.3	NP_008941.2	Q9Y2R4	DDX52_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 52	286	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.					membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			biliary_tract(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(5)|ovary(1)|skin(3)	17		Breast(25;0.00637)|Ovarian(249;0.15)				ATTCCTTACCAAACTTTTTAG	0.343																																					p.D287fs		Atlas-INDEL	.											.	DDX52	40	.	0			c.859delG						.						116.0	110.0	112.0					17																	35988606		2203	4300	6503	SO:0001630	splice_region_variant	11056	exon6			.	AF077033	CCDS11323.1	17q21.1	2014-05-06			ENSG00000141141	ENSG00000278053		"""DEAD-boxes"""	20038	protein-coding gene	gene with protein product		612500				11124703	Standard	XM_006721650		Approved	ROK1	uc002hoi.2	Q9Y2R4	OTTHUMG00000188475	ENST00000349699.2:c.859+1T>-	chr17.hg19:g.35988606delA		102.0	0.0		142.0	11.0	NM_007010	Q86YG1|Q8N213|Q9NVE0|Q9Y482	Frame_Shift_Del	DEL	ENST00000349699.2	hg19	CCDS11323.1																																																																																			.	.		0.343	DDX52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256795.1	NM_152300	Frame_Shift_Del
CMBL	134147	hgsc.bcm.edu	37	5	10282342	10282342	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:10282342delA	ENST00000296658.3	-	5	945	c.525delT	c.(523-525)tttfs	p.F175fs	CMBL_ENST00000510532.1_Intron	NM_138809.3	NP_620164.1	Q96DG6	CMBL_HUMAN	carboxymethylenebutenolidase homolog (Pseudomonas)	175						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	hydrolase activity (GO:0016787)			endometrium(1)|large_intestine(1)|lung(9)|skin(1)|stomach(1)	13						CATTTTCAGCAAAAATGAACA	0.408																																					p.A176fs		Atlas-INDEL	.											.	CMBL	24	.	0			c.526delG						.						98.0	101.0	100.0					5																	10282342		2203	4300	6503	SO:0001589	frameshift_variant	134147	exon5			.		CCDS3878.1	5p15.2	2010-06-25	2006-09-12		ENSG00000164237	ENSG00000164237	3.1.-.-		25090	protein-coding gene	gene with protein product		613379	"""carboxymethylenebutenolidase-like (Pseudomonas)"""			3804974, 20177059	Standard	NM_138809		Approved	FLJ23617	uc003jes.3	Q96DG6	OTTHUMG00000131043	ENST00000296658.3:c.525delT	chr5.hg19:g.10282342delA	ENSP00000296658:p.Phe175fs	109.0	0.0		178.0	13.0	NM_138809	D3DTC7|Q8TED6	Frame_Shift_Del	DEL	ENST00000296658.3	hg19	CCDS3878.1																																																																																			.	.		0.408	CMBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253689.1	NM_138809	
KCNAB1	7881	hgsc.bcm.edu	37	3	155838473	155838473	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:155838473delG	ENST00000490337.1	+	1	137	c.73delG	c.(73-75)gggfs	p.G25fs	KCNAB1_ENST00000389636.5_Frame_Shift_Del_p.G25fs	NM_172160.2	NP_751892.1	Q14722	KCAB1_HUMAN	potassium voltage-gated channel, shaker-related subfamily, beta member 1	25					learning or memory (GO:0007611)|potassium ion transport (GO:0006813)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium channel regulator activity (GO:0015459)|voltage-gated potassium channel activity (GO:0005249)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	28			LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)			GAGACAGTCTGGGTTTTCTGT	0.542																																					p.S24fs		Atlas-Indel,Pindel	.											.	KCNAB1	176	.	0			c.72delT						.						98.0	108.0	105.0					3																	155838473		2203	4300	6503	SO:0001589	frameshift_variant	7881	exon1			.	U33428	CCDS3174.1, CCDS3175.1, CCDS33882.1	3q26.1	2006-11-29			ENSG00000169282	ENSG00000169282		"""Potassium channels"", ""Aldo-keto reductases"""	6228	protein-coding gene	gene with protein product		601141				8838324, 7499366	Standard	NM_172160		Approved	AKR6A3, KCNA1B, hKvBeta3, Kvb1.3, hKvb3	uc003far.2	Q14722	OTTHUMG00000158552	ENST00000490337.1:c.73delG	chr3.hg19:g.155838473delG	ENSP00000419952:p.Gly25fs	109.0	0.0		128.0	26.0	NM_172160	A8K9H8|A8KAD4|B3KPZ4|Q13031|Q13302|Q16547|Q6PI60|Q99869	Frame_Shift_Del	DEL	ENST00000490337.1	hg19	CCDS3174.1																																																																																			.	.		0.542	KCNAB1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351411.1	NM_003471	
LRP1B	53353	hgsc.bcm.edu	37	2	141272298	141272298	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:141272298delT	ENST00000389484.3	-	51	9164	c.8193delA	c.(8191-8193)aaafs	p.K2731fs		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	2731	LDL-receptor class A 16. {ECO:0000255|PROSITE-ProRule:PRU00124}.				protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		TAGAAATACATTTTTGTGCGG	0.378										TSP Lung(27;0.18)																											p.C2732fs	Colon(99;50 2074 2507 20106)	Atlas-INDEL	.											.	LRP1B	1315	.	0			c.8194delT						.						112.0	105.0	107.0					2																	141272298		2203	4300	6503	SO:0001589	frameshift_variant	53353	exon51			.	AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"""Low density lipoprotein receptors"""	6693	protein-coding gene	gene with protein product	"""LRP-deleted in tumors"""	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.8193delA	chr2.hg19:g.141272298delT	ENSP00000374135:p.Lys2731fs	145.0	0.0		194.0	12.0	NM_018557	Q8WY29|Q8WY30|Q8WY31	Frame_Shift_Del	DEL	ENST00000389484.3	hg19	CCDS2182.1																																																																																			.	.		0.378	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557	
CAMK1D	57118	hgsc.bcm.edu	37	10	12856212	12856212	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:12856212delT	ENST00000378847.3	+	7	997	c.660delT	c.(658-660)cctfs	p.P220fs	CAMK1D_ENST00000378845.1_Frame_Shift_Del_p.P220fs	NM_153498.2	NP_705718.1	Q8IU85	KCC1D_HUMAN	calcium/calmodulin-dependent protein kinase ID	220	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				inflammatory response (GO:0006954)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of neuron projection development (GO:0010976)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of phagocytosis (GO:0050766)|positive regulation of respiratory burst (GO:0060267)|regulation of dendrite development (GO:0050773)|regulation of granulocyte chemotaxis (GO:0071622)	calcium- and calmodulin-dependent protein kinase complex (GO:0005954)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)			endometrium(3)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|skin(1)|stomach(1)	16				GBM - Glioblastoma multiforme(1;3.16e-05)		GCTACCCTCCTTTTTATGATG	0.473																																					p.P220fs		Atlas-INDEL	.											.	CAMK1D	99	.	0			c.659delC						.						91.0	81.0	84.0					10																	12856212		2203	4300	6503	SO:0001589	frameshift_variant	57118	exon7			.	AF286366	CCDS7091.1, CCDS7092.1	10p13	2003-11-05			ENSG00000183049	ENSG00000183049			19341	protein-coding gene	gene with protein product		607957				11050006	Standard	XM_006717481		Approved	CKLiK	uc001ilo.3	Q8IU85	OTTHUMG00000017683	ENST00000378847.3:c.660delT	chr10.hg19:g.12856212delT	ENSP00000368124:p.Pro220fs	159.0	0.0		191.0	13.0	NM_153498	B0YIY0|Q9HD31	Frame_Shift_Del	DEL	ENST00000378847.3	hg19	CCDS7091.1																																																																																			.	.		0.473	CAMK1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046820.1	NM_020397	
LINGO4	339398	hgsc.bcm.edu	37	1	151773948	151773948	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:151773948delT	ENST00000368820.3	-	2	2170	c.1233delA	c.(1231-1233)aaafs	p.K411fs	RP11-98D18.17_ENST00000601909.1_lincRNA	NM_001004432.2	NP_001004432.1	Q6UY18	LIGO4_HUMAN	leucine rich repeat and Ig domain containing 4	411	LRRCT.					integral component of membrane (GO:0016021)				breast(2)|cervix(1)|endometrium(4)|large_intestine(5)|lung(4)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	21	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.14)		LUSC - Lung squamous cell carcinoma(543;0.181)			TCAGGGCTGGTTTGCAGGTGA	0.617																																					p.P412fs		Atlas-INDEL	.											.	LINGO4	51	.	0			c.1234delC						.						43.0	43.0	43.0					1																	151773948		2203	4299	6502	SO:0001589	frameshift_variant	339398	exon2			.		CCDS30855.1	1q21.3	2013-01-11	2007-02-01	2007-02-01	ENSG00000213171	ENSG00000213171		"""Immunoglobulin superfamily / I-set domain containing"""	31814	protein-coding gene	gene with protein product		609794	"""leucine rich repeat neuronal 6D"""	LRRN6D			Standard	NM_001004432		Approved		uc001ezf.1	Q6UY18	OTTHUMG00000013059	ENST00000368820.3:c.1233delA	chr1.hg19:g.151773948delT	ENSP00000357810:p.Lys411fs	91.0	0.0		162.0	10.0	NM_001004432		Frame_Shift_Del	DEL	ENST00000368820.3	hg19	CCDS30855.1																																																																																			.	.		0.617	LINGO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036639.1	XM_291387	
ITGB2	3689	hgsc.bcm.edu	37	21	46309403	46309403	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr21:46309403delC	ENST00000397850.2	-	14	2117	c.1665delG	c.(1663-1665)gggfs	p.G555fs	ITGB2_ENST00000355153.4_Frame_Shift_Del_p.G555fs|ITGB2_ENST00000397854.3_Frame_Shift_Del_p.G498fs|ITGB2_ENST00000302347.5_Frame_Shift_Del_p.G555fs|ITGB2_ENST00000397857.1_Frame_Shift_Del_p.G555fs|ITGB2_ENST00000397852.1_Frame_Shift_Del_p.G555fs			P05107	ITB2_HUMAN	integrin, beta 2 (complement component 3 receptor 3 and 4 subunit)	555	Cysteine-rich tandem repeats.				apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|cell-matrix adhesion (GO:0007160)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|neutrophil chemotaxis (GO:0030593)|receptor clustering (GO:0043113)|regulation of cell shape (GO:0008360)|regulation of immune response (GO:0050776)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integrin alphaL-beta2 complex (GO:0034687)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|vesicle (GO:0031982)	cell adhesion molecule binding (GO:0050839)|glycoprotein binding (GO:0001948)|ICAM-3 receptor activity (GO:0030369)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)			breast(2)|central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(6)|lung(14)|ovary(4)|skin(3)	35				Colorectal(79;0.0669)	Simvastatin(DB00641)	AGAAGCAGAGCCCCCTCCCTG	0.697																																					p.L556fs		Atlas-INDEL	.											.	ITGB2	107	.	0			c.1666delC						.						24.0	20.0	22.0					21																	46309403		2160	4257	6417	SO:0001589	frameshift_variant	3689	exon13			.	AK222505	CCDS13716.1	21q22.3	2014-09-17	2006-03-02		ENSG00000160255	ENSG00000160255		"""CD molecules"", ""Complement system"", ""Integrins"""	6155	protein-coding gene	gene with protein product		600065	"""integrin, beta 2 (antigen CD18 (p95), lymphocyte function-associated antigen 1; macrophage antigen 1 (mac-1) beta subunit)"""	CD18, MFI7			Standard	NM_000211		Approved	LFA-1, MAC-1	uc002zgf.3	P05107	OTTHUMG00000090257	ENST00000397850.2:c.1665delG	chr21.hg19:g.46309403delC	ENSP00000380948:p.Gly555fs	159.0	0.0		174.0	11.0	NM_000211	B3KTS8|D3DSM1|Q16418|Q53HS5|Q9UD72	Frame_Shift_Del	DEL	ENST00000397850.2	hg19	CCDS13716.1																																																																																			.	.		0.697	ITGB2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206566.2	NM_000211	
CEP41	95681	hgsc.bcm.edu	37	7	130039927	130039927	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:130039927delT	ENST00000223208.5	-	10	1196	c.926delA	c.(925-927)aagfs	p.K309fs	CEP41_ENST00000343969.5_Intron|CEP41_ENST00000541543.1_Intron	NM_001257158.1|NM_018718.2	NP_001244087.1|NP_061188.1	Q9BYV8	CEP41_HUMAN	centrosomal protein 41kDa	309					cilium assembly (GO:0042384)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|protein polyglutamylation (GO:0018095)|protein transport (GO:0015031)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytosol (GO:0005829)|membrane (GO:0016020)|primary cilium (GO:0072372)											ATATTCTATCTTTTTTAAGTC	0.453																																					p.K309fs		Atlas-INDEL	.											TSGA14,bladder,carcinoma,0,1	.	.	.	0			c.927delG						.						70.0	76.0	74.0					7																	130039927		2203	4300	6503	SO:0001589	frameshift_variant	95681	exon10			.	AJ278890	CCDS5821.1, CCDS59078.1, CCDS59079.1, CCDS59080.1	7q32	2014-02-20	2011-10-04	2011-10-04	ENSG00000106477	ENSG00000106477			12370	protein-coding gene	gene with protein product		610523	"""testis specific, 14"""	TSGA14		14654843, 22246503	Standard	NM_018718		Approved	DKFZp762H1311, FLJ22445, JBTS15	uc003vpz.4	Q9BYV8	OTTHUMG00000157823	ENST00000223208.5:c.926delA	chr7.hg19:g.130039927delT	ENSP00000223208:p.Lys309fs	62.0	0.0		115.0	11.0	NM_018718	A4D1M0|B4DQ35|F5H0V6|Q7Z496|Q86TM1|Q8NFU8|Q9H6A3|Q9NPV3	Frame_Shift_Del	DEL	ENST00000223208.5	hg19	CCDS5821.1																																																																																			.	.		0.453	CEP41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349702.2	NM_018718	
PAM16	51025	hgsc.bcm.edu	37	16	4391385	4391385	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:4391385delG	ENST00000318059.3	-	3	346	c.209delC	c.(208-210)cctfs	p.P70fs	PAM16_ENST00000576217.1_Frame_Shift_Del_p.P70fs|PAM16_ENST00000573553.1_Frame_Shift_Del_p.P90fs|CORO7-PAM16_ENST00000572274.1_5'UTR|PAM16_ENST00000577031.1_Frame_Shift_Del_p.P70fs|CORO7-PAM16_ENST00000572467.1_Frame_Shift_Del_p.P993fs|PAM16_ENST00000571941.1_Frame_Shift_Del_p.P90fs|PAM16_ENST00000575848.1_Frame_Shift_Del_p.P82fs	NM_016069.9	NP_057153.8	Q9Y3D7	TIM16_HUMAN	presequence translocase-associated motor 16 homolog (S. cerevisiae)	70	J-like.				cellular protein metabolic process (GO:0044267)|protein import into mitochondrial matrix (GO:0030150)|protein targeting to mitochondrion (GO:0006626)	mitochondrial inner membrane presequence translocase complex (GO:0005744)				lung(3)	3						GACCTCCTCAGGGCTCAGCTT	0.652																																					p.P993fs		Atlas-INDEL	.											.	.	.	.	0			c.2979delT						.						34.0	29.0	30.0					16																	4391385		2179	4294	6473	SO:0001589	frameshift_variant	100529144	exon29			.	AK026514	CCDS10512.1	16p13.3	2010-10-12	2010-10-12		ENSG00000217930	ENSG00000217930			29679	protein-coding gene	gene with protein product	"""mitochondria associated protein involved in granulocyte macrophage colony stimulating factor signal transduction"""	614336				10810093, 11750097	Standard	NM_016069		Approved	Magmas, Tim16, TIMM16		Q9Y3D7	OTTHUMG00000129466	ENST00000318059.3:c.209delC	chr16.hg19:g.4391385delG	ENSP00000315693:p.Pro70fs	194.0	0.0		202.0	15.0	NM_001201479	Q6I9Z3|Q9H5X3	Frame_Shift_Del	DEL	ENST00000318059.3	hg19	CCDS10512.1																																																																																			.	.		0.652	PAM16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251629.2	NM_016069	
FAM65B	9750	hgsc.bcm.edu	37	6	24843580	24843580	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:24843580delC	ENST00000259698.4	-	14	1605	c.1430delG	c.(1429-1431)ggtfs	p.G477fs	FAM65B_ENST00000540914.1_Frame_Shift_Del_p.G427fs|FAM65B_ENST00000473070.1_5'Flank|FAM65B_ENST00000538035.1_Frame_Shift_Del_p.G456fs|FAM65B_ENST00000378023.4_Frame_Shift_Del_p.G427fs|FAM65B_ENST00000510784.2_Frame_Shift_Del_p.G461fs	NM_014722.2	NP_055537.2	Q9Y4F9	FA65B_HUMAN	family with sequence similarity 65, member B	477					cell differentiation (GO:0030154)|muscle organ development (GO:0007517)	cell projection (GO:0042995)|cytoskeleton (GO:0005856)|mitochondrion (GO:0005739)				breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	25						GTCATCCATACCCTCATTCTG	0.537																																					p.G477fs		Atlas-INDEL	.											.	FAM65B	134	.	0			c.1431delT						.						111.0	103.0	105.0					6																	24843580		1944	4145	6089	SO:0001589	frameshift_variant	9750	exon14			.	U49187	CCDS47383.1, CCDS47384.1, CCDS69057.1, CCDS69058.1, CCDS75410.1	6p22.3-p21.32	2012-11-30	2008-06-13	2008-06-13	ENSG00000111913	ENSG00000111913			13872	protein-coding gene	gene with protein product	"""myogenesis-related and NCAM-associated protein homolog (chicken)"""	611410	"""chromosome 6 open reading frame 32"""	C6orf32		9205841, 17150207, 17825087	Standard	NM_001286447		Approved	KIAA0386, DIFF48, MYONAP	uc003neo.1	Q9Y4F9	OTTHUMG00000014375	ENST00000259698.4:c.1430delG	chr6.hg19:g.24843580delC	ENSP00000259698:p.Gly477fs	102.0	0.0		177.0	11.0	NM_014722	A6NHP2|Q13529|Q5VV37|Q5VV38|Q9BQ28	Frame_Shift_Del	DEL	ENST00000259698.4	hg19	CCDS47383.1																																																																																			.	.		0.537	FAM65B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040024.2		
SPECC1	92521	hgsc.bcm.edu	37	17	19999991	19999991	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:19999991delC	ENST00000261503.5	+	2	78	c.27delC	c.(25-27)aacfs	p.N9fs	SPECC1_ENST00000395529.3_Frame_Shift_Del_p.N9fs|SPECC1_ENST00000472876.1_Intron|SPECC1_ENST00000395527.4_Frame_Shift_Del_p.N9fs	NM_001033553.2	NP_001028725.1	Q5M775	CYTSB_HUMAN	sperm antigen with calponin homology and coiled-coil domains 1	9					cell adhesion (GO:0007155)	nucleus (GO:0005634)				breast(1)|large_intestine(3)|ovary(4)	8				KIRC - Kidney renal clear cell carcinoma(2;0.166)|Kidney(2;0.196)		AGCCCTGGAACCCAGCCATCA	0.562																																					p.N9fs		Atlas-INDEL	.											.	SPECC1	100	.	0			c.26delA						.						74.0	84.0	81.0					17																	19999991		2203	4300	6503	SO:0001589	frameshift_variant	92521	exon2			.	AY816329, AB041533	CCDS32590.1, CCDS42280.1, CCDS42281.1, CCDS45628.1, CCDS58531.1	17p11.2	2012-11-19	2010-09-17	2010-09-17	ENSG00000128487	ENSG00000128487			30615	protein-coding gene	gene with protein product	"""sperm antigen HCMOGT 1"", ""cytokinesis and spindle organization B"", ""cytospin B"""	608793				15602574, 18763323, 15087372	Standard	NM_001033553		Approved	HCMOGT-1, FLJ36955, NSP, CYTSB	uc002gwq.3	Q5M775	OTTHUMG00000179808	ENST00000261503.5:c.27delC	chr17.hg19:g.19999991delC	ENSP00000261503:p.Asn9fs	168.0	0.0		158.0	11.0	NM_001033553	B4DHH0|B7WNS8|Q5IBP1|Q5IBP2|Q5IBP3|Q5IBP4|Q5M772|Q5M773|Q5M774|Q86XT8|Q8N4U4|Q8WU84|Q9HCQ3	Frame_Shift_Del	DEL	ENST00000261503.5	hg19	CCDS32590.1																																																																																			.	.		0.562	SPECC1-018	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441206.1	NM_152904	
ZNF484	83744	hgsc.bcm.edu	37	9	95609839	95609839	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:95609839delT	ENST00000375495.3	-	5	1378	c.1230delA	c.(1228-1230)aaafs	p.K410fs	ZNF484_ENST00000395506.3_Frame_Shift_Del_p.K412fs|ZNF484_ENST00000332591.6_Frame_Shift_Del_p.K374fs|ANKRD19P_ENST00000473204.1_RNA|ZNF484_ENST00000395505.2_Frame_Shift_Del_p.K374fs	NM_031486.2	NP_113674.1	Q5JVG2	ZN484_HUMAN	zinc finger protein 484	410					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|cervix(1)|kidney(8)|large_intestine(10)|lung(10)|prostate(2)	33						ATACATAAGGTTTTTCTCCTG	0.373																																					p.P413fs		Atlas-INDEL	.											.	ZNF484	81	.	0			c.1237delC						.						69.0	74.0	72.0					9																	95609839		2203	4300	6503	SO:0001589	frameshift_variant	83744	exon4			.	AK091203	CCDS35066.1, CCDS35067.1, CCDS59136.1	9q22.32	2013-01-08			ENSG00000127081	ENSG00000127081		"""Zinc fingers, C2H2-type"", ""-"""	23385	protein-coding gene	gene with protein product							Standard	NM_001007101		Approved	BA526D8.4, FLJ33884	uc004asu.2	Q5JVG2	OTTHUMG00000020236	ENST00000375495.3:c.1230delA	chr9.hg19:g.95609839delT	ENSP00000364645:p.Lys410fs	98.0	0.0		146.0	11.0	NM_001261458	B1AL89|B4DRI2	Frame_Shift_Del	DEL	ENST00000375495.3	hg19	CCDS35066.1																																																																																			.	.		0.373	ZNF484-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000053111.2	XM_046861	
KCTD13	253980	hgsc.bcm.edu	37	16	29922397	29922397	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:29922397delC	ENST00000568000.1	-	5	1656	c.655delG	c.(655-657)gacfs	p.D219fs		NM_178863.3	NP_849194.1	Q8WZ19	BACD1_HUMAN	potassium channel tetramerization domain containing 13	219					cell migration (GO:0016477)|DNA replication (GO:0006260)|negative regulation of Rho protein signal transduction (GO:0035024)|positive regulation of DNA replication (GO:0045740)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein homooligomerization (GO:0051260)|protein ubiquitination (GO:0016567)|stress fiber assembly (GO:0043149)	Cul3-RING ubiquitin ligase complex (GO:0031463)|nucleus (GO:0005634)	GTP-Rho binding (GO:0017049)			breast(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(2)	7						CAGATCTCGTCCCCCAGGACA	0.562																																					p.D219fs		Atlas-INDEL	.											.	KCTD13	19	.	0			c.656delA						.						85.0	71.0	76.0					16																	29922397		2197	4300	6497	SO:0001589	frameshift_variant	253980	exon5			.	AF289573	CCDS10661.1	16p11.2	2013-06-20	2013-06-20		ENSG00000174943	ENSG00000174943			22234	protein-coding gene	gene with protein product	"""polymerase delta-interacting protein 1"", ""TNFAIP1-like"""	608947	"""potassium channel tetramerisation domain containing 13"""			11593007	Standard	NM_178863		Approved	PDIP1, FKSG86, POLDIP1	uc002duv.4	Q8WZ19	OTTHUMG00000132120	ENST00000568000.1:c.655delG	chr16.hg19:g.29922397delC	ENSP00000455785:p.Asp219fs	144.0	0.0		170.0	12.0	NM_178863	A8K0R5|Q96P93|Q96SA1	Frame_Shift_Del	DEL	ENST00000568000.1	hg19	CCDS10661.1																																																																																			.	.		0.562	KCTD13-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255162.2	NM_178863	
SLC12A9	56996	hgsc.bcm.edu	37	7	100459490	100459490	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:100459490delG	ENST00000354161.3	+	12	1793	c.1668delG	c.(1666-1668)aagfs	p.K556fs	SLC12A9_ENST00000415287.1_Frame_Shift_Del_p.K467fs|SLC12A9_ENST00000275729.3_Frame_Shift_Del_p.K467fs|SLC12A9_ENST00000428758.1_Frame_Shift_Del_p.K556fs|SLC12A9_ENST00000540482.1_Frame_Shift_Del_p.K556fs	NM_020246.3	NP_064631.2	Q9BXP2	S12A9_HUMAN	solute carrier family 12, member 9	556					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cation:chloride symporter activity (GO:0015377)			breast(1)|endometrium(2)|kidney(2)|large_intestine(10)|lung(20)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	41	Lung NSC(181;0.041)|all_lung(186;0.0581)					AGCTTAAGAAGGGGGGGCTGT	0.642																																					p.K556fs		Atlas-INDEL	.											.,1	SLC12A9	81	.	0			c.1667delA						.						28.0	32.0	31.0					7																	100459490		2203	4300	6503	SO:0001589	frameshift_variant	56996	exon12			.	AF284422	CCDS5707.1, CCDS59068.1, CCDS59069.1	7q22	2013-07-18	2013-07-18		ENSG00000146828	ENSG00000146828		"""Solute carriers"""	17435	protein-coding gene	gene with protein product	"""cation-chloride cotransporter-interacting protein"""					10871601, 11239002	Standard	NM_020246		Approved	CIP1	uc003uwp.4	Q9BXP2	OTTHUMG00000156045	ENST00000354161.3:c.1668delG	chr7.hg19:g.100459490delG	ENSP00000275730:p.Lys556fs	135.0	0.0		165.0	12.0	NM_001267812	B7Z740|D6W5X0|D6W5X2|F5H8C2|Q9BWL2|Q9BXP1|Q9BYI0|Q9NQR5	Frame_Shift_Del	DEL	ENST00000354161.3	hg19	CCDS5707.1																																																																																			.	.		0.642	SLC12A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342837.1	NM_020246	
DPP3	10072	hgsc.bcm.edu	37	11	66252728	66252728	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:66252728delC	ENST00000360510.2	+	3	420	c.355delC	c.(355-357)cccfs	p.P119fs	DPP3_ENST00000532677.1_Frame_Shift_Del_p.P138fs|DPP3_ENST00000531863.1_Frame_Shift_Del_p.P139fs|DPP3_ENST00000541961.1_Frame_Shift_Del_p.P119fs|DPP3_ENST00000453114.1_Frame_Shift_Del_p.P119fs|DPP3_ENST00000530165.1_Intron			Q9NY33	DPP3_HUMAN	dipeptidyl-peptidase 3	119					proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	dipeptidyl-peptidase activity (GO:0008239)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|skin(2)|stomach(1)	23						TCCCAACTTGCCCAAGGTGAG	0.572																																					p.L118fs		Atlas-INDEL	.											.	DPP3	61	.	0			c.354delG						.						68.0	58.0	61.0					11																	66252728		2200	4295	6495	SO:0001589	frameshift_variant	10072	exon3			.	AB017970	CCDS8141.1, CCDS58147.1	11q12-q13.1	2008-02-05	2006-01-12		ENSG00000254986	ENSG00000254986	3.4.14.4		3008	protein-coding gene	gene with protein product		606818	"""dipeptidylpeptidase III"", ""dipeptidylpeptidase 3"""			10773679	Standard	NM_005700		Approved		uc001oif.2	Q9NY33	OTTHUMG00000167143	ENST00000360510.2:c.355delC	chr11.hg19:g.66252728delC	ENSP00000353701:p.Pro119fs	105.0	0.0		109.0	10.0	NM_130443	B2RDB5|B4DLX4|F5H8L6|O95748|Q969H2|Q9BV67|Q9HAL6	Frame_Shift_Del	DEL	ENST00000360510.2	hg19	CCDS8141.1																																																																																			.	.		0.572	DPP3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393424.2		
PARP14	54625	hgsc.bcm.edu	37	3	122437236	122437236	+	Frame_Shift_Del	DEL	A	A	-	rs61732768	byFrequency	TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:122437236delA	ENST00000474629.2	+	14	4504	c.4238delA	c.(4237-4239)caafs	p.Q1413fs	PARP14_ENST00000475640.1_3'UTR	NM_017554.2	NP_060024.2	Q460N5	PAR14_HUMAN	poly (ADP-ribose) polymerase family, member 14	1413					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	NAD+ ADP-ribosyltransferase activity (GO:0003950)			NS(2)|breast(5)|cervix(2)|endometrium(7)|kidney(5)|large_intestine(8)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	50				GBM - Glioblastoma multiforme(114;0.0531)		CAATCTCCCCAAAAAAAGAAT	0.358																																					p.Q1413fs		Atlas-INDEL	.											.,2	PARP14	242	.	0			c.4237delC						.						86.0	84.0	84.0					3																	122437236		1897	4109	6006	SO:0001589	frameshift_variant	54625	exon14			.	AB033094	CCDS46894.1	3q21	2010-02-16			ENSG00000173193	ENSG00000173193		"""Poly (ADP-ribose) polymerases"""	29232	protein-coding gene	gene with protein product		610028				15273990	Standard	NM_017554		Approved	KIAA1268, pART8	uc003efq.4	Q460N5	OTTHUMG00000159552	ENST00000474629.2:c.4238delA	chr3.hg19:g.122437236delA	ENSP00000418194:p.Gln1413fs	88.0	0.0		158.0	13.0	NM_017554	B4E2H0|Q460N4|Q8J027|Q9H9X9|Q9NV60|Q9ULF2	Frame_Shift_Del	DEL	ENST00000474629.2	hg19	CCDS46894.1																																																																																			.	.		0.358	PARP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356173.2	NM_017554	
EPN1	29924	hgsc.bcm.edu	37	19	56206189	56206189	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:56206189delC	ENST00000270460.6	+	10	1673	c.1362delC	c.(1360-1362)agcfs	p.S454fs	AC010525.7_ENST00000589698.1_lincRNA|EPN1_ENST00000085079.7_Frame_Shift_Del_p.S428fs|AC010525.4_ENST00000585559.1_RNA|EPN1_ENST00000411543.2_Frame_Shift_Del_p.S540fs|AC010525.6_ENST00000587937.1_lincRNA	NM_001130072.1	NP_001123544.1	Q9Y6I3	EPN1_HUMAN	epsin 1	454	Ala/Gly/Pro-rich.				embryonic organ development (GO:0048568)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|female pregnancy (GO:0007565)|in utero embryonic development (GO:0001701)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|Notch signaling pathway (GO:0007219)	coated pit (GO:0005905)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)			endometrium(5)|kidney(1)|large_intestine(2)|lung(8)|skin(1)	17		Colorectal(82;0.00244)|Ovarian(87;0.133)		GBM - Glioblastoma multiforme(193;0.112)		CTGTGGGCAGCCCCCCACCTG	0.687																																					p.S540fs		Atlas-INDEL	.											.	EPN1	98	.	0			c.1619delG						.						19.0	31.0	27.0					19																	56206189		2055	4179	6234	SO:0001589	frameshift_variant	29924	exon10			.	AF073727	CCDS46198.1, CCDS46199.1, CCDS46200.1	19q13.42	2014-08-12			ENSG00000063245	ENSG00000063245			21604	protein-coding gene	gene with protein product		607262				9723620, 10557078	Standard	NM_001130072		Approved		uc002qlx.3	Q9Y6I3	OTTHUMG00000180911	ENST00000270460.6:c.1362delC	chr19.hg19:g.56206189delC	ENSP00000270460:p.Ser454fs	155.0	0.0		188.0	13.0	NM_001130071	Q86ST3|Q9HA18	Frame_Shift_Del	DEL	ENST00000270460.6	hg19	CCDS46199.1																																																																																			.	.		0.687	EPN1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453610.1	NM_013333	
DDIT4L	115265	hgsc.bcm.edu	37	4	101108955	101108955	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:101108955delA	ENST00000273990.2	-	3	675	c.461delT	c.(460-462)ttcfs	p.F155fs	RP11-588P8.1_ENST00000515782.1_RNA|RP11-15B17.1_ENST00000515026.1_RNA	NM_145244.3	NP_660287.1	Q96D03	DDT4L_HUMAN	DNA-damage-inducible transcript 4-like	155					negative regulation of signal transduction (GO:0009968)	cytoplasm (GO:0005737)				breast(2)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|pancreas(2)	12				OV - Ovarian serous cystadenocarcinoma(123;5.75e-09)		TCTACTAAAGAAAAAGTCCCT	0.428																																					p.F154fs		Atlas-INDEL	.											.	DDIT4L	33	.	0			c.462delC						.						90.0	92.0	91.0					4																	101108955		2203	4300	6503	SO:0001589	frameshift_variant	115265	exon3			.	BC013592	CCDS34036.1	4q23	2008-02-05				ENSG00000145358			30555	protein-coding gene	gene with protein product	"""regulated in development and DNA damage response 2"", "" similar to Smhs1 protein"""	607730				12477932	Standard	NM_145244		Approved	REDD2, Rtp801L	uc003hvq.3	Q96D03		ENST00000273990.2:c.461delT	chr4.hg19:g.101108955delA	ENSP00000354830:p.Phe155fs	178.0	0.0		181.0	13.0	NM_145244	B2R7C3	Frame_Shift_Del	DEL	ENST00000273990.2	hg19	CCDS34036.1																																																																																			.	.		0.428	DDIT4L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363423.1	NM_145244	
APOD	347	hgsc.bcm.edu	37	3	195295847	195295847	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:195295847delT	ENST00000343267.3	-	5	855	c.494delA	c.(493-495)aatfs	p.N165fs		NM_001647.3	NP_001638.1	P05090	APOD_HUMAN	apolipoprotein D	165					aging (GO:0007568)|angiogenesis (GO:0001525)|brain development (GO:0007420)|glucose metabolic process (GO:0006006)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|negative regulation of cytokine production involved in inflammatory response (GO:1900016)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of lipoprotein lipid oxidation (GO:0060588)|negative regulation of monocyte chemotactic protein-1 production (GO:0071638)|negative regulation of platelet-derived growth factor receptor signaling pathway (GO:0010642)|negative regulation of protein import into nucleus (GO:0042308)|negative regulation of smooth muscle cell proliferation (GO:0048662)|negative regulation of smooth muscle cell-matrix adhesion (GO:2000098)|negative regulation of T cell migration (GO:2000405)|peripheral nervous system axon regeneration (GO:0014012)|response to axon injury (GO:0048678)|response to drug (GO:0042493)|response to reactive oxygen species (GO:0000302)|tissue regeneration (GO:0042246)	cytosolic ribosome (GO:0022626)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)	cholesterol binding (GO:0015485)|lipid transporter activity (GO:0005319)			breast(1)|endometrium(1)|large_intestine(1)|lung(1)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	9	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)	Lung NSC(153;0.191)	Epithelial(36;1e-21)|all cancers(36;9.02e-20)|OV - Ovarian serous cystadenocarcinoma(49;1.6e-18)|Lung(62;0.000104)|LUSC - Lung squamous cell carcinoma(58;0.000128)	GBM - Glioblastoma multiforme(46;1.66e-05)		AGTCAGGATATTTTTTAGAGA	0.448																																					p.N165fs		Atlas-INDEL	.											.	APOD	28	.	0			c.495delT						.						157.0	160.0	159.0					3																	195295847		2203	4300	6503	SO:0001589	frameshift_variant	347	exon5			.		CCDS33925.1	3q29	2013-09-19			ENSG00000189058	ENSG00000189058		"""Lipocalins"", ""Apolipoproteins"""	612	protein-coding gene	gene with protein product		107740				2439269, 3453108	Standard	NM_001647		Approved		uc003fur.2	P05090	OTTHUMG00000155854	ENST00000343267.3:c.494delA	chr3.hg19:g.195295847delT	ENSP00000345179:p.Asn165fs	198.0	0.0		180.0	11.0	NM_001647	B2R579|D3DNW6|Q6IBG6	Frame_Shift_Del	DEL	ENST00000343267.3	hg19	CCDS33925.1																																																																																			.	.		0.448	APOD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342004.1	NM_001647	
ARID4A	5926	hgsc.bcm.edu	37	14	58796774	58796774	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:58796774delA	ENST00000355431.3	+	11	1166	c.793delA	c.(793-795)aaafs	p.K265fs	ARID4A_ENST00000395168.3_Frame_Shift_Del_p.K265fs|ARID4A_ENST00000431317.2_Frame_Shift_Del_p.K265fs|ARID4A_ENST00000348476.3_Frame_Shift_Del_p.K265fs	NM_002892.3	NP_002883.3	P29374	ARI4A_HUMAN	AT rich interactive domain 4A (RBP1-like)	265					erythrocyte development (GO:0048821)|histone H3-K4 trimethylation (GO:0080182)|histone H3-K9 trimethylation (GO:0036124)|histone H4-K20 trimethylation (GO:0034773)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of gene expression by genetic imprinting (GO:0006349)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|central_nervous_system(1)|cervix(4)|endometrium(8)|kidney(2)|large_intestine(14)|lung(19)|ovary(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	60						TGATAATTGGAAAATGGATAT	0.393																																					p.W264X		Atlas-INDEL	.											.	ARID4A	222	.	0			c.792delG						.						98.0	101.0	100.0					14																	58796774		2203	4300	6503	SO:0001589	frameshift_variant	5926	exon11			.	S57153	CCDS9732.1, CCDS9733.1, CCDS45114.1	14q22.3	2013-02-07	2004-01-28	2004-01-28	ENSG00000032219	ENSG00000032219		"""-"""	9885	protein-coding gene	gene with protein product		180201	"""retinoblastoma-binding protein 1"""	RBBP1		1857421, 8455946	Standard	NM_023000		Approved	RBP1, RBP-1	uc001xdp.3	P29374	OTTHUMG00000140320	ENST00000355431.3:c.793delA	chr14.hg19:g.58796774delA	ENSP00000347602:p.Lys265fs	166.0	0.0		148.0	10.0	NM_002892	Q15991|Q15992|Q15993	Frame_Shift_Del	DEL	ENST00000355431.3	hg19	CCDS9732.1																																																																																			.	.		0.393	ARID4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276927.2	NM_023001	
LILRB2	10288	hgsc.bcm.edu	37	19	54781769	54781769	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:54781769delG	ENST00000391749.4	-	8	1554	c.1283delC	c.(1282-1284)ccafs	p.P429fs	LILRB2_ENST00000314446.5_Frame_Shift_Del_p.P429fs|LILRB2_ENST00000434421.1_Frame_Shift_Del_p.P313fs|LILRB2_ENST00000391748.1_Frame_Shift_Del_p.P429fs|LILRB2_ENST00000391746.1_Frame_Shift_Del_p.P429fs|LILRB2_ENST00000471216.1_5'Flank	NM_001278406.1	NP_001265335.1	Q8N423	LIRB2_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 2	429					cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular defense response (GO:0006968)|cellular response to lipopolysaccharide (GO:0071222)|Fc receptor mediated inhibitory signaling pathway (GO:0002774)|heterotypic cell-cell adhesion (GO:0034113)|immune response (GO:0006955)|immune response-inhibiting cell surface receptor signaling pathway (GO:0002767)|negative regulation of antigen processing and presentation (GO:0002578)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of regulatory T cell differentiation (GO:0045591)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of T cell tolerance induction (GO:0002666)|regulation of dendritic cell differentiation (GO:2001198)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|inhibitory MHC class I receptor activity (GO:0032396)|MHC class I protein binding (GO:0042288)|MHC class Ib protein binding (GO:0023029)|protein phosphatase 1 binding (GO:0008157)|receptor activity (GO:0004872)			breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(30)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	44	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		ACCGGTGGGTGGGGGGCTGGA	0.607																																					p.P428fs		Atlas-INDEL	.											.	LILRB2	94	.	0			c.1284delA						.						19.0	25.0	23.0					19																	54781769		2081	4048	6129	SO:0001589	frameshift_variant	10288	exon8			.	AF000574	CCDS12886.1, CCDS42612.1, CCDS62791.1, CCDS62792.1	19q13.4	2013-01-11			ENSG00000131042	ENSG00000131042		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6606	protein-coding gene	gene with protein product		604815				9151699, 9079806	Standard	XM_006722966		Approved	LIR-2, ILT4, MIR-10, LIR2, CD85d, MIR10	uc002qfb.3	Q8N423	OTTHUMG00000064896	ENST00000391749.4:c.1283delC	chr19.hg19:g.54781769delG	ENSP00000375629:p.Pro429fs	147.0	0.0		242.0	16.0	NM_005874	A8MU67|C9JF29|O75017|Q8NHJ7|Q8NHJ8	Frame_Shift_Del	DEL	ENST00000391749.4	hg19	CCDS12886.1																																																																																			.	.		0.607	LILRB2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139510.1		
C1D	10438	hgsc.bcm.edu	37	2	68270088	68270088	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:68270088delT	ENST00000355848.3	-	5	406	c.359delA	c.(358-360)aatfs	p.N120fs	C1D_ENST00000409302.1_Frame_Shift_Del_p.N120fs|C1D_ENST00000407324.1_Frame_Shift_Del_p.N159fs|C1D_ENST00000410067.3_Frame_Shift_Del_p.N120fs			Q13901	C1D_HUMAN	C1D nuclear receptor corepressor	120	Interaction with NCOR1 and NCOR2. {ECO:0000250}.				apoptotic process (GO:0006915)|maturation of 5.8S rRNA (GO:0000460)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear exosome (RNase complex) (GO:0000176)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|RNA binding (GO:0003723)|transcription corepressor activity (GO:0003714)			lung(2)|urinary_tract(1)	3						CCAGAGGGCATTTTTTACAAA	0.348																																					p.N120fs		Atlas-INDEL	.											.	C1D	11	.	0			c.360delT						.						24.0	28.0	27.0					2																	68270088		2199	4296	6495	SO:0001589	frameshift_variant	10438	exon6			.		CCDS1883.1	2p13-p12	2010-06-10	2010-06-10		ENSG00000197223	ENSG00000197223			29911	protein-coding gene	gene with protein product	"""small unique nuclear receptor co-repressor"""	606997	"""C1D nuclear receptor co-repressor"""			9469821, 17599775, 17412707, 11801738, 9405624	Standard	NM_006333		Approved	SUNCOR, SUN-CoR, LRP1	uc002seb.3	Q13901	OTTHUMG00000129564	ENST00000355848.3:c.359delA	chr2.hg19:g.68270088delT	ENSP00000348107:p.Asn120fs	122.0	0.0		164.0	10.0	NM_001190265	A8K336|D6W5F8|Q05D64	Frame_Shift_Del	DEL	ENST00000355848.3	hg19	CCDS1883.1																																																																																			.	.		0.348	C1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251757.3	NM_006333	
HDX	139324	hgsc.bcm.edu	37	X	83730320	83730320	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:83730320delT	ENST00000297977.5	-	2	197	c.86delA	c.(85-87)aatfs	p.N29fs	HDX_ENST00000373177.2_Frame_Shift_Del_p.N29fs|HDX_ENST00000506585.2_Intron	NM_001177479.1|NM_144657.4	NP_001170950.1|NP_653258.2	Q7Z353	HDX_HUMAN	highly divergent homeobox	29						nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|endometrium(6)|kidney(2)|large_intestine(12)|liver(1)|lung(19)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	48						CTGAAAGCAATTTTTACTTTG	0.328																																					p.N29fs	Pancreas(53;231 1169 36156 43751 51139)	Atlas-INDEL	.											.	HDX	124	.	0			c.87delT						.						99.0	82.0	87.0					X																	83730320		2203	4300	6503	SO:0001589	frameshift_variant	139324	exon2			.	BX538112	CCDS35342.1, CCDS55456.1	Xq21.1	2012-03-09	2007-07-13	2007-07-13	ENSG00000165259	ENSG00000165259		"""Homeoboxes / POU class"""	26411	protein-coding gene	gene with protein product			"""chromosome X open reading frame 43"""	CXorf43			Standard	NM_144657		Approved	FLJ30678	uc004eek.2	Q7Z353	OTTHUMG00000021926	ENST00000297977.5:c.86delA	chrX.hg19:g.83730320delT	ENSP00000297977:p.Asn29fs	146.0	0.0		148.0	10.0	NM_144657	A8K1Y5|B7ZL18|Q5JZB4|Q96NK7	Frame_Shift_Del	DEL	ENST00000297977.5	hg19	CCDS35342.1																																																																																			.	.		0.328	HDX-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057379.2	NM_144657	
ZNF532	55205	hgsc.bcm.edu	37	18	56585671	56585671	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr18:56585671delC	ENST00000336078.4	+	4	928	c.152delC	c.(151-153)tccfs	p.S51fs	ZNF532_ENST00000589288.1_Frame_Shift_Del_p.S51fs|ZNF532_ENST00000591083.1_Frame_Shift_Del_p.S51fs|ZNF532_ENST00000591808.1_Frame_Shift_Del_p.S51fs|ZNF532_ENST00000591230.1_Frame_Shift_Del_p.S51fs	NM_018181.4	NP_060651.2	Q9HCE3	ZN532_HUMAN	zinc finger protein 532	51					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(5)|central_nervous_system(1)|cervix(2)|endometrium(14)|kidney(1)|large_intestine(9)|lung(14)|prostate(1)|skin(4)|urinary_tract(1)	52						GAGGATGACTCCCACGCACCA	0.512																																					p.S51fs		Atlas-INDEL	.											.	ZNF532	108	.	0			c.151delT						.						98.0	78.0	85.0					18																	56585671		2203	4300	6503	SO:0001589	frameshift_variant	55205	exon4			.	AB046849	CCDS11969.1	18q21.32	2005-08-22			ENSG00000074657	ENSG00000074657		"""Zinc fingers, C2H2-type"""	30940	protein-coding gene	gene with protein product						10997877	Standard	XM_005266723		Approved	FLJ10697	uc002lho.3	Q9HCE3	OTTHUMG00000132759	ENST00000336078.4:c.152delC	chr18.hg19:g.56585671delC	ENSP00000338217:p.Ser51fs	83.0	0.0		107.0	10.0	NM_018181	Q4G0V6|Q7L7Z7|Q96QR7|Q9NVJ6	Frame_Shift_Del	DEL	ENST00000336078.4	hg19	CCDS11969.1																																																																																			.	.		0.512	ZNF532-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256130.1	NM_018181	
HLA-DRB5	3127	hgsc.bcm.edu	37	6	32487268	32487268	+	Frame_Shift_Del	DEL	A	A	-	rs75732937	byFrequency	TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:32487268delA	ENST00000374975.3	-	3	593	c.531delT	c.(529-531)attfs	p.I177fs		NM_002125.3	NP_002116.2			major histocompatibility complex, class II, DR beta 5											NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|pancreas(1)|prostate(1)|stomach(2)	10						CTCCATTCTGAATCAGGCCTG	0.547																																					p.Q178fs		Atlas-INDEL	.											.	HLA-DRB5	31	.	0			c.532delC						.						61.0	67.0	65.0					6																	32487268		1928	3907	5835	SO:0001589	frameshift_variant	3127	exon3			.		CCDS4751.1	6p21.3	2013-01-11			ENSG00000198502	ENSG00000198502		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4953	protein-coding gene	gene with protein product		604776					Standard	NM_002125		Approved		uc003obj.3	Q30154	OTTHUMG00000031027	ENST00000374975.3:c.531delT	chr6.hg19:g.32487268delA	ENSP00000364114:p.Ile177fs	117.0	0.0		158.0	10.0	NM_002125		Frame_Shift_Del	DEL	ENST00000374975.3	hg19	CCDS4751.1																																																																																			.	.		0.547	HLA-DRB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076022.2	NM_002125	
SLC4A11	83959	hgsc.bcm.edu	37	20	3218620	3218620	+	5'Flank	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr20:3218620delC	ENST00000380056.3	-	0	0				SLC4A11_ENST00000539553.2_Intron|SLC4A11_ENST00000380059.3_Frame_Shift_Del_p.E31fs	NM_032034.3	NP_114423.1	Q8NBS3	S4A11_HUMAN	solute carrier family 4, sodium borate transporter, member 11						bicarbonate transport (GO:0015701)|borate transmembrane transport (GO:0035445)|borate transport (GO:0046713)|cellular cation homeostasis (GO:0030003)|fluid transport (GO:0042044)|proton transport (GO:0015992)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	bicarbonate transmembrane transporter activity (GO:0015106)|borate transmembrane transporter activity (GO:0046715)|hydrogen ion channel activity (GO:0015252)|inorganic anion exchanger activity (GO:0005452)|protein dimerization activity (GO:0046983)|sodium channel activity (GO:0005272)|symporter activity (GO:0015293)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|liver(1)|lung(16)|ovary(2)|prostate(4)|soft_tissue(1)|urinary_tract(1)	40						GCGGGCCTCTCCCCCTCTCTC	0.617																																					p.E31fs	NSCLC(190;922 2139 10266 10292 38692)	Atlas-INDEL	.											.	SLC4A11	188	.	0			c.92delA						.																																			SO:0001631	upstream_gene_variant	83959	exon1			.	AF336127	CCDS13052.1, CCDS54445.1, CCDS54446.1	20p13	2014-02-14	2007-08-03		ENSG00000088836	ENSG00000088836		"""Solute carriers"""	16438	protein-coding gene	gene with protein product		610206	"""corneal endothelial dystrophy 2 (autosomal recessive)"", ""solute carrier family 4, sodium bicarbonate transporter-like, member 11"", ""corneal dystrophy and perceptive deafness 1"""	CHED2, CDPD1		10843999, 11302728, 16767101	Standard	NM_001174089		Approved	dJ794I6.2, BTR1, NaBC1, FECD4	uc010zqe.2	Q8NBS3	OTTHUMG00000031740		chr20.hg19:g.3218620delC	Exception_encountered	111.0	0.0		147.0	10.0	NM_001174090	B4DKC8|B4DKX9|G3V1M3|Q2TB62|Q2TB63|Q9BXF4|Q9NTW9	Frame_Shift_Del	DEL	ENST00000380056.3	hg19	CCDS13052.1																																																																																			.	.		0.617	SLC4A11-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000077728.1		
NOL10	79954	hgsc.bcm.edu	37	2	10742949	10742949	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:10742949delT	ENST00000381685.5	-	16	1390	c.1285delA	c.(1285-1287)atafs	p.I429fs	NOL10_ENST00000538384.1_Frame_Shift_Del_p.I403fs|NOL10_ENST00000345985.3_Frame_Shift_Del_p.I379fs|AC092687.5_ENST00000414538.1_RNA|NOL10_ENST00000542668.1_Frame_Shift_Del_p.I379fs	NM_024894.3	NP_079170.2	Q9BSC4	NOL10_HUMAN	nucleolar protein 10	429						nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)					Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.172)|OV - Ovarian serous cystadenocarcinoma(76;0.207)		TTCTGTCGTATTTTATCTTTC	0.279																																					p.I429fs		Atlas-INDEL	.											.	NOL10	22	.	0			c.1286delT						.						116.0	120.0	119.0					2																	10742949		2202	4298	6500	SO:0001589	frameshift_variant	79954	exon16			.	AK024137	CCDS1673.2, CCDS58697.1, CCDS58698.1	2p25.1	2008-05-23			ENSG00000115761	ENSG00000115761			25862	protein-coding gene	gene with protein product			"""polyglutamine binding protein 5"""	PQBP5		12477932	Standard	NM_024894		Approved	FLJ14075	uc002raq.3	Q9BSC4	OTTHUMG00000119023	ENST00000381685.5:c.1285delA	chr2.hg19:g.10742949delT	ENSP00000371101:p.Ile429fs	94.0	0.0		156.0	10.0	NM_024894	A8K3R5|B4DLV0|Q53RC9|Q96TA5|Q9H7Y7|Q9H855	Frame_Shift_Del	DEL	ENST00000381685.5	hg19	CCDS1673.2																																																																																			.	.		0.279	NOL10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239227.1	NM_024894	
DNM3	26052	hgsc.bcm.edu	37	1	172356459	172356459	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:172356459delC	ENST00000355305.5	+	19	2420	c.2263delC	c.(2263-2265)cccfs	p.P757fs	DNM3_ENST00000367731.1_Frame_Shift_Del_p.P747fs|DNM3_ENST00000358155.4_Frame_Shift_Del_p.P751fs			Q9UQ16	DYN3_HUMAN	dynamin 3	757					endocytosis (GO:0006897)|filopodium assembly (GO:0046847)|GTP catabolic process (GO:0006184)|synapse assembly (GO:0007416)	dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			NS(1)|breast(3)|endometrium(1)|kidney(1)|large_intestine(9)|lung(16)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	37						CACTCCGGCACCCCCTCCAGT	0.587																																					p.A748fs		Atlas-INDEL	.											.	DNM3	85	.	0			c.2244delA						.						28.0	31.0	30.0					1																	172356459		2053	4188	6241	SO:0001589	frameshift_variant	26052	exon19			.	AL136712	CCDS44276.1, CCDS60356.1	1q24.1	2013-01-10			ENSG00000197959	ENSG00000197959		"""Pleckstrin homology (PH) domain containing"""	29125	protein-coding gene	gene with protein product	"""Dyna III"""	611445				10048485	Standard	NM_015569		Approved	KIAA0820	uc001gie.4	Q9UQ16	OTTHUMG00000034913	ENST00000355305.5:c.2263delC	chr1.hg19:g.172356459delC	ENSP00000347457:p.Pro757fs	81.0	0.0		158.0	11.0	NM_015569	A9Z1Y1|O14982|O95555|Q1MTM8|Q5W129|Q6P2G1|Q9H0P3|Q9H548|Q9NQ68|Q9NQN6	Frame_Shift_Del	DEL	ENST00000355305.5	hg19																																																																																				.	.		0.587	DNM3-003	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000084531.1	NM_015569	
SETD2	29072	hgsc.bcm.edu	37	3	47143010	47143010	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:47143010delA	ENST00000409792.3	-	8	4995	c.4953delT	c.(4951-4953)tttfs	p.F1651fs		NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	1651	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)			breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		GTTTGGTGGTAAAAAACCCAA	0.398			"""N, F, S, Mis"""		clear cell renal carcinoma																																p.T1652fs		Atlas-INDEL	.		Rec	yes		3	3p21.31	29072	SET domain containing 2		E	.	SETD2	721	.	0			c.4954delA						.						157.0	156.0	156.0					3																	47143010		2203	4300	6503	SO:0001589	frameshift_variant	29072	exon8			.	AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"""Chromatin-modifying enzymes / K-methyltransferases"""	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.4953delT	chr3.hg19:g.47143010delA	ENSP00000386759:p.Phe1651fs	128.0	0.0		160.0	12.0	NM_014159	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Frame_Shift_Del	DEL	ENST00000409792.3	hg19	CCDS2749.2																																																																																			.	.		0.398	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159	
CAPN2	824	hgsc.bcm.edu	37	1	223934727	223934727	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:223934727delG	ENST00000295006.5	+	5	898	c.589delG	c.(589-591)gggfs	p.G198fs	CAPN2_ENST00000433674.2_Frame_Shift_Del_p.G120fs	NM_001748.4	NP_001739	P17655	CAN2_HUMAN	calpain 2, (m/II) large subunit	198	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.				blastocyst development (GO:0001824)|cellular response to amino acid stimulus (GO:0071230)|myoblast fusion (GO:0007520)|protein autoprocessing (GO:0016540)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of cytoskeleton organization (GO:0051493)|response to hypoxia (GO:0001666)	chromatin (GO:0000785)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)|pseudopodium (GO:0031143)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|cysteine-type peptidase activity (GO:0008234)|cytoskeletal protein binding (GO:0008092)			breast(3)|endometrium(1)|kidney(1)|large_intestine(9)|lung(10)|prostate(1)|skin(1)|stomach(3)	29				GBM - Glioblastoma multiforme(131;0.109)		AGCGCTATCAGGGGGTGCCAC	0.527																																					p.S196fs		Atlas-INDEL	.											.	CAPN2	69	.	0			c.588delA						.						112.0	107.0	109.0					1																	223934727		2203	4300	6503	SO:0001589	frameshift_variant	824	exon5			.	J04700	CCDS31035.1, CCDS53478.1	1q41-q42	2013-01-10			ENSG00000162909	ENSG00000162909	3.4.22.52	"""EF-hand domain containing"""	1479	protein-coding gene	gene with protein product		114230				2852952, 2539381	Standard	NM_001748		Approved	mCANP, CANPml, CANPL2	uc001hob.4	P17655	OTTHUMG00000037376	ENST00000295006.5:c.589delG	chr1.hg19:g.223934727delG	ENSP00000295006:p.Gly198fs	133.0	0.0		193.0	14.0	NM_001748	A6NDG7|B7ZA96|E7ES58|Q16738|Q6PJT3|Q8WU26|Q9HBB1	Frame_Shift_Del	DEL	ENST00000295006.5	hg19	CCDS31035.1																																																																																			.	.		0.527	CAPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090973.1	NM_001748	
BAIAP2L1	55971	hgsc.bcm.edu	37	7	97939854	97939854	+	Frame_Shift_Del	DEL	G	G	-	rs200900587		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:97939854delG	ENST00000005260.8	-	9	1073	c.858delC	c.(856-858)cccfs	p.P286fs	BAIAP2L1_ENST00000462558.1_5'UTR|RP4-607J23.2_ENST00000608882.1_RNA|RP4-607J23.2_ENST00000609873.1_RNA	NM_018842.4	NP_061330.2	Q9UHR4	BI2L1_HUMAN	BAI1-associated protein 2-like 1	286					filopodium assembly (GO:0046847)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of actin filament polymerization (GO:0030838)|response to bacterium (GO:0009617)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	proline-rich region binding (GO:0070064)			NS(1)|breast(1)|cervix(1)|endometrium(3)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)	23	all_cancers(62;4.34e-10)|all_epithelial(64;5e-10)|Esophageal squamous(72;0.00918)|Lung NSC(181;0.0113)|all_lung(186;0.0126)		STAD - Stomach adenocarcinoma(171;0.215)			CTGAAGGAGCGGGGGGCATCT	0.428																																					p.A287fs		Atlas-INDEL	.											BAIAP2L1,NS,carcinoma,0,1	BAIAP2L1	61	.	0			c.859delG						.						95.0	101.0	99.0					7																	97939854		2203	4300	6503	SO:0001589	frameshift_variant	55971	exon9			.	AF119666	CCDS34687.1	7q22.1	2012-10-04			ENSG00000006453	ENSG00000006453			21649	protein-coding gene	gene with protein product		611877					Standard	NM_018842		Approved	IRTKS	uc003upj.3	Q9UHR4	OTTHUMG00000165117	ENST00000005260.8:c.858delC	chr7.hg19:g.97939854delG	ENSP00000005260:p.Pro286fs	111.0	0.0		169.0	13.0	NM_018842	A4D268|Q75L21|Q75L22|Q96CV4|Q9H5F5|Q9Y2M8	Frame_Shift_Del	DEL	ENST00000005260.8	hg19	CCDS34687.1																																																																																			.	.		0.428	BAIAP2L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334681.1	NM_018842	
CEMIP	57214	hgsc.bcm.edu	37	15	81221438	81221438	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:81221438delG	ENST00000394685.3	+	21	2954	c.2535delG	c.(2533-2535)gtgfs	p.V845fs	KIAA1199_ENST00000356249.5_Frame_Shift_Del_p.V845fs|RP11-351M8.2_ENST00000560873.1_RNA|KIAA1199_ENST00000220244.3_Frame_Shift_Del_p.V845fs			Q8WUJ3	CEMIP_HUMAN		845					hyaluronan catabolic process (GO:0030214)|positive regulation of cell migration (GO:0030335)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of protein kinase C activity (GO:1900020)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|sensory perception of sound (GO:0007605)	clathrin-coated vesicle membrane (GO:0030665)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	clathrin heavy chain binding (GO:0032050)|ER retention sequence binding (GO:0046923)|hyaluronic acid binding (GO:0005540)|hyalurononglucosaminidase activity (GO:0004415)			breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(10)|lung(14)|ovary(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	49						GTGGCAACGTGGGGACGGAAA	0.527																																					p.V845fs		Atlas-INDEL	.											.	KIAA1199	118	.	0			c.2534delT						.						140.0	132.0	135.0					15																	81221438		2203	4300	6503	SO:0001589	frameshift_variant	57214	exon20			.																												ENST00000394685.3:c.2535delG	chr15.hg19:g.81221438delG	ENSP00000378177:p.Val845fs	229.0	0.0		313.0	19.0	NM_018689	Q6L9J5|Q9H1K5|Q9NPN9|Q9ULM1	Frame_Shift_Del	DEL	ENST00000394685.3	hg19	CCDS10315.1																																																																																			.	.		0.527	KIAA1199-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291389.1		
ERO1L	30001	hgsc.bcm.edu	37	14	53119839	53119839	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:53119839delT	ENST00000395686.3	-	12	1226	c.1003delA	c.(1003-1005)attfs	p.I335fs		NM_014584.1	NP_055399.1	Q96HE7	ERO1A_HUMAN	ERO1-like (S. cerevisiae)	335					4-hydroxyproline metabolic process (GO:0019471)|brown fat cell differentiation (GO:0050873)|cell redox homeostasis (GO:0045454)|cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|chaperone mediated protein folding requiring cofactor (GO:0051085)|endoplasmic reticulum unfolded protein response (GO:0030968)|extracellular matrix organization (GO:0030198)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|protein folding (GO:0006457)|protein maturation by protein folding (GO:0022417)|release of sequestered calcium ion into cytosol (GO:0051209)|response to endoplasmic reticulum stress (GO:0034976)|response to temperature stimulus (GO:0009266)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	oxidoreductase activity (GO:0016491)|oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor (GO:0016671)|protein disulfide isomerase activity (GO:0003756)|protein disulfide oxidoreductase activity (GO:0015035)		ERO1L/FERMT2(2)	breast(1)|endometrium(1)|large_intestine(3)|lung(5)|ovary(1)|urinary_tract(1)	12	Breast(41;0.226)					TCATCCTGAATTTTATTTCCA	0.289																																					p.I335fs		Atlas-INDEL	.											.	ERO1L	35	.	0			c.1004delT						.						46.0	50.0	49.0					14																	53119839		2202	4298	6500	SO:0001589	frameshift_variant	30001	exon12			.	AF081886	CCDS9709.1	14q22.1	2010-10-06	2001-11-28		ENSG00000197930	ENSG00000197930			13280	protein-coding gene	gene with protein product		615435	"""ERO1 (S. cerevisiae)-like"""			10671517	Standard	NM_014584		Approved	ERO1A, ERO1-alpha	uc001wzv.3	Q96HE7	OTTHUMG00000140301	ENST00000395686.3:c.1003delA	chr14.hg19:g.53119839delT	ENSP00000379042:p.Ile335fs	140.0	0.0		142.0	10.0	NM_014584	A8K9X4|A8MYW1|Q7LD45|Q9P1Q9|Q9UKV6	Frame_Shift_Del	DEL	ENST00000395686.3	hg19	CCDS9709.1																																																																																			.	.		0.289	ERO1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276892.1	NM_014584	
TAF1A	9015	hgsc.bcm.edu	37	1	222753126	222753126	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:222753126delT	ENST00000352967.4	-	4	568	c.380delA	c.(379-381)aatfs	p.N127fs	TAF1A_ENST00000350027.4_Frame_Shift_Del_p.N127fs|TAF1A_ENST00000465263.1_5'UTR|TAF1A_ENST00000543857.1_Frame_Shift_Del_p.N127fs|TAF1A_ENST00000366890.1_Frame_Shift_Del_p.N13fs|TAF1A_ENST00000391882.1_Frame_Shift_Del_p.N13fs	NM_005681.3	NP_005672.1	Q15573	TAF1A_HUMAN	TATA box binding protein (TBP)-associated factor, RNA polymerase I, A, 48kDa	127					gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase I promoter (GO:0006361)	intracellular membrane-bounded organelle (GO:0043231)|microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|RNA polymerase I transcription factor complex (GO:0000120)	DNA binding (GO:0003677)			kidney(3)|large_intestine(3)|lung(11)|urinary_tract(1)	18				GBM - Glioblastoma multiforme(131;0.0186)		GACGCCAATATTTTTCATCCG	0.338																																					p.N127fs		Atlas-INDEL	.											.	TAF1A	35	.	0			c.381delT						.						106.0	116.0	113.0					1																	222753126		2203	4299	6502	SO:0001589	frameshift_variant	9015	exon4			.	L39060	CCDS1531.1, CCDS1532.1	1q42	2008-02-05	2002-08-29		ENSG00000143498	ENSG00000143498			11532	protein-coding gene	gene with protein product		604903	"""TATA box binding protein (TBP)-associated factor, RNA polymerase I, A, 48kD"""			7801123	Standard	NM_005681		Approved	TAFI48, SL1	uc009xdz.2	Q15573	OTTHUMG00000037544	ENST00000352967.4:c.380delA	chr1.hg19:g.222753126delT	ENSP00000327072:p.Asn127fs	139.0	0.0		202.0	13.0	NM_005681	B2RDZ8|D3DTB7|Q9NWA1	Frame_Shift_Del	DEL	ENST00000352967.4	hg19	CCDS1531.1																																																																																			.	.		0.338	TAF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091493.2	NM_005681	
CHGB	1114	hgsc.bcm.edu	37	20	5904345	5904345	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr20:5904345delG	ENST00000378961.4	+	4	1759	c.1555delG	c.(1555-1557)gggfs	p.G519fs		NM_001819.2	NP_001810.2	P05060	SCG1_HUMAN	chromogranin B (secretogranin 1)	519						extracellular region (GO:0005576)|secretory granule (GO:0030141)	hormone activity (GO:0005179)			breast(7)|kidney(2)|large_intestine(8)|lung(19)|ovary(1)|pancreas(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	47						GAAGAGATTAGGGGAACTGTT	0.458																																					p.L518fs		Atlas-INDEL	.											.	CHGB	112	.	0			c.1554delA						.						69.0	71.0	71.0					20																	5904345		2203	4300	6503	SO:0001589	frameshift_variant	1114	exon4			.		CCDS13092.1	20p12.3	2013-09-19			ENSG00000089199	ENSG00000089199			1930	protein-coding gene	gene with protein product	"""secretogranin B"""	118920		SCG1		3608978	Standard	NM_001819		Approved		uc002wmg.3	P05060	OTTHUMG00000031821	ENST00000378961.4:c.1555delG	chr20.hg19:g.5904345delG	ENSP00000368244:p.Gly519fs	95.0	0.0		163.0	10.0	NM_001819	A8K021|Q59EU9|Q6IBS6|Q9BQV6|Q9UC25|Q9UJA6	Frame_Shift_Del	DEL	ENST00000378961.4	hg19	CCDS13092.1																																																																																			.	.		0.458	CHGB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077897.2	NM_001819	
MSH6	2956	hgsc.bcm.edu	37	2	48025968	48025968	+	Frame_Shift_Del	DEL	G	G	-	rs573638836		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:48025968delG	ENST00000234420.5	+	4	998	c.846delG	c.(844-846)gtgfs	p.V282fs	MSH6_ENST00000540021.1_Frame_Shift_Del_p.V152fs|FBXO11_ENST00000405808.1_Intron|MSH6_ENST00000538136.1_5'UTR	NM_000179.2	NP_000170.1	P52701	MSH6_HUMAN	mutS homolog 6	282					ATP catabolic process (GO:0006200)|determination of adult lifespan (GO:0008340)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|isotype switching (GO:0045190)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|positive regulation of helicase activity (GO:0051096)|reciprocal meiotic recombination (GO:0007131)|response to UV (GO:0009411)|somatic hypermutation of immunoglobulin genes (GO:0016446)|somatic recombination of immunoglobulin gene segments (GO:0016447)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|MutSalpha complex (GO:0032301)|nuclear chromatin (GO:0000790)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|damaged DNA binding (GO:0003684)|DNA-dependent ATPase activity (GO:0008094)|guanine/thymine mispair binding (GO:0032137)|methylated histone binding (GO:0035064)|mismatched DNA binding (GO:0030983)	p.0?(2)		breast(8)|central_nervous_system(29)|cervix(1)|endometrium(32)|haematopoietic_and_lymphoid_tissue(12)|kidney(2)|large_intestine(75)|lung(25)|ovary(3)|prostate(3)|skin(10)|stomach(22)|thyroid(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	229		Acute lymphoblastic leukemia(82;0.0299)|all_hematologic(82;0.0358)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			GCAGTGGAGTGGGGGATAGTG	0.468			"""Mis, N, F, S"""		colorectal	"""colorectal, endometrial, ovarian"""		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome																												p.V282fs		Atlas-INDEL	.	yes	Rec	yes	Hereditary non-polyposis colorectal cancer	2	2p16	2956	mutS homolog 6 (E. coli)		E	.	MSH6	341	.	2	Whole gene deletion(2)	haematopoietic_and_lymphoid_tissue(2)	c.845delT						.						166.0	174.0	171.0					2																	48025968		2203	4300	6503	SO:0001589	frameshift_variant	2956	exon4	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome; ;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	.	U54777	CCDS1836.1, CCDS62906.1, CCDS62907.1	2p16	2014-09-17	2013-09-12		ENSG00000116062	ENSG00000116062			7329	protein-coding gene	gene with protein product		600678	"""mutS (E. coli) homolog 6"", ""mutS homolog 6 (E. coli)"""	GTBP		7604266	Standard	NM_000179		Approved		uc002rwd.4	P52701	OTTHUMG00000129129	ENST00000234420.5:c.846delG	chr2.hg19:g.48025968delG	ENSP00000234420:p.Val282fs	80.0	0.0		130.0	10.0	NM_000179	B4DF41|B4E3I4|F5H2F9|O43706|O43917|Q8TCX4|Q9BTB5	Frame_Shift_Del	DEL	ENST00000234420.5	hg19	CCDS1836.1																																																																																			.	.		0.468	MSH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251180.4	NM_000179	
TOX2	84969	hgsc.bcm.edu	37	20	42694616	42694616	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr20:42694616delC	ENST00000358131.5	+	6	1379	c.1171delC	c.(1171-1173)cccfs	p.P392fs	TOX2_ENST00000372999.1_Frame_Shift_Del_p.P368fs|TOX2_ENST00000423191.2_Frame_Shift_Del_p.P368fs|TOX2_ENST00000341197.4_Frame_Shift_Del_p.P410fs|TOX2_ENST00000435864.2_3'UTR	NM_001098798.1	NP_001092268.1	Q96NM4	TOX2_HUMAN	TOX high mobility group box family member 2	392	Pro-rich.				female gonad development (GO:0008585)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to gonadotropin (GO:0034698)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|skin(2)	26		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.00189)			GCTGTCACTGCCCCCTCACGC	0.706																																					p.L408fs		Atlas-INDEL	.											.	TOX2	158	.	0			c.1224delG						.						27.0	30.0	29.0					20																	42694616		2202	4299	6501	SO:0001589	frameshift_variant	84969	exon7			.	BC007636	CCDS13324.1, CCDS42875.1, CCDS46603.1	20q13.12	2007-03-20	2007-03-20	2007-03-20					16095	protein-coding gene	gene with protein product	"""granulosa cell HMG box 1"""	611163	"""chromosome 20 open reading frame 100"""	C20orf100		14764631	Standard	NM_001098796		Approved	dJ1108D11.2, GCX-1	uc010ggo.3	Q96NM4		ENST00000358131.5:c.1171delC	chr20.hg19:g.42694616delC	ENSP00000350849:p.Pro392fs	115.0	0.0		206.0	16.0	NM_001098797	A8K1J1|E1P5X0|G3XAC7|Q5TE33|Q5TE34|Q5TE35|Q96IC9|Q9BQN5	Frame_Shift_Del	DEL	ENST00000358131.5	hg19	CCDS42875.1																																																																																			.	.		0.706	TOX2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079329.2		
KIF1B	23095	hgsc.bcm.edu	37	1	10327488	10327488	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:10327488delA	ENST00000377086.1	+	6	682	c.480delA	c.(478-480)ccafs	p.P160fs	KIF1B_ENST00000263934.6_Frame_Shift_Del_p.P160fs|KIF1B_ENST00000377083.1_Frame_Shift_Del_p.P160fs|KIF1B_ENST00000377081.1_Frame_Shift_Del_p.P160fs|KIF1B_ENST00000377093.4_Frame_Shift_Del_p.P160fs			O60333	KIF1B_HUMAN	kinesin family member 1B	160	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				anterograde axon cargo transport (GO:0008089)|apoptotic process (GO:0006915)|cytoskeleton-dependent intracellular transport (GO:0030705)|microtubule-based movement (GO:0007018)|mitochondrion transport along microtubule (GO:0047497)|neuromuscular synaptic transmission (GO:0007274)|neuron-neuron synaptic transmission (GO:0007270)|vesicle-mediated transport (GO:0016192)	cytoplasmic vesicle (GO:0031410)|cytoplasmic vesicle membrane (GO:0030659)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinesin binding (GO:0019894)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)			breast(2)|endometrium(7)|kidney(8)|large_intestine(9)|lung(29)|ovary(3)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(2)	71	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.2e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0259)|Colorectal(212;9.79e-07)|COAD - Colon adenocarcinoma(227;0.000143)|BRCA - Breast invasive adenocarcinoma(304;0.000413)|Kidney(185;0.00134)|KIRC - Kidney renal clear cell carcinoma(229;0.0037)|STAD - Stomach adenocarcinoma(132;0.0113)|READ - Rectum adenocarcinoma(331;0.0642)		TGCTGAATCCAAAAAACAAGG	0.398																																					p.P160fs		Atlas-INDEL	.											.	KIF1B	242	.	0			c.479delC						.						103.0	90.0	94.0					1																	10327488		2203	4300	6503	SO:0001589	frameshift_variant	23095	exon6			.	AF257176	CCDS111.1, CCDS112.1	1p36.22	2014-09-17			ENSG00000054523	ENSG00000054523		"""Kinesins"", ""Pleckstrin homology (PH) domain containing"""	16636	protein-coding gene	gene with protein product		605995		CMT2A, CMT2		11389829, 10762626	Standard	NM_015074		Approved	KIAA0591, KLP, HMSNII	uc001aqw.4	O60333	OTTHUMG00000001817	ENST00000377086.1:c.480delA	chr1.hg19:g.10327488delA	ENSP00000366290:p.Pro160fs	144.0	0.0		160.0	10.0	NM_183416	A6NFS8|A6NKQ4|Q4VXC3|Q4VXC4|Q4VXC5|Q4VXC6|Q96Q94|Q9BV80|Q9P280	Frame_Shift_Del	DEL	ENST00000377086.1	hg19																																																																																				.	.		0.398	KIF1B-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000005102.1		
LIPG	9388	hgsc.bcm.edu	37	18	47095818	47095818	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr18:47095818delT	ENST00000261292.4	+	4	749	c.471delT	c.(469-471)gatfs	p.D157fs	LIPG_ENST00000580036.1_Frame_Shift_Del_p.D157fs|LIPG_ENST00000427224.2_Frame_Shift_Del_p.D157fs|LIPG_ENST00000577628.1_Frame_Shift_Del_p.D193fs	NM_006033.2	NP_006024.1	Q9Y5X9	LIPE_HUMAN	lipase, endothelial	157					cell proliferation (GO:0008283)|cholesterol homeostasis (GO:0042632)|high-density lipoprotein particle remodeling (GO:0034375)|lipid metabolic process (GO:0006629)|phospholipid catabolic process (GO:0009395)|phospholipid homeostasis (GO:0055091)|positive regulation of cholesterol transport (GO:0032376)|positive regulation of high-density lipoprotein particle clearance (GO:0010983)|regulation of lipoprotein metabolic process (GO:0050746)|response to nutrient (GO:0007584)|reverse cholesterol transport (GO:0043691)	extracellular space (GO:0005615)	heparin binding (GO:0008201)|lipoprotein lipase activity (GO:0004465)|phosphatidylcholine 1-acylhydrolase activity (GO:0008970)|phospholipase activity (GO:0004620)			autonomic_ganglia(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(2)|skin(2)	18						AGAAGGACGATTTTTCTCTCG	0.542																																					p.D157fs	Pancreas(126;280 1778 12814 26243 34948)	Atlas-INDEL	.											LIPG,NS,carcinoma,0,1	LIPG	47	.	0			c.470delA						.						62.0	58.0	59.0					18																	47095818		2203	4300	6503	SO:0001589	frameshift_variant	9388	exon4			.	AF118767	CCDS11938.1	18q21.1	2006-04-22				ENSG00000101670			6623	protein-coding gene	gene with protein product		603684				10318835, 10192396	Standard	XM_005258390		Approved	EDL	uc002ldv.3	Q9Y5X9		ENST00000261292.4:c.471delT	chr18.hg19:g.47095818delT	ENSP00000261292:p.Asp157fs	154.0	0.0		163.0	10.0	NM_006033	B0LPG6|Q6P9C8|Q6UW82	Frame_Shift_Del	DEL	ENST00000261292.4	hg19	CCDS11938.1																																																																																			.	.		0.542	LIPG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447546.1	NM_006033	
NAV1	89796	hgsc.bcm.edu	37	1	201750396	201750396	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:201750396delC	ENST00000367296.4	+	5	2042	c.1622delC	c.(1621-1623)tccfs	p.S541fs	NAV1_ENST00000367302.1_Frame_Shift_Del_p.S554fs|IPO9-AS1_ENST00000413035.1_RNA|NAV1_ENST00000367300.3_Frame_Shift_Del_p.S541fs|NAV1_ENST00000295624.6_Frame_Shift_Del_p.S541fs|NAV1_ENST00000367295.1_Frame_Shift_Del_p.S150fs|NAV1_ENST00000367297.4_Frame_Shift_Del_p.S541fs	NM_020443.4	NP_065176.3	Q8NEY1	NAV1_HUMAN	neuron navigator 1	541					microtubule bundle formation (GO:0001578)|neuron migration (GO:0001764)	cytoplasm (GO:0005737)|microtubule (GO:0005874)				breast(5)|central_nervous_system(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(10)|lung(29)|ovary(4)|prostate(3)|skin(1)|stomach(2)	70						GCTGTAACTTCCCCCATCACT	0.537																																					p.S541fs		Atlas-INDEL	.											.	NAV1	143	.	0			c.1621delT						.						47.0	47.0	47.0					1																	201750396		2203	4300	6503	SO:0001589	frameshift_variant	89796	exon5			.	AF086348	CCDS1414.1, CCDS1414.2, CCDS53456.1	1q32.3	2008-07-18			ENSG00000134369	ENSG00000134369			15989	protein-coding gene	gene with protein product	"""neuron navigator-1"", ""pore membrane and/or filament interacting like protein 3"""	611628				12079279, 12062803	Standard	NM_020443		Approved	FLJ12560, FLJ14203, KIAA1151, MGC14961, POMFIL3, steerin-1, DKFZp781D0314	uc001gwu.3	Q8NEY1	OTTHUMG00000035766	ENST00000367296.4:c.1622delC	chr1.hg19:g.201750396delC	ENSP00000356265:p.Ser541fs	99.0	0.0		159.0	11.0	NM_020443	A8MS88|Q5SVH1|Q5SVH2|Q5SVH3|Q5SVH7|Q5VUY9|Q8IVL2|Q96II1|Q9H7V9|Q9H9S9|Q9H9T5|Q9UGI1|Q9ULK7|Q9ULR9	Frame_Shift_Del	DEL	ENST00000367296.4	hg19	CCDS1414.2																																																																																			.	.		0.537	NAV1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000087013.1	NM_020443	
RGPD5	84220	hgsc.bcm.edu	37	2	110588995	110588995	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:110588995delG	ENST00000016946.3	+	18	2726	c.2568delG	c.(2566-2568)cagfs	p.Q856fs	RGPD5_ENST00000393283.1_Frame_Shift_Del_p.Q856fs|RGPD5_ENST00000272454.6_Frame_Shift_Del_p.Q856fs	NM_005054.2	NP_005045.2	Q99666	RGPD5_HUMAN	RANBP2-like and GRIP domain containing 5	856					protein targeting to Golgi (GO:0000042)	cytoplasm (GO:0005737)				central_nervous_system(1)	1						ATGGATATCAGGGGTCACAGA	0.438																																					p.Q856fs		Atlas-INDEL	.											.	RGPD5	1	.	0			c.2567delA						.																																			SO:0001589	frameshift_variant	84220	exon18			.	U64675	CCDS2082.1, CCDS2083.1	2q13	2013-01-10			ENSG00000015568	ENSG00000015568		"""Tetratricopeptide (TTC) repeat domain containing"""	32418	protein-coding gene	gene with protein product		612708				15710750, 15815621	Standard	NM_032260		Approved	RGP5, BS-63, DKFZp686I1842		Q99666	OTTHUMG00000130985	ENST00000016946.3:c.2568delG	chr2.hg19:g.110588995delG	ENSP00000016946:p.Gln856fs	80.0	0.0		145.0	10.0	NM_005054	Q53QN2|Q53T03|Q59GM7|Q9H0B2	Frame_Shift_Del	DEL	ENST00000016946.3	hg19	CCDS2082.1																																																																																			.	.		0.438	RGPD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253599.3	NM_005054	
NOXRED1	122945	hgsc.bcm.edu	37	14	77872475	77872475	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:77872475delC	ENST00000380835.2	-	5	852	c.686delG	c.(685-687)ggafs	p.G229fs		NM_001113475.2	NP_001106946.1	Q6NXP6	NXRD1_HUMAN	NADP-dependent oxidoreductase domain containing 1	229					proline biosynthetic process (GO:0006561)		pyrroline-5-carboxylate reductase activity (GO:0004735)			NS(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(3)	9						GAGGATTATTCCCCCTACACA	0.453																																					p.G229fs		Atlas-INDEL	.											.	NOXRED1	23	.	0			c.687delA						.						65.0	55.0	58.0					14																	77872475		1568	3582	5150	SO:0001589	frameshift_variant	122945	exon5			.	AK057371	CCDS45142.1	14q24.3	2011-09-30	2011-09-30	2011-09-30	ENSG00000165555	ENSG00000165555			20487	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 148"""	C14orf148			Standard	NM_001113475		Approved	FLJ32809	uc001xtr.3	Q6NXP6	OTTHUMG00000171554	ENST00000380835.2:c.686delG	chr14.hg19:g.77872475delC	ENSP00000370215:p.Gly229fs	169.0	0.0		150.0	10.0	NM_001113475	B3KQ47|O95435	Frame_Shift_Del	DEL	ENST00000380835.2	hg19	CCDS45142.1																																																																																			.	.		0.453	NOXRED1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414103.1	NM_138791	
SLC1A1	6505	hgsc.bcm.edu	37	9	4561480	4561480	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:4561480delA	ENST00000262352.3	+	3	500	c.264delA	c.(262-264)ggafs	p.G88fs	SLC1A1_ENST00000490167.1_3'UTR	NM_004170.5	NP_004161.4	P43005	EAA3_HUMAN	solute carrier family 1 (neuronal/epithelial high affinity glutamate transporter, system Xag), member 1	88					D-aspartate import (GO:0070779)|ion transport (GO:0006811)|L-glutamate import (GO:0051938)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glutamate binding (GO:0016595)|glutamate:sodium symporter activity (GO:0015501)|L-glutamate transmembrane transporter activity (GO:0005313)|sodium:dicarboxylate symporter activity (GO:0017153)			endometrium(1)|kidney(1)|large_intestine(7)|lung(4)|pancreas(1)|skin(1)	15		Acute lymphoblastic leukemia(2;0.0359)|Breast(48;0.0457)		GBM - Glioblastoma multiforme(50;0.0124)|Lung(218;0.183)	L-Aspartic Acid(DB00128)|Pregabalin(DB00230)	ACGTATCCGGAAAAATTGGTC	0.388																																					p.G88fs		Atlas-INDEL	.											.	SLC1A1	43	.	0			c.263delG						.						328.0	310.0	316.0					9																	4561480		2203	4300	6503	SO:0001589	frameshift_variant	6505	exon3			.		CCDS6452.1	9p24	2013-05-22			ENSG00000106688	ENSG00000106688		"""Solute carriers"""	10939	protein-coding gene	gene with protein product		133550				8020993	Standard	NM_004170		Approved	EAAC1, EAAT3	uc003zij.2	P43005	OTTHUMG00000019468	ENST00000262352.3:c.264delA	chr9.hg19:g.4561480delA	ENSP00000262352:p.Gly88fs	115.0	0.0		140.0	11.0	NM_004170	O75587|Q5VZ24|Q8N199|Q9UEW2	Frame_Shift_Del	DEL	ENST00000262352.3	hg19	CCDS6452.1																																																																																			.	.		0.388	SLC1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051571.1		
ACYP1	97	hgsc.bcm.edu	37	14	75520310	75520310	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:75520310delC	ENST00000238618.3	-	3	240	c.137delG	c.(136-138)ggcfs	p.G46fs	ACYP1_ENST00000555463.1_Frame_Shift_Del_p.G76fs|ACYP1_ENST00000357971.3_3'UTR|ACYP1_ENST00000555694.1_Frame_Shift_Del_p.G46fs|MLH3_ENST00000380968.2_5'Flank|MLH3_ENST00000355774.2_5'Flank|MLH3_ENST00000238662.7_5'Flank|MLH3_ENST00000556257.1_5'Flank	NM_001107.3	NP_001098.1	P07311	ACYP1_HUMAN	acylphosphatase 1, erythrocyte (common) type	46	Acylphosphatase-like. {ECO:0000255|PROSITE-ProRule:PRU00520}.				phosphate-containing compound metabolic process (GO:0006796)	extracellular vesicular exosome (GO:0070062)	acylphosphatase activity (GO:0003998)			large_intestine(2)	2				BRCA - Breast invasive adenocarcinoma(234;0.00646)		TTGCACTGTGCCCCGGTCAGT	0.488																																					p.G46fs		Atlas-INDEL	.											.	ACYP1	6	.	0			c.138delC						.						202.0	177.0	186.0					14																	75520310		2203	4300	6503	SO:0001589	frameshift_variant	97	exon3			.	X84194	CCDS9838.1, CCDS45137.1	14q24.3	2014-08-08			ENSG00000119640	ENSG00000119640	3.6.1.7		179	protein-coding gene	gene with protein product		600875				7796909, 9730610	Standard	NM_001107		Approved		uc001xrg.3	P07311	OTTHUMG00000171767	ENST00000238618.3:c.137delG	chr14.hg19:g.75520310delC	ENSP00000238618:p.Gly46fs	140.0	0.0		147.0	10.0	NM_001107	A6NDV8|B2R590	Frame_Shift_Del	DEL	ENST00000238618.3	hg19	CCDS9838.1																																																																																			.	.		0.488	ACYP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415013.1		
PSMA5	5686	hgsc.bcm.edu	37	1	109954503	109954503	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:109954503delG	ENST00000271308.4	-	6	474	c.454delC	c.(454-456)cagfs	p.Q152fs	PSMA5_ENST00000490870.1_5'UTR|PSMA5_ENST00000538610.1_Frame_Shift_Del_p.Q94fs	NM_002790.3	NP_002781.2	P28066	PSA5_HUMAN	proteasome (prosome, macropain) subunit, alpha type, 5	152					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)|proteasome core complex, alpha-subunit complex (GO:0019773)	threonine-type endopeptidase activity (GO:0004298)			kidney(1)|large_intestine(2)|lung(2)	5		all_epithelial(167;2.83e-05)|all_lung(203;0.00016)|Lung NSC(277;0.000318)|Breast(1374;0.244)		Lung(183;0.045)|Colorectal(144;0.116)|Epithelial(280;0.187)|all cancers(265;0.196)|LUSC - Lung squamous cell carcinoma(189;0.235)		ACTTACAGCTGGGGTCCTTTC	0.373																																					p.Q152fs		Atlas-INDEL	.											.	PSMA5	14	.	0			c.455delA						.						61.0	64.0	63.0					1																	109954503		2203	4300	6503	SO:0001589	frameshift_variant	5686	exon6			.	X61970	CCDS799.1, CCDS55619.1	1p13	2008-02-05			ENSG00000143106	ENSG00000143106		"""Proteasome (prosome, macropain) subunits"""	9534	protein-coding gene	gene with protein product		176844				1888762	Standard	NM_002790		Approved	ZETA	uc001dxn.3	P28066	OTTHUMG00000012001	ENST00000271308.4:c.454delC	chr1.hg19:g.109954503delG	ENSP00000271308:p.Gln152fs	184.0	0.0		265.0	16.0	NM_002790	B2R8F6|B4E2V4|Q3T1C1|Q6IBF7	Frame_Shift_Del	DEL	ENST00000271308.4	hg19	CCDS799.1																																																																																			.	.		0.373	PSMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033192.2	NM_002790	
CDR1	1038	hgsc.bcm.edu	37	X	139866088	139866088	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:139866088delA	ENST00000370532.2	-	1	635	c.444delT	c.(442-444)tttfs	p.F148fs		NM_004065.2	NP_004056.2	P51861	CDR1_HUMAN	cerebellar degeneration-related protein 1, 34kDa	148	6 X 6 AA approximate repeats.									breast(1)|endometrium(3)|large_intestine(3)|lung(11)|prostate(2)|skin(4)|urinary_tract(1)	25	Acute lymphoblastic leukemia(192;7.65e-05)	Lung SC(4;0.051)				TACGTCTTCCAAAAAAGCCAT	0.433																																					p.G149fs		Atlas-INDEL	.											.	CDR1	58	.	0			c.445delG						.						126.0	133.0	131.0					X																	139866088		2202	4300	6502	SO:0001589	frameshift_variant	1038	exon1			.		CCDS14670.1	Xq27.1	2013-06-13	2002-08-29		ENSG00000184258	ENSG00000184258			1798	protein-coding gene	gene with protein product	"""Cerebellar degeneration-related protein-1 (34kD)"""	302650	"""cerebellar degeneration-related protein (34kD)"""	CDR		2326268	Standard	NM_004065		Approved	CDR62A, CDR34	uc004fbg.1	P51861	OTTHUMG00000137398	ENST00000370532.2:c.444delT	chrX.hg19:g.139866088delA	ENSP00000359563:p.Phe148fs	131.0	0.0		213.0	14.0	NM_004065	Q5JXH6	Frame_Shift_Del	DEL	ENST00000370532.2	hg19	CCDS14670.1																																																																																			.	.		0.433	CDR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058583.1	NM_004065	
POLQ	10721	hgsc.bcm.edu	37	3	121192306	121192306	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:121192306delG	ENST00000264233.5	-	21	6562	c.6434delC	c.(6433-6435)ccafs	p.P2145fs		NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	2145					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|single-stranded DNA-dependent ATPase activity (GO:0043142)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(55)|ovary(5)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	120				GBM - Glioblastoma multiforme(114;0.0915)		CTCTCTATTTGGGGGCAACTT	0.383								DNA polymerases (catalytic subunits)																													p.P2145fs	Pancreas(152;907 1925 26081 31236 36904)	Atlas-INDEL	.											.	POLQ	273	.	0			c.6435delA						.						181.0	188.0	186.0					3																	121192306		2203	4300	6503	SO:0001589	frameshift_variant	10721	exon21			.	AF052573	CCDS33833.1	3q13.3	2012-05-18			ENSG00000051341	ENSG00000051341	2.7.7.7	"""DNA polymerases"""	9186	protein-coding gene	gene with protein product		604419				10395804	Standard	NM_199420		Approved	POLH	uc003eee.4	O75417	OTTHUMG00000159396	ENST00000264233.5:c.6434delC	chr3.hg19:g.121192306delG	ENSP00000264233:p.Pro2145fs	102.0	0.0		111.0	11.0	NM_199420	O95160|Q6VMB5	Frame_Shift_Del	DEL	ENST00000264233.5	hg19	CCDS33833.1																																																																																			.	.		0.383	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1	NM_199420	
TCN1	6947	hgsc.bcm.edu	37	11	59626598	59626598	+	Frame_Shift_Del	DEL	T	T	-	rs4987226		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:59626598delT	ENST00000257264.3	-	5	803	c.699delA	c.(697-699)aaafs	p.K233fs	TCN1_ENST00000532419.1_Intron	NM_001062.3	NP_001053.2	P20061	TCO1_HUMAN	transcobalamin I (vitamin B12 binding protein, R binder family)	233	Globular N-terminal alpha domain.				cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|cobalt ion transport (GO:0006824)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cobalamin binding (GO:0031419)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(15)|ovary(2)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	29		all_epithelial(135;0.198)			Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	GACCATTTTCTTTTTTCTCAG	0.403																																					p.E234fs		Atlas-INDEL	.											.	TCN1	64	.	0			c.700delG						.						169.0	160.0	163.0					11																	59626598		2201	4295	6496	SO:0001589	frameshift_variant	6947	exon5			.	J05068	CCDS7978.1	11q11-q12	2008-07-21			ENSG00000134827	ENSG00000134827			11652	protein-coding gene	gene with protein product	"""haptocorin"", ""haptocorrin"""	189905					Standard	NM_001062		Approved	TCI, TC1	uc001noj.2	P20061	OTTHUMG00000167400	ENST00000257264.3:c.699delA	chr11.hg19:g.59626598delT	ENSP00000257264:p.Lys233fs	98.0	0.0		124.0	10.0	NM_001062	A8KAC5|Q8WV77	Frame_Shift_Del	DEL	ENST00000257264.3	hg19	CCDS7978.1																																																																																			.	.		0.403	TCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394503.1	NM_001062	
SAMM50	25813	hgsc.bcm.edu	37	22	44368791	44368791	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr22:44368791delA	ENST00000350028.4	+	6	627	c.470delA	c.(469-471)gaafs	p.E157fs	SAMM50_ENST00000396202.3_Intron|SAMM50_ENST00000493161.1_3'UTR	NM_015380.4	NP_056195.3	Q9Y512	SAM50_HUMAN	SAMM50 sorting and assembly machinery component	157					cellular protein metabolic process (GO:0044267)|protein import into mitochondrial outer membrane (GO:0045040)|protein targeting to mitochondrion (GO:0006626)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrial sorting and assembly machinery complex (GO:0001401)|mitochondrion (GO:0005739)				endometrium(3)|large_intestine(5)|liver(1)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	22		all_neural(38;0.0966)|Ovarian(80;0.105)|Glioma(61;0.222)				GGTCGTGCAGAAAAGGTGACC	0.433																																					p.E157fs		Atlas-INDEL	.											.	SAMM50	30	.	0			c.469delG						.						126.0	131.0	129.0					22																	44368791		2203	4300	6503	SO:0001589	frameshift_variant	25813	exon6			.	AK001087	CCDS14055.1	22q13.31	2013-08-21	2013-08-21	2005-11-20	ENSG00000100347	ENSG00000100347			24276	protein-coding gene	gene with protein product		612058	"""sorting and assembly machinery component 50 homolog (S. cerevisiae)"""			15644312	Standard	NM_015380		Approved	CGI-51, TRG-3, YNL026W, OMP85, TOB55	uc003bej.3	Q9Y512	OTTHUMG00000150557	ENST00000350028.4:c.470delA	chr22.hg19:g.44368791delA	ENSP00000345445:p.Glu157fs	122.0	0.0		138.0	10.0	NM_015380	Q53HC4|Q56VW7|Q969Y9|Q96I46|Q9NW85|Q9UQM9	Frame_Shift_Del	DEL	ENST00000350028.4	hg19	CCDS14055.1																																																																																			.	.		0.433	SAMM50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318898.2	NM_015380	
MUC16	94025	hgsc.bcm.edu	37	19	9085053	9085053	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:9085053delG	ENST00000397910.4	-	1	6965	c.6762delC	c.(6760-6762)cccfs	p.P2254fs		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	2254	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TATCAGGGGAGGGGGAAAAGG	0.453																																					p.S2255fs		Atlas-INDEL	.											.	MUC16	4315	.	0			c.6763delT						.						79.0	76.0	77.0					19																	9085053		1945	4141	6086	SO:0001589	frameshift_variant	94025	exon1			.	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.6762delC	chr19.hg19:g.9085053delG	ENSP00000381008:p.Pro2254fs	89.0	0.0		110.0	10.0	NM_024690	Q6ZQW5|Q96RK2	Frame_Shift_Del	DEL	ENST00000397910.4	hg19	CCDS54212.1																																																																																			.	.		0.453	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
CLTC	1213	hgsc.bcm.edu	37	17	57756782	57756782	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:57756782delA	ENST00000269122.3	+	18	3095	c.2821delA	c.(2821-2823)aaafs	p.K941fs	CLTC_ENST00000579456.1_Intron|CLTC_ENST00000393043.1_Frame_Shift_Del_p.K941fs	NM_004859.3	NP_004850.1	Q00610	CLH1_HUMAN	clathrin, heavy chain (Hc)	941	Heavy chain arm.|Proximal segment.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|mitotic nuclear division (GO:0007067)|negative regulation of hyaluronan biosynthetic process (GO:1900126)|negative regulation of protein localization to plasma membrane (GO:1903077)|osteoblast differentiation (GO:0001649)|post-Golgi vesicle-mediated transport (GO:0006892)|receptor internalization (GO:0031623)|receptor-mediated endocytosis (GO:0006898)|transferrin transport (GO:0033572)	clathrin coat (GO:0030118)|clathrin coat of coated pit (GO:0030132)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin complex (GO:0071439)|clathrin-coated endocytic vesicle membrane (GO:0030669)|clathrin-coated vesicle (GO:0030136)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|spindle (GO:0005819)|trans-Golgi network membrane (GO:0032588)|vesicle (GO:0031982)	clathrin light chain binding (GO:0032051)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|structural molecule activity (GO:0005198)		CLTC/ALK(44)|CLTC/TFE3(2)	breast(2)|large_intestine(6)|ovary(1)	9	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)					TTCCCTCTTCAAAAGTCTTTC	0.403			T	"""ALK, TFE3"""	"""ALCL, renal """																																p.F940fs		Atlas-INDEL	.		Dom	yes		17	17q11-qter	1213	"""clathrin, heavy polypeptide (Hc)"""		L	.	CLTC	124	.	0			c.2820delC						.						75.0	72.0	73.0					17																	57756782		2203	4300	6503	SO:0001589	frameshift_variant	1213	exon18			.	X55878	CCDS32696.1, CCDS74115.1	17q23.1	2013-09-19	2006-09-29		ENSG00000141367	ENSG00000141367			2092	protein-coding gene	gene with protein product		118955	"""clathrin, heavy polypeptide (Hc)"", ""clathrin, heavy chain"", ""clathrin, heavy polypeptide-like 2"""	CLTCL2		1765375, 7584026	Standard	NM_004859		Approved	Hc	uc002ixq.1	Q00610	OTTHUMG00000134279	ENST00000269122.3:c.2821delA	chr17.hg19:g.57756782delA	ENSP00000269122:p.Lys941fs	169.0	0.0		189.0	13.0	NM_004859	D3DU00|Q6N0A0|Q86TF2	Frame_Shift_Del	DEL	ENST00000269122.3	hg19	CCDS32696.1																																																																																			.	.		0.403	CLTC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258859.1	NM_004859	
KRTAP10-4	386672	hgsc.bcm.edu	37	21	45993943	45993943	+	Frame_Shift_Del	DEL	C	C	-	rs587672472		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr21:45993943delC	ENST00000400374.3	+	1	338	c.308delC	c.(307-309)tccfs	p.S103fs	TSPEAR_ENST00000323084.4_Intron|TSPEAR_ENST00000397916.1_5'Flank	NM_198687.1	NP_941960.1	P60372	KR104_HUMAN	keratin associated protein 10-4	103	36 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				NS(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(9)|pancreas(1)|prostate(1)	18						TGTGCCTCCTCCCCCTGCCAG	0.657																																					p.S103fs		Atlas-INDEL	.											.	KRTAP10-4	44	.	0			c.307delT						.						15.0	15.0	15.0					21																	45993943		2086	4131	6217	SO:0001589	frameshift_variant	386672	exon1			.	AB076351	CCDS42957.1	21q22.3	2006-03-13	2004-07-12	2004-07-14	ENSG00000215454	ENSG00000215454		"""Keratin associated proteins"""	20521	protein-coding gene	gene with protein product			"""keratin associated protein 18-4"""	KRTAP18-4			Standard	NM_198687		Approved	KRTAP18.4, KAP10.4	uc002zfk.1	P60372	OTTHUMG00000057641	ENST00000400374.3:c.308delC	chr21.hg19:g.45993943delC	ENSP00000383225:p.Ser103fs	230.0	0.0		262.0	17.0	NM_198687	Q08AS0	Frame_Shift_Del	DEL	ENST00000400374.3	hg19	CCDS42957.1																																																																																			.	.		0.657	KRTAP10-4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128045.1	NM_198687	
FFAR4	338557	hgsc.bcm.edu	37	10	95347278	95347278	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:95347278delT	ENST00000371483.4	+	4	1102	c.1046delT	c.(1045-1047)attfs	p.I349fs	FFAR4_ENST00000371481.4_Frame_Shift_Del_p.I333fs|FFAR4_ENST00000604414.1_Intron	NM_181745.3	NP_859529.2	Q5NUL3	FFAR4_HUMAN	free fatty acid receptor 4	349					hormone secretion (GO:0046879)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of inflammatory response (GO:0050728)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|regulation of glucose transport (GO:0010827)	endocytic vesicle (GO:0030139)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	fatty acid binding (GO:0005504)|taste receptor activity (GO:0008527)										TGGAAGAAAATTTTTTGCTGC	0.418																																					p.I349fs		Atlas-INDEL	.											O3FAR1,colon,carcinoma,0,1	.	.	.	0			c.1045delA						.						119.0	127.0	124.0					10																	95347278		2203	4300	6503	SO:0001589	frameshift_variant	338557	exon4			.		CCDS31248.1, CCDS55720.1	10q23.33	2012-11-16	2012-11-16	2012-11-16	ENSG00000186188	ENSG00000186188		"""GPCR / Class A : Fatty acid receptors"""	19061	protein-coding gene	gene with protein product		609044	"""G protein-coupled receptor 129"", ""G protein-coupled receptor 120"", ""omega-3 fatty acid receptor 1"""	GPR129, GPR120, O3FAR1		20471368, 19723586, 15619630, 20813258	Standard	NM_181745		Approved	PGR4	uc010qnt.2	Q5NUL3	OTTHUMG00000034409	ENST00000371483.4:c.1046delT	chr10.hg19:g.95347278delT	ENSP00000360538:p.Ile349fs	170.0	0.0		195.0	12.0	NM_181745	Q495H1|Q5VY25|Q5VY26|Q7Z605|Q86SM7	Frame_Shift_Del	DEL	ENST00000371483.4	hg19	CCDS31248.1																																																																																			.	.		0.418	FFAR4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000083179.1	NM_181745	
FAT1	2195	hgsc.bcm.edu	37	4	187539266	187539266	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:187539266delC	ENST00000441802.2	-	10	8683	c.8474delG	c.(8473-8475)ggafs	p.G2825fs		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	2825	Cadherin 26. {ECO:0000255|PROSITE- ProRule:PRU00043}.				actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						TACTCTACTTCCCCCTGGCAG	0.438										HNSCC(5;0.00058)																											p.G2825fs	Colon(197;1040 2055 4143 4984 49344)	Atlas-INDEL	.											.	FAT1	500	.	0			c.8475delA						.						109.0	103.0	105.0					4																	187539266		1880	4131	6011	SO:0001589	frameshift_variant	2195	exon10			.	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.8474delG	chr4.hg19:g.187539266delC	ENSP00000406229:p.Gly2825fs	153.0	0.0		129.0	11.0	NM_005245		Frame_Shift_Del	DEL	ENST00000441802.2	hg19	CCDS47177.1																																																																																			.	.		0.438	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245	
FBXO46	23403	hgsc.bcm.edu	37	19	46216117	46216117	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:46216117delC	ENST00000317683.3	-	2	770	c.637delG	c.(637-639)gtgfs	p.V213fs		NM_001080469.1	NP_001073938.1	Q6PJ61	FBX46_HUMAN	F-box protein 46	213										breast(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(6)|ovary(2)|skin(1)	15		Ovarian(192;0.179)|all_neural(266;0.224)		OV - Ovarian serous cystadenocarcinoma(262;0.00568)|GBM - Glioblastoma multiforme(486;0.0844)|Epithelial(262;0.201)		TCAGATCCCACCCCCTTGGCC	0.687																																					p.V213fs		Atlas-INDEL	.											.	FBXO46	34	.	0			c.638delT						.						20.0	23.0	22.0					19																	46216117		2006	4141	6147	SO:0001589	frameshift_variant	23403	exon2			.	BC021978	CCDS46116.1	19q13.3	2008-02-05	2004-06-15	2004-06-16		ENSG00000177051		"""F-boxes /  ""other"""""	25069	protein-coding gene	gene with protein product		609117	"""F-box only protein 34-like"""	FBXO34L		9585442	Standard	NM_001080469		Approved	20D7-FC4, Fbx46	uc002pcz.3	Q6PJ61		ENST00000317683.3:c.637delG	chr19.hg19:g.46216117delC	ENSP00000410007:p.Val213fs	130.0	0.0		130.0	10.0	NM_001080469		Frame_Shift_Del	DEL	ENST00000317683.3	hg19	CCDS46116.1																																																																																			.	.		0.687	FBXO46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459661.1	XM_371179	
MX2	4600	hgsc.bcm.edu	37	21	42767625	42767625	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr21:42767625delG	ENST00000330714.3	+	7	1167	c.983delG	c.(982-984)cggfs	p.R328fs	MX2_ENST00000543692.1_3'UTR|MX2_ENST00000496774.1_3'UTR	NM_002463.1	NP_002454.1	P20592	MX2_HUMAN	MX dynamin-like GTPase 2	328	Dynamin-type G.				cytokine-mediated signaling pathway (GO:0019221)|defense response (GO:0006952)|defense response to virus (GO:0051607)|GTP catabolic process (GO:0006184)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of cell cycle (GO:0051726)|regulation of nucleocytoplasmic transport (GO:0046822)|response to interferon-alpha (GO:0035455)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)	p.R328Q(1)		breast(2)|endometrium(3)|large_intestine(6)|lung(12)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)	34		Prostate(19;1.57e-07)|all_epithelial(19;0.0222)				GTGAAGTGCCGGGGCCAGCAG	0.483																																					p.R328fs		Atlas-INDEL	.											.	MX2	84	.	1	Substitution - Missense(1)	large_intestine(1)	c.982delC						.						109.0	99.0	102.0					21																	42767625		2203	4300	6503	SO:0001589	frameshift_variant	4600	exon7			.		CCDS13672.1	21q22.3	2014-07-15	2014-07-15		ENSG00000183486	ENSG00000183486			7533	protein-coding gene	gene with protein product	"""interferon-regulated resistance GTP-binding protein MXB"", ""second interferon-induced protein p78"""	147890	"""myxovirus (influenza) resistance 2, homolog of murine"", ""myxovirus (influenza virus) resistance 2 (mouse)"""			2481229, 8798556	Standard	NM_002463		Approved	MXB	uc002yzf.1	P20592	OTTHUMG00000086753	ENST00000330714.3:c.983delG	chr21.hg19:g.42767625delG	ENSP00000333657:p.Arg328fs	138.0	0.0		151.0	10.0	NM_002463	B7Z5D3|D3DSI7	Frame_Shift_Del	DEL	ENST00000330714.3	hg19	CCDS13672.1																																																																																			.	.		0.483	MX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195147.1	NM_002463	
CHRNA4	1137	hgsc.bcm.edu	37	20	61981195	61981195	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr20:61981195delG	ENST00000370263.4	-	5	1789	c.1568delC	c.(1567-1569)ccafs	p.P523fs	CHRNA4_ENST00000463705.1_5'UTR	NM_000744.6|NM_001256573.1	NP_000735.1|NP_001243502.1	P43681	ACHA4_HUMAN	cholinergic receptor, nicotinic, alpha 4 (neuronal)	523					action potential (GO:0001508)|B cell activation (GO:0042113)|behavioral response to nicotine (GO:0035095)|calcium ion transport (GO:0006816)|cation transmembrane transport (GO:0098655)|cognition (GO:0050890)|DNA repair (GO:0006281)|exploration behavior (GO:0035640)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|neurological system process (GO:0050877)|regulation of dopamine secretion (GO:0014059)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of membrane potential (GO:0042391)|respiratory gaseous exchange (GO:0007585)|response to hypoxia (GO:0001666)|response to nicotine (GO:0035094)|response to oxidative stress (GO:0006979)|sensory perception of pain (GO:0019233)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|ligand-gated ion channel activity (GO:0015276)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(19)|prostate(3)|skin(3)|soft_tissue(1)	33	all_cancers(38;1.71e-10)				Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Dextromethorphan(DB00514)|Galantamine(DB00674)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Nicotine(DB00184)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)|Varenicline(DB01273)	GGGCTGGTCTGGGGGTGGGAG	0.687																																					p.P523fs		Atlas-INDEL	.											.	CHRNA4	98	.	0			c.1569delA						.						28.0	28.0	28.0					20																	61981195		2195	4297	6492	SO:0001589	frameshift_variant	1137	exon5			.		CCDS13517.1	20q13.33	2013-09-20	2012-02-07		ENSG00000101204	ENSG00000101204		"""Cholinergic receptors"", ""Ligand-gated ion channels / Acetylcholine receptors, nicotinic"""	1958	protein-coding gene	gene with protein product	"""acetylcholine receptor, nicotinic, alpha 4 (neuronal)"""	118504	"""cholinergic receptor, nicotinic, alpha polypeptide 4"""	EBN, EBN1		1505988	Standard	NM_000744		Approved	BFNC	uc002yes.3	P43681	OTTHUMG00000033080	ENST00000370263.4:c.1568delC	chr20.hg19:g.61981195delG	ENSP00000359285:p.Pro523fs	68.0	0.0		147.0	10.0	NM_000744	Q4JGR7|Q4VAQ5|Q4VAQ6	Frame_Shift_Del	DEL	ENST00000370263.4	hg19	CCDS13517.1																																																																																			.	.		0.687	CHRNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080508.3		
ADIPOR1	51094	hgsc.bcm.edu	37	1	202917518	202917518	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:202917518delG	ENST00000340990.5	-	3	470	c.172delC	c.(172-174)cagfs	p.Q58fs	ADIPOR1_ENST00000436244.1_Frame_Shift_Del_p.Q58fs|ADIPOR1_ENST00000367254.3_Frame_Shift_Del_p.Q58fs	NM_015999.4	NP_057083.2	Q96A54	ADR1_HUMAN	adiponectin receptor 1	58					adiponectin-activated signaling pathway (GO:0033211)|fatty acid oxidation (GO:0019395)|hormone-mediated signaling pathway (GO:0009755)|leptin-mediated signaling pathway (GO:0033210)|negative regulation of cell growth (GO:0030308)|positive regulation of insulin receptor signaling pathway (GO:0046628)|positive regulation of JAK-STAT cascade (GO:0046427)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	hormone binding (GO:0042562)|protein kinase binding (GO:0019901)|receptor activity (GO:0004872)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(7)|prostate(2)|skin(1)	16			BRCA - Breast invasive adenocarcinoma(75;0.141)			TCTTCTTCCTGGGGCACTGGG	0.507																																					p.Q58fs		Atlas-INDEL	.											.	ADIPOR1	32	.	0			c.173delA						.						95.0	86.0	89.0					1																	202917518		2203	4300	6503	SO:0001589	frameshift_variant	51094	exon3			.		CCDS1430.1	1q32.1	2012-08-22			ENSG00000159346	ENSG00000159346		"""GPCR / Unclassified : Adiponectin receptors"""	24040	protein-coding gene	gene with protein product		607945				12802337	Standard	XM_006711360		Approved	PAQR1, ACDCR1	uc001gyq.5	Q96A54	OTTHUMG00000041391	ENST00000340990.5:c.172delC	chr1.hg19:g.202917518delG	ENSP00000341785:p.Gln58fs	80.0	0.0		130.0	10.0	NM_015999	B3KMB0|Q53HS7|Q53YY6|Q9Y360	Frame_Shift_Del	DEL	ENST00000340990.5	hg19	CCDS1430.1																																																																																			.	.		0.507	ADIPOR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099160.2	NM_015999	
YAP1	10413	hgsc.bcm.edu	37	11	101984981	101984981	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:101984981delC	ENST00000282441.5	+	2	816	c.428delC	c.(427-429)accfs	p.T143fs	YAP1_ENST00000531439.1_Frame_Shift_Del_p.T143fs|YAP1_ENST00000524575.1_5'UTR|YAP1_ENST00000537274.1_Frame_Shift_Del_p.T143fs|YAP1_ENST00000345877.2_Frame_Shift_Del_p.T143fs|YAP1_ENST00000526343.1_Frame_Shift_Del_p.T143fs	NM_001130145.2|NM_001282101.1	NP_001123617.1|NP_001269030.1	P46937	YAP1_HUMAN	Yes-associated protein 1	143					cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|contact inhibition (GO:0060242)|embryonic heart tube morphogenesis (GO:0003143)|gene expression (GO:0010467)|hippo signaling (GO:0035329)|keratinocyte differentiation (GO:0030216)|lateral mesoderm development (GO:0048368)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|notochord development (GO:0030903)|paraxial mesoderm development (GO:0048339)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell proliferation (GO:0008284)|positive regulation of organ growth (GO:0046622)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of keratinocyte proliferation (GO:0010837)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)|regulation of stem cell proliferation (GO:0072091)|somatic stem cell maintenance (GO:0035019)|transcription initiation from RNA polymerase II promoter (GO:0006367)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			central_nervous_system(1)|large_intestine(1)|lung(1)|ovary(1)	4	all_cancers(8;0.000575)|all_epithelial(12;0.00564)	Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.00936)	Lung(13;0.245)	BRCA - Breast invasive adenocarcinoma(274;0.0189)		GGGACACTGACCCCCACTGGA	0.552																																					p.T143fs	Colon(50;247 1103 7861 28956)	Atlas-INDEL	.											.	YAP1	45	.	0			c.427delA						.						82.0	81.0	81.0					11																	101984981		2203	4299	6502	SO:0001589	frameshift_variant	10413	exon2			.		CCDS8314.1, CCDS44716.1, CCDS8314.2, CCDS53699.1, CCDS53700.1, CCDS60944.1, CCDS73373.1, CCDS73374.1	11q13	2010-03-19	2010-03-19		ENSG00000137693	ENSG00000137693			16262	protein-coding gene	gene with protein product		606608	"""Yes-associated protein 1, 65kDa"""			7782338	Standard	NM_001130145		Approved	YAP65	uc001pgt.3	P46937	OTTHUMG00000167322	ENST00000282441.5:c.428delC	chr11.hg19:g.101984981delC	ENSP00000282441:p.Thr143fs	162.0	0.0		164.0	10.0	NM_001130145	B4DTY1|B7ZA01|E3WEB5|E3WEB6|E9PRV2|F5H202|K0KQ18|K0KYZ8|K0L195|K0L1G3|Q7Z574|Q8IUY9	Frame_Shift_Del	DEL	ENST00000282441.5	hg19	CCDS44716.1																																																																																			.	.		0.552	YAP1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000394151.1	NM_006106	
FLNA	2316	hgsc.bcm.edu	37	X	153596402	153596402	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:153596402delG	ENST00000369850.3	-	3	666	c.430delC	c.(430-432)ctgfs	p.L144fs	FLNA_ENST00000422373.1_Frame_Shift_Del_p.L144fs|FLNA_ENST00000344736.4_Frame_Shift_Del_p.L144fs|FLNA_ENST00000360319.4_Frame_Shift_Del_p.L144fs	NM_001110556.1	NP_001104026.1	P21333	FLNA_HUMAN	filamin A, alpha	144	Actin-binding.|CH 1. {ECO:0000255|PROSITE- ProRule:PRU00044}.				actin crosslink formation (GO:0051764)|actin cytoskeleton reorganization (GO:0031532)|adenylate cyclase-inhibiting dopamine receptor signaling pathway (GO:0007195)|blood coagulation (GO:0007596)|cell junction assembly (GO:0034329)|cilium assembly (GO:0042384)|cytoplasmic sequestering of protein (GO:0051220)|early endosome to late endosome transport (GO:0045022)|epithelial to mesenchymal transition (GO:0001837)|establishment of protein localization (GO:0045184)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of transcription factor import into nucleus (GO:0042993)|protein localization to cell surface (GO:0034394)|protein stabilization (GO:0050821)|receptor clustering (GO:0043113)|spindle assembly involved in mitosis (GO:0090307)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|apical dendrite (GO:0097440)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|Myb complex (GO:0031523)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	actin filament binding (GO:0051015)|Fc-gamma receptor I complex binding (GO:0034988)|glycoprotein binding (GO:0001948)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|Rac GTPase binding (GO:0048365)|Ral GTPase binding (GO:0017160)|Rho GTPase binding (GO:0017048)|signal transducer activity (GO:0004871)|small GTPase binding (GO:0031267)|transcription factor binding (GO:0008134)			breast(6)	6	all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					TGCAGGATCAGGGTCCAGATG	0.617																																					p.L144fs		Atlas-INDEL	.											.	FLNA	373	.	0			c.431delT						.						133.0	142.0	139.0					X																	153596402		2189	4286	6475	SO:0001589	frameshift_variant	2316	exon3			.	X70082	CCDS44021.1, CCDS48194.1	Xq28	2009-07-23	2009-07-23		ENSG00000196924	ENSG00000196924			3754	protein-coding gene	gene with protein product	"""actin binding protein 280"""	300017	"""filamin A, alpha (actin binding protein 280)"""	FLN1, FLN, OPD2, OPD1		8406501, 12612583	Standard	NM_001456		Approved	ABP-280	uc004fkk.2	P21333	OTTHUMG00000022712	ENST00000369850.3:c.430delC	chrX.hg19:g.153596402delG	ENSP00000358866:p.Leu144fs	122.0	0.0		182.0	11.0	NM_001456	E9KL45|Q5HY53|Q5HY55|Q8NF52	Frame_Shift_Del	DEL	ENST00000369850.3	hg19	CCDS48194.1																																																																																			.	.		0.617	FLNA-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058942.3		
SIRPB1	10326	hgsc.bcm.edu	37	20	1551499	1551499	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr20:1551499delG	ENST00000381605.4	-	4	1100	c.1036delC	c.(1036-1038)ctgfs	p.L346fs	RP4-576H24.4_ENST00000564763.1_Intron|SIRPB1_ENST00000381603.3_Intron|SIRPB1_ENST00000262929.5_Intron	NM_006065.3	NP_006056.2	O00241	SIRB1_HUMAN	signal-regulatory protein beta 1	346	Ig-like C1-type 2.				cell surface receptor signaling pathway (GO:0007166)|innate immune response (GO:0045087)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				central_nervous_system(2)|kidney(2)|large_intestine(4)|lung(16)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	31						GAGATCTCCAGGGCATAGCTT	0.507																																					p.L346fs		Atlas-INDEL	.											.	SIRPB1	83	.	0			c.1037delT						.						186.0	174.0	178.0					20																	1551499		2203	4300	6503	SO:0001589	frameshift_variant	10326	exon4			.	Y10376	CCDS13019.1, CCDS42850.1, CCDS46571.1	20p13	2013-01-11			ENSG00000101307	ENSG00000101307		"""Signal-regulatory proteins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C1-set domain containing"""	15928	protein-coding gene	gene with protein product		603889				9062191, 16339511	Standard	NM_001083910		Approved	SIRP-BETA-1, CD172b	uc010gai.3	O00241	OTTHUMG00000031676	ENST00000381605.4:c.1036delC	chr20.hg19:g.1551499delG	ENSP00000371018:p.Leu346fs	115.0	0.0		161.0	10.0	NM_006065	A6NLM2|B2R8V0|Q5TFQ9|Q5TFR0|Q8TB12|Q9H1U5|Q9Y4V0	Frame_Shift_Del	DEL	ENST00000381605.4	hg19	CCDS13019.1																																																																																			.	.		0.507	SIRPB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077555.2	NM_006065	
RAB10	10890	hgsc.bcm.edu	37	2	26257589	26257589	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:26257589delT	ENST00000264710.4	+	1	611	c.112delT	c.(112-114)tttfs	p.F38fs		NM_016131.4	NP_057215.3	P61026	RAB10_HUMAN	RAB10, member RAS oncogene family	38					antigen processing and presentation (GO:0019882)|axonogenesis (GO:0007409)|basolateral protein localization (GO:0061467)|cellular response to insulin stimulus (GO:0032869)|endoplasmic reticulum tubular network organization (GO:0071786)|endosomal transport (GO:0016197)|establishment of neuroblast polarity (GO:0045200)|establishment of protein localization to endoplasmic reticulum membrane (GO:0097051)|establishment of protein localization to membrane (GO:0090150)|Golgi to plasma membrane protein transport (GO:0043001)|Golgi to plasma membrane transport (GO:0006893)|GTP catabolic process (GO:0006184)|membrane organization (GO:0061024)|polarized epithelial cell differentiation (GO:0030859)|protein localization to plasma membrane (GO:0072659)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	cytoplasmic vesicle membrane (GO:0030659)|endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum tubular network (GO:0071782)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|insulin-responsive compartment (GO:0032593)|primary cilium (GO:0072372)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|myosin V binding (GO:0031489)			lung(2)|ovary(1)	3	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CAATACTACCTTTATTTCCAC	0.488																																					p.T37fs		Atlas-INDEL	.											.	RAB10	14	.	0			c.111delC						.						156.0	146.0	149.0					2																	26257589		2203	4300	6503	SO:0001589	frameshift_variant	10890	exon1			.	AF106681	CCDS1720.1	2p23.3	2008-05-21			ENSG00000084733	ENSG00000084733		"""RAB, member RAS oncogene"""	9759	protein-coding gene	gene with protein product	"""ras-related GTP-binding protein"""	612672				7688123	Standard	NM_016131		Approved		uc002rgv.3	P61026	OTTHUMG00000094796	ENST00000264710.4:c.112delT	chr2.hg19:g.26257589delT	ENSP00000264710:p.Phe38fs	173.0	0.0		204.0	13.0	NM_016131	D6W538|O88386|Q6IA52|Q9D7X6|Q9H0T3	Frame_Shift_Del	DEL	ENST00000264710.4	hg19	CCDS1720.1																																																																																			.	.		0.488	RAB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211610.1	NM_016131	
RIMBP3C	150221	hgsc.bcm.edu	37	22	21901827	21901827	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr22:21901827delC	ENST00000433039.1	-	1	3923	c.3439delG	c.(3439-3441)gtafs	p.V1147fs	UBE2L3_ENST00000458578.2_5'Flank|RIMBP3C_ENST00000331505.5_Frame_Shift_Del_p.V1053fs|SCARNA17_ENST00000516334.1_RNA|RN7SKP221_ENST00000410420.1_RNA|SCARNA18_ENST00000516796.1_RNA	NM_001128633.1	NP_001122105.1	A6NJZ7	RIM3C_HUMAN	RIMS binding protein 3C	1147	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.									large_intestine(1)	1						AATTCCAATACGGTGCTCCCA	0.562																																					p.V1147fs		Atlas-INDEL	.											.	RIMBP3C	6	.	0			c.3440delT						.																																			SO:0001589	frameshift_variant	150221	exon1			.		CCDS46669.1	22q11.21	2008-10-21			ENSG00000183246	ENSG00000183246			33892	protein-coding gene	gene with protein product		612701				17855024	Standard	NM_001128633		Approved		uc002zuq.4	A6NJZ7	OTTHUMG00000150825	ENST00000433039.1:c.3439delG	chr22.hg19:g.21901827delC	ENSP00000390630:p.Val1147fs	1.0	0.0		12.0	11.0	NM_001128633		Frame_Shift_Del	DEL	ENST00000433039.1	hg19	CCDS46669.1																																																																																			.	.		0.562	RIMBP3C-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		XM_036942	
CIB3	117286	hgsc.bcm.edu	37	19	16275654	16275654	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:16275654delC	ENST00000269878.4	-	5	466	c.417delG	c.(415-417)gggfs	p.G139fs	CIB3_ENST00000379859.3_Frame_Shift_Del_p.G90fs|CIB3_ENST00000541493.1_5'UTR	NM_054113.2	NP_473454.1	Q96Q77	CIB3_HUMAN	calcium and integrin binding family member 3	139			G -> E (in dbSNP:rs6512087). {ECO:0000269|PubMed:15489334}.				calcium ion binding (GO:0005509)			cervix(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)|skin(2)	16						CGGCACTCAGCCCCCCCCGCG	0.567																																					p.L140X		Atlas-INDEL	.											CIB3,NS,carcinoma,0,3	CIB3	35	.	0			c.418delC						.						131.0	118.0	122.0					19																	16275654		2203	4300	6503	SO:0001589	frameshift_variant	117286	exon5			.	AB050868	CCDS12340.1, CCDS74305.1	19p13.12	2013-01-10						"""EF-hand domain containing"""	24580	protein-coding gene	gene with protein product		610645					Standard	XM_005259728		Approved	KIP3	uc002nds.3	Q96Q77		ENST00000269878.4:c.417delG	chr19.hg19:g.16275654delC	ENSP00000269878:p.Gly139fs	157.0	0.0		167.0	15.0	NM_054113	E7EUX1|Q2M1W0|Q6ISP1	Frame_Shift_Del	DEL	ENST00000269878.4	hg19	CCDS12340.1																																																																																			.	.		0.567	CIB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460351.1	NM_054113	
AADACL4	343066	hgsc.bcm.edu	37	1	12704616	12704616	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:12704616delG	ENST00000376221.1	+	1	51	c.51delG	c.(49-51)ctgfs	p.L17fs		NM_001013630.1	NP_001013652.1	Q5VUY2	ADCL4_HUMAN	arylacetamide deacetylase-like 4	17						integral component of membrane (GO:0016021)	carboxylic ester hydrolase activity (GO:0052689)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(6)|prostate(1)	17	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.000937)|all_lung(284;0.00122)|Colorectal(325;0.00215)|Breast(348;0.0042)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.81e-07)|COAD - Colon adenocarcinoma(227;0.000274)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.00217)|KIRC - Kidney renal clear cell carcinoma(229;0.00579)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0384)		TCTTTTTCCTGGGGGTCTTTG	0.542																																					p.L17fs		Atlas-INDEL	.											.	AADACL4	48	.	0			c.50delT						.						183.0	160.0	168.0					1																	12704616		2203	4300	6503	SO:0001589	frameshift_variant	343066	exon1			.		CCDS30590.1	1p36.21	2010-12-14			ENSG00000204518	ENSG00000204518			32038	protein-coding gene	gene with protein product							Standard	XM_006710608		Approved	OTTHUMG00000001889	uc001auf.3	Q5VUY2	OTTHUMG00000001889	ENST00000376221.1:c.51delG	chr1.hg19:g.12704616delG	ENSP00000365395:p.Leu17fs	153.0	0.0		189.0	12.0	NM_001013630		Frame_Shift_Del	DEL	ENST00000376221.1	hg19	CCDS30590.1																																																																																			.	.		0.542	AADACL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005328.1	NM_001013630	
ABCA13	154664	hgsc.bcm.edu	37	7	48391899	48391899	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:48391899delA	ENST00000435803.1	+	31	10527	c.10503delA	c.(10501-10503)gtafs	p.V3501fs		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	3501					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						CAGATGTGGTAAAAAACCCTT	0.453																																					p.V3501fs		Atlas-INDEL	.											.	ABCA13	1192	.	0			c.10502delT						.						87.0	87.0	87.0					7																	48391899		1951	4154	6105	SO:0001589	frameshift_variant	154664	exon31			.	AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"""ATP binding cassette transporters / subfamily A"""	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.10503delA	chr7.hg19:g.48391899delA	ENSP00000411096:p.Val3501fs	120.0	0.0		162.0	10.0	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Frame_Shift_Del	DEL	ENST00000435803.1	hg19	CCDS47584.1																																																																																			.	.		0.453	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701	
ZNF451	26036	hgsc.bcm.edu	37	6	57012815	57012815	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:57012815delT	ENST00000370706.4	+	10	2176	c.1932delT	c.(1930-1932)cctfs	p.P644fs	RP11-203B9.4_ENST00000587815.1_RNA|RP11-203B9.4_ENST00000591553.1_RNA|RP11-203B9.4_ENST00000592038.1_RNA|RP11-203B9.4_ENST00000586432.1_RNA|RP11-203B9.4_ENST00000586053.1_RNA|ZNF451_ENST00000357489.3_Frame_Shift_Del_p.P644fs|RP11-203B9.4_ENST00000592500.1_RNA|RP11-203B9.4_ENST00000416069.2_RNA|RP11-203B9.4_ENST00000588811.1_RNA|RP11-203B9.4_ENST00000585792.1_RNA|ZNF451_ENST00000491832.2_Frame_Shift_Del_p.P644fs|RP11-203B9.4_ENST00000586466.1_RNA|RP11-203B9.4_ENST00000586668.1_RNA|RP11-203B9.4_ENST00000589263.1_RNA|RP11-203B9.4_ENST00000589549.1_RNA	NM_001031623.2	NP_001026794.1	Q9Y4E5	ZN451_HUMAN	zinc finger protein 451	644					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	32	Lung NSC(77;0.145)		LUSC - Lung squamous cell carcinoma(124;0.0785)|Lung(124;0.13)			GCAGAAAGCCTTTTCATAAGA	0.378																																					p.P644fs		Atlas-INDEL	.											.	ZNF451	181	.	0			c.1931delC						.						87.0	88.0	87.0					6																	57012815		2202	4299	6501	SO:0001589	frameshift_variant	26036	exon10			.	AB011148	CCDS4960.1, CCDS43477.1, CCDS59026.1	6p12.1	2012-08-08			ENSG00000112200	ENSG00000112200		"""Zinc fingers, C2H2-type"""	21091	protein-coding gene	gene with protein product		615708				9628581	Standard	NM_001031623		Approved	KIAA0576, COASTER, dJ417I1.1, KIAA1702	uc003pdm.2	Q9Y4E5	OTTHUMG00000014916	ENST00000370706.4:c.1932delT	chr6.hg19:g.57012815delT	ENSP00000359740:p.Pro644fs	78.0	0.0		157.0	10.0	NM_001031623	Q5VVE9|Q5VVF1|Q86YE4|Q8N380|Q8TD15|Q9C0G1|Q9NQM1	Frame_Shift_Del	DEL	ENST00000370706.4	hg19	CCDS43477.1																																																																																			.	.		0.378	ZNF451-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041035.2	NM_015555	
PNKP	11284	hgsc.bcm.edu	37	19	50368611	50368611	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:50368611delC	ENST00000322344.3	-	4	380	c.271delG	c.(271-273)gacfs	p.D91fs	PNKP_ENST00000596014.1_Frame_Shift_Del_p.D91fs|PNKP_ENST00000600573.1_Frame_Shift_Del_p.D91fs|PNKP_ENST00000600910.1_Frame_Shift_Del_p.D91fs|PNKP_ENST00000595792.1_5'Flank	NM_007254.3	NP_009185.2	Q96T60	PNKP_HUMAN	polynucleotide kinase 3'-phosphatase	91	FHA.				dephosphorylation (GO:0016311)|DNA damage response, detection of DNA damage (GO:0042769)|DNA repair (GO:0006281)|DNA-dependent DNA replication (GO:0006261)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleotide phosphorylation (GO:0046939)|nucleotide-excision repair, DNA damage removal (GO:0000718)|polynucleotide 3' dephosphorylation (GO:0098506)|response to oxidative stress (GO:0006979)|response to radiation (GO:0009314)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity (GO:0046404)|damaged DNA binding (GO:0003684)|double-stranded DNA binding (GO:0003690)|endonuclease activity (GO:0004519)|nucleotide kinase activity (GO:0019201)|polynucleotide 3'-phosphatase activity (GO:0046403)|purine nucleotide binding (GO:0017076)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(10)|ovary(1)|urinary_tract(1)	19		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.107)|Ovarian(192;0.231)		GBM - Glioblastoma multiforme(134;0.0118)|OV - Ovarian serous cystadenocarcinoma(262;0.0134)		TACAGTGTGTCCCCCACCCCC	0.622								Other BER factors																													p.D91fs		Atlas-INDEL	.											.	PNKP	71	.	0			c.272delA						.						64.0	61.0	62.0					19																	50368611		2203	4300	6503	SO:0001589	frameshift_variant	11284	exon4			.	AF126486	CCDS12783.1	19q13.3-q13.4	2008-02-05				ENSG00000039650			9154	protein-coding gene	gene with protein product		605610				10446192, 10446193	Standard	NM_007254		Approved	PNK	uc002pqj.3	Q96T60		ENST00000322344.3:c.271delG	chr19.hg19:g.50368611delC	ENSP00000323511:p.Asp91fs	114.0	0.0		157.0	10.0	NM_007254	Q9BUL2|Q9P1V2|Q9UKU8|Q9UNF8|Q9UNI0	Frame_Shift_Del	DEL	ENST00000322344.3	hg19	CCDS12783.1																																																																																			.	.		0.622	PNKP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465830.1	NM_007254	
MYO18A	399687	hgsc.bcm.edu	37	17	27438464	27438464	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:27438464delG	ENST00000527372.1	-	17	3058	c.2878delC	c.(2878-2880)cggfs	p.R960fs	MYO18A_ENST00000533112.1_Frame_Shift_Del_p.R960fs|MYO18A_ENST00000531253.1_Frame_Shift_Del_p.R960fs|MYO18A_ENST00000354329.4_Frame_Shift_Del_p.R960fs	NM_078471.3	NP_510880.2	Q92614	MY18A_HUMAN	myosin XVIIIA	960	Myosin motor.				actomyosin structure organization (GO:0031032)|cell migration (GO:0016477)|DNA metabolic process (GO:0006259)|Golgi organization (GO:0007030)|Golgi vesicle budding (GO:0048194)|negative regulation of apoptotic process (GO:0043066)|positive regulation of protein secretion (GO:0050714)	actomyosin (GO:0042641)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|myosin complex (GO:0016459)|trans-Golgi network (GO:0005802)	actin filament binding (GO:0051015)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|motor activity (GO:0003774)|poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(6)|kidney(6)|lung(20)|urinary_tract(2)	36			Epithelial(11;4.97e-05)|BRCA - Breast invasive adenocarcinoma(11;0.000221)|all cancers(11;0.000234)|Colorectal(6;0.0102)|COAD - Colon adenocarcinoma(6;0.031)			TGCAGGAGCCGGGGGGCATTC	0.592											OREG0024287	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R960fs	Esophageal Squamous(182;472 2015 7001 15270 22562)	Atlas-INDEL	.											MYO18A_ENST00000527372,colon,carcinoma,0,2	MYO18A	217	.	0			c.2879delG						.						69.0	71.0	70.0					17																	27438464		1919	4134	6053	SO:0001589	frameshift_variant	399687	exon17			.	D86970	CCDS45641.1, CCDS45642.1	17q11.2	2011-09-27			ENSG00000196535	ENSG00000196535		"""Myosins / Myosin superfamily : Class XVIII"""	31104	protein-coding gene	gene with protein product		610067				12761286	Standard	NM_078471		Approved	KIAA0216, MysPDZ	uc002hdt.1	Q92614	OTTHUMG00000166360	ENST00000527372.1:c.2878delC	chr17.hg19:g.27438464delG	ENSP00000437073:p.Arg960fs	135.0	0.0	794	148.0	10.0	NM_078471	Q5H9U3|Q5W9F9|Q5W9G1|Q8IXP8	Frame_Shift_Del	DEL	ENST00000527372.1	hg19	CCDS45642.1																																																																																			.	.		0.592	MYO18A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389396.1	NM_078471	
AP1B1	162	hgsc.bcm.edu	37	22	29736724	29736724	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr22:29736724delG	ENST00000405198.1	-	13	1950	c.1919delC	c.(1918-1920)ccafs	p.P640fs	AP1B1_ENST00000317368.7_Frame_Shift_Del_p.P640fs|AP1B1_ENST00000432560.2_Frame_Shift_Del_p.P640fs|AP1B1_ENST00000402502.1_Frame_Shift_Del_p.P640fs|AP1B1_ENST00000415447.1_Frame_Shift_Del_p.P640fs|AP1B1_ENST00000472057.1_5'UTR|AP1B1_ENST00000356015.2_Frame_Shift_Del_p.P640fs|AP1B1_ENST00000357586.2_Frame_Shift_Del_p.P640fs			Q10567	AP1B1_HUMAN	adaptor-related protein complex 1, beta 1 subunit	640	Pro-rich (stalk region).				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of defense response to virus by virus (GO:0050690)|viral process (GO:0016032)	clathrin adaptor complex (GO:0030131)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)|lysosomal membrane (GO:0005765)|trans-Golgi network membrane (GO:0032588)	protein kinase binding (GO:0019901)|protein transporter activity (GO:0008565)|transporter activity (GO:0005215)			endometrium(3)|large_intestine(4)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	22						GCCGCTCACTGGGGGGCCGAG	0.677																																					p.P640fs		Atlas-INDEL	.											.	AP1B1	72	.	0			c.1920delA						.						18.0	19.0	18.0					22																	29736724		2198	4294	6492	SO:0001589	frameshift_variant	162	exon14			.	L13939	CCDS13855.1, CCDS13856.1, CCDS13856.2, CCDS54515.1	22q12.2	2010-06-18			ENSG00000100280	ENSG00000100280			554	protein-coding gene	gene with protein product		600157		ADTB1, CLAPB2		7987321, 8812422	Standard	NM_145730		Approved	BAM22, AP105A	uc003afj.3	Q10567	OTTHUMG00000151109	ENST00000405198.1:c.1919delC	chr22.hg19:g.29736724delG	ENSP00000384194:p.Pro640fs	114.0	0.0		137.0	11.0	NM_001127	C9JRD1|F8WDL0|P78436|Q20WL3|Q86X54	Frame_Shift_Del	DEL	ENST00000405198.1	hg19	CCDS13855.1																																																																																			.	.		0.677	AP1B1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321374.1	NM_001127	
NAALAD2	10003	hgsc.bcm.edu	37	11	89914834	89914834	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:89914834delT	ENST00000534061.1	+	17	2135	c.1905delT	c.(1903-1905)gatfs	p.D635fs	NAALAD2_ENST00000321955.4_Frame_Shift_Del_p.D602fs|NAALAD2_ENST00000375944.3_Intron	NM_005467.3	NP_005458.1	Q9Y3Q0	NALD2_HUMAN	N-acetylated alpha-linked acidic dipeptidase 2	635					neurotransmitter catabolic process (GO:0042135)|proteolysis (GO:0006508)	integral component of membrane (GO:0016021)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|dipeptidyl-peptidase activity (GO:0008239)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|N-formylglutamate deformylase activity (GO:0050129)|serine-type peptidase activity (GO:0008236)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(12)|lung(32)|pancreas(1)|prostate(3)|skin(5)|stomach(2)	59		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00556)				CTGCTTCAGATTTTCATAAAC	0.289																																					p.D635fs		Atlas-INDEL	.											.	NAALAD2	113	.	0			c.1904delA						.						37.0	41.0	40.0					11																	89914834		2199	4291	6490	SO:0001589	frameshift_variant	10003	exon17			.	AJ012370	CCDS8288.1, CCDS73364.1	11q14.3-q21	2011-08-16			ENSG00000077616	ENSG00000077616	3.4.17.21		14526	protein-coding gene	gene with protein product	"""glutamate carboxypeptidase III"""	611636				10085079	Standard	NM_005467		Approved	NAALADASE2, NAADALASE2, GPCIII	uc001pdf.4	Q9Y3Q0	OTTHUMG00000166368	ENST00000534061.1:c.1905delT	chr11.hg19:g.89914834delT	ENSP00000432481:p.Asp635fs	148.0	0.0		163.0	11.0	NM_005467	B3KQR4|Q4KKV4|Q4VAM9	Frame_Shift_Del	DEL	ENST00000534061.1	hg19	CCDS8288.1																																																																																			.	.		0.289	NAALAD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389424.2	NM_005467	
SPG20	23111	hgsc.bcm.edu	37	13	36878657	36878657	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr13:36878657delT	ENST00000451493.1	-	9	2063	c.1846delA	c.(1846-1848)actfs	p.T616fs	SPG20_ENST00000355182.4_Frame_Shift_Del_p.T616fs|SPG20_ENST00000438666.2_Frame_Shift_Del_p.T616fs|SPG20_ENST00000494062.2_Frame_Shift_Del_p.T616fs	NM_001142295.1	NP_001135767.1	Q8N0X7	SPG20_HUMAN	spastic paraplegia 20 (Troyer syndrome)	616					abscission (GO:0009838)|adipose tissue development (GO:0060612)|cell death (GO:0008219)|cell division (GO:0051301)|lipid particle organization (GO:0034389)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of collateral sprouting in absence of injury (GO:0048698)|neuromuscular process (GO:0050905)|regulation of mitochondrial membrane potential (GO:0051881)	cytoplasm (GO:0005737)|lipid particle (GO:0005811)|midbody (GO:0030496)|mitochondrial outer membrane (GO:0005741)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(10)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	27		Breast(139;0.014)|Lung SC(185;0.0548)|Prostate(109;0.174)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;2.42e-08)|Epithelial(112;1.58e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00128)|BRCA - Breast invasive adenocarcinoma(63;0.0125)|GBM - Glioblastoma multiforme(144;0.026)		TGTGTTGCAGTTTTCTTCACC	0.443																																					p.T616fs		Atlas-INDEL	.											.	SPG20	87	.	0			c.1847delC						.						285.0	245.0	258.0					13																	36878657		2203	4300	6503	SO:0001589	frameshift_variant	23111	exon9			.	AB011182	CCDS9356.1	13q13.1	2008-07-04	2007-04-23		ENSG00000133104	ENSG00000133104			18514	protein-coding gene	gene with protein product	"""spartin"""	607111				6022528, 12134148	Standard	NM_001142294		Approved	KIAA0610, TAHCCP1	uc001uvm.3	Q8N0X7	OTTHUMG00000016730	ENST00000451493.1:c.1846delA	chr13.hg19:g.36878657delT	ENSP00000414147:p.Thr616fs	143.0	0.0		162.0	10.0	NM_015087	O60349|Q86Y67|Q9H1T2|Q9H1T3	Frame_Shift_Del	DEL	ENST00000451493.1	hg19	CCDS9356.1																																																																																			.	.		0.443	SPG20-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044494.2		
RP1	6101	hgsc.bcm.edu	37	8	55539238	55539238	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr8:55539238delA	ENST00000220676.1	+	4	2944	c.2796delA	c.(2794-2796)atafs	p.I932fs		NM_006269.1	NP_006260.1	P56715	RP1_HUMAN	retinitis pigmentosa 1 (autosomal dominant)	932					axoneme assembly (GO:0035082)|cellular response to light stimulus (GO:0071482)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|photoreceptor cell outer segment organization (GO:0035845)|phototransduction, visible light (GO:0007603)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|visual perception (GO:0007601)	axoneme (GO:0005930)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	microtubule binding (GO:0008017)			NS(4)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(29)|lung(69)|ovary(6)|pancreas(1)|prostate(9)|skin(17)|upper_aerodigestive_tract(3)|urinary_tract(2)	169		all_lung(136;0.0831)|Lung NSC(129;0.109)|all_epithelial(80;0.123)	OV - Ovarian serous cystadenocarcinoma(7;4.4e-07)|Epithelial(17;3.37e-05)|all cancers(17;0.000285)			TAAAGCCTATAAAATCAGCTC	0.323																																					p.I932fs	Colon(91;1014 1389 7634 14542 40420)	Atlas-INDEL	.											.	RP1	429	.	0			c.2795delT						.						35.0	38.0	37.0					8																	55539238		2202	4300	6502	SO:0001589	frameshift_variant	6101	exon4			.	AF146592	CCDS6160.1	8q12.1	2013-01-08				ENSG00000104237			10263	protein-coding gene	gene with protein product		603937				1783394	Standard	NM_006269		Approved	DCDC4A	uc003xsd.1	P56715		ENST00000220676.1:c.2796delA	chr8.hg19:g.55539238delA	ENSP00000220676:p.Ile932fs	68.0	0.0		170.0	11.0	NM_006269		Frame_Shift_Del	DEL	ENST00000220676.1	hg19	CCDS6160.1																																																																																			.	.		0.323	RP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378532.2	NM_006269	
CREBBP	1387	hgsc.bcm.edu	37	16	3777763	3777763	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:3777763delC	ENST00000262367.5	-	31	8094	c.7285delG	c.(7285-7287)gacfs	p.D2429fs	CREBBP_ENST00000382070.3_Frame_Shift_Del_p.D2391fs	NM_004380.2	NP_004371.2	Q92793	CBP_HUMAN	CREB binding protein	2429					cellular lipid metabolic process (GO:0044255)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|embryonic digit morphogenesis (GO:0042733)|gene expression (GO:0010467)|germ-line stem cell maintenance (GO:0030718)|histone acetylation (GO:0016573)|homeostatic process (GO:0042592)|innate immune response (GO:0045087)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein complex assembly (GO:0006461)|regulation of smoothened signaling pathway (GO:0008589)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nuclear body (GO:0016604)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|histone acetyltransferase activity (GO:0004402)|MRF binding (GO:0043426)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|central_nervous_system(4)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(125)|kidney(5)|large_intestine(32)|lung(43)|ovary(18)|pancreas(2)|prostate(6)|skin(9)|soft_tissue(1)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(21)	295		Ovarian(90;0.0266)		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)		CCCGTGGTGTCCCCGACCAGG	0.552			"""T, N, F, Mis, O"""	"""MLL, MORF, RUNXBP2"""	"""ALL, AML, DLBCL, B-NHL """		Rubinstein-Taybi syndrome																														p.D2429fs		Atlas-INDEL	.		Dom/Rec	yes		16	16p13.3	1387	CREB binding protein (CBP)	yes	L	.	CREBBP	546	.	0			c.7286delA						.						102.0	104.0	103.0					16																	3777763		2197	4300	6497	SO:0001589	frameshift_variant	1387	exon31			.	U85962	CCDS10509.1, CCDS45399.1	16p13.3	2011-07-01	2008-08-01		ENSG00000005339	ENSG00000005339		"""Chromatin-modifying enzymes / K-acetyltransferases"""	2348	protein-coding gene	gene with protein product		600140	"""Rubinstein-Taybi syndrome"""	RSTS		8413673	Standard	NM_001079846		Approved	RTS, CBP, KAT3A	uc002cvv.3	Q92793	OTTHUMG00000129431	ENST00000262367.5:c.7285delG	chr16.hg19:g.3777763delC	ENSP00000262367:p.Asp2429fs	83.0	0.0		121.0	11.0	NM_004380	D3DUC9|O00147|Q16376|Q4LE28	Frame_Shift_Del	DEL	ENST00000262367.5	hg19	CCDS10509.1																																																																																			.	.		0.552	CREBBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251591.2	NM_004380	
SIPA1L3	23094	hgsc.bcm.edu	37	19	38655235	38655235	+	Frame_Shift_Del	DEL	C	C	-	rs142602797	byFrequency	TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:38655235delC	ENST00000222345.6	+	15	4406	c.3897delC	c.(3895-3897)gacfs	p.D1299fs		NM_015073.1	NP_055888.1	O60292	SI1L3_HUMAN	signal-induced proliferation-associated 1 like 3	1299					hematopoietic progenitor cell differentiation (GO:0002244)|regulation of small GTPase mediated signal transduction (GO:0051056)	extracellular space (GO:0005615)	GTPase activator activity (GO:0005096)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(22)|ovary(2)|prostate(4)|skin(3)	59			Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			CAGAGCAAGACCCCCTCTCCA	0.647																																					p.D1299fs		Atlas-INDEL	.											.	SIPA1L3	150	.	0			c.3896delA						.						73.0	65.0	67.0					19																	38655235		2203	4300	6503	SO:0001589	frameshift_variant	23094	exon15			.	AB011117	CCDS33007.1	19q13.13	2008-02-05			ENSG00000105738	ENSG00000105738			23801	protein-coding gene	gene with protein product							Standard	XM_005258671		Approved	KIAA0545	uc002ohk.3	O60292	OTTHUMG00000073727	ENST00000222345.6:c.3897delC	chr19.hg19:g.38655235delC	ENSP00000222345:p.Asp1299fs	176.0	0.0		191.0	12.0	NM_015073	Q2TV87	Frame_Shift_Del	DEL	ENST00000222345.6	hg19	CCDS33007.1																																																																																			.	.		0.647	SIPA1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000156294.2	XM_032278	
HERC2	8924	hgsc.bcm.edu	37	15	28436339	28436339	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:28436339delT	ENST00000261609.7	-	54	8611	c.8503delA	c.(8503-8505)atgfs	p.M2835fs		NM_004667.5	NP_004658.3			HECT and RLD domain containing E3 ubiquitin protein ligase 2											NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(3)|cervix(3)|endometrium(20)|kidney(11)|large_intestine(33)|lung(95)|ovary(7)|prostate(8)|skin(7)|upper_aerodigestive_tract(8)|urinary_tract(4)	204		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)		TCTACGATCATTTTTAATCTA	0.358																																					p.M2835fs		Atlas-INDEL	.											.	HERC2	501	.	0			c.8504delT						.						97.0	100.0	99.0					15																	28436339		2203	4300	6503	SO:0001589	frameshift_variant	8924	exon54			.	AF071172	CCDS10021.1	15q13	2012-02-23	2012-02-23		ENSG00000128731	ENSG00000128731			4868	protein-coding gene	gene with protein product		605837	"""hect domain and RLD 2"""			9949213	Standard	NM_004667		Approved	jdf2, p528, D15F37S1	uc001zbj.4	O95714	OTTHUMG00000129251	ENST00000261609.7:c.8503delA	chr15.hg19:g.28436339delT	ENSP00000261609:p.Met2835fs	86.0	0.0		116.0	11.0	NM_004667		Frame_Shift_Del	DEL	ENST00000261609.7	hg19	CCDS10021.1																																																																																			.	.		0.358	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667	
HSP90B1	7184	hgsc.bcm.edu	37	12	104331534	104331534	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:104331534delA	ENST00000299767.5	+	6	987	c.805delA	c.(805-807)aaafs	p.K270fs		NM_003299.2	NP_003290.1	P14625	ENPL_HUMAN	heat shock protein 90kDa beta (Grp94), member 1	270					actin rod assembly (GO:0031247)|activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|cellular response to ATP (GO:0071318)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|protein folding (GO:0006457)|protein transport (GO:0015031)|regulation of phosphoprotein phosphatase activity (GO:0043666)|response to hypoxia (GO:0001666)|sequestering of calcium ion (GO:0051208)|toll-like receptor signaling pathway (GO:0002224)	cytosol (GO:0005829)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|midbody (GO:0030496)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|low-density lipoprotein particle receptor binding (GO:0050750)|protein phosphatase binding (GO:0019903)|RNA binding (GO:0003723)|virion binding (GO:0046790)			central_nervous_system(1)|kidney(5)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|skin(1)|urinary_tract(4)	29					Rifabutin(DB00615)	AAATCTCGTCAAAAAATATTC	0.299																																					p.V268fs		Atlas-INDEL	.											.	HSP90B1	72	.	0			c.804delC						.						48.0	51.0	50.0					12																	104331534		2201	4298	6499	SO:0001589	frameshift_variant	7184	exon6			.	AY040226	CCDS9094.1	12q24.2-q24.3	2011-09-02	2006-02-24	2006-02-24		ENSG00000166598		"""Heat shock proteins / HSPC"""	12028	protein-coding gene	gene with protein product		191175	"""tumor rejection antigen (gp96) 1"""	TRA1		16269234	Standard	NM_003299		Approved	GP96, GRP94	uc001tkb.2	P14625	OTTHUMG00000170118	ENST00000299767.5:c.805delA	chr12.hg19:g.104331534delA	ENSP00000299767:p.Lys270fs	162.0	0.0		179.0	11.0	NM_003299	Q96A97	Frame_Shift_Del	DEL	ENST00000299767.5	hg19	CCDS9094.1																																																																																			.	.		0.299	HSP90B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407349.1	NM_003299	
WHSC1L1	54904	hgsc.bcm.edu	37	8	38146052	38146052	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr8:38146052delT	ENST00000317025.8	-	19	3971	c.3454delA	c.(3454-3456)acgfs	p.T1152fs	WHSC1L1_ENST00000433384.2_Frame_Shift_Del_p.T1103fs|WHSC1L1_ENST00000527502.1_Frame_Shift_Del_p.T1152fs	NM_023034.1	NP_075447.1	Q9BZ95	NSD3_HUMAN	Wolf-Hirschhorn syndrome candidate 1-like 1	1152	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				histone lysine methylation (GO:0034968)|histone methylation (GO:0016571)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(3)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	24	Colorectal(12;0.000442)|Esophageal squamous(3;0.0725)	all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.065)	Epithelial(3;3.12e-43)|all cancers(3;1.72e-38)|BRCA - Breast invasive adenocarcinoma(5;2.84e-27)|LUSC - Lung squamous cell carcinoma(2;2.79e-25)|Lung(2;5.03e-23)|COAD - Colon adenocarcinoma(9;0.0511)			CTCCGCTCCGTTTTGATGATC	0.537			T	NUP98	AML																																p.T1152fs		Atlas-INDEL	.		Dom	yes		8	8p12	54904	Wolf-Hirschhorn syndrome candidate 1-like 1 (NSD3)		L	.	WHSC1L1	137	.	0			c.3455delC						.						118.0	116.0	117.0					8																	38146052		1932	4141	6073	SO:0001589	frameshift_variant	54904	exon19			.	AF332469	CCDS6105.1, CCDS43729.1	8p11.2	2013-05-20			ENSG00000147548	ENSG00000147548			12767	protein-coding gene	gene with protein product		607083				10802047, 23269674	Standard	NM_023034		Approved	FLJ20353, NSD3	uc003xli.3	Q9BZ95		ENST00000317025.8:c.3454delA	chr8.hg19:g.38146052delT	ENSP00000313983:p.Thr1152fs	133.0	0.0		130.0	10.0	NM_023034	B7ZL11|D3DSX1|Q1RMD3|Q3B796|Q6ZSA5|Q9BYU8|Q9BYU9|Q9H2M8|Q9H9W9|Q9NXA6	Frame_Shift_Del	DEL	ENST00000317025.8	hg19	CCDS43729.1																																																																																			.	.		0.537	WHSC1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381924.3	NM_023034	
CEACAM3	1084	hgsc.bcm.edu	37	19	42314895	42314895	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:42314895delC	ENST00000357396.3	+	6	894	c.653delC	c.(652-654)gccfs	p.A218fs	CEACAM3_ENST00000344550.4_Frame_Shift_Del_p.G200fs|CEACAM3_ENST00000221999.4_Frame_Shift_Del_p.G200fs	NM_001815.2	NP_001806.2	P40198	CEAM3_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 3	218						integral component of membrane (GO:0016021)				endometrium(2)|kidney(4)|large_intestine(1)|lung(4)|prostate(3)|skin(4)|stomach(1)	19						ACTGCCCAGGCCCCCCTACCC	0.612																																					p.A218fs		Atlas-INDEL	.											.	CEACAM3	37	.	0			c.652delG						.						85.0	76.0	79.0					19																	42314895		2203	4300	6503	SO:0001589	frameshift_variant	1084	exon6			.	E03349	CCDS12586.2, CCDS62685.1	19q13.2	2013-01-11			ENSG00000170956	ENSG00000170956		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	1815	protein-coding gene	gene with protein product		609142		CGM1			Standard	NM_001815		Approved	CD66d	uc002orn.2	P40198	OTTHUMG00000150142	ENST00000357396.3:c.653delC	chr19.hg19:g.42314895delC	ENSP00000349971:p.Ala218fs	131.0	0.0		166.0	13.0	NM_001815	G5E978|Q3KPH9	Frame_Shift_Del	DEL	ENST00000357396.3	hg19	CCDS12586.2																																																																																			.	.		0.612	CEACAM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316509.2	NM_001815	
ATP11C	286410	hgsc.bcm.edu	37	X	138869386	138869386	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:138869386delA	ENST00000327569.3	-	15	1645	c.1547delT	c.(1546-1548)ttafs	p.L516fs	ATP11C_ENST00000361648.2_Frame_Shift_Del_p.L516fs|ATP11C_ENST00000359686.2_Frame_Shift_Del_p.L516fs|ATP11C_ENST00000370557.1_Frame_Shift_Del_p.L513fs|ATP11C_ENST00000370543.1_Frame_Shift_Del_p.L516fs|ATP11C_ENST00000460773.1_5'UTR	NM_173694.4	NP_775965	Q8NB49	AT11C_HUMAN	ATPase, class VI, type 11C	516					ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|positive regulation of B cell differentiation (GO:0045579)|pre-B cell differentiation (GO:0002329)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			breast(2)|central_nervous_system(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(31)|ovary(5)|prostate(1)|skin(3)	75	Acute lymphoblastic leukemia(192;0.000127)					TCGATTTCCTAAAAATGTGAA	0.294																																					p.L516fs		Atlas-INDEL	.											.	ATP11C	319	.	0			c.1548delA						.						101.0	83.0	89.0					X																	138869386		2201	4298	6499	SO:0001589	frameshift_variant	286410	exon15			.	AJ580094	CCDS14668.1, CCDS35410.1	Xq27.1	2011-06-09	2007-09-19		ENSG00000101974	ENSG00000101974		"""ATPases / P-type"""	13554	protein-coding gene	gene with protein product		300516	"""ATPase, Class VI, type 11C"""			11015572	Standard	NM_173694		Approved	ATPIG, ATPIQ	uc004faz.3	Q8NB49	OTTHUMG00000022538	ENST00000327569.3:c.1547delT	chrX.hg19:g.138869386delA	ENSP00000332756:p.Leu516fs	149.0	0.0		147.0	10.0	NM_001010986	Q5JT69|Q5JT70|Q5JT71|Q5JT72|Q5JT73|Q6ZND5|Q6ZU50|Q6ZUP7|Q70IJ9|Q70IK0|Q8WX24	Frame_Shift_Del	DEL	ENST00000327569.3	hg19	CCDS14668.1																																																																																			.	.		0.294	ATP11C-008	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354945.1	NM_173694	
CDKN2A	1029	hgsc.bcm.edu	37	9	21967542	21967542	+	IGR	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:21967542delC	ENST00000304494.5	-	0	1218				C9orf53_ENST00000441769.2_3'UTR|RP11-145E5.5_ENST00000404796.2_Intron	NM_000077.4	NP_000068.1	P42771	CD2A1_HUMAN	cyclin-dependent kinase inhibitor 2A						cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cellular senescence (GO:2000774)|positive regulation of macrophage apoptotic process (GO:2000111)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|Ras protein signal transduction (GO:0007265)|replicative senescence (GO:0090399)|senescence-associated heterochromatin focus assembly (GO:0035986)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|senescence-associated heterochromatin focus (GO:0035985)	cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|NF-kappaB binding (GO:0051059)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)	p.0(1)|p.0?(1)		NS(28)|adrenal_gland(6)|autonomic_ganglia(11)|biliary_tract(74)|bone(84)|breast(46)|central_nervous_system(522)|cervix(23)|endometrium(14)|eye(4)|genital_tract(15)|haematopoietic_and_lymphoid_tissue(698)|kidney(39)|large_intestine(11)|liver(92)|lung(365)|meninges(18)|oesophagus(239)|ovary(98)|pancreas(263)|pleura(94)|prostate(13)|salivary_gland(10)|skin(541)|small_intestine(1)|soft_tissue(93)|stomach(48)|thymus(4)|thyroid(24)|upper_aerodigestive_tract(436)|urinary_tract(283)|vulva(2)	4199		all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;2.37e-290)|Lung NSC(2;1.26e-139)|all_lung(2;4.48e-131)|Glioma(2;3.26e-60)|all_neural(2;2.1e-52)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;2.74e-34)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00162)|Colorectal(97;0.172)		all cancers(2;0)|GBM - Glioblastoma multiforme(3;0)|Lung(2;4.07e-74)|Epithelial(2;1.08e-61)|LUSC - Lung squamous cell carcinoma(2;3.82e-48)|LUAD - Lung adenocarcinoma(2;4.56e-26)|OV - Ovarian serous cystadenocarcinoma(39;7.64e-10)|BRCA - Breast invasive adenocarcinoma(2;5.01e-09)|STAD - Stomach adenocarcinoma(4;4.63e-07)|Kidney(2;5.79e-07)|KIRC - Kidney renal clear cell carcinoma(2;7.27e-07)|COAD - Colon adenocarcinoma(8;5.15e-05)		GATATGAGGTCCCCCTAGAGT	0.428		17								HNSCC(2;<9.43e_08)|TSP Lung(5;3.83e-07)																											.		Atlas-INDEL	.											.	.	.	.	2	Whole gene deletion(2)	lung(2)	.						.																																			SO:0001628	intergenic_variant	51198	.			.	L27211	CCDS6510.1, CCDS6511.1, CCDS6511.2, CCDS56565.1	9p21	2014-09-17	2012-03-08		ENSG00000147889	ENSG00000147889			1787	protein-coding gene	gene with protein product		600160	"""cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4)"""	CDKN2, MLM		8152487, 7606716	Standard	NM_058195		Approved	CDK4I, p16, INK4a, MTS1, CMM2, ARF, p19, p14, INK4, p16INK4a, p19Arf	uc003zpk.3	P42771	OTTHUMG00000019686		chr9.hg19:g.21967542delC		123.0	0.0		176.0	11.0	.	A5X2G7|D3DRK1|O95440|Q15191|Q5VVJ5|Q96B52|Q9NP05	RNA	DEL	ENST00000304494.5	hg19	CCDS6510.1																																																																																			.	.		0.428	CDKN2A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000051915.1	NM_000077	
MYO18B	84700	hgsc.bcm.edu	37	22	26164213	26164213	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr22:26164213delG	ENST00000407587.2	+	4	499	c.330delG	c.(328-330)gagfs	p.E110fs	MYO18B_ENST00000335473.7_Frame_Shift_Del_p.E110fs|MYO18B_ENST00000536101.1_Frame_Shift_Del_p.E110fs			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	110	Ser-rich.					cytoplasm (GO:0005737)|nucleus (GO:0005634)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(6)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(27)|liver(2)|lung(60)|ovary(7)|prostate(8)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	146						AGGAGAGCGAGGGGTCCCGCA	0.597																																					p.E110fs		Atlas-INDEL	.											.	MYO18B	322	.	0			c.329delA						.						59.0	66.0	64.0					22																	26164213		1980	4145	6125	SO:0001589	frameshift_variant	84700	exon4			.	AJ310931	CCDS54507.1	22q12.1	2011-09-27			ENSG00000133454	ENSG00000133454		"""Myosins / Myosin superfamily : Class XVIII"""	18150	protein-coding gene	gene with protein product		607295				12209013, 12547197	Standard	NM_032608		Approved	BK125H2.1	uc003abz.1	Q8IUG5	OTTHUMG00000151129	ENST00000407587.2:c.330delG	chr22.hg19:g.26164213delG	ENSP00000386096:p.Glu110fs	120.0	0.0		158.0	10.0	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Frame_Shift_Del	DEL	ENST00000407587.2	hg19																																																																																				.	.		0.597	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608	
LAMP1	3916	hgsc.bcm.edu	37	13	113960838	113960838	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr13:113960838delA	ENST00000332556.4	+	2	294	c.100delA	c.(100-102)aaafs	p.K34fs	LAMP1_ENST00000397181.3_Frame_Shift_Del_p.K34fs	NM_005561.3	NP_005552.3	P11279	LAMP1_HUMAN	lysosomal-associated membrane protein 1	34	First lumenal domain.			VKNGNGTA -> MARGGRVR (in Ref. 7; AAA59524). {ECO:0000305}.	autophagic cell death (GO:0048102)|autophagy (GO:0006914)|establishment of protein localization to organelle (GO:0072594)|Golgi to lysosome transport (GO:0090160)|granzyme-mediated apoptotic signaling pathway (GO:0008626)|positive regulation of natural killer cell degranulation (GO:0043323)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|protein stabilization (GO:0050821)|regulation of organelle transport along microtubule (GO:1902513)	alveolar lamellar body (GO:0097208)|cytolytic granule (GO:0044194)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|lysosome (GO:0005764)|melanosome (GO:0042470)|membrane (GO:0016020)|multivesicular body (GO:0005771)|neuronal cell body (GO:0043025)|phagolysosome membrane (GO:0061474)|sarcolemma (GO:0042383)	enzyme binding (GO:0019899)			NS(1)|central_nervous_system(2)|endometrium(3)|large_intestine(4)|lung(2)|prostate(1)|skin(1)|stomach(2)	16	Lung NSC(43;0.0161)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0482)|all_epithelial(44;0.0148)|all_lung(25;0.0271)|Lung NSC(25;0.0977)|Breast(118;0.188)	all cancers(43;0.025)|GBM - Glioblastoma multiforme(44;0.206)|Epithelial(84;0.246)			GTTTATGGTGAAAAATGGCAA	0.498																																					p.V33fs		Atlas-INDEL	.											.	LAMP1	41	.	0			c.99delG						.						167.0	163.0	165.0					13																	113960838		2025	4189	6214	SO:0001589	frameshift_variant	3916	exon2			.	J03263	CCDS41909.1	13q34	2011-11-24			ENSG00000185896	ENSG00000185896		"""CD molecules"""	6499	protein-coding gene	gene with protein product		153330					Standard	NM_005561		Approved	CD107a	uc001vtm.1	P11279	OTTHUMG00000017380	ENST00000332556.4:c.100delA	chr13.hg19:g.113960838delA	ENSP00000333298:p.Lys34fs	152.0	0.0		162.0	10.0	NM_005561	B4DWL3|Q8WU33|Q96I40|Q9BRD2|Q9NP13	Frame_Shift_Del	DEL	ENST00000332556.4	hg19	CCDS41909.1																																																																																			.	.		0.498	LAMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045876.2		
DCHS1	8642	hgsc.bcm.edu	37	11	6647877	6647877	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:6647877delG	ENST00000299441.3	-	15	6681	c.6270delC	c.(6268-6270)cccfs	p.P2090fs		NM_003737.2	NP_003728.1	Q96JQ0	PCD16_HUMAN	dachsous cadherin-related 1	2090	Cadherin 20. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|calcium-dependent cell-cell adhesion (GO:0016339)|cochlea development (GO:0090102)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|neural tube development (GO:0021915)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|post-anal tail morphogenesis (GO:0036342)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(16)|liver(1)|lung(41)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	103		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GGACGGCCCTGGGGGAGACAA	0.532																																					p.R2091fs		Atlas-INDEL	.											.	DCHS1	277	.	0			c.6271delA						.						131.0	130.0	130.0					11																	6647877		2201	4296	6497	SO:0001589	frameshift_variant	8642	exon15			.	AB000895	CCDS7771.1	11p15.4	2013-10-04	2013-10-04	2004-09-03	ENSG00000166341	ENSG00000166341		"""Cadherins / Cadherin-related"""	13681	protein-coding gene	gene with protein product	"""cadherin-related family member 6"""	603057	"""protocadherin 16"", ""dachsous 1 (Drosophila)"""	CDH25, PCDH16		9199196	Standard	XM_005253207		Approved	FIB1, KIAA1773, FLJ11790, CDHR6	uc001mem.1	Q96JQ0	OTTHUMG00000133398	ENST00000299441.3:c.6270delC	chr11.hg19:g.6647877delG	ENSP00000299441:p.Pro2090fs	116.0	0.0		160.0	10.0	NM_003737	O15098	Frame_Shift_Del	DEL	ENST00000299441.3	hg19	CCDS7771.1																																																																																			.	.		0.532	DCHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257258.1	NM_003737	
COL7A1	1294	hgsc.bcm.edu	37	3	48631052	48631052	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:48631052delC	ENST00000328333.8	-	3	451	c.344delG	c.(343-345)ggcfs	p.G115fs	COL7A1_ENST00000454817.1_Frame_Shift_Del_p.G115fs	NM_000094.3	NP_000085.1	Q02388	CO7A1_HUMAN	collagen, type VII, alpha 1	115	Nonhelical region (NC1).|VWFA 1. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen type VII trimer (GO:0005590)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(3)|breast(8)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(57)|ovary(7)|prostate(5)|skin(9)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	137				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		GCGAGTGTTGCCCCCCTTGTA	0.617																																					p.G115fs		Atlas-INDEL	.											.	COL7A1	320	.	0			c.345delC						.						138.0	119.0	126.0					3																	48631052		2203	4300	6503	SO:0001589	frameshift_variant	1294	exon3			.	L02870	CCDS2773.1	3p21.1	2014-09-17	2008-08-01		ENSG00000114270	ENSG00000114270		"""Collagens"", ""Fibronectin type III domain containing"""	2214	protein-coding gene	gene with protein product	"""collagen VII, alpha-1 polypeptide"", ""LC collagen"""	120120	"""epidermolysis bullosa, dystrophic, dominant and recessive"""	EBDCT, EBD1, EBR1		1871109	Standard	NM_000094		Approved		uc003ctz.2	Q02388	OTTHUMG00000133541	ENST00000328333.8:c.344delG	chr3.hg19:g.48631052delC	ENSP00000332371:p.Gly115fs	149.0	0.0		167.0	12.0	NM_000094	Q14054|Q16507	Frame_Shift_Del	DEL	ENST00000328333.8	hg19	CCDS2773.1																																																																																			.	.		0.617	COL7A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257519.1	NM_000094	
GLG1	2734	hgsc.bcm.edu	37	16	74525009	74525009	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:74525009delC	ENST00000422840.2	-	8	1338	c.1339delG	c.(1339-1341)gagfs	p.E447fs	GLG1_ENST00000447066.2_Frame_Shift_Del_p.E436fs|GLG1_ENST00000205061.5_Frame_Shift_Del_p.E447fs	NM_001145667.1	NP_001139139.1	Q92896	GSLG1_HUMAN	golgi glycoprotein 1	447					blood coagulation (GO:0007596)|bone morphogenesis (GO:0060349)|leukocyte migration (GO:0050900)|negative regulation of protein processing (GO:0010955)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|regulation of chondrocyte differentiation (GO:0032330)	extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			breast(2)|cervix(2)|endometrium(6)|kidney(8)|large_intestine(6)|lung(28)|ovary(3)|prostate(1)|skin(1)	57						TGTTCAATCTCCCCCCGACAG	0.512																																					p.E447fs		Atlas-INDEL	.											.	GLG1	106	.	0			c.1340delA						.						176.0	147.0	157.0					16																	74525009		2198	4300	6498	SO:0001589	frameshift_variant	2734	exon8			.		CCDS32485.1, CCDS45526.1, CCDS45527.1	16q22-q23	2010-02-12	2010-02-12			ENSG00000090863			4316	protein-coding gene	gene with protein product		600753	"""golgi apparatus protein 1"""			8530051, 7531823	Standard	NM_012201		Approved	MG-160, ESL-1, CFR-1	uc002fcx.3	Q92896		ENST00000422840.2:c.1339delG	chr16.hg19:g.74525009delC	ENSP00000405984:p.Glu447fs	185.0	0.0		182.0	12.0	NM_001145667	B7Z8Y4|D3DUJ7|Q13221|Q6P9D1	Frame_Shift_Del	DEL	ENST00000422840.2	hg19	CCDS45527.1																																																																																			.	.		0.512	GLG1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000435750.1	NM_012201	
DMRTB1	63948	hgsc.bcm.edu	37	1	53925136	53925136	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:53925136delA	ENST00000371445.3	+	1	65	c.10delA	c.(10-12)aaafs	p.K4fs		NM_033067.1	NP_149056.1	Q96MA1	DMRTB_HUMAN	DMRT-like family B with proline-rich C-terminal, 1	4					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			large_intestine(3)|lung(5)|ovary(1)|skin(1)	10						AATGGCCGACAAAATGGTGCG	0.627																																					p.D3fs		Atlas-INDEL	.											.	DMRTB1	38	.	0			c.9delC						.						50.0	44.0	46.0					1																	53925136		2202	4300	6502	SO:0001589	frameshift_variant	63948	exon1			.	AJ291671	CCDS581.1	1p32	2008-08-29			ENSG00000143006	ENSG00000143006			13913	protein-coding gene	gene with protein product		614805					Standard	NM_033067		Approved		uc001cvq.1	Q96MA1	OTTHUMG00000008080	ENST00000371445.3:c.10delA	chr1.hg19:g.53925136delA	ENSP00000360500:p.Lys4fs	185.0	0.0		174.0	11.0	NM_033067	Q96SD2	Frame_Shift_Del	DEL	ENST00000371445.3	hg19	CCDS581.1																																																																																			.	.		0.627	DMRTB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022110.1		
COL9A2	1298	hgsc.bcm.edu	37	1	40773421	40773421	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:40773421delG	ENST00000372748.3	-	18	1004	c.908delC	c.(907-909)ccafs	p.P303fs	COL9A2_ENST00000466267.1_5'Flank	NM_001852.3	NP_001843.1	Q14055	CO9A2_HUMAN	collagen, type IX, alpha 2	303	Triple-helical region 3 (COL3).				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type IX trimer (GO:0005594)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(4)|stomach(2)|urinary_tract(2)	22	Lung NSC(20;4.38e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;2.08e-17)			GTTGATGCCTGGGGGGCCCTA	0.627																																					p.P303fs		Atlas-INDEL	.											.	COL9A2	63	.	0			c.909delA						.						43.0	40.0	41.0					1																	40773421		2203	4300	6503	SO:0001589	frameshift_variant	1298	exon18			.	M95610	CCDS450.1	1p33-p32	2013-01-16			ENSG00000049089	ENSG00000049089		"""Proteoglycans / Extracellular Matrix : Collagen proteoglycans"", ""Collagens"""	2218	protein-coding gene	gene with protein product		120260		EDM2		8454052, 8528240, 1429648	Standard	NM_001852		Approved	MED	uc001cfh.1	Q14055	OTTHUMG00000005761	ENST00000372748.3:c.908delC	chr1.hg19:g.40773421delG	ENSP00000361834:p.Pro303fs	180.0	0.0		176.0	11.0	NM_001852	B2RMP9	Frame_Shift_Del	DEL	ENST00000372748.3	hg19	CCDS450.1																																																																																			.	.		0.627	COL9A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015764.3	NM_001852	
TNR	7143	hgsc.bcm.edu	37	1	175372615	175372615	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:175372615delC	ENST00000367674.2	-	4	1345	c.637delG	c.(637-639)gtgfs	p.V213fs	TNR_ENST00000263525.2_Frame_Shift_Del_p.V213fs			Q92752	TENR_HUMAN	tenascin R	213	Cys-rich.				associative learning (GO:0008306)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|locomotory exploration behavior (GO:0035641)|long-term synaptic potentiation (GO:0060291)|negative regulation of axon extension involved in regeneration (GO:0048692)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of synaptic transmission (GO:0050805)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transmission of nerve impulse (GO:0051971)|synapse organization (GO:0050808)|telencephalon cell migration (GO:0022029)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)				NS(3)|breast(7)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|lung(98)|ovary(4)|pancreas(5)|prostate(4)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	177	Renal(580;0.146)					TCCACACACACCCCCCGGCTG	0.607																																					p.V213fs		Atlas-INDEL	.											.	TNR	399	.	0			c.638delT						.						104.0	109.0	107.0					1																	175372615		2203	4300	6503	SO:0001589	frameshift_variant	7143	exon4			.	X98085	CCDS1318.1	1q24	2013-02-11	2012-07-12		ENSG00000116147	ENSG00000116147		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	11953	protein-coding gene	gene with protein product	"""restrictin"", ""janusin"""	601995				8626505, 8940128	Standard	NM_003285		Approved		uc009wwu.1	Q92752	OTTHUMG00000034876	ENST00000367674.2:c.637delG	chr1.hg19:g.175372615delC	ENSP00000356646:p.Val213fs	88.0	0.0		165.0	10.0	NM_003285	C9J563|Q15568|Q5R3G0	Frame_Shift_Del	DEL	ENST00000367674.2	hg19	CCDS1318.1																																																																																			.	.		0.607	TNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084414.4	NM_003285	
CREB1	1385	hgsc.bcm.edu	37	2	208442310	208442310	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:208442310delC	ENST00000432329.2	+	8	1063	c.812delC	c.(811-813)tccfs	p.S271fs	CREB1_ENST00000353267.3_Frame_Shift_Del_p.S257fs|CREB1_ENST00000430624.1_Frame_Shift_Del_p.S257fs|CREB1_ENST00000374397.4_Intron	NM_134442.3	NP_604391.1	P16220	CREB1_HUMAN	cAMP responsive element binding protein 1	271					activation of phospholipase C activity (GO:0007202)|axon guidance (GO:0007411)|cellular response to zinc ion (GO:0071294)|circadian rhythm (GO:0007623)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|lactation (GO:0007595)|lung saccule development (GO:0060430)|memory (GO:0007613)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of transcription by competitive promoter binding (GO:0010944)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|pituitary gland development (GO:0021983)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of hormone secretion (GO:0046887)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|regulation of cell size (GO:0008361)|response to drug (GO:0042493)|response to glucagon (GO:0033762)|response to organic substance (GO:0010033)|secretory granule organization (GO:0033363)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|synaptic transmission (GO:0007268)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription from RNA polymerase II promoter (GO:0006366)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|Type I pneumocyte differentiation (GO:0060509)|viral process (GO:0016032)	nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	cAMP response element binding (GO:0035497)|enzyme binding (GO:0019899)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription cofactor activity (GO:0003712)		EWSR1/CREB1(44)	NS(1)|breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|upper_aerodigestive_tract(1)	5				LUSC - Lung squamous cell carcinoma(261;0.0768)|Epithelial(149;0.127)|Lung(261;0.145)	Adenosine monophosphate(DB00131)|Naloxone(DB01183)	ATGGCATCCTCCCCAGCACTT	0.468			T	EWSR1	"""clear cell sarcoma, angiomatoid fibrous histiocytoma"""																																p.S271fs		Atlas-INDEL	.		Dom	yes		2	2q34	1385	cAMP responsive element binding protein 1		M	.	CREB1	21	.	0			c.811delT						.						142.0	117.0	125.0					2																	208442310		2203	4300	6503	SO:0001589	frameshift_variant	1385	exon8			.	M27691	CCDS2374.1, CCDS2375.1	2q34	2013-01-10			ENSG00000118260	ENSG00000118260		"""basic leucine zipper proteins"""	2345	protein-coding gene	gene with protein product		123810					Standard	NM_134442		Approved		uc002vcc.3	P16220	OTTHUMG00000132936	ENST00000432329.2:c.812delC	chr2.hg19:g.208442310delC	ENSP00000387699:p.Ser271fs	139.0	0.0		181.0	12.0	NM_134442	P21934|Q6V963|Q9UMA7	Frame_Shift_Del	DEL	ENST00000432329.2	hg19	CCDS2375.1																																																																																			.	.		0.468	CREB1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256467.3	NM_134442	
CCDC168	643677	hgsc.bcm.edu	37	13	103383806	103383806	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr13:103383806delT	ENST00000322527.2	-	1	5353	c.5354delA	c.(5353-5355)aatfs	p.N1785fs		NM_001146197.1	NP_001139669.1	Q8NDH2	CC168_HUMAN	coiled-coil domain containing 168	1785																	AGTAAGCTTATTTTTTTCTTT	0.358																																					p.N6414fs		Atlas-INDEL	.											.	.	.	.	0			c.19242delT						.						113.0	95.0	101.0					13																	103383806		692	1590	2282	SO:0001589	frameshift_variant	643677	exon4			.		CCDS73596.1	13q33.1	2014-06-17	2011-08-09	2011-08-09	ENSG00000175820	ENSG00000175820			26851	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 40"""	C13orf40			Standard	NM_001146197		Approved	FLJ40176	uc001vpm.3	Q8NDH2	OTTHUMG00000187287	ENST00000322527.2:c.5354delA	chr13.hg19:g.103383806delT	ENSP00000320232:p.Asn1785fs	132.0	0.0		205.0	13.0	NM_001146197	Q8N800	Frame_Shift_Del	DEL	ENST00000322527.2	hg19																																																																																				.	.		0.358	CCDC168-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001146197	
LIMCH1	22998	hgsc.bcm.edu	37	4	41668635	41668635	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:41668635delA	ENST00000313860.7	+	16	2248	c.2194delA	c.(2194-2196)aaafs	p.K732fs	LIMCH1_ENST00000513024.1_Frame_Shift_Del_p.K561fs|LIMCH1_ENST00000512632.1_Intron|LIMCH1_ENST00000503057.1_Frame_Shift_Del_p.K1117fs|LIMCH1_ENST00000509277.1_Frame_Shift_Del_p.K566fs|LIMCH1_ENST00000512946.1_Frame_Shift_Del_p.K732fs|LIMCH1_ENST00000396595.3_Frame_Shift_Del_p.K578fs|LIMCH1_ENST00000511496.1_Frame_Shift_Del_p.K573fs|LIMCH1_ENST00000514096.1_Frame_Shift_Del_p.K573fs|LIMCH1_ENST00000512820.1_Frame_Shift_Del_p.K720fs|LIMCH1_ENST00000508501.1_Frame_Shift_Del_p.K732fs|LIMCH1_ENST00000381753.4_Frame_Shift_Del_p.K566fs	NM_014988.2	NP_055803.2	Q9UPQ0	LIMC1_HUMAN	LIM and calponin homology domains 1	732					actomyosin structure organization (GO:0031032)		zinc ion binding (GO:0008270)			central_nervous_system(2)|endometrium(1)|large_intestine(9)|lung(17)|ovary(3)|pancreas(1)|prostate(3)|skin(5)	41						ATTTCTGGACAAAATGCCTGA	0.418																																					p.D731fs		Atlas-INDEL	.											.	LIMCH1	233	.	0			c.2193delC						.						116.0	99.0	104.0					4																	41668635		2203	4300	6503	SO:0001589	frameshift_variant	22998	exon16			.	AB029025	CCDS33977.1, CCDS47047.1, CCDS54763.1, CCDS54764.1, CCDS54765.1, CCDS75119.1, CCDS75121.1	4p13	2007-06-14		2008-01-09	ENSG00000064042	ENSG00000064042			29191	protein-coding gene	gene with protein product						10470851	Standard	XM_005248057		Approved	DKFZP686A01247, LIMCH1A, LMO7B	uc003gvz.4	Q9UPQ0	OTTHUMG00000160575	ENST00000313860.7:c.2194delA	chr4.hg19:g.41668635delA	ENSP00000316891:p.Lys732fs	104.0	0.0		148.0	11.0	NM_014988	A8MXC3|E9PHM7|Q503B5|Q5CZB1|Q5CZB6|Q5H9S8|Q68E07|Q6PJ44|Q7Z3G5|Q8N3S9|Q8N6M2	Frame_Shift_Del	DEL	ENST00000313860.7	hg19	CCDS33977.1																																																																																			.	.		0.418	LIMCH1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000361249.2	NM_014988	
PLEKHA3	65977	hgsc.bcm.edu	37	2	179355529	179355529	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:179355529delA	ENST00000234453.5	+	3	703	c.301delA	c.(301-303)aaafs	p.K102fs	PLEKHA3_ENST00000461474.1_3'UTR	NM_019091.3	NP_061964.3	Q9HB20	PKHA3_HUMAN	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 3	102						Golgi apparatus (GO:0005794)|membrane (GO:0016020)	1-phosphatidylinositol binding (GO:0005545)|phospholipid binding (GO:0005543)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)	11			OV - Ovarian serous cystadenocarcinoma(117;0.0112)|Epithelial(96;0.0266)|all cancers(119;0.0865)			TACAAGGACTAAAAAAGAAAA	0.383																																					p.T100fs		Atlas-INDEL	.											.	PLEKHA3	25	.	0			c.300delT						.						47.0	47.0	47.0					2																	179355529		2203	4300	6503	SO:0001589	frameshift_variant	65977	exon3			.	AF286162	CCDS33336.1	2q31.2	2013-01-10	2002-01-14		ENSG00000116095	ENSG00000116095		"""Pleckstrin homology (PH) domain containing"""	14338	protein-coding gene	gene with protein product	"""four-phosphate-adaptor protein 1"""	607774	"""pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3"""			11001876, 15107860	Standard	NM_019091		Approved	FAPP1	uc002umn.3	Q9HB20	OTTHUMG00000154446	ENST00000234453.5:c.301delA	chr2.hg19:g.179355529delA	ENSP00000234453:p.Lys102fs	131.0	0.0		192.0	14.0	NM_019091	Q4ZG69|Q86TQ1|Q9NXT3	Frame_Shift_Del	DEL	ENST00000234453.5	hg19	CCDS33336.1																																																																																			.	.		0.383	PLEKHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335241.2	NM_019091	
ACACA	31	hgsc.bcm.edu	37	17	35487101	35487101	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:35487101delC	ENST00000394406.2	-	46	5802	c.5612delG	c.(5611-5613)ggcfs	p.G1871fs	ACACA_ENST00000335166.5_Frame_Shift_Del_p.G1793fs|ACACA_ENST00000361253.5_5'UTR|ACACA_ENST00000353139.5_Frame_Shift_Del_p.G1908fs|ACACA_ENST00000360679.3_Frame_Shift_Del_p.G1813fs	NM_198836.1	NP_942133.1	Q13085	ACACA_HUMAN	acetyl-CoA carboxylase alpha	1871	Carboxyltransferase.				acetyl-CoA metabolic process (GO:0006084)|biotin metabolic process (GO:0006768)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|lipid homeostasis (GO:0055088)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|malonyl-CoA biosynthetic process (GO:2001295)|multicellular organismal protein metabolic process (GO:0044268)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|small molecule metabolic process (GO:0044281)|tissue homeostasis (GO:0001894)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)			NS(2)|breast(5)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(24)|lung(23)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	83		Breast(25;0.00157)|Ovarian(249;0.15)			Biotin(DB00121)	AATCTGGATGCCCCCCAGCTG	0.493																																					p.G1908fs	Colon(23;82 258 739 2117 10493 24037 27661 34815 35438 36249)	Atlas-INDEL	.											.	ACACA	395	.	0			c.5724delC						.						182.0	162.0	169.0					17																	35487101		2203	4300	6503	SO:0001589	frameshift_variant	31	exon46			.	U19822	CCDS11317.1, CCDS11318.1, CCDS42302.1, CCDS42303.1	17q21	2014-05-06	2010-04-30		ENSG00000132142	ENSG00000278540	6.4.1.2		84	protein-coding gene	gene with protein product	"""acetyl-CoA carboxylase 1"""	200350	"""acetyl-Coenzyme A carboxylase alpha"""	ACAC, ACC			Standard	NM_198837		Approved	ACC1	uc002hno.3	Q13085	OTTHUMG00000188463	ENST00000394406.2:c.5612delG	chr17.hg19:g.35487101delC	ENSP00000377928:p.Gly1871fs	200.0	0.0		192.0	13.0	NM_198834	B2RP68|Q6KEV6|Q6XDA8|Q7Z2G8|Q7Z561|Q7Z563|Q7Z564|Q86WB2|Q86WB3	Frame_Shift_Del	DEL	ENST00000394406.2	hg19	CCDS11317.1																																																																																			.	.		0.493	ACACA-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256696.1	NM_198836	
TDRD1	56165	hgsc.bcm.edu	37	10	115987018	115987018	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:115987018delA	ENST00000251864.2	+	23	3516	c.3363delA	c.(3361-3363)gcafs	p.A1121fs	TDRD1_ENST00000369282.1_Intron|TDRD1_ENST00000369281.2_Frame_Shift_Del_p.A1007fs|TDRD1_ENST00000369280.1_Intron|TDRD1_ENST00000422662.1_Intron	NM_198795.1	NP_942090.1	Q9BXT4	TDRD1_HUMAN	tudor domain containing 1	1121					DNA methylation involved in gamete generation (GO:0043046)|gene silencing by RNA (GO:0031047)|germ cell development (GO:0007281)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|P granule (GO:0043186)|pi-body (GO:0071546)	metal ion binding (GO:0046872)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(15)|ovary(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(5)	48		Colorectal(252;0.172)|Breast(234;0.188)		Epithelial(162;0.0343)|all cancers(201;0.0754)		TTGGTCTGGCAAAAAACATCA	0.358																																					p.A1121fs		Atlas-INDEL	.											.	TDRD1	126	.	0			c.3362delC						.						172.0	165.0	167.0					10																	115987018		2203	4300	6503	SO:0001589	frameshift_variant	56165	exon23			.	AF285606	CCDS7588.1	10q26.11	2013-01-23			ENSG00000095627	ENSG00000095627		"""Tudor domain containing"""	11712	protein-coding gene	gene with protein product	"""cancer/testis antigen 41.1"""	605796				11279525	Standard	NM_198795		Approved	CT41.1	uc001lbg.1	Q9BXT4	OTTHUMG00000019083	ENST00000251864.2:c.3363delA	chr10.hg19:g.115987018delA	ENSP00000251864:p.Ala1121fs	194.0	0.0		209.0	13.0	NM_198795	A6NEN3|A6NMN2|B3KVI4|B4E2L5|D3DRC2|Q4G0Y8|Q6P518|Q9H7B3	Frame_Shift_Del	DEL	ENST00000251864.2	hg19	CCDS7588.1																																																																																			.	.		0.358	TDRD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
PXN	5829	hgsc.bcm.edu	37	12	120652962	120652962	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:120652962delC	ENST00000228307.7	-	8	1189	c.1048delG	c.(1048-1050)gtcfs	p.V350fs	PXN_ENST00000538144.1_5'UTR|PXN-AS1_ENST00000542265.1_RNA|PXN-AS1_ENST00000535200.1_RNA|PXN_ENST00000458477.2_Frame_Shift_Del_p.V183fs|PXN_ENST00000536957.1_Frame_Shift_Del_p.V348fs|PXN_ENST00000424649.2_Frame_Shift_Del_p.V316fs|PXN_ENST00000267257.7_Frame_Shift_Del_p.V364fs|PXN_ENST00000397506.3_Frame_Shift_Del_p.V162fs	NM_001080855.2	NP_001074324.1	P49023	PAXI_HUMAN	paxillin	350					activation of MAPK activity (GO:0000187)|branching morphogenesis of an epithelial tube (GO:0048754)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cellular component movement (GO:0006928)|cellular response to reactive oxygen species (GO:0034614)|cytoskeleton organization (GO:0007010)|epidermal growth factor receptor signaling pathway (GO:0007173)|focal adhesion assembly (GO:0048041)|growth hormone receptor signaling pathway (GO:0060396)|integrin-mediated signaling pathway (GO:0007229)|lamellipodium assembly (GO:0030032)|muscle contraction (GO:0006936)|peptidyl-tyrosine phosphorylation (GO:0018108)|regulation of cell shape (GO:0008360)|signal complex assembly (GO:0007172)|signal transduction (GO:0007165)|substrate adhesion-dependent cell spreading (GO:0034446)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	beta-catenin binding (GO:0008013)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			breast(1)|endometrium(5)|kidney(2)|large_intestine(1)|lung(5)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					ACTGTGGCGACCCCCAGCTTG	0.687																																					p.V364fs		Atlas-INDEL	.											.	PXN	69	.	0			c.1091delT						.						18.0	21.0	20.0					12																	120652962		2166	4268	6434	SO:0001589	frameshift_variant	5829	exon7			.	U14588	CCDS44996.1, CCDS44997.1, CCDS44998.1, CCDS58281.1	12q24	2006-01-23			ENSG00000089159	ENSG00000089159			9718	protein-coding gene	gene with protein product		602505				7534286	Standard	NM_001080855		Approved		uc001txv.3	P49023	OTTHUMG00000169169	ENST00000228307.7:c.1048delG	chr12.hg19:g.120652962delC	ENSP00000228307:p.Val350fs	249.0	0.0		210.0	13.0	NM_001243756	B2RAI3|B7ZMB4|O14970|O14971|O60360|Q5HYA4	Frame_Shift_Del	DEL	ENST00000228307.7	hg19	CCDS44997.1																																																																																			.	.		0.687	PXN-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000402679.4	NM_002859	
HHLA1	10086	hgsc.bcm.edu	37	8	133116366	133116366	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr8:133116366delA	ENST00000414222.1	-	2	127	c.128delT	c.(127-129)ttafs	p.L43fs	HHLA1_ENST00000434736.2_Frame_Shift_Del_p.L43fs	NM_001145095.1	NP_001138567.1	C9JL84	HHLA1_HUMAN	HERV-H LTR-associating 1	43						extracellular region (GO:0005576)				endometrium(6)|kidney(1)|lung(2)|skin(1)|stomach(2)	12						TGTTGTAGGTAAAAAGGTCAT	0.408																																					p.L43fs		Atlas-INDEL	.											.	HHLA1	35	.	0			c.129delA						.						255.0	224.0	234.0					8																	133116366		692	1591	2283	SO:0001589	frameshift_variant	10086	exon2			.	AF110315		8q24	2011-03-01			ENSG00000132297	ENSG00000132297			4904	protein-coding gene	gene with protein product		604109		PLA2L		10329003	Standard	NM_001145095		Approved		uc011liy.1	C9JL84	OTTHUMG00000140390	ENST00000414222.1:c.128delT	chr8.hg19:g.133116366delA	ENSP00000388322:p.Leu43fs	79.0	0.0		187.0	14.0	NM_001145095		Frame_Shift_Del	DEL	ENST00000414222.1	hg19																																																																																				.	.		0.408	HHLA1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		XR_017860	
PRAP1	118471	hgsc.bcm.edu	37	10	135165935	135165935	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:135165935delC	ENST00000433452.2	+	5	719	c.447delC	c.(445-447)cacfs	p.H149fs	PRAP1_ENST00000463201.1_3'UTR|RP11-122K13.7_ENST00000452591.1_RNA|FUOM_ENST00000465384.1_5'Flank|PRAP1_ENST00000423766.1_Frame_Shift_Del_p.H150fs|PRAP1_ENST00000458230.1_Frame_Shift_Del_p.H140fs|ZNF511_ENST00000368554.4_Frame_Shift_Del_p.H308fs			Q96NZ9	PRAP1_HUMAN	proline-rich acidic protein 1	149						extracellular region (GO:0005576)				large_intestine(1)|lung(2)	3		all_cancers(35;7.01e-07)|all_epithelial(44;1.45e-05)|Lung NSC(174;0.027)|all_lung(145;0.0384)|all_neural(114;0.0726)|Glioma(114;0.172)|Melanoma(40;0.175)		all cancers(32;7.08e-06)|OV - Ovarian serous cystadenocarcinoma(35;7.88e-06)|Epithelial(32;9.48e-06)		ACATCTACCACCCCCAGTAGG	0.652																																					p.H149fs		Atlas-INDEL	.											.	PRAP1	20	.	0			c.446delA						.						71.0	67.0	69.0					10																	135165935		2203	4300	6503	SO:0001589	frameshift_variant	118471	exon5			.	AF421885	CCDS7679.1	10q26.3	2012-10-01			ENSG00000165828	ENSG00000165828			23304	protein-coding gene	gene with protein product		609776				14583459, 20674898	Standard	NM_001145201		Approved	UPA		Q96NZ9	OTTHUMG00000019312	ENST00000433452.2:c.447delC	chr10.hg19:g.135165935delC	ENSP00000416126:p.His149fs	114.0	0.0		163.0	10.0	NM_145202	B7ZL57|B7ZL58|E9KL31|Q5VWY4|Q7Z4X5|Q8IWR3|Q8NCS2	Frame_Shift_Del	DEL	ENST00000433452.2	hg19	CCDS7679.1																																																																																			.	.		0.652	PRAP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000051132.1	NM_145202	
STRN	6801	hgsc.bcm.edu	37	2	37129784	37129784	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:37129784delT	ENST00000263918.4	-	5	610	c.602delA	c.(601-603)aatfs	p.N201fs	STRN_ENST00000379213.2_Frame_Shift_Del_p.N189fs	NM_003162.3	NP_003153.2	O43815	STRN_HUMAN	striatin, calmodulin binding protein	201					dendrite development (GO:0016358)|locomotory behavior (GO:0007626)|negative regulation of cell proliferation (GO:0008285)|tight junction assembly (GO:0070830)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|tight junction (GO:0005923)	armadillo repeat domain binding (GO:0070016)|calmodulin binding (GO:0005516)|estrogen receptor binding (GO:0030331)|protein complex binding (GO:0032403)|protein phosphatase 2A binding (GO:0051721)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(16)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	33		Ovarian(717;0.0129)|all_hematologic(82;0.21)				TGAGTCCTGATTTTTGTCATC	0.393																																					p.N201fs		Atlas-INDEL	.											.	STRN	71	.	0			c.603delT						.						203.0	186.0	192.0					2																	37129784		2203	4300	6503	SO:0001589	frameshift_variant	6801	exon5			.	AJ223814	CCDS1784.1	2p22.2	2013-01-10	2001-11-28		ENSG00000115808	ENSG00000115808		"""WD repeat domain containing"""	11424	protein-coding gene	gene with protein product		614765	"""striatin, calmodulin-binding protein"""			9693043, 8769426	Standard	NM_003162		Approved	SG2NA	uc002rpn.3	O43815	OTTHUMG00000100959	ENST00000263918.4:c.602delA	chr2.hg19:g.37129784delT	ENSP00000263918:p.Asn201fs	145.0	0.0		202.0	15.0	NM_003162	Q3KP65|Q53TQ8|Q9NP38	Frame_Shift_Del	DEL	ENST00000263918.4	hg19	CCDS1784.1																																																																																			.	.		0.393	STRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218568.1		
ETV1	2115	hgsc.bcm.edu	37	7	14027750	14027750	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:14027750delT	ENST00000430479.1	-	4	761	c.94delA	c.(94-96)agafs	p.R32fs	ETV1_ENST00000403527.1_5'Flank|ETV1_ENST00000242066.5_Frame_Shift_Del_p.R32fs|ETV1_ENST00000403685.1_Frame_Shift_Del_p.R32fs|ETV1_ENST00000476720.2_5'Flank|ETV1_ENST00000399357.3_5'Flank|ETV1_ENST00000405218.2_Frame_Shift_Del_p.R32fs|ETV1_ENST00000405358.4_Frame_Shift_Del_p.R46fs|ETV1_ENST00000343495.5_Frame_Shift_Del_p.R32fs|ETV1_ENST00000420159.2_5'Flank|ETV1_ENST00000405192.2_Frame_Shift_Del_p.R32fs	NM_004956.4	NP_004947.2	P50549	ETV1_HUMAN	ets variant 1	32					axon guidance (GO:0007411)|cell differentiation (GO:0030154)|mechanosensory behavior (GO:0007638)|muscle organ development (GO:0007517)|peripheral nervous system neuron development (GO:0048935)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)		TMPRSS2/ETV1(34)|ACSL3_ENST00000357430/ETV1(2)|EWSR1/ETV1(7)|KLK2/ETV1(3)|SLC45A3/ETV1(3)|HNRNPA2B1/ETV1(8)	breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(9)|lung(15)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	31						ATGAATTTTCTTTTCCTGACA	0.383			T	"""EWSR1, TMPRSS2, SLC45A3, C15orf21, HNRNPA2B1. ACSL3"""	"""Ewing sarcoma, prostate"""																																p.R32fs		Atlas-INDEL	.		Dom	yes		7	7p22	2115	ets variant gene 1		"""M, E"""	.	ETV1	138	.	0			c.95delG						.						148.0	153.0	151.0					7																	14027750		2184	4288	6472	SO:0001589	frameshift_variant	2115	exon3			.		CCDS55083.1, CCDS55084.1, CCDS55085.1, CCDS55086.1, CCDS55087.1, CCDS55088.1	7p22	2008-09-12	2008-09-12		ENSG00000006468	ENSG00000006468			3490	protein-coding gene	gene with protein product		600541	"""ets variant gene 1"""			1340465	Standard	NM_004956		Approved	ER81	uc003ssw.4	P50549	OTTHUMG00000152403	ENST00000430479.1:c.94delA	chr7.hg19:g.14027750delT	ENSP00000405327:p.Arg32fs	189.0	0.0		185.0	12.0	NM_001163149	A4D118|B2R768|B7Z2I4|B7Z618|B7Z9P2|C9JT37|E9PHB1|F5GXR2|O75849|Q4KMQ6|Q59GA7|Q6AI30|Q9UQ71|Q9Y636	Frame_Shift_Del	DEL	ENST00000430479.1	hg19	CCDS55088.1																																																																																			.	.		0.383	ETV1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326111.1	NM_004956	
IFT88	8100	hgsc.bcm.edu	37	13	21148532	21148532	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr13:21148532delA	ENST00000319980.6	+	4	362	c.35delA	c.(34-36)caafs	p.Q12fs	IFT88_ENST00000351808.5_Frame_Shift_Del_p.Q3fs|IFT88_ENST00000537103.1_Frame_Shift_Del_p.Q3fs|IFT88_ENST00000382778.4_Frame_Shift_Del_p.Q12fs	NM_175605.3	NP_783195.2	Q13099	IFT88_HUMAN	intraflagellar transport 88	12					anterior/posterior pattern specification (GO:0009952)|cardiac muscle cell differentiation (GO:0055007)|cardiac septum morphogenesis (GO:0060411)|cilium morphogenesis (GO:0060271)|cochlea development (GO:0090102)|cytoplasmic microtubule organization (GO:0031122)|determination of left/right symmetry (GO:0007368)|embryonic digit morphogenesis (GO:0042733)|epidermal stem cell homeostasis (GO:0036334)|epidermis development (GO:0008544)|epithelial cell morphogenesis (GO:0003382)|eye development (GO:0001654)|forebrain morphogenesis (GO:0048853)|heart formation (GO:0060914)|inner ear receptor stereocilium organization (GO:0060122)|kidney development (GO:0001822)|liver development (GO:0001889)|lung vasculature development (GO:0060426)|negative regulation of epithelial cell proliferation (GO:0050680)|Notch signaling pathway (GO:0007219)|palate development (GO:0060021)|pancreas development (GO:0031016)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|protein localization (GO:0008104)|regulation of autophagic vacuole assembly (GO:2000785)|regulation of cilium assembly (GO:1902017)|regulation of fat cell differentiation (GO:0045598)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|regulation of protein processing (GO:0070613)|regulation of smoothened signaling pathway (GO:0008589)|response to fluid shear stress (GO:0034405)|smoothened signaling pathway (GO:0007224)|sperm axoneme assembly (GO:0007288)|spermatid nucleus elongation (GO:0007290)|spinal cord dorsal/ventral patterning (GO:0021513)|telencephalon development (GO:0021537)	acrosomal membrane (GO:0002080)|apical part of cell (GO:0045177)|axonemal basal plate (GO:0097541)|centriole (GO:0005814)|ciliary basal body (GO:0036064)|ciliary base (GO:0097546)|ciliary tip (GO:0097542)|cilium (GO:0005929)|intraciliary transport particle B (GO:0030992)|kinocilium (GO:0060091)|motile cilium (GO:0031514)|motile primary cilium (GO:0031512)|photoreceptor connecting cilium (GO:0032391)				breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	27		all_cancers(29;5.79e-25)|all_epithelial(30;2.57e-20)|all_lung(29;3.13e-16)|Lung SC(185;0.0262)|Ovarian(182;0.0825)|Hepatocellular(188;0.244)		all cancers(112;0.000667)|Epithelial(112;0.00119)|OV - Ovarian serous cystadenocarcinoma(117;0.0141)|Lung(94;0.0183)|LUSC - Lung squamous cell carcinoma(192;0.0528)		CAAATGATGCAAAATGTGCAC	0.353																																					p.Q12fs		Atlas-INDEL	.											.	IFT88	83	.	0			c.34delC						.						92.0	86.0	88.0					13																	21148532		2203	4300	6503	SO:0001589	frameshift_variant	8100	exon4			.	AK058172	CCDS31944.1, CCDS31945.1	13q12.1	2014-07-03	2014-07-03	2005-11-02	ENSG00000032742	ENSG00000032742		"""Intraflagellar transport homologs"", ""Tetratricopeptide (TTC) repeat domain containing"""	20606	protein-coding gene	gene with protein product	"""polaris homolog"""	600595	"""tetratricopeptide repeat domain 10"", ""intraflagellar transport 88 homolog (Chlamydomonas)"""	TTC10		7633404	Standard	XM_005266546		Approved	hTg737, Tg737, D13S1056E, MGC26259	uc001uni.3	Q13099	OTTHUMG00000016517	ENST00000319980.6:c.35delA	chr13.hg19:g.21148532delA	ENSP00000323580:p.Gln12fs	211.0	0.0		322.0	21.0	NM_175605	A2A491|B4DUS2|Q5SZJ6|Q8N719	Frame_Shift_Del	DEL	ENST00000319980.6	hg19	CCDS31944.1																																																																																			.	.		0.353	IFT88-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044075.3	NM_006531	
CMYA5	202333	hgsc.bcm.edu	37	5	79031144	79031144	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:79031144delT	ENST00000446378.2	+	2	6587	c.6556delT	c.(6556-6558)tttfs	p.F2187fs		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	2187					negative regulation of calcineurin-NFAT signaling cascade (GO:0070885)|negative regulation of protein phosphatase type 2B activity (GO:0032513)|regulation of skeletal muscle adaptation (GO:0014733)	costamere (GO:0043034)				NS(2)|breast(4)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(37)|lung(34)|ovary(6)|pancreas(2)|prostate(5)|skin(5)|stomach(11)|upper_aerodigestive_tract(3)|urinary_tract(1)	128		Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262)		OV - Ovarian serous cystadenocarcinoma(54;9.85e-46)|Epithelial(54;3.38e-40)|all cancers(79;3.43e-35)		GTCCAGCTTGTTTTTTGGATC	0.433																																					p.L2185fs		Atlas-INDEL	.											.	CMYA5	643	.	0			c.6555delG						.						72.0	71.0	71.0					5																	79031144		1876	4124	6000	SO:0001589	frameshift_variant	202333	exon2			.	AW755254, AL831986	CCDS47238.1	5q14.1	2013-02-11			ENSG00000164309	ENSG00000164309		"""Tripartite motif containing / Tripartite motif containing"", ""A-kinase anchor proteins"", ""Fibronectin type III domain containing"""	14305	protein-coding gene	gene with protein product	"""genethonin-3"", ""tripartite motif-containing 76"""	612193	"""chromosome 5 open reading frame 10"""	C5orf10		14688250	Standard	NM_153610		Approved	myospryn, SPRYD2, DKFZp451G223, TRIM76	uc003kgc.3	Q8N3K9	OTTHUMG00000162548	ENST00000446378.2:c.6556delT	chr5.hg19:g.79031144delT	ENSP00000394770:p.Phe2187fs	98.0	0.0		150.0	13.0	NM_153610	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	Frame_Shift_Del	DEL	ENST00000446378.2	hg19	CCDS47238.1																																																																																			.	.		0.433	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610	
DDX49	54555	hgsc.bcm.edu	37	19	19030629	19030629	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:19030629delC	ENST00000247003.4	+	1	146	c.79delC	c.(79-81)cccfs	p.P27fs	COPE_ENST00000600932.1_5'Flank|COPE_ENST00000262812.4_5'Flank|COPE_ENST00000349893.4_5'Flank|DDX49_ENST00000438170.2_5'UTR|COPE_ENST00000351079.4_5'Flank|AC002985.3_ENST00000596918.1_Intron	NM_019070.4	NP_061943.2	Q9Y6V7	DDX49_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 49	27							ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(6)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)	18			Epithelial(12;0.0289)			GCAGCCCACGCCCGTGCAGCT	0.652																																					p.T26fs		Atlas-INDEL	.											.	DDX49	37	.	0			c.78delG						.						28.0	29.0	29.0					19																	19030629		2201	4300	6501	SO:0001589	frameshift_variant	54555	exon1			.		CCDS12390.1	19p12	2008-02-05				ENSG00000105671		"""DEAD-boxes"""	18684	protein-coding gene	gene with protein product							Standard	NM_019070		Approved	FLJ10432	uc002nkq.2	Q9Y6V7		ENST00000247003.4:c.79delC	chr19.hg19:g.19030629delC	ENSP00000247003:p.Pro27fs	143.0	0.0		164.0	10.0	NM_019070	E7ENA0|Q53FJ1|Q9BVQ8	Frame_Shift_Del	DEL	ENST00000247003.4	hg19	CCDS12390.1																																																																																			.	.		0.652	DDX49-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464593.1	NM_019070	
ATP2C2	9914	hgsc.bcm.edu	37	16	84486788	84486788	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:84486788delG	ENST00000262429.4	+	19	1965	c.1876delG	c.(1876-1878)gggfs	p.G626fs	ATP2C2_ENST00000420010.2_3'UTR|ATP2C2_ENST00000416219.2_Frame_Shift_Del_p.G626fs	NM_014861.2	NP_055676.2	O75185	AT2C2_HUMAN	ATPase, Ca++ transporting, type 2C, member 2	626					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|prostate(3)|skin(5)|urinary_tract(1)	33						AGCCATGTCCGGGGAGGAGGT	0.657																																					p.S625fs		Atlas-INDEL	.											.	ATP2C2	75	.	0			c.1875delC						.						45.0	52.0	50.0					16																	84486788		2041	4182	6223	SO:0001589	frameshift_variant	9914	exon19			.	AK091051	CCDS42207.1, CCDS67088.1	16q24.1	2010-04-20			ENSG00000064270	ENSG00000064270	3.6.3.8	"""ATPases / P-type"""	29103	protein-coding gene	gene with protein product	"""secretory pathway calcium ATPase 2"""	613082				9734811	Standard	XM_006721355		Approved	KIAA0703, SPCA2	uc002fhx.3	O75185		ENST00000262429.4:c.1876delG	chr16.hg19:g.84486788delG	ENSP00000262429:p.Gly626fs	103.0	0.0		150.0	10.0	NM_014861	B4DU76|E7ES94|Q5HYC3|Q5S053|Q68CQ2	Frame_Shift_Del	DEL	ENST00000262429.4	hg19	CCDS42207.1																																																																																			.	.		0.657	ATP2C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433404.1	NM_014861	
USP34	9736	hgsc.bcm.edu	37	2	61571112	61571112	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:61571112delG	ENST00000398571.2	-	16	2414	c.2338delC	c.(2338-2340)cagfs	p.Q780fs		NM_014709.3	NP_055524.3	Q70CQ2	UBP34_HUMAN	ubiquitin specific peptidase 34	780					positive regulation of canonical Wnt signaling pathway (GO:0090263)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)		cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			autonomic_ganglia(1)|breast(14)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(52)|ovary(8)|prostate(10)|skin(6)|urinary_tract(2)	138			Epithelial(17;0.229)			GCACTAACCTGGGAGCTACTA	0.378																																					p.Q780fs		Atlas-INDEL	.											.	USP34	334	.	0			c.2339delA						.						110.0	98.0	102.0					2																	61571112		1899	4130	6029	SO:0001589	frameshift_variant	9736	exon16			.	AB011142	CCDS42686.1	2p16.1-p15	2005-08-08	2005-08-08		ENSG00000115464	ENSG00000115464		"""Ubiquitin-specific peptidases"""	20066	protein-coding gene	gene with protein product		615295	"""ubiquitin specific protease 34"""			12838346	Standard	NM_014709		Approved	KIAA0570, KIAA0729	uc002sbe.3	Q70CQ2	OTTHUMG00000152265	ENST00000398571.2:c.2338delC	chr2.hg19:g.61571112delG	ENSP00000381577:p.Gln780fs	152.0	0.0		149.0	10.0	NM_014709	A8MWD0|B3KWU9|O60316|O94834|Q3B777|Q6P6C9|Q7L8P6|Q8N3T9|Q8TBW2|Q9UGA1	Frame_Shift_Del	DEL	ENST00000398571.2	hg19	CCDS42686.1																																																																																			.	.		0.378	USP34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325650.4		
CYP4B1	1580	hgsc.bcm.edu	37	1	47284387	47284387	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:47284387delC	ENST00000271153.4	+	12	1473	c.1437delC	c.(1435-1437)gacfs	p.D479fs	CYP4B1_ENST00000371919.4_Frame_Shift_Del_p.D465fs|CYP4B1_ENST00000371923.4_Frame_Shift_Del_p.D480fs|CYP4B1_ENST00000452782.2_Frame_Shift_Del_p.D317fs			P13584	CP4B1_HUMAN	cytochrome P450, family 4, subfamily B, polypeptide 1	479					biphenyl metabolic process (GO:0018879)|exogenous drug catabolic process (GO:0042738)|fluorene metabolic process (GO:0018917)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|drug binding (GO:0008144)|fluorene oxygenase activity (GO:0018585)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)			NS(2)|breast(1)|endometrium(2)|kidney(1)|large_intestine(12)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	36	Acute lymphoblastic leukemia(166;0.155)				Midazolam(DB00683)|Phenobarbital(DB01174)|Thiamine(DB00152)	TCTCTCTGGACCCCTCACGGC	0.577																																					p.D480fs		Atlas-INDEL	.											.	CYP4B1	81	.	0			c.1439delA						.						163.0	140.0	148.0					1																	47284387		2203	4300	6503	SO:0001589	frameshift_variant	1580	exon12			.	BC017758	CCDS542.1, CCDS41328.1	1p33	2013-11-11	2003-01-14		ENSG00000142973	ENSG00000142973		"""Cytochrome P450s"""	2644	protein-coding gene	gene with protein product		124075	"""cytochrome P450, subfamily IVB, polypeptide 1"""				Standard	NM_000779		Approved		uc001cqn.4	P13584	OTTHUMG00000007984	ENST00000271153.4:c.1437delC	chr1.hg19:g.47284387delC	ENSP00000271153:p.Asp479fs	163.0	0.0		156.0	10.0	NM_001099772	Q1HBI2|Q8TD85|Q8WWF2|Q8WWU9|Q8WWV0	Frame_Shift_Del	DEL	ENST00000271153.4	hg19	CCDS542.1																																																																																			.	.		0.577	CYP4B1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000021911.1	NM_000779	
NLRP6	171389	hgsc.bcm.edu	37	11	281492	281492	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:281492delC	ENST00000312165.5	+	4	1758	c.1758delC	c.(1756-1758)tgcfs	p.C586fs	NLRP6_ENST00000534750.1_Frame_Shift_Del_p.C586fs	NM_138329.1	NP_612202.2	P59044	NALP6_HUMAN	NLR family, pyrin domain containing 6	586					G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of immune response (GO:0050777)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|regulation of inflammatory response (GO:0050727)|response to bacterium (GO:0009617)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|vasopressin receptor activity (GO:0005000)			breast(1)|skin(1)|upper_aerodigestive_tract(2)	4		all_cancers(49;1.12e-06)|all_epithelial(84;0.000375)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;4.28e-28)|Epithelial(43;2.47e-27)|OV - Ovarian serous cystadenocarcinoma(40;4.66e-21)|BRCA - Breast invasive adenocarcinoma(625;3.57e-05)|Lung(200;0.0485)|LUSC - Lung squamous cell carcinoma(625;0.122)		GACAGGGCTGCCCCGGAGTGG	0.672																																					p.C586fs		Atlas-INDEL	.											.	NLRP6	4	.	0			c.1757delG						.						29.0	34.0	32.0					11																	281492		2202	4300	6502	SO:0001589	frameshift_variant	171389	exon4			.	AF479748	CCDS7693.1, CCDS60680.1	11p15	2006-12-08	2006-12-08	2006-12-08	ENSG00000174885	ENSG00000174885		"""Nucleotide-binding domain and leucine rich repeat containing"""	22944	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 6"""	609650	"""NACHT, leucine rich repeat and PYD containing 6"""	NALP6		12563287, 12019269	Standard	NM_138329		Approved	PYPAF5, PAN3, CLR11.4	uc010qvs.3	P59044	OTTHUMG00000119070	ENST00000312165.5:c.1758delC	chr11.hg19:g.281492delC	ENSP00000309767:p.Cys586fs	124.0	0.0		153.0	10.0	NM_138329	A8K9F3|E9PJZ8	Frame_Shift_Del	DEL	ENST00000312165.5	hg19	CCDS7693.1																																																																																			.	.		0.672	NLRP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239283.1	NM_138329	
TCP1	6950	hgsc.bcm.edu	37	6	160202000	160202000	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:160202000delT	ENST00000321394.7	-	8	1220	c.940delA	c.(940-942)aggfs	p.R314fs	TCP1_ENST00000392168.2_Frame_Shift_Del_p.R159fs|SNORA20_ENST00000384662.1_RNA|TCP1_ENST00000420894.2_Frame_Shift_Del_p.R314fs|TCP1_ENST00000544255.1_Frame_Shift_Del_p.R90fs	NM_030752.2	NP_110379.2	P17987	TCPA_HUMAN	t-complex 1	314					'de novo' posttranslational protein folding (GO:0051084)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)|tubulin complex assembly (GO:0007021)	acrosomal vesicle (GO:0001669)|cell body (GO:0044297)|centrosome (GO:0005813)|chaperonin-containing T-complex (GO:0005832)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|nuclear heterochromatin (GO:0005720)|pericentriolar material (GO:0000242)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|unfolded protein binding (GO:0051082)			breast(1)|endometrium(4)|large_intestine(3)|lung(2)	10		Breast(66;1.53e-05)|Ovarian(120;0.024)		OV - Ovarian serous cystadenocarcinoma(65;4.05e-20)|BRCA - Breast invasive adenocarcinoma(81;1.1e-06)		TTAAGGTCCCTTTTTAAAACT	0.393																																					p.R314fs		Atlas-INDEL	.											.	TCP1	37	.	0			c.941delG						.						127.0	127.0	127.0					6																	160202000		2203	4300	6503	SO:0001589	frameshift_variant	6950	exon8			.	X52882	CCDS5269.1, CCDS43522.1	6q25-q27	2012-10-02			ENSG00000120438	ENSG00000120438		"""Heat Shock Proteins / Chaperonins"""	11655	protein-coding gene	gene with protein product		186980				3476253, 3653076	Standard	NM_030752		Approved	D6S230E, CCT1, Ccta	uc003qsr.3	P17987	OTTHUMG00000015937	ENST00000321394.7:c.940delA	chr6.hg19:g.160202000delT	ENSP00000317334:p.Arg314fs	213.0	0.0		179.0	12.0	NM_030752	E1P5B2|Q15556|Q5TCM3	Frame_Shift_Del	DEL	ENST00000321394.7	hg19	CCDS5269.1																																																																																			.	.		0.393	TCP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042917.2	NM_030752	
COL9A1	1297	hgsc.bcm.edu	37	6	71010083	71010083	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:71010083delG	ENST00000357250.6	-	3	253	c.95delC	c.(94-96)cctfs	p.P32fs	COL9A1_ENST00000370496.3_Frame_Shift_Del_p.P32fs	NM_001851.4	NP_001842.3	P20849	CO9A1_HUMAN	collagen, type IX, alpha 1	32	Nonhelical region (NC4).				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|organ morphogenesis (GO:0009887)|tissue homeostasis (GO:0001894)	collagen type IX trimer (GO:0005594)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(44)|ovary(5)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)	80						GGAATTGACAGGGAATCCTGC	0.308																																					p.P32fs		Atlas-INDEL	.											.	COL9A1	228	.	0			c.96delT						.						105.0	96.0	99.0					6																	71010083		2203	4300	6503	SO:0001589	frameshift_variant	1297	exon3			.		CCDS4971.1, CCDS47447.1	6q13	2013-05-07			ENSG00000112280	ENSG00000112280		"""Proteoglycans / Extracellular Matrix : Collagen proteoglycans"", ""Collagens"""	2217	protein-coding gene	gene with protein product		120210				1429648	Standard	NM_001851		Approved		uc003pfg.4	P20849	OTTHUMG00000014988	ENST00000357250.6:c.95delC	chr6.hg19:g.71010083delG	ENSP00000349790:p.Pro32fs	134.0	0.0		165.0	12.0	NM_001851	Q13699|Q13700|Q5TF52|Q6P467|Q96BM8|Q99225|Q9H151|Q9H152|Q9Y6P2|Q9Y6P3	Frame_Shift_Del	DEL	ENST00000357250.6	hg19	CCDS4971.1																																																																																			.	.		0.308	COL9A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041131.2		
DHX40	79665	hgsc.bcm.edu	37	17	57656854	57656854	+	Frame_Shift_Del	DEL	C	C	-	rs375795771		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:57656854delC	ENST00000251241.4	+	9	1242	c.1095delC	c.(1093-1095)ttcfs	p.F365fs	DHX40_ENST00000451169.2_Frame_Shift_Del_p.F317fs|DHX40_ENST00000425628.3_Frame_Shift_Del_p.F288fs	NM_024612.4	NP_078888.4	Q8IX18	DHX40_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 40	365	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.						ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|nucleic acid binding (GO:0003676)			endometrium(7)|large_intestine(6)|lung(6)|prostate(1)	20	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)					ATGGTGGCTTCGTGAAGCAGT	0.358																																					p.F365fs		Atlas-INDEL	.											.	DHX40	40	.	0			c.1094delT						.						38.0	57.0	53.0					17																	57656854		984	4080	5064	SO:0001589	frameshift_variant	79665	exon9			.	AF260270	CCDS11617.1, CCDS54150.1	17q22	2014-01-28	2003-06-13	2003-06-20		ENSG00000108406		"""DEAH-boxes"""	18018	protein-coding gene	gene with protein product		607570	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 40 (RNA helicase)"""	DDX40			Standard	NM_024612		Approved	ARG147, PAD, FLJ22060	uc002ixn.2	Q8IX18		ENST00000251241.4:c.1095delC	chr17.hg19:g.57656854delC	ENSP00000251241:p.Phe365fs	3.0	0.0		10.0	10.0	NM_024612	B3KTJ5|C9JR60|Q5JPH4|Q8TC86|Q8WY53|Q9BXM1|Q9H6M9	Frame_Shift_Del	DEL	ENST00000251241.4	hg19	CCDS11617.1																																																																																			.	.		0.358	DHX40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446095.1	NM_024612	
NCOA1	8648	hgsc.bcm.edu	37	2	24920612	24920612	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:24920612delT	ENST00000406961.1	+	11	1546	c.894delT	c.(892-894)gctfs	p.A298fs	NCOA1_ENST00000538539.1_Frame_Shift_Del_p.A298fs|NCOA1_ENST00000348332.3_Frame_Shift_Del_p.A298fs|NCOA1_ENST00000405141.1_Frame_Shift_Del_p.A298fs|NCOA1_ENST00000288599.5_Frame_Shift_Del_p.A298fs|NCOA1_ENST00000395856.3_Frame_Shift_Del_p.A298fs|NCOA1_ENST00000407230.1_Frame_Shift_Del_p.A147fs			Q15788	NCOA1_HUMAN	nuclear receptor coactivator 1	298					androgen receptor signaling pathway (GO:0030521)|cellular lipid metabolic process (GO:0044255)|cellular response to hormone stimulus (GO:0032870)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|estrous cycle phase (GO:0060206)|hippocampus development (GO:0021766)|histone H4 acetylation (GO:0043967)|hypothalamus development (GO:0021854)|labyrinthine layer morphogenesis (GO:0060713)|lactation (GO:0007595)|male gonad development (GO:0008584)|male mating behavior (GO:0060179)|ovulation cycle (GO:0042698)|positive regulation of apoptotic process (GO:0043065)|positive regulation of female receptivity (GO:0045925)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter by galactose (GO:0000435)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cellular response to drug (GO:2001038)|response to estradiol (GO:0032355)|response to progesterone (GO:0032570)|response to retinoic acid (GO:0032526)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|neuron projection (GO:0043005)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|protein N-terminus binding (GO:0047485)|RNA polymerase II regulatory region DNA binding (GO:0001012)|RNA polymerase II transcription coactivator activity (GO:0001105)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)		PAX3/NCOA1(8)	breast(3)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(26)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	53	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GCATTTATGCTTTTTTCCAAC	0.388			T	PAX3	alveolar rhadomyosarcoma																																p.A298fs		Atlas-INDEL	.		Dom	yes		2	2p23	8648	nuclear receptor coactivator 1		M	.	NCOA1	210	.	0			c.893delC						.						129.0	124.0	126.0					2																	24920612		2203	4300	6503	SO:0001589	frameshift_variant	8648	exon9			.	U40396	CCDS1712.1, CCDS1713.1, CCDS42660.1	2p23	2011-07-01			ENSG00000084676	ENSG00000084676		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Basic helix-loop-helix proteins"""	7668	protein-coding gene	gene with protein product		602691				7481822, 9575154	Standard	XM_005264625		Approved	SRC1, F-SRC-1, NCoA-1, KAT13A, RIP160, bHLHe74	uc002rfk.3	Q15788	OTTHUMG00000125523	ENST00000406961.1:c.894delT	chr2.hg19:g.24920612delT	ENSP00000385216:p.Ala298fs	101.0	0.0		182.0	11.0	NM_147223	O00150|O43792|O43793|Q13071|Q13420|Q2T9G5|Q53SX3|Q6GVI5|Q7KYV3	Frame_Shift_Del	DEL	ENST00000406961.1	hg19	CCDS1712.1																																																																																			.	.		0.388	NCOA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000246852.3	NM_147223	
U2AF1L4	199746	hgsc.bcm.edu	37	19	36236292	36236292	+	Start_Codon_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:36236292delT	ENST00000412391.2	-	0	14				IGFLR1_ENST00000246532.1_5'Flank|U2AF1L4_ENST00000292879.5_Start_Codon_Del|AC002398.11_ENST00000585365.1_RNA|IGFLR1_ENST00000588992.1_5'Flank|IGFLR1_ENST00000344990.3_5'Flank|IGFLR1_ENST00000592537.1_5'Flank|AC002398.11_ENST00000591091.1_RNA|LIN37_ENST00000301159.9_5'Flank|PSENEN_ENST00000591949.1_5'Flank|PSENEN_ENST00000222266.2_5'Flank|AC002398.9_ENST00000591613.2_5'Flank|PSENEN_ENST00000587708.2_5'UTR|AD000671.6_ENST00000589807.1_Start_Codon_Del|U2AF1L4_ENST00000588100.1_5'UTR|U2AF1L4_ENST00000378975.3_Start_Codon_Del			Q8WU68	U2AF4_HUMAN	U2 small nuclear RNA auxiliary factor 1-like 4						mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	spliceosomal complex (GO:0005681)	metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(2)|prostate(1)	8	all_lung(56;3.33e-07)|Lung NSC(56;5.02e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			TATTCAGCCATTTTTACCCAA	0.572																																					p.M1fs		Atlas-INDEL	.											.	U2AF1L4	34	.	0			c.2delT						.						123.0	136.0	132.0					19																	36236292		2203	4300	6503	SO:0001582	initiator_codon_variant	199746	exon1			.	BC021186, AY569437	CCDS12473.1, CCDS42551.1	19q13.13	2013-02-12	2006-04-12	2006-04-12		ENSG00000161265		"""RNA binding motif (RRM) containing"""	23020	protein-coding gene	gene with protein product		601080	"""U2(RNU2) small nuclear RNA auxiliary factor 1-like 3"", ""U2 small nuclear RNA auxiliary factor 1-like 3"""	U2AF1L3		8586425, 11739736	Standard	NM_001040425		Approved	MGC33901, U2af26	uc002obf.3	Q8WU68			chr19.hg19:g.36236292delT		124.0	0.0		146.0	12.0	NM_144987	A6NKI8|Q56UU3	Frame_Shift_Del	DEL	ENST00000412391.2	hg19																																																																																				.	.		0.572	U2AF1L4-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_144987	
SSC5D	284297	hgsc.bcm.edu	37	19	56002276	56002276	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:56002276delG	ENST00000389623.6	+	6	747	c.724delG	c.(724-726)gggfs	p.G243fs	SSC5D_ENST00000587166.1_Frame_Shift_Del_p.G243fs	NM_001144950.1	NP_001138422.1	A1L4H1	SRCRL_HUMAN	scavenger receptor cysteine rich family, 5 domains	243	SRCR 2. {ECO:0000255|PROSITE- ProRule:PRU00196}.				defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|detection of bacterial lipoprotein (GO:0042494)|innate immune response (GO:0045087)|multicellular organismal development (GO:0007275)|negative regulation of interleukin-8 secretion (GO:2000483)|receptor-mediated endocytosis (GO:0006898)	cytoplasm (GO:0005737)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|intracellular (GO:0005622)|membrane (GO:0016020)	extracellular matrix binding (GO:0050840)|fibronectin binding (GO:0001968)|laminin binding (GO:0043236)|scavenger receptor activity (GO:0005044)			NS(1)|breast(1)|skin(2)	4						ACTGGGCTGTGGGGGGGCGCT	0.721																																					p.C241fs		Atlas-INDEL	.											.,2	SSC5D	65	.	0			c.723delT						.						13.0	22.0	20.0					19																	56002276		691	1586	2277	SO:0001589	frameshift_variant	284297	exon6			.		CCDS46196.1, CCDS59424.1	19q13.42	2014-07-09	2014-07-09		ENSG00000179954	ENSG00000179954			26641	protein-coding gene	gene with protein product	"""soluble scavenger with 5 domains"""		"""scavenger receptor cysteine rich domain containing (5 domains)"""			19535143	Standard	NM_001144950		Approved	FLJ35258	uc002qlg.4	A1L4H1		ENST00000389623.6:c.724delG	chr19.hg19:g.56002276delG	ENSP00000374274:p.Gly243fs	31.0	0.0		161.0	10.0	NM_001195267	B5MDQ5|C7S7T9|C7S7U0|K7EP70	Frame_Shift_Del	DEL	ENST00000389623.6	hg19	CCDS46196.1																																																																																			.	.		0.721	SSC5D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453345.2	XM_001718392	
STRC	161497	hgsc.bcm.edu	37	15	43909880	43909880	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:43909880delG	ENST00000450892.2	-	2	816	c.739delC	c.(739-741)ctcfs	p.L247fs	STRC_ENST00000541030.1_5'UTR	NM_153700.2	NP_714544.1	Q7RTU9	STRC_HUMAN	stereocilin	247					auditory receptor cell stereocilium organization (GO:0060088)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)	kinocilium (GO:0060091)|stereocilium bundle tip (GO:0032426)				skin(4)	4		all_cancers(109;3.26e-15)|all_epithelial(112;1.48e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.56e-07)		GCAGCATAGAGGGGGGCCCCC	0.592																																					p.L247fs		Atlas-INDEL	.											.	STRC	58	.	0			c.740delT						.						1.0	2.0	2.0					15																	43909880		536	1524	2060	SO:0001589	frameshift_variant	161497	exon2			.	BK000138	CCDS10098.1	15q15.3	2010-02-26			ENSG00000242866	ENSG00000242866			16035	protein-coding gene	gene with protein product		606440		DFNB16		11687802, 9429146	Standard	NM_153700		Approved		uc001zsf.3	Q7RTU9	OTTHUMG00000059899	ENST00000450892.2:c.739delC	chr15.hg19:g.43909880delG	ENSP00000401513:p.Leu247fs	75.0	0.0		110.0	10.0	NM_153700		Frame_Shift_Del	DEL	ENST00000450892.2	hg19	CCDS10098.1																																																																																			.	.		0.592	STRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133140.1	NM_153700	
KRTAP5-10	387273	hgsc.bcm.edu	37	11	71276925	71276925	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:71276925delG	ENST00000398531.1	+	1	317	c.292delG	c.(292-294)gggfs	p.G99fs	KRTAP5-10_ENST00000376536.4_Intron	NM_001012710.1	NP_001012728.1	Q6L8G5	KR510_HUMAN	keratin associated protein 5-10	99	7 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)				endometrium(2)|large_intestine(1)|lung(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	12						TGGCTCCTGTGGGGGCTCCAA	0.682																																					p.C97fs		Atlas-INDEL	.											.	KRTAP5-10	37	.	0			c.291delT						.						33.0	53.0	46.0					11																	71276925		2100	4221	6321	SO:0001589	frameshift_variant	387273	exon1			.	AB126079	CCDS41684.1	11q13.4	2008-02-05			ENSG00000204572	ENSG00000204572		"""Keratin associated proteins"""	23605	protein-coding gene	gene with protein product						15144888	Standard	NM_001012710		Approved	KRTAP5.10	uc001oqt.1	Q6L8G5	OTTHUMG00000057585	ENST00000398531.1:c.292delG	chr11.hg19:g.71276925delG	ENSP00000381542:p.Gly99fs	78.0	0.0		166.0	11.0	NM_001012710	B9EHA4	Frame_Shift_Del	DEL	ENST00000398531.1	hg19	CCDS41684.1																																																																																			.	.		0.682	KRTAP5-10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000127968.2		
ABL1	25	hgsc.bcm.edu	37	9	133759994	133759995	+	Frame_Shift_Del	DEL	GA	GA	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	GA	GA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:133759994_133759995delGA	ENST00000318560.5	+	11	2698_2699	c.2317_2318delGA	c.(2317-2319)gacfs	p.D773fs		NM_005157.4	NP_005148.2	P00519	ABL1_HUMAN	ABL proto-oncogene 1, non-receptor tyrosine kinase	773					actin cytoskeleton organization (GO:0030036)|autophagy (GO:0006914)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to dopamine (GO:1903351)|cellular response to oxidative stress (GO:0034599)|DNA damage induced protein phosphorylation (GO:0006975)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|mismatch repair (GO:0006298)|mitochondrial depolarization (GO:0051882)|mitotic nuclear division (GO:0007067)|muscle cell differentiation (GO:0042692)|negative regulation of phospholipase C activity (GO:1900275)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of ubiquitin-protein transferase activity (GO:0051444)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of autophagy (GO:0010506)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of endocytosis (GO:0030100)|regulation of response to DNA damage stimulus (GO:2001020)|regulation of transcription, DNA-templated (GO:0006355)|response to oxidative stress (GO:0006979)|signal transduction in response to DNA damage (GO:0042770)	actin cytoskeleton (GO:0015629)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|mitogen-activated protein kinase binding (GO:0051019)|nicotinate-nucleotide adenylyltransferase activity (GO:0004515)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|proline-rich region binding (GO:0070064)|protein C-terminus binding (GO:0008022)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|SH3 domain binding (GO:0017124)|syntaxin binding (GO:0019905)			breast(3)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1149)|kidney(3)|large_intestine(7)|lung(15)|ovary(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	1195		all_hematologic(13;0.0361)|Acute lymphoblastic leukemia(5;0.0543)|Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.4e-05)	Adenosine triphosphate(DB00171)|Bosutinib(DB06616)|Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Ponatinib(DB08901)|Regorafenib(DB08896)	GAACAGGTCTGACCAGGTGACC	0.569			"""T, Mis"""	"""BCR, ETV6, NUP214"""	"""CML, ALL, T-ALL"""																																p.791_792del		Atlas-Indel,Pindel	.		Dom	yes		9	9q34.1	25	v-abl Abelson murine leukemia viral oncogene homolog 1		L	.	ABL1	1632	.	0			c.2373_2374del						.																																			SO:0001589	frameshift_variant	25	exon11			.	M14752	CCDS35165.1, CCDS35166.1	9q34.1	2014-09-17	2014-06-26		ENSG00000097007	ENSG00000097007		"""SH2 domain containing"""	76	protein-coding gene	gene with protein product		189980	"""v-abl Abelson murine leukemia viral oncogene homolog 1"", ""c-abl oncogene 1, receptor tyrosine kinase"", ""c-abl oncogene 1, non-receptor tyrosine kinase"""	ABL		1857987, 12626632	Standard	NM_007313		Approved	JTK7, c-ABL, p150	uc004bzv.3	P00519	OTTHUMG00000020813	ENST00000318560.5:c.2317_2318delGA	chr9.hg19:g.133759994_133759995delGA	ENSP00000323315:p.Asp773fs	36.0	0.0		32.0	13.0	NM_007313	A3KFJ3|Q13869|Q13870|Q16133|Q17R61|Q45F09	Frame_Shift_Del	DEL	ENST00000318560.5	hg19	CCDS35166.1																																																																																			.	.		0.569	ABL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054684.1	NM_007313	
LYST	1130	hgsc.bcm.edu	37	1	235880039	235880039	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:235880039delT	ENST00000389794.3	-	41	9774	c.9600delA	c.(9598-9600)aaafs	p.K3200fs	LYST_ENST00000389793.2_Frame_Shift_Del_p.K3200fs|LYST_ENST00000473037.1_5'UTR			Q99698	LYST_HUMAN	lysosomal trafficking regulator	3200	BEACH. {ECO:0000255|PROSITE- ProRule:PRU00026}.				blood coagulation (GO:0007596)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|defense response to virus (GO:0051607)|endosome to lysosome transport via multivesicular body sorting pathway (GO:0032510)|leukocyte chemotaxis (GO:0030595)|lysosome organization (GO:0007040)|mast cell secretory granule organization (GO:0033364)|melanosome organization (GO:0032438)|microtubule-based process (GO:0007017)|natural killer cell mediated cytotoxicity (GO:0042267)|neutrophil mediated immunity (GO:0002446)|phospholipid homeostasis (GO:0055091)|phospholipid metabolic process (GO:0006644)|pigmentation (GO:0043473)|positive regulation of natural killer cell activation (GO:0032816)|response to drug (GO:0042493)|secretion of lysosomal enzymes (GO:0033299)|T cell mediated immunity (GO:0002456)	cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)				NS(1)|breast(13)|central_nervous_system(3)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(27)|lung(66)|ovary(7)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	162	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00246)|Prostate(94;0.0771)|Acute lymphoblastic leukemia(190;0.228)	OV - Ovarian serous cystadenocarcinoma(106;0.000674)			AACGATCTTCTTTTTCTTTAT	0.289																																					p.E3201fs		Atlas-INDEL	.											.	LYST	370	.	0			c.9601delG						.						69.0	71.0	70.0					1																	235880039		2200	4297	6497	SO:0001589	frameshift_variant	1130	exon41			.	U70064	CCDS31062.1	1q42.1-q42.2	2014-09-17	2004-12-09	2004-12-10	ENSG00000143669	ENSG00000143669		"""WD repeat domain containing"""	1968	protein-coding gene	gene with protein product		606897	"""Chediak-Higashi syndrome 1"""	CHS1		8717042, 8896560	Standard	NM_000081		Approved	CHS	uc001hxj.3	Q99698	OTTHUMG00000040527	ENST00000389794.3:c.9600delA	chr1.hg19:g.235880039delT	ENSP00000374444:p.Lys3200fs	103.0	0.0		220.0	15.0	NM_000081	O43274|Q5T2U9|Q96TD7|Q96TD8|Q99709|Q9H133	Frame_Shift_Del	DEL	ENST00000389794.3	hg19	CCDS31062.1																																																																																			.	.		0.289	LYST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097533.5		
CCDC171	203238	hgsc.bcm.edu	37	9	15623298	15623298	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:15623298delA	ENST00000380701.3	+	7	1037	c.709delA	c.(709-711)aaafs	p.K237fs	CCDC171_ENST00000297641.3_Frame_Shift_Del_p.K237fs|CCDC171_ENST00000535968.1_Frame_Shift_Del_p.K237fs	NM_173550.2	NP_775821.2	Q6TFL3	CC171_HUMAN	coiled-coil domain containing 171	237	Glu-rich.																TATGCATAAGAAAGTAGAAAA	0.363																																					p.K236fs		Atlas-INDEL	.											.	.	.	.	0			c.708delG						.						131.0	133.0	132.0					9																	15623298		2203	4300	6503	SO:0001589	frameshift_variant	203238	exon7			.	AY422473	CCDS6481.1	9p22.2	2012-03-26	2012-03-26	2012-03-26	ENSG00000164989	ENSG00000164989			29828	protein-coding gene	gene with protein product	"""myosin tail domain containing protein"""		"""chromosome 9 open reading frame 93"""	C9orf93		14702039	Standard	NM_173550		Approved	FLJ39267, FLJ46740, Em:AL513423.1, bA778P13.1, bA536D16.1	uc003zmd.3	Q6TFL3	OTTHUMG00000019584	ENST00000380701.3:c.709delA	chr9.hg19:g.15623298delA	ENSP00000370077:p.Lys237fs	147.0	0.0		180.0	11.0	NM_173550	B7ZM22|Q5SU58|Q6P1W1|Q6ZR13|Q8N1Z4|Q8N8L3|Q8TBR2	Frame_Shift_Del	DEL	ENST00000380701.3	hg19	CCDS6481.1																																																																																			.	.		0.363	CCDC171-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051768.4	NM_173550	
CFAP53	220136	hgsc.bcm.edu	37	18	47787507	47787507	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr18:47787507delT	ENST00000398545.4	-	3	517	c.400delA	c.(400-402)actfs	p.T134fs		NM_145020.3	NP_659457.2														endometrium(1)|kidney(4)|large_intestine(6)|lung(6)|ovary(1)|pancreas(1)|skin(1)	20				STAD - Stomach adenocarcinoma(97;2.66e-05)|Colorectal(21;7.57e-05)|Lung(128;0.00932)|READ - Rectum adenocarcinoma(32;0.164)		AGTAATTTAGTTTTCTCTCTC	0.338																																					p.T134fs		Atlas-INDEL	.											.	CCDC11	59	.	0			c.401delC						.						170.0	159.0	162.0					18																	47787507		1802	4076	5878	SO:0001589	frameshift_variant	220136	exon3			.																												ENST00000398545.4:c.400delA	chr18.hg19:g.47787507delT	ENSP00000381553:p.Thr134fs	88.0	0.0		155.0	11.0	NM_145020		Frame_Shift_Del	DEL	ENST00000398545.4	hg19	CCDS11940.2																																																																																			.	.		0.338	CCDC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255922.3		
FAM21A	387680	hgsc.bcm.edu	37	10	47915896	47915896	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:47915896delA	ENST00000358474.5	+	15	1303	c.1303delA	c.(1303-1305)aaafs	p.K435fs		NM_018232.1	NP_060702.1	Q5SNT6	FA21B_HUMAN		435					retrograde transport, endosome to Golgi (GO:0042147)	early endosome (GO:0005769)|membrane (GO:0016020)|WASH complex (GO:0071203)				endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	10						ATCTTCCAGCAAAAATCTCAA	0.403																																					p.S434fs		Atlas-INDEL	.											.	FAM21B	31	.	0			c.1302delC						.						20.0	29.0	27.0					10																	47915896		1763	4023	5786	SO:0001589	frameshift_variant	55747	exon15			.																												ENST00000358474.5:c.1303delA	chr10.hg19:g.47915896delA	ENSP00000351259:p.Lys435fs	203.0	0.0		190.0	16.0	NM_018232		Frame_Shift_Del	DEL	ENST00000358474.5	hg19	CCDS44379.1																																																																																			.	.		0.403	FAM21B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047871.2		
TAF2	6873	hgsc.bcm.edu	37	8	120759116	120759116	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr8:120759116delA	ENST00000378164.2	-	23	3235	c.2937delT	c.(2935-2937)tttfs	p.F979fs	TAF2_ENST00000519355.1_5'UTR	NM_003184.3	NP_003175	Q6P1X5	TAF2_HUMAN	TAF2 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 150kDa	979					G2/M transition of mitotic cell cycle (GO:0000086)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to organic cyclic compound (GO:0014070)|transcription initiation from RNA polymerase II promoter (GO:0006367)	transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	metallopeptidase activity (GO:0008237)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(2)|breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(21)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	49	Lung NSC(37;9.35e-07)|Ovarian(258;0.011)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)			TACTGAGGCCAAAAAGTGTGA	0.408																																					p.G980fs		Atlas-INDEL	.											.	TAF2	204	.	0			c.2938delG						.						114.0	100.0	105.0					8																	120759116		2203	4300	6503	SO:0001589	frameshift_variant	6873	exon23			.	AF040701	CCDS34937.1	8q24	2012-07-18	2002-08-29	2001-12-07	ENSG00000064313	ENSG00000064313			11536	protein-coding gene	gene with protein product		604912	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, B, 150kD"""	TAF2B		9774672, 9418870	Standard	NM_003184		Approved	TAFII150, CIF150	uc003you.3	Q6P1X5	OTTHUMG00000165009	ENST00000378164.2:c.2937delT	chr8.hg19:g.120759116delA	ENSP00000367406:p.Phe979fs	74.0	0.0		173.0	13.0	NM_003184	B2RE82|O43487|O43604|O60668|Q86WW7|Q8IWK4	Frame_Shift_Del	DEL	ENST00000378164.2	hg19	CCDS34937.1																																																																																			.	.		0.408	TAF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381436.1	NM_003184	
SH3D21	79729	hgsc.bcm.edu	37	1	36785322	36785322	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:36785322delC	ENST00000426732.2	+	13	995	c.710delC	c.(709-711)accfs	p.T237fs	SH3D21_ENST00000453908.2_Frame_Shift_Del_p.T353fs|SH3D21_ENST00000505871.1_Frame_Shift_Del_p.T242fs|EVA1B_ENST00000490466.1_5'Flank|SH3D21_ENST00000312808.4_5'UTR			A4FU49	SH321_HUMAN	SH3 domain containing 21	237						extracellular vesicular exosome (GO:0070062)				endometrium(1)|large_intestine(6)|lung(4)|pancreas(1)	12						GTGAAGAGAACCCCCATGCCG	0.627																																					p.T353fs		Atlas-INDEL	.											.	SH3D21	73	.	0			c.1057delA						.						29.0	42.0	38.0					1																	36785322		2194	4296	6490	SO:0001589	frameshift_variant	79729	exon14			.	AK056459	CCDS30674.1, CCDS30674.2	1p34.3	2011-02-21	2011-02-21	2011-02-21	ENSG00000214193	ENSG00000214193			26236	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 113"""	C1orf113		12477932	Standard	NM_024676		Approved	FLJ22938	uc010oia.1	A4FU49	OTTHUMG00000007868	ENST00000426732.2:c.710delC	chr1.hg19:g.36785322delC	ENSP00000408613:p.Thr237fs	228.0	0.0		247.0	16.0	NM_001162530	B4DLI6|D3DPS6|J3KQM5|Q5VTK7|Q86XZ6|Q8N445|Q96DN4|Q9H5W5	Frame_Shift_Del	DEL	ENST00000426732.2	hg19																																																																																				.	.		0.627	SH3D21-202	KNOWN	basic	protein_coding	protein_coding		NM_024676	
PHTF2	57157	hgsc.bcm.edu	37	7	77579071	77579071	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:77579071delT	ENST00000248550.7	+	16	2112	c.2036delT	c.(2035-2037)cttfs	p.L679fs	PHTF2_ENST00000416283.2_Frame_Shift_Del_p.L645fs|PHTF2_ENST00000422959.2_Frame_Shift_Del_p.L645fs|PHTF2_ENST00000275575.7_Intron|PHTF2_ENST00000307305.8_Frame_Shift_Del_p.L641fs			Q8N3S3	PHTF2_HUMAN	putative homeodomain transcription factor 2	679					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(2)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)	19						TCGTTAACACTTTTTCTCCTA	0.338																																					p.L645fs		Atlas-INDEL	.											.	PHTF2	104	.	0			c.1933delC						.						129.0	116.0	120.0					7																	77579071		1850	4085	5935	SO:0001589	frameshift_variant	57157	exon15			.	AL136883	CCDS47621.1, CCDS47622.1, CCDS47623.1, CCDS47624.1	7q11.23-q21	2008-02-01			ENSG00000006576	ENSG00000006576			13411	protein-coding gene	gene with protein product						10729229	Standard	NM_020432		Approved	DKFZp434D166	uc003ugq.4	Q8N3S3	OTTHUMG00000155557	ENST00000248550.7:c.2036delT	chr7.hg19:g.77579071delT	ENSP00000248550:p.Leu679fs	143.0	0.0		201.0	13.0	NM_001127357	A0JP04|A0JP05|A4D1C2|E9PEE3|G5E9H7|Q6NW35|Q8TBW4|Q9H099	Frame_Shift_Del	DEL	ENST00000248550.7	hg19																																																																																				.	.		0.338	PHTF2-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000340638.2	NM_020432	
DHX57	90957	hgsc.bcm.edu	37	2	39033812	39033812	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:39033812delA	ENST00000295373.6	-	22	3831	c.3705delT	c.(3703-3705)tttfs	p.F1235fs		NM_198963.1	NP_945314.1	Q6P158	DHX57_HUMAN	DEAH (Asp-Glu-Ala-Asp/His) box polypeptide 57	1235							ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(9)|kidney(2)|large_intestine(15)|lung(20)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	62		all_hematologic(82;0.248)				TGGTCTTCTGAAATTTTCCTT	0.363																																					p.Q1236fs	Melanoma(191;1090 2095 4375 23729 47341)	Atlas-INDEL	.											.	DHX57	127	.	0			c.3706delC						.						124.0	114.0	117.0					2																	39033812		2203	4300	6503	SO:0001589	frameshift_variant	90957	exon22			.	AF070590	CCDS1800.1	2p22.3	2008-02-05			ENSG00000163214	ENSG00000163214		"""DEAH-boxes"""	20086	protein-coding gene	gene with protein product							Standard	NM_198963		Approved	DDX57	uc002rrf.3	Q6P158	OTTHUMG00000102103	ENST00000295373.6:c.3705delT	chr2.hg19:g.39033812delA	ENSP00000295373:p.Phe1235fs	124.0	0.0		183.0	12.0	NM_198963	A2RRC7|Q53SI4|Q6P9G1|Q7Z6H3|Q8NG17|Q96M33	Frame_Shift_Del	DEL	ENST00000295373.6	hg19	CCDS1800.1																																																																																			.	.		0.363	DHX57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219940.2	NM_145646	
DSC2	1824	hgsc.bcm.edu	37	18	28649035	28649035	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr18:28649035delT	ENST00000280904.6	-	15	2776	c.2333delA	c.(2332-2334)aacfs	p.N778fs	DSC2_ENST00000251081.6_Frame_Shift_Del_p.N778fs	NM_024422.3	NP_077740.1	Q02487	DSC2_HUMAN	desmocollin 2	778					bundle of His cell to Purkinje myocyte communication (GO:0086069)|cardiac muscle cell-cardiac muscle cell adhesion (GO:0086042)|cell adhesion (GO:0007155)|cellular response to starvation (GO:0009267)|homophilic cell adhesion (GO:0007156)|regulation of heart rate by cardiac conduction (GO:0086091)|ventricular cardiac muscle cell action potential (GO:0086005)	cell-cell adherens junction (GO:0005913)|cytoplasmic vesicle (GO:0031410)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(2)|kidney(1)|large_intestine(2)|lung(12)|ovary(2)|prostate(1)|skin(1)	21			OV - Ovarian serous cystadenocarcinoma(10;0.0241)			CTGACCTCCGTTTTTGATTCC	0.542																																					p.N778fs		Atlas-INDEL	.											.	DSC2	168	.	0			c.2334delC						.						72.0	66.0	68.0					18																	28649035		2203	4300	6503	SO:0001589	frameshift_variant	1824	exon15			.	X56807	CCDS11892.1, CCDS11893.1	18q12.1	2014-09-17			ENSG00000134755	ENSG00000134755		"""Cadherins / Major cadherins"""	3036	protein-coding gene	gene with protein product		125645		DSC3		7774948	Standard	NM_024422		Approved	CDHF2	uc002kwl.4	Q02487	OTTHUMG00000131981	ENST00000280904.6:c.2333delA	chr18.hg19:g.28649035delT	ENSP00000280904:p.Asn778fs	119.0	0.0		156.0	11.0	NM_024422		Frame_Shift_Del	DEL	ENST00000280904.6	hg19	CCDS11892.1																																																																																			.	.		0.542	DSC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254943.1	NM_004949	
MOV10	4343	hgsc.bcm.edu	37	1	113243060	113243060	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:113243060delC	ENST00000413052.2	+	21	3333	c.2943delC	c.(2941-2943)ctcfs	p.L981fs	RP11-426L16.10_ENST00000471038.2_5'Flank|MOV10_ENST00000369644.1_Frame_Shift_Del_p.L925fs|MOV10_ENST00000357443.2_Frame_Shift_Del_p.L981fs|MOV10_ENST00000369645.1_Frame_Shift_Del_p.L981fs|MOV10_ENST00000468624.1_3'UTR	NM_001130079.1|NM_020963.3	NP_001123551.1|NP_066014.1	Q9HCE1	MOV10_HUMAN	Mov10 RISC complex RNA helicase	981					epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|mRNA cleavage involved in gene silencing by miRNA (GO:0035279)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|extracellular space (GO:0005615)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(3)|large_intestine(6)|lung(15)|ovary(5)|prostate(1)|skin(3)|urinary_tract(3)	38	Lung SC(450;0.246)	all_cancers(81;3.31e-11)|all_epithelial(167;5.69e-10)|all_lung(203;3.73e-05)|Breast(1374;0.000525)|Lung NSC(69;0.000954)|Ovarian(761;0.0367)|Lung SC(238;0.114)		OV - Ovarian serous cystadenocarcinoma(397;3.99e-67)|all cancers(265;1e-62)|Epithelial(280;4.78e-61)|Lung(183;0.0234)|Colorectal(144;0.0686)|READ - Rectum adenocarcinoma(129;0.0929)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)|BRCA - Breast invasive adenocarcinoma(282;0.24)		ATGACTACCTCCCCCAGGAGC	0.612																																					p.L981fs		Atlas-INDEL	.											.	MOV10	74	.	0			c.2942delT						.						74.0	77.0	76.0					1																	113243060		2203	4300	6503	SO:0001589	frameshift_variant	4343	exon21			.	AL833353	CCDS853.1, CCDS65615.1	1p13.2	2014-07-02	2014-07-02		ENSG00000155363	ENSG00000155363			7200	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 113"""	610742	"""Mov10 (Moloney leukemia virus 10, mouse) homolog"", ""Mov10, Moloney leukemia virus 10, homolog (mouse)"""			12226669	Standard	NM_001286072		Approved	gb110, MGC2948, fSAP113	uc001eck.3	Q9HCE1	OTTHUMG00000011906	ENST00000413052.2:c.2943delC	chr1.hg19:g.113243060delC	ENSP00000399797:p.Leu981fs	169.0	0.0		173.0	12.0	NM_020963	Q5JR03|Q8TEF0|Q9BSY3|Q9BUJ9	Frame_Shift_Del	DEL	ENST00000413052.2	hg19	CCDS853.1																																																																																			.	.		0.612	MOV10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032906.1	NM_020963	
LINC00283	100874057	hgsc.bcm.edu	37	13	103394930	103394930	+	RNA	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr13:103394930delA	ENST00000430111.1	+	0	0									long intergenic non-protein coding RNA 283																		TTGATCTATTAAATCAACTTC	0.338																																					p.L2706fs		Atlas-INDEL	.											.	.	.	.	0			c.8118delA						.						77.0	57.0	63.0					13																	103394930		692	1590	2282			643677	exon4			.			13q33.1	2012-10-12	2011-08-10	2011-08-10	ENSG00000231633	ENSG00000231633		"""Long non-coding RNAs"""	38809	non-coding RNA	RNA, long non-coding			"""non-protein coding RNA 283"""	NCRNA00283			Standard			Approved				OTTHUMG00000017311		chr13.hg19:g.103394930delA		94.0	0.0		143.0	10.0	NM_001146197		Frame_Shift_Del	DEL	ENST00000430111.1	hg19																																																																																				.	.		0.338	LINC00283-001	KNOWN	not_organism_supported|basic	antisense	antisense	OTTHUMT00000045714.1		
TRIM33	51592	hgsc.bcm.edu	37	1	114942160	114942160	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:114942160delT	ENST00000358465.2	-	18	3122	c.3039delA	c.(3037-3039)aaafs	p.K1013fs	TRIM33_ENST00000369543.2_Frame_Shift_Del_p.K1013fs|TRIM33_ENST00000450349.2_Frame_Shift_Del_p.K645fs	NM_015906.3	NP_056990.3	Q9UPN9	TRI33_HUMAN	tripartite motif containing 33	1013	Bromo. {ECO:0000255|PROSITE- ProRule:PRU00035}.				gene expression (GO:0010467)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|protein ubiquitination (GO:0016567)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	co-SMAD binding (GO:0070410)|DNA binding (GO:0003677)|ligase activity (GO:0016874)|R-SMAD binding (GO:0070412)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.H1014fs*10(1)		breast(2)|central_nervous_system(5)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(10)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	48	all_epithelial(7;0.000132)|all_lung(7;0.00106)|Lung SC(450;0.184)	all_cancers(81;3.03e-08)|all_epithelial(167;3.24e-08)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		GTTGGGAATGTTTTTTCTGAA	0.348			T	RET	papillary thyroid																																p.H1014fs		Atlas-INDEL	.		Dom	yes		1	1p13	51592	""" tripartite motif-containing 33 (PTC7,TIF1G)"""		E	.,1	TRIM33	115	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.3040delC						.						144.0	155.0	152.0					1																	114942160		2203	4300	6503	SO:0001589	frameshift_variant	51592	exon18			.	AF220136	CCDS872.1, CCDS873.1	1p13.1	2014-02-17	2011-01-25		ENSG00000197323	ENSG00000197323		"""Tripartite motif containing / Tripartite motif containing"", ""Zinc fingers, PHD-type"", ""RING-type (C3HC4) zinc fingers"""	16290	protein-coding gene	gene with protein product	"""transcriptional intermediary factor 1 gamma"", ""ret-fused gene 7"""	605769	"""tripartite motif-containing 33"""			11331580, 10022127	Standard	XM_005270936		Approved	TIF1GAMMA, FLJ11429, KIAA1113, TIFGAMMA, RFG7, TF1G, TIF1G, PTC7	uc001eew.3	Q9UPN9	OTTHUMG00000011891	ENST00000358465.2:c.3039delA	chr1.hg19:g.114942160delT	ENSP00000351250:p.Lys1013fs	207.0	0.0		188.0	13.0	NM_033020	O95855|Q5TG72|Q5TG73|Q5TG74|Q9C017|Q9UJ79	Frame_Shift_Del	DEL	ENST00000358465.2	hg19	CCDS872.1																																																																																			.	.		0.348	TRIM33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032854.1	NM_015906	
NOBOX	135935	hgsc.bcm.edu	37	7	144096920	144096920	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:144096920delT	ENST00000467773.1	-	6	1083	c.1084delA	c.(1084-1086)atgfs	p.M362fs	NOBOX_ENST00000223140.5_Frame_Shift_Del_p.M245fs|NOBOX_ENST00000483238.1_Frame_Shift_Del_p.M330fs	NM_001080413.3	NP_001073882.3	O60393	NOBOX_HUMAN	NOBOX oogenesis homeobox	362					oogenesis (GO:0048477)|ovarian follicle development (GO:0001541)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)|prostate(1)	26	Melanoma(164;0.14)					AGTTTCTCCATTTTTCGCCAC	0.532																																					p.M362fs		Atlas-INDEL	.											.	NOBOX	130	.	0			c.1085delT						.						97.0	100.0	99.0					7																	144096920		1954	4153	6107	SO:0001589	frameshift_variant	135935	exon6			.			7q35	2011-06-20			ENSG00000106410	ENSG00000106410		"""Homeoboxes / PRD class"""	22448	protein-coding gene	gene with protein product	"""newborn ovary homeobox-encoding gene"""	610934				11804785, 16597639	Standard	NM_001080413		Approved	OG2, Og2x	uc022aoj.1	O60393	OTTHUMG00000158051	ENST00000467773.1:c.1084delA	chr7.hg19:g.144096920delT	ENSP00000419457:p.Met362fs	168.0	0.0		161.0	12.0	NM_001080413	A6NCD3|A8MZN5	Frame_Shift_Del	DEL	ENST00000467773.1	hg19																																																																																				.	.		0.532	NOBOX-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000350095.1	XM_001134420	
TMEM244	253582	hgsc.bcm.edu	37	6	130166960	130166960	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:130166960delA	ENST00000368143.1	-	2	153	c.71delT	c.(70-72)ttcfs	p.F24fs	TMEM244_ENST00000438392.1_Frame_Shift_Del_p.F24fs	NM_001010876.1	NP_001010876.1	Q5VVB8	TM244_HUMAN	transmembrane protein 244	24						integral component of membrane (GO:0016021)											CACAGTGTAGAAAAGAATGAC	0.398																																					p.F24fs		Atlas-INDEL	.											.	.	.	.	0			c.72delC						.						113.0	103.0	106.0					6																	130166960		2203	4300	6503	SO:0001589	frameshift_variant	253582	exon2			.		CCDS34536.1	6q22.33	2012-02-21	2012-02-21	2012-02-21	ENSG00000203756	ENSG00000203756			21571	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 191"""	C6orf191			Standard	NM_001010876		Approved	bA174C7.4	uc003qbs.3	Q5VVB8	OTTHUMG00000015553	ENST00000368143.1:c.71delT	chr6.hg19:g.130166960delA	ENSP00000357125:p.Phe24fs	122.0	0.0		151.0	10.0	NM_001010876		Frame_Shift_Del	DEL	ENST00000368143.1	hg19	CCDS34536.1																																																																																			.	.		0.398	TMEM244-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042194.1	NM_001010876	
POU5F1	5460	hgsc.bcm.edu	37	6	31138149	31138149	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:31138149delC	ENST00000259915.8	-	1	321	c.249delG	c.(247-249)gggfs	p.G83fs	POU5F1_ENST00000441888.3_Intron	NM_002701.4	NP_002692.2	Q01860	PO5F1_HUMAN	POU class 5 homeobox 1	83					anatomical structure morphogenesis (GO:0009653)|blastocyst development (GO:0001824)|BMP signaling pathway involved in heart induction (GO:0003130)|cardiac cell fate determination (GO:0060913)|cell fate commitment involved in formation of primary germ layer (GO:0060795)|endodermal cell fate specification (GO:0001714)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|negative regulation of gene silencing by miRNA (GO:0060965)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of asymmetric cell division (GO:0009786)|regulation of gene expression (GO:0010468)|regulation of heart induction by regulation of canonical Wnt signaling pathway (GO:0090081)|regulation of methylation-dependent chromatin silencing (GO:0090308)|regulation of transcription, DNA-templated (GO:0006355)|response to wounding (GO:0009611)|somatic stem cell maintenance (GO:0035019)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|miRNA binding (GO:0035198)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)		EWSR1/POU5F1(10)	breast(1)|large_intestine(2)|lung(3)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	13					Dopamine(DB00988)|Norepinephrine(DB00368)	GGGGCACTAGCCCCACTCCAA	0.687			T	EWSR1	sarcoma																																p.L84X		Atlas-INDEL	.		Dom	yes		6	6p21.31	5460	"""POU domain, class 5, transcription factor 1"""		M	.	POU5F1	25	.	0			c.250delC						.						31.0	31.0	31.0					6																	31138149		1510	2708	4218	SO:0001589	frameshift_variant	5460	exon1			.	Z11898	CCDS34391.1, CCDS47398.1, CCDS47398.2, CCDS75420.1	6p21.33	2011-06-20	2007-07-13		ENSG00000204531	ENSG00000204531		"""Homeoboxes / POU class"""	9221	protein-coding gene	gene with protein product		164177	"""POU domain class 5, transcription factor 1"""	OTF3		1408763	Standard	NM_002701		Approved	OCT3, Oct4, MGC22487	uc003nsv.3	Q01860	OTTHUMG00000031206	ENST00000259915.8:c.249delG	chr6.hg19:g.31138149delC	ENSP00000259915:p.Gly83fs	78.0	0.0		200.0	13.0	NM_002701	A6NCS1|A6NLL8|D2IYK4|P31359|Q15167|Q15168|Q16422|Q5STF3|Q5STF4	Frame_Shift_Del	DEL	ENST00000259915.8	hg19	CCDS34391.1																																																																																			.	.		0.687	POU5F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076413.4	NM_002701	
TRPV3	162514	hgsc.bcm.edu	37	17	3424284	3424284	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:3424284delA	ENST00000576742.1	-	14	2114	c.1793delT	c.(1792-1794)ttgfs	p.L599fs	TRPV3_ENST00000301365.4_Frame_Shift_Del_p.L599fs|TRPV3_ENST00000572519.1_Frame_Shift_Del_p.L599fs	NM_001258205.1|NM_145068.3	NP_001245134.1|NP_659505.1	Q8NET8	TRPV3_HUMAN	transient receptor potential cation channel, subfamily V, member 3	599					calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|negative regulation of hair cycle (GO:0042636)|positive regulation of calcium ion import (GO:0090280)|response to heat (GO:0009408)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium channel activity (GO:0005262)			breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(12)|ovary(5)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	35					Menthol(DB00825)	AAATCCAAGCAAAAACACGAT	0.333																																					p.L598fs		Atlas-INDEL	.											.	TRPV3	85	.	0			c.1794delG						.						85.0	78.0	81.0					17																	3424284		2201	4300	6501	SO:0001589	frameshift_variant	162514	exon14			.	AF514998	CCDS11029.1, CCDS58500.1	17p13.3	2013-01-10			ENSG00000167723	ENSG00000167723		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	18084	protein-coding gene	gene with protein product		607066				12016205, 12077606, 16382100	Standard	NM_001258205		Approved	VRL3	uc002fvr.3	Q8NET8	OTTHUMG00000090695	ENST00000576742.1:c.1793delT	chr17.hg19:g.3424284delA	ENSP00000461518:p.Leu599fs	160.0	0.0		178.0	12.0	NM_001258205	Q8NDW7|Q8NET9|Q8NFH2	Frame_Shift_Del	DEL	ENST00000576742.1	hg19	CCDS11029.1																																																																																			.	.		0.333	TRPV3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000207379.2	NM_145068	
DCLRE1C	64421	hgsc.bcm.edu	37	10	14950883	14950883	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:14950883delG	ENST00000378278.2	-	14	1640	c.1603delC	c.(1603-1605)cagfs	p.Q535fs	DCLRE1C_ENST00000357717.2_Frame_Shift_Del_p.Q420fs|DCLRE1C_ENST00000378289.4_Intron|DCLRE1C_ENST00000378255.1_Frame_Shift_Del_p.Q415fs|DCLRE1C_ENST00000453695.2_Frame_Shift_Del_p.Q415fs|DCLRE1C_ENST00000492201.1_5'UTR|DCLRE1C_ENST00000378242.1_Frame_Shift_Del_p.Q188fs|DCLRE1C_ENST00000378246.2_Frame_Shift_Del_p.Q420fs|DCLRE1C_ENST00000378258.1_Frame_Shift_Del_p.Q415fs|DCLRE1C_ENST00000378249.1_Frame_Shift_Del_p.Q420fs|DCLRE1C_ENST00000396817.2_Frame_Shift_Del_p.Q415fs|DCLRE1C_ENST00000378254.1_Frame_Shift_Del_p.Q415fs			Q96SD1	DCR1C_HUMAN	DNA cross-link repair 1C	535					B cell differentiation (GO:0030183)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA recombination (GO:0006310)|double-strand break repair (GO:0006302)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|response to ionizing radiation (GO:0010212)|telomere maintenance (GO:0000723)	nucleus (GO:0005634)	5'-3' exonuclease activity (GO:0008409)|single-stranded DNA endodeoxyribonuclease activity (GO:0000014)			breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)	17						GAAGAATTCTGGGAGGAGATG	0.463								Non-homologous end-joining																													p.Q535fs		Atlas-INDEL	.											.	DCLRE1C	136	.	0			c.1604delA						.						75.0	73.0	74.0					10																	14950883		2203	4300	6503	SO:0001589	frameshift_variant	64421	exon14			.	BC022254	CCDS7105.1, CCDS31149.1, CCDS31150.1	10p13	2014-09-17	2010-06-24		ENSG00000152457	ENSG00000152457			17642	protein-coding gene	gene with protein product	"""PSO2 homolog (S. cerevisiae)"""	605988	"""severe combined immunodeficiency, type a (Athabascan)"", ""DNA cross-link repair 1C (PSO2 homolog, S. cerevisiae)"""	SCIDA		11336668, 9443881	Standard	XM_005252558		Approved	ARTEMIS, FLJ11360, SNM1C, A-SCID	uc001inn.3	Q96SD1	OTTHUMG00000017716	ENST00000378278.2:c.1603delC	chr10.hg19:g.14950883delG	ENSP00000367527:p.Gln535fs	101.0	0.0		132.0	12.0	NM_001033855	D3DRT6|Q1HCL2|Q5JSR4|Q5JSR5|Q5JSR7|Q5JSR8|Q5JSR9|Q5JSS0|Q5JSS7|Q6PK14|Q8N101|Q8N132|Q8TBW9|Q9BVW9|Q9HAM4	Frame_Shift_Del	DEL	ENST00000378278.2	hg19	CCDS31149.1																																																																																			.	.		0.463	DCLRE1C-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046934.1	NM_022487	
NLGN2	57555	hgsc.bcm.edu	37	17	7319293	7319293	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:7319293delG	ENST00000302926.2	+	6	1574	c.1501delG	c.(1501-1503)gggfs	p.G501fs	NLGN2_ENST00000575301.1_Frame_Shift_Del_p.G501fs	NM_020795.2	NP_065846.1	Q8NFZ4	NLGN2_HUMAN	neuroligin 2	501					cell-cell junction maintenance (GO:0045217)|gephyrin clustering (GO:0097116)|locomotory exploration behavior (GO:0035641)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|protein localization to synapse (GO:0035418)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|regulation of synaptic transmission (GO:0050804)|sensory perception of pain (GO:0019233)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)|synapse organization (GO:0050808)|terminal button organization (GO:0072553)	cell junction (GO:0030054)|cell surface (GO:0009986)|inhibitory synapse (GO:0060077)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|neurexin family protein binding (GO:0042043)|receptor activity (GO:0004872)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(7)|prostate(2)|skin(3)	22		Prostate(122;0.157)				TGCGGCGCACGGGGATGAACT	0.607																																					p.H500fs		Atlas-INDEL	.											.	NLGN2	61	.	0			c.1500delC						.						77.0	61.0	66.0					17																	7319293		2203	4300	6503	SO:0001589	frameshift_variant	57555	exon6			.	AB037787	CCDS11103.1	17p13.2	2008-07-18			ENSG00000169992	ENSG00000169992			14290	protein-coding gene	gene with protein product		606479				10767552, 10819331	Standard	NM_020795		Approved	KIAA1366	uc002ggt.1	Q8NFZ4	OTTHUMG00000108138	ENST00000302926.2:c.1501delG	chr17.hg19:g.7319293delG	ENSP00000305288:p.Gly501fs	172.0	0.0		154.0	10.0	NM_020795	Q9P2I1	Frame_Shift_Del	DEL	ENST00000302926.2	hg19	CCDS11103.1																																																																																			.	.		0.607	NLGN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226941.2	NM_020795	
C3orf35	339883	hgsc.bcm.edu	37	3	37476531	37476531	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:37476531delA	ENST00000328376.5	+	6	1402	c.423delA	c.(421-423)acafs	p.T141fs	C3orf35_ENST00000481400.1_3'UTR	NM_178339.2	NP_848029.2	Q8IVJ8	APRG1_HUMAN	chromosome 3 open reading frame 35	141						integral component of membrane (GO:0016021)				NS(1)|central_nervous_system(1)|endometrium(3)|large_intestine(1)|lung(2)|ovary(1)|pancreas(1)|urinary_tract(1)	11						CCTGGAAAACAAAATTAGGAG	0.537																																					p.T141fs		Atlas-INDEL	.											.	C3orf35	21	.	0			c.422delC						.						47.0	51.0	50.0					3																	37476531		1915	4122	6037	SO:0001589	frameshift_variant	339883	exon6			.	AJ493599	CCDS43065.1, CCDS46792.1	3p22.3	2014-05-22			ENSG00000198590	ENSG00000198590			24082	protein-coding gene	gene with protein product	"""AP20 region protein"", ""APRG1 tumor suppressor candidate"""	611429				12543795	Standard	NM_178342		Approved	APRG1	uc003cha.4	Q8IVJ8	OTTHUMG00000155923	ENST00000328376.5:c.423delA	chr3.hg19:g.37476531delA	ENSP00000331625:p.Thr141fs	95.0	0.0		138.0	10.0	NM_178339	B7ZMA0|Q8IVJ5|Q8IVJ9	Frame_Shift_Del	DEL	ENST00000328376.5	hg19	CCDS43065.1																																																																																			.	.		0.537	C3orf35-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000342344.2	NM_178338	
C4orf47	441054	hgsc.bcm.edu	37	4	186353241	186353241	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:186353241delT	ENST00000378850.4	+	2	228	c.206delT	c.(205-207)attfs	p.I69fs		NM_001114357.1	NP_001107829.1	A7E2U8	CD047_HUMAN	chromosome 4 open reading frame 47	69										breast(2)|endometrium(1)	3						TTTGTAAGGATTTTTGAAGGT	0.403																																					p.I69fs		Atlas-INDEL	.											.	C4orf47	13	.	0			c.205delA						.						111.0	99.0	103.0					4																	186353241		692	1591	2283	SO:0001589	frameshift_variant	441054	exon2			.	AY947525, BC127739, BC141967	CCDS47169.1	4q35.1	2008-07-18			ENSG00000205129	ENSG00000205129			34346	protein-coding gene	gene with protein product						12477932	Standard	NM_001114357		Approved	LOC441054	uc003ixt.2	A7E2U8	OTTHUMG00000160458	ENST00000378850.4:c.206delT	chr4.hg19:g.186353241delT	ENSP00000368127:p.Ile69fs	175.0	0.0		162.0	11.0	NM_001114357	Q5BLP7	Frame_Shift_Del	DEL	ENST00000378850.4	hg19	CCDS47169.1																																																																																			.	.		0.403	C4orf47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360667.1	NM_001114357	
DNAH14	127602	hgsc.bcm.edu	37	1	225328686	225328686	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:225328686delA	ENST00000445597.2	+	17	3268	c.3268delA	c.(3268-3270)aaafs	p.K1090fs	DNAH14_ENST00000439375.2_Frame_Shift_Del_p.K1474fs|DNAH14_ENST00000430092.1_Frame_Shift_Del_p.K1474fs			Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy chain 14	1090					microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(2)|breast(3)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(2)|lung(2)|skin(2)|stomach(1)	27						TTTACTACTTAAAAATATCTT	0.333																																					p.L1473fs		Atlas-INDEL	.											.	DNAH14	300	.	0			c.4419delT						.						54.0	51.0	52.0					1																	225328686		692	1591	2283	SO:0001589	frameshift_variant	127602	exon27			.	U61741	CCDS41472.1, CCDS44322.1	1q42.13	2009-02-12	2006-09-04		ENSG00000185842	ENSG00000185842		"""Axonemal dyneins"""	2945	protein-coding gene	gene with protein product		603341	"""dynein, axonemal, heavy polypeptide 14"", ""chromosome 1 open reading frame 67"""	C1orf67		8812413	Standard	NM_144989		Approved	Dnahc14, HL-18, HL18, DKFZp781B1548, MGC27277	uc001how.2	Q0VDD8	OTTHUMG00000037447	ENST00000445597.2:c.3268delA	chr1.hg19:g.225328686delA	ENSP00000409472:p.Lys1090fs	89.0	0.0		154.0	10.0	NM_001373	A6NG62|A6NNL2|Q0VDD9|Q4VXC7|Q4VXG4|Q4VXG5|Q5VU33|Q5VU34	Frame_Shift_Del	DEL	ENST00000445597.2	hg19																																																																																				.	.		0.333	DNAH14-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000331217.3	XM_059166	
HERC2	8924	hgsc.bcm.edu	37	15	28366565	28366565	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:28366565delA	ENST00000261609.7	-	86	13307	c.13199delT	c.(13198-13200)ttcfs	p.F4400fs		NM_004667.5	NP_004658.3			HECT and RLD domain containing E3 ubiquitin protein ligase 2											NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(3)|cervix(3)|endometrium(20)|kidney(11)|large_intestine(33)|lung(95)|ovary(7)|prostate(8)|skin(7)|upper_aerodigestive_tract(8)|urinary_tract(4)	204		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)		TACTTTCCGGAAAGCCGCCTC	0.438																																					p.F4400fs		Atlas-INDEL	.											.	HERC2	501	.	0			c.13200delC						.						110.0	105.0	106.0					15																	28366565		2203	4300	6503	SO:0001589	frameshift_variant	8924	exon86			.	AF071172	CCDS10021.1	15q13	2012-02-23	2012-02-23		ENSG00000128731	ENSG00000128731			4868	protein-coding gene	gene with protein product		605837	"""hect domain and RLD 2"""			9949213	Standard	NM_004667		Approved	jdf2, p528, D15F37S1	uc001zbj.4	O95714	OTTHUMG00000129251	ENST00000261609.7:c.13199delT	chr15.hg19:g.28366565delA	ENSP00000261609:p.Phe4400fs	132.0	0.0		162.0	10.0	NM_004667		Frame_Shift_Del	DEL	ENST00000261609.7	hg19	CCDS10021.1																																																																																			.	.		0.438	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667	
GPR158	57512	hgsc.bcm.edu	37	10	25887118	25887118	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:25887118delA	ENST00000376351.3	+	11	2922	c.2563delA	c.(2563-2565)aaafs	p.K856fs	GPR158_ENST00000490549.1_3'UTR	NM_020752.2	NP_065803.2	Q5T848	GP158_HUMAN	G protein-coupled receptor 158	856					protein localization to plasma membrane (GO:0072659)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(5)|cervix(1)|endometrium(9)|kidney(10)|large_intestine(20)|lung(56)|ovary(4)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	119						CCTGTCGGGTAAAAAACTAAC	0.507																																					p.G854fs		Atlas-INDEL	.											.	GPR158	255	.	0			c.2562delT						.						82.0	92.0	88.0					10																	25887118		2203	4300	6503	SO:0001589	frameshift_variant	57512	exon11			.	AB032962	CCDS31166.1	10p12.31	2012-08-21			ENSG00000151025	ENSG00000151025		"""GPCR / Class C : Orphans"""	23689	protein-coding gene	gene with protein product		614573					Standard	NM_020752		Approved	KIAA1136	uc001isj.3	Q5T848	OTTHUMG00000017832	ENST00000376351.3:c.2563delA	chr10.hg19:g.25887118delA	ENSP00000365529:p.Lys856fs	93.0	0.0		148.0	11.0	NM_020752	Q6QR81|Q9ULT3	Frame_Shift_Del	DEL	ENST00000376351.3	hg19	CCDS31166.1																																																																																			.	.		0.507	GPR158-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047248.2	XM_166110	
NOBOX	135935	hgsc.bcm.edu	37	7	144096122	144096122	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:144096122delG	ENST00000467773.1	-	8	1389	c.1390delC	c.(1390-1392)caafs	p.Q464fs	NOBOX_ENST00000223140.5_Frame_Shift_Del_p.Q347fs|NOBOX_ENST00000483238.1_Frame_Shift_Del_p.Q432fs	NM_001080413.3	NP_001073882.3	O60393	NOBOX_HUMAN	NOBOX oogenesis homeobox	464	Pro-rich.				oogenesis (GO:0048477)|ovarian follicle development (GO:0001541)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)|prostate(1)	26	Melanoma(164;0.14)					GGCATCAGTTGGGGGGTGTGG	0.637																																					p.Q464fs		Atlas-INDEL	.											.	NOBOX	130	.	0			c.1391delA						.						10.0	11.0	10.0					7																	144096122		1905	4132	6037	SO:0001589	frameshift_variant	135935	exon8			.			7q35	2011-06-20			ENSG00000106410	ENSG00000106410		"""Homeoboxes / PRD class"""	22448	protein-coding gene	gene with protein product	"""newborn ovary homeobox-encoding gene"""	610934				11804785, 16597639	Standard	NM_001080413		Approved	OG2, Og2x	uc022aoj.1	O60393	OTTHUMG00000158051	ENST00000467773.1:c.1390delC	chr7.hg19:g.144096122delG	ENSP00000419457:p.Gln464fs	223.0	0.0		193.0	13.0	NM_001080413	A6NCD3|A8MZN5	Frame_Shift_Del	DEL	ENST00000467773.1	hg19																																																																																				.	.		0.637	NOBOX-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000350095.1	XM_001134420	
ZFPM2	23414	hgsc.bcm.edu	37	8	106573666	106573666	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr8:106573666delG	ENST00000407775.2	+	4	627	c.377delG	c.(376-378)tggfs	p.W126fs	ZFPM2_ENST00000520492.1_5'UTR|ZFPM2_ENST00000517361.1_5'UTR	NM_012082.3	NP_036214.2	Q8WW38	FOG2_HUMAN	zinc finger protein, FOG family member 2	126					blood coagulation (GO:0007596)|embryonic organ development (GO:0048568)|gonadal mesoderm development (GO:0007506)|in utero embryonic development (GO:0001701)|lung development (GO:0030324)|negative regulation of cell death (GO:0060548)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of female gonad development (GO:2000195)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract septum morphogenesis (GO:0003148)|positive regulation of male gonad development (GO:2000020)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|right ventricular cardiac muscle tissue morphogenesis (GO:0003221)|vasculogenesis (GO:0001570)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|nucleic acid binding transcription factor activity (GO:0001071)|RNA polymerase II transcription coactivator activity (GO:0001105)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.W126L(1)		NS(4)|breast(6)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(11)|liver(2)|lung(48)|ovary(4)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	99			OV - Ovarian serous cystadenocarcinoma(57;8.28e-08)			GGAACAACCTGGGGGCCGTTT	0.433																																					p.W126fs		Atlas-INDEL	.											.	ZFPM2	219	.	1	Substitution - Missense(1)	lung(1)	c.376delT						.						56.0	57.0	57.0					8																	106573666		1844	4080	5924	SO:0001589	frameshift_variant	23414	exon4			.	AF119334	CCDS47908.1	8q23	2013-01-10	2012-11-27		ENSG00000169946	ENSG00000169946		"""Zinc fingers, C2H2-type"", ""Zinc fingers, C2HC-type containing"""	16700	protein-coding gene	gene with protein product		603693	"""zinc finger protein, multitype 2"""			9927675, 10438528	Standard	NM_012082		Approved	FOG2, hFOG-2, ZNF89B, ZC2HC11B	uc003ymd.3	Q8WW38	OTTHUMG00000164818	ENST00000407775.2:c.377delG	chr8.hg19:g.106573666delG	ENSP00000384179:p.Trp126fs	49.0	0.0		155.0	11.0	NM_012082	Q32MA6|Q9NPL7|Q9NPS4|Q9UNI5	Frame_Shift_Del	DEL	ENST00000407775.2	hg19	CCDS47908.1																																																																																			.	.		0.433	ZFPM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380614.1		
FSIP1	161835	hgsc.bcm.edu	37	15	39910069	39910069	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:39910069delA	ENST00000350221.3	-	11	1775	c.1566delT	c.(1564-1566)tttfs	p.F522fs		NM_152597.4	NP_689810.3	Q8NA03	FSIP1_HUMAN	fibrous sheath interacting protein 1	522										NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(4)|ovary(2)|skin(4)|stomach(2)|urinary_tract(1)	23		all_cancers(109;2.66e-19)|all_epithelial(112;2.66e-16)|Lung NSC(122;1.5e-11)|all_lung(180;4.03e-10)|Melanoma(134;0.0575)|Ovarian(310;0.0827)|Colorectal(260;0.119)		GBM - Glioblastoma multiforme(113;8.22e-06)|BRCA - Breast invasive adenocarcinoma(123;0.142)		TCTTCGACATAAAATAGTCTT	0.408																																					p.M523fs		Atlas-INDEL	.											.	FSIP1	53	.	0			c.1567delA						.						106.0	100.0	102.0					15																	39910069		2200	4297	6497	SO:0001589	frameshift_variant	161835	exon11			.	BC045191	CCDS10050.1	15q14	2012-11-19			ENSG00000150667	ENSG00000150667			21674	protein-coding gene	gene with protein product		615795				14702039	Standard	NM_152597		Approved	FLJ35989	uc001zki.3	Q8NA03	OTTHUMG00000172456	ENST00000350221.3:c.1566delT	chr15.hg19:g.39910069delA	ENSP00000280236:p.Phe522fs	122.0	0.0		198.0	13.0	NM_152597	Q6X2C8|Q86Y89	Frame_Shift_Del	DEL	ENST00000350221.3	hg19	CCDS10050.1																																																																																			.	.		0.408	FSIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252118.2	NM_152597	
ANKRD20A4	728747	hgsc.bcm.edu	37	9	69386012	69386012	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:69386012delA	ENST00000357336.3	+	3	730	c.449delA	c.(448-450)gaafs	p.E150fs		NM_001098805.1	NP_001092275.1	Q4UJ75	A20A4_HUMAN	ankyrin repeat domain 20 family, member A4	150										breast(1)|large_intestine(1)|liver(1)|lung(9)|pancreas(2)|skin(2)	16						TCACTGGCAGAAAAACTGCTT	0.418																																					p.E150fs		Atlas-INDEL	.											.	ANKRD20A4	38	.	0			c.448delG						.						1.0	1.0	1.0					9																	69386012		77	175	252	SO:0001589	frameshift_variant	728747	exon3			.		CCDS43828.1	9q21.11	2013-01-10			ENSG00000172014	ENSG00000172014		"""Ankyrin repeat domain containing"""	31982	protein-coding gene	gene with protein product							Standard	NM_001098805		Approved	OTTHUMG00000066855	uc004afn.3	Q4UJ75	OTTHUMG00000066855	ENST00000357336.3:c.449delA	chr9.hg19:g.69386012delA	ENSP00000349891:p.Glu150fs	99.0	0.0		91.0	11.0	NM_001098805		Frame_Shift_Del	DEL	ENST00000357336.3	hg19	CCDS43828.1																																																																																			.	.		0.418	ANKRD20A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143287.3	NM_001098805	
CNGB1	1258	hgsc.bcm.edu	37	16	57953155	57953155	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:57953155delG	ENST00000251102.8	-	20	1865	c.1805delC	c.(1804-1806)ccafs	p.P602fs	CNGB1_ENST00000564448.1_Frame_Shift_Del_p.P596fs	NM_001297.4	NP_001288.3	Q14028	CNGB1_HUMAN	cyclic nucleotide gated channel beta 1	602					cation transport (GO:0006812)|cytosolic calcium ion homeostasis (GO:0051480)|detection of light stimulus involved in visual perception (GO:0050908)|phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|protein heterotetramerization (GO:0051290)|regulation of membrane potential (GO:0042391)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina homeostasis (GO:0001895)|rhodopsin mediated signaling pathway (GO:0016056)|sensory perception of smell (GO:0007608)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|intracellular cyclic nucleotide activated cation channel complex (GO:0017071)|plasma membrane (GO:0005886)|terminal bouton (GO:0043195)|transmembrane transporter complex (GO:1902495)	cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|ligand-gated ion channel activity (GO:0015276)|voltage-gated potassium channel activity (GO:0005249)			breast(7)|cervix(2)|endometrium(4)|kidney(2)|large_intestine(11)|liver(1)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	54						TTTCTTGGCTGGGGCTGTGGG	0.567																																					p.P602fs	Colon(156;1293 1853 16336 28962 38659)	Atlas-INDEL	.											.	CNGB1	105	.	0			c.1806delA						.						70.0	73.0	72.0					16																	57953155		1953	4166	6119	SO:0001589	frameshift_variant	1258	exon20			.	AF042498	CCDS42169.1, CCDS45495.1, CCDS67042.1	16q13	2013-02-14			ENSG00000070729	ENSG00000070729		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	2151	protein-coding gene	gene with protein product	"""glutamic acid-rich protein"""	600724		CNCG2, CNCG3L		8766832, 7590744, 16382102	Standard	NM_001297		Approved	RCNC2, RCNCb, GARP, GAR1, CNGB1B, RP45	uc002emt.2	Q14028	OTTHUMG00000154810	ENST00000251102.8:c.1805delC	chr16.hg19:g.57953155delG	ENSP00000251102:p.Pro602fs	200.0	0.0		228.0	14.0	NM_001297	H3BN09|O43636|Q13059|Q14029|Q9UMG2	Frame_Shift_Del	DEL	ENST00000251102.8	hg19	CCDS42169.1																																																																																			.	.		0.567	CNGB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337167.2	NM_001297	
NPHP3	27031	hgsc.bcm.edu	37	3	132438560	132438560	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:132438560delT	ENST00000337331.5	-	2	594	c.508delA	c.(508-510)aggfs	p.R170fs	NPHP3-AS1_ENST00000504440.1_RNA|NPHP3_ENST00000343113.4_Frame_Shift_Del_p.R170fs|NPHP3_ENST00000326682.8_Frame_Shift_Del_p.R170fs|NPHP3_ENST00000476742.1_5'Flank|NPHP3-AS1_ENST00000489343.1_RNA	NM_153240.4	NP_694972.3	Q7Z494	NPHP3_HUMAN	nephronophthisis 3 (adolescent)	170					atrial septum development (GO:0003283)|cilium morphogenesis (GO:0060271)|convergent extension involved in gastrulation (GO:0060027)|determination of intestine left/right asymmetry (GO:0071908)|determination of left/right symmetry (GO:0007368)|determination of liver left/right asymmetry (GO:0071910)|determination of pancreatic left/right asymmetry (GO:0035469)|determination of stomach left/right asymmetry (GO:0071909)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|establishment or maintenance of cell polarity (GO:0007163)|extracellular matrix organization (GO:0030198)|heart looping (GO:0001947)|kidney development (GO:0001822)|kidney morphogenesis (GO:0060993)|lipid metabolic process (GO:0006629)|lung development (GO:0030324)|maintenance of organ identity (GO:0048496)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|photoreceptor cell maintenance (GO:0045494)|regulation of cAMP metabolic process (GO:0030814)|regulation of planar cell polarity pathway involved in neural tube closure (GO:2000167)|regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000095)|ureter development (GO:0072189)|Wnt signaling pathway (GO:0016055)	cilium (GO:0005929)|primary cilium (GO:0072372)				NS(1)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(5)|lung(15)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						TTGAATTGCCTTTTAACTTTA	0.303																																					p.R170fs		Atlas-INDEL	.											.	NPHP3	110	.	0			c.509delG						.						156.0	152.0	154.0					3																	132438560		2202	4300	6502	SO:0001589	frameshift_variant	27031	exon2			.	AB056657	CCDS3078.1	3q22	2014-07-18			ENSG00000113971	ENSG00000113971		"""Tetratricopeptide (TTC) repeat domain containing"""	7907	protein-coding gene	gene with protein product	"""nephrocystin-3"", ""Meckel syndrome, type 7"", ""cilia and flagella associated protein 31"""	608002				12872122, 15381417	Standard	NM_153240		Approved	NPH3, KIAA2000, FLJ30691, FLJ36696, MKS7, SLSN3, CFAP31	uc003epe.2	Q7Z494	OTTHUMG00000159713	ENST00000337331.5:c.508delA	chr3.hg19:g.132438560delT	ENSP00000338766:p.Arg170fs	122.0	0.0		152.0	11.0	NM_153240	Q5JPE3|Q5JPE6|Q68D99|Q6NVH3|Q7Z492|Q7Z493|Q8N9R2|Q8NCM5|Q96N70|Q96NK2	Frame_Shift_Del	DEL	ENST00000337331.5	hg19	CCDS3078.1																																																																																			.	.		0.303	NPHP3-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357020.2	NM_153240	
HLTF	6596	hgsc.bcm.edu	37	3	148778638	148778638	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:148778638delT	ENST00000310053.5	-	11	1361	c.1168delA	c.(1168-1170)actfs	p.T390fs	HLTF_ENST00000392912.2_Frame_Shift_Del_p.T390fs|HLTF_ENST00000465259.1_Frame_Shift_Del_p.T390fs|HLTF_ENST00000494055.1_Frame_Shift_Del_p.T390fs	NM_003071.3|NM_139048.2	NP_003062.2|NP_620636.1	Q14527	HLTF_HUMAN	helicase-like transcription factor	390					chromatin modification (GO:0016568)|protein ubiquitination (GO:0016567)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(18)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	47			LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)			TGGACAGCAGTTTTTCTTCTA	0.289																																					p.T390fs		Atlas-INDEL	.											.	HLTF	87	.	0			c.1169delC						.						54.0	52.0	53.0					3																	148778638		2202	4292	6494	SO:0001589	frameshift_variant	6596	exon11			.	L34673	CCDS33875.1	3q25.1-q26.1	2006-11-09	2006-11-09	2006-11-09	ENSG00000071794	ENSG00000071794		"""RING-type (C3HC4) zinc fingers"""	11099	protein-coding gene	gene with protein product		603257	"""SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 3"""	SNF2L3, SMARCA3		7558014	Standard	NM_139048		Approved	HIP116A, HLTF1, RNF80	uc003ewr.1	Q14527	OTTHUMG00000159534	ENST00000310053.5:c.1168delA	chr3.hg19:g.148778638delT	ENSP00000308944:p.Thr390fs	120.0	0.0		143.0	10.0	NM_139048	D3DNH3|Q14536|Q16051|Q7KYJ6|Q86YA5|Q92652|Q96KM9	Frame_Shift_Del	DEL	ENST00000310053.5	hg19	CCDS33875.1																																																																																			.	.		0.289	HLTF-003	KNOWN	alternative_3_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356064.1		
SLC44A5	204962	hgsc.bcm.edu	37	1	75684228	75684228	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:75684228delT	ENST00000370855.5	-	17	1589	c.1476delA	c.(1474-1476)aaafs	p.K492fs	SLC44A5_ENST00000370859.3_Frame_Shift_Del_p.K492fs|SLC44A5_ENST00000535611.1_Frame_Shift_Del_p.K362fs	NM_152697.4	NP_689910.2	Q8NCS7	CTL5_HUMAN	solute carrier family 44, member 5	492					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				kidney(1)|large_intestine(13)|lung(35)|ovary(2)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	61						TGTCATCAGGTTTTTTCATGG	0.418																																					p.P493fs		Atlas-INDEL	.											.	SLC44A5	231	.	0			c.1477delC						.						174.0	162.0	166.0					1																	75684228		2203	4300	6503	SO:0001589	frameshift_variant	204962	exon17			.	BC034580	CCDS667.1, CCDS44164.1	1p31.1	2013-05-22			ENSG00000137968	ENSG00000137968		"""Solute carriers"""	28524	protein-coding gene	gene with protein product						15715662	Standard	NM_152697		Approved	MGC34032, CTL5	uc001dgu.3	Q8NCS7	OTTHUMG00000009721	ENST00000370855.5:c.1476delA	chr1.hg19:g.75684228delT	ENSP00000359892:p.Lys492fs	113.0	0.0		136.0	10.0	NM_152697	B5MCU3|Q4G0K0|Q8NA44|Q8NB86	Frame_Shift_Del	DEL	ENST00000370855.5	hg19	CCDS667.1																																																																																			.	.		0.418	SLC44A5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026921.1	NM_152697	
MYOCD	93649	hgsc.bcm.edu	37	17	12666622	12666622	+	Frame_Shift_Del	DEL	A	A	-	rs369384824	byFrequency	TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:12666622delA	ENST00000343344.4	+	13	2478	c.2478delA	c.(2476-2478)ctafs	p.L826fs	RP11-1090M7.1_ENST00000584772.1_RNA|MYOCD_ENST00000425538.1_Frame_Shift_Del_p.L874fs			Q8IZQ8	MYCD_HUMAN	myocardin	826					cardiac muscle cell differentiation (GO:0055007)|cardiac ventricle development (GO:0003231)|cardiocyte differentiation (GO:0035051)|cell growth involved in cardiac muscle cell development (GO:0061049)|cellular component maintenance (GO:0043954)|cellular response to growth factor stimulus (GO:0071363)|cellular response to hypoxia (GO:0071456)|digestive tract development (GO:0048565)|ductus arteriosus closure (GO:0097070)|hepatic stellate cell activation (GO:0035733)|lung alveolus development (GO:0048286)|negative regulation of beta-amyloid clearance (GO:1900222)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of skeletal muscle cell differentiation (GO:2001015)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cardiac muscle cell differentiation (GO:2000727)|positive regulation of cardiac vascular smooth muscle cell differentiation (GO:2000724)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA binding (GO:0043388)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle cell differentiation (GO:0051152)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003257)|positive regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation (GO:2000721)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of cell growth by extracellular stimulus (GO:0001560)|regulation of histone acetylation (GO:0035065)|regulation of myoblast differentiation (GO:0045661)|regulation of smooth muscle cell differentiation (GO:0051150)|response to hypoxia (GO:0001666)|smooth muscle cell differentiation (GO:0051145)|urinary bladder development (GO:0060157)|uterus development (GO:0060065)|vasculogenesis (GO:0001570)|ventricular cardiac muscle cell differentiation (GO:0055012)	nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|protein domain specific binding (GO:0019904)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(11)|liver(2)|lung(33)|ovary(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	70				UCEC - Uterine corpus endometrioid carcinoma (92;0.0969)		TCACCCTTCTAAAAATTGGGA	0.478																																					p.L874fs		Atlas-INDEL	.											.	MYOCD	291	.	0			c.2621delT						.						73.0	71.0	71.0					17																	12666622		2203	4300	6503	SO:0001589	frameshift_variant	93649	exon14			.	AF532596	CCDS11163.1, CCDS54091.1	17p11.2	2004-03-01			ENSG00000141052	ENSG00000141052			16067	protein-coding gene	gene with protein product		606127				11439182, 12397177	Standard	XM_005256863		Approved	MYCD	uc002gno.2	Q8IZQ8	OTTHUMG00000058767	ENST00000343344.4:c.2478delA	chr17.hg19:g.12666622delA	ENSP00000341835:p.Leu826fs	170.0	0.0		179.0	11.0	NM_001146312	Q5UBU5|Q8N7Q1	Frame_Shift_Del	DEL	ENST00000343344.4	hg19	CCDS11163.1																																																																																			.	.		0.478	MYOCD-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129950.1	NM_153604	
DNAH6	1768	hgsc.bcm.edu	37	2	84913642	84913642	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:84913642delT	ENST00000237449.6	+	43	7106	c.7098delT	c.(7096-7098)tatfs	p.Y2366fs	DNAH6_ENST00000602588.1_Frame_Shift_Del_p.Y338fs|DNAH6_ENST00000389394.3_Frame_Shift_Del_p.Y2366fs|DNAH6_ENST00000398278.2_Frame_Shift_Del_p.Y2317fs			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	2366					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(9)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	57						ACCTGGAATATTTTTTGAATA	0.259																																					p.Y2366fs		Atlas-INDEL	.											.	DNAH6	194	.	0			c.7097delA						.						101.0	85.0	90.0					2																	84913642		692	1587	2279	SO:0001589	frameshift_variant	1768	exon44			.	U61736	CCDS46348.1	2p11.2	2011-05-24	2006-09-04		ENSG00000115423	ENSG00000115423		"""Axonemal dyneins"""	2951	protein-coding gene	gene with protein product		603336	"""dynein, axonemal, heavy polypeptide 6"", ""dynein heavy chain-like 1"""	DNHL1		8812413	Standard	NM_001370		Approved	Dnahc6, HL-2, FLJ37357	uc010fgb.3	Q9C0G6	OTTHUMG00000128957	ENST00000237449.6:c.7098delT	chr2.hg19:g.84913642delT	ENSP00000237449:p.Tyr2366fs	251.0	0.0		254.0	16.0	NM_001370	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Frame_Shift_Del	DEL	ENST00000237449.6	hg19	CCDS46348.1																																																																																			.	.		0.259	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370	
CLEC4F	165530	hgsc.bcm.edu	37	2	71043906	71043906	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:71043906delT	ENST00000272367.2	-	4	683	c.607delA	c.(607-609)agcfs	p.S204fs	CLEC4F_ENST00000426626.1_Frame_Shift_Del_p.S204fs	NM_001258027.1|NM_173535.2	NP_001244956.1|NP_775806.2	Q8N1N0	CLC4F_HUMAN	C-type lectin domain family 4, member F	204					endocytosis (GO:0006897)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			endometrium(1)|large_intestine(5)|lung(18)|ovary(5)|prostate(5)|skin(1)|upper_aerodigestive_tract(2)	37						TCTAAACTGCTTTTTAAGAAA	0.443																																					p.S203fs	Colon(107;10 2157 6841 26035)	Atlas-INDEL	.											.	CLEC4F	95	.	0			c.608delG						.						98.0	94.0	96.0					2																	71043906		2203	4300	6503	SO:0001589	frameshift_variant	165530	exon4			.	AK096429	CCDS1910.1	2p13.3	2008-02-05	2005-02-09	2005-02-11	ENSG00000152672	ENSG00000152672		"""C-type lectin domain containing"""	25357	protein-coding gene	gene with protein product			"""C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 13"""	CLECSF13		8889548, 1846367	Standard	NM_001258027		Approved	FLJ39110, KCLR	uc002shf.3	Q8N1N0	OTTHUMG00000129713	ENST00000272367.2:c.607delA	chr2.hg19:g.71043906delT	ENSP00000272367:p.Ser204fs	149.0	0.0		172.0	11.0	NM_001258027	A4QPA5	Frame_Shift_Del	DEL	ENST00000272367.2	hg19	CCDS1910.1																																																																																			.	.		0.443	CLEC4F-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251922.1	NM_173535	
FOXD4L1	200350	hgsc.bcm.edu	37	2	114257385	114257385	+	Frame_Shift_Del	DEL	C	C	-	rs369834731		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:114257385delC	ENST00000306507.5	+	1	725	c.552delC	c.(550-552)gacfs	p.D184fs		NM_012184.4	NP_036316.1	Q9NU39	FX4L1_HUMAN	forkhead box D4-like 1	184					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(10)|prostate(1)|skin(2)	26						GGAGCCTGGACCCCGCCTCCC	0.652																																					p.D184fs		Atlas-INDEL	.											.	FOXD4L1	48	.	0			c.551delA						.						49.0	65.0	59.0					2																	114257385		2114	4099	6213	SO:0001589	frameshift_variant	200350	exon1			.	AF452723	CCDS2117.1	2q14.1	2008-02-05			ENSG00000184492	ENSG00000184492			18521	protein-coding gene	gene with protein product		611084				12421752, 15233989	Standard	NM_012184		Approved	FOXD5	uc002tjw.4	Q9NU39	OTTHUMG00000131359	ENST00000306507.5:c.552delC	chr2.hg19:g.114257385delC	ENSP00000302756:p.Asp184fs	125.0	0.0		181.0	11.0	NM_012184	B3KWN1|B9EGF3	Frame_Shift_Del	DEL	ENST00000306507.5	hg19	CCDS2117.1																																																																																			.	.		0.652	FOXD4L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254148.1	NM_012184	
ADRBK1	156	hgsc.bcm.edu	37	11	67048975	67048975	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:67048975delG	ENST00000308595.5	+	9	983	c.693delG	c.(691-693)cagfs	p.Q231fs	ADRBK1_ENST00000526285.1_Frame_Shift_Del_p.Q231fs	NM_001619.3	NP_001610.2	P25098	ARBK1_HUMAN	adrenergic, beta, receptor kinase 1	231	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of phospholipase C activity (GO:0007202)|cardiac muscle contraction (GO:0060048)|desensitization of G-protein coupled receptor protein signaling pathway (GO:0002029)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|heart development (GO:0007507)|innate immune response (GO:0045087)|negative regulation of striated muscle contraction (GO:0045988)|negative regulation of the force of heart contraction by chemical signal (GO:0003108)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of catecholamine secretion (GO:0033605)|receptor internalization (GO:0031623)|signal transduction (GO:0007165)|tachykinin receptor signaling pathway (GO:0007217)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	alpha-2A adrenergic receptor binding (GO:0031694)|ATP binding (GO:0005524)|beta-adrenergic receptor kinase activity (GO:0047696)|Edg-2 lysophosphatidic acid receptor binding (GO:0031755)|G-protein coupled receptor kinase activity (GO:0004703)|protein kinase activity (GO:0004672)			cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(2)|liver(2)|lung(8)|prostate(2)	22			BRCA - Breast invasive adenocarcinoma(15;2.26e-06)		Adenosine triphosphate(DB00171)	AGATGAAGCAGGGGGAGACCC	0.657																																					p.Q231fs		Atlas-INDEL	.											.	ADRBK1	51	.	0			c.692delA						.						79.0	71.0	74.0					11																	67048975		2200	4295	6495	SO:0001589	frameshift_variant	156	exon9			.	X61157	CCDS8156.1	11q13	2013-01-10			ENSG00000173020	ENSG00000173020		"""Pleckstrin homology (PH) domain containing"""	289	protein-coding gene	gene with protein product		109635				2037065	Standard	NM_001619		Approved	GRK2, BARK1	uc009yrn.1	P25098	OTTHUMG00000167104	ENST00000308595.5:c.693delG	chr11.hg19:g.67048975delG	ENSP00000312262:p.Gln231fs	91.0	0.0		154.0	10.0	NM_001619	B0ZBE1|Q13837|Q6GTT3	Frame_Shift_Del	DEL	ENST00000308595.5	hg19	CCDS8156.1																																																																																			.	.		0.657	ADRBK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393153.1	NM_001619	
ATRX	546	hgsc.bcm.edu	37	X	76938413	76938413	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:76938413delT	ENST00000373344.5	-	9	2549	c.2335delA	c.(2335-2337)aggfs	p.R779fs	ATRX_ENST00000395603.3_Frame_Shift_Del_p.R741fs|ATRX_ENST00000480283.1_5'UTR	NM_000489.3	NP_000480.3	P46100	ATRX_HUMAN	alpha thalassemia/mental retardation syndrome X-linked	779					ATP catabolic process (GO:0006200)|cellular response to hydroxyurea (GO:0072711)|chromatin remodeling (GO:0006338)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA duplex unwinding (GO:0032508)|DNA methylation (GO:0006306)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication-independent nucleosome assembly (GO:0006336)|forebrain development (GO:0030900)|negative regulation of telomeric RNA transcription from RNA pol II promoter (GO:1901581)|nucleosome assembly (GO:0006334)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of telomere maintenance (GO:0032206)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|replication fork processing (GO:0031297)|seminiferous tubule development (GO:0072520)|Sertoli cell development (GO:0060009)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nuclear heterochromatin (GO:0005720)|nucleolus (GO:0005730)|nucleus (GO:0005634)|SWI/SNF superfamily-type complex (GO:0070603)|telomeric heterochromatin (GO:0031933)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA translocase activity (GO:0015616)|helicase activity (GO:0004386)|histone binding (GO:0042393)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)	p.?(1)		bone(1)|breast(6)|central_nervous_system(31)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(15)|kidney(14)|large_intestine(1)|liver(1)|lung(40)|ovary(2)|pancreas(13)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	145						TTTCGTTTCCTTTTTCCTTTA	0.338			"""Mis, F, N"""		"""Pancreatic neuroendocrine tumors, paediatric GBM"""		ATR-X (alpha thalassemia/mental retardation) syndrome																														p.R779fs		Atlas-INDEL	.		Rec	yes		X	Xq21.1	546	alpha thalassemia/mental retardation syndrome X-linked	yes	E	.	ATRX	833	.	1	Unknown(1)	bone(1)	c.2336delG						.						133.0	139.0	137.0					X																	76938413		2203	4295	6498	SO:0001589	frameshift_variant	546	exon9			.	U72937	CCDS14434.1, CCDS14435.1	Xq21.1	2014-06-17	2010-06-24		ENSG00000085224	ENSG00000085224			886	protein-coding gene	gene with protein product	"""RAD54 homolog (S. cerevisiae)"""	300032	"""alpha thalassemia/mental retardation syndrome X-linked (RAD54 (S. cerevisiae) homolog)"", ""Juberg-Marsidi syndrome"""	RAD54, JMS		7874112, 1415255, 8503439, 8630485	Standard	NM_000489		Approved	XH2, XNP	uc004ecp.4	P46100	OTTHUMG00000022686	ENST00000373344.5:c.2335delA	chrX.hg19:g.76938413delT	ENSP00000362441:p.Arg779fs	134.0	0.0		197.0	12.0	NM_000489	D3DTE2|P51068|Q15886|Q59FB5|Q59H31|Q5H9A2|Q5JWI4|Q7Z2J1|Q9H0Z1|Q9NTS3	Frame_Shift_Del	DEL	ENST00000373344.5	hg19	CCDS14434.1																																																																																			.	.		0.338	ATRX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058860.2	NM_000489	
LARP1	23367	hgsc.bcm.edu	37	5	154181822	154181822	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:154181822delG	ENST00000336314.4	+	11	1765	c.1741delG	c.(1741-1743)gggfs	p.G582fs		NM_015315.3	NP_056130.2	Q6PKG0	LARP1_HUMAN	La ribonucleoprotein domain family, member 1	659					cell proliferation (GO:0008283)|positive regulation of macroautophagy (GO:0016239)|positive regulation of translation (GO:0045727)|TOR signaling (GO:0031929)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	eukaryotic initiation factor 4E binding (GO:0008190)|mRNA 3'-UTR binding (GO:0003730)|mRNA 5'-UTR binding (GO:0048027)|poly(A) RNA binding (GO:0044822)|RNA cap binding (GO:0000339)|translation activator activity (GO:0008494)|translation initiation factor binding (GO:0031369)			breast(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(9)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	33	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			CCGGCACCCAGGGGGGGACCG	0.547																																					p.P580fs		Atlas-INDEL	.											.	LARP1	187	.	0			c.1740delA						.						79.0	76.0	77.0					5																	154181822		2203	4300	6503	SO:0001589	frameshift_variant	23367	exon11			.	AB018274	CCDS4328.1	5q33.2	2014-02-12			ENSG00000155506	ENSG00000155506		"""La ribonucleoprotein domain containing"""	29531	protein-coding gene	gene with protein product		612059				9872452, 10878606	Standard	NM_015315		Approved	LARP, KIAA0731, MGC19556	uc003lvo.4	Q6PKG0	OTTHUMG00000130191	ENST00000336314.4:c.1741delG	chr5.hg19:g.154181822delG	ENSP00000336721:p.Gly582fs	119.0	0.0		157.0	16.0	NM_015315	O94836|Q8N4M2|Q8NB73|Q9UFD7	Frame_Shift_Del	DEL	ENST00000336314.4	hg19	CCDS4328.1																																																																																			.	.		0.547	LARP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252509.1	NM_033551	
NCAPG	64151	hgsc.bcm.edu	37	4	17816898	17816898	+	Splice_Site	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:17816898delT	ENST00000251496.2	+	5	868	c.692delT	c.(691-693)gtt>gt	p.V231fs		NM_022346.4	NP_071741.2	Q9BPX3	CND3_HUMAN	non-SMC condensin I complex, subunit G	231					mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|condensin complex (GO:0000796)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(11)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)	27				STAD - Stomach adenocarcinoma(129;0.18)		ATTTTTAAGGTTTTAGCTGAA	0.318																																					p.V231fs		Atlas-INDEL	.											.	NCAPG	76	.	0			c.691delG						.						46.0	48.0	47.0					4																	17816898		2202	4296	6498	SO:0001630	splice_region_variant	64151	exon5			.	AF331796	CCDS3424.1	4p15.32	2014-01-15			ENSG00000109805	ENSG00000109805			24304	protein-coding gene	gene with protein product	"""chromosome condensation protein G"""	606280				10910072, 11136719	Standard	NM_022346		Approved	FLJ12450, hCAP-G, CAP-G, YCG1	uc003gpp.4	Q9BPX3	OTTHUMG00000128539	ENST00000251496.2:c.691-1T>-	chr4.hg19:g.17816898delT		103.0	0.0		111.0	10.0	NM_022346	Q3MJE0|Q96SV9|Q9BUR3|Q9BVY1|Q9H914|Q9H9Z6|Q9HBI9	Frame_Shift_Del	DEL	ENST00000251496.2	hg19	CCDS3424.1																																																																																			.	.		0.318	NCAPG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250375.1	NM_022346	Frame_Shift_Del
CAMK2A	815	hgsc.bcm.edu	37	5	149636381	149636381	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:149636381delC	ENST00000348628.6	-	5	951	c.286delG	c.(286-288)gaafs	p.E96fs	CAMK2A_ENST00000398376.3_Frame_Shift_Del_p.E96fs	NM_015981.3|NM_171825.2	NP_057065.2|NP_741960.1	Q9UQM7	KCC2A_HUMAN	calcium/calmodulin-dependent protein kinase II alpha	96	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				calcium ion transport (GO:0006816)|cytokine-mediated signaling pathway (GO:0019221)|G1/S transition of mitotic cell cycle (GO:0000082)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of neurotransmitter secretion (GO:0046928)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|kinase activity (GO:0016301)|protein homodimerization activity (GO:0042803)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(6)|skin(1)|stomach(1)	15		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TCAAACAGTTCCCCACCAGTG	0.587																																					p.E96fs		Atlas-INDEL	.											.	CAMK2A	42	.	0			c.287delA						.						67.0	70.0	69.0					5																	149636381		2059	4203	6262	SO:0001589	frameshift_variant	815	exon5			.	AB023185	CCDS43386.1, CCDS43387.1	5q32	2013-09-20	2008-10-30		ENSG00000070808	ENSG00000070808	2.7.11.17		1460	protein-coding gene	gene with protein product	"""CaM-kinase II alpha chain"", ""calcium/calmodulin-dependent protein kinase II alpha-B subunit"", ""CaM kinase II alpha subunit"", ""CaMK-II alpha subunit"", ""calcium/calmodulin-dependent protein kinase type II alpha chain"""	114078	"""calcium/calmodulin-dependent protein kinase (CaM kinase) II alpha"""	CAMKA		10231032, 3475713	Standard	NM_015981		Approved	KIAA0968, CaMKIINalpha	uc003lrt.2	Q9UQM7	OTTHUMG00000134281	ENST00000348628.6:c.286delG	chr5.hg19:g.149636381delC	ENSP00000261793:p.Glu96fs	155.0	0.0		177.0	12.0	NM_171825	Q9UL21|Q9Y2H4|Q9Y352	Frame_Shift_Del	DEL	ENST00000348628.6	hg19	CCDS43386.1																																																																																			.	.		0.587	CAMK2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258869.2	NM_015981	
ZNF667	63934	hgsc.bcm.edu	37	19	56953129	56953129	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:56953129delT	ENST00000504904.3	-	7	1954	c.1235delA	c.(1234-1236)aagfs	p.K413fs	ZNF667_ENST00000591790.1_3'UTR|ZNF667_ENST00000342634.3_Frame_Shift_Del_p.K541fs|ZNF667_ENST00000292069.6_Frame_Shift_Del_p.K413fs			Q5HYK9	ZN667_HUMAN	zinc finger protein 667	413					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(18)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)	38		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0615)		AAATAGTTTCTTTTTCTTTGT	0.333																																					p.K412fs		Atlas-INDEL	.											.	ZNF667	95	.	0			c.1236delG						.						54.0	53.0	53.0					19																	56953129		2203	4300	6503	SO:0001589	frameshift_variant	63934	exon5			.		CCDS12944.1	19q13.43	2013-01-08				ENSG00000198046		"""Zinc fingers, C2H2-type"", ""-"""	28854	protein-coding gene	gene with protein product		611024					Standard	NM_022103		Approved	FLJ14011	uc002qnd.3	Q5HYK9		ENST00000504904.3:c.1235delA	chr19.hg19:g.56953129delT	ENSP00000439402:p.Lys413fs	129.0	0.0		145.0	10.0	NM_022103	B2RMS6|B9EK36|Q6B093|Q9H807	Frame_Shift_Del	DEL	ENST00000504904.3	hg19	CCDS12944.1																																																																																			.	.		0.333	ZNF667-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458394.1	NM_022103	
CBLB	868	hgsc.bcm.edu	37	3	105452913	105452913	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:105452913delT	ENST00000264122.4	-	9	1464	c.1143delA	c.(1141-1143)aaafs	p.K381fs	CBLB_ENST00000394027.3_Frame_Shift_Del_p.K403fs|CBLB_ENST00000403724.1_Frame_Shift_Del_p.K381fs|CBLB_ENST00000545639.1_3'UTR|CBLB_ENST00000405772.1_Frame_Shift_Del_p.K381fs	NM_170662.3	NP_733762.2	Q13191	CBLB_HUMAN	Cbl proto-oncogene B, E3 ubiquitin protein ligase	381					cell surface receptor signaling pathway (GO:0007166)|immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|negative regulation of alpha-beta T cell proliferation (GO:0046642)|negative regulation of T cell receptor signaling pathway (GO:0050860)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of T cell anergy (GO:0002669)|signal transduction (GO:0007165)|T cell activation (GO:0042110)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|ligase activity (GO:0016874)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(8)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(3)|stomach(2)|urinary_tract(2)	49						TCTTGACATCTTTGTCATTCT	0.413			Mis S		AML																																p.D382fs	GBM(93;588 1337 9788 29341 43499)	Atlas-INDEL	.		Rec	yes		3	3q13.11	868	Cas-Br-M (murine) ecotropic retroviral transforming sequence b		L	.	CBLB	118	.	0			c.1144delG						.						108.0	101.0	103.0					3																	105452913		2203	4300	6503	SO:0001589	frameshift_variant	868	exon9			.	U26710	CCDS2948.1	3q	2013-07-09	2013-07-09		ENSG00000114423	ENSG00000114423		"""RING-type (C3HC4) zinc fingers"""	1542	protein-coding gene	gene with protein product		604491	"""Cas-Br-M (murine) ectropic retroviral transforming sequence b"", ""Cas-Br-M (murine) ecotropic retroviral transforming sequence b"""			7784085	Standard	XM_005247853		Approved	RNF56, Cbl-b	uc003dwc.3	Q13191	OTTHUMG00000150654	ENST00000264122.4:c.1143delA	chr3.hg19:g.105452913delT	ENSP00000264122:p.Lys381fs	216.0	0.0		250.0	15.0	NM_170662	A8K9S7|B7WNM4|Q13192|Q13193|Q3LIC0|Q63Z43|Q8IVC5	Frame_Shift_Del	DEL	ENST00000264122.4	hg19	CCDS2948.1																																																																																			.	.		0.413	CBLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319417.2	NM_170662	
VPS13C	54832	hgsc.bcm.edu	37	15	62243167	62243167	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:62243167delG	ENST00000261517.5	-	40	4586	c.4513delC	c.(4513-4515)cttfs	p.L1506fs	VPS13C_ENST00000395898.3_Frame_Shift_Del_p.L1463fs|VPS13C_ENST00000395896.4_Frame_Shift_Del_p.L1506fs|VPS13C_ENST00000249837.3_Frame_Shift_Del_p.L1463fs	NM_020821.2	NP_065872.1			vacuolar protein sorting 13 homolog C (S. cerevisiae)											NS(3)|breast(4)|endometrium(4)|kidney(9)|large_intestine(26)|lung(46)|ovary(5)|prostate(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	117						ATTTTCAGAAGGGGTTCGTCA	0.289																																					p.L1505fs		Atlas-INDEL	.											.	VPS13C	506	.	0			c.4514delT						.						46.0	46.0	46.0					15																	62243167		2202	4295	6497	SO:0001589	frameshift_variant	54832	exon40			.	AJ608770	CCDS10180.1, CCDS32257.1, CCDS45272.1, CCDS58367.1	15q21.3	2009-07-09	2006-04-04		ENSG00000129003	ENSG00000129003			23594	protein-coding gene	gene with protein product		608879	"""vacuolar protein sorting 13C (yeast)"""				Standard	NM_018080		Approved	FLJ20136, FLJ10381, KIAA1421	uc002agz.3	Q709C8	OTTHUMG00000132801	ENST00000261517.5:c.4513delC	chr15.hg19:g.62243167delG	ENSP00000261517:p.Leu1506fs	146.0	0.0		250.0	16.0	NM_020821		Frame_Shift_Del	DEL	ENST00000261517.5	hg19	CCDS32257.1																																																																																			.	.		0.289	VPS13C-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415997.1	NM_017684	
SPATA25	128497	hgsc.bcm.edu	37	20	44515612	44515612	+	Frame_Shift_Del	DEL	C	C	-	rs529491989		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr20:44515612delC	ENST00000372519.3	-	2	272	c.228delG	c.(226-228)gggfs	p.G76fs		NM_080608.3	NP_542175.1	Q9BR10	SPT25_HUMAN	spermatogenesis associated 25	76					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											CCCAGCTAGTCCCCCCAGGGC	0.627																																					p.T77fs		Atlas-INDEL	.											.	.	.	.	0			c.229delA						.						98.0	104.0	102.0					20																	44515612		2203	4300	6503	SO:0001589	frameshift_variant	128497	exon2			.	AL008726	CCDS13383.1	20q13.12	2011-11-24	2011-11-24	2011-11-24	ENSG00000149634	ENSG00000149634			16158	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 165"""	C20orf165		19240080	Standard	NM_080608		Approved	dJ337O18.8, TSG23	uc002xqf.3	Q9BR10	OTTHUMG00000032628	ENST00000372519.3:c.228delG	chr20.hg19:g.44515612delC	ENSP00000361597:p.Gly76fs	127.0	0.0		187.0	15.0	NM_080608		Frame_Shift_Del	DEL	ENST00000372519.3	hg19	CCDS13383.1																																																																																			.	.		0.627	SPATA25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079541.1		
MCM3AP	8888	hgsc.bcm.edu	37	21	47700452	47700452	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr21:47700452delA	ENST00000397708.1	-	4	1735	c.1481delT	c.(1480-1482)ttgfs	p.L494fs	MCM3AP_ENST00000291688.1_Frame_Shift_Del_p.L494fs			O60318	GANP_HUMAN	minichromosome maintenance complex component 3 associated protein	494	DNA primase.				DNA replication (GO:0006260)|immune system process (GO:0002376)|mRNA transport (GO:0051028)|protein import into nucleus (GO:0006606)	cytosol (GO:0005829)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	DNA binding (GO:0003677)|transferase activity, transferring acyl groups (GO:0016746)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(10)|kidney(5)|large_intestine(17)|lung(24)|ovary(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	72	Breast(49;0.112)					GTCTTTATGCAAACTTTTCCC	0.348																																					p.L494fs		Atlas-INDEL	.											.	MCM3AP	146	.	0			c.1482delG						.						74.0	79.0	77.0					21																	47700452		2203	4300	6503	SO:0001589	frameshift_variant	8888	exon3			.	AB005543	CCDS13734.1	21q22.3	2012-12-19	2007-04-04		ENSG00000160294	ENSG00000160294			6946	protein-coding gene	gene with protein product	"""germinal-centre associated nuclear protein"""	603294	"""minichromosome maintenance deficient (S. cerevisiae) 3-associated protein"", ""MCM3 minichromosome maintenance deficient 3 (S. cerevisiae) associated protein"""			9712829, 16914116, 21195085	Standard	XM_005261205		Approved	Map80, KIAA0572, GANP, SAC3	uc002zir.1	O60318	OTTHUMG00000090630	ENST00000397708.1:c.1481delT	chr21.hg19:g.47700452delA	ENSP00000380820:p.Leu494fs	228.0	0.0		261.0	16.0	NM_003906	C9JL56|Q2M3C1|Q6PJP6|Q9BSY5|Q9UMT4	Frame_Shift_Del	DEL	ENST00000397708.1	hg19	CCDS13734.1																																																																																			.	.		0.348	MCM3AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207254.1	NM_003906	
IL17RE	132014	hgsc.bcm.edu	37	3	9952818	9952818	+	Frame_Shift_Del	DEL	T	T	-	rs370860056		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:9952818delT	ENST00000383814.3	+	10	1091	c.986delT	c.(985-987)gttfs	p.V329fs	IL17RE_ENST00000295980.3_Frame_Shift_Del_p.V329fs|IL17RE_ENST00000454190.2_Frame_Shift_Del_p.V329fs|IL17RE_ENST00000421412.1_Frame_Shift_Del_p.V362fs	NM_153480.1	NP_705613.1	Q8NFR9	I17RE_HUMAN	interleukin 17 receptor E	329					inflammatory response (GO:0006954)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(11)|skin(1)	21				OV - Ovarian serous cystadenocarcinoma(96;5.34e-64)		CAGTGGTATGTTTTGGAGAAG	0.552																																					p.V369fs		Atlas-INDEL	.											.	IL17RE	62	.	0			c.1105delG						.						153.0	150.0	151.0					3																	9952818		2203	4300	6503	SO:0001589	frameshift_variant	132014	exon11			.	AF458069	CCDS2589.1, CCDS54552.1	3p25.3	2008-02-05			ENSG00000163701	ENSG00000163701		"""Interleukins and interleukin receptors"""	18439	protein-coding gene	gene with protein product		614995					Standard	NM_153480		Approved	FLJ23658	uc003btu.3	Q8NFR9	OTTHUMG00000128649	ENST00000383814.3:c.986delT	chr3.hg19:g.9952818delT	ENSP00000373325:p.Val329fs	158.0	0.0		210.0	13.0	NM_153483	B2RB34|B2RNR1|B9EH65|Q6P532|Q8N8H7|Q8N8H8|Q8TEC2	Frame_Shift_Del	DEL	ENST00000383814.3	hg19	CCDS2589.1																																																																																			.	.		0.552	IL17RE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250529.1	NM_153480	
PPAT	5471	hgsc.bcm.edu	37	4	57267544	57267544	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:57267544delA	ENST00000264220.2	-	7	975	c.838delT	c.(838-840)tgtfs	p.C280fs	PPAT_ENST00000507648.1_5'Flank	NM_002703.4	NP_002694.3	Q06203	PUR1_HUMAN	phosphoribosyl pyrophosphate amidotransferase	280					'de novo' IMP biosynthetic process (GO:0006189)|cellular response to drug (GO:0035690)|cellular response to insulin stimulus (GO:0032869)|G1/S transition of mitotic cell cycle (GO:0000082)|glutamine catabolic process (GO:0006543)|kidney development (GO:0001822)|lactation (GO:0007595)|maternal process involved in female pregnancy (GO:0060135)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleoside metabolic process (GO:0009116)|organ regeneration (GO:0031100)|protein homotetramerization (GO:0051289)|purine nucleobase biosynthetic process (GO:0009113)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide biosynthetic process (GO:0006164)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	4 iron, 4 sulfur cluster binding (GO:0051539)|amidophosphoribosyltransferase activity (GO:0004044)|metal ion binding (GO:0046872)			cervix(1)|endometrium(2)|large_intestine(6)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)	20	Glioma(25;0.08)|all_neural(26;0.101)				Fluorouracil(DB00544)|L-Glutamine(DB00130)|Mercaptopurine(DB01033)	TCAAAGATACAAAAAGCCACT	0.348																																					p.C280fs		Atlas-INDEL	.											.	PPAT	41	.	0			c.839delG						.						184.0	188.0	187.0					4																	57267544		2203	4299	6502	SO:0001589	frameshift_variant	5471	exon7			.		CCDS3505.1	4q12	2012-10-02			ENSG00000128059	ENSG00000128059	2.4.2.14		9238	protein-coding gene	gene with protein product		172450					Standard	NM_002703		Approved	GPAT, PRAT	uc003hbr.3	Q06203	OTTHUMG00000128842	ENST00000264220.2:c.838delT	chr4.hg19:g.57267544delA	ENSP00000264220:p.Cys280fs	190.0	0.0		179.0	11.0	NM_002703		Frame_Shift_Del	DEL	ENST00000264220.2	hg19	CCDS3505.1																																																																																			.	.		0.348	PPAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250781.2	NM_002703	
PCMT1	5110	hgsc.bcm.edu	37	6	150123486	150123486	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:150123486delA	ENST00000367380.5	+	7	862	c.655delA	c.(655-657)aaafs	p.K219fs	PCMT1_ENST00000544496.1_Frame_Shift_Del_p.K184fs|PCMT1_ENST00000367384.2_Frame_Shift_Del_p.K277fs|PCMT1_ENST00000464889.1_Frame_Shift_Del_p.K277fs|PCMT1_ENST00000367378.1_Frame_Shift_Del_p.K277fs	NM_001252049.1|NM_001252050.1|NM_001252051.1|NM_001252052.1|NM_005389.2	NP_001238978.1|NP_001238979.1|NP_001238980.1|NP_001238981.1|NP_005380.2	P22061	PIMT_HUMAN	protein-L-isoaspartate (D-aspartate) O-methyltransferase	219					protein methylation (GO:0006479)|protein repair (GO:0030091)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	protein-L-isoaspartate (D-aspartate) O-methyltransferase activity (GO:0004719)			kidney(1)|large_intestine(2)|lung(4)|ovary(1)	8		Ovarian(120;0.0907)	BRCA - Breast invasive adenocarcinoma(37;0.221)	OV - Ovarian serous cystadenocarcinoma(155;5.63e-13)|GBM - Glioblastoma multiforme(68;0.207)		TTTAACAGATAAAGAAAAGCA	0.433																																					p.D276fs		Atlas-INDEL	.											.	PCMT1	27	.	0			c.828delT						.						111.0	108.0	109.0					6																	150123486		2203	4300	6503	SO:0001589	frameshift_variant	5110	exon7			.		CCDS5219.1, CCDS5219.2, CCDS59041.1, CCDS75533.1, CCDS75534.1	6q22.3-q24	2008-02-05			ENSG00000120265	ENSG00000120265	2.1.1.77		8728	protein-coding gene	gene with protein product		176851				1478665, 10343128	Standard	NM_005389		Approved		uc003qne.3	P22061	OTTHUMG00000015794	ENST00000367380.5:c.655delA	chr6.hg19:g.150123486delA	ENSP00000356350:p.Lys219fs	164.0	0.0		182.0	11.0	NM_005389	A8K109|J3KP72|Q14661|Q16556|Q5VYC1|Q5VYC2|Q93061|Q96II9|Q99625|Q9BQV7|Q9BQV8|Q9NP03	Frame_Shift_Del	DEL	ENST00000367380.5	hg19																																																																																				.	.		0.433	PCMT1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding			
C4A	720	hgsc.bcm.edu	37	6	31964732	31964732	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:31964732delC	ENST00000428956.2	+	29	3887	c.3803delC	c.(3802-3804)gccfs	p.A1268fs	C4A_ENST00000498271.1_Frame_Shift_Del_p.A1268fs	NM_007293.2	NP_009224.2	P0C0L4	CO4A_HUMAN	complement component 4A (Rodgers blood group)	1268					complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of apoptotic cell clearance (GO:2000427)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	complement component C1q binding (GO:0001849)|endopeptidase inhibitor activity (GO:0004866)									Intravenous Immunoglobulin(DB00028)	ACAGCCTACGCCCTGCTGCAC	0.652																																					p.A1268fs		Atlas-INDEL	.											.	C4A	15	.	0			c.3802delG						.						4.0	8.0	7.0					6																	31964732		329	1219	1548	SO:0001589	frameshift_variant	720	exon29			.	L26261, M14823, X77491, AY224378	CCDS47404.1, CCDS59005.1	6p21.3	2014-09-17	2006-01-19		ENSG00000244731	ENSG00000244731		"""Blood group antigens"", ""Complement system"""	1323	protein-coding gene	gene with protein product		120810	"""complement component 4A"""				Standard	NM_001252204		Approved	CPAMD2, C4S, CO4, C4, C4A3, C4A2, C4A4, C4A6, C4B, RG		P0C0L4	OTTHUMG00000031186	ENST00000428956.2:c.3803delC	chr6.hg19:g.31964732delC	ENSP00000396688:p.Ala1268fs	88.0	0.0		150.0	10.0	NM_007293	A6H8M8|A6NHJ5|A7E2V2|B0QZR6|B0V2C8|B2RUT6|B7ZVZ6|P01028|P78445|Q13160|Q13906|Q14033|Q14835|Q4LE82|Q5JNX2|Q5JQM8|Q6P4R1|Q6U2E5|Q6U2E8|Q6U2F0|Q6U2F3|Q6U2F4|Q6U2F6|Q6U2F8|Q6U2G0|Q96EG2|Q96SA8|Q9NPK5|Q9UIP5	Frame_Shift_Del	DEL	ENST00000428956.2	hg19	CCDS47404.1																																																																																			.	.		0.652	C4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076364.3	NM_007293	
SCYL2	55681	hgsc.bcm.edu	37	12	100729661	100729661	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:100729661delG	ENST00000360820.2	+	16	2439	c.2002delG	c.(2002-2004)gggfs	p.G668fs		NM_017988.4	NP_060458.3	Q6P3W7	SCYL2_HUMAN	SCY1-like 2 (S. cerevisiae)	668					endosome to lysosome transport (GO:0008333)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of clathrin-mediated endocytosis (GO:2000370)|positive regulation of receptor internalization (GO:0002092)|receptor internalization involved in canonical Wnt signaling pathway (GO:2000286)	cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(4)|lung(15)|ovary(2)|skin(1)	41						TAAAGAGGACGGGTTACAGAA	0.358																																					p.D667fs		Atlas-INDEL	.											.	SCYL2	99	.	0			c.2001delC						.						81.0	89.0	86.0					12																	100729661		2203	4300	6503	SO:0001589	frameshift_variant	55681	exon16			.	AB037781	CCDS9076.1	12q23.1	2005-01-20				ENSG00000136021			19286	protein-coding gene	gene with protein product						10718198	Standard	NM_017988		Approved	KIAA1360	uc001thn.3	Q6P3W7	OTTHUMG00000170319	ENST00000360820.2:c.2002delG	chr12.hg19:g.100729661delG	ENSP00000354061:p.Gly668fs	98.0	0.0		148.0	10.0	NM_017988	A8KAB5|Q96EF4|Q96ST4|Q9H7V5|Q9NVH3|Q9P2I7	Frame_Shift_Del	DEL	ENST00000360820.2	hg19	CCDS9076.1																																																																																			.	.		0.358	SCYL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408493.2	NM_017988	
KMT2C	58508	hgsc.bcm.edu	37	7	151874093	151874093	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:151874093delT	ENST00000262189.6	-	38	8663	c.8445delA	c.(8443-8445)aaafs	p.K2815fs	KMT2C_ENST00000355193.2_Frame_Shift_Del_p.K2815fs	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	2815					histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)										TAACAGTGGATTTTTTCTGTG	0.323																																					p.S2816fs		Atlas-INDEL	.											.	MLL3	1564	.	0			c.8446delT						.						151.0	145.0	147.0					7																	151874093		2203	4300	6503	SO:0001589	frameshift_variant	58508	exon38			.	AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	13726	protein-coding gene	gene with protein product		606833	"""myeloid/lymphoid or mixed-lineage leukemia 3"""	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.8445delA	chr7.hg19:g.151874093delT	ENSP00000262189:p.Lys2815fs	158.0	0.0		221.0	16.0	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Frame_Shift_Del	DEL	ENST00000262189.6	hg19	CCDS5931.1																																																																																			.	.		0.323	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3		
PROB1	389333	hgsc.bcm.edu	37	5	138727890	138727890	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:138727890delG	ENST00000434752.2	-	1	2995	c.2881delC	c.(2881-2883)ctcfs	p.L961fs	MZB1_ENST00000302125.8_5'Flank|MZB1_ENST00000457570.2_5'Flank|MZB1_ENST00000412103.2_5'Flank	NM_001161546.1	NP_001155018.1	E7EW31	PROB1_HUMAN	proline-rich basic protein 1	961	Pro-rich.																GGGCTGCCGAGGGCCTGCGGG	0.726																																					p.L961fs		Atlas-INDEL	.											.	.	.	.	0			c.2882delT						.						9.0	17.0	15.0					5																	138727890		688	1585	2273	SO:0001589	frameshift_variant	389333	exon1			.	AK316483	CCDS54909.1	5q31.2	2012-10-01	2012-10-01	2012-10-01	ENSG00000228672	ENSG00000228672			41906	protein-coding gene	gene with protein product			"""chromosome 5 open reading frame 65"""	C5orf65			Standard	NM_001161546		Approved		uc011czc.1	E7EW31		ENST00000434752.2:c.2881delC	chr5.hg19:g.138727890delG	ENSP00000416033:p.Leu961fs	55.0	0.0		127.0	10.0	NM_001161546	B4E007	Frame_Shift_Del	DEL	ENST00000434752.2	hg19	CCDS54909.1																																																																																			.	.		0.726	PROB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000470735.1	NM_001161546	
MPG	4350	hgsc.bcm.edu	37	16	129299	129299	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:129299delC	ENST00000219431.4	+	2	239	c.8delC	c.(7-9)accfs	p.T3fs	MPG_ENST00000475280.1_Intron|MPG_ENST00000397817.1_Intron|RHBDF1_ENST00000454039.2_5'Flank	NM_002434.3	NP_002425.2	P29372	3MG_HUMAN	N-methylpurine-DNA glycosylase	3					base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|depurination (GO:0045007)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA repair (GO:0006281)	mitochondrial nucleoid (GO:0042645)|nucleoplasm (GO:0005654)	alkylbase DNA N-glycosylase activity (GO:0003905)|damaged DNA binding (GO:0003684)|DNA-3-methyladenine glycosylase activity (GO:0008725)|DNA-3-methylguanine glycosylase activity (GO:0052822)|DNA-7-methyladenine glycosylase activity (GO:0052821)|DNA-7-methylguanine glycosylase activity (GO:0043916)			endometrium(4)|kidney(1)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	9		all_cancers(16;9.01e-08)|all_epithelial(16;7.64e-07)|Hepatocellular(780;0.000325)|Lung NSC(18;0.0104)|all_lung(18;0.0239)				aggatggtcacccccgctttg	0.552								Base excision repair (BER), DNA glycosylases																													p.T3fs		Atlas-INDEL	.											.,1	MPG	26	.	0			c.7delA						.						112.0	95.0	101.0					16																	129299		2193	4294	6487	SO:0001589	frameshift_variant	4350	exon2			.		CCDS32345.1, CCDS32346.1, CCDS42087.1	16p13.3	2008-07-29			ENSG00000103152	ENSG00000103152	3.2.2.21		7211	protein-coding gene	gene with protein product	"""alkyladenine DNA glycosylase"""	156565				1874728	Standard	NM_002434		Approved	MDG	uc002cfo.4	P29372	OTTHUMG00000047887	ENST00000219431.4:c.8delC	chr16.hg19:g.129299delC	ENSP00000219431:p.Thr3fs	159.0	0.0		177.0	11.0	NM_002434	G5E9E2|Q13770|Q15275|Q15961|Q5J9I4|Q96BZ6|Q96S33|Q9NNX5	Frame_Shift_Del	DEL	ENST00000219431.4	hg19	CCDS32346.1																																																																																			.	.		0.552	MPG-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109121.4		
TPPP2	122664	hgsc.bcm.edu	37	14	21498757	21498757	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:21498757delA	ENST00000321760.6	+	2	165	c.17delA	c.(16-18)gaafs	p.E6fs	AL161668.5_ENST00000533984.1_lincRNA|RP11-998D10.1_ENST00000531638.1_5'Flank|NDRG2_ENST00000403829.3_Intron|TPPP2_ENST00000460647.2_Frame_Shift_Del_p.E6fs|TPPP2_ENST00000530140.2_Frame_Shift_Del_p.E6fs	NM_173846.4	NP_776245.2	P59282	TPPP2_HUMAN	tubulin polymerization-promoting protein family member 2	6						cytoplasm (GO:0005737)				endometrium(1)|large_intestine(2)|lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	9	all_cancers(95;0.000759)		OV - Ovarian serous cystadenocarcinoma(11;6.85e-11)|Epithelial(56;9.49e-09)|all cancers(55;3.84e-08)	GBM - Glioblastoma multiforme(265;0.0191)		TCAGAGGCAGAAAAAACATTC	0.522																																					p.E6fs		Atlas-INDEL	.											.,1	TPPP2	22	.	0			c.16delG						.						78.0	55.0	63.0					14																	21498757		2203	4300	6503	SO:0001589	frameshift_variant	122664	exon2			.	AY072034	CCDS9566.1	14q11.2	2014-01-21	2007-05-02	2007-05-02	ENSG00000179636	ENSG00000179636			19293	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 8"""	C14orf8		15590652, 17105200	Standard	NM_173846		Approved	p25beta, p18, CT152	uc001vzh.3	P59282	OTTHUMG00000029642	ENST00000321760.6:c.17delA	chr14.hg19:g.21498757delA	ENSP00000317595:p.Glu6fs	172.0	0.0		181.0	11.0	NM_173846	Q2VYF3	Frame_Shift_Del	DEL	ENST00000321760.6	hg19	CCDS9566.1																																																																																			.	.		0.522	TPPP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073914.3	NM_173846	
RYR1	6261	hgsc.bcm.edu	37	19	39008261	39008261	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:39008261delG	ENST00000359596.3	+	66	9948	c.9948delG	c.(9946-9948)ctgfs	p.L3316fs	RYR1_ENST00000360985.3_Frame_Shift_Del_p.L3316fs|RYR1_ENST00000355481.4_Frame_Shift_Del_p.L3316fs			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	3316					calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	ACTCCCTGCTGGGGAATATCC	0.682																																					p.L3316fs		Atlas-INDEL	.											.	RYR1	708	.	0			c.9947delT						.						48.0	47.0	47.0					19																	39008261		2203	4300	6503	SO:0001589	frameshift_variant	6261	exon66			.	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"""Ion channels / Ryanodine receptors"""	10483	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 137"""	180901	"""central core disease of muscle"""	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.9948delG	chr19.hg19:g.39008261delG	ENSP00000352608:p.Leu3316fs	155.0	0.0		234.0	16.0	NM_001042723	Q16314|Q16368|Q9NPK1|Q9P1U4	Frame_Shift_Del	DEL	ENST00000359596.3	hg19	CCDS33011.1																																																																																			.	.		0.682	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1		
FAT3	120114	hgsc.bcm.edu	37	11	92533028	92533028	+	Frame_Shift_Del	DEL	C	C	-	rs370953208		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:92533028delC	ENST00000298047.6	+	9	6866	c.6849delC	c.(6847-6849)aacfs	p.N2283fs	FAT3_ENST00000525166.1_Frame_Shift_Del_p.N2133fs|FAT3_ENST00000409404.2_Frame_Shift_Del_p.N2283fs			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	2283	Cadherin 20. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				TAAATGACAACCCCCCTATTT	0.428										TCGA Ovarian(4;0.039)																											p.N2283fs		Atlas-INDEL	.											.	FAT3	1822	.	0			c.6848delA						.						99.0	89.0	92.0					11																	92533028		1917	4130	6047	SO:0001589	frameshift_variant	120114	exon9			.	AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"""Cadherins / Cadherin-related"""	23112	protein-coding gene	gene with protein product	"""cadherin-related family member 10"""	612483	"""FAT tumor suppressor homolog 3 (Drosophila)"""			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.6849delC	chr11.hg19:g.92533028delC	ENSP00000298047:p.Asn2283fs	86.0	0.0		120.0	10.0	NM_001008781	B5MDB0|Q96AU6	Frame_Shift_Del	DEL	ENST00000298047.6	hg19																																																																																				.	.		0.428	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781	
PDE1C	5137	hgsc.bcm.edu	37	7	31793035	31793035	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:31793035delT	ENST00000396191.1	-	18	2548	c.2093delA	c.(2092-2094)aagfs	p.K698fs	PDE1C_ENST00000321453.7_Frame_Shift_Del_p.K698fs|PDE1C_ENST00000396193.1_Frame_Shift_Del_p.K758fs	NM_001191057.1	NP_001177986.1	Q14123	PDE1C_HUMAN	phosphodiesterase 1C, calmodulin-dependent 70kDa	698					activation of phospholipase C activity (GO:0007202)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)	cytosol (GO:0005829)	calmodulin-dependent cyclic-nucleotide phosphodiesterase activity (GO:0004117)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(38)|prostate(4)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	81			GBM - Glioblastoma multiforme(11;0.216)		Caffeine(DB00201)	GTTCTGAATCTTTTTCATTTT	0.468																																					p.K758fs		Atlas-INDEL	.											.	PDE1C	465	.	0			c.2274delG						.						390.0	385.0	387.0					7																	31793035		876	1991	2867	SO:0001589	frameshift_variant	5137	exon19			.	U40371	CCDS5437.1, CCDS55099.1, CCDS55100.1	7p15.1-p14.3	2008-05-15	2002-08-29		ENSG00000154678	ENSG00000154678	3.1.4.17	"""Phosphodiesterases"""	8776	protein-coding gene	gene with protein product		602987	"""phosphodiesterase 1C, calmodulin-dependent (70kD)"""			8557689	Standard	XM_005249769		Approved	Hcam3	uc003tco.2	Q14123	OTTHUMG00000023836	ENST00000396191.1:c.2093delA	chr7.hg19:g.31793035delT	ENSP00000379494:p.Lys698fs	181.0	0.0		189.0	13.0	NM_001191058	B3KPC6|E9PE92|Q14124|Q8NB10	Frame_Shift_Del	DEL	ENST00000396191.1	hg19	CCDS55099.1																																																																																			.	.		0.468	PDE1C-006	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000328458.1		
TUBB3	10381	hgsc.bcm.edu	37	16	90001894	90001894	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:90001894delC	ENST00000315491.7	+	4	1158	c.1035delC	c.(1033-1035)atcfs	p.I345fs	TUBB3_ENST00000556922.1_Frame_Shift_Del_p.I692fs|TUBB3_ENST00000555576.1_Intron|TUBB3_ENST00000554444.1_Frame_Shift_Del_p.I273fs|TUBB3_ENST00000304984.5_Frame_Shift_Del_p.I273fs	NM_006086.3	NP_006077.2	Q13509	TBB3_HUMAN	tubulin, beta 3 class III	345					'de novo' posttranslational protein folding (GO:0051084)|axon guidance (GO:0007411)|cellular protein metabolic process (GO:0044267)|microtubule-based process (GO:0007017)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|ovary(3)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(1)	17		all_cancers(9;1.69e-11)|Lung NSC(15;8.94e-06)|all_lung(18;1.39e-05)|all_neural(9;0.00581)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.0273)	Ixabepilone(DB04845)	TGGAGTGGATCCCCAACAACG	0.617																																					p.I345fs		Atlas-INDEL	.											.	TUBB3	49	.	0			c.1034delT						.						189.0	159.0	169.0					16																	90001894		2198	4300	6498	SO:0001589	frameshift_variant	10381	exon4			.	BC000748	CCDS10988.1, CCDS56012.1	16q24.3	2014-02-04	2011-10-10		ENSG00000198211	ENSG00000198211		"""Tubulins"""	20772	protein-coding gene	gene with protein product	"""class III beta-tubulin"""	602661	"""tubulin, beta 3"", ""fibrosis of extraocular muscles, congenital, 3"""	FEOM3		9473684, 8098743, 20074521	Standard	NM_006086		Approved	beta-4, CFEOM3, CFEOM3A	uc002fph.2	Q13509	OTTHUMG00000138985	ENST00000315491.7:c.1035delC	chr16.hg19:g.90001894delC	ENSP00000320295:p.Ile345fs	125.0	0.0		168.0	12.0	NM_006086	A8K854|Q9BTZ0|Q9BW10	Frame_Shift_Del	DEL	ENST00000315491.7	hg19	CCDS10988.1																																																																																			.	.		0.617	TUBB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272874.1	NM_006086	
TDRD6	221400	hgsc.bcm.edu	37	6	46660975	46660975	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:46660975delA	ENST00000316081.6	+	1	5110	c.5110delA	c.(5110-5112)aaafs	p.K1704fs	TDRD6_ENST00000544460.1_Frame_Shift_Del_p.K1704fs	NM_001010870.2	NP_001010870.1	O60522	TDRD6_HUMAN	tudor domain containing 6	1704					germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|P granule (GO:0043186)				NS(1)|breast(9)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(25)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	80			Lung(136;0.192)			GACTGGTATTAAAAGTGCTCT	0.333																																					p.I1703fs		Atlas-INDEL	.											.	TDRD6	205	.	0			c.5109delT						.						30.0	35.0	33.0					6																	46660975		2172	4283	6455	SO:0001589	frameshift_variant	221400	exon1			.	AF039442	CCDS34470.1, CCDS55017.1	6p12.3	2013-01-23			ENSG00000180113	ENSG00000180113		"""Tudor domain containing"""	21339	protein-coding gene	gene with protein product	"""cancer/testis antigen 41.2"", ""spermatogenesis associated 36"""	611200				9610721	Standard	NM_001010870		Approved	NY-CO-45, bA446F17.4, CT41.2, SPATA36	uc003oyj.3	O60522	OTTHUMG00000014788	ENST00000316081.6:c.5110delA	chr6.hg19:g.46660975delA	ENSP00000346065:p.Lys1704fs	84.0	0.0		164.0	10.0	NM_001168359	B3KWU2|F5H5M3|Q5HYB1|Q5VTS4|Q6ZMX5	Frame_Shift_Del	DEL	ENST00000316081.6	hg19	CCDS34470.1																																																																																			.	.		0.333	TDRD6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040800.1	XM_166443	
FSTL4	23105	hgsc.bcm.edu	37	5	132553042	132553042	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:132553042delT	ENST00000265342.7	-	13	1736	c.1487delA	c.(1486-1488)aatfs	p.N496fs	CTB-49A3.2_ENST00000509051.1_RNA|CTB-49A3.2_ENST00000502776.1_RNA	NM_015082.1	NP_055897.1	Q6MZW2	FSTL4_HUMAN	follistatin-like 4	496						extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(8)|skin(2)|upper_aerodigestive_tract(1)	23		all_cancers(142;0.244)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			CTGGGTTGCATTTTTTTCTCT	0.493																																					p.N496fs		Atlas-INDEL	.											.	FSTL4	74	.	0			c.1488delT						.						87.0	85.0	86.0					5																	132553042		2203	4300	6503	SO:0001589	frameshift_variant	23105	exon13			.	AB028984	CCDS34238.1	5q31.1	2013-01-29			ENSG00000053108	ENSG00000053108		"""EF-hand domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	21389	protein-coding gene	gene with protein product						10470851, 15527507	Standard	NM_015082		Approved	KIAA1061	uc003kyn.1	Q6MZW2	OTTHUMG00000162729	ENST00000265342.7:c.1487delA	chr5.hg19:g.132553042delT	ENSP00000265342:p.Asn496fs	137.0	0.0		180.0	12.0	NM_015082	Q8TBU0|Q9UPU1	Frame_Shift_Del	DEL	ENST00000265342.7	hg19	CCDS34238.1																																																																																			.	.		0.493	FSTL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370212.1	XM_048786	
EFTUD2	9343	hgsc.bcm.edu	37	17	42929803	42929803	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:42929803delA	ENST00000426333.2	-	26	2986	c.2689delT	c.(2689-2691)tctfs	p.S897fs	EFTUD2_ENST00000591382.1_Frame_Shift_Del_p.S897fs|EFTUD2_ENST00000592576.1_Frame_Shift_Del_p.S887fs|EFTUD2_ENST00000402521.3_Frame_Shift_Del_p.S862fs	NM_001142605.1|NM_001258354.1|NM_004247.3	NP_001136077.1|NP_001245283.1|NP_004238.3	Q15029	U5S1_HUMAN	elongation factor Tu GTP binding domain containing 2	897					gene expression (GO:0010467)|GTP catabolic process (GO:0006184)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	Cajal body (GO:0015030)|catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	32		Prostate(33;0.109)				ACAGACAGAGAAAAGGCTTGT	0.557																																					p.S897fs	Ovarian(10;65 485 10258 29980 30707)	Atlas-INDEL	.											.	EFTUD2	85	.	0			c.2690delC						.						76.0	66.0	69.0					17																	42929803		2203	4300	6503	SO:0001589	frameshift_variant	9343	exon26			.	D21163	CCDS11489.1, CCDS45707.1, CCDS59295.1	17q21.31	2014-08-12			ENSG00000108883	ENSG00000108883			30858	protein-coding gene	gene with protein product	"""U5 snRNP specific protein, 116 kD"""	603892				9233818	Standard	NM_004247		Approved	U5-116KD, Snrp116, Snu114, SNRNP116	uc002ihn.2	Q15029	OTTHUMG00000179865	ENST00000426333.2:c.2689delT	chr17.hg19:g.42929803delA	ENSP00000392094:p.Ser897fs	157.0	0.0		156.0	13.0	NM_004247	B4DK30|B4DMC0|D3DX58|K7EJ81|Q9BUR0	Frame_Shift_Del	DEL	ENST00000426333.2	hg19	CCDS11489.1																																																																																			.	.		0.557	EFTUD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448672.1	NM_004247	
DHX34	9704	hgsc.bcm.edu	37	19	47884149	47884149	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:47884149delC	ENST00000328771.4	+	15	3408	c.3059delC	c.(3058-3060)accfs	p.T1020fs		NM_014681.5	NP_055496.2	Q14147	DHX34_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 34	1020					negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process (GO:0000956)	membrane (GO:0016020)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(8)|ovary(5)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36		all_cancers(25;1.65e-09)|all_epithelial(76;9.95e-08)|all_lung(116;7.27e-07)|Lung NSC(112;1.6e-06)|Ovarian(192;0.0139)|all_neural(266;0.026)|Breast(70;0.0503)		all cancers(93;7.16e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000489)|GBM - Glioblastoma multiforme(486;0.00413)|Epithelial(262;0.0132)		ATCCCAGCCACCCCCCATCTT	0.592																																					p.T1020fs		Atlas-INDEL	.											.	DHX34	98	.	0			c.3058delA						.						97.0	93.0	94.0					19																	47884149		2203	4300	6503	SO:0001589	frameshift_variant	9704	exon15			.	D50924	CCDS12700.1	19q13.3	2003-06-13	2003-06-13	2003-06-13	ENSG00000134815	ENSG00000134815		"""DEAH-boxes"""	16719	protein-coding gene	gene with protein product		615475	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 34"""	DDX34		10708517, 8590280	Standard	NM_014681		Approved	KIAA0134	uc010xyn.2	Q14147	OTTHUMG00000149959	ENST00000328771.4:c.3059delC	chr19.hg19:g.47884149delC	ENSP00000331907:p.Thr1020fs	103.0	0.0		158.0	11.0	NM_014681	B4DMY8	Frame_Shift_Del	DEL	ENST00000328771.4	hg19	CCDS12700.1																																																																																			.	.		0.592	DHX34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314313.3	NM_014681	
NEDD9	4739	hgsc.bcm.edu	37	6	11190264	11190264	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:11190264delG	ENST00000379446.5	-	5	2004	c.1838delC	c.(1837-1839)cctfs	p.P613fs	NEDD9_ENST00000504387.1_Frame_Shift_Del_p.P613fs|RP3-510L9.1_ENST00000500636.2_RNA	NM_001271033.1|NM_006403.3	NP_001257962.1|NP_006394.1	Q14511	CASL_HUMAN	neural precursor cell expressed, developmentally down-regulated 9	613					actin filament bundle assembly (GO:0051017)|cell adhesion (GO:0007155)|cytoskeleton organization (GO:0007010)|integrin-mediated signaling pathway (GO:0007229)|mitotic nuclear division (GO:0007067)|regulation of growth (GO:0040008)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|spindle (GO:0005819)|spindle pole (GO:0000922)				endometrium(3)|kidney(2)|large_intestine(8)|liver(1)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26	Breast(50;0.0768)|Ovarian(93;0.152)	all_hematologic(90;0.135)	Epithelial(50;0.0647)|all cancers(50;0.179)			GCTACAGTCAGGGGCCTGCTC	0.577																																					p.P613fs		Atlas-INDEL	.											.	NEDD9	191	.	0			c.1839delT						.						99.0	88.0	92.0					6																	11190264		2203	4300	6503	SO:0001589	frameshift_variant	4739	exon6			.	L43821	CCDS4520.1, CCDS34340.1, CCDS47373.1, CCDS75400.1	6p25-p24	2011-04-13			ENSG00000111859	ENSG00000111859		"""Cas scaffolding proteins"""	7733	protein-coding gene	gene with protein product	"""Cas scaffolding protein family member 2"", ""Cas-like"""	602265					Standard	NM_182966		Approved	HEF1, CAS-L, CASS2	uc003mzv.2	Q14511	OTTHUMG00000014255	ENST00000379446.5:c.1838delC	chr6.hg19:g.11190264delG	ENSP00000368759:p.Pro613fs	112.0	0.0		164.0	13.0	NM_001142393	A8K9G7|A8MSJ9|G5E9Y9|Q5T9R4|Q5XKI0	Frame_Shift_Del	DEL	ENST00000379446.5	hg19	CCDS4520.1																																																																																			.	.		0.577	NEDD9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039853.2	NM_006403	
VCX3B	425054	hgsc.bcm.edu	37	X	8433809	8433809	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:8433809delA	ENST00000381032.1	+	3	433	c.126delA	c.(124-126)ggafs	p.G42fs	VCX3B_ENST00000381029.4_Frame_Shift_Del_p.G42fs|VCX3B_ENST00000440654.2_Frame_Shift_Del_p.G42fs|VCX3B_ENST00000444481.1_Frame_Shift_Del_p.G42fs|VCX3B_ENST00000453306.1_Frame_Shift_Del_p.G42fs	NM_001001888.3	NP_001001888.3	Q9H321	VCX3B_HUMAN	variable charge, X-linked 3B	42						nucleolus (GO:0005730)|nucleus (GO:0005634)				NS(1)|large_intestine(1)|lung(2)|prostate(1)|skin(3)|urinary_tract(3)	11						CCAAGAAGGGAAAAGCAGTTC	0.632																																					p.G42fs		Atlas-INDEL	.											.	VCX3B	34	.	0			c.125delG						.						1.0	1.0	1.0					X																	8433809		146	519	665	SO:0001589	frameshift_variant	425054	exon3			.		CCDS48077.1, CCDS48077.2	Xp22.31	2009-01-14			ENSG00000205642	ENSG00000205642			31838	protein-coding gene	gene with protein product							Standard	NM_001001888		Approved	VCX-C	uc011mht.2	Q9H321	OTTHUMG00000021106	ENST00000381032.1:c.126delA	chrX.hg19:g.8433809delA	ENSP00000370420:p.Gly42fs	135.0	0.0		229.0	15.0	NM_001001888	C9JS46|Q4KN12	Frame_Shift_Del	DEL	ENST00000381032.1	hg19	CCDS48077.2																																																																																			.	.		0.632	VCX3B-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055691.1		
XIRP2	129446	hgsc.bcm.edu	37	2	168105629	168105629	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:168105629delA	ENST00000409195.1	+	9	7816	c.7727delA	c.(7726-7728)caafs	p.Q2576fs	XIRP2_ENST00000409273.1_Frame_Shift_Del_p.Q2354fs|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000295237.9_Frame_Shift_Del_p.Q2576fs	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	2401					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						ACTCAAAGCCAAAATCAACAC	0.338																																					p.Q2576fs		Atlas-INDEL	.											XIRP2,NS,carcinoma,0,1	XIRP2	914	.	0			c.7726delC						.						96.0	90.0	92.0					2																	168105629		1831	4081	5912	SO:0001589	frameshift_variant	129446	exon9			.	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"""myomaxin"""	609778	"""cardiomyopathy associated 3"""	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.7727delA	chr2.hg19:g.168105629delA	ENSP00000386840:p.Gln2576fs	134.0	0.0		182.0	11.0	NM_152381	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Frame_Shift_Del	DEL	ENST00000409195.1	hg19	CCDS42769.1																																																																																			.	.		0.338	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381	
RBM46	166863	hgsc.bcm.edu	37	4	155720193	155720193	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:155720193delA	ENST00000281722.3	+	4	1114	c.879delA	c.(877-879)ggafs	p.G293fs	RBM46_ENST00000510397.1_Frame_Shift_Del_p.G293fs|RBM46_ENST00000514866.1_Frame_Shift_Del_p.G293fs	NM_144979.3	NP_659416.1	Q8TBY0	RBM46_HUMAN	RNA binding motif protein 46	293	RRM 3. {ECO:0000255|PROSITE- ProRule:PRU00176}.						nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(7)|skin(3)|urinary_tract(2)	26	all_hematologic(180;0.24)	Renal(120;0.0854)				TTATGAATGGAAAATGCATTG	0.388																																					p.G293fs		Atlas-INDEL	.											.	RBM46	76	.	0			c.878delG						.						91.0	83.0	86.0					4																	155720193		2203	4300	6503	SO:0001589	frameshift_variant	166863	exon4			.	BC028588	CCDS3790.1, CCDS64085.1, CCDS64086.1	4q32.1	2013-02-12				ENSG00000151962		"""RNA binding motif (RRM) containing"""	28401	protein-coding gene	gene with protein product	"""cancer/testis antigen 68"""					12477932	Standard	NM_144979		Approved	MGC27016, CT68	uc003ioo.4	Q8TBY0		ENST00000281722.3:c.879delA	chr4.hg19:g.155720193delA	ENSP00000281722:p.Gly293fs	149.0	0.0		148.0	10.0	NM_144979	B3KWU8|B4DZ27	Frame_Shift_Del	DEL	ENST00000281722.3	hg19	CCDS3790.1																																																																																			.	.		0.388	RBM46-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365259.1	NM_144979	
TGM6	343641	hgsc.bcm.edu	37	20	2384126	2384126	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr20:2384126delC	ENST00000202625.2	+	8	1134	c.1073delC	c.(1072-1074)accfs	p.T358fs	TGM6_ENST00000381423.1_Frame_Shift_Del_p.T358fs	NM_198994.2	NP_945345.2	O95932	TGM3L_HUMAN	transglutaminase 6	358					cell death (GO:0008219)|peptide cross-linking (GO:0018149)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			breast(1)|endometrium(6)|kidney(2)|large_intestine(2)|lung(32)|ovary(4)|prostate(1)|skin(4)	52					L-Glutamine(DB00130)	CTGGATGCCACCCCCCAGGAG	0.582																																					p.T358fs		Atlas-INDEL	.											.	TGM6	126	.	0			c.1072delA						.						58.0	56.0	57.0					20																	2384126		2203	4300	6503	SO:0001589	frameshift_variant	343641	exon8			.	AF540970	CCDS13025.1, CCDS58761.1	20p13	2010-12-19	2004-07-05	2004-07-07	ENSG00000166948	ENSG00000166948		"""Transglutaminases"""	16255	protein-coding gene	gene with protein product	"""spinocerebellar ataxia 35"""	613900	"""transglutaminase 3-like"""	TGM3L		11390390, 21106500	Standard	NM_198994		Approved	dJ734P14.3, TGY, SCA35	uc002wfy.1	O95932	OTTHUMG00000031692	ENST00000202625.2:c.1073delC	chr20.hg19:g.2384126delC	ENSP00000202625:p.Thr358fs	120.0	0.0		154.0	10.0	NM_198994	Q5JXU4|Q5JXU5|Q719M2|Q719M3|Q9Y4U8	Frame_Shift_Del	DEL	ENST00000202625.2	hg19	CCDS13025.1																																																																																			.	.		0.582	TGM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077581.2	NM_198994	
NTNG2	84628	hgsc.bcm.edu	37	9	135042407	135042407	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:135042407delC	ENST00000393229.3	+	2	965	c.189delC	c.(187-189)gacfs	p.D63fs	NTNG2_ENST00000393228.4_Frame_Shift_Del_p.D63fs|NTNG2_ENST00000372179.3_Frame_Shift_Del_p.D63fs|NTNG2_ENST00000360670.3_Frame_Shift_Del_p.D63fs	NM_032536.2	NP_115925.2	Q96CW9	NTNG2_HUMAN	netrin G2	63	Laminin N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00466}.				axonogenesis (GO:0007409)	anchored component of plasma membrane (GO:0046658)|axon (GO:0030424)				central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(10)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	29				OV - Ovarian serous cystadenocarcinoma(145;1.23e-05)|Epithelial(140;0.000173)		CATGTGGAGACCCCCCTGAGA	0.592																																					p.D63fs		Atlas-INDEL	.											.	NTNG2	66	.	0			c.188delA						.						104.0	109.0	108.0					9																	135042407		2203	4300	6503	SO:0001589	frameshift_variant	84628	exon2			.	AB058760	CCDS6946.1	9q34	2013-03-01	2003-12-02	2003-12-03	ENSG00000196358	ENSG00000196358		"""Netrins"""	14288	protein-coding gene	gene with protein product	"""Netrin-G2"""		"""netrin G1"""	NTNG1			Standard	NM_032536		Approved	KIAA1857, Lmnt2	uc004cbh.2	Q96CW9	OTTHUMG00000020835	ENST00000393229.3:c.189delC	chr9.hg19:g.135042407delC	ENSP00000376921:p.Asp63fs	164.0	0.0		200.0	12.0	NM_032536	Q5JUJ2|Q6UXY0|Q96JH0	Frame_Shift_Del	DEL	ENST00000393229.3	hg19	CCDS6946.1																																																																																			.	.		0.592	NTNG2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054779.1	NM_032536	
FAM120AOS	158293	hgsc.bcm.edu	37	9	96209929	96209929	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:96209929delT	ENST00000375412.5	-	3	1617	c.735delA	c.(733-735)aaafs	p.K245fs	FAM120AOS_ENST00000423591.1_Frame_Shift_Del_p.K63fs|FAM120AOS_ENST00000479094.1_5'UTR	NM_198841.2	NP_942138.2	Q5T036	F120S_HUMAN	family with sequence similarity 120A opposite strand	245										kidney(1)|large_intestine(1)|lung(3)|skin(1)	6						GTGTTGGTGGTTTTGTGGTTT	0.353																																					p.P246fs		Atlas-INDEL	.											FAM120AOS,NS,carcinoma,0,1	FAM120AOS	13	.	0			c.736delC						.						225.0	210.0	215.0					9																	96209929		2203	4300	6503	SO:0001589	frameshift_variant	158293	exon3			.	AK056096	CCDS6705.1	9q22.32	2008-02-05	2006-07-04	2006-07-04	ENSG00000188938	ENSG00000188938			23389	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 10 opposite strand"""	C9orf10OS		14585507	Standard	NM_198841		Approved		uc004atu.4	Q5T036	OTTHUMG00000020251	ENST00000375412.5:c.735delA	chr9.hg19:g.96209929delT	ENSP00000364561:p.Lys245fs	149.0	0.0		156.0	12.0	NM_198841	A6NN20	Frame_Shift_Del	DEL	ENST00000375412.5	hg19	CCDS6705.1																																																																																			.	.		0.353	FAM120AOS-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053154.1		
SPATA31A5	727905	hgsc.bcm.edu	37	9	41506041	41506041	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:41506041delC	ENST00000377621.1	+	4	3342	c.3313delC	c.(3313-3315)cccfs	p.P1106fs	RP11-100J16.5_ENST00000429787.2_RNA	NM_001113541.1	NP_001107013.1	Q5VU36	S31A5_HUMAN	SPATA31 subfamily A, member 5	1106					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											GCCAATGTTTCCCCCTATTCA	0.488																																					p.F1104fs		Atlas-INDEL	.											.	.	.	.	0			c.3312delT						.																																			SO:0001589	frameshift_variant	727905	exon4			.			9p12	2012-10-15	2012-10-12	2012-10-12	ENSG00000233788				32005	protein-coding gene	gene with protein product			"""family with sequence similarity 75, member A5"""	FAM75A5		20850414	Standard	NM_001113541		Approved	OTTHUMG00000013204	uc004abu.4	Q5VU36	OTTHUMG00000013204	ENST00000377621.1:c.3313delC	chr9.hg19:g.41506041delC	ENSP00000366847:p.Pro1106fs	105.0	0.0		175.0	11.0	NM_001113541		Frame_Shift_Del	DEL	ENST00000377621.1	hg19	CCDS47970.1																																																																																			.	.		0.488	SPATA31A5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036962.1	NM_001113541	
CTIF	9811	hgsc.bcm.edu	37	18	46288021	46288021	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr18:46288021delG	ENST00000256413.3	+	9	1627	c.1332delG	c.(1330-1332)gagfs	p.E444fs	CTIF_ENST00000382998.4_Frame_Shift_Del_p.E446fs	NM_014772.2	NP_055587.1	O43310	CTIF_HUMAN	CBP80/20-dependent translation initiation factor	444	MIF4G.				nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of translational initiation (GO:0006446)	cytoplasm (GO:0005737)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)			breast(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(14)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	31						TTATGGTGGAGGGGACCAAGT	0.632																																					p.E446fs		Atlas-INDEL	.											.	CTIF	102	.	0			c.1337delA						.						76.0	74.0	75.0					18																	46288021		2203	4300	6503	SO:0001589	frameshift_variant	9811	exon10			.	AB007887	CCDS11935.1, CCDS45864.1	18q21.1	2011-01-20	2011-01-20	2011-01-20	ENSG00000134030	ENSG00000134030			23925	protein-coding gene	gene with protein product		613178	"""KIAA0427"""	KIAA0427		9455477, 19648179	Standard	NM_014772		Approved		uc002ldd.3	O43310	OTTHUMG00000132656	ENST00000256413.3:c.1332delG	chr18.hg19:g.46288021delG	ENSP00000256413:p.Glu444fs	109.0	0.0		141.0	11.0	NM_001142397	B3KTR8|Q8IVD5	Frame_Shift_Del	DEL	ENST00000256413.3	hg19	CCDS11935.1																																																																																			.	.		0.632	CTIF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255907.1	NM_014772	
FAT1	2195	hgsc.bcm.edu	37	4	187628769	187628769	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:187628769delA	ENST00000441802.2	-	2	2422	c.2213delT	c.(2212-2214)ttcfs	p.F738fs		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	738	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						GGAGTTCATGAAAATTACACT	0.433										HNSCC(5;0.00058)																											p.F738fs	Colon(197;1040 2055 4143 4984 49344)	Atlas-INDEL	.											.	FAT1	500	.	0			c.2214delC						.						70.0	67.0	68.0					4																	187628769		1887	4106	5993	SO:0001589	frameshift_variant	2195	exon2			.	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.2213delT	chr4.hg19:g.187628769delA	ENSP00000406229:p.Phe738fs	123.0	0.0		124.0	10.0	NM_005245		Frame_Shift_Del	DEL	ENST00000441802.2	hg19	CCDS47177.1																																																																																			.	.		0.433	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245	
TNR	7143	hgsc.bcm.edu	37	1	175375844	175375844	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:175375844delC	ENST00000367674.2	-	3	715	c.7delG	c.(7-9)gcafs	p.A3fs	TNR_ENST00000263525.2_Frame_Shift_Del_p.A3fs			Q92752	TENR_HUMAN	tenascin R	3					associative learning (GO:0008306)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|locomotory exploration behavior (GO:0035641)|long-term synaptic potentiation (GO:0060291)|negative regulation of axon extension involved in regeneration (GO:0048692)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of synaptic transmission (GO:0050805)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transmission of nerve impulse (GO:0051971)|synapse organization (GO:0050808)|telencephalon cell migration (GO:0022029)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)				NS(3)|breast(7)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|lung(98)|ovary(4)|pancreas(5)|prostate(4)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	177	Renal(580;0.146)					TCCCCATCTGCCCCCATCCTC	0.532																																					p.A3fs		Atlas-INDEL	.											.	TNR	399	.	0			c.8delC						.						103.0	98.0	100.0					1																	175375844		2203	4300	6503	SO:0001589	frameshift_variant	7143	exon3			.	X98085	CCDS1318.1	1q24	2013-02-11	2012-07-12		ENSG00000116147	ENSG00000116147		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	11953	protein-coding gene	gene with protein product	"""restrictin"", ""janusin"""	601995				8626505, 8940128	Standard	NM_003285		Approved		uc009wwu.1	Q92752	OTTHUMG00000034876	ENST00000367674.2:c.7delG	chr1.hg19:g.175375844delC	ENSP00000356646:p.Ala3fs	97.0	0.0		166.0	10.0	NM_003285	C9J563|Q15568|Q5R3G0	Frame_Shift_Del	DEL	ENST00000367674.2	hg19	CCDS1318.1																																																																																			.	.		0.532	TNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084414.4	NM_003285	
DONSON	29980	hgsc.bcm.edu	37	21	34954281	34954281	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr21:34954281delT	ENST00000303071.5	-	7	1193	c.1127delA	c.(1126-1128)aagfs	p.K376fs	DONSON_ENST00000432378.1_Frame_Shift_Del_p.K376fs|DONSON_ENST00000453626.1_Frame_Shift_Del_p.K376fs|DONSON_ENST00000303113.6_Frame_Shift_Del_p.K362fs	NM_017613.3	NP_060083.1	Q9NYP3	DONS_HUMAN	downstream neighbor of SON	376					multicellular organismal development (GO:0007275)	nucleus (GO:0005634)				central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(1)|ovary(1)	11						TATGTCTGGCTTTTTAATTTT	0.368																																					p.K376fs		Atlas-INDEL	.											.	DONSON	34	.	0			c.1128delG						.						98.0	98.0	98.0					21																	34954281		2203	4300	6503	SO:0001589	frameshift_variant	29980	exon7			.	AF000002	CCDS13632.1	21q22.1	2008-07-31			ENSG00000159147	ENSG00000159147			2993	protein-coding gene	gene with protein product		611428		C21orf60		10773462, 10950926	Standard	NM_017613		Approved	B17, C2TA, DKFZP434M035	uc002ysk.4	Q9NYP3	OTTHUMG00000065904	ENST00000303071.5:c.1127delA	chr21.hg19:g.34954281delT	ENSP00000307143:p.Lys376fs	195.0	0.0		164.0	11.0	NM_017613	Q8NC53|Q9NSR9|Q9NVZ5|Q9NYP1|Q9NYP2	Frame_Shift_Del	DEL	ENST00000303071.5	hg19	CCDS13632.1																																																																																			.	.		0.368	DONSON-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141184.1	NM_017613	
COL19A1	1310	hgsc.bcm.edu	37	6	70610184	70610184	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:70610184delA	ENST00000322773.4	+	4	322	c.220delA	c.(220-222)aaafs	p.K74fs		NM_001858.4	NP_001849.2	Q14993	COJA1_HUMAN	collagen, type XIX, alpha 1	74	Laminin G-like.				cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|single organismal cell-cell adhesion (GO:0016337)|skeletal muscle tissue development (GO:0007519)|skeletal system development (GO:0001501)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|protein binding, bridging (GO:0030674)			breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(8)|lung(54)|ovary(3)|prostate(2)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(2)	109						TGAAAGTGATAAAACCTGTTT	0.264																																					p.D73fs		Atlas-INDEL	.											.	COL19A1	232	.	0			c.219delT						.						75.0	76.0	76.0					6																	70610184		2203	4298	6501	SO:0001589	frameshift_variant	1310	exon4			.		CCDS4970.1	6q12-q13	2013-01-16			ENSG00000082293	ENSG00000082293		"""Collagens"""	2196	protein-coding gene	gene with protein product		120165				7916703, 9143499	Standard	NM_001858		Approved		uc003pfc.1	Q14993	OTTHUMG00000014987	ENST00000322773.4:c.220delA	chr6.hg19:g.70610184delA	ENSP00000316030:p.Lys74fs	163.0	0.0		164.0	11.0	NM_001858	Q00559|Q05850|Q12885|Q13676|Q14DH1|Q5JUF0|Q5T424|Q9H572|Q9NPZ2|Q9NQP2	Frame_Shift_Del	DEL	ENST00000322773.4	hg19	CCDS4970.1																																																																																			.	.		0.264	COL19A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041127.1		
ELF1	1997	hgsc.bcm.edu	37	13	41523943	41523943	+	Splice_Site	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr13:41523943delT	ENST00000239882.3	-	5	842	c.528delA	c.(526-528)aaa>aa	p.K176fs	ELF1_ENST00000498824.1_5'UTR|ELF1_ENST00000442101.1_Splice_Site_p.K152fs	NM_172373.3	NP_758961.1	P32519	ELF1_HUMAN	E74-like factor 1 (ets domain transcription factor)	176					cell differentiation (GO:0030154)|negative regulation of T cell receptor signaling pathway (GO:0050860)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokine production (GO:0001817)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(12)|ovary(1)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	37		Lung NSC(96;8.3e-05)|Prostate(109;0.0233)|Breast(139;0.0296)|Lung SC(185;0.0367)		all cancers(112;1.87e-08)|Epithelial(112;8.45e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000202)|GBM - Glioblastoma multiforme(144;0.00266)|BRCA - Breast invasive adenocarcinoma(63;0.072)		CCCACCTACCTTTTTTCCTCT	0.423																																					p.G177fs		Atlas-INDEL	.											.	ELF1	65	.	0			c.529delG						.						197.0	194.0	195.0					13																	41523943		2203	4300	6503	SO:0001630	splice_region_variant	1997	exon5			.	M82882	CCDS9374.1	13q13	2008-07-18			ENSG00000120690	ENSG00000120690			3316	protein-coding gene	gene with protein product		189973				1545787	Standard	NM_001145353		Approved		uc001uxs.3	P32519	OTTHUMG00000016783	ENST00000239882.3:c.529+1A>-	chr13.hg19:g.41523943delT		214.0	0.0		270.0	17.0	NM_172373	B4E2I5|E9PDQ9|Q8N6F6|Q9UDE1	Frame_Shift_Del	DEL	ENST00000239882.3	hg19	CCDS9374.1																																																																																			.	.		0.423	ELF1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044654.3	NM_172373	Frame_Shift_Del
AHNAK2	113146	hgsc.bcm.edu	37	14	105418454	105418454	+	Frame_Shift_Del	DEL	T	T	-	rs200174203	byFrequency	TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:105418454delT	ENST00000333244.5	-	7	3453	c.3334delA	c.(3334-3336)agcfs	p.S1112fs	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1112						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			GCCTTGGGGCTTTTCAGGTCC	0.647																																					p.S1112fs		Atlas-INDEL	.											.	AHNAK2	719	.	0			c.3335delG						.						116.0	145.0	136.0					14																	105418454		1882	4115	5997	SO:0001589	frameshift_variant	113146	exon7			.	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"""chromosome 14 open reading frame 78"""	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.3334delA	chr14.hg19:g.105418454delT	ENSP00000353114:p.Ser1112fs	153.0	0.0		177.0	11.0	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Frame_Shift_Del	DEL	ENST00000333244.5	hg19	CCDS45177.1																																																																																			.	.		0.647	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
OR5T3	390154	hgsc.bcm.edu	37	11	56020026	56020026	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:56020026delA	ENST00000303059.3	+	1	351	c.351delA	c.(349-351)gcafs	p.A117fs		NM_001004747.1	NP_001004747.1	Q8NGG3	OR5T3_HUMAN	olfactory receptor, family 5, subfamily T, member 3	117						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(23)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	39	Esophageal squamous(21;0.00448)					ATTTCCTGGCAAAAAATAAAT	0.363																																					p.A117fs		Atlas-INDEL	.											.	OR5T3	98	.	0			c.350delC						.						136.0	138.0	137.0					11																	56020026		2201	4295	6496	SO:0001589	frameshift_variant	390154	exon1			.	AB065837	CCDS31524.1	11q11	2012-08-09			ENSG00000172489	ENSG00000172489		"""GPCR / Class A : Olfactory receptors"""	15297	protein-coding gene	gene with protein product							Standard	NM_001004747		Approved	OR5T3Q	uc010rjd.2	Q8NGG3	OTTHUMG00000166852	ENST00000303059.3:c.351delA	chr11.hg19:g.56020026delA	ENSP00000305403:p.Ala117fs	100.0	0.0		157.0	10.0	NM_001004747	Q6IFC7	Frame_Shift_Del	DEL	ENST00000303059.3	hg19	CCDS31524.1																																																																																			.	.		0.363	OR5T3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391599.1	NM_001004747	
HTR1E	3354	hgsc.bcm.edu	37	6	87725971	87725971	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:87725971delT	ENST00000305344.5	+	2	1622	c.919delT	c.(919-921)tttfs	p.F308fs		NM_000865.2	NP_000856.1	P28566	5HT1E_HUMAN	5-hydroxytryptamine (serotonin) receptor 1E, G protein-coupled	308	Agonist binding. {ECO:0000250}.				adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|negative regulation of cAMP metabolic process (GO:0030815)|serotonin receptor signaling pathway (GO:0007210)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|serotonin binding (GO:0051378)|serotonin receptor activity (GO:0004993)			breast(3)|endometrium(2)|kidney(3)|large_intestine(11)|lung(15)|ovary(2)|prostate(2)|skin(3)	41		all_cancers(76;7.11e-06)|Acute lymphoblastic leukemia(125;1.2e-09)|Prostate(29;3.51e-09)|all_hematologic(105;7.43e-06)|all_epithelial(107;0.00819)		BRCA - Breast invasive adenocarcinoma(108;0.055)	Aripiprazole(DB01238)|Clozapine(DB00363)|Eletriptan(DB00216)|Ergoloid mesylate(DB01049)|Ketamine(DB01221)|Loxapine(DB00408)|Methysergide(DB00247)|Olanzapine(DB00334)|Quetiapine(DB01224)|Ziprasidone(DB00246)	CTGGCTGCCATTTTTCATCAA	0.512																																					p.P306fs		Atlas-INDEL	.											.	HTR1E	89	.	0			c.918delA						.						159.0	160.0	160.0					6																	87725971		2203	4300	6503	SO:0001589	frameshift_variant	3354	exon2			.		CCDS5006.1	6q14-q15	2013-06-19	2012-02-03		ENSG00000168830	ENSG00000168830		"""5-HT (serotonin) receptors"", ""GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"""	5291	protein-coding gene	gene with protein product		182132	"""5-hydroxytryptamine (serotonin) receptor 1E"""			1608964	Standard	NM_000865		Approved	5-HT1E	uc003pli.3	P28566	OTTHUMG00000015154	ENST00000305344.5:c.919delT	chr6.hg19:g.87725971delT	ENSP00000307766:p.Phe308fs	195.0	0.0		200.0	12.0	NM_000865	E1P503|Q9P1Y1	Frame_Shift_Del	DEL	ENST00000305344.5	hg19	CCDS5006.1																																																																																			.	.		0.512	HTR1E-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000472488.2	NM_000865	
KL	9365	hgsc.bcm.edu	37	13	33628034	33628034	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr13:33628034delA	ENST00000380099.3	+	2	958	c.950delA	c.(949-951)caafs	p.Q317fs	KL_ENST00000487852.1_3'UTR|KL_ENST00000426690.2_Frame_Shift_Del_p.Q10fs	NM_004795.3	NP_004786.2	Q9UEF7	KLOT_HUMAN	klotho	317	Glycosyl hydrolase-1 1.				acute inflammatory response (GO:0002526)|aging (GO:0007568)|calcium ion homeostasis (GO:0055074)|carbohydrate metabolic process (GO:0005975)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of bone mineralization (GO:0030501)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-glucosidase activity (GO:0008422)|beta-glucuronidase activity (GO:0004566)|fibroblast growth factor binding (GO:0017134)|signal transducer activity (GO:0004871)|vitamin D binding (GO:0005499)			breast(2)|endometrium(5)|kidney(3)|large_intestine(10)|lung(14)|ovary(2)|skin(5)	41	all_epithelial(80;0.133)	Ovarian(182;1.78e-06)|Breast(139;4.08e-05)|Hepatocellular(188;0.00886)|Lung SC(185;0.0262)		GBM - Glioblastoma multiforme(144;7.13e-230)|all cancers(112;1.33e-165)|OV - Ovarian serous cystadenocarcinoma(117;1.09e-113)|Epithelial(112;3.79e-112)|Lung(94;8.52e-27)|LUSC - Lung squamous cell carcinoma(192;1.4e-13)|Kidney(163;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(186;5.63e-08)|BRCA - Breast invasive adenocarcinoma(63;1.41e-05)		AAAGAATGTCAAAAATCTCTG	0.453																																					p.Q317fs		Atlas-INDEL	.											.	KL	106	.	0			c.949delC						.						171.0	163.0	165.0					13																	33628034		2203	4300	6503	SO:0001589	frameshift_variant	9365	exon2			.	AB005142	CCDS9347.1	13q12	2008-02-05			ENSG00000133116	ENSG00000133116			6344	protein-coding gene	gene with protein product		604824				9464267	Standard	NM_004795		Approved		uc001uus.3	Q9UEF7	OTTHUMG00000017408	ENST00000380099.3:c.950delA	chr13.hg19:g.33628034delA	ENSP00000369442:p.Gln317fs	122.0	0.0		144.0	10.0	NM_004795	Q5VZ95|Q96KV5|Q96KW5|Q9UEI9|Q9Y4F0	Frame_Shift_Del	DEL	ENST00000380099.3	hg19	CCDS9347.1																																																																																			.	.		0.453	KL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045987.1		
KDELC1	79070	hgsc.bcm.edu	37	13	103449216	103449216	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr13:103449216delT	ENST00000376004.4	-	2	662	c.326delA	c.(325-327)aatfs	p.N109fs	BIVM_ENST00000419638.1_5'Flank|KDELC1_ENST00000460338.1_5'UTR|BIVM_ENST00000257336.1_5'Flank|BIVM_ENST00000448849.2_5'Flank	NM_024089.2	NP_076994.2	Q6UW63	KDEL1_HUMAN	KDEL (Lys-Asp-Glu-Leu) containing 1	109				N -> S (in Ref. 2; BAD96287). {ECO:0000305}.		endoplasmic reticulum lumen (GO:0005788)				central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(9)|ovary(1)|prostate(1)|skin(1)	19	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.211)					CACCTTCAGATTTTTGTAGCT	0.363																																					p.N109fs		Atlas-INDEL	.											.	KDELC1	66	.	0			c.327delT						.						131.0	127.0	128.0					13																	103449216		2203	4300	6503	SO:0001589	frameshift_variant	79070	exon2			.	BC001297	CCDS9504.1	13q33	2010-11-18			ENSG00000134901	ENSG00000134901			19350	protein-coding gene	gene with protein product		611613					Standard	NM_024089		Approved	MGC5302, EP58	uc001vpq.4	Q6UW63	OTTHUMG00000017307	ENST00000376004.4:c.326delA	chr13.hg19:g.103449216delT	ENSP00000365172:p.Asn109fs	117.0	0.0		147.0	11.0	NM_024089	Q53HL3|Q9BVD2	Frame_Shift_Del	DEL	ENST00000376004.4	hg19	CCDS9504.1																																																																																			.	.		0.363	KDELC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045699.1		
SPATA31A6	389730	hgsc.bcm.edu	37	9	43625186	43625186	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:43625186delA	ENST00000332857.6	-	4	3529	c.3501delT	c.(3499-3501)tttfs	p.F1167fs	SPATA31A6_ENST00000496386.1_5'Flank	NM_001145196.1	NP_001138668.1	Q5VVP1	S31A6_HUMAN	SPATA31 subfamily A, member 6	1167					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											AAATCCACTGAAAAAATTGCT	0.428																																					p.Q1168fs		Atlas-INDEL	.											FAM75A6,bladder,carcinoma,0,1	.	.	.	0			c.3502delC						.						128.0	134.0	132.0					9																	43625186		632	1548	2180	SO:0001589	frameshift_variant	389730	exon4			.		CCDS75837.1	9p11.2	2012-10-15	2012-10-12	2012-10-12	ENSG00000185775	ENSG00000185775			32006	protein-coding gene	gene with protein product			"""family with sequence similarity 75, member A6"""	FAM75A6		20850414	Standard	NM_001145196		Approved	OTTHUMG00000013224	uc011lrb.2	Q5VVP1	OTTHUMG00000013224	ENST00000332857.6:c.3501delT	chr9.hg19:g.43625186delA	ENSP00000329825:p.Phe1167fs	362.0	0.0		284.0	19.0	NM_001145196		Frame_Shift_Del	DEL	ENST00000332857.6	hg19	CCDS47973.1																																																																																			.	.		0.428	SPATA31A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036987.1	NM_001145196	
BCL11A	53335	hgsc.bcm.edu	37	2	60688969	60688969	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:60688969delG	ENST00000335712.6	-	4	1305	c.1078delC	c.(1078-1080)ctcfs	p.L360fs	BCL11A_ENST00000358510.4_Frame_Shift_Del_p.L326fs|BCL11A_ENST00000477659.1_5'UTR|BCL11A_ENST00000538214.1_Frame_Shift_Del_p.L326fs|BCL11A_ENST00000356842.4_Frame_Shift_Del_p.L360fs|BCL11A_ENST00000537768.1_Intron|BCL11A_ENST00000359629.5_Intron	NM_022893.3	NP_075044.2	Q9H165	BC11A_HUMAN	B-cell CLL/lymphoma 11A (zinc finger protein)	360	Pro-rich.				B cell differentiation (GO:0030183)|negative regulation of axon extension (GO:0030517)|negative regulation of collateral sprouting (GO:0048671)|negative regulation of dendrite development (GO:2000171)|negative regulation of neuron projection development (GO:0010977)|negative regulation of protein homooligomerization (GO:0032463)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of collateral sprouting (GO:0048672)|positive regulation of neuron projection development (GO:0010976)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein sumoylation (GO:0016925)|regulation of dendrite development (GO:0050773)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|nuclear body (GO:0016604)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|transcription corepressor activity (GO:0003714)			NS(1)|breast(6)|central_nervous_system(6)|endometrium(4)|kidney(1)|large_intestine(8)|lung(25)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	59			LUSC - Lung squamous cell carcinoma(5;9.29e-08)|Lung(5;1.34e-06)|Epithelial(17;0.0562)|all cancers(80;0.199)			AGAGGAGGGAGGGGGGGCGTC	0.632			T	IGH@	B-CLL																																p.L360fs		Atlas-INDEL	.		Dom	yes		2	2p13	53335	B-cell CLL/lymphoma 11A		L	.	BCL11A	298	.	0			c.1079delT						.						39.0	48.0	44.0					2																	60688969		2198	4297	6495	SO:0001589	frameshift_variant	53335	exon4			.	AJ404611	CCDS1861.1, CCDS1862.1, CCDS46295.1	2p16.1	2013-01-08	2002-05-08		ENSG00000119866	ENSG00000119866		"""Zinc fingers, C2H2-type"""	13221	protein-coding gene	gene with protein product		606557	"""ecotropic viral integration site 9"""	EVI9		11719382, 18245381	Standard	NM_018014		Approved	BCL11A-XL, BCL11A-L, BCL11A-S, CTIP1, HBFQTL5, ZNF856	uc002sae.1	Q9H165	OTTHUMG00000129420	ENST00000335712.6:c.1078delC	chr2.hg19:g.60688969delG	ENSP00000338774:p.Leu360fs	147.0	0.0		147.0	10.0	NM_022893	D6W5D7|Q86W14|Q8WU92|Q96JL6|Q9H163|Q9H164|Q9H3G9|Q9NWA7	Frame_Shift_Del	DEL	ENST00000335712.6	hg19	CCDS1862.1																																																																																			.	.		0.632	BCL11A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251579.2	NM_022893	
IGF2BP3	10643	hgsc.bcm.edu	37	7	23387322	23387322	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:23387322delC	ENST00000258729.3	-	7	1071	c.715delG	c.(715-717)gctfs	p.A240fs		NM_006547.2	NP_006538.2	O00425	IF2B3_HUMAN	insulin-like growth factor 2 mRNA binding protein 3	240	KH 1. {ECO:0000255|PROSITE- ProRule:PRU00117}.				anatomical structure morphogenesis (GO:0009653)|gene expression (GO:0010467)|mRNA transport (GO:0051028)|negative regulation of translation (GO:0017148)|regulation of cytokine biosynthetic process (GO:0042035)|translation (GO:0006412)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	mRNA 3'-UTR binding (GO:0003730)|mRNA 5'-UTR binding (GO:0048027)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|translation regulator activity (GO:0045182)			breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(14)|ovary(2)|prostate(2)|skin(4)|stomach(1)	34						TTCTCAGCAGCCCCCGCATTT	0.458																																					p.A239fs		Atlas-INDEL	.											.	IGF2BP3	71	.	0			c.716delC						.						103.0	93.0	96.0					7																	23387322		2203	4300	6503	SO:0001589	frameshift_variant	10643	exon7			.	AF117108	CCDS5382.1	7p15.3	2014-02-19			ENSG00000136231	ENSG00000136231		"""RNA binding motif (RRM) containing"""	28868	protein-coding gene	gene with protein product	"""IGF II mRNA binding protein 3"", ""cancer/testis antigen 98"""	608259				9891060, 9178771	Standard	NM_006547		Approved	IMP-3, CT98, IMP3	uc003swg.3	O00425	OTTHUMG00000128445	ENST00000258729.3:c.715delG	chr7.hg19:g.23387322delC	ENSP00000258729:p.Ala240fs	166.0	0.0		206.0	14.0	NM_006547	A0A4Z5|Q63HM0|Q6MZZ2|Q86VB1	Frame_Shift_Del	DEL	ENST00000258729.3	hg19	CCDS5382.1																																																																																			.	.		0.458	IGF2BP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250243.2	NM_006547	
APBA2	321	hgsc.bcm.edu	37	15	29346583	29346583	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:29346583delC	ENST00000558402.1	+	5	1095	c.496delC	c.(496-498)cccfs	p.P166fs	APBA2_ENST00000558259.1_Frame_Shift_Del_p.P166fs|APBA2_ENST00000411764.1_Frame_Shift_Del_p.P166fs|APBA2_ENST00000561069.1_Frame_Shift_Del_p.P166fs|APBA2_ENST00000558330.1_Frame_Shift_Del_p.P166fs			Q99767	APBA2_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 2	166					in utero embryonic development (GO:0001701)|locomotory behavior (GO:0007626)|multicellular organism growth (GO:0035264)|nervous system development (GO:0007399)|protein transport (GO:0015031)|regulation of gene expression (GO:0010468)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)	beta-amyloid binding (GO:0001540)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(7)|liver(2)|lung(33)|stomach(1)|urinary_tract(1)	59		all_lung(180;1.73e-12)|Breast(32;2.89e-05)|Colorectal(260;0.234)		all cancers(64;7.44e-11)|Epithelial(43;5.74e-10)|GBM - Glioblastoma multiforme(186;0.026)|BRCA - Breast invasive adenocarcinoma(123;0.0286)|Lung(196;0.24)		CGGCCAACTGCCCATTCCGGA	0.647																																					p.L165fs		Atlas-INDEL	.											.	APBA2	132	.	0			c.495delG						.						41.0	41.0	41.0					15																	29346583		2203	4300	6503	SO:0001589	frameshift_variant	321	exon3			.	AB014719	CCDS10022.1, CCDS45197.1	15q11-q12	2008-07-18	2008-07-18		ENSG00000034053	ENSG00000034053			579	protein-coding gene	gene with protein product		602712	"""X11-like"", ""amyloid beta (A4) precursor protein-binding, family A, member 2 (X11-like)"""	X11L, MINT2		8955346	Standard	NM_005503		Approved	D15S1518E, LIN-10, MGC:14091, HsT16821	uc001zck.3	Q99767	OTTHUMG00000129255	ENST00000558402.1:c.496delC	chr15.hg19:g.29346583delC	ENSP00000453293:p.Pro166fs	159.0	0.0		159.0	10.0	NM_005503	E9PGI4|O60571|Q5XKC0	Frame_Shift_Del	DEL	ENST00000558402.1	hg19	CCDS10022.1																																																																																			.	.		0.647	APBA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251362.3	NM_005503	
PAK2	5062	hgsc.bcm.edu	37	3	196541368	196541368	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:196541368delG	ENST00000327134.3	+	11	1304	c.982delG	c.(982-984)gggfs	p.G329fs		NM_002577.4	NP_002568.2	Q13177	PAK2_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 2	329	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.			G -> R (in Ref. 3; AAA75468). {ECO:0000305}.	apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis (GO:2001271)|negative regulation of protein kinase activity (GO:0006469)|peptidyl-serine phosphorylation (GO:0018105)|phosphorylation (GO:0016310)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein tyrosine kinase activity (GO:0061098)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of defense response to virus by virus (GO:0050690)|regulation of growth (GO:0040008)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activator activity (GO:0030296)			breast(1)|cervix(1)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(2)	12	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;1.07e-23)|all cancers(36;6.38e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.5e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00405)		ATACCTTGCTGGGGGGTCACT	0.408																																					p.A327fs		Atlas-INDEL	.											.	PAK2	113	.	0			c.981delT						.						164.0	159.0	161.0					3																	196541368		2203	4300	6503	SO:0001589	frameshift_variant	5062	exon11			.	U24153	CCDS3321.1	3q29	2008-06-17	2008-06-17			ENSG00000180370	2.7.11.1		8591	protein-coding gene	gene with protein product	"""S6/H4 kinase"""	605022	"""p21 (CDKN1A)-activated kinase 2"""			7744004, 7618083	Standard	NM_002577		Approved	PAK65, PAKgamma	uc003fwy.4	Q13177		ENST00000327134.3:c.982delG	chr3.hg19:g.196541368delG	ENSP00000314067:p.Gly329fs	152.0	0.0		222.0	14.0	NM_002577	Q13154|Q6ISC3	Frame_Shift_Del	DEL	ENST00000327134.3	hg19	CCDS3321.1																																																																																			.	.		0.408	PAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340548.1	NM_002577	
ARF1	375	hgsc.bcm.edu	37	1	228284858	228284858	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:228284858delA	ENST00000541182.1	+	2	305	c.43delA	c.(43-45)aaafs	p.K16fs	ARF1_ENST00000540651.1_Frame_Shift_Del_p.K16fs|MIR3620_ENST00000584469.1_RNA|ARF1_ENST00000478424.1_3'UTR|ARF1_ENST00000272102.5_Frame_Shift_Del_p.K16fs	NM_001024227.1|NM_001024228.1	NP_001019398.1|NP_001019399.1	P84077	ARF1_HUMAN	ADP-ribosylation factor 1	16					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cellular copper ion homeostasis (GO:0006878)|COPI coating of Golgi vesicle (GO:0048205)|dendritic spine organization (GO:0097061)|GTP catabolic process (GO:0006184)|long term synaptic depression (GO:0060292)|membrane organization (GO:0061024)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|post-Golgi vesicle-mediated transport (GO:0006892)|protein transport (GO:0015031)|regulation of Arp2/3 complex-mediated actin nucleation (GO:0034315)|regulation of defense response to virus by virus (GO:0050690)|regulation of receptor internalization (GO:0002090)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi membrane (GO:0000139)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|receptor signaling protein activity (GO:0005057)			breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(4)	10		Prostate(94;0.0405)				CCTTTTTGGCAAAAAAGAAAT	0.547																																					p.G14fs		Atlas-INDEL	.											.,1	ARF1	24	.	0			c.42delC						.						121.0	101.0	108.0					1																	228284858		2203	4300	6503	SO:0001589	frameshift_variant	375	exon2			.	M84326	CCDS1565.1	1q42.13	2014-01-30			ENSG00000143761	ENSG00000143761		"""ADP-ribosylation factors"", ""Endogenous ligands"""	652	protein-coding gene	gene with protein product		103180				1577740	Standard	NM_001658		Approved		uc001hrr.3	P84077	OTTHUMG00000037595	ENST00000541182.1:c.43delA	chr1.hg19:g.228284858delA	ENSP00000440005:p.Lys16fs	105.0	0.0		162.0	10.0	NM_001024228	P10947|P32889	Frame_Shift_Del	DEL	ENST00000541182.1	hg19	CCDS1565.1																																																																																			.	.		0.547	ARF1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091650.1	NM_001024227	
PRR3	80742	hgsc.bcm.edu	37	6	30525950	30525950	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:30525950delC	ENST00000376560.3	+	2	589	c.130delC	c.(130-132)cccfs	p.P45fs	PRR3_ENST00000376557.3_Intron|PRR3_ENST00000498336.1_3'UTR|GNL1_ENST00000376621.3_5'Flank	NM_025263.3	NP_079539.2	P79522	PRR3_HUMAN	proline rich 3	45	Pro-rich.						metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			lung(1)|ovary(1)	2						TCTGGGCCCTCCCCCCATGGC	0.502																																					p.P43fs		Atlas-Indel,Pindel	.											.	PRR3	5	.	0			c.129delT						.						95.0	97.0	96.0					6																	30525950		1161	2503	3664	SO:0001589	frameshift_variant	80742	exon2			.	AK074531	CCDS43440.1, CCDS43441.1	6p21.32	2013-01-18	2004-05-27		ENSG00000204576	ENSG00000204576		"""Zinc fingers, CCCH-type domain containing"""	21149	protein-coding gene	gene with protein product			"""proline-rich polpeptide 3"""				Standard	NM_025263		Approved	CAT56, Em:AB014077.1, Em:AB023052.2	uc003nqi.2	P79522	OTTHUMG00000031037	ENST00000376560.3:c.130delC	chr6.hg19:g.30525950delC	ENSP00000365744:p.Pro45fs	91.0	0.0		135.0	12.0	NM_025263	A1A4H4|Q5RJB5|Q5STN6	Frame_Shift_Del	DEL	ENST00000376560.3	hg19	CCDS43440.1																																																																																			.	.		0.502	PRR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076033.2	NM_025263	
SIPA1L1	26037	hgsc.bcm.edu	37	14	72196875	72196875	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:72196875delG	ENST00000555818.1	+	18	5129	c.4781delG	c.(4780-4782)aggfs	p.R1594fs	SIPA1L1_ENST00000381232.3_Frame_Shift_Del_p.R1573fs|SIPA1L1_ENST00000537413.1_Frame_Shift_Del_p.R1048fs|SIPA1L1_ENST00000554874.1_3'UTR|SIPA1L1_ENST00000358550.2_Frame_Shift_Del_p.R1573fs	NM_001284247.1|NM_015556.1	NP_001271176.1|NP_056371.1	O43166	SI1L1_HUMAN	signal-induced proliferation-associated 1 like 1	1594					actin cytoskeleton reorganization (GO:0031532)|activation of Rap GTPase activity (GO:0032861)|ephrin receptor signaling pathway (GO:0048013)|regulation of axonogenesis (GO:0050770)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of Rap GTPase activity (GO:0032317)|regulation of synaptic plasticity (GO:0048167)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	GTPase activator activity (GO:0005096)			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(11)|kidney(1)|large_intestine(22)|liver(2)|lung(25)|ovary(3)|prostate(3)|skin(3)|stomach(1)	78				all cancers(60;0.00169)|BRCA - Breast invasive adenocarcinoma(234;0.00912)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)		AATAGCCAGAGGGAGCACTTT	0.597																																					p.R1594fs		Atlas-INDEL	.											.	SIPA1L1	219	.	0			c.4780delA						.						106.0	90.0	95.0					14																	72196875		2203	4300	6503	SO:0001589	frameshift_variant	26037	exon18			.	AB007900	CCDS9807.1, CCDS61490.1, CCDS61491.1	14q24.1	2003-12-11				ENSG00000197555			20284	protein-coding gene	gene with protein product						9858596	Standard	XM_005267514		Approved	KIAA0440, E6TP1	uc001xmr.1	O43166		ENST00000555818.1:c.4781delG	chr14.hg19:g.72196875delG	ENSP00000450832:p.Arg1594fs	167.0	0.0		185.0	13.0	NM_015556	J3KP19|O95321|Q9UDU4|Q9UNU4	Frame_Shift_Del	DEL	ENST00000555818.1	hg19	CCDS9807.1																																																																																			.	.		0.597	SIPA1L1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412806.1	NM_015556	
TTN	7273	hgsc.bcm.edu	37	2	179391906	179391906	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:179391906delT	ENST00000591111.1	-	313	103110	c.102886delA	c.(102886-102888)atcfs	p.I34296fs	TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000591466.1_RNA|TTN-AS1_ENST00000585625.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000589842.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000587576.1_RNA|TTN-AS1_ENST00000588244.1_RNA|TTN-AS1_ENST00000588804.1_RNA|TTN-AS1_ENST00000588257.1_RNA|TTN-AS1_ENST00000592182.1_RNA|TTN-AS1_ENST00000585487.1_RNA|TTN-AS1_ENST00000590040.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000588716.1_RNA|TTN_ENST00000342175.6_Frame_Shift_Del_p.I27064fs|TTN_ENST00000589042.1_Frame_Shift_Del_p.I35937fs|TTN-AS1_ENST00000587944.1_RNA|TTN-AS1_ENST00000591867.1_RNA|TTN-AS1_ENST00000431259.2_RNA|TTN_ENST00000342992.6_Frame_Shift_Del_p.I33369fs|TTN_ENST00000460472.2_Frame_Shift_Del_p.I26872fs|TTN-AS1_ENST00000587568.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000592836.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000442329.2_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN_ENST00000359218.5_Frame_Shift_Del_p.I26997fs|TTN-AS1_ENST00000589391.1_RNA|TTN-AS1_ENST00000604571.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000592161.1_RNA|TTN-AS1_ENST00000585358.1_RNA|TTN-AS1_ENST00000589434.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000450692.2_RNA|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	34296	Ig-like 152.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TGACTGTGGATTTTTCTTCCA	0.453																																					p.I35937fs		Atlas-INDEL	.											.	TTN	18412	.	0			c.107810delT						.						180.0	158.0	165.0					2																	179391906		1929	4132	6061	SO:0001589	frameshift_variant	7273	exon363			.	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.102886delA	chr2.hg19:g.179391906delT	ENSP00000465570:p.Ile34296fs	221.0	0.0		281.0	17.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Frame_Shift_Del	DEL	ENST00000591111.1	hg19																																																																																				.	.		0.453	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
CLK2	1196	hgsc.bcm.edu	37	1	155240721	155240721	+	Frame_Shift_Del	DEL	C	C	-	rs371622938		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:155240721delC	ENST00000368361.4	-	2	363	c.48delG	c.(46-48)gggfs	p.G16fs	CLK2_ENST00000355560.4_Frame_Shift_Del_p.G16fs|CLK2_ENST00000497188.1_5'Flank|CLK2_ENST00000361168.5_Frame_Shift_Del_p.G16fs|CLK2_ENST00000536801.1_Frame_Shift_Del_p.G16fs			P49760	CLK2_HUMAN	CDC-like kinase 2	16					negative regulation of gluconeogenesis (GO:0045721)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of RNA splicing (GO:0043484)|response to ionizing radiation (GO:0010212)|response to retinoic acid (GO:0032526)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			endometrium(4)|lung(12)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	22	all_lung(78;2.32e-23)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			CACGGTAACTCCCCCGGCTGC	0.552								Other conserved DNA damage response genes																													p.S17fs		Atlas-INDEL	.											.	CLK2	55	.	0			c.49delA						.						127.0	122.0	123.0					1																	155240721		2203	4300	6503	SO:0001589	frameshift_variant	1196	exon2			.	L29218	CCDS1107.1, CCDS72939.1	1q21	2008-05-02			ENSG00000176444	ENSG00000176444		"""CDC-like kinases"""	2069	protein-coding gene	gene with protein product		602989				7990150, 9856501	Standard	XM_005244876		Approved	clk2	uc001fjw.3	P49760	OTTHUMG00000035873	ENST00000368361.4:c.48delG	chr1.hg19:g.155240721delC	ENSP00000357345:p.Gly16fs	93.0	0.0		174.0	12.0	NM_003993	B1AVS9|B5MBX6|Q96CQ0	Frame_Shift_Del	DEL	ENST00000368361.4	hg19																																																																																				.	.		0.552	CLK2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000087391.1	NM_003993	
ZNF217	7764	hgsc.bcm.edu	37	20	52193620	52193620	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr20:52193620delA	ENST00000371471.2	-	4	2108	c.1683delT	c.(1681-1683)tttfs	p.F561fs	RP4-724E16.2_ENST00000424252.1_RNA|ZNF217_ENST00000302342.3_Frame_Shift_Del_p.F561fs			O75362	ZN217_HUMAN	zinc finger protein 217	561					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(13)|lung(17)|ovary(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	50	all_cancers(1;6.75e-17)|all_epithelial(1;1.76e-18)|Breast(2;3.83e-14)|Lung NSC(4;9.04e-07)|all_lung(4;2.5e-06)|Ovarian(1;0.0398)		BRCA - Breast invasive adenocarcinoma(1;9.88e-17)|Epithelial(1;1.56e-14)|all cancers(1;9.44e-13)|STAD - Stomach adenocarcinoma(23;0.0474)|Colorectal(105;0.198)			TGGCACCATCAAAAAATCTTT	0.443																																					p.D562fs		Atlas-INDEL	.											.	ZNF217	227	.	0			c.1684delG						.						129.0	125.0	126.0					20																	52193620		2203	4300	6503	SO:0001589	frameshift_variant	7764	exon3			.	AF041259	CCDS13443.1	20q13.2	2013-01-08			ENSG00000171940	ENSG00000171940		"""Zinc fingers, C2H2-type"""	13009	protein-coding gene	gene with protein product		602967				9671742	Standard	NM_006526		Approved	ZABC1	uc002xwq.4	O75362	OTTHUMG00000032764	ENST00000371471.2:c.1683delT	chr20.hg19:g.52193620delA	ENSP00000360526:p.Phe561fs	81.0	0.0		126.0	12.0	NM_006526	E1P5Y6|Q14DB8	Frame_Shift_Del	DEL	ENST00000371471.2	hg19	CCDS13443.1																																																																																			.	.		0.443	ZNF217-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079757.2	NM_006526	
GPR22	2845	hgsc.bcm.edu	37	7	107115730	107115730	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:107115730delA	ENST00000304402.4	+	3	2568	c.1225delA	c.(1225-1227)aaafs	p.K409fs	COG5_ENST00000393603.2_Intron|COG5_ENST00000475638.2_Intron|COG5_ENST00000297135.3_Intron|COG5_ENST00000347053.3_Intron	NM_005295.2	NP_005286.2	Q99680	GPR22_HUMAN	G protein-coupled receptor 22	409					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)			large_intestine(3)|lung(6)|ovary(2)|stomach(1)	12						GATAGATCCTAAAAGAAACAA	0.338																																					p.P408fs		Atlas-INDEL	.											.	GPR22	43	.	0			c.1224delT						.						35.0	40.0	38.0					7																	107115730		2195	4281	6476	SO:0001589	frameshift_variant	2845	exon3			.	U66581	CCDS5744.1	7q22-q31.1	2012-08-21			ENSG00000172209	ENSG00000172209		"""GPCR / Class A : Orphans"""	4477	protein-coding gene	gene with protein product		601910				9073069	Standard	NM_005295		Approved		uc003vef.3	Q99680	OTTHUMG00000154902	ENST00000304402.4:c.1225delA	chr7.hg19:g.107115730delA	ENSP00000302676:p.Lys409fs	118.0	0.0		163.0	10.0	NM_005295	O14554	Frame_Shift_Del	DEL	ENST00000304402.4	hg19	CCDS5744.1																																																																																			.	.		0.338	GPR22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337598.1		
CDC73	79577	hgsc.bcm.edu	37	1	193111006	193111006	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:193111006delA	ENST00000367435.3	+	7	723	c.539delA	c.(538-540)gaafs	p.E180fs		NM_024529.4	NP_078805.3	Q6P1J9	CDC73_HUMAN	cell division cycle 73	180					cell cycle (GO:0007049)|cellular response to lipopolysaccharide (GO:0071222)|endodermal cell fate commitment (GO:0001711)|histone H2B ubiquitination (GO:0033523)|histone monoubiquitination (GO:0010390)|mRNA polyadenylation (GO:0006378)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of mRNA 3'-end processing (GO:0031442)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|protein destabilization (GO:0031648)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	Cdc73/Paf1 complex (GO:0016593)|nucleus (GO:0005634)	RNA polymerase II core binding (GO:0000993)			breast(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(14)|ovary(1)|pancreas(1)|parathyroid(51)|skin(1)|upper_aerodigestive_tract(1)	87						ATGTCAGTGGAAAAAATTGCT	0.328																																					p.E180fs		Atlas-INDEL	.											.	CDC73	163	.	0			c.538delG						.						45.0	42.0	43.0					1																	193111006		2203	4300	6503	SO:0001589	frameshift_variant	79577	exon7			.	AF312865	CCDS1382.1	1q25	2014-09-17	2013-01-17	2005-07-20	ENSG00000134371	ENSG00000134371			16783	protein-coding gene	gene with protein product	"""Paf1/RNA polymerase II complex component"""	607393	"""chromosome 1 open reading frame 28"", ""hyperparathyroidism 2 (with jaw tumor)"", ""cell division cycle 73, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae)"", ""hyperparathyroidism 1"""	C1orf28, HRPT2, HRPT1		11318611, 15632063, 18755853	Standard	NM_024529		Approved	parafibromin, FIHP	uc001gtb.3	Q6P1J9	OTTHUMG00000035676	ENST00000367435.3:c.539delA	chr1.hg19:g.193111006delA	ENSP00000356405:p.Glu180fs	103.0	0.0		153.0	10.0	NM_024529	A6NLZ8|B2RBR2|Q6PK51|Q96A07|Q9H245|Q9H5L7	Frame_Shift_Del	DEL	ENST00000367435.3	hg19	CCDS1382.1																																																																																			.	.		0.328	CDC73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086696.2	NM_024529	
CLTCL1	8218	hgsc.bcm.edu	37	22	19209481	19209481	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr22:19209481delT	ENST00000263200.10	-	16	2626	c.2554delA	c.(2554-2556)agafs	p.R852fs	CLTCL1_ENST00000353891.5_Frame_Shift_Del_p.R852fs|CLTCL1_ENST00000427926.1_Frame_Shift_Del_p.R852fs	NM_007098.3	NP_009029.3	P53675	CLH2_HUMAN	clathrin, heavy chain-like 1	852	Heavy chain arm.|Proximal segment.				anatomical structure morphogenesis (GO:0009653)|intracellular protein transport (GO:0006886)|mitotic nuclear division (GO:0007067)|positive regulation of glucose import (GO:0046326)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)	clathrin coat of coated pit (GO:0030132)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|coated vesicle (GO:0030135)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|spindle (GO:0005819)|trans-Golgi network (GO:0005802)	signal transducer activity (GO:0004871)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(2)|endometrium(9)|kidney(3)|large_intestine(11)|lung(9)|ovary(5)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49	Colorectal(54;0.0993)					TACCTATTTCTTTTTTCTACT	0.418			T	?	ALCL																																p.R852fs		Atlas-INDEL	.		Dom	yes		22	22q11.21	8218	"""clathrin, heavy polypeptide-like 1"""		L	CLTCL1,NS,carcinoma,0,1	CLTCL1	115	.	0			c.2555delG						.						111.0	115.0	114.0					22																	19209481		1941	4119	6060	SO:0001589	frameshift_variant	8218	exon16			.		CCDS46662.1, CCDS54497.1, CCDS46662.2, CCDS54497.2	22q11.2	2008-06-10	2006-09-29		ENSG00000070371	ENSG00000070371			2093	protein-coding gene	gene with protein product		601273	"""clathrin, heavy polypeptide-like 1"""	CLTCL		8844170, 15133132	Standard	NM_007098		Approved	CLTD, CLH22, CHC22	uc021wle.1	P53675	OTTHUMG00000150109	ENST00000263200.10:c.2554delA	chr22.hg19:g.19209481delT	ENSP00000445677:p.Arg852fs	112.0	0.0		165.0	12.0	NM_001835	B7Z7U5|Q14017|Q15808|Q15809	Frame_Shift_Del	DEL	ENST00000263200.10	hg19	CCDS46662.1																																																																																			.	.		0.418	CLTCL1-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316397.5	NM_007098	
CNTFR	1271	hgsc.bcm.edu	37	9	34556395	34556395	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:34556395delT	ENST00000378980.3	-	7	919	c.626delA	c.(625-627)aatfs	p.N209fs	CNTFR_ENST00000351266.4_Frame_Shift_Del_p.N209fs	NM_001207011.1|NM_147164.2	NP_001193940.1|NP_671693.1	P26992	CNTFR_HUMAN	ciliary neurotrophic factor receptor	209	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				brainstem development (GO:0003360)|ciliary neurotrophic factor-mediated signaling pathway (GO:0070120)|negative regulation of neuron apoptotic process (GO:0043524)|nervous system development (GO:0007399)|positive regulation of cell proliferation (GO:0008284)|sex differentiation (GO:0007548)|signal transduction (GO:0007165)|skeletal muscle organ development (GO:0060538)|suckling behavior (GO:0001967)	anchored component of membrane (GO:0031225)|CNTFR-CLCF1 complex (GO:0097059)|extrinsic component of membrane (GO:0019898)|plasma membrane (GO:0005886)	ciliary neurotrophic factor receptor activity (GO:0004897)|cytokine binding (GO:0019955)|receptor binding (GO:0005102)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(4)|ovary(4)|skin(1)	15	all_epithelial(49;0.0899)		STAD - Stomach adenocarcinoma(86;0.212)	GBM - Glioblastoma multiforme(74;0.00494)		GGCTACCACATTTTCTGGAGG	0.552																																					p.N209fs		Atlas-INDEL	.											.	CNTFR	46	.	0			c.627delT						.						67.0	65.0	66.0					9																	34556395		2203	4300	6503	SO:0001589	frameshift_variant	1271	exon7			.	M73238	CCDS6558.1	9p13	2013-02-11			ENSG00000122756	ENSG00000122756		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	2170	protein-coding gene	gene with protein product		118946				1648265	Standard	NM_001842		Approved		uc003zuq.2	P26992	OTTHUMG00000019821	ENST00000378980.3:c.626delA	chr9.hg19:g.34556395delT	ENSP00000368265:p.Asn209fs	90.0	0.0		140.0	10.0	NM_147164	Q5U050	Frame_Shift_Del	DEL	ENST00000378980.3	hg19	CCDS6558.1																																																																																			.	.		0.552	CNTFR-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052176.1		
FAM184B	27146	hgsc.bcm.edu	37	4	17660011	17660011	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:17660011delG	ENST00000265018.3	-	10	2211	c.1999delC	c.(1999-2001)ctgfs	p.L667fs		NM_015688.1	NP_056503.1	Q9ULE4	F184B_HUMAN	family with sequence similarity 184, member B	667										NS(1)|central_nervous_system(1)|endometrium(1)|prostate(1)	4						AGCATGCGCAGGGCTCTCTGG	0.607																																					p.L667fs		Atlas-INDEL	.											.	FAM184B	38	.	0			c.2000delT						.						72.0	66.0	68.0					4																	17660011		692	1591	2283	SO:0001589	frameshift_variant	27146	exon10			.		CCDS47033.1	4p16	2009-04-22			ENSG00000047662	ENSG00000047662			29235	protein-coding gene	gene with protein product						10574462	Standard	NM_015688		Approved	KIAA1276	uc003gpm.4	Q9ULE4	OTTHUMG00000160287	ENST00000265018.3:c.1999delC	chr4.hg19:g.17660011delG	ENSP00000265018:p.Leu667fs	145.0	0.0		156.0	10.0	NM_015688		Frame_Shift_Del	DEL	ENST00000265018.3	hg19	CCDS47033.1																																																																																			.	.		0.607	FAM184B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360137.1	NM_015688	
OGFR	11054	hgsc.bcm.edu	37	20	61444462	61444462	+	Frame_Shift_Del	DEL	G	G	-	rs369405396		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr20:61444462delG	ENST00000290291.6	+	7	1520	c.1495delG	c.(1495-1497)gggfs	p.G499fs	OGFR_ENST00000370461.1_Frame_Shift_Del_p.G447fs	NM_007346.2	NP_031372.2	Q9NZT2	OGFR_HUMAN	opioid growth factor receptor	499					opioid receptor signaling pathway (GO:0038003)|regulation of cell growth (GO:0001558)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	opioid receptor activity (GO:0004985)			endometrium(2)|kidney(1)|lung(4)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)	17	Breast(26;3.65e-08)					CAGTGAGAACGGGGTTGAGGA	0.682																																					p.N498fs		Atlas-INDEL	.											OGFR,NS,carcinoma,0,1	OGFR	63	.	0			c.1494delC						.						21.0	24.0	23.0					20																	61444462		2164	4259	6423	SO:0001589	frameshift_variant	11054	exon7			.	AF109134	CCDS13504.1	20q13.3	2008-05-02			ENSG00000060491	ENSG00000060491			15768	protein-coding gene	gene with protein product		606459				10677613	Standard	NM_007346		Approved	7-60	uc002ydj.3	Q9NZT2	OTTHUMG00000032937	ENST00000290291.6:c.1495delG	chr20.hg19:g.61444462delG	ENSP00000290291:p.Gly499fs	63.0	0.0		152.0	10.0	NM_007346	O96029|Q4VXW5|Q96CM2|Q9BQW1|Q9H4H0|Q9H7J5|Q9NZT3|Q9NZT4	Frame_Shift_Del	DEL	ENST00000290291.6	hg19	CCDS13504.1																																																																																			.	.		0.682	OGFR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080067.1		
SEMG1	6406	hgsc.bcm.edu	37	20	43836178	43836178	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr20:43836178delA	ENST00000372781.3	+	2	297	c.240delA	c.(238-240)cgafs	p.R80fs	SEMG1_ENST00000244069.6_Frame_Shift_Del_p.R80fs	NM_003007.3	NP_002998.1	P04279	SEMG1_HUMAN	semenogelin I	80	Repeat-rich region. {ECO:0000250}.				insemination (GO:0007320)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|secretory granule (GO:0030141)	structural molecule activity (GO:0005198)			cervix(1)|endometrium(2)|kidney(3)|large_intestine(3)|liver(1)|lung(12)|prostate(1)|skin(6)|stomach(2)|urinary_tract(1)	32		Myeloproliferative disorder(115;0.0122)				ACCAGTCCCGAAAAAGTCAGC	0.383																																					p.R80fs		Atlas-INDEL	.											.	SEMG1	71	.	0			c.239delG						.						148.0	133.0	138.0					20																	43836178		2203	4300	6503	SO:0001589	frameshift_variant	6406	exon2			.		CCDS13345.1	20q12-q13.2	2009-08-06			ENSG00000124233	ENSG00000124233			10742	protein-coding gene	gene with protein product	"""semen coagulating protein"", ""cancer/testis antigen 103"""	182140		SEMG		2912989, 15563730	Standard	NM_003007		Approved	CT103		P04279	OTTHUMG00000032565	ENST00000372781.3:c.240delA	chr20.hg19:g.43836178delA	ENSP00000361867:p.Arg80fs	156.0	0.0		280.0	17.0	NM_003007	Q53ZV0|Q53ZV1|Q53ZV2|Q6X4I9|Q6Y809|Q6Y822|Q6Y823|Q86U64|Q96QM3	Frame_Shift_Del	DEL	ENST00000372781.3	hg19	CCDS13345.1																																																																																			.	.		0.383	SEMG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079416.3	NM_003007	
SPAG1	6674	hgsc.bcm.edu	37	8	101199429	101199429	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr8:101199429delT	ENST00000388798.2	+	8	974	c.783delT	c.(781-783)gctfs	p.A261fs	SPAG1_ENST00000520643.1_Frame_Shift_Del_p.A261fs|SPAG1_ENST00000251809.3_Frame_Shift_Del_p.A261fs|SPAG1_ENST00000520508.1_Frame_Shift_Del_p.A261fs|Y_RNA_ENST00000362797.1_RNA	NM_003114.4	NP_003105.2	Q07617	SPAG1_HUMAN	sperm associated antigen 1	261					axonemal dynein complex assembly (GO:0070286)|single fertilization (GO:0007338)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	GTP binding (GO:0005525)|hydrolase activity (GO:0016787)			central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(10)|ovary(2)|pancreas(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	30	all_cancers(14;2.35e-05)|all_epithelial(15;5.2e-08)|Lung NSC(17;0.000283)|all_lung(17;0.000823)	Breast(495;0.195)	Epithelial(11;1.12e-09)|all cancers(13;1.26e-07)|OV - Ovarian serous cystadenocarcinoma(57;4.37e-05)|STAD - Stomach adenocarcinoma(118;0.0525)	KIRC - Kidney renal clear cell carcinoma(542;0.00178)|READ - Rectum adenocarcinoma(644;0.236)		GGAATAGTGCTTTTCAGGATT	0.358																																					p.A261fs		Atlas-INDEL	.											.	SPAG1	80	.	0			c.782delC						.						85.0	85.0	85.0					8																	101199429		2203	4300	6503	SO:0001589	frameshift_variant	6674	exon8			.	AF311312	CCDS34930.1	8q22	2014-01-21			ENSG00000104450	ENSG00000104450		"""Tetratricopeptide (TTC) repeat domain containing"""	11212	protein-coding gene	gene with protein product		603395				16368546	Standard	NM_172218		Approved	SP75, FLJ32920, HSD-3.8, TPIS, CT140	uc003yjh.2	Q07617	OTTHUMG00000164706	ENST00000388798.2:c.783delT	chr8.hg19:g.101199429delT	ENSP00000373450:p.Ala261fs	87.0	0.0		156.0	10.0	NM_003114	A6NP70|B3KQ58|G3XAM3|Q7Z5G1	Frame_Shift_Del	DEL	ENST00000388798.2	hg19	CCDS34930.1																																																																																			.	.		0.358	SPAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379853.2	NM_172218	
ZNF527	84503	hgsc.bcm.edu	37	19	37879579	37879579	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:37879579delA	ENST00000436120.2	+	5	735	c.628delA	c.(628-630)aaafs	p.K210fs	ZNF527_ENST00000587349.1_Intron	NM_032453.1	NP_115829.1	Q8NB42	ZN527_HUMAN	zinc finger protein 527	210					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	33			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			AATTGAATATAAAAGACTCCA	0.333																																					p.Y209X		Atlas-INDEL	.											.	ZNF527	78	.	0			c.627delT						.						50.0	50.0	50.0					19																	37879579		1807	4062	5869	SO:0001589	frameshift_variant	84503	exon5			.	AB058732, AK091585	CCDS42559.1	19q13.1	2013-01-08			ENSG00000189164	ENSG00000189164		"""Zinc fingers, C2H2-type"", ""-"""	29385	protein-coding gene	gene with protein product						11347906	Standard	NM_032453		Approved	KIAA1829	uc010efk.1	Q8NB42	OTTHUMG00000048173	ENST00000436120.2:c.628delA	chr19.hg19:g.37879579delA	ENSP00000390179:p.Lys210fs	87.0	0.0		151.0	10.0	NM_032453	B4DVL5	Frame_Shift_Del	DEL	ENST00000436120.2	hg19	CCDS42559.1																																																																																			.	.		0.333	ZNF527-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458434.1	NM_032453	
MCCC1	56922	hgsc.bcm.edu	37	3	182788998	182788998	+	Splice_Site	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:182788998delT	ENST00000265594.4	-	6	785	c.639delA	c.(637-639)aaa>aa	p.K213fs	MCCC1_ENST00000492597.1_Splice_Site_p.K104fs|MCCC1_ENST00000539926.1_Splice_Site_p.K78fs	NM_020166.3	NP_064551.3	Q96RQ3	MCCA_HUMAN	methylcrotonoyl-CoA carboxylase 1 (alpha)	213	ATP-grasp. {ECO:0000255|PROSITE- ProRule:PRU00409}.|Biotin carboxylation.				biotin metabolic process (GO:0006768)|branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|leucine catabolic process (GO:0006552)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)|methylcrotonoyl-CoA carboxylase activity (GO:0004485)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|liver(1)|lung(17)|ovary(1)|pancreas(2)|prostate(1)|skin(2)	40	all_cancers(143;1.84e-14)|Ovarian(172;0.0355)		all cancers(12;1.8e-44)|Epithelial(37;3.23e-38)|LUSC - Lung squamous cell carcinoma(7;5.04e-25)|Lung(8;5.03e-23)|OV - Ovarian serous cystadenocarcinoma(80;5.07e-21)		Biotin(DB00121)	ACAATCTTACTTTTCCTCCTC	0.433																																					.		Atlas-INDEL	.											.	MCCC1	87	.	0			c.639+1A>-						.						107.0	112.0	110.0					3																	182788998		2203	4300	6503	SO:0001630	splice_region_variant	56922	exon7			.	AF310972	CCDS3241.1	3q27.1	2010-04-30	2010-04-30		ENSG00000078070	ENSG00000078070	6.4.1.4		6936	protein-coding gene	gene with protein product		609010	"""methylcrotonoyl-Coenzyme A carboxylase 1 (alpha)"""			11170888	Standard	XR_241502		Approved	MCCA	uc003fle.3	Q96RQ3	OTTHUMG00000158355	ENST00000265594.4:c.639+1A>-	chr3.hg19:g.182788998delT		144.0	0.0		250.0	17.0	NM_020166	Q59ES4|Q9H959|Q9NS97	Splice_Site	DEL	ENST00000265594.4	hg19	CCDS3241.1																																																																																			.	.		0.433	MCCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350775.1	NM_020166	Frame_Shift_Del
TM6SF1	53346	hgsc.bcm.edu	37	15	83790732	83790732	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:83790732delT	ENST00000322019.9	+	5	732	c.458delT	c.(457-459)gttfs	p.V153fs	TM6SF1_ENST00000565774.1_Frame_Shift_Del_p.V153fs|TM6SF1_ENST00000379386.4_Frame_Shift_Del_p.V156fs|TM6SF1_ENST00000379390.6_Frame_Shift_Del_p.V153fs			Q9BZW5	TM6S1_HUMAN	transmembrane 6 superfamily member 1	153						integral component of membrane (GO:0016021)				endometrium(1)|kidney(3)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	15						AGTGTTGTTGTTTTTGTGCCA	0.318																																					p.V153fs		Atlas-INDEL	.											.	TM6SF1	38	.	0			c.457delG						.						254.0	242.0	246.0					15																	83790732		2203	4299	6502	SO:0001589	frameshift_variant	53346	exon5			.	AF255922	CCDS10323.1, CCDS45338.1	15q24-q26	2003-04-04			ENSG00000136404	ENSG00000136404			11860	protein-coding gene	gene with protein product		606562				11124529	Standard	NM_001144903		Approved		uc002bjp.3	Q9BZW5	OTTHUMG00000147365	ENST00000322019.9:c.458delT	chr15.hg19:g.83790732delT	ENSP00000317000:p.Val153fs	148.0	0.0		220.0	15.0	NM_001144903	A8K7T5|H3BU56|Q4U0U5	Frame_Shift_Del	DEL	ENST00000322019.9	hg19	CCDS10323.1																																																																																			.	.		0.318	TM6SF1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000304009.1	NM_023003	
C10orf105	414152	hgsc.bcm.edu	37	10	73476077	73476077	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:73476077delG	ENST00000441508.2	-	2	217	c.18delC	c.(16-18)cccfs	p.P6fs	CDH23_ENST00000224721.6_Intron|C10orf105_ENST00000398786.2_Frame_Shift_Del_p.P6fs	NM_001164375.2	NP_001157847.1	Q8TEF2	CJ105_HUMAN	chromosome 10 open reading frame 105	6						integral component of membrane (GO:0016021)											TGGCGAGGCTGGGGCCCTCTG	0.622																																					p.S7fs		Atlas-INDEL	.											.	C10orf105	11	.	0			c.19delA						.						22.0	31.0	29.0					10																	73476077		692	1591	2283	SO:0001589	frameshift_variant	414152	exon2			.	AK074172	CCDS44430.1	10q22.1	2012-06-01			ENSG00000214688	ENSG00000214688			20304	protein-coding gene	gene with protein product							Standard	NM_001164375		Approved	FLJ00245	uc001jsa.2	Q8TEF2	OTTHUMG00000018427	ENST00000441508.2:c.18delC	chr10.hg19:g.73476077delG	ENSP00000403151:p.Pro6fs	182.0	0.0		178.0	11.0	NM_001168390		Frame_Shift_Del	DEL	ENST00000441508.2	hg19	CCDS44430.1																																																																																			.	.		0.622	C10orf105-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048551.2	NM_001164375	
PDE12	201626	hgsc.bcm.edu	37	3	57545384	57545384	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:57545384delG	ENST00000311180.8	+	3	1586	c.1483delG	c.(1483-1485)gggfs	p.G495fs	PDE12_ENST00000487257.1_3'UTR	NM_177966.5	NP_808881.3	Q6L8Q7	PDE12_HUMAN	phosphodiesterase 12	495					mRNA processing (GO:0006397)	mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|poly(A)-specific ribonuclease activity (GO:0004535)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(2)|liver(4)|lung(3)|ovary(3)|prostate(1)|skin(1)|urinary_tract(1)	20				KIRC - Kidney renal clear cell carcinoma(284;0.011)|Kidney(284;0.0127)		TATATTTTGTGGGGACTTTAA	0.433																																					p.C494fs	Colon(125;308 1634 19198 50622 50717)	Atlas-INDEL	.											.	PDE12	32	.	0			c.1482delT						.						101.0	100.0	101.0					3																	57545384		2203	4300	6503	SO:0001589	frameshift_variant	201626	exon3			.	AK074423	CCDS33772.1	3p14.3	2013-10-11			ENSG00000174840	ENSG00000174840			25386	protein-coding gene	gene with protein product	"""2'-phosphodiesterase"""					15231837	Standard	NM_177966		Approved	DKFZp667B1218, 2'-PDE	uc003diw.4	Q6L8Q7	OTTHUMG00000158599	ENST00000311180.8:c.1483delG	chr3.hg19:g.57545384delG	ENSP00000309142:p.Gly495fs	166.0	0.0		211.0	13.0	NM_177966	B4DTU8|Q8IYU3|Q8NDU2|Q8TE78	Frame_Shift_Del	DEL	ENST00000311180.8	hg19	CCDS33772.1																																																																																			.	.		0.433	PDE12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351440.2	NM_177966	
DDX58	23586	hgsc.bcm.edu	37	9	32488833	32488833	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:32488833delT	ENST00000379883.2	-	7	1009	c.852delA	c.(850-852)aaafs	p.K284fs	DDX58_ENST00000542096.1_Frame_Shift_Del_p.K213fs|DDX58_ENST00000379868.1_Frame_Shift_Del_p.K81fs|DDX58_ENST00000545044.1_Frame_Shift_Del_p.K81fs|DDX58_ENST00000379882.1_Frame_Shift_Del_p.K239fs	NM_014314.3	NP_055129.2	O95786	DDX58_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 58	284	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.|Interaction with ZC3HAV1.				cytoplasmic pattern recognition receptor signaling pathway in response to virus (GO:0039528)|detection of virus (GO:0009597)|innate immune response (GO:0045087)|negative regulation of type I interferon production (GO:0032480)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell migration (GO:0030334)|regulation of type III interferon production (GO:0034344)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|RIG-I signaling pathway (GO:0039529)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	ATP binding (GO:0005524)|double-stranded DNA binding (GO:0003690)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|identical protein binding (GO:0042802)|single-stranded RNA binding (GO:0003727)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|liver(1)|lung(9)|ovary(2)|pancreas(1)|prostate(1)	27			LUSC - Lung squamous cell carcinoma(29;0.00813)	GBM - Glioblastoma multiforme(74;0.00056)		CTTGTGGGAATTTTTTAAGAT	0.323																																					p.F285fs		Atlas-INDEL	.											.	DDX58	82	.	0			c.853delT						.						72.0	65.0	68.0					9																	32488833		2203	4300	6503	SO:0001589	frameshift_variant	23586	exon7			.	AF038963	CCDS6526.1	9p12	2011-08-05			ENSG00000107201	ENSG00000107201		"""DEAD-boxes"""	19102	protein-coding gene	gene with protein product	"""RNA helicase RIG-I"", ""retinoic acid inducible gene I"""	609631				21690088	Standard	NM_014314		Approved	RIG-I, FLJ13599, DKFZp434J1111	uc003zra.3	O95786	OTTHUMG00000019746	ENST00000379883.2:c.852delA	chr9.hg19:g.32488833delT	ENSP00000369213:p.Lys284fs	140.0	0.0		187.0	12.0	NM_014314	A2RU81|Q5HYE1|Q5VYT1|Q9NT04	Frame_Shift_Del	DEL	ENST00000379883.2	hg19	CCDS6526.1																																																																																			.	.		0.323	DDX58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052011.1	NM_014314	
ANKRD26	22852	hgsc.bcm.edu	37	10	27324168	27324168	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:27324168delT	ENST00000376087.4	-	24	3376	c.3211delA	c.(3211-3213)agtfs	p.S1071fs	ANKRD26_ENST00000376070.3_Frame_Shift_Del_p.S628fs|ANKRD26_ENST00000436985.2_Frame_Shift_Del_p.S1087fs	NM_001256053.1|NM_014915.2	NP_001242982.1|NP_055730.2	Q9UPS8	ANR26_HUMAN	ankyrin repeat domain 26	1070					glucose homeostasis (GO:0042593)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of organ growth (GO:0046621)|regulation of fatty acid metabolic process (GO:0019217)|regulation of feeding behavior (GO:0060259)	actin filament (GO:0005884)|centrosome (GO:0005813)				breast(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|lung(30)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|urinary_tract(2)	70						TTGAGTTTACTTTCAGTTTTA	0.358																																					p.S1071fs		Atlas-INDEL	.											.	ANKRD26	179	.	0			c.3212delG						.						84.0	82.0	82.0					10																	27324168		1838	4092	5930	SO:0001589	frameshift_variant	22852	exon24			.	AB028997	CCDS41499.1	10p12.1	2014-09-17			ENSG00000107890	ENSG00000107890		"""Ankyrin repeat domain containing"""	29186	protein-coding gene	gene with protein product		610855	"""thrombocytopenia 2 (autosomal dominant)"""	THC2		10470851, 21211618	Standard	NM_014915		Approved	KIAA1074	uc009xku.1	Q9UPS8	OTTHUMG00000017851	ENST00000376087.4:c.3211delA	chr10.hg19:g.27324168delT	ENSP00000365255:p.Ser1071fs	138.0	0.0		135.0	10.0	NM_014915	A6NH29|Q2TAZ3|Q6ZR14|Q9H1Q1|Q9NSK9|Q9NTD5|Q9NW69	Frame_Shift_Del	DEL	ENST00000376087.4	hg19	CCDS41499.1																																																																																			.	.		0.358	ANKRD26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047296.1		
PAPOLA	10914	hgsc.bcm.edu	37	14	96991682	96991682	+	Frame_Shift_Del	DEL	A	A	-	rs35783174		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:96991682delA	ENST00000216277.8	+	4	505	c.285delA	c.(283-285)ggafs	p.G95fs	PAPOLA_ENST00000557471.1_Frame_Shift_Del_p.G95fs|PAPOLA_ENST00000554130.1_Intron|PAPOLA_ENST00000557320.1_Frame_Shift_Del_p.G95fs|PAPOLA_ENST00000392990.2_Frame_Shift_Del_p.G95fs	NM_032632.4	NP_116021.2	P51003	PAPOA_HUMAN	poly(A) polymerase alpha	95					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA splicing, via spliceosome (GO:0000398)|RNA polyadenylation (GO:0043631)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|polynucleotide adenylyltransferase activity (GO:0004652)|RNA binding (GO:0003723)			breast(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(6)|skin(1)|urinary_tract(1)	21		all_cancers(154;0.0555)|all_epithelial(191;0.149)|Melanoma(154;0.155)		COAD - Colon adenocarcinoma(157;0.213)		ATGTTGGAGGAAAAATTTTTA	0.299																																					p.G95fs	NSCLC(19;254 734 11908 35501 39234)	Atlas-INDEL	.											.	PAPOLA	58	.	0			c.284delG						.						56.0	62.0	60.0					14																	96991682		2203	4298	6501	SO:0001589	frameshift_variant	10914	exon4			.	X76770	CCDS9946.1, CCDS58334.1, CCDS58335.1	14q32.1-q32.2	2008-02-08				ENSG00000090060	2.7.7.19		14981	protein-coding gene	gene with protein product		605553				8302877, 10429366	Standard	NM_032632		Approved	PAP	uc001yfq.3	P51003		ENST00000216277.8:c.285delA	chr14.hg19:g.96991682delA	ENSP00000216277:p.Gly95fs	112.0	0.0		135.0	10.0	NM_001252006	Q86SX4|Q86TV0|Q8IYF5|Q9BVU2	Frame_Shift_Del	DEL	ENST00000216277.8	hg19	CCDS9946.1																																																																																			.	.		0.299	PAPOLA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413411.2		
AZI2	64343	hgsc.bcm.edu	37	3	28373874	28373874	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:28373874delT	ENST00000479665.1	-	6	1164	c.633delA	c.(631-633)aaafs	p.K211fs	AZI2_ENST00000334100.6_Frame_Shift_Del_p.K211fs|AZI2_ENST00000457172.1_Frame_Shift_Del_p.K211fs|AZI2_ENST00000295748.3_5'UTR|AZI2_ENST00000420543.2_Frame_Shift_Del_p.K211fs	NM_022461.3	NP_071906.1	Q9H6S1	AZI2_HUMAN	5-azacytidine induced 2	211					dendritic cell differentiation (GO:0097028)|dendritic cell proliferation (GO:0044565)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|interferon-alpha production (GO:0032607)|interferon-gamma production (GO:0032609)|interleukin-6 production (GO:0032635)|mitotic cell cycle (GO:0000278)|T cell activation (GO:0042110)|tumor necrosis factor production (GO:0032640)	cytoplasm (GO:0005737)				cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	15						AAATGCTTAGTTTTTGGAGAT	0.313																																					p.L212X		Atlas-INDEL	.											AZI2,NS,carcinoma,0,1	AZI2	33	.	0			c.634delC						.						199.0	185.0	190.0					3																	28373874		2203	4300	6503	SO:0001589	frameshift_variant	64343	exon6			.	AC093142	CCDS2647.1, CCDS46782.1, CCDS46783.1	3p23	2006-03-01			ENSG00000163512	ENSG00000163512			24002	protein-coding gene	gene with protein product		609916				10580148	Standard	NM_001134432		Approved	NAP1, FLJ21939, AZ2	uc003ceb.4	Q9H6S1	OTTHUMG00000130573	ENST00000479665.1:c.633delA	chr3.hg19:g.28373874delT	ENSP00000419371:p.Lys211fs	141.0	0.0		199.0	16.0	NM_001134432	A8K3M2|C9JB40|H7BXU6|Q86W99|Q9BQF1	Frame_Shift_Del	DEL	ENST00000479665.1	hg19	CCDS2647.1																																																																																			.	.		0.313	AZI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252998.2	NM_203326	
UBE2E1	7324	hgsc.bcm.edu	37	3	23929187	23929187	+	Frame_Shift_Del	DEL	A	A	-	rs564357209	byFrequency	TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:23929187delA	ENST00000306627.3	+	4	552	c.333delA	c.(331-333)ccafs	p.P111fs	UBE2E1_ENST00000475680.1_3'UTR|UBE2E1_ENST00000424381.1_Frame_Shift_Del_p.P78fs|UBE2E1_ENST00000346855.3_Frame_Shift_Del_p.P94fs|UBE2E1_ENST00000467766.1_Frame_Shift_Del_p.P78fs	NM_003341.4	NP_003332.1	P51965	UB2E1_HUMAN	ubiquitin-conjugating enzyme E2E 1	111					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cytokine-mediated signaling pathway (GO:0019221)|histone H2B ubiquitination (GO:0033523)|histone monoubiquitination (GO:0010390)|ISG15-protein conjugation (GO:0032020)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K48-linked ubiquitination (GO:0070936)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	ATP binding (GO:0005524)|ISG15 ligase activity (GO:0042296)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(2)|large_intestine(4)	7						TCAAGCCTCCAAAGGTAAGAA	0.383																																					p.P111fs		Atlas-INDEL	.											.	UBE2E1	15	.	0			c.332delC						.						106.0	102.0	103.0					3																	23929187		2203	4300	6503	SO:0001589	frameshift_variant	7324	exon4			.	X92963	CCDS2638.1, CCDS2639.1, CCDS56244.1	3p24.2	2011-05-19	2011-05-19		ENSG00000170142	ENSG00000170142		"""Ubiquitin-conjugating enzymes E2"""	12477	protein-coding gene	gene with protein product		602916	"""ubiquitin-conjugating enzyme E2E 1 (homologous to yeast UBC4/5)"", ""ubiquitin-conjugating enzyme E2E 1 (UBC4/5 homolog, yeast)"""			8576257	Standard	NM_003341		Approved	UbcH6	uc003cch.3	P51965	OTTHUMG00000130483	ENST00000306627.3:c.333delA	chr3.hg19:g.23929187delA	ENSP00000303709:p.Pro111fs	139.0	0.0		179.0	11.0	NM_003341	B2RBX4|C9J8K2|K4DI90	Frame_Shift_Del	DEL	ENST00000306627.3	hg19	CCDS2638.1																																																																																			.	.		0.383	UBE2E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252882.2	NM_003341	
POLR1A	25885	hgsc.bcm.edu	37	2	86265933	86265933	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:86265933delT	ENST00000263857.6	-	27	4302	c.3924delA	c.(3922-3924)aaafs	p.K1308fs	POLR1A_ENST00000409681.1_Frame_Shift_Del_p.K1308fs			O95602	RPA1_HUMAN	polymerase (RNA) I polypeptide A, 194kDa	1308					gene expression (GO:0010467)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase I complex (GO:0005736)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|cervix(2)|endometrium(8)|kidney(3)|large_intestine(12)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	63						ATTTGTTCTGTTTTTCTTCCA	0.502																																					p.Q1309fs		Atlas-INDEL	.											.	POLR1A	137	.	0			c.3925delC						.						106.0	99.0	101.0					2																	86265933		1952	4164	6116	SO:0001589	frameshift_variant	25885	exon27			.	AK025568	CCDS42706.1	2p11.2	2013-01-21			ENSG00000068654	ENSG00000068654		"""RNA polymerase subunits"""	17264	protein-coding gene	gene with protein product						9236775	Standard	NM_015425		Approved	DKFZP586M0122, FLJ21915, RPO1-4, RPA1	uc002sqs.3	O95602	OTTHUMG00000153165	ENST00000263857.6:c.3924delA	chr2.hg19:g.86265933delT	ENSP00000263857:p.Lys1308fs	157.0	0.0		220.0	14.0	NM_015425	B7Z7T0|D6W5M0|Q0VG05|Q9UEH0|Q9UFT9	Frame_Shift_Del	DEL	ENST00000263857.6	hg19	CCDS42706.1																																																																																			.	.		0.502	POLR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329830.2	NM_015425	
CECR1	51816	hgsc.bcm.edu	37	22	17690247	17690247	+	Splice_Site	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr22:17690247delT	ENST00000399839.1	-	2	591	c.321delA	c.(319-321)aaa>aa	p.K107fs	CECR1_ENST00000262607.3_Splice_Site_p.K107fs|CECR1_ENST00000399837.2_Splice_Site_p.K107fs|CECR1_ENST00000449907.2_Splice_Site_p.K65fs	NM_001282227.1|NM_001282228.1	NP_001269156.1|NP_001269157.1	Q9NZK5	CECR1_HUMAN	cat eye syndrome chromosome region, candidate 1	107					adenosine catabolic process (GO:0006154)|hypoxanthine salvage (GO:0043103)|inosine biosynthetic process (GO:0046103)|multicellular organismal development (GO:0007275)	extracellular space (GO:0005615)	adenosine deaminase activity (GO:0004000)|adenosine receptor binding (GO:0031685)|growth factor activity (GO:0008083)|heparin binding (GO:0008201)|protein homodimerization activity (GO:0042803)|proteoglycan binding (GO:0043394)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(6)|liver(1)|lung(10)|ovary(2)|prostate(2)|stomach(1)	25		all_epithelial(15;0.0152)|Lung NSC(13;0.0875)|all_lung(157;0.106)				AAACCTTACCTTTTGGCATCA	0.483																																					p.G108fs		Atlas-INDEL	.											.	CECR1	77	.	0			c.322delG						.						56.0	53.0	54.0					22																	17690247		2203	4300	6503	SO:0001630	splice_region_variant	51816	exon1			.	AF190746	CCDS13742.1, CCDS13743.1, CCDS63395.1, CCDS74809.1	22q11.2	2008-02-22			ENSG00000093072	ENSG00000093072			1839	protein-coding gene	gene with protein product		607575		IDGFL		10756095	Standard	NM_001282225		Approved	ADGF	uc002zmk.1	Q9NZK5	OTTHUMG00000030726	ENST00000399839.1:c.322+1A>-	chr22.hg19:g.17690247delT		163.0	0.0		161.0	10.0	NM_017424	A8K9H4|Q6ICF1|Q86UB6|Q8NCJ2|Q96K41	Frame_Shift_Del	DEL	ENST00000399839.1	hg19	CCDS13742.1																																																																																			.	.		0.483	CECR1-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316079.1		Frame_Shift_Del
SLC3A2	6520	hgsc.bcm.edu	37	11	62649372	62649372	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:62649372delG	ENST00000377890.2	+	5	903	c.735delG	c.(733-735)aagfs	p.K245fs	SLC3A2_ENST00000536981.1_5'UTR|SLC3A2_ENST00000338663.7_Frame_Shift_Del_p.K144fs|SLC3A2_ENST00000535296.1_Frame_Shift_Del_p.K214fs|SLC3A2_ENST00000377892.1_Frame_Shift_Del_p.K276fs|SLC3A2_ENST00000377891.2_Frame_Shift_Del_p.K246fs|SLC3A2_ENST00000377889.2_Frame_Shift_Del_p.K183fs|SLC3A2_ENST00000538682.1_3'UTR	NM_002394.5	NP_002385.3	P08195	4F2_HUMAN	solute carrier family 3 (amino acid transporter heavy chain), member 2	245					amino acid transport (GO:0006865)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|carbohydrate metabolic process (GO:0005975)|cell growth (GO:0016049)|ion transport (GO:0006811)|leucine import (GO:0060356)|leukocyte migration (GO:0050900)|response to exogenous dsRNA (GO:0043330)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|tryptophan transport (GO:0015827)	cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium:sodium antiporter activity (GO:0005432)|catalytic activity (GO:0003824)|cation binding (GO:0043169)|double-stranded RNA binding (GO:0003725)|neutral amino acid transmembrane transporter activity (GO:0015175)|poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(3)|large_intestine(2)|lung(12)|ovary(1)|prostate(1)|skin(2)	22						CAGGTCTGAAGGGGCGTCTCG	0.592																																					p.K246fs		Atlas-INDEL	.											.	SLC3A2	55	.	0			c.737delA						.						84.0	84.0	84.0					11																	62649372		2201	4298	6499	SO:0001589	frameshift_variant	6520	exon5			.		CCDS8039.2, CCDS31588.1, CCDS31589.1, CCDS31590.1	11q12-q22	2013-07-19	2013-07-19		ENSG00000168003	ENSG00000168003		"""Solute carriers"""	11026	protein-coding gene	gene with protein product	"""antigen identified by monoclonal antibodies 4F2, TRA1.10, TROP4, and T43"", ""antigen defined by monoclonal antibody 4F2"", ""heavy chain"", ""4F2 heavy chain"", ""CD98 heavy chain"", ""monoclonal antibody 44D7"", ""4F2 cell-surface antigen heavy chain"", ""lymphocyte activation antigen 4F2 large subunit"""	158070	"""solute carrier family 3 (activators of dibasic and neutral amino acid transport), member 2"""	MDU1		3036867	Standard	NM_001012662		Approved	4T2HC, 4F2, NACAE, CD98, CD98HC, 4F2HC	uc001nwd.3	P08195	OTTHUMG00000074091	ENST00000377890.2:c.735delG	chr11.hg19:g.62649372delG	ENSP00000367122:p.Lys245fs	99.0	0.0		122.0	10.0	NM_001012662	Q13543	Frame_Shift_Del	DEL	ENST00000377890.2	hg19	CCDS8039.2																																																																																			.	.		0.592	SLC3A2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000157306.1	NM_001012661	
CPSF3L	54973	hgsc.bcm.edu	37	1	1256455	1256455	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:1256455delC	ENST00000435064.1	-	2	129	c.47delG	c.(46-48)ggcfs	p.G16fs	CPSF3L_ENST00000450926.2_Frame_Shift_Del_p.G16fs|CPSF3L_ENST00000411962.1_Intron|CPSF3L_ENST00000545578.1_5'UTR|CPSF3L_ENST00000421495.2_Intron|RP5-890O3.9_ENST00000444968.1_RNA|CPSF3L_ENST00000419704.1_Frame_Shift_Del_p.G16fs|CPSF3L_ENST00000540437.1_Frame_Shift_Del_p.G22fs	NM_001256460.1|NM_017871.5	NP_001243389.1|NP_060341.2	Q5TA45	INT11_HUMAN	cleavage and polyadenylation specific factor 3-like	16					snRNA processing (GO:0016180)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|integrator complex (GO:0032039)	hydrolase activity (GO:0016787)			endometrium(4)|kidney(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(3)	13	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;6.71e-35)|OV - Ovarian serous cystadenocarcinoma(86;4.35e-21)|Colorectal(212;0.000166)|COAD - Colon adenocarcinoma(227;0.000196)|Kidney(185;0.00235)|BRCA - Breast invasive adenocarcinoma(365;0.00255)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0349)|Lung(427;0.201)		GCAGCTTCGGCCCACGTCCTG	0.647																																					p.G22fs		Atlas-INDEL	.											.	CPSF3L	33	.	0			c.66delC						.						101.0	91.0	95.0					1																	1256455		2203	4300	6503	SO:0001589	frameshift_variant	54973	exon4			.	AL136813	CCDS21.1, CCDS57959.1, CCDS57960.1, CCDS57961.1, CCDS72678.1	1p36.33	2008-02-05			ENSG00000127054	ENSG00000127054			26052	protein-coding gene	gene with protein product	"""integrator complex subunit 11"""	611354				15684398, 16239144	Standard	NM_001256456		Approved	FLJ20542, RC-68, CPSF73L, INT11, INTS11	uc001aee.2	Q5TA45	OTTHUMG00000003330	ENST00000435064.1:c.47delG	chr1.hg19:g.1256455delC	ENSP00000413493:p.Gly16fs	194.0	0.0		199.0	12.0	NM_001256456	A8K5S2|B3KPR3|B4DM87|G3V1S5|Q5TA46|Q5TA48|Q5TA52|Q5TA53|Q5TA54|Q7L3D7|Q96HY1|Q9BW36|Q9H0F9|Q9H8R5|Q9HAA6|Q9NWX9	Frame_Shift_Del	DEL	ENST00000435064.1	hg19	CCDS21.1																																																																																			.	.		0.647	CPSF3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009360.2	NM_017871	
GOLGA2	2801	hgsc.bcm.edu	37	9	131036199	131036199	+	Frame_Shift_Del	DEL	T	T	-	rs142168936		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:131036199delT	ENST00000421699.2	-	2	149	c.137delA	c.(136-138)aagfs	p.K49fs	GOLGA2_ENST00000609374.1_Frame_Shift_Del_p.K37fs|GOLGA2_ENST00000490628.1_Frame_Shift_Del_p.K49fs|SWI5_ENST00000418976.1_5'Flank|SWI5_ENST00000608796.1_5'Flank|SWI5_ENST00000419867.2_5'Flank|SWI5_ENST00000320188.5_5'Flank|SWI5_ENST00000495313.1_5'Flank	NM_004486.4	NP_004477.3	Q08379	GOGA2_HUMAN	golgin A2	49	Poly-Lys.				mitotic cell cycle (GO:0000278)	cis-Golgi network (GO:0005801)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)				NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(10)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	34						TTTCTTCTTCTTTTTCGCTCC	0.468																																					p.K46fs		Atlas-INDEL	.											.	GOLGA2	69	.	0			c.138delG						.						157.0	172.0	167.0					9																	131036199		2203	4300	6503	SO:0001589	frameshift_variant	2801	exon2			.	L06147	CCDS6896.2	9q34.13	2010-06-28	2010-02-12		ENSG00000167110	ENSG00000167110			4425	protein-coding gene	gene with protein product	"""Golgi matrix protein GM130"", ""SY11 protein"""	602580	"""golgi autoantigen, golgin subfamily a, 2"""			8315394	Standard	NM_004486		Approved	GM130, golgin-95	uc011maw.2	Q08379	OTTHUMG00000020732	ENST00000421699.2:c.137delA	chr9.hg19:g.131036199delT	ENSP00000416097:p.Lys49fs	182.0	0.0		187.0	14.0	NM_004486	Q6GRM9|Q9BRB0|Q9NYF9	Frame_Shift_Del	DEL	ENST00000421699.2	hg19	CCDS6896.2																																																																																			.	.		0.468	GOLGA2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054358.2	NM_004486	
TBX10	347853	hgsc.bcm.edu	37	11	67402373	67402373	+	Frame_Shift_Del	DEL	G	G	-	rs144542807		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:67402373delG	ENST00000335385.3	-	3	378	c.291delC	c.(289-291)cccfs	p.P97fs		NM_005995.4	NP_005986.2	O75333	TBX10_HUMAN	T-box 10	97					anatomical structure morphogenesis (GO:0009653)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|lung(4)|ovary(1)	7						TCACCTGGAAGGGGGGGAACA	0.677																																					p.F98fs		Atlas-INDEL	.											.	TBX10	25	.	0			c.292delT						.						50.0	49.0	49.0					11																	67402373		2200	4294	6494	SO:0001589	frameshift_variant	347853	exon3			.	AH006177	CCDS31621.1	11q13.2	2005-10-11	2004-10-05		ENSG00000167800	ENSG00000167800		"""T-boxes"""	11593	protein-coding gene	gene with protein product		604648	"""T-box 7"""	TBX7		9545502	Standard	NM_005995		Approved	TBX13	uc001omp.3	O75333	OTTHUMG00000167291	ENST00000335385.3:c.291delC	chr11.hg19:g.67402373delG	ENSP00000335191:p.Pro97fs	107.0	0.0		178.0	11.0	NM_005995	Q14D64|Q86XS3	Frame_Shift_Del	DEL	ENST00000335385.3	hg19	CCDS31621.1																																																																																			.	.		0.677	TBX10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394034.1	NM_005995	
C10orf55	414236	hgsc.bcm.edu	37	10	75673438	75673438	+	Intron	DEL	G	G	-	rs549461157	byFrequency	TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:75673438delG	ENST00000409178.1	-	3	268				PLAU_ENST00000372764.3_Frame_Shift_Del_p.R201fs|PLAU_ENST00000372762.4_Frame_Shift_Del_p.R165fs|C10orf55_ENST00000412307.2_Intron|PLAU_ENST00000446342.1_Frame_Shift_Del_p.R184fs|PLAU_ENST00000494287.1_3'UTR	NM_001001791.2	NP_001001791.2	Q5SWW7	CJ055_HUMAN	chromosome 10 open reading frame 55											endometrium(1)	1	Prostate(51;0.0112)					AGGAGGCACCGGGGGGGCTCT	0.587																																					p.R201fs		Atlas-INDEL	.											.,1	PLAU	47	.	0			c.601delC						.		,,	17,4245		5,7,2119					,,	2.0	0.9			66	27,8227		11,5,4111	no	frameshift,frameshift,intron	PLAU,C10orf55	NM_002658.3,NM_001145031.1,NM_001001791.2	,,	16,12,6230	A1A1,A1R,RR		0.3271,0.3989,0.3516	,,	,,		44,12472				SO:0001627	intron_variant	5328	exon7			.		CCDS53541.1	10q22.2	2012-05-24			ENSG00000222047	ENSG00000222047			31008	protein-coding gene	gene with protein product							Standard	NM_001001791		Approved	bA417O11.3	uc001jvz.2	Q5SWW7	OTTHUMG00000018496	ENST00000409178.1:c.73-605C>-	chr10.hg19:g.75673438delG		156.0	0.0		186.0	12.0	NM_002658	Q3KRG4|Q8NAK4	Frame_Shift_Del	DEL	ENST00000409178.1	hg19	CCDS53541.1																																																																																			.	.		0.587	C10orf55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048746.1	NM_001001791	
TAOK2	9344	hgsc.bcm.edu	37	16	29998911	29998911	+	Frame_Shift_Del	DEL	G	G	-	rs200539809		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:29998911delG	ENST00000308893.4	+	16	4361	c.3318delG	c.(3316-3318)gtgfs	p.V1106fs	TAOK2_ENST00000543033.1_Frame_Shift_Del_p.V993fs|TAOK2_ENST00000416441.2_Frame_Shift_Del_p.V933fs|TAOK2_ENST00000279394.3_Intron	NM_001252043.1|NM_016151.3	NP_001238972.1|NP_057235.2	Q9UL54	TAOK2_HUMAN	TAO kinase 2	1106					actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|apoptotic process (GO:0006915)|cell migration (GO:0016477)|cellular response to DNA damage stimulus (GO:0006974)|focal adhesion assembly (GO:0048041)|G2 DNA damage checkpoint (GO:0031572)|positive regulation of JNK cascade (GO:0046330)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein targeting to membrane (GO:0006612)|regulation of cell growth (GO:0001558)|regulation of cell shape (GO:0008360)|response to stress (GO:0006950)|stress-activated MAPK cascade (GO:0051403)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleolus (GO:0005730)|nucleus (GO:0005634)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|mitogen-activated protein kinase kinase binding (GO:0031434)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(3)|large_intestine(5)|lung(8)|ovary(1)|prostate(3)|skin(1)	22						GTGGGGCTGTGGGGGACCGGG	0.697																																					p.V1106fs		Atlas-INDEL	.											.	TAOK2	142	.	0			c.3317delT						.						52.0	61.0	58.0					16																	29998911		2197	4299	6496	SO:0001589	frameshift_variant	9344	exon16			.	AB020688	CCDS10662.1, CCDS10663.1, CCDS58448.1	16p11.2	2008-02-05			ENSG00000149930	ENSG00000149930			16835	protein-coding gene	gene with protein product		613199				10048485, 9786855	Standard	NM_016151		Approved	TAO1, KIAA0881, PSK, PSK1, TAO2, MAP3K17	uc002dva.2	Q9UL54	OTTHUMG00000132111	ENST00000308893.4:c.3318delG	chr16.hg19:g.29998911delG	ENSP00000310094:p.Val1106fs	104.0	0.0		179.0	13.0	NM_016151	A5PKY1|A7MCZ2|B2RN35|B7ZM88|O94957|Q6UW73|Q7LC09|Q9NSW2	Frame_Shift_Del	DEL	ENST00000308893.4	hg19	CCDS10663.1																																																																																			.	.		0.697	TAOK2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255152.2	NM_016151	
SLC38A11	151258	hgsc.bcm.edu	37	2	165755103	165755103	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:165755103delA	ENST00000409149.3	-	11	1356	c.1065delT	c.(1063-1065)tttfs	p.F355fs	RNA5SP111_ENST00000411386.1_RNA|SLC38A11_ENST00000409662.1_Frame_Shift_Del_p.F355fs|SLC38A11_ENST00000409058.1_Frame_Shift_Del_p.F386fs|SLC38A11_ENST00000303735.4_Frame_Shift_Del_p.F333fs	NM_001199148.1	NP_001186077.1	Q08AI6	S38AB_HUMAN	solute carrier family 38, member 11	355					amino acid transport (GO:0006865)|sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)				endometrium(2)|large_intestine(4)|lung(8)|ovary(1)	15						TGACGAATCCAAAAACCATCA	0.433																																					p.G356fs		Atlas-INDEL	.											.	SLC38A11	41	.	0			c.1066delG						.						130.0	114.0	119.0					2																	165755103		2203	4300	6503	SO:0001589	frameshift_variant	151258	exon11			.		CCDS2224.1, CCDS56142.1	2q24.3	2013-05-22			ENSG00000169507	ENSG00000169507		"""Solute carriers"""	26836	protein-coding gene	gene with protein product							Standard	NM_173512		Approved	FLJ39822, AVT2	uc002ucw.2	Q08AI6	OTTHUMG00000132144	ENST00000409149.3:c.1065delT	chr2.hg19:g.165755103delA	ENSP00000386272:p.Phe355fs	135.0	0.0		179.0	11.0	NM_001199148	B4DF99|Q8N887	Frame_Shift_Del	DEL	ENST00000409149.3	hg19	CCDS56142.1																																																																																			.	.		0.433	SLC38A11-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333390.1	NM_173512	
ITGB8	3696	hgsc.bcm.edu	37	7	20438514	20438514	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:20438514delA	ENST00000222573.4	+	9	1862	c.1178delA	c.(1177-1179)gaafs	p.E393fs	ITGB8_ENST00000537992.1_Frame_Shift_Del_p.E258fs	NM_002214.2	NP_002205.1	P26012	ITB8_HUMAN	integrin, beta 8	393					cartilage development (GO:0051216)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|ganglioside metabolic process (GO:0001573)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of gene expression (GO:0010629)|placenta blood vessel development (GO:0060674)|positive regulation of gene expression (GO:0010628)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integrin alphav-beta8 complex (GO:0034686)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	extracellular matrix protein binding (GO:1990430)|receptor activity (GO:0004872)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(17)|prostate(2)|skin(4)|stomach(2)|urinary_tract(1)	37						GTTCAGGTGGAAAACCAGGTA	0.418																																					p.E393fs		Atlas-INDEL	.											.	ITGB8	159	.	0			c.1177delG						.						100.0	97.0	98.0					7																	20438514		2203	4300	6503	SO:0001589	frameshift_variant	3696	exon9			.		CCDS5370.1	7p15.3	2010-03-23			ENSG00000105855	ENSG00000105855		"""Integrins"""	6163	protein-coding gene	gene with protein product		604160					Standard	XM_005249751		Approved		uc003suu.3	P26012	OTTHUMG00000023594	ENST00000222573.4:c.1178delA	chr7.hg19:g.20438514delA	ENSP00000222573:p.Glu393fs	135.0	0.0		181.0	12.0	NM_002214	A4D133|B4DHD4	Frame_Shift_Del	DEL	ENST00000222573.4	hg19	CCDS5370.1																																																																																			.	.		0.418	ITGB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059915.3	NM_002214	
ADCY6	112	hgsc.bcm.edu	37	12	49170245	49170245	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:49170245delG	ENST00000307885.4	-	6	2195	c.1501delC	c.(1501-1503)ctgfs	p.L501fs	ADCY6_ENST00000550422.1_Frame_Shift_Del_p.L501fs|ADCY6_ENST00000357869.3_Frame_Shift_Del_p.L501fs|ADCY6_ENST00000552090.1_5'UTR	NM_015270.3	NP_056085.1	O43306	ADCY6_HUMAN	adenylate cyclase 6	501					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cAMP biosynthetic process (GO:0006171)|cellular response to catecholamine stimulus (GO:0071870)|cellular response to glucagon stimulus (GO:0071377)|cellular response to prostaglandin E stimulus (GO:0071380)|dopamine receptor signaling pathway (GO:0007212)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|negative regulation of neuron projection development (GO:0010977)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cilium (GO:0005929)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)			breast(1)|endometrium(6)|kidney(1)|large_intestine(2)|lung(16)|prostate(1)|skin(1)|urinary_tract(1)	29						TGGTTGGCCAGGGTCACATCA	0.647																																					p.L501fs		Atlas-INDEL	.											.	ADCY6	81	.	0			c.1502delT						.						61.0	56.0	58.0					12																	49170245		2203	4299	6502	SO:0001589	frameshift_variant	112	exon7			.		CCDS8767.1, CCDS8768.1	12q12-q13	2013-02-04				ENSG00000174233	4.6.1.1	"""Adenylate cyclases"""	237	protein-coding gene	gene with protein product		600294					Standard	NM_015270		Approved	AC6	uc001rsh.4	O43306		ENST00000307885.4:c.1501delC	chr12.hg19:g.49170245delG	ENSP00000311405:p.Leu501fs	128.0	0.0		104.0	10.0	NM_020983	Q9NR75|Q9UDB0	Frame_Shift_Del	DEL	ENST00000307885.4	hg19	CCDS8767.1																																																																																			.	.		0.647	ADCY6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408863.1	NM_020983	
GLYCTK	132158	hgsc.bcm.edu	37	3	52328238	52328238	+	IGR	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:52328238delC	ENST00000436784.2	+	0	1982				GLYCTK-AS1_ENST00000493616.1_RNA|GLYCTK_ENST00000354773.4_3'UTR|GLYCTK-AS1_ENST00000472761.1_RNA|MIR135A1_ENST00000385191.1_RNA			Q8IVS8	GLCTK_HUMAN	glycerate kinase						protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|glycerate kinase activity (GO:0008887)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|urinary_tract(1)	9				BRCA - Breast invasive adenocarcinoma(193;3.56e-05)|Kidney(197;0.00171)|KIRC - Kidney renal clear cell carcinoma(197;0.00194)|OV - Ovarian serous cystadenocarcinoma(275;0.235)		CGCTGGCTGTCCCCGCCGTGC	0.592																																					.		Atlas-INDEL	.											.	.	.	.	0			.						.						83.0	87.0	86.0					3																	52328238		1568	3582	5150	SO:0001628	intergenic_variant	406925	.			.		CCDS2852.1, CCDS46841.1	3p21.1	2008-01-22			ENSG00000168237	ENSG00000168237	2.7.1.31		24247	protein-coding gene	gene with protein product		610516				16753811	Standard	NM_145262		Approved	HBEBP4, HBEBP2	uc003ddo.3	Q8IVS8	OTTHUMG00000158380		chr3.hg19:g.52328238delC		164.0	0.0		152.0	10.0	.	Q0P630|Q2EZ43|Q6Y2K6|Q7Z6G5|Q86YR8|Q8TED2|Q8WTY2	RNA	DEL	ENST00000436784.2	hg19	CCDS2852.1																																																																																			.	.		0.592	GLYCTK-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350835.1	NM_145262	
PPP4R1L	55370	hgsc.bcm.edu	37	20	56826860	56826860	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr20:56826860delG	ENST00000334187.8	-	6	509	c.496delC	c.(496-498)cgafs	p.R166fs	PPP4R1L_ENST00000244070.3_Frame_Shift_Del_p.R137fs|PPP4R1L_ENST00000462333.1_5'UTR			Q9P1A2	PP4RL_HUMAN	protein phosphatase 4, regulatory subunit 1-like	166																	TCACAGAATCGGGGGAGTAGC	0.343																																					.		Atlas-INDEL	.											.	PPP4R1L	1	.	0			.						.																																			SO:0001589	frameshift_variant	55370	.			.	AF119843		20q13.32	2013-03-28			ENSG00000124224	ENSG00000124224			15755	other	unknown				C20orf192		14702039, 11780052	Standard	NR_003505		Approved	bA196N14.4, bA196N14.5	uc002xyy.1	Q9P1A2	OTTHUMG00000032838	ENST00000334187.8:c.496delC	chr20.hg19:g.56826860delG	ENSP00000335579:p.Arg166fs	173.0	0.0		286.0	20.0	.	B4DRM4|Q96LY6|Q9BZ17|Q9BZ18	RNA	DEL	ENST00000334187.8	hg19																																																																																				.	.		0.343	PPP4R1L-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NR_003505	
EDAR	10913	hgsc.bcm.edu	37	2	109546604	109546604	+	Frame_Shift_Del	DEL	G	G	-	rs375891208		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:109546604delG	ENST00000258443.2	-	3	576	c.146delC	c.(145-147)ccgfs	p.P49fs	EDAR_ENST00000376651.1_Frame_Shift_Del_p.P49fs|EDAR_ENST00000409271.1_Frame_Shift_Del_p.P49fs	NM_022336.3	NP_071731.1	Q9UNE0	EDAR_HUMAN	ectodysplasin A receptor	49					apoptotic process (GO:0006915)|cell differentiation (GO:0030154)|epidermis development (GO:0008544)|hair follicle development (GO:0001942)|odontogenesis of dentin-containing tooth (GO:0042475)|pigmentation (GO:0043473)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|salivary gland cavitation (GO:0060662)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(6)|prostate(1)|skin(1)	16						CGGCCCACACGGGGGGCACTC	0.632																																					p.P49fs		Atlas-INDEL	.											.,1	EDAR	49	.	0			c.147delG						.						54.0	49.0	51.0					2																	109546604		2203	4300	6503	SO:0001589	frameshift_variant	10913	exon3			.	AF130988	CCDS2081.1	2q13	2013-05-22	2004-08-09		ENSG00000135960	ENSG00000135960		"""Tumor necrosis factor receptor superfamily"""	2895	protein-coding gene	gene with protein product		604095	"""ectodysplasin 1, anhidrotic receptor"""	ED3, DL		10431241, 9375732	Standard	NM_022336		Approved	ED5, EDA3, Edar, ED1R, EDA1R	uc002teq.4	Q9UNE0	OTTHUMG00000130982	ENST00000258443.2:c.146delC	chr2.hg19:g.109546604delG	ENSP00000258443:p.Pro49fs	196.0	0.0		258.0	17.0	NM_022336	B2R9H2|B4DLC5|D3DX74|E9PC98|Q52LL5|Q9UND9	Frame_Shift_Del	DEL	ENST00000258443.2	hg19	CCDS2081.1																																																																																			.	.		0.632	EDAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253595.1		
APEX2	27301	hgsc.bcm.edu	37	X	55033694	55033694	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:55033694delG	ENST00000374987.3	+	6	1449	c.1383delG	c.(1381-1383)gcgfs	p.A461fs	ALAS2_ENST00000498636.1_5'Flank	NM_014481.2	NP_055296.2	Q9UBZ4	APEX2_HUMAN	APEX nuclease (apurinic/apyrimidinic endonuclease) 2	461					base-excision repair (GO:0006284)|cell cycle (GO:0007049)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA catabolic process, exonucleolytic (GO:0000738)|DNA recombination (GO:0006310)	mitochondrial inner membrane (GO:0005743)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|double-stranded DNA 3'-5' exodeoxyribonuclease activity (GO:0008311)|zinc ion binding (GO:0008270)			breast(1)|endometrium(8)|large_intestine(4)|lung(6)|prostate(1)|urinary_tract(1)	21						CTGTGCTGGCGGGGCCCTTGC	0.582								Other BER factors																													p.A461fs		Atlas-INDEL	.											.	APEX2	50	.	0			c.1382delC						.						41.0	32.0	35.0					X																	55033694		2203	4300	6503	SO:0001589	frameshift_variant	27301	exon6			.	AB021260	CCDS14365.1	Xp11.23	2014-02-18			ENSG00000169188	ENSG00000169188	4.2.99.18		17889	protein-coding gene	gene with protein product	"""zinc finger, GRF-type containing 2"""	300773				11376153	Standard	NM_014481		Approved	APEXL2, APE2, XTH2, ZGRF2	uc004dtz.4	Q9UBZ4	OTTHUMG00000021642	ENST00000374987.3:c.1383delG	chrX.hg19:g.55033694delG	ENSP00000364126:p.Ala461fs	122.0	0.0		147.0	10.0	NM_014481	Q9Y5X7	Frame_Shift_Del	DEL	ENST00000374987.3	hg19	CCDS14365.1																																																																																			.	.		0.582	APEX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056845.1		
SLC1A2	6506	hgsc.bcm.edu	37	11	35333900	35333900	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:35333900delC	ENST00000278379.3	-	4	688	c.406delG	c.(406-408)gtcfs	p.V136fs	SLC1A2_ENST00000395753.1_Frame_Shift_Del_p.V127fs|SLC1A2_ENST00000606205.1_Frame_Shift_Del_p.V136fs|SLC1A2_ENST00000395750.1_Frame_Shift_Del_p.V127fs	NM_004171.3	NP_004162.2	P43004	EAA2_HUMAN	solute carrier family 1 (glial high affinity glutamate transporter), member 2	136					adult behavior (GO:0030534)|cellular response to extracellular stimulus (GO:0031668)|D-aspartate import (GO:0070779)|ion transport (GO:0006811)|L-glutamate import (GO:0051938)|multicellular organism growth (GO:0035264)|multicellular organismal aging (GO:0010259)|positive regulation of glucose import (GO:0046326)|response to amino acid (GO:0043200)|response to drug (GO:0042493)|response to wounding (GO:0009611)|synaptic transmission (GO:0007268)|telencephalon development (GO:0021537)|transmembrane transport (GO:0055085)|visual behavior (GO:0007632)	axolemma (GO:0030673)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glutamate:sodium symporter activity (GO:0015501)|L-glutamate transmembrane transporter activity (GO:0005313)|sodium:dicarboxylate symporter activity (GO:0017153)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(11)|ovary(2)|prostate(1)|urinary_tract(1)	24	all_lung(20;0.211)|all_epithelial(35;0.234)	all_hematologic(20;0.109)	STAD - Stomach adenocarcinoma(6;0.00731)			ACCAGAATGACCCCCAGTACT	0.552																																					p.V136fs	NSCLC(100;1273 1575 12993 16869 47409)|Ovarian(164;45 1946 8965 30452 48454)	Atlas-INDEL	.											.	SLC1A2	54	.	0			c.407delT						.						179.0	165.0	170.0					11																	35333900		2202	4298	6500	SO:0001589	frameshift_variant	6506	exon4			.	AB209444	CCDS31459.1, CCDS55756.1	11p13-p12	2013-05-22			ENSG00000110436	ENSG00000110436		"""Solute carriers"""	10940	protein-coding gene	gene with protein product		600300				1448170	Standard	NM_004171		Approved	GLT-1, EAAT2	uc001mwd.3	P43004	OTTHUMG00000044391	ENST00000278379.3:c.406delG	chr11.hg19:g.35333900delC	ENSP00000278379:p.Val136fs	140.0	0.0		157.0	11.0	NM_004171	B4DQE9|Q14417|Q541G6|U3KQQ4	Frame_Shift_Del	DEL	ENST00000278379.3	hg19	CCDS31459.1																																																																																			.	.		0.552	SLC1A2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000258181.1	NM_004171	
MAPK4	5596	hgsc.bcm.edu	37	18	48190827	48190827	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr18:48190827delG	ENST00000400384.2	+	2	1535	c.499delG	c.(499-501)gggfs	p.G167fs	MAPK4_ENST00000588540.1_Frame_Shift_Del_p.G167fs|MAPK4_ENST00000592595.1_Frame_Shift_Del_p.G167fs|MAPK4_ENST00000587823.1_3'UTR|MAPK4_ENST00000540640.1_Intron	NM_002747.3	NP_002738.2	P31152	MK04_HUMAN	mitogen-activated protein kinase 4	167	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell cycle (GO:0007049)|MAPK cascade (GO:0000165)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|MAP kinase activity (GO:0004707)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)			lung(4)|skin(3)|upper_aerodigestive_tract(1)	8		Colorectal(6;0.0297)		Colorectal(21;0.156)		GCTCAAGATTGGGGATTTCGG	0.552																																					p.I166fs		Atlas-INDEL	.											.	MAPK4	75	.	0			c.498delT						.						67.0	68.0	68.0					18																	48190827		2173	4281	6454	SO:0001589	frameshift_variant	5596	exon2			.	X59727	CCDS42437.1	18q21.1	2012-10-02			ENSG00000141639	ENSG00000141639		"""Mitogen-activated protein kinase cascade / Kinases"""	6878	protein-coding gene	gene with protein product		176949		PRKM4		8290275	Standard	XM_005258299		Approved	Erk3-related, Erk4	uc002lev.3	P31152	OTTHUMG00000179853	ENST00000400384.2:c.499delG	chr18.hg19:g.48190827delG	ENSP00000383234:p.Gly167fs	106.0	0.0		157.0	10.0	NM_002747	A1A4C4|Q0VG04	Frame_Shift_Del	DEL	ENST00000400384.2	hg19	CCDS42437.1																																																																																			.	.		0.552	MAPK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448631.2	NM_002747	
PIK3CD	5293	hgsc.bcm.edu	37	1	9713912	9713912	+	Intron	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:9713912delT	ENST00000377346.4	+	1	58				C1orf200_ENST00000377320.3_Frame_Shift_Del_p.K143fs|PIK3CD_ENST00000536656.1_Intron	NM_005026.3	NP_005017.3	O00329	PK3CD_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit delta						adaptive immune response (GO:0002250)|B cell activation (GO:0042113)|B cell chemotaxis (GO:0035754)|B cell homeostasis (GO:0001782)|B cell receptor signaling pathway (GO:0050853)|cytokine production (GO:0001816)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|mast cell chemotaxis (GO:0002551)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|natural killer cell activation (GO:0030101)|natural killer cell chemotaxis (GO:0035747)|natural killer cell differentiation (GO:0001779)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil chemotaxis (GO:0030593)|neutrophil extravasation (GO:0072672)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|protein phosphorylation (GO:0006468)|respiratory burst involved in defense response (GO:0002679)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|T cell activation (GO:0042110)|T cell chemotaxis (GO:0010818)|T cell differentiation (GO:0030217)|T cell receptor signaling pathway (GO:0050852)	cytosol (GO:0005829)|mast cell granule (GO:0042629)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)			central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(12)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	31	all_lung(157;0.222)	all_lung(118;2.44e-05)|Lung NSC(185;4.08e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00314)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0231)|Colorectal(212;7.52e-08)|COAD - Colon adenocarcinoma(227;1.78e-05)|Kidney(185;0.000322)|KIRC - Kidney renal clear cell carcinoma(229;0.00114)|BRCA - Breast invasive adenocarcinoma(304;0.0021)|STAD - Stomach adenocarcinoma(132;0.00395)|READ - Rectum adenocarcinoma(331;0.0419)	Caffeine(DB00201)	CTTGGTCCTCTTTTGGTGCTT	0.522																																					.		Atlas-INDEL	.											.	C1orf200	19	.	0			.						.						96.0	98.0	98.0					1																	9713912		1888	4120	6008	SO:0001627	intron_variant	644997	.			.		CCDS104.1	1p36.2	2014-09-17	2012-07-13		ENSG00000171608	ENSG00000171608	2.7.1.153		8977	protein-coding gene	gene with protein product	"""phosphatidylinositol 3-kinase, catalytic, delta polypeptide"", ""phosphoinositide-3-kinase C"""	602839	"""phosphoinositide-3-kinase, catalytic, delta polypeptide"""			9113989, 9455486	Standard	NM_005026		Approved	p110D	uc001aqb.4	O00329	OTTHUMG00000001450	ENST00000377346.4:c.-138+2052T>-	chr1.hg19:g.9713912delT		166.0	0.0		181.0	11.0	.	A6NCG0|G1FFP1|O15445|Q5SR49	RNA	DEL	ENST00000377346.4	hg19	CCDS104.1																																																																																			.	.		0.522	PIK3CD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004235.1	NM_005026	
MYNN	55892	hgsc.bcm.edu	37	3	169504444	169504444	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:169504444delT	ENST00000349841.5	+	8	2474	c.1811delT	c.(1810-1812)attfs	p.I604fs	MYNN_ENST00000356716.4_Frame_Shift_Del_p.I604fs|MYNN_ENST00000544106.1_Frame_Shift_Del_p.I575fs	NM_018657.4	NP_061127.1	Q9NPC7	MYNN_HUMAN	myoneurin	604					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16	all_cancers(22;9.55e-22)|all_epithelial(15;2.04e-26)|all_lung(20;5.05e-16)|Lung NSC(18;2.19e-15)|Ovarian(172;0.000223)|Breast(254;0.197)		Epithelial(2;4.03e-64)|all cancers(2;2.19e-58)|Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.00676)			CCACAGTTGATTTTTTTACAA	0.368																																					p.I604fs		Atlas-INDEL	.											.	MYNN	36	.	0			c.1810delA						.						50.0	51.0	51.0					3																	169504444		2203	4300	6503	SO:0001589	frameshift_variant	55892	exon8			.	AF148848	CCDS3207.1, CCDS54671.1	3q26.31	2013-01-09			ENSG00000085274	ENSG00000085274		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	14955	protein-coding gene	gene with protein product		606042				10873615	Standard	NM_001185118		Approved	SBBIZ1, ZBTB31, ZNF902	uc010hwo.3	Q9NPC7		ENST00000349841.5:c.1811delT	chr3.hg19:g.169504444delT	ENSP00000326240:p.Ile604fs	137.0	0.0		154.0	11.0	NM_018657	B2R6C9|Q6QHA6|Q6QHA7|Q6R3G1|Q6R3G2|Q6R4A0|Q7Z716|Q7Z717|Q86Z11|Q86Z12|Q9NS01|Q9UIW8	Frame_Shift_Del	DEL	ENST00000349841.5	hg19	CCDS3207.1																																																																																			.	.		0.368	MYNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467801.1	NM_018657	
MME	4311	hgsc.bcm.edu	37	3	154834710	154834710	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:154834710delA	ENST00000460393.1	+	7	709	c.589delA	c.(589-591)aaafs	p.K198fs	MME_ENST00000462745.1_Frame_Shift_Del_p.K198fs|MME_ENST00000493237.1_Frame_Shift_Del_p.K198fs|MME_ENST00000360490.2_Frame_Shift_Del_p.K198fs|MME_ENST00000492661.1_Frame_Shift_Del_p.K198fs	NM_000902.3|NM_007287.2	NP_000893.2|NP_009218.2	P08473	NEP_HUMAN	membrane metallo-endopeptidase	198					angiotensin maturation (GO:0002003)|beta-amyloid metabolic process (GO:0050435)|cellular protein metabolic process (GO:0044267)|cellular response to cytokine stimulus (GO:0071345)|cellular response to UV-A (GO:0071492)|cellular response to UV-B (GO:0071493)|creatinine metabolic process (GO:0046449)|kidney development (GO:0001822)|peptide metabolic process (GO:0006518)|proteolysis (GO:0006508)|replicative senescence (GO:0090399)|sensory perception of pain (GO:0019233)	axon (GO:0030424)|brush border (GO:0005903)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|neuron projection terminus (GO:0044306)|plasma membrane (GO:0005886)|synapse (GO:0045202)|synaptic vesicle (GO:0008021)	endopeptidase activity (GO:0004175)|metalloendopeptidase activity (GO:0004222)|peptide binding (GO:0042277)|zinc ion binding (GO:0008270)	p.K197E(1)		central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(31)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	64		all_neural(597;0.00391)|Myeloproliferative disorder(1037;0.0122)	LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.135)		Candoxatril(DB00616)|Liraglutide(DB06655)	TAAATATGGGAAAAAAGTCCT	0.299																																					p.G196fs		Atlas-INDEL	.											.	MME	133	.	1	Substitution - Missense(1)	endometrium(1)	c.588delG						.						58.0	62.0	60.0					3																	154834710		2203	4296	6499	SO:0001589	frameshift_variant	4311	exon7			.		CCDS3172.1	3q25.2	2012-01-31	2007-02-21		ENSG00000196549	ENSG00000196549	3.4.24.11	"""CD molecules"""	7154	protein-coding gene	gene with protein product	"""neutral endopeptidase"", ""enkephalinase"", ""neprilysin"""	120520					Standard	NM_007287		Approved	CALLA, CD10, NEP	uc003fad.1	P08473	OTTHUMG00000158455	ENST00000460393.1:c.589delA	chr3.hg19:g.154834710delA	ENSP00000418525:p.Lys198fs	133.0	0.0		221.0	14.0	NM_007287	A8K6U6|D3DNJ9|Q3MIX4	Frame_Shift_Del	DEL	ENST00000460393.1	hg19	CCDS3172.1																																																																																			.	.		0.299	MME-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351076.1	NM_000902	
LINC01098	285501	hgsc.bcm.edu	37	4	178882055	178882055	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:178882055delA	ENST00000507870.1	+	3	514	c.52delA	c.(52-54)aaafs	p.K19fs																	lung(8)|prostate(1)	9						TGCAATCTGGAAAAAGTACGG	0.318																																					.		Atlas-INDEL	.											.	.	.	.	0			.						.						123.0	122.0	122.0					4																	178882055		1801	4074	5875	SO:0001589	frameshift_variant	0	.			.																												ENST00000507870.1:c.52delA	chr4.hg19:g.178882055delA	ENSP00000421352:p.Lys19fs	126.0	0.0		166.0	11.0	.		RNA	DEL	ENST00000507870.1	hg19																																																																																				.	.		0.318	RP11-389E17.1-001	PUTATIVE	basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000361922.1		
SBF2	81846	hgsc.bcm.edu	37	11	9864304	9864304	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:9864304delT	ENST00000256190.8	-	25	3261	c.3124delA	c.(3124-3126)acafs	p.T1042fs	RNU7-28P_ENST00000516759.1_RNA|RP11-1H15.2_ENST00000533659.1_RNA	NM_030962.3	NP_112224.1	Q86WG5	MTMRD_HUMAN	SET binding factor 2	1042					cell death (GO:0008219)|myelination (GO:0042552)|positive regulation of Rab GTPase activity (GO:0032851)|protein tetramerization (GO:0051262)	membrane (GO:0016020)|vacuolar membrane (GO:0005774)	phosphatase activity (GO:0016791)|phosphatase regulator activity (GO:0019208)|phosphatidylinositol binding (GO:0035091)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(4)|endometrium(8)|kidney(2)|large_intestine(8)|lung(16)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	48				all cancers(16;2.88e-11)|Epithelial(150;3.61e-10)|BRCA - Breast invasive adenocarcinoma(625;0.00887)		TTCACAATTGTTTTTGAGAAG	0.363																																					p.T1042fs		Atlas-INDEL	.											.	SBF2	146	.	0			c.3125delC						.						117.0	100.0	106.0					11																	9864304		2201	4294	6495	SO:0001589	frameshift_variant	81846	exon25			.	AB051553	CCDS31427.1	11p15.3	2014-09-17	2004-11-12	2004-11-12	ENSG00000133812	ENSG00000133812		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"", ""DENN/MADD domain containing"", ""Pleckstrin homology (PH) domain containing"""	2135	protein-coding gene	gene with protein product	"""myotubularin related 13"""	607697	"""Charcot-Marie-Tooth neuropathy 4B2 (autosomal recessive, with myelin outfolding)"", ""DENN/MADD domain containing 7B"""	CMT4B2		10644431	Standard	NM_030962		Approved	KIAA1766, MTMR13, DENND7B	uc001mib.2	Q86WG5	OTTHUMG00000165890	ENST00000256190.8:c.3124delA	chr11.hg19:g.9864304delT	ENSP00000256190:p.Thr1042fs	143.0	0.0		197.0	12.0	NM_030962	Q3MJF0|Q68DQ3|Q6P459|Q6PJD1|Q7Z325|Q7Z621|Q86VE2|Q96FE2|Q9C097	Frame_Shift_Del	DEL	ENST00000256190.8	hg19	CCDS31427.1																																																																																			.	.		0.363	SBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386911.2	NM_030962	
COL9A1	1297	hgsc.bcm.edu	37	6	70963135	70963135	+	Intron	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:70963135delA	ENST00000357250.6	-	26	1878				COL9A1_ENST00000489611.1_Intron|COL9A1_ENST00000370499.4_Intron|COL9A1_ENST00000320755.7_Intron	NM_001851.4	NP_001842.3	P20849	CO9A1_HUMAN	collagen, type IX, alpha 1						axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|organ morphogenesis (GO:0009887)|tissue homeostasis (GO:0001894)	collagen type IX trimer (GO:0005594)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(44)|ovary(5)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)	80						GGTACACCCTAAAAGAATACA	0.368																																					.		Atlas-INDEL	.											.	COL9A1	228	.	0			c.1720-2T>-						.						107.0	102.0	104.0					6																	70963135		2203	4300	6503	SO:0001627	intron_variant	1297	exon27			.		CCDS4971.1, CCDS47447.1	6q13	2013-05-07			ENSG00000112280	ENSG00000112280		"""Proteoglycans / Extracellular Matrix : Collagen proteoglycans"", ""Collagens"""	2217	protein-coding gene	gene with protein product		120210				1429648	Standard	NM_001851		Approved		uc003pfg.4	P20849	OTTHUMG00000014988	ENST00000357250.6:c.1720-3T>-	chr6.hg19:g.70963135delA		212.0	0.0		257.0	20.0	NM_001851	Q13699|Q13700|Q5TF52|Q6P467|Q96BM8|Q99225|Q9H151|Q9H152|Q9Y6P2|Q9Y6P3	Splice_Site	DEL	ENST00000357250.6	hg19	CCDS4971.1																																																																																			.	.		0.368	COL9A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041131.2		
ABCB4	5244	hgsc.bcm.edu	37	7	87081038	87081038	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:87081038delA	ENST00000265723.4	-	7	720	c.609delT	c.(607-609)tttfs	p.F203fs	ABCB4_ENST00000358400.3_Frame_Shift_Del_p.F203fs|ABCB4_ENST00000359206.3_Frame_Shift_Del_p.F203fs|ABCB4_ENST00000453593.1_Frame_Shift_Del_p.F203fs|ABCB4_ENST00000545634.1_Frame_Shift_Del_p.F203fs	NM_000443.3|NM_018849.2	NP_000434.1|NP_061337.1	P21439	MDR3_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 4	203	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				cellular lipid metabolic process (GO:0044255)|lipid metabolic process (GO:0006629)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intercellular canaliculus (GO:0046581)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|xenobiotic-transporting ATPase activity (GO:0008559)			breast(5)|endometrium(7)|kidney(2)|large_intestine(15)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	77	Esophageal squamous(14;0.0058)|all_lung(186;0.201)|Lung NSC(181;0.203)				Colchicine(DB01394)|Etravirine(DB06414)|Silodosin(DB06207)	TGAATCCTGCAAAAAACGTGG	0.448																																					p.A204fs		Atlas-INDEL	.											.	ABCB4	177	.	0			c.610delG						.						192.0	158.0	169.0					7																	87081038		2203	4300	6503	SO:0001589	frameshift_variant	5244	exon7			.	M23234	CCDS5605.1, CCDS5606.1, CCDS5607.1	7q21	2012-03-14			ENSG00000005471	ENSG00000005471		"""ATP binding cassette transporters / subfamily B"""	45	protein-coding gene	gene with protein product		171060		PGY3, MDR3		2892668, 11313316	Standard	NM_018850		Approved	MDR2, PFIC-3, GBD1	uc003uiv.1	P21439	OTTHUMG00000023396	ENST00000265723.4:c.609delT	chr7.hg19:g.87081038delA	ENSP00000265723:p.Phe203fs	137.0	0.0		182.0	13.0	NM_018850	A0A2V7|A4D1D3|A4D1D4|A4D1D5|D6W5P3|D6W5P4|Q14813	Frame_Shift_Del	DEL	ENST00000265723.4	hg19	CCDS5606.1																																																																																			.	.		0.448	ABCB4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000336083.1	NM_000443	
PNPLA4	8228	hgsc.bcm.edu	37	X	7894068	7894068	+	Frame_Shift_Del	DEL	T	T	-	rs375654820		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:7894068delT	ENST00000381042.4	-	2	263	c.93delA	c.(91-93)aaafs	p.K31fs	PNPLA4_ENST00000444736.1_Frame_Shift_Del_p.K31fs|PNPLA4_ENST00000537427.1_Intron	NM_004650.2	NP_004641.1	P41247	PLPL4_HUMAN	patatin-like phospholipase domain containing 4	31	Patatin.				lipid catabolic process (GO:0016042)		triglyceride lipase activity (GO:0004806)			kidney(1)|large_intestine(3)|lung(2)|prostate(1)	7		Colorectal(8;0.0329)|Medulloblastoma(8;0.232)				CCTTCACAAGTTTTTTGCCAT	0.468											OREG0019651	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L32fs		Atlas-INDEL	.											.	PNPLA4	24	.	0			c.94delC						.						94.0	77.0	83.0					X																	7894068		2203	4299	6502	SO:0001589	frameshift_variant	8228	exon2			.	U03886	CCDS14129.1, CCDS55368.1	Xp22.3	2014-03-14			ENSG00000006757	ENSG00000006757	3.1.1.3	"""Patatin-like phospholipase domain containing"""	24887	protein-coding gene	gene with protein product		300102				7806223, 16799181, 19029121	Standard	NM_004650		Approved	DXS1283E, GS2, iPLA2eta	uc011mhr.1	P41247	OTTHUMG00000021103	ENST00000381042.4:c.93delA	chrX.hg19:g.7894068delT	ENSP00000370430:p.Lys31fs	159.0	0.0	645	154.0	10.0	NM_004650	A8K1H3|B4E362|Q8WW83	Frame_Shift_Del	DEL	ENST00000381042.4	hg19	CCDS14129.1																																																																																			.	.		0.468	PNPLA4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055687.1	NM_004650	
PLEKHA8P1	51054	hgsc.bcm.edu	37	12	45567655	45567655	+	RNA	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:45567655delT	ENST00000256692.5	-	0	1030					NR_037144.1		O95397	PKHA9_HUMAN	pleckstrin homology domain containing, family A member 8 pseudogene 1							cytoplasm (GO:0005737)	glycolipid binding (GO:0051861)|glycolipid transporter activity (GO:0017089)			breast(1)|endometrium(2)|kidney(2)|large_intestine(8)|lung(10)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26						ATTGTCATGATTTTTCAGGTT	0.398																																					.		Atlas-INDEL	.											PLEKHA8P1,NS,carcinoma,0,1	PLEKHA8P1	38	.	0			.						.						151.0	146.0	148.0					12																	45567655		2203	4300	6503			51054	.			.	AF103731		12q12	2010-11-24	2010-11-24	2010-11-24	ENSG00000134297	ENSG00000134297			30222	pseudogene	pseudogene	"""putative glycolipid transfer protein"""		"""pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 9"""	PLEKHA9		12477932	Standard	NR_037144		Approved	FLJ14156	uc001rom.2	O95397			chr12.hg19:g.45567655delT		205.0	0.0		246.0	15.0	.		RNA	DEL	ENST00000256692.5	hg19																																																																																				.	.		0.398	PLEKHA8P1-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000404814.1	NR_037144	
ADCY1	107	hgsc.bcm.edu	37	7	45743294	45743294	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:45743294delG	ENST00000297323.7	+	16	2689	c.2667delG	c.(2665-2667)atgfs	p.M889fs		NM_021116.2	NP_066939.1	Q08828	ADCY1_HUMAN	adenylate cyclase 1 (brain)	889					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|axonogenesis (GO:0007409)|cellular response to glucagon stimulus (GO:0071377)|circadian rhythm (GO:0007623)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|long-term memory (GO:0007616)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of circadian rhythm (GO:0042752)|response to drug (GO:0042493)|response to lithium ion (GO:0010226)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(14)|lung(33)|ovary(4)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	71					Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)	GCAACAACATGGGGGTGGAGT	0.577																																					p.M889fs		Atlas-INDEL	.											.	ADCY1	187	.	0			c.2666delT						.						146.0	133.0	137.0					7																	45743294		2203	4300	6503	SO:0001589	frameshift_variant	107	exon16			.	L05500	CCDS34631.1, CCDS75593.1	7p13-p12	2013-02-04			ENSG00000164742	ENSG00000164742	4.6.1.1	"""Adenylate cyclases"""	232	protein-coding gene	gene with protein product		103072				8314585	Standard	NM_021116		Approved	AC1	uc003tne.4	Q08828	OTTHUMG00000155420	ENST00000297323.7:c.2667delG	chr7.hg19:g.45743294delG	ENSP00000297323:p.Met889fs	215.0	0.0		249.0	15.0	NM_021116	A4D2L8|Q75MI1	Frame_Shift_Del	DEL	ENST00000297323.7	hg19	CCDS34631.1																																																																																			.	.		0.577	ADCY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340055.2	NM_021116	
RYR2	6262	hgsc.bcm.edu	37	1	237693788	237693788	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:237693788delA	ENST00000366574.2	+	25	3201	c.2884delA	c.(2884-2886)aaafs	p.K963fs	RYR2_ENST00000360064.6_Frame_Shift_Del_p.K961fs|RYR2_ENST00000542537.1_Frame_Shift_Del_p.K947fs	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	963	4 X approximate repeats.				BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			AGACAAGGTGAAAAAAATGAA	0.358																																					p.V961fs		Atlas-INDEL	.											.	RYR2	1273	.	0			c.2883delG						.						103.0	95.0	98.0					1																	237693788		1861	4097	5958	SO:0001589	frameshift_variant	6262	exon25			.	X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"""Ion channels / Ryanodine receptors"", ""EF-hand domain containing"""	10484	protein-coding gene	gene with protein product		180902	"""arrhythmogenic right ventricular dysplasia 2"""	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.2884delA	chr1.hg19:g.237693788delA	ENSP00000355533:p.Lys963fs	70.0	0.0		131.0	10.0	NM_001035	Q15411|Q546N8|Q5T3P2	Frame_Shift_Del	DEL	ENST00000366574.2	hg19	CCDS55691.1																																																																																			.	.		0.358	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035	
NOP14	8602	hgsc.bcm.edu	37	4	2950011	2950011	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:2950011delT	ENST00000314262.6	-	9	1455	c.1407delA	c.(1405-1407)aaafs	p.K469fs	NOP14_ENST00000502735.1_Frame_Shift_Del_p.K469fs|NOP14-AS1_ENST00000507702.1_RNA|NOP14_ENST00000416614.2_Frame_Shift_Del_p.K469fs|NOP14-AS1_ENST00000515194.1_RNA|NOP14-AS1_ENST00000505731.1_RNA|NOP14-AS1_ENST00000503709.1_RNA|NOP14_ENST00000398071.4_Frame_Shift_Del_p.K469fs	NM_003703.1	NP_003694.1	P78316	NOP14_HUMAN	NOP14 nucleolar protein	469					endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000480)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000447)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000472)|maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000462)|ribosomal small subunit biogenesis (GO:0042274)|rRNA processing (GO:0006364)	90S preribosome (GO:0030686)|membrane (GO:0016020)|mitochondrion (GO:0005739)|Noc4p-Nop14p complex (GO:0030692)|nucleolus (GO:0005730)|nucleus (GO:0005634)|small-subunit processome (GO:0032040)	enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|snoRNA binding (GO:0030515)			NS(1)|endometrium(2)|kidney(3)|large_intestine(9)|lung(12)|pancreas(1)|skin(1)|urinary_tract(1)	30						GTACTTCTAATTTTGCTTTGT	0.483																																					p.L470X		Atlas-INDEL	.											.	NOP14	69	.	0			c.1408delT						.						312.0	248.0	269.0					4																	2950011		2203	4300	6503	SO:0001589	frameshift_variant	8602	exon9			.	AB000467	CCDS33945.1	4p16.3	2012-12-10	2012-12-10	2008-10-13	ENSG00000087269	ENSG00000087269			16821	protein-coding gene	gene with protein product	"""NOP14 homolog (S. cerevisiae)"""	611526	"""chromosome 4 open reading frame 9"", ""nucleolar protein 14"", ""nucleolar protein 14 homolog (yeast)"", ""NOP14 nucleolar protein homolog (yeast)"""	C4orf9, NOL14		9734812, 11694595	Standard	XR_241655		Approved	RES4-25, UTP2	uc003ggj.1	P78316	OTTHUMG00000159911	ENST00000314262.6:c.1407delA	chr4.hg19:g.2950011delT	ENSP00000315674:p.Lys469fs	134.0	0.0		158.0	10.0	NM_003703	D3DVR6|Q7LGI5|Q7Z6K0|Q8TBR6	Frame_Shift_Del	DEL	ENST00000314262.6	hg19	CCDS33945.1																																																																																			.	.		0.483	NOP14-002	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000358135.2	NM_003703	
AKAP6	9472	hgsc.bcm.edu	37	14	33290855	33290855	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:33290855delC	ENST00000280979.4	+	13	4006	c.3836delC	c.(3835-3837)gccfs	p.A1279fs	AKAP6_ENST00000557272.1_Intron	NM_004274.4	NP_004265.3	Q13023	AKAP6_HUMAN	A kinase (PRKA) anchor protein 6	1279					action potential (GO:0001508)|cAMP-mediated signaling (GO:0019933)|cellular response to cAMP (GO:0071320)|cellular response to cytokine stimulus (GO:0071345)|negative regulation of cAMP biosynthetic process (GO:0030818)|positive regulation of calcineurin-NFAT signaling cascade (GO:0070886)|positive regulation of cell growth (GO:0030307)|positive regulation of cell growth involved in cardiac muscle cell development (GO:0061051)|positive regulation of delayed rectifier potassium channel activity (GO:1902261)|positive regulation of NFAT protein import into nucleus (GO:0051533)|positive regulation of potassium ion transmembrane transport (GO:1901381)|positive regulation of protein phosphatase type 2B activity (GO:0032514)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|protein targeting (GO:0006605)|regulation of membrane repolarization (GO:0060306)|regulation of protein kinase A signaling (GO:0010738)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)	calcium channel complex (GO:0034704)|caveola (GO:0005901)|cytoplasm (GO:0005737)|intercalated disc (GO:0014704)|junctional sarcoplasmic reticulum membrane (GO:0014701)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)	adenylate cyclase binding (GO:0008179)|ion channel binding (GO:0044325)|protein anchor (GO:0043495)|protein complex scaffold (GO:0032947)|protein kinase A binding (GO:0051018)|protein kinase A regulatory subunit binding (GO:0034237)			NS(2)|breast(10)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(25)|lung(42)|ovary(5)|pancreas(2)|prostate(3)|skin(9)|urinary_tract(2)	122	Breast(36;0.0388)|Prostate(35;0.15)		LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00677)|STAD - Stomach adenocarcinoma(7;0.116)	GBM - Glioblastoma multiforme(265;0.019)		AATATTACTGCCCCCTCTAGT	0.463																																					p.A1279fs	Melanoma(49;821 1200 7288 13647 42351)	Atlas-INDEL	.											.	AKAP6	308	.	0			c.3835delG						.						83.0	69.0	74.0					14																	33290855		2203	4300	6503	SO:0001589	frameshift_variant	9472	exon13			.	AB002309	CCDS9644.1	14q12	2008-08-11			ENSG00000151320	ENSG00000151320		"""A-kinase anchor proteins"""	376	protein-coding gene	gene with protein product	"""protein kinase A anchoring protein 6"""	604691				7721854, 9205841	Standard	NM_004274		Approved	KIAA0311, mAKAP, AKAP100, PRKA6, ADAP6	uc001wrq.3	Q13023	OTTHUMG00000140207	ENST00000280979.4:c.3836delC	chr14.hg19:g.33290855delC	ENSP00000280979:p.Ala1279fs	121.0	0.0		156.0	11.0	NM_004274	A7E242|A7E2D4|O15028	Frame_Shift_Del	DEL	ENST00000280979.4	hg19	CCDS9644.1																																																																																			.	.		0.463	AKAP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276617.2	NM_004274	
HEATR4	399671	hgsc.bcm.edu	37	14	73945358	73945358	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:73945358delA	ENST00000553558.1	-	18	3355	c.3034delT	c.(3034-3036)tctfs	p.S1012fs	HEATR4_ENST00000560393.1_Frame_Shift_Del_p.S965fs|HEATR4_ENST00000334988.2_Frame_Shift_Del_p.S1012fs|HEATR4_ENST00000566478.1_5'UTR|RP1-240K6.3_ENST00000515412.2_RNA	NM_001220484.1	NP_001207413.1	Q86WZ0	HEAT4_HUMAN	HEAT repeat containing 4	1012										breast(3)|endometrium(2)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	28				BRCA - Breast invasive adenocarcinoma(234;0.00386)|OV - Ovarian serous cystadenocarcinoma(108;0.0719)		ATGATGGGAGAAAAAAATGTT	0.458																																					p.S1012fs		Atlas-INDEL	.											.	HEATR4	126	.	0			c.3035delC						.						91.0	90.0	90.0					14																	73945358		2203	4300	6503	SO:0001589	frameshift_variant	399671	exon17			.	BC047590	CCDS9815.1, CCDS9815.2	14q24.3	2013-09-20			ENSG00000187105	ENSG00000187105			16761	protein-coding gene	gene with protein product						15489334	Standard	NM_203309		Approved	MGC48595	uc021rwf.2	Q86WZ0	OTTHUMG00000171602	ENST00000553558.1:c.3034delT	chr14.hg19:g.73945358delA	ENSP00000450444:p.Ser1012fs	121.0	0.0		129.0	10.0	NM_203309	B7Z7V9|E9KL41	Frame_Shift_Del	DEL	ENST00000553558.1	hg19	CCDS9815.2																																																																																			.	.		0.458	HEATR4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414422.2	NM_203309	
EPB41L3	23136	hgsc.bcm.edu	37	18	5428316	5428316	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr18:5428316delC	ENST00000341928.2	-	9	1401	c.1061delG	c.(1060-1062)ggafs	p.G354fs	EPB41L3_ENST00000540638.2_Frame_Shift_Del_p.G354fs|EPB41L3_ENST00000544123.1_Frame_Shift_Del_p.G354fs|EPB41L3_ENST00000342933.3_Frame_Shift_Del_p.G354fs|EPB41L3_ENST00000542652.2_5'UTR|EPB41L3_ENST00000400111.3_Frame_Shift_Del_p.G354fs	NM_012307.2	NP_036439.2	Q9Y2J2	E41L3_HUMAN	erythrocyte membrane protein band 4.1-like 3	354	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				apoptotic process (GO:0006915)|cortical actin cytoskeleton organization (GO:0030866)|cortical cytoskeleton organization (GO:0030865)|cytoskeletal anchoring at plasma membrane (GO:0007016)|myelin maintenance (GO:0043217)|neuron projection morphogenesis (GO:0048812)|paranodal junction assembly (GO:0030913)|protein localization to juxtaparanode region of axon (GO:0071205)|protein localization to paranode region of axon (GO:0002175)|protein localization to plasma membrane (GO:0072659)|regulation of cell shape (GO:0008360)	axolemma (GO:0030673)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|juxtaparanode region of axon (GO:0044224)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)			breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(24)|lung(52)|ovary(5)|prostate(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	105						ACTTACCTCTCCCGGCCGGAT	0.438																																					p.G354fs		Atlas-INDEL	.											.	EPB41L3	222	.	0			c.1062delA						.						117.0	111.0	113.0					18																	5428316		2203	4300	6503	SO:0001589	frameshift_variant	23136	exon9			.	AB023204	CCDS11838.1, CCDS62381.1, CCDS62382.1	18p11.32	2006-06-28			ENSG00000082397	ENSG00000082397			3380	protein-coding gene	gene with protein product		605331				9828140, 9892180	Standard	NM_012307		Approved	DAL1, KIAA0987, 4.1B	uc002kmt.1	Q9Y2J2	OTTHUMG00000131562	ENST00000341928.2:c.1061delG	chr18.hg19:g.5428316delC	ENSP00000343158:p.Gly354fs	123.0	0.0		160.0	10.0	NM_012307	B7Z4I5|F5GX05|O95713|Q9BRP5	Frame_Shift_Del	DEL	ENST00000341928.2	hg19	CCDS11838.1																																																																																			.	.		0.438	EPB41L3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254424.1	NM_012307	
ATG5	9474	hgsc.bcm.edu	37	6	106727570	106727570	+	Frame_Shift_Del	DEL	T	T	-	rs34601838	byFrequency	TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:106727570delT	ENST00000369076.3	-	5	767	c.444delA	c.(442-444)aaafs	p.K148fs	ATG5_ENST00000360666.4_Intron|ATG5_ENST00000369070.1_Frame_Shift_Del_p.K70fs|ATG5_ENST00000343245.3_Frame_Shift_Del_p.K148fs	NM_004849.2	NP_004840.1	Q9H1Y0	ATG5_HUMAN	autophagy related 5	148					apoptotic process (GO:0006915)|autophagic vacuole assembly (GO:0000045)|autophagy (GO:0006914)|blood vessel remodeling (GO:0001974)|heart contraction (GO:0060047)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of type I interferon production (GO:0032480)|negative stranded viral RNA replication (GO:0039689)|otolith development (GO:0048840)|post-translational protein modification (GO:0043687)|regulation of cilium assembly (GO:1902017)|regulation of cytokine secretion involved in immune response (GO:0002739)|response to drug (GO:0042493)|response to fungus (GO:0009620)|vasodilation (GO:0042311)|ventricular cardiac muscle cell development (GO:0055015)	autophagic vacuole (GO:0005776)|axoneme (GO:0005930)|cytoplasm (GO:0005737)|membrane (GO:0016020)|pre-autophagosomal structure membrane (GO:0034045)				endometrium(1)|large_intestine(5)|lung(1)|prostate(1)	8	Breast(9;0.0296)	all_cancers(87;0.000301)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.0612)|Lung NSC(302;0.216)	BRCA - Breast invasive adenocarcinoma(8;0.00802)	OV - Ovarian serous cystadenocarcinoma(136;0.128)|Epithelial(106;0.159)|all cancers(137;0.18)		GCTTGTGATCTTTTTTCTGCA	0.318																																					p.D149fs		Atlas-INDEL	.											.	ATG5	23	.	0			c.445delG						.						116.0	107.0	110.0					6																	106727570		2203	4300	6503	SO:0001589	frameshift_variant	9474	exon5			.	Y11588	CCDS5055.1, CCDS69159.1, CCDS75498.1	6q21	2014-02-12	2012-06-06	2005-09-11	ENSG00000057663	ENSG00000057663			589	protein-coding gene	gene with protein product		604261	"""APG5 (autophagy 5, S. cerevisiae)-like"", ""APG5 autophagy 5-like (S. cerevisiae)"", ""ATG5 autophagy related 5 homolog (S. cerevisiae)"""	APG5L		9563500, 11349150, 15778222	Standard	NM_001286111		Approved	ASP, APG5, hAPG5	uc003prf.3	Q9H1Y0	OTTHUMG00000016193	ENST00000369076.3:c.444delA	chr6.hg19:g.106727570delT	ENSP00000358072:p.Lys148fs	178.0	0.0		161.0	10.0	NM_004849	O60875|Q5JVR2|Q68DI4|Q9H2B8|Q9HCZ7	Frame_Shift_Del	DEL	ENST00000369076.3	hg19	CCDS5055.1																																																																																			.	.		0.318	ATG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043476.1	NM_004849	
PRODH	5625	hgsc.bcm.edu	37	22	18905911	18905911	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr22:18905911delG	ENST00000357068.6	-	11	1610	c.1345delC	c.(1345-1347)cagfs	p.Q449fs	PRODH_ENST00000334029.2_Frame_Shift_Del_p.Q341fs|PRODH_ENST00000420436.1_Frame_Shift_Del_p.Q341fs	NM_016335.4	NP_057419	O43272	PROD_HUMAN	proline dehydrogenase (oxidase) 1	449					4-hydroxyproline catabolic process (GO:0019470)|cellular nitrogen compound metabolic process (GO:0034641)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|proline catabolic process (GO:0006562)|proline catabolic process to glutamate (GO:0010133)|proline metabolic process (GO:0006560)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)	FAD binding (GO:0071949)|proline dehydrogenase activity (GO:0004657)			breast(1)|endometrium(3)|lung(4)|upper_aerodigestive_tract(1)	9					L-Proline(DB00172)	GCTCGCTCCTGGGCCAGGTAT	0.652																																					p.Q449fs		Atlas-INDEL	.											.	PRODH	42	.	0			c.1346delA						.						98.0	91.0	93.0					22																	18905911		2203	4300	6503	SO:0001589	frameshift_variant	5625	exon12			.	AF010310	CCDS13754.1, CCDS56223.1	22q11.2	2014-07-10	2001-12-05		ENSG00000100033	ENSG00000100033	1.5.5.2		9453	protein-coding gene	gene with protein product		606810	"""proline dehydrogenase (proline oxidase )"""			9385373, 10192398	Standard	NM_001195226		Approved	HSPOX2, PRODH1, PIG6, PRODH2, TP53I6	uc002zok.4	O43272	OTTHUMG00000150163	ENST00000357068.6:c.1345delC	chr22.hg19:g.18905911delG	ENSP00000349577:p.Gln449fs	169.0	0.0		224.0	14.0	NM_016335	A6NF53|O14680|Q0P507|Q147W8|Q504W1|Q59FI8|Q6NV86|Q9UF13	Frame_Shift_Del	DEL	ENST00000357068.6	hg19	CCDS13754.1																																																																																			.	.		0.652	PRODH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316637.2	NM_016335	
OTUD7B	56957	hgsc.bcm.edu	37	1	149922079	149922079	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:149922079delA	ENST00000369135.4	-	8	1185	c.891delT	c.(889-891)tttfs	p.F297fs		NM_020205.2	NP_064590.2	Q6GQQ9	OTU7B_HUMAN	OTU deubiquitinase 7B	297	Catalytic.|OTU. {ECO:0000255|PROSITE- ProRule:PRU00139}.|TRAF-binding.				mucosal immune response (GO:0002385)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of interleukin-8 production (GO:0032717)|negative regulation of protein localization to nucleus (GO:1900181)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein K11-linked deubiquitination (GO:0035871)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)|DNA binding (GO:0003677)|Lys48-specific deubiquitinase activity (GO:1990380)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			breast(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(18)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39	Breast(34;0.0009)|Ovarian(49;0.0265)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.247)			CAAAGACGTGAAACTCTTCAA	0.532																																					p.H298fs		Atlas-INDEL	.											.	OTUD7B	76	.	0			c.892delC						.						74.0	75.0	75.0					1																	149922079		2030	4195	6225	SO:0001589	frameshift_variant	56957	exon8			.	AJ293573	CCDS72903.1	1q21.2	2014-02-24	2014-02-24	2006-07-07	ENSG00000163113	ENSG00000264522		"""OTU domain containing"""	16683	protein-coding gene	gene with protein product		611748	"""zinc finger, A20 domain containing 1"", ""OTU domain containing 7B"""	ZA20D1		11463333, 23827681	Standard	NM_020205		Approved	CEZANNE	uc001etn.3	Q6GQQ9	OTTHUMG00000012291	ENST00000369135.4:c.891delT	chr1.hg19:g.149922079delA	ENSP00000358131:p.Phe297fs	85.0	0.0		179.0	12.0	NM_020205	B7Z643|D3DUZ8|Q5SZ60|Q8WWA7|Q9NQ53|Q9UFF4	Frame_Shift_Del	DEL	ENST00000369135.4	hg19	CCDS41389.1																																																																																			.	.		0.532	OTUD7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034146.3	NM_020205	
USP9X	8239	hgsc.bcm.edu	37	X	41069811	41069811	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:41069811delT	ENST00000324545.8	+	33	5698	c.5065delT	c.(5065-5067)tttfs	p.F1690fs	USP9X_ENST00000378308.2_Frame_Shift_Del_p.F1690fs	NM_001039590.2|NM_001039591.2	NP_001034679.2|NP_001034680.2	Q93008	USP9X_HUMAN	ubiquitin specific peptidase 9, X-linked	1690	USP.				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						TGCTTTAGAATTTTTTAATTC	0.353																																					p.E1688fs	Ovarian(172;1807 2695 35459 49286)	Atlas-INDEL	.											.	USP9X	385	.	0			c.5064delA						.						114.0	109.0	111.0					X																	41069811		2172	4290	6462	SO:0001589	frameshift_variant	8239	exon33			.	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.5065delT	chrX.hg19:g.41069811delT	ENSP00000316357:p.Phe1690fs	113.0	0.0		160.0	12.0	NM_001039591	O75550|Q8WWT3|Q8WX12	Frame_Shift_Del	DEL	ENST00000324545.8	hg19	CCDS43930.1																																																																																			.	.		0.353	USP9X-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000056250.4	NM_004652	
PPWD1	23398	hgsc.bcm.edu	37	5	64859205	64859205	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:64859205delA	ENST00000261308.5	+	1	140	c.68delA	c.(67-69)gaafs	p.E23fs	CENPK_ENST00000510354.1_5'Flank|CENPK_ENST00000510693.1_5'Flank|CENPK_ENST00000508421.1_5'Flank|CENPK_ENST00000506282.2_5'Flank|CENPK_ENST00000514814.1_5'Flank|CENPK_ENST00000396679.1_5'Flank|PPWD1_ENST00000538977.1_5'UTR|PPWD1_ENST00000535264.1_5'UTR	NM_015342.3	NP_056157.1	Q96BP3	PPWD1_HUMAN	peptidylprolyl isomerase domain and WD repeat containing 1	23					mRNA splicing, via spliceosome (GO:0000398)|protein folding (GO:0006457)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)	19		Lung NSC(167;7.21e-05)|Prostate(74;0.0174)|Ovarian(174;0.186)		Lung(70;0.00451)		GAGGAACCGGAAAAAACAGAA	0.562																																					p.E23fs		Atlas-INDEL	.											.,1	PPWD1	47	.	0			c.67delG						.						72.0	75.0	74.0					5																	64859205		2203	4300	6503	SO:0001589	frameshift_variant	23398	exon1			.	AK025679	CCDS3985.1, CCDS64161.1, CCDS64162.1	5q12.3	2013-01-09			ENSG00000113593	ENSG00000113593		"""WD repeat domain containing"""	28954	protein-coding gene	gene with protein product						7584044	Standard	NM_015342		Approved	KIAA0073	uc003jtv.5	Q96BP3	OTTHUMG00000131226	ENST00000261308.5:c.68delA	chr5.hg19:g.64859205delA	ENSP00000261308:p.Glu23fs	108.0	0.0		154.0	10.0	NM_015342	B4DWR9|Q15002|Q7KZ89	Frame_Shift_Del	DEL	ENST00000261308.5	hg19	CCDS3985.1																																																																																			.	.		0.562	PPWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253970.2	NM_015342	
LEPREL4	10609	hgsc.bcm.edu	37	17	39959614	39959614	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:39959614delC	ENST00000355468.3	-	8	1682	c.1216delG	c.(1216-1218)gagfs	p.E406fs	LEPREL4_ENST00000393928.1_Frame_Shift_Del_p.E406fs			Q92791	SC65_HUMAN	leprecan-like 4	406	Asp/Glu-rich (acidic).				synaptonemal complex assembly (GO:0007130)	condensed nuclear chromosome (GO:0000794)|nucleolus (GO:0005730)|synaptonemal complex (GO:0000795)				endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|urinary_tract(1)	8						TAGTCACCCTCCCCCTCAAAC	0.627																																					p.E406fs		Atlas-INDEL	.											.	LEPREL4	20	.	0			c.1217delA						.						188.0	147.0	161.0					17																	39959614		2203	4300	6503	SO:0001589	frameshift_variant	10609	exon7			.	BC001047	CCDS11408.1	17q12	2013-05-03	2002-08-29		ENSG00000141696	ENSG00000141696			16946	protein-coding gene	gene with protein product			"""nucleolar autoantigen (55kD)"", ""rat synaptonemal complex protein"""			8862517	Standard	NM_006455		Approved	SC65, NO55	uc002hxt.3	Q92791	OTTHUMG00000133501	ENST00000355468.3:c.1216delG	chr17.hg19:g.39959614delC	ENSP00000347649:p.Glu406fs	252.0	0.0		219.0	14.0	NM_006455	Q53GI6|Q9H4F6	Frame_Shift_Del	DEL	ENST00000355468.3	hg19	CCDS11408.1																																																																																			.	.		0.627	LEPREL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257439.2		
C1orf27	54953	hgsc.bcm.edu	37	1	186367553	186367553	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:186367553delA	ENST00000287859.6	+	10	1014	c.889delA	c.(889-891)aaafs	p.K297fs	C1orf27_ENST00000432021.3_Frame_Shift_Del_p.K274fs|OCLM_ENST00000574641.1_5'Flank|AL596220.1_ENST00000598663.1_5'Flank|C1orf27_ENST00000419367.3_Frame_Shift_Del_p.K265fs|C1orf27_ENST00000367470.3_Frame_Shift_Del_p.K274fs	NM_017847.5	NP_060317.3	Q5SWX8	ODR4_HUMAN	chromosome 1 open reading frame 27	297						integral component of membrane (GO:0016021)	oxidoreductase activity (GO:0016491)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(2)|lung(3)|ovary(1)	9						CAGTAAACCCAAAGTTAAAGA	0.373																																					p.P296fs		Atlas-INDEL	.											.	C1orf27	41	.	0			c.888delC						.						88.0	82.0	84.0					1																	186367553		1861	4111	5972	SO:0001589	frameshift_variant	54953	exon10			.	BC003397	CCDS53448.1, CCDS53449.1, CCDS53450.1	1q25	2012-06-25			ENSG00000157181	ENSG00000157181			24299	protein-coding gene	gene with protein product	"""transactivated by recombinant transforming growth factor beta"""	609335				12868032	Standard	NM_017847		Approved	FLJ20505, odr-4, TTG1	uc021pgj.1	Q5SWX8	OTTHUMG00000035579	ENST00000287859.6:c.889delA	chr1.hg19:g.186367553delA	ENSP00000287859:p.Lys297fs	99.0	0.0		160.0	14.0	NM_017847	B4DNY0|E9PFR7|Q19CC6|Q8WYB6|Q9BTS2|Q9H6A6|Q9NX06	Frame_Shift_Del	DEL	ENST00000287859.6	hg19	CCDS53448.1																																																																																			.	.		0.373	C1orf27-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086352.2	NM_017847	
SLC35C2	51006	hgsc.bcm.edu	37	20	44979150	44979150	+	Frame_Shift_Del	DEL	G	G	-	rs199919922		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr20:44979150delG	ENST00000372227.1	-	10	1521	c.981delC	c.(979-981)cccfs	p.P327fs	SLC35C2_ENST00000243896.2_Frame_Shift_Del_p.P327fs|SLC35C2_ENST00000372229.1_Frame_Shift_Del_p.P194fs|SLC35C2_ENST00000493599.1_5'UTR|SLC35C2_ENST00000543605.1_Frame_Shift_Del_p.P356fs|SLC35C2_ENST00000372230.5_Frame_Shift_Del_p.P327fs|SLC35C2_ENST00000317734.8_Frame_Shift_Del_p.P306fs	NM_001281458.1|NM_001281460.1	NP_001268387.1|NP_001268389.1	Q9NQQ7	S35C2_HUMAN	solute carrier family 35 (GDP-fucose transporter), member C2	327					negative regulation of gene expression (GO:0010629)|positive regulation of Notch signaling pathway (GO:0045747)|protein O-linked fucosylation (GO:0036066)|transport (GO:0006810)	cis-Golgi network (GO:0005801)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(2)|prostate(1)	16		Myeloproliferative disorder(115;0.0122)				TCAAGGCCTTGGGGCCACCAT	0.592																																					p.K328fs		Atlas-INDEL	.											.	SLC35C2	35	.	0			c.982delA						.						38.0	41.0	40.0					20																	44979150		2203	4300	6503	SO:0001589	frameshift_variant	51006	exon10			.		CCDS13396.1, CCDS13397.1, CCDS63292.1	20q13.12	2013-07-17	2013-07-17	2003-10-10	ENSG00000080189	ENSG00000080189		"""Solute carriers"""	17117	protein-coding gene	gene with protein product			"""ovarian cancer overexpressed 1"", ""solute carrier family 35, member C2"""	C20orf5, OVCOV1		10810093, 11549316	Standard	NM_173179		Approved	CGI-15, bA394O2.1	uc002xrq.3	Q9NQQ7	OTTHUMG00000033050	ENST00000372227.1:c.981delC	chr20.hg19:g.44979150delG	ENSP00000361301:p.Pro327fs	125.0	0.0		180.0	11.0	NM_173179	B7Z6V6|E1P5T0|Q53GK3|Q5JW05|Q96CJ8|Q9Y304	Frame_Shift_Del	DEL	ENST00000372227.1	hg19	CCDS13396.1																																																																																			.	.		0.592	SLC35C2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080363.1	NM_015945	
POU1F1	5449	hgsc.bcm.edu	37	3	87309133	87309133	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:87309133delA	ENST00000350375.2	-	6	911	c.787delT	c.(787-789)tgcfs	p.C263fs	POU1F1_ENST00000560656.1_3'UTR|POU1F1_ENST00000344265.3_Frame_Shift_Del_p.C289fs	NM_000306.2	NP_000297.1	P28069	PIT1_HUMAN	POU class 1 homeobox 1	263					B cell differentiation (GO:0030183)|cell fate specification (GO:0001708)|determination of adult lifespan (GO:0008340)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nuclear transport (GO:0051169)|positive regulation of cell proliferation (GO:0008284)|positive regulation of inositol trisphosphate biosynthetic process (GO:0032962)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of insulin-like growth factor receptor signaling pathway (GO:0043567)|somatotropin secreting cell development (GO:0060133)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription coactivator activity (GO:0001105)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|large_intestine(5)|liver(1)|lung(7)|prostate(2)|skin(2)	18	all_cancers(8;0.104)|Lung SC(3;0.184)	Lung NSC(201;0.0777)		LUSC - Lung squamous cell carcinoma(29;0.00229)|Lung(72;0.00677)		CTCCGGTTGCAAAACCAAACT	0.383																																					p.C289fs		Atlas-INDEL	.											.	POU1F1	70	.	0			c.866delG						.						94.0	96.0	95.0					3																	87309133		2202	4300	6502	SO:0001589	frameshift_variant	5449	exon6			.	D10216	CCDS2919.1, CCDS46873.1	3p11.2	2011-06-20	2007-07-13		ENSG00000064835	ENSG00000064835		"""Homeoboxes / POU class"""	9210	protein-coding gene	gene with protein product	"""growth hormone factor 1"""	173110	"""POU domain class 1, transcription factor 1"""	PIT1		1956794	Standard	NM_001122757		Approved	GHF-1, POU1F1a	uc010hoj.1	P28069	OTTHUMG00000158992	ENST00000350375.2:c.787delT	chr3.hg19:g.87309133delA	ENSP00000263781:p.Cys263fs	194.0	0.0		231.0	14.0	NM_001122757	O75757|Q15132|Q15133|Q9UD34|Q9UEL3	Frame_Shift_Del	DEL	ENST00000350375.2	hg19	CCDS2919.1																																																																																			.	.		0.383	POU1F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352827.1	NM_000306	
WDR41	55255	hgsc.bcm.edu	37	5	76729042	76729042	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:76729042delT	ENST00000296679.4	-	13	1673	c.1298delA	c.(1297-1299)aatfs	p.N433fs	WDR41_ENST00000512033.1_5'UTR|WDR41_ENST00000507029.1_Frame_Shift_Del_p.N378fs|WDR41_ENST00000414719.2_Frame_Shift_Del_p.N179fs	NM_018268.2	NP_060738.2	Q9HAD4	WDR41_HUMAN	WD repeat domain 41	433						lysosomal membrane (GO:0005765)				NS(1)|autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(5)	14		all_lung(232;0.000961)|Lung NSC(167;0.0011)|Ovarian(174;0.0105)|Prostate(461;0.059)		OV - Ovarian serous cystadenocarcinoma(54;6.3e-50)|Epithelial(54;2.04e-44)|all cancers(79;6.84e-40)		TCGCTCTCCATTTTTCCACAA	0.338																																					p.N433fs		Atlas-INDEL	.											.	WDR41	29	.	0			c.1299delT						.						96.0	98.0	97.0					5																	76729042		2203	4300	6503	SO:0001589	frameshift_variant	55255	exon13			.	AF115511	CCDS4038.1	5q14	2013-01-09			ENSG00000164253	ENSG00000164253		"""WD repeat domain containing"""	25601	protein-coding gene	gene with protein product						12477932	Standard	NM_018268		Approved	FLJ10904	uc003kff.1	Q9HAD4	OTTHUMG00000102169	ENST00000296679.4:c.1298delA	chr5.hg19:g.76729042delT	ENSP00000296679:p.Asn433fs	153.0	0.0		162.0	10.0	NM_018268	B4DT55|Q7Z792|Q8IWG3|Q8IXA9|Q8NDA7|Q9NV62	Frame_Shift_Del	DEL	ENST00000296679.4	hg19	CCDS4038.1																																																																																			.	.		0.338	WDR41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220014.2	NM_018268	
NPAS4	266743	hgsc.bcm.edu	37	11	66193455	66193455	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:66193455delT	ENST00000311034.2	+	8	2580	c.2404delT	c.(2404-2406)tttfs	p.F802fs		NM_178864.3	NP_849195.2	Q8IUM7	NPAS4_HUMAN	neuronal PAS domain protein 4	802					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)			breast(4)|endometrium(2)|kidney(3)|large_intestine(11)|liver(2)|lung(20)|ovary(1)|prostate(3)|skin(3)	49						GGAACCAACGTTTTGAATAAG	0.498																																					p.T801fs		Atlas-INDEL	.											.	NPAS4	133	.	0			c.2403delG						.						197.0	169.0	179.0					11																	66193455		2200	4295	6495	SO:0001589	frameshift_variant	266743	exon8			.	AB049469	CCDS8138.1	11q13.2	2013-05-21			ENSG00000174576	ENSG00000174576		"""Basic helix-loop-helix proteins"""	18983	protein-coding gene	gene with protein product		608554				14701734	Standard	NM_178864		Approved	PASD10, NXF, Le-PAS, bHLHe79	uc001ohx.1	Q8IUM7	OTTHUMG00000167045	ENST00000311034.2:c.2404delT	chr11.hg19:g.66193455delT	ENSP00000311196:p.Phe802fs	129.0	0.0		181.0	12.0	NM_178864	B7ZL81|Q8N8S5|Q8N9Q9	Frame_Shift_Del	DEL	ENST00000311034.2	hg19	CCDS8138.1																																																																																			.	.		0.498	NPAS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392634.1	NM_178864	
KIF9	64147	hgsc.bcm.edu	37	3	47282419	47282419	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:47282419delT	ENST00000265529.3	-	18	2476	c.1796delA	c.(1795-1797)aacfs	p.N599fs	KIF9_ENST00000487440.1_5'UTR|KIF9_ENST00000352910.4_Frame_Shift_Del_p.N441fs|KIF9_ENST00000335044.2_Frame_Shift_Del_p.N599fs|KIF9_ENST00000452770.2_Frame_Shift_Del_p.N599fs|KIF9-AS1_ENST00000429315.3_RNA|KIF9_ENST00000444589.2_Frame_Shift_Del_p.N534fs			Q9HAQ2	KIF9_HUMAN	kinesin family member 9	599					ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|extracellular matrix disassembly (GO:0022617)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|organelle disassembly (GO:1903008)|regulation of podosome assembly (GO:0071801)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|podosome (GO:0002102)|vesicle (GO:0031982)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|protein dimerization activity (GO:0046983)			central_nervous_system(1)|endometrium(2)|large_intestine(8)|lung(15)|skin(4)|stomach(2)|upper_aerodigestive_tract(2)	34		Acute lymphoblastic leukemia(5;0.164)		BRCA - Breast invasive adenocarcinoma(193;0.000284)|KIRC - Kidney renal clear cell carcinoma(197;0.00609)|Kidney(197;0.007)		GATGGATTTGTTTTCTTTGAA	0.483																																					p.N599fs	Colon(44;962 1147 15977 24541)	Atlas-INDEL	.											.	KIF9	59	.	0			c.1797delC						.						146.0	135.0	138.0					3																	47282419		2203	4300	6503	SO:0001589	frameshift_variant	64147	exon17			.	AF311212	CCDS2751.1, CCDS2752.1	3p21.31	2008-03-03			ENSG00000088727	ENSG00000088727		"""Kinesins"""	16666	protein-coding gene	gene with protein product		607910				11483511	Standard	NM_022342		Approved	MGC104186	uc003cqx.3	Q9HAQ2	OTTHUMG00000133512	ENST00000265529.3:c.1796delA	chr3.hg19:g.47282419delT	ENSP00000265529:p.Asn599fs	122.0	0.0		146.0	10.0	NM_182902	Q86Z28|Q9H8A4	Frame_Shift_Del	DEL	ENST00000265529.3	hg19	CCDS2752.1																																																																																			.	.		0.483	KIF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257475.2		
LTK	4058	hgsc.bcm.edu	37	15	41796336	41796336	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:41796336delG	ENST00000263800.6	-	20	2549	c.2453delC	c.(2452-2454)ccafs	p.P818fs	LTK_ENST00000561619.1_Frame_Shift_Del_p.P516fs|LTK_ENST00000453182.2_Frame_Shift_Del_p.P688fs|LTK_ENST00000355166.5_Frame_Shift_Del_p.P757fs	NM_002344.5	NP_002335.2	P29376	LTK_HUMAN	leukocyte receptor tyrosine kinase	818					cell proliferation (GO:0008283)|cellular response to retinoic acid (GO:0071300)|negative regulation of apoptotic process (GO:0043066)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol 3-kinase signaling (GO:0014065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of neuron projection development (GO:0010976)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(16)|skin(3)|urinary_tract(1)	26		all_cancers(109;1.89e-19)|all_epithelial(112;2.28e-16)|Lung NSC(122;5.34e-11)|all_lung(180;1.33e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.172)		OV - Ovarian serous cystadenocarcinoma(18;2.1e-17)|GBM - Glioblastoma multiforme(113;1.34e-06)|Colorectal(105;0.0148)|BRCA - Breast invasive adenocarcinoma(123;0.113)		CTGGGGCTGTGGGGGTCTTAG	0.602										TSP Lung(18;0.14)																											p.P818fs		Atlas-INDEL	.											.	LTK	117	.	0			c.2454delA						.						44.0	51.0	48.0					15																	41796336		2203	4300	6503	SO:0001589	frameshift_variant	4058	exon20			.	D16105	CCDS10077.1, CCDS10078.1, CCDS45237.1	15q15.1-q21.1	2009-07-10	2008-01-23		ENSG00000062524	ENSG00000062524	2.7.10.1		6721	protein-coding gene	gene with protein product		151520	"""leukocyte tyrosine kinase"""			2320375	Standard	NM_206961		Approved	TYK1	uc001zoa.3	P29376	OTTHUMG00000130339	ENST00000263800.6:c.2453delC	chr15.hg19:g.41796336delG	ENSP00000263800:p.Pro818fs	170.0	0.0		157.0	11.0	NM_002344	A6NNJ8|B4DL89|E9PFX4	Frame_Shift_Del	DEL	ENST00000263800.6	hg19	CCDS10077.1																																																																																			.	.		0.602	LTK-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252690.2		
PLEC	5339	hgsc.bcm.edu	37	8	144991218	144991218	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr8:144991218delG	ENST00000322810.4	-	32	13351	c.13182delC	c.(13180-13182)cccfs	p.P4394fs	PLEC_ENST00000354589.3_Frame_Shift_Del_p.P4257fs|PLEC_ENST00000436759.2_Frame_Shift_Del_p.P4284fs|PLEC_ENST00000345136.3_Frame_Shift_Del_p.P4257fs|PLEC_ENST00000527096.1_Frame_Shift_Del_p.P4280fs|PLEC_ENST00000398774.2_Frame_Shift_Del_p.P4225fs|PLEC_ENST00000356346.3_Frame_Shift_Del_p.P4243fs|PLEC_ENST00000357649.2_Frame_Shift_Del_p.P4261fs|PLEC_ENST00000354958.2_Frame_Shift_Del_p.P4235fs	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	4394	Globular 2.				apoptotic process (GO:0006915)|cell junction assembly (GO:0034329)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|poly(A) RNA binding (GO:0044822)|structural constituent of muscle (GO:0008307)			NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						CGGGGCTGATGGGGTAGGAGG	0.682																																					p.I4395fs		Atlas-INDEL	.											.	PLEC	1144	.	0			c.13183delA						.						38.0	48.0	45.0					8																	144991218		2042	4190	6232	SO:0001589	frameshift_variant	5339	exon32			.	U53204	CCDS43769.1, CCDS43770.1, CCDS43771.1, CCDS43772.1, CCDS43773.1, CCDS43774.1, CCDS43775.1, CCDS47936.1	8q24	2010-02-04	2010-02-04	2010-02-04	ENSG00000178209	ENSG00000178209			9069	protein-coding gene	gene with protein product		601282	"""plectin 1, intermediate filament binding protein, 500kD"", ""epidermolysis bullosa simplex 1 (Ogna)"", ""plectin 1, intermediate filament binding protein 500kDa"""	EBS1, PLEC1		8633055, 8696340	Standard	XM_005250976		Approved	PCN, PLTN	uc003zaf.1	Q15149	OTTHUMG00000165291	ENST00000322810.4:c.13182delC	chr8.hg19:g.144991218delG	ENSP00000323856:p.Pro4394fs	99.0	0.0		248.0	15.0	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Frame_Shift_Del	DEL	ENST00000322810.4	hg19	CCDS43772.1																																																																																			.	.		0.682	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445	
RAD18	56852	hgsc.bcm.edu	37	3	8977726	8977726	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:8977726delT	ENST00000264926.2	-	7	834	c.718delA	c.(718-720)aggfs	p.R240fs		NM_020165.3	NP_064550.3	Q9NS91	RAD18_HUMAN	RAD18 E3 ubiquitin protein ligase	240					DNA repair (GO:0006281)|negative regulation of DNA recombination (GO:0045910)|protein ubiquitination (GO:0016567)|response to UV (GO:0009411)|spermatogenesis (GO:0007283)	chromatin (GO:0000785)|nucleus (GO:0005634)|replication fork (GO:0005657)|XY body (GO:0001741)	damaged DNA binding (GO:0003684)|ligase activity (GO:0016874)|polyubiquitin binding (GO:0031593)|ubiquitin protein ligase binding (GO:0031625)|Y-form DNA binding (GO:0000403)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|large_intestine(4)|lung(3)|ovary(2)|prostate(1)|skin(3)	15				OV - Ovarian serous cystadenocarcinoma(96;0.0552)		AGCGGCTTCCTTTTGTGAACA	0.338								Rad6 pathway																													p.R240fs		Atlas-INDEL	.											.	RAD18	52	.	0			c.719delG						.						79.0	79.0	79.0					3																	8977726		2203	4300	6503	SO:0001589	frameshift_variant	56852	exon7			.		CCDS2571.1	3p25-p24	2014-08-04	2014-08-04		ENSG00000070950	ENSG00000070950		"""RING-type (C3HC4) zinc fingers"""	18278	protein-coding gene	gene with protein product		605256	"""RAD18 homolog (S. cerevisiae)"""			10884424, 10908344	Standard	NM_020165		Approved	RNF73	uc003brd.3	Q9NS91	OTTHUMG00000090545	ENST00000264926.2:c.718delA	chr3.hg19:g.8977726delT	ENSP00000264926:p.Arg240fs	131.0	0.0		175.0	11.0	NM_020165	Q58F55|Q9NRT6	Frame_Shift_Del	DEL	ENST00000264926.2	hg19	CCDS2571.1																																																																																			.	.		0.338	RAD18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207071.2	NM_020165	
PLIN1	5346	hgsc.bcm.edu	37	15	90210976	90210976	+	Frame_Shift_Del	DEL	G	G	-	rs8179070	byFrequency	TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:90210976delG	ENST00000300055.5	-	7	985	c.820delC	c.(820-822)cggfs	p.R276fs	PLIN1_ENST00000430628.2_Frame_Shift_Del_p.R276fs	NM_002666.4	NP_002657.3	O60240	PLIN1_HUMAN	perilipin 1	276					lipid metabolic process (GO:0006629)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|lipid particle (GO:0005811)	lipid binding (GO:0008289)			NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(4)|skin(2)	13						CTCCTCCGCCGGGACACCGCC	0.667																																					p.R274fs		Atlas-INDEL	.											.	PLIN1	36	.	0			c.821delG						.						65.0	45.0	52.0					15																	90210976		2186	4280	6466	SO:0001589	frameshift_variant	5346	exon7			.	AB005293	CCDS10353.1	15q26	2009-08-12	2009-08-12	2009-08-12	ENSG00000166819	ENSG00000166819		"""Perilipins"""	9076	protein-coding gene	gene with protein product		170290	"""perilipin"""	PLIN		9521880, 19638644	Standard	NM_002666		Approved		uc010upx.1	O60240	OTTHUMG00000149813	ENST00000300055.5:c.820delC	chr15.hg19:g.90210976delG	ENSP00000300055:p.Arg276fs	97.0	0.0		150.0	11.0	NM_001145311	Q8N5Y6	Frame_Shift_Del	DEL	ENST00000300055.5	hg19	CCDS10353.1																																																																																			.	.		0.667	PLIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313424.2	NM_002666	
MTCL1	23255	hgsc.bcm.edu	37	18	8825894	8825894	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr18:8825894delG	ENST00000306329.11	+	13	5343	c.5343delG	c.(5341-5343)aagfs	p.K1781fs	SOGA2_ENST00000400050.3_Frame_Shift_Del_p.K1421fs|SOGA2_ENST00000517570.1_Frame_Shift_Del_p.K1421fs|SOGA2_ENST00000359865.3_Frame_Shift_Del_p.K1462fs|SOGA2_ENST00000518815.1_Frame_Shift_Del_p.K787fs|SOGA2_ENST00000306285.7_Frame_Shift_Del_p.K787fs																							CCTTCCAGAAGGGGCTGCGGG	0.642																																					p.K1462fs		Atlas-INDEL	.											.	.	.	.	0			c.4385delA						.						35.0	41.0	39.0					18																	8825894		2201	4296	6497	SO:0001589	frameshift_variant	23255	exon15			.																												ENST00000306329.11:c.5343delG	chr18.hg19:g.8825894delG	ENSP00000305027:p.Lys1781fs	125.0	0.0		155.0	10.0	NM_015210		Frame_Shift_Del	DEL	ENST00000306329.11	hg19																																																																																				.	.		0.642	SOGA2-015	PUTATIVE	basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000444141.1		
NBEAL1	65065	hgsc.bcm.edu	37	2	203974873	203974873	+	Splice_Site	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:203974873delT	ENST00000449802.1	+	14	2196	c.1863delT	c.(1861-1863)agt>ag	p.S621fs		NM_001114132.1	NP_001107604.1	Q6ZS30	NBEL1_HUMAN	neurobeachin-like 1	621										NS(1)|breast(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(8)|liver(1)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	37						TTTTTTTTAGTTTTTTTACAG	0.348																																					.		Atlas-INDEL	.											.	NBEAL1	266	.	0			c.1863-1T>-						.						201.0	159.0	172.0					2																	203974873		692	1591	2283	SO:0001630	splice_region_variant	65065	exon14			.	AY172970	CCDS46495.1	2q33	2013-01-10			ENSG00000144426	ENSG00000144426		"""WD repeat domain containing"""	20681	protein-coding gene	gene with protein product		609816	"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 17"", ""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 16"""	ALS2CR17, ALS2CR16		15193433	Standard	NM_001114132		Approved	MGC164581	uc002uzt.3	Q6ZS30	OTTHUMG00000154129	ENST00000449802.1:c.1863-1T>-	chr2.hg19:g.203974873delT		98.0	0.0		166.0	11.0	NM_001114132	A6NHD5|Q6Y876|Q6ZP36|Q6ZQY5|Q8N8R4|Q96Q30|Q96Q31	Splice_Site	DEL	ENST00000449802.1	hg19	CCDS46495.1																																																																																			.	.		0.348	NBEAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333982.4		Frame_Shift_Del
DHX32	55760	hgsc.bcm.edu	37	10	127542640	127542640	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:127542640delT	ENST00000284690.3	-	4	1472	c.982delA	c.(982-984)agafs	p.R328fs	DHX32_ENST00000284688.6_Intron|DHX32_ENST00000368721.1_5'UTR	NM_018180.2	NP_060650.2	Q7L7V1	DHX32_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 32	328						mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(2)|stomach(1)	29		all_lung(145;0.00751)|Lung NSC(174;0.0115)|Colorectal(57;0.0846)|all_neural(114;0.0936)				ACTTGGCATCTTTTTTCTGTT	0.403																																					p.R328fs		Atlas-INDEL	.											.	DHX32	67	.	0			c.983delG						.						154.0	153.0	153.0					10																	127542640		2203	4300	6503	SO:0001589	frameshift_variant	55760	exon4			.		CCDS7652.1	10q26.11-q26.2	2008-01-07	2004-01-29	2004-01-30	ENSG00000089876	ENSG00000089876		"""DEAH-boxes"""	16717	protein-coding gene	gene with protein product		607960	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 32"""	DDX32			Standard	NM_018180		Approved	FLJ10889, FLJ10694, DHLP1	uc001ljf.1	Q7L7V1	OTTHUMG00000019238	ENST00000284690.3:c.982delA	chr10.hg19:g.127542640delT	ENSP00000284690:p.Arg328fs	148.0	0.0		156.0	10.0	NM_018180	A8MSV2|D3DRF9|Q49AG5|Q5T3L0|Q5T3L5|Q96NY1|Q9BUN0|Q9H769|Q9NSL5|Q9NV74|Q9NVJ7	Frame_Shift_Del	DEL	ENST00000284690.3	hg19	CCDS7652.1																																																																																			.	.		0.403	DHX32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050945.2	NM_018180	
MYH3	4621	hgsc.bcm.edu	37	17	10546255	10546255	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:10546255delA	ENST00000583535.1	-	15	1556	c.1469delT	c.(1468-1470)ttcfs	p.F490fs	MYH3_ENST00000226209.7_Frame_Shift_Del_p.F490fs	NM_002470.3	NP_002461.2	P11055	MYH3_HUMAN	myosin, heavy chain 3, skeletal muscle, embryonic	490	Myosin motor.				actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|embryonic limb morphogenesis (GO:0030326)|face morphogenesis (GO:0060325)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|sarcomere organization (GO:0045214)|skeletal muscle contraction (GO:0003009)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(5)|large_intestine(18)|lung(30)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	83						GTGGTGGTTGAAAAACTGTTG	0.453																																					p.F490fs		Atlas-INDEL	.											.	MYH3	227	.	0			c.1470delC						.						131.0	120.0	124.0					17																	10546255		2203	4297	6500	SO:0001589	frameshift_variant	4621	exon15			.		CCDS11157.1	17p13.1	2013-09-19	2006-09-29		ENSG00000109063	ENSG00000109063		"""Myosins / Myosin superfamily : Class II"""	7573	protein-coding gene	gene with protein product	"""myosin, skeletal, heavy chain, embryonic 1"", ""muscle embryonic myosin heavy chain 3"""	160720	"""myosin, heavy polypeptide 3, skeletal muscle, embryonic"""			2726495	Standard	NM_002470		Approved	MYHC-EMB, MYHSE1, HEMHC, SMHCE	uc002gmq.2	P11055	OTTHUMG00000130367	ENST00000583535.1:c.1469delT	chr17.hg19:g.10546255delA	ENSP00000464317:p.Phe490fs	108.0	0.0		110.0	10.0	NM_002470	Q15492	Frame_Shift_Del	DEL	ENST00000583535.1	hg19	CCDS11157.1																																																																																			.	.		0.453	MYH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252734.2	NM_002470	
PACRG	135138	hgsc.bcm.edu	37	6	163483224	163483224	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:163483224delT	ENST00000337019.3	+	4	558	c.334delT	c.(334-336)tttfs	p.F113fs	PACRG_ENST00000366889.2_Frame_Shift_Del_p.F113fs|PACRG_ENST00000366888.2_Frame_Shift_Del_p.F113fs	NM_152410.2	NP_689623.2	Q96M98	PACRG_HUMAN	PARK2 co-regulated	113					spermatid development (GO:0007286)	cell body (GO:0044297)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|sperm midpiece (GO:0097225)				endometrium(2)|large_intestine(6)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20		Breast(66;2.41e-05)|Ovarian(120;0.0245)|Prostate(117;0.0273)|all_neural(5;0.0416)|Glioma(2;0.203)		OV - Ovarian serous cystadenocarcinoma(33;4.31e-19)|GBM - Glioblastoma multiforme(2;7.42e-11)|BRCA - Breast invasive adenocarcinoma(81;3.19e-05)|KIRC - Kidney renal clear cell carcinoma(3;0.205)|Kidney(3;0.242)		TCTGCCTCTGTTTTTTGATGG	0.448																																					p.L111fs		Atlas-INDEL	.											.	PACRG	48	.	0			c.333delG						.						109.0	110.0	109.0					6																	163483224		2203	4300	6503	SO:0001589	frameshift_variant	135138	exon3			.	AK057286	CCDS5284.1, CCDS43524.1	6q26	2004-07-01			ENSG00000112530	ENSG00000112530			19152	protein-coding gene	gene with protein product		608427				12547187	Standard	NM_001080378		Approved	PARK2CRG, FLJ32724, Glup, HAK005771	uc003qua.3	Q96M98	OTTHUMG00000016116	ENST00000337019.3:c.334delT	chr6.hg19:g.163483224delT	ENSP00000337946:p.Phe113fs	165.0	0.0		210.0	13.0	NM_001080379	E1P5B5|Q6IMB8|Q8IZM1|Q8NHP5|Q9H1V9	Frame_Shift_Del	DEL	ENST00000337019.3	hg19	CCDS5284.1																																																																																			.	.		0.448	PACRG-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000400424.1	NM_152410	
OR10G2	26534	hgsc.bcm.edu	37	14	22102864	22102864	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:22102864delC	ENST00000542433.1	-	1	232	c.135delG	c.(133-135)gggfs	p.G45fs		NM_001005466.1	NP_001005466.1	Q8NGC3	O10G2_HUMAN	olfactory receptor, family 10, subfamily G, member 2	45						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(12)|prostate(1)|skin(2)|stomach(2)	22	all_cancers(95;0.00113)	Acute lymphoblastic leukemia(2;0.0279)		GBM - Glioblastoma multiforme(265;0.0142)		TGAGCAGGTTCCCCAGCTGAG	0.512																																					p.N46fs		Atlas-INDEL	.											.	OR10G2	35	.	0			c.136delA						.						75.0	73.0	74.0					14																	22102864		2203	4300	6503	SO:0001589	frameshift_variant	26534	exon1			.		CCDS32047.1	14q11.2	2013-09-24			ENSG00000255582	ENSG00000255582		"""GPCR / Class A : Olfactory receptors"""	8170	protein-coding gene	gene with protein product						8188290	Standard	NM_001005466		Approved		uc010tmc.2	Q8NGC3	OTTHUMG00000168890	ENST00000542433.1:c.135delG	chr14.hg19:g.22102864delC	ENSP00000445383:p.Gly45fs	243.0	0.0		231.0	14.0	NM_001005466	B2RPD0	Frame_Shift_Del	DEL	ENST00000542433.1	hg19	CCDS32047.1																																																																																			.	.		0.512	OR10G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401525.1		
MXRA7	439921	hgsc.bcm.edu	37	17	74681205	74681205	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:74681205delC	ENST00000355797.3	-	3	457	c.449delG	c.(448-450)ggafs	p.G150fs	MXRA7_ENST00000588114.1_5'UTR|MXRA7_ENST00000592148.1_Frame_Shift_Del_p.G193fs|MXRA7_ENST00000449428.2_Frame_Shift_Del_p.G150fs|MXRA7_ENST00000585519.1_5'UTR|MXRA7_ENST00000375036.2_Frame_Shift_Del_p.G150fs|MXRA7_ENST00000589082.1_5'UTR	NM_001008528.1	NP_001008528.1	P84157	MXRA7_HUMAN	matrix-remodelling associated 7	150						integral component of membrane (GO:0016021)				kidney(1)|large_intestine(2)|lung(2)|skin(1)	6						GTACTGGTTTCCCCTCAGCTT	0.617																																					p.G150fs		Atlas-INDEL	.											.	MXRA7	11	.	0			c.450delA						.						157.0	148.0	151.0					17																	74681205		2203	4300	6503	SO:0001589	frameshift_variant	439921	exon3			.	BC053983	CCDS32745.1, CCDS32746.1, CCDS45786.1	17q25.1	2007-08-01				ENSG00000182534			7541	protein-coding gene	gene with protein product							Standard	XM_005257382		Approved	FLJ46603, TMAP1, PS1TP1	uc002jsk.1	P84157		ENST00000355797.3:c.449delG	chr17.hg19:g.74681205delC	ENSP00000348050:p.Gly150fs	158.0	0.0		152.0	10.0	NM_001008529	Q0P5W3	Frame_Shift_Del	DEL	ENST00000355797.3	hg19	CCDS32745.1																																																																																			.	.		0.617	MXRA7-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000450983.1	NM_001008529	
GRB14	2888	hgsc.bcm.edu	37	2	165378510	165378510	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:165378510delA	ENST00000263915.3	-	6	1334	c.796delT	c.(796-798)tctfs	p.S266fs	GRB14_ENST00000543549.1_Frame_Shift_Del_p.S179fs	NM_004490.2	NP_004481.2	Q14449	GRB14_HUMAN	growth factor receptor-bound protein 14	266	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				blood coagulation (GO:0007596)|leukocyte migration (GO:0050900)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)			breast(3)|endometrium(2)|large_intestine(6)|lung(10)|ovary(7)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	32						CCTTTAGTAGAAAAATATAAA	0.299																																					p.S266fs		Atlas-INDEL	.											.	GRB14	73	.	0			c.797delC						.						51.0	56.0	54.0					2																	165378510		2195	4285	6480	SO:0001589	frameshift_variant	2888	exon6			.		CCDS2222.1	2q22-q24	2013-02-14			ENSG00000115290	ENSG00000115290		"""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	4565	protein-coding gene	gene with protein product		601524				8812444	Standard	XM_005246477		Approved		uc002ucl.3	Q14449	OTTHUMG00000132135	ENST00000263915.3:c.796delT	chr2.hg19:g.165378510delA	ENSP00000263915:p.Ser266fs	136.0	0.0		213.0	13.0	NM_004490	B7Z7F9|Q7Z6I1	Frame_Shift_Del	DEL	ENST00000263915.3	hg19	CCDS2222.1																																																																																			.	.		0.299	GRB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255180.2		
PRKAG2	51422	hgsc.bcm.edu	37	7	151372597	151372597	+	Frame_Shift_Del	DEL	G	G	-	rs41317142		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:151372597delG	ENST00000287878.4	-	4	1097	c.593delC	c.(592-594)ccgfs	p.P198fs	PRKAG2_ENST00000492843.1_Frame_Shift_Del_p.P74fs|PRKAG2_ENST00000461529.1_5'Flank|PRKAG2_ENST00000433631.2_Frame_Shift_Del_p.P74fs|PRKAG2_ENST00000392801.2_Frame_Shift_Del_p.P154fs	NM_016203.3	NP_057287.2	Q9UGJ0	AAKG2_HUMAN	protein kinase, AMP-activated, gamma 2 non-catalytic subunit	198					ATP biosynthetic process (GO:0006754)|carnitine shuttle (GO:0006853)|cell cycle arrest (GO:0007050)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|glycogen metabolic process (GO:0005977)|insulin receptor signaling pathway (GO:0008286)|intracellular signal transduction (GO:0035556)|membrane organization (GO:0061024)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of protein kinase activity (GO:0045860)|regulation of fatty acid biosynthetic process (GO:0042304)|regulation of fatty acid metabolic process (GO:0019217)|regulation of fatty acid oxidation (GO:0046320)|regulation of glucose import (GO:0046324)|regulation of glycolytic process (GO:0006110)|small molecule metabolic process (GO:0044281)|sterol biosynthetic process (GO:0016126)	AMP-activated protein kinase complex (GO:0031588)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleoplasm (GO:0005654)	ADP binding (GO:0043531)|AMP binding (GO:0016208)|ATP binding (GO:0005524)|cAMP-dependent protein kinase inhibitor activity (GO:0004862)|cAMP-dependent protein kinase regulator activity (GO:0008603)|phosphorylase kinase regulator activity (GO:0008607)|protein kinase activator activity (GO:0030295)|protein kinase binding (GO:0019901)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|upper_aerodigestive_tract(1)	26	all_neural(206;0.187)	all_hematologic(28;0.0605)	OV - Ovarian serous cystadenocarcinoma(82;0.00252)	UCEC - Uterine corpus endometrioid carcinoma (81;0.185)	Acetylsalicylic acid(DB00945)	CCCTGTGTCCGGGGGGGAAGA	0.582																																					p.P198fs		Atlas-INDEL	.											.,4	PRKAG2	86	.	0			c.594delG						.						93.0	85.0	88.0					7																	151372597		2203	4300	6503	SO:0001589	frameshift_variant	51422	exon4			.	AF087875	CCDS5928.1, CCDS43683.1, CCDS47752.1	7q35-q36	2014-09-17			ENSG00000106617	ENSG00000106617			9386	protein-coding gene	gene with protein product	"""AMPK gamma2"""	602743				8557660, 8621499	Standard	NM_024429		Approved	AAKG, AAKG2, H91620p, WPWS, CMH6	uc003wkk.3	Q9UGJ0	OTTHUMG00000157324	ENST00000287878.4:c.593delC	chr7.hg19:g.151372597delG	ENSP00000287878:p.Pro198fs	111.0	0.0		174.0	14.0	NM_016203	Q53Y07|Q6NUI0|Q75MP4|Q9NUZ9|Q9UDN8|Q9ULX8	Frame_Shift_Del	DEL	ENST00000287878.4	hg19	CCDS5928.1																																																																																			.	.		0.582	PRKAG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348440.2	NM_016203	
MICALCL	84953	hgsc.bcm.edu	37	11	12345559	12345559	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:12345559delA	ENST00000256186.2	+	5	1868	c.1577delA	c.(1576-1578)gaafs	p.E526fs		NM_032867.2	NP_116256.2	Q6ZW33	MICLK_HUMAN	MICAL C-terminal like	526					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)	mitogen-activated protein kinase binding (GO:0051019)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(5)|lung(5)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)	30				Epithelial(150;0.00177)		AAGAAGCTAGAAAAAGCAATG	0.368																																					p.E526fs		Atlas-INDEL	.											.	MICALCL	59	.	0			c.1576delG						.						81.0	82.0	81.0					11																	12345559		1821	4077	5898	SO:0001589	frameshift_variant	84953	exon5			.	BK000463	CCDS41620.1	11p15.3	2005-11-01			ENSG00000133808	ENSG00000133808			25933	protein-coding gene	gene with protein product		612355				12110185	Standard	NM_032867		Approved	FLJ14966	uc001mkg.1	Q6ZW33	OTTHUMG00000165777	ENST00000256186.2:c.1577delA	chr11.hg19:g.12345559delA	ENSP00000256186:p.Glu526fs	136.0	0.0		178.0	11.0	NM_032867	Q7RTP7|Q96JU6	Frame_Shift_Del	DEL	ENST00000256186.2	hg19	CCDS41620.1																																																																																			.	.		0.368	MICALCL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386164.1	NM_032867	
ATP13A1	57130	hgsc.bcm.edu	37	19	19774122	19774122	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:19774122delC	ENST00000357324.6	-	1	380	c.354delG	c.(352-354)gggfs	p.G118fs	ATP13A1_ENST00000291503.5_5'Flank	NM_020410.2	NP_065143.2	Q9HD20	AT131_HUMAN	ATPase type 13A1	118						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|liver(2)|lung(7)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	29						CAGACCAATGCCCCGAGAGGA	0.687																																					p.H119fs	Esophageal Squamous(142;920 1789 9047 14684 24777)	Atlas-INDEL	.											.	ATP13A1	82	.	0			c.355delC						.						10.0	14.0	13.0					19																	19774122		1545	3561	5106	SO:0001589	frameshift_variant	57130	exon1			.	AK056420	CCDS32970.2	19p13.11	2010-04-20	2005-01-12	2005-01-12	ENSG00000105726	ENSG00000105726		"""ATPases / P-type"""	24215	protein-coding gene	gene with protein product	"""cation transporting ATPase"""		"""ATPase type 13A"""	ATP13A		11347906	Standard	NM_020410		Approved	KIAA1825, FLJ31858, CGI-152	uc002nnh.4	Q9HD20	OTTHUMG00000153016	ENST00000357324.6:c.354delG	chr19.hg19:g.19774122delC	ENSP00000349877:p.Gly118fs	187.0	0.0		191.0	12.0	NM_020410	B3KPJ2|B3KTA7|Q6NT90|Q6ZMG7|Q9H6C6	Frame_Shift_Del	DEL	ENST00000357324.6	hg19	CCDS32970.2																																																																																			.	.		0.687	ATP13A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329005.1	NM_020410	
NAIP	4671	hgsc.bcm.edu	37	5	70307197	70307197	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:70307197delT	ENST00000517649.1	-	5	863	c.573delA	c.(571-573)aaafs	p.K191fs	NAIP_ENST00000194097.4_Frame_Shift_Del_p.K191fs|NAIP_ENST00000523981.1_Intron|NAIP_ENST00000508426.2_Frame_Shift_Del_p.K191fs|NAIP_ENST00000503719.2_Intron	NM_004536.2	NP_004527.2	Q13075	BIRC1_HUMAN	NLR family, apoptosis inhibitory protein	191					inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of neuron apoptotic process (GO:0043524)|nervous system development (GO:0007399)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|metal ion binding (GO:0046872)			central_nervous_system(1)	1		Lung NSC(167;4.15e-05)|Prostate(74;0.00996)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;3.04e-60)|Epithelial(20;7.09e-58)|all cancers(19;1.13e-53)|Lung(70;0.0174)		CCGTGTCCTGTTTACCTATAT	0.438																																					p.Q192fs		Atlas-INDEL	.											.	NAIP	38	.	0			c.574delC						.						122.0	106.0	111.0					5																	70307197		2202	4296	6498	SO:0001589	frameshift_variant	4671	exon5			.	U19251	CCDS4009.1, CCDS43327.1	5q13.2	2010-06-16	2006-12-08	2006-12-08	ENSG00000249437	ENSG00000249437		"""Baculoviral IAP repeat containing"", ""Nucleotide-binding domain and leucine rich repeat containing"""	7634	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and BIR domain containing 1"", ""NLR family, BIR domain containing 1"""	600355	"""baculoviral IAP repeat-containing 1"""	BIRC1		7813013	Standard	NM_022892		Approved	NLRB1	uc003jyj.1	Q13075	OTTHUMG00000163318	ENST00000517649.1:c.573delA	chr5.hg19:g.70307197delT	ENSP00000428657:p.Lys191fs	145.0	0.0		163.0	10.0	NM_004536	B9EG72|E9PHD1|O75857|Q13730|Q59GI6|Q8TDZ4|Q99796	Frame_Shift_Del	DEL	ENST00000517649.1	hg19	CCDS4009.1																																																																																			.	.		0.438	NAIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372649.6	NM_004536	
DYRK1A	1859	hgsc.bcm.edu	37	21	38852951	38852951	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr21:38852951delA	ENST00000398960.2	+	4	414	c.339delA	c.(337-339)gcafs	p.A113fs	DYRK1A_ENST00000321219.8_Frame_Shift_Del_p.A113fs|DYRK1A_ENST00000451934.1_Frame_Shift_Del_p.A113fs|DYRK1A_ENST00000398956.2_Frame_Shift_Del_p.A113fs|DYRK1A_ENST00000339659.4_Frame_Shift_Del_p.A104fs|DYRK1A_ENST00000462274.1_3'UTR|DYRK1A_ENST00000338785.3_Frame_Shift_Del_p.A113fs	NM_001396.3|NM_130438.2	NP_001387.2|NP_569122.1	Q13627	DYR1A_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1A	113					circadian rhythm (GO:0007623)|mitotic cell cycle (GO:0000278)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|nervous system development (GO:0007399)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of protein deacetylation (GO:0090312)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)|tau protein binding (GO:0048156)			breast(4)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(5)|lung(10)|ovary(3)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						TTTACTATGCAAAAAAGAAGC	0.363																																					p.A113fs	Melanoma(114;464 1602 31203 43785 45765)	Atlas-INDEL	.											.	DYRK1A	85	.	0			c.338delC						.						98.0	97.0	98.0					21																	38852951		2203	4300	6503	SO:0001589	frameshift_variant	1859	exon4			.	U52373	CCDS13653.1, CCDS13654.1, CCDS42925.1, CCDS42926.1	21q22.13	2010-04-21			ENSG00000157540	ENSG00000157540			3091	protein-coding gene	gene with protein product		600855		DYRK1, DYRK, MNBH		9284911	Standard	NM_130436		Approved		uc002ywk.3	Q13627	OTTHUMG00000086657	ENST00000398960.2:c.339delA	chr21.hg19:g.38852951delA	ENSP00000381932:p.Ala113fs	101.0	0.0		108.0	10.0	NM_001396	O60769|Q92582|Q92810|Q9UNM5	Frame_Shift_Del	DEL	ENST00000398960.2	hg19	CCDS42925.1																																																																																			.	.		0.363	DYRK1A-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194804.1	NM_001396	
MTFR2	113115	hgsc.bcm.edu	37	6	136562707	136562707	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:136562707delT	ENST00000420702.1	-	5	778	c.389delA	c.(388-390)aatfs	p.N130fs	MTFR2_ENST00000451457.2_Frame_Shift_Del_p.N130fs	NM_001099286.1	NP_001092756.1	Q6P444	MTFR2_HUMAN	mitochondrial fission regulator 2	130					aerobic respiration (GO:0009060)|mitochondrial fission (GO:0000266)|mitochondrion organization (GO:0007005)	mitochondrion (GO:0005739)											AGGCAGGTCATTTTTCACAGT	0.398																																					p.N130fs		Atlas-INDEL	.											.	.	.	.	0			c.390delT						.						107.0	98.0	101.0					6																	136562707		2203	4300	6503	SO:0001589	frameshift_variant	113115	exon5			.	BC011716	CCDS5176.1	6q23.2	2012-11-30	2012-11-29	2012-11-29	ENSG00000146410	ENSG00000146410			21115	protein-coding gene	gene with protein product			"""DUF729 domain containing 1"", ""family with sequence similarity 54, member A"""	DUFD1, FAM54A			Standard	NM_138419		Approved		uc003qgt.1	Q6P444	OTTHUMG00000015643	ENST00000420702.1:c.389delA	chr6.hg19:g.136562707delT	ENSP00000395232:p.Asn130fs	116.0	0.0		138.0	10.0	NM_138419	A8K8D8|E1P585|Q5JWR7|Q6ZUE8|Q7L3U6|Q9BZ39	Frame_Shift_Del	DEL	ENST00000420702.1	hg19	CCDS5176.1																																																																																			.	.		0.398	MTFR2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042378.2	NM_138419	
DSG3	1830	hgsc.bcm.edu	37	18	29037066	29037066	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr18:29037066delA	ENST00000257189.4	+	3	278	c.195delA	c.(193-195)tcafs	p.S65fs		NM_001944.2	NP_001935.2	P32926	DSG3_HUMAN	desmoglein 3	65	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|homophilic cell adhesion (GO:0007156)	cell junction (GO:0030054)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(2)|cervix(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(28)|ovary(4)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)	62			OV - Ovarian serous cystadenocarcinoma(10;0.00504)			AAGATAACTCAAAAAGAAACC	0.343																																					p.S65X		Atlas-INDEL	.											.	DSG3	172	.	0			c.194delC						.						108.0	102.0	104.0					18																	29037066		2203	4300	6503	SO:0001589	frameshift_variant	1830	exon3			.	M76482	CCDS11898.1	18q12.1	2010-06-24	2010-06-24		ENSG00000134757	ENSG00000134757		"""Cadherins / Major cadherins"""	3050	protein-coding gene	gene with protein product	"""pemphigus vulgaris antigen"""	169615	"""desmoglein 3 (pemphigus vulgaris antigen)"""			1601426	Standard	NM_001944		Approved	CDHF6	uc002kws.3	P32926	OTTHUMG00000131985	ENST00000257189.4:c.195delA	chr18.hg19:g.29037066delA	ENSP00000257189:p.Ser65fs	86.0	0.0		139.0	10.0	NM_001944	A8K2V2	Frame_Shift_Del	DEL	ENST00000257189.4	hg19	CCDS11898.1																																																																																			.	.		0.343	DSG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254949.1	NM_001944	
ZNF222	7673	hgsc.bcm.edu	37	19	44537092	44537092	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:44537092delA	ENST00000187879.8	+	4	1427	c.1265delA	c.(1264-1266)gaafs	p.E422fs	ZNF223_ENST00000591793.1_Intron|ZNF222_ENST00000391960.3_Frame_Shift_Del_p.E462fs	NM_013360.2	NP_037492.2	Q9UK12	ZN222_HUMAN	zinc finger protein 222	422					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(7)|lung(6)|ovary(3)|prostate(1)|skin(1)|urinary_tract(1)	20		Prostate(69;0.0435)				CACAGTGGAGAAAACCCATCC	0.393																																					p.E462fs		Atlas-INDEL	.											.	ZNF222	90	.	0			c.1384delG						.						71.0	74.0	73.0					19																	44537092		2203	4300	6503	SO:0001589	frameshift_variant	7673	exon4			.	AF187988	CCDS33045.1, CCDS46098.1	19q13.2	2013-01-08				ENSG00000159885		"""Zinc fingers, C2H2-type"", ""-"""	13015	protein-coding gene	gene with protein product							Standard	NM_013360		Approved		uc002oye.3	Q9UK12		ENST00000187879.8:c.1265delA	chr19.hg19:g.44537092delA	ENSP00000187879:p.Glu422fs	77.0	0.0		157.0	10.0	NM_001129996	G5E9B9|Q8N6G7|Q9P1U5	Frame_Shift_Del	DEL	ENST00000187879.8	hg19	CCDS33045.1																																																																																			.	.		0.393	ZNF222-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000460465.2		
ZKSCAN3	80317	hgsc.bcm.edu	37	6	28333941	28333941	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:28333941delA	ENST00000377255.3	+	7	1793	c.1496delA	c.(1495-1497)caafs	p.Q499fs	ZKSCAN3_ENST00000341464.5_Frame_Shift_Del_p.Q351fs|ZKSCAN3_ENST00000252211.2_Frame_Shift_Del_p.Q499fs	NM_001242894.1	NP_001229823.1	Q9BRR0	ZKSC3_HUMAN	zinc finger with KRAB and SCAN domains 3	499					autophagy (GO:0006914)|lysosome organization (GO:0007040)|negative regulation of autophagy (GO:0010507)|negative regulation of cellular senescence (GO:2000773)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(4)|large_intestine(3)|lung(8)|pancreas(1)|skin(2)|stomach(2)|urinary_tract(1)	21						ATTGAACATCAAAAAATCCAC	0.408																																					p.Q499fs		Atlas-INDEL	.											.	ZKSCAN3	50	.	0			c.1495delC						.						79.0	82.0	81.0					6																	28333941		2203	4300	6503	SO:0001589	frameshift_variant	80317	exon6			.	U71601	CCDS4650.1, CCDS56408.1	6p22.1	2013-01-09	2007-02-20	2007-02-20		ENSG00000189298		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	13853	protein-coding gene	gene with protein product		612791	"""zinc finger protein 306"", ""zinc finger protein 309"""	ZNF306, ZNF309		10520746, 22531714	Standard	NM_024493		Approved	Zfp47, ZF47, ZSCAN35	uc003nle.4	Q9BRR0	OTTHUMG00000014521	ENST00000377255.3:c.1496delA	chr6.hg19:g.28333941delA	ENSP00000366465:p.Gln499fs	84.0	0.0		140.0	11.0	NM_024493	B2R8W2|B3KVC0|H7BXX1|Q5VXH3|Q92972|Q9H4T3	Frame_Shift_Del	DEL	ENST00000377255.3	hg19	CCDS4650.1																																																																																			.	.		0.408	ZKSCAN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040189.3	NM_024493	
NEFH	4744	hgsc.bcm.edu	37	22	29885884	29885884	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr22:29885884delC	ENST00000310624.6	+	4	2288	c.2255delC	c.(2254-2256)tccfs	p.S752fs		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	758	30 X 6 AA repeats of K-S-P-[AEPV]-[EAK]- [AEVK].|Tail.				axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						AAGGCCAAGTCCCCAGAGAAG	0.552																																					p.S752fs		Atlas-INDEL	.											.	NEFH	178	.	0			c.2254delT						.						96.0	95.0	95.0					22																	29885884		2203	4300	6503	SO:0001589	frameshift_variant	4744	exon4			.		CCDS13858.1	22q12.2	2013-01-16	2008-09-19		ENSG00000100285	ENSG00000100285		"""Intermediate filaments type IV"""	7737	protein-coding gene	gene with protein product		162230	"""neurofilament, heavy polypeptide 200kDa"""				Standard	NM_021076		Approved		uc003afo.3	P12036	OTTHUMG00000151155	ENST00000310624.6:c.2255delC	chr22.hg19:g.29885884delC	ENSP00000311997:p.Ser752fs	135.0	0.0		164.0	11.0	NM_021076	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	Frame_Shift_Del	DEL	ENST00000310624.6	hg19	CCDS13858.1																																																																																			.	.		0.552	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076	
SCOC	60592	hgsc.bcm.edu	37	4	141302170	141302170	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:141302170delA	ENST00000608372.1	+	4	419	c.392delA	c.(391-393)gaafs	p.E131fs	SCOC_ENST00000394205.3_Frame_Shift_Del_p.E94fs|SCOC_ENST00000394201.4_Frame_Shift_Del_p.E54fs|SCOC_ENST00000512749.1_Frame_Shift_Del_p.E54fs|SCOC_ENST00000502535.1_Frame_Shift_Del_p.E54fs|SCOC_ENST00000510586.1_Frame_Shift_Del_p.E54fs|SCOC_ENST00000338517.4_Frame_Shift_Del_p.E94fs|SCOC_ENST00000506597.1_Frame_Shift_Del_p.E103fs|SCOC_ENST00000394203.3_Frame_Shift_Del_p.E94fs|SCOC_ENST00000506322.1_Frame_Shift_Del_p.E54fs			Q9UIL1	SCOC_HUMAN	short coiled-coil protein	131					positive regulation of macroautophagy (GO:0016239)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)				kidney(1)|large_intestine(1)|lung(2)|skin(1)	5	all_hematologic(180;0.162)					CTAAAATCAGAAAACCAAGTT	0.313																																					p.E131fs		Atlas-INDEL	.											.	SCOC	11	.	0			c.391delG						.						51.0	56.0	55.0					4																	141302170		2203	4298	6501	SO:0001589	frameshift_variant	60592	exon4			.	AK027797	CCDS3750.1, CCDS54806.1, CCDS54807.1	4q28.3	2014-05-22	2003-03-19		ENSG00000153130	ENSG00000153130			20335	protein-coding gene	gene with protein product			"""short coiled coil protein"""			11303027	Standard	NM_032547		Approved	HRIHFB2072, SCOCO	uc011che.1	Q9UIL1	OTTHUMG00000133416	ENST00000608372.1:c.392delA	chr4.hg19:g.141302170delA	ENSP00000477352:p.Glu131fs	161.0	0.0		165.0	11.0	NM_001153484	B7WPH7|D3DNY7|E9PB65|Q6P5T9|Q7L2Y0|Q7Z4P2|Q96JY9|Q9BZB2	Frame_Shift_Del	DEL	ENST00000608372.1	hg19	CCDS54806.1																																																																																			.	.		0.313	SCOC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257274.2		
TTN	7273	hgsc.bcm.edu	37	2	179438689	179438689	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:179438689delG	ENST00000591111.1	-	276	67471	c.67247delC	c.(67246-67248)ccafs	p.P22418fs	TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Frame_Shift_Del_p.P15186fs|TTN_ENST00000589042.1_Frame_Shift_Del_p.P24059fs|TTN_ENST00000342992.6_Frame_Shift_Del_p.P21491fs|TTN_ENST00000460472.2_Frame_Shift_Del_p.P14994fs|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN_ENST00000359218.5_Frame_Shift_Del_p.P15119fs|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	22418	Ig-like 116.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TGTTGGAGGTGGGCGGCCTGA	0.403																																					p.P24057fs		Atlas-INDEL	.											.	TTN	18412	.	0			c.72171delA						.						62.0	59.0	60.0					2																	179438689		1867	4106	5973	SO:0001589	frameshift_variant	7273	exon326			.	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.67247delC	chr2.hg19:g.179438689delG	ENSP00000465570:p.Pro22418fs	147.0	0.0		192.0	12.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Frame_Shift_Del	DEL	ENST00000591111.1	hg19																																																																																				.	.		0.403	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
COL6A3	1293	hgsc.bcm.edu	37	2	238277223	238277223	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:238277223delG	ENST00000295550.4	-	10	5335	c.4883delC	c.(4882-4884)cctfs	p.P1630fs	COL6A3_ENST00000353578.4_Frame_Shift_Del_p.P1424fs|COL6A3_ENST00000346358.4_Frame_Shift_Del_p.P1430fs|COL6A3_ENST00000347401.3_Frame_Shift_Del_p.P1429fs|COL6A3_ENST00000472056.1_Frame_Shift_Del_p.P1023fs|COL6A3_ENST00000409809.1_Frame_Shift_Del_p.P1424fs	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	1630	Nonhelical region.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		TGAAGGAGGAGGGGTGTCCAC	0.468																																					p.P1628fs		Atlas-INDEL	.											.	COL6A3	608	.	0			c.4884delT						.						61.0	63.0	63.0					2																	238277223		2203	4300	6503	SO:0001589	frameshift_variant	1293	exon10			.	X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"""Collagens"""	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.4883delC	chr2.hg19:g.238277223delG	ENSP00000295550:p.Pro1630fs	117.0	0.0		129.0	10.0	NM_004369	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Frame_Shift_Del	DEL	ENST00000295550.4	hg19	CCDS33412.1																																																																																			.	.		0.468	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369	
ATXN7L2	127002	hgsc.bcm.edu	37	1	110033680	110033680	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:110033680delC	ENST00000369870.3	+	10	1510	c.1495delC	c.(1495-1497)cccfs	p.P500fs	ATXN7L2_ENST00000459635.1_3'UTR|CYB561D1_ENST00000393709.3_5'Flank	NM_153340.4	NP_699171.3	Q5T6C5	AT7L2_HUMAN	ataxin 7-like 2	500								p.T501fs*21(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(1)|skin(1)	17		all_epithelial(167;0.00197)|all_lung(203;0.00291)|Lung NSC(277;0.00453)		Colorectal(144;0.0129)|Lung(183;0.0426)|Epithelial(280;0.0675)|READ - Rectum adenocarcinoma(129;0.0693)|all cancers(265;0.071)|LUSC - Lung squamous cell carcinoma(189;0.228)		AGCCTCCATGCCCCCCACCAA	0.662											OREG0013635	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.M498fs		Atlas-INDEL	.											.,1	ATXN7L2	60	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.1494delG						.						37.0	42.0	41.0					1																	110033680		2203	4300	6503	SO:0001589	frameshift_variant	127002	exon10			.	BC037582	CCDS30794.1	1p13.2	2008-02-05			ENSG00000162650	ENSG00000162650			28713	protein-coding gene	gene with protein product						12477932	Standard	NM_153340		Approved	MGC46534, FLJ00381	uc001dxr.3	Q5T6C5	OTTHUMG00000011027	ENST00000369870.3:c.1495delC	chr1.hg19:g.110033680delC	ENSP00000358886:p.Pro500fs	164.0	0.0	1424	162.0	11.0	NM_153340		Frame_Shift_Del	DEL	ENST00000369870.3	hg19	CCDS30794.1																																																																																			.	.		0.662	ATXN7L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030331.1	NM_153340	
AGO2	27161	hgsc.bcm.edu	37	8	141595382	141595382	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr8:141595382delG	ENST00000220592.5	-	2	163	c.51delC	c.(49-51)cccfs	p.P17fs	AGO2_ENST00000519980.1_Frame_Shift_Del_p.P17fs|AGO2_ENST00000517293.1_5'UTR	NM_012154.3	NP_036286.2	Q9UKV8	AGO2_HUMAN	argonaute RISC catalytic component 2	17					epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|innate immune response (GO:0045087)|mRNA cleavage involved in gene silencing by miRNA (GO:0035279)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|negative regulation of translational initiation (GO:0045947)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|post-embryonic development (GO:0009791)|pre-miRNA processing (GO:0031054)|regulation of transcription, DNA-templated (GO:0006355)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|transcription, DNA-templated (GO:0006351)|translation (GO:0006412)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)|micro-ribonucleoprotein complex (GO:0035068)|mRNA cap binding complex (GO:0005845)|nucleus (GO:0005634)|polysome (GO:0005844)|ribonucleoprotein complex (GO:0030529)|RISC complex (GO:0016442)	endoribonuclease activity (GO:0004521)|endoribonuclease activity, cleaving siRNA-paired mRNA (GO:0070551)|metal ion binding (GO:0046872)|miRNA binding (GO:0035198)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|RNA 7-methylguanosine cap binding (GO:0000340)|siRNA binding (GO:0035197)|translation initiation factor activity (GO:0003743)										ATCCTTGGATGGGGGGCGGCG	0.592																																					p.I18fs		Atlas-INDEL	.											.	.	.	.	0			c.52delA						.						54.0	59.0	57.0					8																	141595382		2203	4300	6503	SO:0001589	frameshift_variant	27161	exon2			.	AF121255	CCDS6380.1, CCDS55279.1	8q24.3	2013-02-15	2013-02-15	2013-02-15	ENSG00000123908	ENSG00000123908		"""Argonaute/PIWI family"""	3263	protein-coding gene	gene with protein product	"""argonaute 2"""	606229	"""eukaryotic translation initiation factor 2C, 2"""	EIF2C2		10534406, 12906857	Standard	NM_012154		Approved	hAGO2, Q10	uc003yvn.3	Q9UKV8	OTTHUMG00000164232	ENST00000220592.5:c.51delC	chr8.hg19:g.141595382delG	ENSP00000220592:p.Pro17fs	98.0	0.0		181.0	12.0	NM_012154	Q8TCZ5|Q8WV58|Q96ID1	Frame_Shift_Del	DEL	ENST00000220592.5	hg19	CCDS6380.1																																																																																			.	.		0.592	AGO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377866.4		
AKAP7	9465	hgsc.bcm.edu	37	6	131540900	131540900	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:131540900delA	ENST00000431975.2	+	7	900	c.802delA	c.(802-804)aaafs	p.K269fs	AKAP7_ENST00000368123.4_Frame_Shift_Del_p.K247fs|AKAP7_ENST00000537868.1_Frame_Shift_Del_p.K5fs|AKAP7_ENST00000263050.3_Frame_Shift_Del_p.K5fs|AKAP7_ENST00000541650.1_Frame_Shift_Del_p.K268fs	NM_016377.3	NP_057461.2	Q9P0M2	AKA7G_HUMAN	A kinase (PRKA) anchor protein 7	269						cytosol (GO:0005829)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|nucleotide binding (GO:0000166)|protein kinase A binding (GO:0051018)			endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(2)|prostate(1)|stomach(1)	13	Breast(56;0.152)			GBM - Glioblastoma multiforme(226;0.0184)|OV - Ovarian serous cystadenocarcinoma(155;0.0345)		CATGCTGAAGAAAAAACAAAG	0.279																																					p.K267fs		Atlas-INDEL	.											.	AKAP7	61	.	0			c.801delG						.						78.0	84.0	82.0					6																	131540900		2202	4299	6501	SO:0001589	frameshift_variant	9465	exon7			.	AF047715	CCDS5142.1, CCDS5143.1, CCDS5144.1, CCDS5142.2	6q23.2	2012-10-24			ENSG00000118507	ENSG00000118507		"""A-kinase anchor proteins"""	377	protein-coding gene	gene with protein product		604693				9545239	Standard	NM_016377		Approved	AKAP18, AKAP15	uc003qck.4	O43687	OTTHUMG00000015563	ENST00000431975.2:c.802delA	chr6.hg19:g.131540900delA	ENSP00000405252:p.Lys269fs	242.0	0.0		208.0	15.0	NM_016377	B4DUC3|Q9HCZ8	Frame_Shift_Del	DEL	ENST00000431975.2	hg19	CCDS5142.2																																																																																			.	.		0.279	AKAP7-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042209.2	NM_004842	
GK5	256356	hgsc.bcm.edu	37	3	141917719	141917719	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:141917719delA	ENST00000392993.2	-	5	619	c.468delT	c.(466-468)tttfs	p.F156fs	GK5_ENST00000544571.1_Frame_Shift_Del_p.F156fs	NM_001039547.2	NP_001034636.1	Q6ZS86	GLPK5_HUMAN	glycerol kinase 5 (putative)	156					glycerol catabolic process (GO:0019563)		ATP binding (GO:0005524)|glycerol kinase activity (GO:0004370)			kidney(1)|large_intestine(1)|lung(7)|urinary_tract(1)	10						AACTGGCTGTAAAAAGTCGTT	0.348																																					p.T157fs		Atlas-INDEL	.											.	GK5	45	.	0			c.469delA						.						81.0	80.0	81.0					3																	141917719		2203	4300	6503	SO:0001589	frameshift_variant	256356	exon5			.	BX648681	CCDS33871.1	3q23	2014-02-12	2006-09-21		ENSG00000175066	ENSG00000175066		"""Glycerol kinases"""	28635	protein-coding gene	gene with protein product						12477932	Standard	NM_001039547		Approved	MGC40579	uc003euq.2	Q6ZS86	OTTHUMG00000133572	ENST00000392993.2:c.468delT	chr3.hg19:g.141917719delA	ENSP00000418001:p.Phe156fs	158.0	0.0		192.0	12.0	NM_001039547	B2R9I2|D3DNG2|Q8N2A7|Q8N5E6	Frame_Shift_Del	DEL	ENST00000392993.2	hg19	CCDS33871.1																																																																																			.	.		0.348	GK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353999.1	NM_001039547	
PRSS53	339105	hgsc.bcm.edu	37	16	31098992	31098992	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:31098992delG	ENST00000280606.6	-	3	261	c.108delC	c.(106-108)cccfs	p.P36fs	RP11-196G11.1_ENST00000529564.1_Frame_Shift_Del_p.P111fs	NM_001039503.2	NP_001034592.1	Q2L4Q9	PRS53_HUMAN	protease, serine, 53	36	Peptidase S1 1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			large_intestine(1)|lung(3)	4						CCTGAGGCTTGGGGGGGCCGG	0.647																																					p.K37fs		Atlas-INDEL	.											.,1	PRSS53	29	.	0			c.109delA						.						21.0	26.0	25.0					16																	31098992		2009	4177	6186	SO:0001589	frameshift_variant	339105	exon3			.		CCDS42153.1	16p11.2	2010-05-07			ENSG00000151006	ENSG00000151006		"""Serine peptidases / Serine peptidases"""	34407	protein-coding gene	gene with protein product	"""polyserase 3"""	610561				16566820	Standard	NM_001039503		Approved	POL3S	uc002eaq.3	Q2L4Q9	OTTHUMG00000047358	ENST00000280606.6:c.108delC	chr16.hg19:g.31098992delG	ENSP00000280606:p.Pro36fs	114.0	0.0		128.0	11.0	NM_001039503		Frame_Shift_Del	DEL	ENST00000280606.6	hg19	CCDS42153.1																																																																																			.	.		0.647	PRSS53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000108580.4	NM_001081268	
MSL3	10943	hgsc.bcm.edu	37	X	11776451	11776451	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:11776451delC	ENST00000312196.4	+	1	174	c.69delC	c.(67-69)gacfs	p.D23fs	MSL3_ENST00000380693.3_5'Flank|MSL3_ENST00000337339.2_Frame_Shift_Del_p.D23fs|MSL3_ENST00000361672.2_5'UTR|MSL3_ENST00000398527.2_5'Flank	NM_078629.3	NP_523353.2	Q8N5Y2	MS3L1_HUMAN	male-specific lethal 3 homolog (Drosophila)	23					chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|multicellular organismal development (GO:0007275)|transcription from RNA polymerase II promoter (GO:0006366)	MSL complex (GO:0072487)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|methylated histone binding (GO:0035064)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(3)|cervix(1)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)|urinary_tract(1)	19						TCGAGCCTGACCCCACCAAGG	0.687																																					p.D23fs		Atlas-INDEL	.											.	MSL3	88	.	0			c.68delA						.						28.0	21.0	24.0					X																	11776451		2193	4297	6490	SO:0001589	frameshift_variant	10943	exon1			.	AF117065	CCDS14147.1, CCDS14148.1, CCDS14149.1, CCDS55369.1, CCDS65213.1	Xp22.3	2008-10-29	2008-10-29	2008-10-29	ENSG00000005302	ENSG00000005302			7370	protein-coding gene	gene with protein product		300609	"""male-specific lethal-3 (Drosophila)-like 1"", ""male-specific lethal 3-like 1 (Drosophila)"""	MSL3L1		10395802, 10908644	Standard	NM_078628		Approved		uc004cuw.3	Q8N5Y2	OTTHUMG00000021132	ENST00000312196.4:c.69delC	chrX.hg19:g.11776451delC	ENSP00000312244:p.Asp23fs	111.0	0.0		127.0	11.0	NM_078628	A6NCU2|A6NHW8|A8K165|B4DUV8|B7Z227|Q9UG70|Q9Y5Z8	Frame_Shift_Del	DEL	ENST00000312196.4	hg19	CCDS14147.1																																																																																			.	.		0.687	MSL3-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055757.1	NM_006800	
TRAP1	10131	hgsc.bcm.edu	37	16	3708188	3708188	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:3708188delG	ENST00000246957.5	-	18	2145	c.2057delC	c.(2056-2058)cctfs	p.P686fs	DNASE1_ENST00000414110.2_Intron|TRAP1_ENST00000538171.1_Frame_Shift_Del_p.P633fs|TRAP1_ENST00000575671.1_Frame_Shift_Del_p.P477fs	NM_016292.2	NP_057376.2	Q12931	TRAP1_HUMAN	TNF receptor-associated protein 1	686					chaperone-mediated protein folding (GO:0061077)|negative regulation of cellular respiration (GO:1901856)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|regulation of reactive oxygen species metabolic process (GO:2000377)|response to stress (GO:0006950)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|tumor necrosis factor receptor binding (GO:0005164)			central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19		Ovarian(90;0.0261)				CATGGCCCTAGGGTCGTCAAC	0.547																																					p.P686fs		Atlas-INDEL	.											.	TRAP1	53	.	0			c.2058delT						.						60.0	57.0	58.0					16																	3708188		2197	4300	6497	SO:0001589	frameshift_variant	10131	exon18			.	AF154108	CCDS10508.1, CCDS61824.1	16p13.3	2011-09-02			ENSG00000126602	ENSG00000126602		"""Heat shock proteins / HSPC"""	16264	protein-coding gene	gene with protein product		606219				10652318, 7876093	Standard	NM_016292		Approved	HSP75, HSP90L	uc002cvt.4	Q12931	OTTHUMG00000129427	ENST00000246957.5:c.2057delC	chr16.hg19:g.3708188delG	ENSP00000246957:p.Pro686fs	112.0	0.0		141.0	10.0	NM_016292	B4DR68|D3DUC8|F5H897|O43642|O75235|Q9UHL5	Frame_Shift_Del	DEL	ENST00000246957.5	hg19	CCDS10508.1																																																																																			.	.		0.547	TRAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251586.2	NM_016292	
RP11-383M4.6	0	hgsc.bcm.edu	37	9	84545071	84545071	+	lincRNA	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:84545071delA	ENST00000585776.1	-	0	4416				RP11-383M4.2_ENST00000427387.1_lincRNA|SPATA31D4_ENST00000341875.4_RNA																							TTCTTTTCTGAAAAGGTGATT	0.378																																					p.L96fs		Atlas-INDEL	.											.	.	.	.	0			c.288delG						.						1.0	3.0	2.0					9																	84545071		109	575	684			389761	exon3			.																													chr9.hg19:g.84545071delA		158.0	0.0		182.0	12.0	NM_001145197		Frame_Shift_Del	DEL	ENST00000585776.1	hg19																																																																																				.	.		0.378	RP11-383M4.6-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000453562.1		
GPR126	57211	hgsc.bcm.edu	37	6	142741019	142741019	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:142741019delT	ENST00000230173.6	+	22	3573	c.3097delT	c.(3097-3099)tttfs	p.F1034fs	GPR126_ENST00000296932.8_Frame_Shift_Del_p.F1006fs|GPR126_ENST00000367608.2_Frame_Shift_Del_p.F1006fs|GPR126_ENST00000367609.3_Frame_Shift_Del_p.F1034fs	NM_020455.5	NP_065188	Q86SQ4	GP126_HUMAN	G protein-coupled receptor 126	1034					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(12)|lung(10)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	36	Breast(32;0.176)			OV - Ovarian serous cystadenocarcinoma(155;9.33e-06)|GBM - Glioblastoma multiforme(68;0.00121)		TGGAGTCATGTTTTTTCTGAA	0.383																																					p.M1032fs		Atlas-INDEL	.											.	GPR126	192	.	0			c.3096delG						.						219.0	195.0	202.0					6																	142741019		1898	4125	6023	SO:0001589	frameshift_variant	57211	exon22			.	AK027843	CCDS47489.1, CCDS47490.1, CCDS47491.1, CCDS55064.1	6q23.1-q24.3	2014-08-08			ENSG00000112414	ENSG00000112414		"""-"", ""GPCR / Class B : Orphans"""	13841	protein-coding gene	gene with protein product		612243				12565841	Standard	NM_001032395		Approved	FLJ14937	uc010khe.3	Q86SQ4	OTTHUMG00000015709	ENST00000230173.6:c.3097delT	chr6.hg19:g.142741019delT	ENSP00000230173:p.Phe1034fs	215.0	0.0		221.0	15.0	NM_198569	Q5TGN7|Q6DHZ4|Q6F3F5|Q6F3F6|Q6F3F7|Q6F3F8|Q6MZU7|Q8IXA4|Q8NC14|Q96JW0	Frame_Shift_Del	DEL	ENST00000230173.6	hg19	CCDS47490.1																																																																																			.	.		0.383	GPR126-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000042487.2		
PCDHGA1	56114	hgsc.bcm.edu	37	5	140711785	140711785	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:140711785delG	ENST00000517417.1	+	1	1534	c.1534delG	c.(1534-1536)gggfs	p.G512fs	PCDHGA1_ENST00000378105.3_Frame_Shift_Del_p.G512fs|AC005618.6_ENST00000606901.1_lincRNA	NM_018912.2	NP_061735.1	Q9Y5H4	PCDG1_HUMAN	protocadherin gamma subfamily A, 1	512	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(18)|lung(32)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTCCGACACTGGGGTCCTGTA	0.552																																					p.T511fs		Atlas-INDEL	.											.	PCDHGA1	397	.	0			c.1533delT						.						136.0	148.0	144.0					5																	140711785		2203	4300	6503	SO:0001589	frameshift_variant	56114	exon1			.	AF152318	CCDS54922.1	5q31	2010-01-26				ENSG00000204956		"""Cadherins / Protocadherins : Clustered"""	8696	other	protocadherin		606288				10380929	Standard	NM_018912		Approved	PCDH-GAMMA-A1		Q9Y5H4		ENST00000517417.1:c.1534delG	chr5.hg19:g.140711785delG	ENSP00000431083:p.Gly512fs	111.0	0.0		149.0	11.0	NM_018912	Q2M273|Q9Y5D6	Frame_Shift_Del	DEL	ENST00000517417.1	hg19	CCDS54922.1																																																																																			.	.		0.552	PCDHGA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374737.1	NM_018912	
ZCWPW1	55063	hgsc.bcm.edu	37	7	100013617	100013617	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:100013617delT	ENST00000398027.2	-	8	979	c.732delA	c.(730-732)aaafs	p.K244fs	ZCWPW1_ENST00000360951.4_Frame_Shift_Del_p.K245fs|ZCWPW1_ENST00000490721.1_Frame_Shift_Del_p.K124fs|ZCWPW1_ENST00000324725.6_Frame_Shift_Del_p.K124fs	NM_017984.4	NP_060454.3	Q9H0M4	ZCPW1_HUMAN	zinc finger, CW type with PWWP domain 1	244							zinc ion binding (GO:0008270)			breast(1)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|skin(1)	16	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					TTATCTCTCCTTTTTGCTGGT	0.443																																					p.G246fs		Atlas-INDEL	.											.	ZCWPW1	41	.	0			c.736delG						.						258.0	238.0	244.0					7																	100013617		1901	4118	6019	SO:0001589	frameshift_variant	55063	exon8			.	AK000919	CCDS43623.1, CCDS59067.1	7q22.1	2012-02-10	2004-11-03		ENSG00000078487	ENSG00000078487			23486	protein-coding gene	gene with protein product			"""zinc finger, CW-type with PWWP domain 1"""			11230166, 14607086, 20826339	Standard	NM_017984		Approved	FLJ10057, DKFZp434N0510, ZCW1	uc003uut.4	Q9H0M4	OTTHUMG00000159537	ENST00000398027.2:c.732delA	chr7.hg19:g.100013617delT	ENSP00000381109:p.Lys244fs	153.0	0.0		207.0	14.0	NM_001258008	A8MVF5|B4DUQ2|Q8NA98|Q9BUD0|Q9NWF7	Frame_Shift_Del	DEL	ENST00000398027.2	hg19	CCDS43623.1																																																																																			.	.		0.443	ZCWPW1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356083.1	NM_017984	
FER1L6	654463	hgsc.bcm.edu	37	8	125115501	125115501	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr8:125115501delA	ENST00000522917.1	+	39	5446	c.5240delA	c.(5239-5241)caafs	p.Q1747fs	FER1L6_ENST00000399018.1_Frame_Shift_Del_p.Q1747fs|FER1L6-AS2_ENST00000520031.1_RNA	NM_001039112.2	NP_001034201.2	Q2WGJ9	FR1L6_HUMAN	fer-1-like family member 6	1747						integral component of membrane (GO:0016021)				NS(2)|breast(3)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(18)|liver(1)|lung(49)|ovary(5)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(1)	118	Lung NSC(37;4.1e-12)|Ovarian(258;0.00438)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00186)			ATATTCCAGCAAAAACGTGTG	0.483																																					p.Q1747fs		Atlas-INDEL	.											.	FER1L6	268	.	0			c.5239delC						.						151.0	147.0	148.0					8																	125115501		1910	4133	6043	SO:0001589	frameshift_variant	654463	exon39			.	AB196633	CCDS43767.1	8q24.13	2014-06-27	2014-06-27		ENSG00000214814	ENSG00000214814			28065	protein-coding gene	gene with protein product			"""fer-1-like 6 (C. elegans)"""				Standard	NM_001039112		Approved	C8ORFK23	uc003yqw.3	Q2WGJ9	OTTHUMG00000164998	ENST00000522917.1:c.5240delA	chr8.hg19:g.125115501delA	ENSP00000428280:p.Gln1747fs	94.0	0.0		188.0	12.0	NM_001039112		Frame_Shift_Del	DEL	ENST00000522917.1	hg19	CCDS43767.1																																																																																			.	.		0.483	FER1L6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381400.1	NM_001039112	
ABCF1	23	hgsc.bcm.edu	37	6	30553664	30553664	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:30553664delA	ENST00000326195.8	+	17	1721	c.1609delA	c.(1609-1611)aaafs	p.K538fs	ABCF1_ENST00000376545.3_Frame_Shift_Del_p.K500fs|ABCF1_ENST00000396515.4_Intron|MIR877_ENST00000401282.1_RNA	NM_001025091.1	NP_001020262.1	Q8NE71	ABCF1_HUMAN	ATP-binding cassette, sub-family F (GCN20), member 1	538	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				inflammatory response (GO:0006954)|positive regulation of translation (GO:0045727)|translation (GO:0006412)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|polysomal ribosome (GO:0042788)|ribosome (GO:0005840)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|poly(A) RNA binding (GO:0044822)|ribosome binding (GO:0043022)|translation activator activity (GO:0008494)|translation factor activity, nucleic acid binding (GO:0008135)			breast(2)|endometrium(1)|kidney(2)|large_intestine(6)|lung(5)|ovary(3)|skin(2)	21						AGTGACCTTCAAAAAGATGTA	0.527																																					p.F536fs		Atlas-INDEL	.											.	ABCF1	61	.	0			c.1608delC						.						21.0	17.0	18.0					6																	30553664		1510	2708	4218	SO:0001589	frameshift_variant	23	exon17			.	AF027302	CCDS34380.1, CCDS34381.1	6p21.33	2012-03-14			ENSG00000204574	ENSG00000204574		"""ATP binding cassette transporters / subfamily F"""	70	protein-coding gene	gene with protein product		603429		ABC50		9790762	Standard	NM_001025091		Approved	EST123147	uc003nql.3	Q8NE71	OTTHUMG00000031094	ENST00000326195.8:c.1609delA	chr6.hg19:g.30553664delA	ENSP00000313603:p.Lys538fs	57.0	0.0		123.0	10.0	NM_001025091	A2BF75|O14897|Q69YP6	Frame_Shift_Del	DEL	ENST00000326195.8	hg19	CCDS34380.1																																																																																			.	.		0.527	ABCF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076137.3		
ANKS1B	56899	hgsc.bcm.edu	37	12	99446958	99446958	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:99446958delT	ENST00000547776.2	-	17	2754	c.2755delA	c.(2755-2757)atcfs	p.I919fs	ANKS1B_ENST00000546568.1_Frame_Shift_Del_p.I145fs|ANKS1B_ENST00000546960.1_Frame_Shift_Del_p.I145fs|ANKS1B_ENST00000549493.2_Frame_Shift_Del_p.I145fs|ANKS1B_ENST00000332712.7_Frame_Shift_Del_p.I145fs|ANKS1B_ENST00000549558.2_Frame_Shift_Del_p.I145fs|ANKS1B_ENST00000549025.2_Frame_Shift_Del_p.I88fs|ANKS1B_ENST00000550693.2_Frame_Shift_Del_p.I145fs|ANKS1B_ENST00000547010.1_Frame_Shift_Del_p.I495fs|ANKS1B_ENST00000329257.7_Frame_Shift_Del_p.I919fs|ANKS1B_ENST00000547446.1_Frame_Shift_Del_p.I114fs	NM_152788.4	NP_690001.3	Q7Z6G8	ANS1B_HUMAN	ankyrin repeat and sterile alpha motif domain containing 1B	919	SAM 2. {ECO:0000255|PROSITE- ProRule:PRU00184}.					cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	ephrin receptor binding (GO:0046875)			NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(15)|lung(38)|pancreas(1)|prostate(2)|skin(1)	70		all_cancers(3;0.0197)|all_epithelial(3;0.0101)|Esophageal squamous(3;0.0559)|Breast(359;0.209)		OV - Ovarian serous cystadenocarcinoma(2;2.89e-08)|Epithelial(2;6.12e-08)|all cancers(2;4.07e-06)		ACCTCCCAGATTTTTTTCAAC	0.373																																					p.I919fs		Atlas-INDEL	.											.	ANKS1B	180	.	0			c.2756delT						.						41.0	39.0	40.0					12																	99446958		1835	4089	5924	SO:0001589	frameshift_variant	56899	exon17			.	AF145204	CCDS55864.1, CCDS55865.1, CCDS55866.1, CCDS55867.1, CCDS55868.1, CCDS55869.1, CCDS55870.1, CCDS55871.1, CCDS55872.1	12q23.1	2013-01-10						"""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	24600	protein-coding gene	gene with protein product		607815				10490826, 12415113	Standard	NM_020140		Approved	EB-1, AIDA-1, cajalin-2, ANKS2	uc001tge.2	Q7Z6G8		ENST00000547776.2:c.2755delA	chr12.hg19:g.99446958delT	ENSP00000449629:p.Ile919fs	187.0	0.0		200.0	12.0	NM_152788	A5PKY5|A7E259|A8K153|A8MSN4|B4DFP6|B4DH98|F8VPM3|F8VZR9|F8WC27|Q5XLJ0|Q6IVB5|Q6NUS4|Q7Z6G6|Q7Z6G7|Q8TAP3|Q9NRX7|Q9Y5K9	Frame_Shift_Del	DEL	ENST00000547776.2	hg19	CCDS55872.1																																																																																			.	.		0.373	ANKS1B-003	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000408421.3	NM_020140	
CDH9	1007	hgsc.bcm.edu	37	5	26988315	26988315	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:26988315delT	ENST00000231021.4	-	2	298	c.126delA	c.(124-126)aaafs	p.K42fs		NM_016279.3	NP_057363.3	Q9ULB4	CADH9_HUMAN	cadherin 9, type 2 (T1-cadherin)	42					adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(25)|lung(80)|ovary(5)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	137						TACCGTCATCTTTTGTCAGAC	0.403																																					p.D43fs	Melanoma(8;187 585 15745 40864 52829)	Atlas-INDEL	.											.	CDH9	305	.	0			c.127delG						.						138.0	132.0	134.0					5																	26988315		2203	4300	6503	SO:0001589	frameshift_variant	1007	exon2			.	AB035302	CCDS3893.1	5p14	2010-01-26			ENSG00000113100	ENSG00000113100		"""Cadherins / Major cadherins"""	1768	protein-coding gene	gene with protein product		609974				2059658	Standard	NM_016279		Approved		uc003jgs.1	Q9ULB4	OTTHUMG00000090671	ENST00000231021.4:c.126delA	chr5.hg19:g.26988315delT	ENSP00000231021:p.Lys42fs	207.0	0.0		205.0	14.0	NM_016279	Q3B7I5	Frame_Shift_Del	DEL	ENST00000231021.4	hg19	CCDS3893.1																																																																																			.	.		0.403	CDH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207352.1	NM_016279	
GTSE1	51512	hgsc.bcm.edu	37	22	46704068	46704068	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr22:46704068delA	ENST00000454366.1	+	3	313	c.101delA	c.(100-102)gaafs	p.E34fs		NM_016426.6	NP_057510	Q9NYZ3	GTSE1_HUMAN	G-2 and S-phase expressed 1	15					DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|microtubule-based process (GO:0007017)	cytoplasmic microtubule (GO:0005881)|membrane (GO:0016020)				NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(3)	27		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00462)		TTGGCCGATGAAAAATTTGAC	0.373																																					p.E34fs	GBM(153;542 1915 12487 29016 50495)	Atlas-INDEL	.											.	GTSE1	100	.	0			c.100delG						.						130.0	131.0	131.0					22																	46704068		2203	4300	6503	SO:0001589	frameshift_variant	51512	exon3			.	AF223408	CCDS14074.2	22q13.2-q13.3	2008-06-10			ENSG00000075218	ENSG00000075218			13698	protein-coding gene	gene with protein product		607477				10974554, 10984615, 12750368	Standard	NM_016426		Approved	GTSE-1, B99	uc011aqy.2	Q9NYZ3	OTTHUMG00000150486	ENST00000454366.1:c.101delA	chr22.hg19:g.46704068delA	ENSP00000415430:p.Glu34fs	127.0	0.0		174.0	11.0	NM_016426	B0QYM3|Q20WK2|Q53GX5|Q5R3I6|Q6DHX4|Q9BRE0|Q9UGZ9|Q9Y557	Frame_Shift_Del	DEL	ENST00000454366.1	hg19	CCDS14074.2																																																																																			.	.		0.373	GTSE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318360.2	NM_016426	
PIK3C2A	5286	hgsc.bcm.edu	37	11	17150951	17150951	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:17150951delA	ENST00000265970.7	-	12	2294	c.2295delT	c.(2293-2295)tttfs	p.F765fs	PIK3C2A_ENST00000540361.1_Frame_Shift_Del_p.F385fs|PIK3C2A_ENST00000531428.1_Intron	NM_002645.2	NP_002636.2	O00443	P3C2A_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 alpha	765	C2 PI3K-type. {ECO:0000255|PROSITE- ProRule:PRU00041, ECO:0000255|PROSITE- ProRule:PRU00880}.				clathrin coat assembly (GO:0048268)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|exocytosis (GO:0006887)|insulin receptor signaling pathway (GO:0008286)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|small molecule metabolic process (GO:0044281)|vascular smooth muscle contraction (GO:0014829)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol binding (GO:0035091)			central_nervous_system(4)|endometrium(5)|kidney(5)|large_intestine(7)|lung(24)|ovary(3)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	58						TTAAAATTCCAAAAAGAGTAA	0.348																																					p.G766fs		Atlas-INDEL	.											.	PIK3C2A	148	.	0			c.2296delG						.						80.0	87.0	84.0					11																	17150951		2200	4292	6492	SO:0001589	frameshift_variant	5286	exon12			.	Y13367	CCDS7824.1	11p15.5-p14	2012-07-13	2012-07-13			ENSG00000011405	2.7.1.154		8971	protein-coding gene	gene with protein product		603601	"""phosphoinositide-3-kinase, class 2, alpha polypeptide"""			9337861	Standard	NM_002645		Approved	PI3K-C2alpha	uc001mmq.4	O00443		ENST00000265970.7:c.2295delT	chr11.hg19:g.17150951delA	ENSP00000265970:p.Phe765fs	126.0	0.0		167.0	13.0	NM_002645	B0LPH2|B4E2G4|Q14CQ9	Frame_Shift_Del	DEL	ENST00000265970.7	hg19	CCDS7824.1																																																																																			.	.		0.348	PIK3C2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387553.1	NM_002645	
NFIX	4784	hgsc.bcm.edu	37	19	13184726	13184726	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:13184726delT	ENST00000592199.1	+	5	704	c.704delT	c.(703-705)gttfs	p.V235fs	AC007787.2_ENST00000588095.1_RNA|NFIX_ENST00000358552.3_Frame_Shift_Del_p.V234fs|NFIX_ENST00000585575.1_Frame_Shift_Del_p.V227fs|NFIX_ENST00000587760.1_Frame_Shift_Del_p.V227fs|NFIX_ENST00000397661.2_Frame_Shift_Del_p.V235fs|NFIX_ENST00000588680.1_3'UTR|NFIX_ENST00000360105.4_Frame_Shift_Del_p.V238fs|NFIX_ENST00000588228.1_Frame_Shift_Del_p.V188fs|NFIX_ENST00000587260.1_Frame_Shift_Del_p.V234fs			Q14938	NFIX_HUMAN	nuclear factor I/X (CCAAT-binding transcription factor)	235					astrocyte differentiation (GO:0048708)|cerebellar granule cell differentiation (GO:0021707)|cerebellar Purkinje cell layer development (GO:0021680)|DNA replication (GO:0006260)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(1)|skin(1)|urinary_tract(1)	11			OV - Ovarian serous cystadenocarcinoma(19;8.2e-22)			CCAGCTCCTGTTGCAACAGCA	0.597																																					p.V243fs		Atlas-INDEL	.											.	NFIX	61	.	0			c.727delG						.						74.0	81.0	79.0					19																	13184726		1955	4138	6093	SO:0001589	frameshift_variant	4784	exon5			.	U18761	CCDS45996.1, CCDS59359.1	19p13.3	2008-02-05				ENSG00000008441			7788	protein-coding gene	gene with protein product		164005				8340106, 7590749	Standard	NM_001271043		Approved	NF1A	uc010xmx.2	Q14938		ENST00000592199.1:c.704delT	chr19.hg19:g.13184726delT	ENSP00000467512:p.Val235fs	131.0	0.0		152.0	10.0	NM_001271043	B4DM25|O60413|Q0VG09|Q12859|Q13050|Q13052|Q5U094|Q9UPH1|Q9Y6R8	Frame_Shift_Del	DEL	ENST00000592199.1	hg19																																																																																				.	.		0.597	NFIX-013	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000452763.1	NM_002501	
ERICH3	127254	hgsc.bcm.edu	37	1	75112405	75112405	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:75112405delT	ENST00000326665.5	-	3	407	c.189delA	c.(187-189)aaafs	p.K63fs		NM_001002912.4	NP_001002912.4	Q5RHP9	ERIC3_HUMAN		63										NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(23)|lung(123)|ovary(3)|prostate(10)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)	184						CCCGGATATATTTTTGATGAT	0.259																																					p.Y64fs		Atlas-INDEL	.											.	C1orf173	380	.	0			c.190delT						.						28.0	26.0	26.0					1																	75112405		2084	4072	6156	SO:0001589	frameshift_variant	127254	exon3			.																												ENST00000326665.5:c.189delA	chr1.hg19:g.75112405delT	ENSP00000322609:p.Lys63fs	166.0	0.0		208.0	14.0	NM_001002912	Q68DL8|Q6GMR8|Q6ZSF9|Q8ND41	Frame_Shift_Del	DEL	ENST00000326665.5	hg19	CCDS30755.1																																																																																			.	.		0.259	C1orf173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026516.1		
DOCK5	80005	hgsc.bcm.edu	37	8	25240190	25240190	+	Splice_Site	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr8:25240190delA	ENST00000276440.7	+	40	4071	c.4027delA	c.(4027-4029)aaa>aa	p.K1344fs		NM_024940.6	NP_079216.4	Q9H7D0	DOCK5_HUMAN	dedicator of cytokinesis 5	1344	DHR-2.				positive regulation of GTPase activity (GO:0043547)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(9)|large_intestine(13)|lung(20)|ovary(3)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	72		all_cancers(63;0.0361)|Ovarian(32;0.000711)|all_epithelial(46;0.0153)|Hepatocellular(4;0.115)|Prostate(55;0.13)|Breast(100;0.143)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0267)|Epithelial(17;1.07e-11)|Colorectal(74;0.0276)|COAD - Colon adenocarcinoma(73;0.0828)		TGTTTTCCAGAAAAAAAGGGC	0.408																																					.	Pancreas(145;34 1887 3271 10937 30165)	Atlas-INDEL	.											.	DOCK5	167	.	0			c.4027-1A>-						.						85.0	80.0	82.0					8																	25240190		2203	4300	6503	SO:0001630	splice_region_variant	80005	exon40			.		CCDS6047.1	8p21.2	2009-04-17			ENSG00000147459	ENSG00000147459			23476	protein-coding gene	gene with protein product						12432077	Standard	NM_024940		Approved	FLJ21034	uc003xeg.3	Q9H7D0	OTTHUMG00000131991	ENST00000276440.7:c.4027-1A>-	chr8.hg19:g.25240190delA		74.0	0.0		78.0	10.0	NM_024940	B2RNY0|Q5XKD5|Q6AI11|Q6PJS6|Q6ZTS6	Splice_Site	DEL	ENST00000276440.7	hg19	CCDS6047.1																																																																																			.	.		0.408	DOCK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254955.2	NM_024940	Frame_Shift_Del
WDR70	55100	hgsc.bcm.edu	37	5	37703139	37703139	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:37703139delT	ENST00000265107.4	+	13	1522	c.1366delT	c.(1366-1368)tttfs	p.F456fs	RNU6-484P_ENST00000384016.1_RNA	NM_018034.2	NP_060504.1	Q9NW82	WDR70_HUMAN	WD repeat domain 70	456							enzyme binding (GO:0019899)			central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(5)|lung(18)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37	all_lung(31;0.000285)		COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			ACTTGTTTTCTTTGAGCGTAG	0.413																																					p.F455fs		Atlas-INDEL	.											.	WDR70	76	.	0			c.1365delC						.						122.0	111.0	115.0					5																	37703139		2203	4300	6503	SO:0001589	frameshift_variant	55100	exon13			.	BC009648	CCDS34147.1	5p13.2	2013-01-09			ENSG00000082068	ENSG00000082068		"""WD repeat domain containing"""	25495	protein-coding gene	gene with protein product						12477932	Standard	NM_018034		Approved	FLJ10233	uc003jkv.3	Q9NW82	OTTHUMG00000162263	ENST00000265107.4:c.1366delT	chr5.hg19:g.37703139delT	ENSP00000265107:p.Phe456fs	163.0	0.0		194.0	14.0	NM_018034	Q9H053	Frame_Shift_Del	DEL	ENST00000265107.4	hg19	CCDS34147.1																																																																																			.	.		0.413	WDR70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368294.1	NM_018034	
USP19	10869	hgsc.bcm.edu	37	3	49153294	49153294	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:49153294delG	ENST00000398888.2	-	10	1564	c.1246delC	c.(1246-1248)ctgfs	p.L416fs	USP19_ENST00000488993.1_5'Flank|USP19_ENST00000434032.2_Frame_Shift_Del_p.L517fs|USP19_ENST00000398898.2_Frame_Shift_Del_p.L456fs|USP19_ENST00000417901.1_Frame_Shift_Del_p.L519fs|USP19_ENST00000398896.1_Frame_Shift_Del_p.L224fs|USP19_ENST00000398892.3_Frame_Shift_Del_p.L456fs|USP19_ENST00000453664.1_Frame_Shift_Del_p.L507fs	NM_006677.2	NP_006668.1	O94966	UBP19_HUMAN	ubiquitin specific peptidase 19	416					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|negative regulation of skeletal muscle tissue development (GO:0048642)|positive regulation of cell cycle process (GO:0090068)|protein deubiquitination (GO:0016579)|regulation of cellular response to hypoxia (GO:1900037)|regulation of protein stability (GO:0031647)|response to endoplasmic reticulum stress (GO:0034976)|skeletal muscle atrophy (GO:0014732)	cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)|ubiquitin-specific protease activity (GO:0004843)			NS(1)|breast(3)|endometrium(5)|kidney(2)|large_intestine(10)|lung(5)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	38				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		TGGCCTGTCAGGGGGTGGGGA	0.607																																					p.L519fs		Atlas-INDEL	.											.	USP19	158	.	0			c.1556delT						.						57.0	60.0	59.0					3																	49153294		1964	4142	6106	SO:0001589	frameshift_variant	10869	exon11			.	AB020698	CCDS43090.1, CCDS56254.1, CCDS56255.1, CCDS56256.1	3p21.31	2005-10-13	2005-08-08		ENSG00000172046	ENSG00000172046		"""Zinc fingers, MYND-type"", ""Ubiquitin-specific peptidases"""	12617	protein-coding gene	gene with protein product		614471	"""ubiquitin specific protease 19"""			12838346	Standard	NM_001199160		Approved	KIAA0891, ZMYND9	uc011bch.2	O94966	OTTHUMG00000133611	ENST00000398888.2:c.1246delC	chr3.hg19:g.49153294delG	ENSP00000381863:p.Leu416fs	171.0	0.0		205.0	13.0	NM_001199161	A5PKX8|A6H8U2|B4DGT3|B4DTZ0|E7EN22|E7ETS0|E9PEG8|Q3KQW4|Q641Q9|Q6NZY8|Q86XV9	Frame_Shift_Del	DEL	ENST00000398888.2	hg19	CCDS43090.1																																																																																			.	.		0.607	USP19-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257721.1	NM_006677	
ASPM	259266	hgsc.bcm.edu	37	1	197115430	197115430	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:197115430delC	ENST00000367409.4	-	1	394	c.138delG	c.(136-138)aggfs	p.R46fs	ASPM_ENST00000294732.7_Frame_Shift_Del_p.R46fs	NM_018136.4	NP_060606.3	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle) homolog, microcephaly associated (Drosophila)	46					developmental growth (GO:0048589)|forebrain neuroblast division (GO:0021873)|maintenance of centrosome location (GO:0051661)|mitotic nuclear division (GO:0007067)|negative regulation of asymmetric cell division (GO:0045769)|negative regulation of neuron differentiation (GO:0045665)|neuron migration (GO:0001764)|oogenesis (GO:0048477)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of neuroblast proliferation (GO:0002052)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle pole (GO:0000922)				breast(6)|central_nervous_system(2)|cervix(2)|endometrium(10)|kidney(9)|large_intestine(28)|liver(1)|lung(87)|ovary(5)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(3)	165						GGAAAGGAGACCTGCAGAAGT	0.672																																					p.S47fs		Atlas-INDEL	.											.	ASPM	444	.	0			c.139delT						.						89.0	97.0	94.0					1																	197115430		2203	4300	6503	SO:0001589	frameshift_variant	259266	exon1			.	AY367065	CCDS1389.1, CCDS55672.1	1q31	2008-02-05	2006-09-12		ENSG00000066279	ENSG00000066279			19048	protein-coding gene	gene with protein product		605481	"""microcephaly, primary autosomal recessive 5"", ""asp (abnormal spindle)-like, microcephaly associated (Drosophila)"""	MCPH5		11078481	Standard	NM_018136		Approved	Calmbp1, ASP, FLJ10517, FLJ10549	uc001gtu.3	Q8IZT6	OTTHUMG00000036277	ENST00000367409.4:c.138delG	chr1.hg19:g.197115430delC	ENSP00000356379:p.Arg46fs	57.0	0.0		104.0	10.0	NM_001206846	Q4G1H1|Q5VYL3|Q86UX4|Q8IUL2|Q8IZJ7|Q8IZJ8|Q8IZJ9|Q8N4D1|Q9NVS1|Q9NVT6	Frame_Shift_Del	DEL	ENST00000367409.4	hg19	CCDS1389.1																																																																																			.	.		0.672	ASPM-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000088256.1	NM_018136	
PEAK1	79834	hgsc.bcm.edu	37	15	77472174	77472174	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:77472174delT	ENST00000560626.2	-	4	2570	c.2095delA	c.(2095-2097)aggfs	p.R699fs	PEAK1_ENST00000312493.4_Frame_Shift_Del_p.R699fs|PEAK1_ENST00000558305.1_Frame_Shift_Del_p.R699fs			Q9H792	PEAK1_HUMAN	pseudopodium-enriched atypical kinase 1	699					cell migration (GO:0016477)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|substrate adhesion-dependent cell spreading (GO:0034446)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										ACTGAGCCCCTTTTATGCTCT	0.448																																					p.R699fs		Atlas-INDEL	.											.	.	.	.	0			c.2096delG						.						161.0	152.0	154.0					15																	77472174		1900	4133	6033	SO:0001589	frameshift_variant	0	exon5			.		CCDS42062.1	15q24.3	2013-09-27			ENSG00000173517	ENSG00000173517			29431	protein-coding gene	gene with protein product		614248				16879967, 20534451	Standard	NM_024776		Approved	KIAA2002, sgk269		Q9H792	OTTHUMG00000172618	ENST00000560626.2:c.2095delA	chr15.hg19:g.77472174delT	ENSP00000452796:p.Arg699fs	126.0	0.0		144.0	10.0	NM_024776	Q6ZS78|Q8NAZ4|Q8NCM3|Q8TEG7	Frame_Shift_Del	DEL	ENST00000560626.2	hg19	CCDS42062.1																																																																																			.	.		0.448	PEAK1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419483.3		
UBXN7	26043	hgsc.bcm.edu	37	3	196089423	196089423	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:196089423delA	ENST00000296328.4	-	9	1044	c.970delT	c.(970-972)tctfs	p.S324fs	UBXN7_ENST00000428095.1_Frame_Shift_Del_p.S162fs|UBXN7_ENST00000535858.1_Frame_Shift_Del_p.S176fs	NM_015562.1	NP_056377.1	O94888	UBXN7_HUMAN	UBX domain protein 7	324						Cdc48p-Npl4p-Ufd1p AAA ATPase complex (GO:0034098)|nucleus (GO:0005634)	transcription factor binding (GO:0008134)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)			NS(1)|endometrium(2)|large_intestine(4)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	18						TCACTGCCAGAAAAAAGTTCA	0.438																																					p.S324fs		Atlas-INDEL	.											.	UBXN7	43	.	0			c.971delC						.						105.0	100.0	102.0					3																	196089423		1845	4099	5944	SO:0001589	frameshift_variant	26043	exon9			.	AB018337	CCDS43191.1	3q29	2012-07-06	2008-07-25	2008-07-25	ENSG00000163960	ENSG00000163960		"""UBX domain containing"""	29119	protein-coding gene	gene with protein product			"""UBX domain containing 7"""	UBXD7		9872452, 22537386	Standard	NM_015562		Approved	KIAA0794	uc003fwm.4	O94888	OTTHUMG00000155639	ENST00000296328.4:c.970delT	chr3.hg19:g.196089423delA	ENSP00000296328:p.Ser324fs	152.0	0.0		163.0	10.0	NM_015562	D3DXB3|Q6ZP77|Q86X20|Q8N327	Frame_Shift_Del	DEL	ENST00000296328.4	hg19	CCDS43191.1																																																																																			.	.		0.438	UBXN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340938.2	XM_087353	
GPR113	165082	hgsc.bcm.edu	37	2	26540962	26540962	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:26540962delG	ENST00000311519.1	-	2	207	c.208delC	c.(208-210)ctafs	p.L70fs	GPR113_ENST00000421160.2_Intron|GPR113_ENST00000459892.1_Intron|GPR113_ENST00000333478.6_Intron|GPR113_ENST00000541401.1_Intron	NM_001145168.1	NP_001138640.1	Q8IZF5	GP113_HUMAN	G protein-coupled receptor 113	70					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(5)|ovary(4)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	24	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CTAGAAGATAGGGGGATGGGG	0.577																																					p.L70fs		Atlas-INDEL	.											.	GPR113	134	.	0			c.209delT						.						57.0	63.0	61.0					2																	26540962		692	1591	2283	SO:0001589	frameshift_variant	165082	exon2			.	AB083619	CCDS33159.2, CCDS46238.1, CCDS46239.1	2p24.1	2014-08-08			ENSG00000173567	ENSG00000173567		"""-"", ""GPCR / Class B : Orphans"""	18989	protein-coding gene	gene with protein product						12435584	Standard	NM_153835		Approved	hGPCR37, PGR23	uc002rhe.4	Q8IZF5	OTTHUMG00000150225	ENST00000311519.1:c.208delC	chr2.hg19:g.26540962delG	ENSP00000307831:p.Leu70fs	107.0	0.0		161.0	13.0	NM_001145168	B4DF15|E9PEV1|Q53TA5|Q6UXT7|Q6UXX3|Q86SL7|Q8IXD8|Q8TDT3	Frame_Shift_Del	DEL	ENST00000311519.1	hg19	CCDS46239.1																																																																																			.	.		0.577	GPR113-004	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000316892.1	NM_153835	
LINCMD1	101154644	hgsc.bcm.edu	37	6	52013737	52013737	+	lincRNA	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:52013737delC	ENST00000418518.2	-	0	238				MIR133B_ENST00000362210.1_RNA																							AAGAAAGATGCCCCCTGCTCT	0.517																																					.		Atlas-INDEL	.											.	.	.	.	0			.						.						69.0	67.0	67.0					6																	52013737		1568	3582	5150			442890	.			.																													chr6.hg19:g.52013737delC		68.0	0.0		92.0	10.0	.		RNA	DEL	ENST00000418518.2	hg19																																																																																				.	.		0.517	MIR133BHG-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000040895.1		
PSMD2	5708	hgsc.bcm.edu	37	3	184025287	184025287	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:184025287delT	ENST00000310118.4	+	17	2735	c.2177delT	c.(2176-2178)attfs	p.I726fs	PSMD2_ENST00000435761.1_Frame_Shift_Del_p.I567fs|EIF2B5_ENST00000444495.1_Intron|PSMD2_ENST00000439383.1_Frame_Shift_Del_p.I596fs	NM_002808.3	NP_002799.3	Q13200	PSMD2_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 2	726					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of protein catabolic process (GO:0042176)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)	enzyme regulator activity (GO:0030234)			breast(1)|central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(5)|liver(1)|lung(12)|prostate(3)|upper_aerodigestive_tract(2)	27	all_cancers(143;1.54e-10)|Ovarian(172;0.0339)		Epithelial(37;1.53e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)		Bortezomib(DB00188)	TATAACTCCATTTTTGCCATG	0.458																																					p.I726fs	Colon(24;313 636 6917 9932 15554)	Atlas-INDEL	.											.	PSMD2	56	.	0			c.2176delA						.						90.0	89.0	89.0					3																	184025287		2203	4300	6503	SO:0001589	frameshift_variant	5708	exon17			.	AK095245	CCDS3258.1, CCDS63853.1, CCDS63854.1	3q27.3	2008-05-22			ENSG00000175166	ENSG00000175166		"""Proteasome (prosome, macropain) subunits"""	9559	protein-coding gene	gene with protein product		606223				8774743	Standard	NM_002808		Approved	S2, P97, TRAP2, MGC14274, Rpn1	uc003fnn.1	Q13200	OTTHUMG00000156796	ENST00000310118.4:c.2177delT	chr3.hg19:g.184025287delT	ENSP00000310129:p.Ile726fs	120.0	0.0		159.0	11.0	NM_002808	B4DX07|B4DXY1|E7EW34|E9PCS3|Q12932|Q15321|Q53XQ4|Q96I12	Frame_Shift_Del	DEL	ENST00000310118.4	hg19	CCDS3258.1																																																																																			.	.		0.458	PSMD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345843.1	NM_002808	
NUAK2	81788	hgsc.bcm.edu	37	1	205275421	205275421	+	Frame_Shift_Del	DEL	A	A	-	rs4951197	byFrequency	TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:205275421delA	ENST00000367157.3	-	5	711	c.585delT	c.(583-585)ggtfs	p.G195fs		NM_030952.1	NP_112214.1			NUAK family, SNF1-like kinase, 2											breast(3)|kidney(3)|large_intestine(4)|lung(4)|ovary(3)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	23	Breast(84;0.186)		BRCA - Breast invasive adenocarcinoma(75;0.117)			GGTTGGAGAGACCGAAGTCAG	0.562																																					p.L196fs		Atlas-INDEL	.											.	NUAK2	107	.	0			c.586delC						.						113.0	108.0	110.0					1																	205275421		2203	4300	6503	SO:0001589	frameshift_variant	81788	exon5			.	AK074830	CCDS1453.1	1q32.1	2008-02-05			ENSG00000163545	ENSG00000163545			29558	protein-coding gene	gene with protein product	"""SNF1/AMP activated protein kinase"""	608131				11230166	Standard	NM_030952		Approved	SNARK, FLJ90349	uc001hce.3	Q9H093	OTTHUMG00000037196	ENST00000367157.3:c.585delT	chr1.hg19:g.205275421delA	ENSP00000356125:p.Gly195fs	94.0	0.0		167.0	11.0	NM_030952		Frame_Shift_Del	DEL	ENST00000367157.3	hg19	CCDS1453.1																																																																																			.	.		0.562	NUAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090390.1	NM_030952	
ASIC4	55515	hgsc.bcm.edu	37	2	220402417	220402417	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:220402417delG	ENST00000347842.3	+	8	1803	c.1789delG	c.(1789-1791)gggfs	p.G598fs	ASIC4_ENST00000358078.4_Frame_Shift_Del_p.G617fs	NM_182847.2	NP_878267.2	Q96FT7	ASIC4_HUMAN	acid-sensing (proton-gated) ion channel family member 4	598					ion transmembrane transport (GO:0034220)|sodium ion transmembrane transport (GO:0035725)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)	ion channel activity (GO:0005216)|sodium channel activity (GO:0005272)|sodium ion transmembrane transporter activity (GO:0015081)										GACCTCCACTGGGGGCATCTC	0.612																																					p.T596fs		Atlas-INDEL	.											.	.	.	.	0			c.1788delT						.						32.0	31.0	31.0					2																	220402417		2202	4300	6502	SO:0001589	frameshift_variant	55515	exon8			.	AJ271643	CCDS2442.1	2q36.1	2012-02-22	2012-02-22	2012-02-22	ENSG00000072182	ENSG00000072182		"""Ion channels / Acid-sensing (proton-gated) ion channels"""	21263	protein-coding gene	gene with protein product		606715	"""amiloride-sensitive cation channel 4, pituitary"", ""amiloride-sensitive cation channel family member 4, pituitary"""	ACCN4		10852210	Standard	NM_182847		Approved	BNAC4	uc002vma.3	Q96FT7	OTTHUMG00000058928	ENST00000347842.3:c.1789delG	chr2.hg19:g.220402417delG	ENSP00000326627:p.Gly598fs	125.0	0.0		159.0	10.0	NM_182847	Q53SB7|Q6GMS1|Q6PIN9|Q9NQA4	Frame_Shift_Del	DEL	ENST00000347842.3	hg19	CCDS2442.1																																																																																			.	.		0.612	ASIC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000130263.1	NM_018674	
RBM27	54439	hgsc.bcm.edu	37	5	145608566	145608566	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:145608566delC	ENST00000265271.5	+	4	527	c.361delC	c.(361-363)cccfs	p.P121fs	RBM27_ENST00000506502.1_Frame_Shift_Del_p.P121fs	NM_018989.1	NP_061862.1	Q9P2N5	RBM27_HUMAN	RNA binding motif protein 27	121					mRNA processing (GO:0006397)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(1)|central_nervous_system(3)|endometrium(4)|kidney(5)|large_intestine(7)|liver(2)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	39			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			ATATCCTAGTCCCCAGAAGAC	0.398																																					p.S120fs		Atlas-INDEL	.											.	RBM27	119	.	0			c.360delT						.						151.0	146.0	147.0					5																	145608566		1568	3582	5150	SO:0001589	frameshift_variant	54439	exon4			.	AL833706	CCDS43378.1	5q32	2013-01-09				ENSG00000091009		"""Zinc fingers, CCCH-type domain containing"", ""RNA binding motif (RRM) containing"""	29243	protein-coding gene	gene with protein product	"""acidic rich RS domain containing 1"""					10718198, 15741184	Standard	NM_018989		Approved	KIAA1311, ARRS1, Psc1, ZC3H18	uc003lnz.4	Q9P2N5		ENST00000265271.5:c.361delC	chr5.hg19:g.145608566delC	ENSP00000265271:p.Pro121fs	171.0	0.0		164.0	14.0	NM_018989	Q8IYW9	Frame_Shift_Del	DEL	ENST00000265271.5	hg19	CCDS43378.1																																																																																			.	.		0.398	RBM27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373420.1	XM_291128	
PLXNA1	5361	hgsc.bcm.edu	37	3	126710277	126710277	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:126710277delG	ENST00000393409.2	+	2	1245	c.1245delG	c.(1243-1245)ctgfs	p.L415fs	PLXNA1_ENST00000251772.4_Frame_Shift_Del_p.L392fs	NM_032242.3	NP_115618.3	Q9UIW2	PLXA1_HUMAN	plexin A1	415	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|multicellular organismal development (GO:0007275)|regulation of smooth muscle cell migration (GO:0014910)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	receptor activity (GO:0004872)|semaphorin receptor activity (GO:0017154)			breast(3)|central_nervous_system(5)|endometrium(10)|kidney(5)|large_intestine(4)|lung(32)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	67				GBM - Glioblastoma multiforme(114;0.155)		ACCAGCCCCTGGGGGGCACAG	0.647																																					p.L415fs		Atlas-INDEL	.											.	PLXNA1	185	.	0			c.1244delT						.						47.0	42.0	44.0					3																	126710277		2203	4299	6502	SO:0001589	frameshift_variant	5361	exon2			.	X87832	CCDS33847.1, CCDS33847.2	3q21.2	2006-12-19				ENSG00000114554		"""Plexins"""	9099	protein-coding gene	gene with protein product		601055		PLXN1		8570614	Standard	NM_032242		Approved	NOV	uc003ejg.3	Q9UIW2		ENST00000393409.2:c.1245delG	chr3.hg19:g.126710277delG	ENSP00000377061:p.Leu415fs	196.0	0.0		215.0	14.0	NM_032242		Frame_Shift_Del	DEL	ENST00000393409.2	hg19	CCDS33847.2																																																																																			.	.		0.647	PLXNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356451.1	NM_032242	
KLHDC8A	55220	hgsc.bcm.edu	37	1	205308534	205308534	+	Frame_Shift_Del	DEL	C	C	-	rs369573058		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:205308534delC	ENST00000367156.3	-	7	1361	c.545delG	c.(544-546)ggafs	p.G182fs	KLHDC8A_ENST00000460687.1_Frame_Shift_Del_p.G48fs|KLHDC8A_ENST00000539253.1_Frame_Shift_Del_p.G182fs|KLHDC8A_ENST00000367155.3_Frame_Shift_Del_p.G182fs|KLHDC8A_ENST00000537168.1_Frame_Shift_Del_p.G69fs	NM_001271863.1	NP_001258792.1	Q8IYD2	KLD8A_HUMAN	kelch domain containing 8A	182										breast(1)|endometrium(3)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	14	Breast(84;0.23)		BRCA - Breast invasive adenocarcinoma(75;0.117)			GGACTGTCGTCCCCCTGGGGG	0.542																																					p.G182fs		Atlas-INDEL	.											.	KLHDC8A	31	.	0			c.546delA						.						30.0	29.0	29.0					1																	205308534		2203	4300	6503	SO:0001589	frameshift_variant	55220	exon5			.		CCDS30985.1	1q32.1	2008-02-05			ENSG00000162873	ENSG00000162873			25573	protein-coding gene	gene with protein product		614503					Standard	NM_018203		Approved	FLJ10748	uc031prx.1	Q8IYD2	OTTHUMG00000037199	ENST00000367156.3:c.545delG	chr1.hg19:g.205308534delC	ENSP00000356124:p.Gly182fs	67.0	0.0		161.0	10.0	NM_001271864	B3KU70|Q9NVG5	Frame_Shift_Del	DEL	ENST00000367156.3	hg19	CCDS30985.1																																																																																			.	.		0.542	KLHDC8A-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090397.1	NM_018203	
GH2	2689	hgsc.bcm.edu	37	17	61958073	61958073	+	Intron	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:61958073delC	ENST00000423893.2	-	4	518				GH2_ENST00000449787.2_Intron|GH2_ENST00000332800.7_Frame_Shift_Del_p.G172fs|GH2_ENST00000456543.2_Intron			P01242	SOM2_HUMAN	growth hormone 2						JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)	extracellular region (GO:0005576)	hormone activity (GO:0005179)			breast(3)|large_intestine(3)|lung(14)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)	24						GTGTTTCTCTCCCCAGTCCCT	0.567																																					p.G172fs		Atlas-INDEL	.											.	GH2	73	.	0			c.516delA						.						77.0	81.0	79.0					17																	61958073		2203	4300	6503	SO:0001627	intron_variant	2689	exon4			.	J03756	CCDS11647.1, CCDS11648.1, CCDS45757.1, CCDS45758.1	17q22-q24	2014-01-30						"""Endogenous ligands"""	4262	protein-coding gene	gene with protein product	"""placental-specific growth hormone"", ""placenta-specific growth hormone"""	139240				6306568	Standard	NM_002059		Approved	GH-V, GHV, GHL, hGH-V	uc002jcl.2	P01242		ENST00000423893.2:c.456+58G>-	chr17.hg19:g.61958073delC		124.0	0.0		168.0	11.0	NM_022557	B1A4H5|B1A4H7|O14643|O14644|P09587	Frame_Shift_Del	DEL	ENST00000423893.2	hg19	CCDS11647.1																																																																																			.	.		0.567	GH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417665.1	NM_002059	
AP4E1	23431	hgsc.bcm.edu	37	15	51289642	51289642	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:51289642delA	ENST00000261842.5	+	18	2572	c.2466delA	c.(2464-2466)tcafs	p.S822fs	AP4E1_ENST00000560508.1_Frame_Shift_Del_p.S747fs	NM_001252127.1|NM_007347.4	NP_001239056.1|NP_031373.2	Q9UPM8	AP4E1_HUMAN	adaptor-related protein complex 4, epsilon 1 subunit	822					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)		GTTCTTTGTCAAATGTGGCAT	0.348																																					p.S822X		Atlas-INDEL	.											.	AP4E1	78	.	0			c.2465delC						.						127.0	123.0	124.0					15																	51289642		2196	4294	6490	SO:0001589	frameshift_variant	23431	exon18			.	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.2466delA	chr15.hg19:g.51289642delA	ENSP00000261842:p.Ser822fs	107.0	0.0		163.0	11.0	NM_007347	A0AVD6|A1L4A9|A6NNX7|H0YKX4|Q68D31|Q9Y588	Frame_Shift_Del	DEL	ENST00000261842.5	hg19	CCDS32240.1																																																																																			.	.		0.348	AP4E1-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418656.1		
CDH16	1014	hgsc.bcm.edu	37	16	66947073	66947073	+	Frame_Shift_Del	DEL	G	G	-	rs532055028		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:66947073delG	ENST00000299752.4	-	9	1208	c.1015delC	c.(1015-1017)cgtfs	p.R339fs	CDH16_ENST00000570262.1_Frame_Shift_Del_p.R259fs|CDH16_ENST00000565796.1_Frame_Shift_Del_p.R339fs|CDH16_ENST00000568632.1_Frame_Shift_Del_p.R242fs|CDH16_ENST00000394055.3_Frame_Shift_Del_p.R339fs	NM_001204744.1|NM_001204745.1|NM_004062.3	NP_001191673.1|NP_001191674.1|NP_004053.1	O75309	CAD16_HUMAN	cadherin 16, KSP-cadherin	339					calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)	basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(3)|large_intestine(10)|lung(15)|ovary(2)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	41		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0877)|Epithelial(162;0.203)		GTGGGGTCACGGGGAGGGCAG	0.582																																					p.R339fs		Atlas-INDEL	.											.	CDH16	91	.	0			c.1016delG						.						157.0	148.0	151.0					16																	66947073		2200	4300	6500	SO:0001589	frameshift_variant	1014	exon9			.	AF016272	CCDS10823.1, CCDS56002.1, CCDS58471.1, CCDS58472.1	16q22.1	2010-01-26			ENSG00000166589	ENSG00000166589		"""Cadherins / Major cadherins"""	1755	protein-coding gene	gene with protein product		603118				9721215, 7615566	Standard	NM_004062		Approved		uc002eql.3	O75309	OTTHUMG00000137518	ENST00000299752.4:c.1015delC	chr16.hg19:g.66947073delG	ENSP00000299752:p.Arg339fs	120.0	0.0		127.0	10.0	NM_004062	B4DPA8|H3BPD3|Q6UW93	Frame_Shift_Del	DEL	ENST00000299752.4	hg19	CCDS10823.1																																																																																			.	.		0.582	CDH16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268839.2	NM_004062	
DLC1	10395	hgsc.bcm.edu	37	8	13356655	13356655	+	Frame_Shift_Del	DEL	T	T	-	rs34242235	byFrequency	TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr8:13356655delT	ENST00000276297.4	-	2	1335	c.926delA	c.(925-927)aagfs	p.K309fs	DLC1_ENST00000316609.5_Frame_Shift_Del_p.K309fs|DLC1_ENST00000511869.1_Frame_Shift_Del_p.K309fs	NM_182643.2	NP_872584.2	Q96QB1	RHG07_HUMAN	DLC1 Rho GTPase activating protein	309					actin cytoskeleton organization (GO:0030036)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|focal adhesion assembly (GO:0048041)|forebrain development (GO:0030900)|heart morphogenesis (GO:0003007)|hindbrain morphogenesis (GO:0021575)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of stress fiber assembly (GO:0051497)|neural tube closure (GO:0001843)|positive regulation of execution phase of apoptosis (GO:1900119)|positive regulation of protein dephosphorylation (GO:0035307)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	lipid binding (GO:0008289)|Rho GTPase activator activity (GO:0005100)|SH2 domain binding (GO:0042169)			NS(2)|breast(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(39)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	110						TGCCTTGACCTTTGGTGGACT	0.478																																					p.K309fs		Atlas-INDEL	.											.	DLC1	411	.	0			c.927delG						.						202.0	180.0	187.0					8																	13356655		2203	4300	6503	SO:0001589	frameshift_variant	10395	exon2			.	AF035119	CCDS5989.1, CCDS5990.1, CCDS5991.1, CCDS5991.2, CCDS55201.1	8p22	2014-06-20	2014-06-20		ENSG00000164741	ENSG00000164741		"""Rho GTPase activating proteins"", ""StAR-related lipid transfer (START) domain containing"""	2897	protein-coding gene	gene with protein product	"""StAR-related lipid transfer (START) domain containing 12"""	604258	"""deleted in liver cancer 1"""			9605766, 11214970	Standard	NM_182643		Approved	HP, ARHGAP7, STARD12, DLC-1, p122-RhoGAP	uc003wwm.2	Q96QB1	OTTHUMG00000090825	ENST00000276297.4:c.926delA	chr8.hg19:g.13356655delT	ENSP00000276297:p.Lys309fs	188.0	0.0		162.0	10.0	NM_182643	B4DR10|B8PTI0|E9PDZ8|E9PF76|E9PGY9|O14868|O43199|Q7Z5R8|Q86UC6|Q9C0E0|Q9H7A2	Frame_Shift_Del	DEL	ENST00000276297.4	hg19	CCDS5989.1																																																																																			.	.		0.478	DLC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207632.2	NM_182643, NM_006094	
CHD2	1106	hgsc.bcm.edu	37	15	93540530	93540530	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:93540530delG	ENST00000394196.4	+	30	4850	c.3782delG	c.(3781-3783)tggfs	p.W1261fs	CHD2_ENST00000557381.1_Frame_Shift_Del_p.W1261fs	NM_001271.3	NP_001262.3	O14647	CHD2_HUMAN	chromodomain helicase DNA binding protein 2	1261					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)			GATGTAGAGTGGGGGGTGGAA	0.413																																					p.W1261fs		Atlas-INDEL	.											.	CHD2	280	.	0			c.3781delT						.						139.0	138.0	138.0					15																	93540530		2197	4298	6495	SO:0001589	frameshift_variant	1106	exon30			.	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.3782delG	chr15.hg19:g.93540530delG	ENSP00000377747:p.Trp1261fs	142.0	0.0		170.0	12.0	NM_001271	C6G482|Q96IP5	Frame_Shift_Del	DEL	ENST00000394196.4	hg19	CCDS10374.2																																																																																			.	.		0.413	CHD2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000313528.3	NM_001271	
FAM160A1	729830	hgsc.bcm.edu	37	4	152571011	152571011	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:152571011delC	ENST00000505231.1	+	9	1977	c.1818delC	c.(1816-1818)ggcfs	p.G606fs	FAM160A1_ENST00000435205.1_Frame_Shift_Del_p.G606fs			Q05DH4	F16A1_HUMAN	family with sequence similarity 160, member A1	606										endometrium(2)|kidney(1)	3						AGGTTTCAGGCCCCCCAGCAC	0.552																																					p.G606fs		Atlas-INDEL	.											.	FAM160A1	60	.	0			c.1817delG						.						56.0	65.0	62.0					4																	152571011		692	1591	2283	SO:0001589	frameshift_variant	729830	exon11			.		CCDS47146.1	4q31.3	2012-11-30			ENSG00000164142	ENSG00000164142			34237	protein-coding gene	gene with protein product							Standard	NM_001109977		Approved	FLJ43373	uc003imj.2	Q05DH4	OTTHUMG00000161675	ENST00000505231.1:c.1818delC	chr4.hg19:g.152571011delC	ENSP00000421580:p.Gly606fs	141.0	0.0		113.0	12.0	NM_001109977	Q6ZUS2	Frame_Shift_Del	DEL	ENST00000505231.1	hg19	CCDS47146.1																																																																																			.	.		0.552	FAM160A1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365691.1	NM_001109977	
COL7A1	1294	hgsc.bcm.edu	37	3	48610137	48610137	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:48610137delT	ENST00000328333.8	-	87	6974	c.6867delA	c.(6865-6867)aaafs	p.K2289fs	COL7A1_ENST00000454817.1_Frame_Shift_Del_p.K2257fs	NM_000094.3	NP_000085.1	Q02388	CO7A1_HUMAN	collagen, type VII, alpha 1	2289	Triple-helical region.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen type VII trimer (GO:0005590)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(3)|breast(8)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(57)|ovary(7)|prostate(5)|skin(9)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	137				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		CAGGTTCTCCTTTAGGTCCGA	0.632																																					p.G2290fs		Atlas-INDEL	.											.	COL7A1	320	.	0			c.6868delG						.						24.0	30.0	28.0					3																	48610137		2201	4297	6498	SO:0001589	frameshift_variant	1294	exon87			.	L02870	CCDS2773.1	3p21.1	2014-09-17	2008-08-01		ENSG00000114270	ENSG00000114270		"""Collagens"", ""Fibronectin type III domain containing"""	2214	protein-coding gene	gene with protein product	"""collagen VII, alpha-1 polypeptide"", ""LC collagen"""	120120	"""epidermolysis bullosa, dystrophic, dominant and recessive"""	EBDCT, EBD1, EBR1		1871109	Standard	NM_000094		Approved		uc003ctz.2	Q02388	OTTHUMG00000133541	ENST00000328333.8:c.6867delA	chr3.hg19:g.48610137delT	ENSP00000332371:p.Lys2289fs	136.0	0.0		192.0	12.0	NM_000094	Q14054|Q16507	Frame_Shift_Del	DEL	ENST00000328333.8	hg19	CCDS2773.1																																																																																			.	.		0.632	COL7A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257519.1	NM_000094	
RP3-470B24.5	0	hgsc.bcm.edu	37	6	168377111	168377111	+	lincRNA	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:168377111delG	ENST00000538528.1	-	0	508																											AGAAGACAGTGGGGGTCATTC	0.632																																					p.T75fs		Atlas-INDEL	.											.	.	.	.	0			c.223delA						.						4.0	5.0	5.0					6																	168377111		613	1467	2080			0	exon1			.																													chr6.hg19:g.168377111delG		108.0	0.0		165.0	10.0	NM_001129895		Frame_Shift_Del	DEL	ENST00000538528.1	hg19																																																																																				.	.		0.632	RP3-470B24.5-201	KNOWN	basic	lincRNA	lincRNA			
CALHM1	255022	hgsc.bcm.edu	37	10	105215220	105215220	+	Frame_Shift_Del	DEL	G	G	-	rs184539423		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:105215220delG	ENST00000329905.5	-	2	976	c.840delC	c.(838-840)cccfs	p.P280fs	RP11-225H22.4_ENST00000411906.1_RNA|CALHM2_ENST00000393235.1_5'Flank	NM_001001412.3	NP_001001412.3	Q8IU99	CAHM1_HUMAN	calcium homeostasis modulator 1	280					ATP transport (GO:0015867)|cation transport (GO:0006812)|protein homooligomerization (GO:0051260)|regulation of ion transmembrane transport (GO:0034765)|sensory perception of bitter taste (GO:0050913)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)	calcium activated cation channel activity (GO:0005227)|calcium channel activity (GO:0005262)|identical protein binding (GO:0042802)|voltage-gated ion channel activity (GO:0005244)			large_intestine(2)|liver(1)|lung(5)|ovary(1)	9						CCGCACCATCGGGGGTCGTGG	0.632																																					p.D281fs		Atlas-INDEL	.											.	CALHM1	33	.	0			c.841delG						.						47.0	37.0	40.0					10																	105215220		2203	4300	6503	SO:0001589	frameshift_variant	255022	exon2			.	BC036208	CCDS7550.1	10q24.33	2008-07-02	2008-07-02	2008-07-02	ENSG00000185933	ENSG00000185933			23494	protein-coding gene	gene with protein product		612234	"""family with sequence similarity 26, member C"""	FAM26C		18585350	Standard	NM_001001412		Approved		uc001kxe.2	Q8IU99	OTTHUMG00000018991	ENST00000329905.5:c.840delC	chr10.hg19:g.105215220delG	ENSP00000329926:p.Pro280fs	185.0	0.0		172.0	11.0	NM_001001412	Q5W091	Frame_Shift_Del	DEL	ENST00000329905.5	hg19	CCDS7550.1																																																																																			.	.		0.632	CALHM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050165.1	NM_001001412	
SDS	10993	hgsc.bcm.edu	37	12	113835064	113835064	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:113835064delC	ENST00000257549.4	-	6	681	c.559delG	c.(559-561)gacfs	p.D187fs		NM_006843.2	NP_006834.2	P20132	SDHL_HUMAN	serine dehydratase	187					gluconeogenesis (GO:0006094)|L-serine catabolic process (GO:0006565)|pyruvate biosynthetic process (GO:0042866)|response to amino acid (GO:0043200)|response to cobalamin (GO:0033590)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	L-serine ammonia-lyase activity (GO:0003941)|L-threonine ammonia-lyase activity (GO:0004794)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)			large_intestine(2)|lung(6)|pancreas(1)|prostate(1)|urinary_tract(1)	11					L-Serine(DB00133)	ACAGGCACGTCCCCCCAGCCC	0.662																																					p.D187fs		Atlas-INDEL	.											.	SDS	35	.	0			c.560delA						.						74.0	63.0	67.0					12																	113835064		2203	4300	6503	SO:0001589	frameshift_variant	10993	exon6			.	J05037	CCDS9169.1	12q24.13	2014-06-24			ENSG00000135094	ENSG00000135094	4.3.1.17		10691	protein-coding gene	gene with protein product	"""L-serine ammonia-lyase"""	182128				2674117	Standard	NM_006843		Approved	SDH	uc001tvg.3	P20132	OTTHUMG00000169554	ENST00000257549.4:c.559delG	chr12.hg19:g.113835064delC	ENSP00000257549:p.Asp187fs	231.0	0.0		223.0	14.0	NM_006843	A8K9P5	Frame_Shift_Del	DEL	ENST00000257549.4	hg19	CCDS9169.1																																																																																			.	.		0.662	SDS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404790.1	NM_006843	
ZNF350	59348	hgsc.bcm.edu	37	19	52468815	52468815	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:52468815delT	ENST00000243644.4	-	5	1118	c.891delA	c.(889-891)aaafs	p.K297fs	ZNF350_ENST00000600703.1_5'Flank|HCCAT3_ENST00000600253.1_RNA|HCCAT3_ENST00000595010.1_RNA	NM_021632.3	NP_067645.3	Q9GZX5	ZN350_HUMAN	zinc finger protein 350	297					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|endometrium(3)|kidney(3)|large_intestine(7)|lung(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	26		all_neural(266;0.0505)		GBM - Glioblastoma multiforme(134;0.00124)|OV - Ovarian serous cystadenocarcinoma(262;0.0179)		GGATGAAGCCTTTTCCACATT	0.408																																					p.G298fs		Atlas-INDEL	.											.	ZNF350	48	.	0			c.892delG						.						119.0	113.0	115.0					19																	52468815		2203	4300	6503	SO:0001589	frameshift_variant	59348	exon5			.	AF295096	CCDS12845.1	19q13.41	2013-05-23			ENSG00000256683	ENSG00000256683		"""Zinc fingers, C2H2-type"", ""-"""	16656	protein-coding gene	gene with protein product		605422				11090615, 11161714	Standard	NM_021632		Approved	ZBRK1, ZFQR	uc002pyd.3	Q9GZX5	OTTHUMG00000182538	ENST00000243644.4:c.891delA	chr19.hg19:g.52468815delT	ENSP00000243644:p.Lys297fs	87.0	0.0		152.0	10.0	NM_021632	Q96G73|Q9HAQ4	Frame_Shift_Del	DEL	ENST00000243644.4	hg19	CCDS12845.1																																																																																			.	.		0.408	ZNF350-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462278.1	NM_021632	
L3MBTL1	26013	hgsc.bcm.edu	37	20	42143323	42143323	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr20:42143323delC	ENST00000427442.2	+	4	502	c.343delC	c.(343-345)cccfs	p.P116fs	L3MBTL1_ENST00000373135.3_Frame_Shift_Del_p.P48fs|L3MBTL1_ENST00000444063.1_Frame_Shift_Del_p.P48fs|L3MBTL1_ENST00000418998.1_Frame_Shift_Del_p.P116fs|L3MBTL1_ENST00000373134.1_Frame_Shift_Del_p.P48fs|L3MBTL1_ENST00000457824.1_3'UTR			Q9Y468	LMBL1_HUMAN	l(3)mbt-like 1 (Drosophila)	48					chromatin modification (GO:0016568)|hemopoiesis (GO:0030097)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of cell cycle (GO:0051726)|regulation of megakaryocyte differentiation (GO:0045652)|regulation of mitosis (GO:0007088)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|condensed chromosome (GO:0000793)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|identical protein binding (GO:0042802)|methylated histone binding (GO:0035064)|nucleosomal histone binding (GO:0031493)|nucleosome binding (GO:0031491)|SAM domain binding (GO:0032093)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|large_intestine(3)|ovary(1)|skin(2)	7						AGTGGAGCAGCCCCCGAGCCC	0.682																																					p.Q114fs		Atlas-INDEL	.											.	L3MBTL1	105	.	0			c.342delG						.						19.0	20.0	20.0					20																	42143323		2180	4274	6454	SO:0001589	frameshift_variant	26013	exon4			.	U89358	CCDS13319.1, CCDS46602.1, CCDS46602.2	20q13.12	2013-01-10	2010-09-03	2010-09-03	ENSG00000185513	ENSG00000185513		"""Zinc fingers, C2HC-type containing"", ""Sterile alpha motif (SAM) domain containing"""	15905	protein-coding gene	gene with protein product	"""lethal (3) malignant brain tumor l(3)"""	608802	"""l(3)mbt (Drosophila)-like"", ""l(3)mbt-like (Drosophila)"""	L3MBTL		10445843, 17540172	Standard	NM_032107		Approved	ZC2HC3, dJ138B7.3, DKFZp586P1522, KIAA0681	uc010zwh.2	Q9Y468	OTTHUMG00000032503	ENST00000427442.2:c.343delC	chr20.hg19:g.42143323delC	ENSP00000402107:p.Pro116fs	104.0	0.0		160.0	10.0	NM_032107	B4DRC9|E1P5W7|Q5H8Y8|Q5H8Y9|Q8IUV7|Q9H1E6|Q9H1G5|Q9UG06|Q9UJB9|Q9Y4C9	Frame_Shift_Del	DEL	ENST00000427442.2	hg19	CCDS46602.2																																																																																			.	.		0.682	L3MBTL1-007	KNOWN	upstream_ATG|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079300.3	NM_032107	
ARHGAP10	79658	hgsc.bcm.edu	37	4	148744064	148744064	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:148744064delT	ENST00000336498.3	+	3	507	c.268delT	c.(268-270)tttfs	p.F90fs		NM_024605.3	NP_078881.3	Q5T5U3	RHG21_HUMAN	Rho GTPase activating protein 10	0	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				establishment of Golgi localization (GO:0051683)|Golgi organization (GO:0007030)|maintenance of Golgi location (GO:0051684)|organelle transport along microtubule (GO:0072384)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)			autonomic_ganglia(2)|endometrium(5)|kidney(2)|large_intestine(4)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	33	all_hematologic(180;0.151)	Renal(17;0.0166)		GBM - Glioblastoma multiforme(119;0.0423)		CTTACGTGAATTTTCAAATTT	0.358																																					p.E89fs		Atlas-INDEL	.											.	ARHGAP10	92	.	0			c.267delA						.						90.0	87.0	88.0					4																	148744064		2203	4300	6503	SO:0001589	frameshift_variant	79658	exon3			.	BC047914	CCDS34075.1	4q31.23	2013-09-20			ENSG00000071205	ENSG00000071205		"""Rho GTPase activating proteins"""	26099	protein-coding gene	gene with protein product		609746				8288572	Standard	NM_024605		Approved	FLJ20896, FLJ41791, GRAF2	uc003ilf.3	A1A4S6	OTTHUMG00000161460	ENST00000336498.3:c.268delT	chr4.hg19:g.148744064delT	ENSP00000336923:p.Phe90fs	124.0	0.0		157.0	10.0	NM_024605	Q0VF98|Q7Z3P7|Q8N3A2|Q8NI19|Q8TBV5|Q9P2C3	Frame_Shift_Del	DEL	ENST00000336498.3	hg19	CCDS34075.1																																																																																			.	.		0.358	ARHGAP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365005.1	NM_024605	
TTC39C	125488	hgsc.bcm.edu	37	18	21698147	21698147	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr18:21698147delA	ENST00000317571.3	+	8	1373	c.1137delA	c.(1135-1137)ctafs	p.L379fs	RP11-799B12.2_ENST00000583782.1_RNA|TTC39C_ENST00000304621.6_Frame_Shift_Del_p.L318fs|TTC39C_ENST00000540918.2_Frame_Shift_Del_p.L72fs	NM_001135993.1	NP_001129465.1	Q8N584	TT39C_HUMAN	tetratricopeptide repeat domain 39C	379										breast(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(1)	19						TTGAGAGGCTAAAAAATGAGT	0.448																																					p.L379fs		Atlas-INDEL	.											.	TTC39C	83	.	0			c.1136delT						.						131.0	119.0	123.0					18																	21698147		2203	4300	6503	SO:0001589	frameshift_variant	125488	exon8			.	AK091080	CCDS32804.1, CCDS45839.1, CCDS58616.1	18q11.2	2014-02-07	2008-06-23	2008-06-23	ENSG00000168234	ENSG00000168234		"""Tetratricopeptide (TTC) repeat domain containing"""	26595	protein-coding gene	gene with protein product			"""chromosome 18 open reading frame 17"""	C18orf17		14702039	Standard	NM_153211		Approved	FLJ33761, HsT2697	uc002kuw.3	Q8N584	OTTHUMG00000179403	ENST00000317571.3:c.1137delA	chr18.hg19:g.21698147delA	ENSP00000323645:p.Leu379fs	115.0	0.0		129.0	11.0	NM_001135993	B7WP63|J3QRR1|Q0VAJ2|Q8N284	Frame_Shift_Del	DEL	ENST00000317571.3	hg19	CCDS45839.1																																																																																			.	.		0.448	TTC39C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446107.1	NM_153211	
GCC2	9648	hgsc.bcm.edu	37	2	109088158	109088158	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:109088158delA	ENST00000309863.6	+	6	3087	c.2373delA	c.(2371-2373)gcafs	p.A791fs		NM_181453.3	NP_852118	Q8IWJ2	GCC2_HUMAN	GRIP and coiled-coil domain containing 2	791					Golgi ribbon formation (GO:0090161)|late endosome to Golgi transport (GO:0034499)|microtubule anchoring (GO:0034453)|microtubule organizing center organization (GO:0031023)|protein localization to Golgi apparatus (GO:0034067)|protein targeting to Golgi (GO:0000042)|protein targeting to lysosome (GO:0006622)|recycling endosome to Golgi transport (GO:0071955)|regulation of protein exit from endoplasmic reticulum (GO:0070861)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	identical protein binding (GO:0042802)			breast(8)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(10)|lung(19)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	54						AATCCTTGGCAAAAATAAATG	0.368																																					p.A791fs		Atlas-Indel,Pindel	.											.	GCC2	129	.	0			c.2372delC						.						61.0	64.0	63.0					2																	109088158		2203	4297	6500	SO:0001589	frameshift_variant	9648	exon6			.	BC020645	CCDS33268.1	2q12.3	2008-02-05	2004-03-05		ENSG00000135968	ENSG00000135968			23218	protein-coding gene	gene with protein product		612711	"""GRIP and coiled-coil domain-containing 2"""			12446665	Standard	NM_181453		Approved	GCC185, KIAA0336	uc002tec.3	Q8IWJ2	OTTHUMG00000153214	ENST00000309863.6:c.2373delA	chr2.hg19:g.109088158delA	ENSP00000307939:p.Ala791fs	274.0	0.0		347.0	21.0	NM_181453	A6H8X8|O15045|Q4ZG46|Q8TDH3|Q9H2G8	Frame_Shift_Del	DEL	ENST00000309863.6	hg19	CCDS33268.1																																																																																			.	.		0.368	GCC2-014	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358516.3	NM_014635	
NOB1	28987	hgsc.bcm.edu	37	16	69782138	69782138	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:69782138delA	ENST00000268802.5	-	7	850	c.821delT	c.(820-822)ttcfs	p.F274fs		NM_014062.1	NP_054781.1	Q9ULX3	NOB1_HUMAN	NIN1/RPN12 binding protein 1 homolog (S. cerevisiae)	274					visual perception (GO:0007601)	nucleus (GO:0005634)	metal ion binding (GO:0046872)			breast(2)|cervix(1)|endometrium(1)|large_intestine(1)|lung(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11						TACATACTTGAAACAGCCATG	0.537																																					p.F274fs		Atlas-INDEL	.											.	NOB1	24	.	0			c.822delC						.						62.0	56.0	58.0					16																	69782138		2198	4300	6498	SO:0001589	frameshift_variant	28987	exon7			.	AB026125	CCDS10884.1	16q22.1	2008-02-05	2006-04-20	2006-04-20	ENSG00000141101	ENSG00000141101			29540	protein-coding gene	gene with protein product	"""nin one binding protein"""	613586	"""PSMD8 binding protein 1"""	PSMD8BP1		16172919	Standard	NM_014062		Approved	NOB1P, ART-4, MST158	uc002exs.4	Q9ULX3	OTTHUMG00000137576	ENST00000268802.5:c.821delT	chr16.hg19:g.69782138delA	ENSP00000268802:p.Phe274fs	136.0	0.0		164.0	10.0	NM_014062	Q7L6B7|Q7M4M4|Q7Z4B5|Q9NWB0	Frame_Shift_Del	DEL	ENST00000268802.5	hg19	CCDS10884.1																																																																																			.	.		0.537	NOB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268958.2	NM_014062	
C11orf84	144097	hgsc.bcm.edu	37	11	63586276	63586276	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:63586276delC	ENST00000294244.4	+	5	1035	c.736delC	c.(736-738)cccfs	p.P247fs		NM_138471.1	NP_612480.1	Q9BUA3	CK084_HUMAN	chromosome 11 open reading frame 84	247	Pro-rich.									endometrium(3)|kidney(1)|lung(3)|skin(1)	8						CCTTCCAGAGCCCCCATCGCC	0.632																																					p.E245fs		Atlas-INDEL	.											.	C11orf84	33	.	0			c.735delG						.						64.0	65.0	65.0					11																	63586276		2201	4298	6499	SO:0001589	frameshift_variant	144097	exon5			.	BC007540	CCDS31594.1	11q13.1	2014-02-10			ENSG00000168005	ENSG00000168005			25115	protein-coding gene	gene with protein product						12477932	Standard	NM_138471		Approved		uc001nxt.3	Q9BUA3	OTTHUMG00000167746	ENST00000294244.4:c.736delC	chr11.hg19:g.63586276delC	ENSP00000294244:p.Pro247fs	97.0	0.0		117.0	10.0	NM_138471	Q68CV7|Q6PHS2|Q96IH0	Frame_Shift_Del	DEL	ENST00000294244.4	hg19	CCDS31594.1																																																																																			.	.		0.632	C11orf84-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396084.1	NM_138471	
UIMC1	51720	hgsc.bcm.edu	37	5	176396191	176396191	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:176396191delT	ENST00000377227.4	-	6	697	c.565delA	c.(565-567)actfs	p.T189fs	UIMC1_ENST00000503273.1_5'Flank|UIMC1_ENST00000506128.1_Frame_Shift_Del_p.T189fs|UIMC1_ENST00000511320.1_Frame_Shift_Del_p.T189fs|UIMC1_ENST00000377219.2_Frame_Shift_Del_p.T189fs			Q96RL1	UIMC1_HUMAN	ubiquitin interaction motif containing 1	189	Necessary for interaction with NR6A1 N- terminus.				double-strand break repair (GO:0006302)|G2 DNA damage checkpoint (GO:0031572)|histone H2A K63-linked deubiquitination (GO:0070537)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of DNA repair (GO:0045739)|response to ionizing radiation (GO:0010212)|transcription, DNA-templated (GO:0006351)	BRCA1-A complex (GO:0070531)|nucleus (GO:0005634)	histone binding (GO:0042393)|K63-linked polyubiquitin binding (GO:0070530)			NS(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(5)|ovary(4)|pancreas(1)|prostate(1)|skin(1)	21	all_cancers(89;7.96e-05)|Renal(175;0.000269)|Lung NSC(126;0.00476)|all_lung(126;0.00806)	Medulloblastoma(196;0.0145)|all_neural(177;0.0325)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TCCTCTTCAGTTTTTTCAGTG	0.498																																					p.T189fs		Atlas-INDEL	.											.	UIMC1	55	.	0			c.566delC						.						66.0	66.0	66.0					5																	176396191		2203	4300	6503	SO:0001589	frameshift_variant	51720	exon6			.	AF349313	CCDS4408.1	5q35.2	2008-02-05			ENSG00000087206	ENSG00000087206			30298	protein-coding gene	gene with protein product	"""receptor associated protein 80"""	609433				12080054	Standard	NM_001199297		Approved	RAP80	uc021yin.1	Q96RL1	OTTHUMG00000130852	ENST00000377227.4:c.565delA	chr5.hg19:g.176396191delT	ENSP00000366434:p.Thr189fs	171.0	0.0		238.0	16.0	NM_016290	A8MSA1|B3KMZ1|B4E3N2|Q5XKQ1|Q7Z3W7|Q8N5B9|Q9BZR1|Q9BZR5|Q9UHX7	Frame_Shift_Del	DEL	ENST00000377227.4	hg19	CCDS4408.1																																																																																			.	.		0.498	UIMC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253422.1	NM_016290	
ARNT	405	hgsc.bcm.edu	37	1	150808762	150808762	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:150808762delG	ENST00000358595.5	-	7	894	c.694delC	c.(694-696)ctgfs	p.L232fs	ARNT_ENST00000468970.1_5'UTR|ARNT_ENST00000354396.2_Frame_Shift_Del_p.L232fs|ARNT_ENST00000505755.1_Frame_Shift_Del_p.L217fs|ARNT_ENST00000515192.1_Frame_Shift_Del_p.L223fs	NM_001197325.1|NM_001668.3|NM_178427.2	NP_001184254.1|NP_001659.1|NP_848514.1	P27540	ARNT_HUMAN	aryl hydrocarbon receptor nuclear translocator	232	PAS 1. {ECO:0000255|PROSITE- ProRule:PRU00140}.				cell differentiation (GO:0030154)|cellular response to hypoxia (GO:0071456)|embryonic placenta development (GO:0001892)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of glycolytic process (GO:0045821)|positive regulation of hormone biosynthetic process (GO:0046886)|positive regulation of protein sumoylation (GO:0033235)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0043619)|response to hypoxia (GO:0001666)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	aryl hydrocarbon receptor activity (GO:0004874)|aryl hydrocarbon receptor binding (GO:0017162)|enhancer binding (GO:0035326)|protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(11)|prostate(2)|skin(4)|stomach(1)	34	all_lung(15;9e-35)|Lung NSC(24;3.45e-31)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.108)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.02)|BRCA - Breast invasive adenocarcinoma(12;0.00606)|LUSC - Lung squamous cell carcinoma(543;0.211)			TCACCTGTCAGGGCATTTTCT	0.423			T	ETV6	AML																																p.L232fs		Atlas-INDEL	.		Dom	yes		1	1q21	405	aryl hydrocarbon receptor nuclear translocator		L	.	ARNT	68	.	0			c.695delT						.						92.0	73.0	79.0					1																	150808762		2203	4300	6503	SO:0001589	frameshift_variant	405	exon7			.	AF001307	CCDS970.1, CCDS971.1, CCDS65641.1, CCDS65642.1	1q21	2013-05-21			ENSG00000143437	ENSG00000143437		"""Basic helix-loop-helix proteins"""	700	protein-coding gene	gene with protein product		126110					Standard	NM_001668		Approved	HIF-1beta, bHLHe2	uc001evr.2	P27540	OTTHUMG00000035011	ENST00000358595.5:c.694delC	chr1.hg19:g.150808762delG	ENSP00000351407:p.Leu232fs	75.0	0.0		194.0	12.0	NM_001668	B2R9H1|C4AMA1|F8WAP6|Q59ED4|Q5QP39|Q8NDC7	Frame_Shift_Del	DEL	ENST00000358595.5	hg19	CCDS970.1																																																																																			.	.		0.423	ARNT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000084741.2		
SRP72	6731	hgsc.bcm.edu	37	4	57333820	57333820	+	Frame_Shift_Del	DEL	G	G	-	rs17524437	byFrequency	TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:57333820delG	ENST00000342756.5	+	1	740	c.19delG	c.(19-21)gggfs	p.G8fs	SRP72_ENST00000504757.1_Frame_Shift_Del_p.G8fs|SRP72_ENST00000510663.1_Frame_Shift_Del_p.G8fs	NM_006947.3	NP_008878.3	O76094	SRP72_HUMAN	signal recognition particle 72kDa	8					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|response to drug (GO:0042493)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|signal recognition particle, endoplasmic reticulum targeting (GO:0005786)	7S RNA binding (GO:0008312)|poly(A) RNA binding (GO:0044822)|signal recognition particle binding (GO:0005047)			breast(2)|endometrium(4)|kidney(1)|large_intestine(4)|liver(2)|lung(7)|ovary(2)	22	Glioma(25;0.08)|all_neural(26;0.101)					CGGCGGCAGCGGGGGGGTGTC	0.642																																					p.S6fs		Atlas-INDEL	.											.,1	SRP72	59	.	0			c.18delC						.						14.0	16.0	15.0					4																	57333820		2193	4293	6486	SO:0001589	frameshift_variant	6731	exon1			.	AF069765	CCDS3506.1, CCDS58898.1	4q11	2013-01-10	2002-08-29		ENSG00000174780	ENSG00000174780		"""Tetratricopeptide (TTC) repeat domain containing"""	11303	protein-coding gene	gene with protein product		602122	"""signal recognition particle 72kD"""			9224693, 9857079	Standard	NM_006947		Approved		uc003hbv.3	O76094	OTTHUMG00000128843	ENST00000342756.5:c.19delG	chr4.hg19:g.57333820delG	ENSP00000342181:p.Gly8fs	135.0	0.0		134.0	10.0	NM_001267722	G5E9Z8|Q7Z3C0	Frame_Shift_Del	DEL	ENST00000342756.5	hg19	CCDS3506.1																																																																																			.	.		0.642	SRP72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250782.7		
ABL2	27	hgsc.bcm.edu	37	1	179078242	179078242	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:179078242delC	ENST00000502732.1	-	12	2363	c.2160delG	c.(2158-2160)gggfs	p.G720fs	ABL2_ENST00000507173.1_Intron|ABL2_ENST00000512653.1_Frame_Shift_Del_p.G705fs|ABL2_ENST00000511413.1_Intron|ABL2_ENST00000504405.1_Intron|ABL2_ENST00000344730.3_Intron|ABL2_ENST00000408940.3_Frame_Shift_Del_p.G684fs|ABL2_ENST00000367623.4_Frame_Shift_Del_p.G699fs	NM_001168236.1|NM_001168237.1|NM_001168238.1|NM_007314.3	NP_001161708.1|NP_001161709.1|NP_001161710.1|NP_009298.1	P42684	ABL2_HUMAN	ABL proto-oncogene 2, non-receptor tyrosine kinase	720	F-actin-binding. {ECO:0000250}.				actin filament bundle assembly (GO:0051017)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cellular protein modification process (GO:0006464)|cellular response to retinoic acid (GO:0071300)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of neuron projection development (GO:0010976)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of phospholipase C activity (GO:0010863)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of autophagy (GO:0010506)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of endocytosis (GO:0030100)|signal transduction (GO:0007165)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)	actin filament binding (GO:0051015)|actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)			breast(8)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(9)|lung(32)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	65					Adenosine triphosphate(DB00171)|Dasatinib(DB01254)	GTGCAAAGCTCCCCCCATAGC	0.567			T	ETV6	AML																																p.S721fs		Atlas-INDEL	.		Dom	yes		1	1q24-q25	27	v-abl Abelson murine leukemia viral oncogene homolog 2		L	.	ABL2	307	.	0			c.2161delA						.						53.0	55.0	54.0					1																	179078242		2203	4300	6503	SO:0001589	frameshift_variant	27	exon12			.	M14904	CCDS30947.1, CCDS41441.1, CCDS44282.1, CCDS44283.1, CCDS41441.2, CCDS53435.1, CCDS53436.1, CCDS53437.1, CCDS53438.1	1q25.2	2014-06-26	2014-06-26		ENSG00000143322	ENSG00000143322		"""SH2 domain containing"""	77	protein-coding gene	gene with protein product	"""Abelson-related gene"""	164690	"""v-abl Abelson murine leukemia viral oncogene homolog 2 (arg, Abelson-related gene)"", ""v-abl Abelson murine leukemia viral oncogene homolog 2"", ""c-abl oncogene 2, non-receptor tyrosine kinase"""	ABLL		3787260	Standard	NM_001136001		Approved	ARG	uc001gmi.4	P42684	OTTHUMG00000035199	ENST00000502732.1:c.2160delG	chr1.hg19:g.179078242delC	ENSP00000427562:p.Gly720fs	80.0	0.0		148.0	10.0	NM_007314	A0M8X0|B7UEF2|B7UEF3|B7UEF4|B7UEF5|Q5T0X6|Q5W0C5|Q6NZY6|Q7Z301	Frame_Shift_Del	DEL	ENST00000502732.1	hg19	CCDS30947.1																																																																																			.	.		0.567	ABL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000085174.3	NM_005158	
TMC4	147798	hgsc.bcm.edu	37	19	54672280	54672280	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:54672280delG	ENST00000376591.4	-	4	718	c.587delC	c.(586-588)ccafs	p.P196fs	TMC4_ENST00000476013.2_5'UTR|TMC4_ENST00000301187.4_Frame_Shift_Del_p.P190fs	NM_001145303.1|NM_144686.2	NP_001138775|NP_653287.2	Q7Z404	TMC4_HUMAN	transmembrane channel-like 4	196					ion transport (GO:0006811)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(2)|endometrium(7)|large_intestine(4)|lung(6)|pancreas(1)|skin(1)|urinary_tract(1)	22	all_cancers(19;0.0065)|all_epithelial(19;0.00348)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)					GGGAGGGCCTGGGGGAGCGCC	0.647											OREG0025670	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P196fs		Atlas-INDEL	.											.	TMC4	89	.	0			c.588delA						.						25.0	21.0	23.0					19																	54672280		2181	4282	6463	SO:0001589	frameshift_variant	147798	exon4			.	AY236492	CCDS12882.1, CCDS46174.1	19q13.42	2008-02-05			ENSG00000167608	ENSG00000167608			22998	protein-coding gene	gene with protein product						12812529, 12906855	Standard	XM_005277069		Approved		uc010erf.3	Q7Z404	OTTHUMG00000066485	ENST00000376591.4:c.587delC	chr19.hg19:g.54672280delG	ENSP00000365776:p.Pro196fs	127.0	0.0	1002	195.0	13.0	NM_001145303	Q7Z5M3|Q8N5E4|Q8TBS7	Frame_Shift_Del	DEL	ENST00000376591.4	hg19	CCDS46174.1																																																																																			.	.		0.647	TMC4-011	NOVEL	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000156164.2		
FRMD7	90167	hgsc.bcm.edu	37	X	131211907	131211907	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:131211907delA	ENST00000298542.4	-	12	2313	c.2138delT	c.(2137-2139)ttafs	p.L713fs	FRMD7_ENST00000370879.1_Frame_Shift_Del_p.L593fs|FRMD7_ENST00000464296.1_Frame_Shift_Del_p.L698fs	NM_194277.2	NP_919253.1	Q6ZUT3	FRMD7_HUMAN	FERM domain containing 7	713					regulation of neuron projection development (GO:0010975)	cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|growth cone (GO:0030426)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)				breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(12)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	24	Acute lymphoblastic leukemia(192;0.000127)					CTTTTAAGCTAAAAAGTAATT	0.363																																					p.L713fs		Atlas-INDEL	.											.	FRMD7	69	.	0			c.2139delA						.			0,3721		0,0,0,1592,537	95.0	84.0	88.0			5.7	1.0	X		89	2,6482		0,1,1,2356,1769	no	frameshift	FRMD7	NM_194277.2		0,1,1,3948,2306	A1A1,A1R,A1,RR,R		0.0308,0.0,0.0196			131211907	2,10203	2203	4300	6503	SO:0001589	frameshift_variant	90167	exon12			.	AL161984	CCDS35397.1	Xq26.2	2014-09-17	2006-09-01	2006-09-01	ENSG00000165694	ENSG00000165694			8079	protein-coding gene	gene with protein product		300628	"""nystagmus 1, congenital"""	NYS, NYS1		2063919, 17013395	Standard	NM_194277		Approved	FLJ43346	uc004ewn.3	Q6ZUT3	OTTHUMG00000022421	ENST00000298542.4:c.2138delT	chrX.hg19:g.131211907delA	ENSP00000298542:p.Leu713fs	181.0	0.0		233.0	14.0	NM_194277	C0LLJ3|Q5JX99	Frame_Shift_Del	DEL	ENST00000298542.4	hg19	CCDS35397.1																																																																																			.	.		0.363	FRMD7-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355031.1	NM_194277	
SLC47A2	146802	hgsc.bcm.edu	37	17	19617255	19617255	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:19617255delC	ENST00000325411.5	-	4	376	c.326delG	c.(325-327)ggcfs	p.G109fs	SLC47A2_ENST00000463318.1_5'UTR|SLC47A2_ENST00000350657.5_Frame_Shift_Del_p.G109fs	NM_152908.3	NP_690872.2	Q86VL8	S47A2_HUMAN	solute carrier family 47 (multidrug and toxin extrusion), member 2	109					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antiporter activity (GO:0015297)|drug transmembrane transporter activity (GO:0015238)			endometrium(2)|kidney(3)|large_intestine(2)|lung(1)|ovary(1)	9	all_cancers(12;2.3e-05)|all_epithelial(12;0.0024)|Breast(13;0.245)				Aciclovir(DB00787)	CAGGATCACGCCCACGTGCTT	0.662																																					p.G109fs		Atlas-INDEL	.											.	SLC47A2	61	.	0			c.327delC						.						74.0	69.0	71.0					17																	19617255		2203	4300	6503	SO:0001589	frameshift_variant	146802	exon4			.	AB250364	CCDS11211.1, CCDS58530.1	17p11.2	2013-07-17	2013-07-17		ENSG00000180638	ENSG00000180638		"""Solute carriers"""	26439	protein-coding gene	gene with protein product	"""multidrug and toxin extrusion 2"""	609833				16996621, 16807400	Standard	NM_152908		Approved	FLJ31196, MATE2, MATE2-K	uc002gwf.4	Q86VL8	OTTHUMG00000059464	ENST00000325411.5:c.326delG	chr17.hg19:g.19617255delC	ENSP00000326671:p.Gly109fs	133.0	0.0		131.0	11.0	NM_152908	A0JBX9|A0P8Z7|Q63HJ9|Q8IV44|Q96NA1	Frame_Shift_Del	DEL	ENST00000325411.5	hg19	CCDS11211.1																																																																																			.	.		0.662	SLC47A2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000132242.2	NM_152908	
DIP2A	23181	hgsc.bcm.edu	37	21	47977529	47977529	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr21:47977529delC	ENST00000417564.2	+	31	3682	c.3661delC	c.(3661-3663)cccfs	p.P1222fs	DIP2A_ENST00000318711.7_Frame_Shift_Del_p.P1223fs|DIP2A_ENST00000400274.1_Frame_Shift_Del_p.P1218fs			Q14689	DIP2A_HUMAN	DIP2 disco-interacting protein 2 homolog A (Drosophila)	1222					multicellular organismal development (GO:0007275)|negative regulation of gene expression (GO:0010629)|regulation of apoptotic process (GO:0042981)	cell surface (GO:0009986)|nucleus (GO:0005634)	catalytic activity (GO:0003824)			cervix(1)|endometrium(7)|kidney(2)|large_intestine(6)|lung(22)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Breast(49;0.0933)			Epithelial(3;3.12e-06)|OV - Ovarian serous cystadenocarcinoma(3;5.68e-06)|all cancers(3;4.08e-05)|Colorectal(79;0.0129)|COAD - Colon adenocarcinoma(84;0.0824)		AGTGCTGGTGCCCCCGCTGGA	0.642																																					p.V1220fs		Atlas-INDEL	.											.	DIP2A	332	.	0			c.3660delG						.						34.0	42.0	40.0					21																	47977529		2116	4213	6329	SO:0001589	frameshift_variant	23181	exon31			.	AF490768	CCDS46655.1, CCDS46656.1, CCDS46657.1, CCDS54490.1, CCDS54491.1	21q22.3	2010-08-20	2006-01-13	2006-01-13	ENSG00000160305	ENSG00000160305			17217	protein-coding gene	gene with protein product		607711	"""chromosome 21 open reading frame 106"""	C21orf106			Standard	NM_015151		Approved	Dip2, KIAA0184	uc002zjo.2	Q14689	OTTHUMG00000090717	ENST00000417564.2:c.3661delC	chr21.hg19:g.47977529delC	ENSP00000392066:p.Pro1222fs	124.0	0.0		125.0	11.0	NM_015151	A6P4T3|B4E0F0|E7EMA5|Q8IVA3|Q8N4S2|Q8TD89|Q96ML9	Frame_Shift_Del	DEL	ENST00000417564.2	hg19	CCDS46655.1																																																																																			.	.		0.642	DIP2A-012	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376736.1	NM_015151	
ALDH4A1	8659	hgsc.bcm.edu	37	1	19213000	19213000	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:19213000delA	ENST00000375341.3	-	4	512	c.255delT	c.(253-255)tttfs	p.F85fs	ALDH4A1_ENST00000538839.1_Frame_Shift_Del_p.F85fs|ALDH4A1_ENST00000290597.5_Frame_Shift_Del_p.F85fs|ALDH4A1_ENST00000538309.1_Frame_Shift_Del_p.F25fs|RP13-279N23.2_ENST00000494072.3_3'UTR|ALDH4A1_ENST00000454547.1_5'Flank	NM_003748.3	NP_003739.2	P30038	AL4A1_HUMAN	aldehyde dehydrogenase 4 family, member A1	85					4-hydroxyproline catabolic process (GO:0019470)|cellular nitrogen compound metabolic process (GO:0034641)|glutamate biosynthetic process (GO:0006537)|proline biosynthetic process (GO:0006561)|proline catabolic process (GO:0006562)|proline catabolic process to glutamate (GO:0010133)|proline metabolic process (GO:0006560)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)	1-pyrroline-5-carboxylate dehydrogenase activity (GO:0003842)|aldehyde dehydrogenase (NAD) activity (GO:0004029)|electron carrier activity (GO:0009055)|identical protein binding (GO:0042802)			cervix(2)|endometrium(1)|large_intestine(3)|lung(8)|prostate(1)	15		Colorectal(325;3.46e-05)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Renal(390;0.000518)|Breast(348;0.000812)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00479)|BRCA - Breast invasive adenocarcinoma(304;3.67e-05)|Kidney(64;0.000182)|KIRC - Kidney renal clear cell carcinoma(64;0.00269)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		GTCCATGGTTAAAAGGCTGAA	0.562																																					p.N86fs		Atlas-INDEL	.											.	ALDH4A1	72	.	0			c.256delA						.						152.0	112.0	126.0					1																	19213000		2203	4300	6503	SO:0001589	frameshift_variant	8659	exon4			.	U24266	CCDS188.1, CCDS53272.1	1p36	2008-02-05			ENSG00000159423	ENSG00000159423	1.5.1.12	"""Aldehyde dehydrogenases"""	406	protein-coding gene	gene with protein product		606811		ALDH4		8621661	Standard	NM_003748		Approved	P5CDh	uc001bbc.3	P30038	OTTHUMG00000002443	ENST00000375341.3:c.255delT	chr1.hg19:g.19213000delA	ENSP00000364490:p.Phe85fs	135.0	0.0		142.0	13.0	NM_003748	A8K1Q7|B4DGE4|D2D4A3|Q16882|Q53HU4|Q5JNV6|Q8IZ38|Q96IF0|Q9UDI6	Frame_Shift_Del	DEL	ENST00000375341.3	hg19	CCDS188.1																																																																																			.	.		0.562	ALDH4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006954.1		
MAP3K8	1326	hgsc.bcm.edu	37	10	30740592	30740592	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:30740592delA	ENST00000263056.1	+	6	1488	c.792delA	c.(790-792)acafs	p.T264fs	MAP3K8_ENST00000542547.1_Frame_Shift_Del_p.T264fs|MAP3K8_ENST00000375321.1_Frame_Shift_Del_p.T264fs	NM_001244134.1|NM_005204.3	NP_001231063.1|NP_005195.2	P41279	M3K8_HUMAN	mitogen-activated protein kinase kinase kinase 8	264	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell cycle (GO:0007049)|protein phosphorylation (GO:0006468)|T cell costimulation (GO:0031295)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|MAP kinase kinase kinase activity (GO:0004709)|protein serine/threonine kinase activity (GO:0004674)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23		Prostate(175;0.151)				TCATGTCCACAAAAGCTGTTT	0.323																																					p.T264fs		Atlas-INDEL	.											.	MAP3K8	46	.	0			c.791delC						.						86.0	86.0	86.0					10																	30740592		2203	4300	6503	SO:0001589	frameshift_variant	1326	exon5			.	D14497	CCDS7166.1	10p11.2	2011-06-09			ENSG00000107968	ENSG00000107968		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6860	protein-coding gene	gene with protein product		191195		COT, ESTF		2072910, 8479752	Standard	NM_005204		Approved	Tpl-2, EST, c-COT, MEKK8	uc009xlf.2	P41279	OTTHUMG00000017889	ENST00000263056.1:c.792delA	chr10.hg19:g.30740592delA	ENSP00000263056:p.Thr264fs	94.0	0.0		120.0	11.0	NM_001244134	A8K2Q5|D3DRX1|Q14275|Q5T855|Q9HC81	Frame_Shift_Del	DEL	ENST00000263056.1	hg19	CCDS7166.1																																																																																			.	.		0.323	MAP3K8-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047416.2	NM_005204	
NUDT6	11162	hgsc.bcm.edu	37	4	123833749	123833749	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:123833749delT	ENST00000304430.5	-	3	505	c.472delA	c.(472-474)atafs	p.I158fs	NUDT6_ENST00000339154.2_5'UTR|NUDT6_ENST00000502270.1_5'UTR	NM_007083.4	NP_009014.2	P53370	NUDT6_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 6	158	Nudix hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00794}.					mitochondrion (GO:0005739)|nucleus (GO:0005634)	growth factor activity (GO:0008083)|hydrolase activity (GO:0016787)			endometrium(2)|lung(1)|prostate(1)|skin(1)|stomach(1)	6						ACAACCAGTATTTTTCTAGTA	0.289																																					p.I158fs		Atlas-INDEL	.											.	NUDT6	50	.	0			c.473delT						.						58.0	59.0	59.0					4																	123833749		1800	4056	5856	SO:0001589	frameshift_variant	11162	exon3			.	AF019632	CCDS3729.1, CCDS43268.1	4q26	2011-02-21			ENSG00000170917	ENSG00000170917		"""Nudix motif containing"""	8053	protein-coding gene	gene with protein product		606261				7984147, 10022609	Standard	NM_198041		Approved	gfg-1, gfg, FGF2AS, FGF-AS	uc003iew.3	P53370	OTTHUMG00000039507	ENST00000304430.5:c.472delA	chr4.hg19:g.123833749delT	ENSP00000306070:p.Ile158fs	123.0	0.0		182.0	11.0	NM_007083	A8K756|O95097|Q9UQD9	Frame_Shift_Del	DEL	ENST00000304430.5	hg19	CCDS43268.1																																																																																			.	.		0.289	NUDT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095331.3	NM_007083	
DHX30	22907	hgsc.bcm.edu	37	3	47884619	47884619	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:47884619delG	ENST00000445061.1	+	9	1220	c.813delG	c.(811-813)gtgfs	p.V271fs	DHX30_ENST00000457607.1_Frame_Shift_Del_p.V299fs|DHX30_ENST00000446256.2_Frame_Shift_Del_p.V232fs|DHX30_ENST00000348968.4_Frame_Shift_Del_p.V243fs	NM_138615.2	NP_619520.1	Q7L2E3	DHX30_HUMAN	DEAH (Asp-Glu-Ala-His) box helicase 30	271						cytoplasm (GO:0005737)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|chromatin binding (GO:0003682)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)			endometrium(3)|kidney(1)|large_intestine(11)|lung(13)|ovary(4)|pancreas(1)|prostate(1)|skin(3)	37				BRCA - Breast invasive adenocarcinoma(193;0.000696)|KIRC - Kidney renal clear cell carcinoma(197;0.00609)|Kidney(197;0.007)		TCCATACTGTGGGCACCAAGA	0.532																																					p.V271fs		Atlas-INDEL	.											.	DHX30	101	.	0			c.812delT						.						167.0	153.0	158.0					3																	47884619		2203	4300	6503	SO:0001589	frameshift_variant	22907	exon9			.	AB020697	CCDS2759.1	3p24.3-p22.1	2013-07-16	2013-07-16	2003-06-13	ENSG00000132153	ENSG00000132153		"""DEAH-boxes"""	16716	protein-coding gene	gene with protein product			"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 30"", ""DEAH (Asp-Glu-Ala-His) box polypeptide 30"""	DDX30		10048485, 18022663	Standard	NM_138615		Approved	KIAA0890, FLJ11214	uc003cru.3	Q7L2E3	OTTHUMG00000133522	ENST00000445061.1:c.813delG	chr3.hg19:g.47884619delG	ENSP00000405620:p.Val271fs	148.0	0.0		177.0	12.0	NM_138615	A8K5F1|O94965|Q7Z753|Q96CH4|Q9NUQ0	Frame_Shift_Del	DEL	ENST00000445061.1	hg19	CCDS2759.1																																																																																			.	.		0.532	DHX30-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257495.2	NM_138615	
C1orf228	339541	hgsc.bcm.edu	37	1	45155414	45155414	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:45155414delT	ENST00000458657.2	+	3	352	c.45delT	c.(43-45)agtfs	p.S15fs	C1orf228_ENST00000535358.1_Frame_Shift_Del_p.S15fs|C1orf228_ENST00000444751.1_3'UTR			Q6PIY5	CA228_HUMAN	chromosome 1 open reading frame 228	15										central_nervous_system(1)	1						GGCTCTTAAGTTTTTTACAGG	0.488																																					p.S15fs		Atlas-INDEL	.											.	C1orf228	15	.	0			c.44delG						.						53.0	46.0	48.0					1																	45155414		692	1591	2283	SO:0001589	frameshift_variant	339541	exon2			.	AL122004, AY254217, BC026115	CCDS53311.1	1p34.1	2011-02-22	2009-03-17	2009-03-17	ENSG00000198520	ENSG00000198520			34345	protein-coding gene	gene with protein product			"""non-protein coding RNA 82"""	NCRNA00082		12477932	Standard	NM_001145636		Approved	MGC33556, p40	uc001cmf.2	Q6PIY5	OTTHUMG00000007834	ENST00000458657.2:c.45delT	chr1.hg19:g.45155414delT	ENSP00000420716:p.Ser15fs	128.0	0.0		177.0	15.0	NM_001145636	A1KXE5	Frame_Shift_Del	DEL	ENST00000458657.2	hg19	CCDS53311.1																																																																																			.	.		0.488	C1orf228-013	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023125.2	NM_001145636	
WDR11	55717	hgsc.bcm.edu	37	10	122625230	122625230	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:122625230delT	ENST00000263461.6	+	7	1214	c.968delT	c.(967-969)attfs	p.I323fs		NM_018117.11	NP_060587.8	Q8WWQ0	PHIP_HUMAN	WD repeat domain 11	1332					cytoskeleton organization (GO:0007010)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell morphogenesis (GO:0022604)|regulation of growth (GO:0040008)|regulation of protein phosphorylation (GO:0001932)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin receptor binding (GO:0005158)|lysine-acetylated histone binding (GO:0070577)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(9)|prostate(2)|skin(2)|stomach(5)	38						TATAATAACATTTTTACCACT	0.303																																					p.I323fs		Atlas-INDEL	.											.	WDR11	95	.	0			c.967delA						.						78.0	76.0	77.0					10																	122625230		2201	4295	6496	SO:0001589	frameshift_variant	55717	exon7			.	AF320223	CCDS7619.1	10q26	2013-01-21	2010-01-06	2010-01-06	ENSG00000120008	ENSG00000120008		"""WD repeat domain containing"""	13831	protein-coding gene	gene with protein product		606417	"""bromodomain and WD repeat domain containing 2"""	BRWD2		10718198, 11536051	Standard	NM_018117		Approved	KIAA1351, FLJ10506, WDR15, HH14, DR11	uc021pzt.1	Q9BZH6	OTTHUMG00000019171	ENST00000263461.6:c.968delT	chr10.hg19:g.122625230delT	ENSP00000263461:p.Ile323fs	108.0	0.0		148.0	13.0	NM_018117	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Frame_Shift_Del	DEL	ENST00000263461.6	hg19	CCDS7619.1																																																																																			.	.		0.303	WDR11-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050707.2		
PLK1	5347	hgsc.bcm.edu	37	16	23695373	23695373	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:23695373delC	ENST00000300093.4	+	5	1110	c.999delC	c.(997-999)gacfs	p.D333fs	CTD-2196E14.5_ENST00000566143.1_RNA	NM_005030.3	NP_005021.2	P53350	PLK1_HUMAN	polo-like kinase 1	333					activation of mitotic anaphase-promoting complex activity (GO:0007092)|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|centrosome organization (GO:0051297)|cytokinesis (GO:0000910)|establishment of protein localization (GO:0045184)|G2 DNA damage checkpoint (GO:0031572)|G2/M transition of mitotic cell cycle (GO:0000086)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|microtubule bundle formation (GO:0001578)|mitotic cell cycle (GO:0000278)|mitotic cytokinesis (GO:0000281)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic sister chromatid segregation (GO:0000070)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|peptidyl-serine phosphorylation (GO:0018105)|polar body extrusion after meiotic divisions (GO:0040038)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of proteolysis (GO:0045862)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein destabilization (GO:0031648)|protein localization to chromatin (GO:0071168)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell cycle (GO:0051726)|regulation of mitotic cell cycle (GO:0007346)|regulation of mitotic metaphase/anaphase transition (GO:0030071)|regulation of protein binding (GO:0043393)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|response to antibiotic (GO:0046677)	centrosome (GO:0005813)|condensed nuclear chromosome outer kinetochore (GO:0000942)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)|spindle midzone (GO:0051233)|spindle pole (GO:0000922)	anaphase-promoting complex binding (GO:0010997)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|microtubule binding (GO:0008017)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23				GBM - Glioblastoma multiforme(48;0.0156)		GCAGCCTGGACCCCAGCAACC	0.547																																					p.D333fs	Colon(12;240 564 27038 33155)	Atlas-INDEL	.											.	PLK1	67	.	0			c.998delA						.						103.0	108.0	107.0					16																	23695373		2197	4300	6497	SO:0001589	frameshift_variant	5347	exon5			.		CCDS10616.1	16p	2013-01-17	2010-06-24	2004-01-28	ENSG00000166851	ENSG00000166851			9077	protein-coding gene	gene with protein product		602098	"""polo-like kinase (Drosophila)"""	PLK		8127874	Standard	NM_005030		Approved		uc002dlz.1	P53350	OTTHUMG00000096984	ENST00000300093.4:c.999delC	chr16.hg19:g.23695373delC	ENSP00000300093:p.Asp333fs	115.0	0.0		153.0	10.0	NM_005030	Q15153|Q99746	Frame_Shift_Del	DEL	ENST00000300093.4	hg19	CCDS10616.1																																																																																			.	.		0.547	PLK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214057.2	NM_005030	
CABP2	51475	hgsc.bcm.edu	37	11	67290137	67290137	+	Frame_Shift_Del	DEL	G	G	-	rs559061168	byFrequency	TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:67290137delG	ENST00000294288.4	-	2	162	c.93delC	c.(91-93)cccfs	p.P31fs	CABP2_ENST00000353903.5_Intron	NM_016366.2	NP_057450.2	Q9NPB3	CABP2_HUMAN	calcium binding protein 2	31					signal transduction (GO:0007165)	Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(2)|large_intestine(1)|lung(3)|prostate(1)|skin(2)	9						ggctggagctggggctggggc	0.726																																					p.S32fs		Atlas-INDEL	.											.	CABP2	25	.	0			c.94delA						.						5.0	6.0	5.0					11																	67290137		1933	3696	5629	SO:0001589	frameshift_variant	51475	exon2			.	AF169154	CCDS8170.1	11q13.1	2013-01-10			ENSG00000167791	ENSG00000167791		"""EF-hand domain containing"""	1385	protein-coding gene	gene with protein product		607314				10625670	Standard	NM_016366		Approved		uc001omc.1	Q9NPB3	OTTHUMG00000168014	ENST00000294288.4:c.93delC	chr11.hg19:g.67290137delG	ENSP00000294288:p.Pro31fs	39.0	0.0		139.0	10.0	NM_016366		Frame_Shift_Del	DEL	ENST00000294288.4	hg19	CCDS8170.1																																																																																			.	.		0.726	CABP2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000397516.1		
MAP4K5	11183	hgsc.bcm.edu	37	14	50933308	50933308	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:50933308delT	ENST00000013125.4	-	11	1048	c.730delA	c.(730-732)acafs	p.T244fs	Y_RNA_ENST00000364703.1_RNA|MAP4K5_ENST00000557578.1_5'Flank	NM_006575.4|NM_198794.2	NP_006566.2|NP_942089.1	Q9Y4K4	M4K5_HUMAN	mitogen-activated protein kinase kinase kinase kinase 5	244	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of JUN kinase activity (GO:0007257)|intracellular signal transduction (GO:0035556)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	15	all_epithelial(31;0.000415)|Breast(41;0.0102)					CACCATTTTGTTTTGTCCTTT	0.279																																					p.T244fs		Atlas-INDEL	.											.	MAP4K5	48	.	0			c.731delC						.						45.0	39.0	41.0					14																	50933308		1604	3619	5223	SO:0001589	frameshift_variant	11183	exon11			.	U77129		14q11.2-q21	2011-06-09				ENSG00000012983		"""Mitogen-activated protein kinase cascade / Kinase kinase kinase kinases"""	6867	protein-coding gene	gene with protein product	"""germinal center kinase-related"""	604923				9038372, 8274451	Standard	NM_198794		Approved	KHS1, GCKR, KHS	uc001wyb.3	Q9Y4K4		ENST00000013125.4:c.730delA	chr14.hg19:g.50933308delT	ENSP00000013125:p.Thr244fs	112.0	0.0		159.0	10.0	NM_006575	Q8IYF6	Frame_Shift_Del	DEL	ENST00000013125.4	hg19																																																																																				.	.		0.279	MAP4K5-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000410880.1	NM_006575	
SUCLA2	8803	hgsc.bcm.edu	37	13	48562793	48562793	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr13:48562793delT	ENST00000378654.3	-	4	473	c.417delA	c.(415-417)aaafs	p.K139fs	SUCLA2_ENST00000544100.1_Frame_Shift_Del_p.K5fs|SUCLA2_ENST00000534875.1_Frame_Shift_Del_p.K81fs|SUCLA2_ENST00000497202.1_5'UTR|SUCLA2_ENST00000543413.1_Frame_Shift_Del_p.K81fs	NM_003850.2	NP_003841.1	Q9P2R7	SUCB1_HUMAN	succinate-CoA ligase, ADP-forming, beta subunit	139	ATP-grasp.				cellular metabolic process (GO:0044237)|small molecule metabolic process (GO:0044281)|succinate metabolic process (GO:0006105)|succinyl-CoA metabolic process (GO:0006104)|succinyl-CoA pathway (GO:0006781)|tricarboxylic acid cycle (GO:0006099)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|succinate-CoA ligase (ADP-forming) activity (GO:0004775)			central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(5)|lung(3)|skin(4)	15		all_cancers(8;1.13e-24)|all_epithelial(8;1.78e-13)|all_lung(13;2.85e-06)|Breast(56;0.000141)|Lung NSC(96;0.000226)|all_hematologic(8;0.000885)|Prostate(109;0.00132)|Acute lymphoblastic leukemia(8;0.0167)|Myeloproliferative disorder(33;0.039)|Hepatocellular(98;0.0556)|Lung SC(185;0.102)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(144;2.1e-06)	Succinic acid(DB00139)	TGGTAAACAATTTTTTCCCAA	0.348																																					p.L140fs		Atlas-INDEL	.											.	SUCLA2	40	.	0			c.418delT						.						95.0	87.0	90.0					13																	48562793		2202	4299	6501	SO:0001589	frameshift_variant	8803	exon4			.	AF058953	CCDS9406.1	13q12.2-q13.3	2010-04-16			ENSG00000136143	ENSG00000136143	6.2.1.5		11448	protein-coding gene	gene with protein product		603921				9765291	Standard	NM_003850		Approved		uc001vbs.3	Q9P2R7	OTTHUMG00000016889	ENST00000378654.3:c.417delA	chr13.hg19:g.48562793delT	ENSP00000367923:p.Lys139fs	118.0	0.0		160.0	10.0	NM_003850	B2RDE7|O95194|Q5T9Q4|Q5T9Q6|Q9NV21|Q9NVP7	Frame_Shift_Del	DEL	ENST00000378654.3	hg19	CCDS9406.1																																																																																			.	.		0.348	SUCLA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044852.1		
SMTNL1	219537	hgsc.bcm.edu	37	11	57310817	57310817	+	Intron	DEL	A	A	-	rs373299953		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:57310817delA	ENST00000399154.2	+	2	621				SMTNL1_ENST00000527972.1_Frame_Shift_Del_p.A234fs|SMTNL1_ENST00000457912.1_Frame_Shift_Del_p.A252fs			A8MU46	SMTL1_HUMAN	smoothelin-like 1						negative regulation of vasodilation (GO:0045908)|positive regulation of vasoconstriction (GO:0045907)	contractile fiber (GO:0043292)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(2)|large_intestine(1)|lung(4)|ovary(1)	8						AGGCTGATGCAAAAGAGGAGG	0.567																																					p.A234fs		Atlas-INDEL	.											.	SMTNL1	68	.	0			c.701delC						.						39.0	41.0	40.0					11																	57310817		2116	4229	6345	SO:0001627	intron_variant	219537	exon1			.	BX116227		11q12.1	2006-02-02				ENSG00000214872			32394	protein-coding gene	gene with protein product	"""calponin homology-associated smooth muscle protein"""	613664				15327999	Standard	NM_001105565		Approved	CHASM	uc021qjh.1	A8MU46		ENST00000399154.2:c.621+3A>-	chr11.hg19:g.57310817delA		129.0	0.0		151.0	10.0	NM_001105565		Frame_Shift_Del	DEL	ENST00000399154.2	hg19																																																																																				.	.		0.567	SMTNL1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_166203	
CDK5RAP2	55755	hgsc.bcm.edu	37	9	123152026	123152026	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:123152026delT	ENST00000349780.4	-	37	5797	c.5618delA	c.(5617-5619)aacfs	p.N1873fs	CDK5RAP2_ENST00000480467.1_5'UTR|CDK5RAP2_ENST00000360190.4_Frame_Shift_Del_p.N1794fs|CDK5RAP2_ENST00000360822.3_Frame_Shift_Del_p.N1841fs|CDK5RAP2_ENST00000359309.3_Frame_Shift_Del_p.N1832fs	NM_018249.4	NP_060719.4	Q96SN8	CK5P2_HUMAN	CDK5 regulatory subunit associated protein 2	1873	Interaction with PCNT and AKAP9.				brain development (GO:0007420)|centrosome organization (GO:0051297)|chromosome segregation (GO:0007059)|establishment of mitotic spindle orientation (GO:0000132)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule bundle formation (GO:0001578)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|negative regulation of centriole replication (GO:0046600)|negative regulation of neuron differentiation (GO:0045665)|neurogenesis (GO:0022008)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of neuron differentiation (GO:0045664)|regulation of spindle checkpoint (GO:0090231)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|pericentriolar material (GO:0000242)|perinuclear region of cytoplasm (GO:0048471)|spindle pole (GO:0000922)	calmodulin binding (GO:0005516)|microtubule binding (GO:0008017)|protein kinase binding (GO:0019901)|transcription regulatory region DNA binding (GO:0044212)|tubulin binding (GO:0015631)			breast(6)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(12)|lung(21)|ovary(2)|prostate(2)|skin(6)|urinary_tract(1)	58						TACCTCCAGGTTTCCTCTGGC	0.512																																					p.N1873fs		Atlas-INDEL	.											.	CDK5RAP2	157	.	0			c.5619delC						.						161.0	136.0	144.0					9																	123152026		2203	4300	6503	SO:0001589	frameshift_variant	55755	exon37			.	BK005504	CCDS6823.1, CCDS43871.1, CCDS75888.1	9q33.3	2014-02-21			ENSG00000136861	ENSG00000136861			18672	protein-coding gene	gene with protein product	"""centrosomin"""	608201	"""microcephaly, primary autosomal recessive 3"""	MCPH3		10721722, 17764569, 24466316	Standard	NM_018249		Approved	C48, FLJ10867, CEP215	uc004bkf.4	Q96SN8	OTTHUMG00000021043	ENST00000349780.4:c.5618delA	chr9.hg19:g.123152026delT	ENSP00000343818:p.Asn1873fs	156.0	0.0		157.0	11.0	NM_018249	Q5JV18|Q7Z3L4|Q7Z3U1|Q7Z7I6|Q9BSW0|Q9H6J6|Q9HCD9|Q9NV90|Q9UIW9	Frame_Shift_Del	DEL	ENST00000349780.4	hg19	CCDS6823.1																																																																																			.	.		0.512	CDK5RAP2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055535.1	NM_018249	
KTN1	3895	hgsc.bcm.edu	37	14	56114751	56114751	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:56114751delA	ENST00000395314.3	+	20	2284	c.2216delA	c.(2215-2217)gaafs	p.E739fs	KTN1_ENST00000554507.1_Frame_Shift_Del_p.E34fs|KTN1_ENST00000438792.2_Frame_Shift_Del_p.E739fs|KTN1_ENST00000395311.1_Frame_Shift_Del_p.E739fs|KTN1_ENST00000416613.1_Frame_Shift_Del_p.E739fs|KTN1_ENST00000413890.2_Frame_Shift_Del_p.E739fs|KTN1_ENST00000395308.1_Frame_Shift_Del_p.E739fs|KTN1_ENST00000395309.3_Frame_Shift_Del_p.E739fs	NM_001079521.1	NP_001072989.1	Q86UP2	KTN1_HUMAN	kinectin 1 (kinesin receptor)	739					microtubule-based movement (GO:0007018)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			breast(4)|central_nervous_system(1)|large_intestine(8)|lung(1)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	19						AGCATTCAAGAAAAAGATGAG	0.269			T	RET	papillary thryoid																																p.E739fs		Atlas-INDEL	.		Dom	yes		14	14q22.1	3895	kinectin 1 (kinesin receptor)		E	.	KTN1	147	.	0			c.2215delG						.						59.0	62.0	61.0					14																	56114751		2203	4298	6501	SO:0001589	frameshift_variant	3895	exon20			.		CCDS41957.1, CCDS41958.1, CCDS41959.1	14q22.1	2008-05-02			ENSG00000126777	ENSG00000126777			6467	protein-coding gene	gene with protein product		600381				9605849	Standard	NM_001079521		Approved	KIAA0004, CG1	uc001xcc.3	Q86UP2	OTTHUMG00000140312	ENST00000395314.3:c.2216delA	chr14.hg19:g.56114751delA	ENSP00000378725:p.Glu739fs	176.0	0.0		160.0	10.0	NM_004986	B4DZ88|Q13999|Q14707|Q15387|Q17RZ5|Q5GGW3|Q86W57	Frame_Shift_Del	DEL	ENST00000395314.3	hg19	CCDS41957.1																																																																																			.	.		0.269	KTN1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276912.2		
CHMP6	79643	hgsc.bcm.edu	37	17	78969500	78969500	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:78969500delA	ENST00000325167.5	+	4	368	c.290delA	c.(289-291)gaafs	p.E97fs		NM_024591.4	NP_078867.2	Q96FZ7	CHMP6_HUMAN	charged multivesicular body protein 6	97					endosomal transport (GO:0016197)|membrane organization (GO:0061024)|protein transport (GO:0015031)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	protein N-terminus binding (GO:0047485)			lung(2)|ovary(1)	3	all_neural(118;0.101)		BRCA - Breast invasive adenocarcinoma(99;0.0175)|OV - Ovarian serous cystadenocarcinoma(97;0.0524)			ACCCAGATCGAAATGAAAGTG	0.582																																					p.E97fs		Atlas-INDEL	.											.	CHMP6	16	.	0			c.289delG						.						103.0	94.0	97.0					17																	78969500		2203	4300	6503	SO:0001589	frameshift_variant	79643	exon4			.	BC010108	CCDS11774.1	17q25.3	2014-08-13	2011-09-21		ENSG00000176108	ENSG00000176108		"""Charged multivesicular body proteins"""	25675	protein-coding gene	gene with protein product		610901	"""chromatin modifying protein 6"""			11559748, 15511219	Standard	NM_024591		Approved	FLJ11749, VPS20	uc002jyw.4	Q96FZ7	OTTHUMG00000177645	ENST00000325167.5:c.290delA	chr17.hg19:g.78969500delA	ENSP00000317468:p.Glu97fs	162.0	0.0		198.0	14.0	NM_024591	A8K7U0|Q53FU4|Q9HAE8	Frame_Shift_Del	DEL	ENST00000325167.5	hg19	CCDS11774.1																																																																																			.	.		0.582	CHMP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438215.1	NM_024591	
ERICH6B	220081	hgsc.bcm.edu	37	13	46154112	46154112	+	Intron	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr13:46154112delA	ENST00000298738.2	-	7	1084					NM_182542.2	NP_872348.2	Q5W0A0	ERI6B_HUMAN												breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)	5						AACATGCTCTAAAAAAGAATA	0.348																																					.		Atlas-INDEL	.											.	FAM194B	42	.	0			c.920-2T>-						.						96.0	94.0	95.0					13																	46154112		692	1591	2283	SO:0001627	intron_variant	220081	exon8			.																												ENST00000298738.2:c.920-3T>-	chr13.hg19:g.46154112delA		108.0	0.0		183.0	11.0	NM_182542	Q96MB5	Splice_Site	DEL	ENST00000298738.2	hg19	CCDS45045.1																																																																																			.	.		0.348	FAM194B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044781.3		
SIGLEC6	946	hgsc.bcm.edu	37	19	52034030	52034030	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:52034030delG	ENST00000425629.3	-	3	765	c.611delC	c.(610-612)ccafs	p.P204fs	SIGLEC6_ENST00000343300.4_Frame_Shift_Del_p.P204fs|SIGLEC6_ENST00000436458.1_Frame_Shift_Del_p.P168fs|SIGLEC6_ENST00000346477.3_Frame_Shift_Del_p.P204fs|SIGLEC6_ENST00000391797.3_Frame_Shift_Del_p.P193fs|SIGLEC6_ENST00000474054.1_5'Flank|SIGLEC6_ENST00000359982.4_Frame_Shift_Del_p.P204fs	NM_001245.5	NP_001236.4	O43699	SIGL6_HUMAN	sialic acid binding Ig-like lectin 6	204	Ig-like C2-type 1.				cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)			endometrium(3)|kidney(1)|large_intestine(6)|liver(1)|lung(15)|ovary(1)|stomach(1)	28		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.00115)|OV - Ovarian serous cystadenocarcinoma(262;0.0165)		CTGGGGCCGTGGGGTGATTGT	0.637																																					p.P204fs		Atlas-INDEL	.											.	SIGLEC6	142	.	0			c.612delA						.						63.0	69.0	67.0					19																	52034030		2203	4300	6503	SO:0001589	frameshift_variant	946	exon3			.	D86358	CCDS12834.3, CCDS12835.3, CCDS12836.3, CCDS54307.1, CCDS54308.1, CCDS59417.1	19q13.3	2013-01-29			ENSG00000105492	ENSG00000105492		"""Sialic acid binding Ig-like lectins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10875	protein-coding gene	gene with protein product		604405		CD33L, CD33L1		9465907	Standard	NM_001245		Approved	OB-BP1, SIGLEC-6, CD327	uc002pwy.3	O43699	OTTHUMG00000133571	ENST00000425629.3:c.611delC	chr19.hg19:g.52034030delG	ENSP00000401502:p.Pro204fs	126.0	0.0		159.0	14.0	NM_198845	A8MV71|B2RTS8|C9JBE5|F8WA78|O15388|O43700	Frame_Shift_Del	DEL	ENST00000425629.3	hg19	CCDS12834.3																																																																																			.	.		0.637	SIGLEC6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257670.3	NM_001245	
NOL6	65083	hgsc.bcm.edu	37	9	33464082	33464082	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:33464082delG	ENST00000379471.2	-	22	2944	c.2857delC	c.(2857-2859)caafs	p.Q953fs	NOL6_ENST00000464829.1_Intron|NOL6_ENST00000455041.2_Frame_Shift_Del_p.Q901fs			Q9H6R4	NOL6_HUMAN	nucleolar protein 6 (RNA-associated)	953					rRNA processing (GO:0006364)	condensed nuclear chromosome (GO:0000794)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(4)|kidney(4)|large_intestine(5)|lung(8)|ovary(2)|prostate(2)|skin(2)	27			LUSC - Lung squamous cell carcinoma(29;0.00788)	GBM - Glioblastoma multiforme(74;0.152)		TTGCGGTCTTGGGGGGTAACA	0.567																																					p.Q953fs		Atlas-INDEL	.											.	NOL6	85	.	0			c.2858delA						.						140.0	125.0	130.0					9																	33464082		2203	4300	6503	SO:0001589	frameshift_variant	65083	exon22			.	AF361079	CCDS6543.1, CCDS6544.1	9p12	2013-02-22	2013-02-22		ENSG00000165271	ENSG00000165271			19910	protein-coding gene	gene with protein product		611532	"""nucleolar protein family 6 (RNA-associated)"""			11895476, 15590835	Standard	NM_022917		Approved	bA311H10.1, Nrap, FLJ21959, MGC14896, MGC14921, MGC20838, UTP22	uc003zsz.3	Q9H6R4	OTTHUMG00000000394	ENST00000379471.2:c.2857delC	chr9.hg19:g.33464082delG	ENSP00000368784:p.Gln953fs	137.0	0.0		167.0	11.0	NM_022917	Q5T5M3|Q5T5M4|Q7L4G6|Q8N6I0|Q8TEY9|Q8TEZ0|Q8TEZ1|Q9H675	Frame_Shift_Del	DEL	ENST00000379471.2	hg19																																																																																				.	.		0.567	NOL6-005	NOVEL	non_canonical_TEC|basic	protein_coding	protein_coding	OTTHUMT00000001019.2	NM_022917	
NR2E1	7101	hgsc.bcm.edu	37	6	108499301	108499301	+	Frame_Shift_Del	DEL	C	C	-	rs143132592	byFrequency	TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:108499301delC	ENST00000368986.4	+	5	1206	c.498delC	c.(496-498)tacfs	p.Y166fs	NR2E1_ENST00000484978.1_3'UTR|NR2E1_ENST00000368983.3_Frame_Shift_Del_p.Y203fs	NM_003269.3	NP_003260.1	Q9Y466	NR2E1_HUMAN	nuclear receptor subfamily 2, group E, member 1	166					aggressive behavior (GO:0002118)|amygdala development (GO:0021764)|anterior commissure morphogenesis (GO:0021960)|behavioral fear response (GO:0001662)|cell fate commitment (GO:0045165)|cerebral cortex neuron differentiation (GO:0021895)|dentate gyrus development (GO:0021542)|extracellular matrix organization (GO:0030198)|forebrain generation of neurons (GO:0021872)|gene expression (GO:0010467)|glial cell migration (GO:0008347)|layer formation in cerebral cortex (GO:0021819)|long-term synaptic potentiation (GO:0060291)|negative regulation of apoptotic process (GO:0043066)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron differentiation (GO:0045665)|nervous system development (GO:0007399)|olfactory bulb development (GO:0021772)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell cycle (GO:0045787)|positive regulation of neural precursor cell proliferation (GO:2000179)|positive regulation of stem cell proliferation (GO:2000648)|regulation of cell migration involved in sprouting angiogenesis (GO:0090049)|regulation of dendrite morphogenesis (GO:0048814)|regulation of timing of neuron differentiation (GO:0060164)|retina development in camera-type eye (GO:0060041)|social behavior (GO:0035176)|somatic stem cell maintenance (GO:0035019)|transcription initiation from RNA polymerase II promoter (GO:0006367)|visual perception (GO:0007601)	nucleoplasm (GO:0005654)	RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(4)|liver(1)|lung(16)|prostate(1)|skin(3)	30		all_cancers(87;8.13e-05)|Acute lymphoblastic leukemia(125;3.07e-08)|all_hematologic(75;3.33e-06)|all_epithelial(87;0.00866)|Colorectal(196;0.0637)		BRCA - Breast invasive adenocarcinoma(108;0.013)|Epithelial(106;0.0521)|all cancers(137;0.068)|OV - Ovarian serous cystadenocarcinoma(136;0.0689)		CTACCCAGTACCCCCATGAAG	0.463																																					p.Y166fs		Atlas-INDEL	.											.	NR2E1	57	.	0			c.497delA						.						95.0	91.0	93.0					6																	108499301		2203	4300	6503	SO:0001589	frameshift_variant	7101	exon5			.	Y13276	CCDS5063.1, CCDS69165.1	6q21	2013-01-16			ENSG00000112333	ENSG00000112333		"""Nuclear hormone receptors"""	7973	protein-coding gene	gene with protein product		603849		TLX		9628820	Standard	NM_003269		Approved	TLL, XTLL	uc003psg.3	Q9Y466	OTTHUMG00000015319	ENST00000368986.4:c.498delC	chr6.hg19:g.108499301delC	ENSP00000357982:p.Tyr166fs	122.0	0.0		157.0	10.0	NM_003269	Q6ZMP8	Frame_Shift_Del	DEL	ENST00000368986.4	hg19	CCDS5063.1																																																																																			.	.		0.463	NR2E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041712.2		
RIC8A	60626	hgsc.bcm.edu	37	11	211289	211289	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:211289delG	ENST00000526104.1	+	5	2253	c.909delG	c.(907-909)atgfs	p.M303fs	RIC8A_ENST00000325207.5_Frame_Shift_Del_p.M303fs|RIC8A_ENST00000527696.1_Frame_Shift_Del_p.M297fs			Q9NPQ8	RIC8A_HUMAN	RIC8 guanine nucleotide exchange factor A	303					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|basement membrane organization (GO:0071711)|cell migration involved in gastrulation (GO:0042074)|cell-cell adhesion involved in gastrulation (GO:0070586)|in utero embryonic development (GO:0001701)|vasculature development (GO:0001944)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)			endometrium(3)|kidney(1)|large_intestine(3)|lung(3)|pancreas(1)|prostate(1)|skin(1)	13		all_cancers(49;9.23e-07)|all_epithelial(84;0.000315)|Breast(177;0.00122)|Ovarian(85;0.0202)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;4.45e-27)|Epithelial(43;2.94e-26)|OV - Ovarian serous cystadenocarcinoma(40;5.86e-21)|BRCA - Breast invasive adenocarcinoma(625;3.57e-05)|Lung(200;0.105)|LUSC - Lung squamous cell carcinoma(625;0.122)		CGGAGTTCATGGGAGTGAATA	0.577																																					p.M303fs		Atlas-INDEL	.											.	RIC8A	45	.	0			c.908delT						.						129.0	111.0	117.0					11																	211289		2203	4300	6503	SO:0001589	frameshift_variant	60626	exon5			.	AK022870	CCDS7690.1, CCDS65982.1	11p15.5	2013-08-05	2013-08-05		ENSG00000177963	ENSG00000177963			29550	protein-coding gene	gene with protein product		609146	"""resistance to inhibitors of cholinesterase 8 homolog A (C. elegans)"""			10985349, 11230166	Standard	XM_005253052		Approved	synembryn, synembryn-A	uc001lof.3	Q9NPQ8	OTTHUMG00000119069	ENST00000526104.1:c.909delG	chr11.hg19:g.211289delG	ENSP00000432008:p.Met303fs	150.0	0.0		158.0	10.0	NM_021932	Q0P508|Q2T9J1|Q7Z352|Q96EZ1|Q96SZ2|Q9H064|Q9H5H3|Q9H9E7	Frame_Shift_Del	DEL	ENST00000526104.1	hg19																																																																																				.	.		0.577	RIC8A-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000384761.1	NM_021932	
SLCO6A1	133482	hgsc.bcm.edu	37	5	101774421	101774421	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:101774421delT	ENST00000506729.1	-	7	1347	c.1176delA	c.(1174-1176)aaafs	p.K392fs	SLCO6A1_ENST00000389019.3_Frame_Shift_Del_p.K330fs|SLCO6A1_ENST00000514551.1_5'UTR|SLCO6A1_ENST00000379807.3_Frame_Shift_Del_p.K392fs|SLCO6A1_ENST00000513675.1_Intron|SLCO6A1_ENST00000379810.1_Intron			Q86UG4	SO6A1_HUMAN	solute carrier organic anion transporter family, member 6A1	392						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(17)|lung(22)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	60		all_cancers(142;8e-09)|all_epithelial(76;2.83e-12)|Prostate(80;0.00125)|Colorectal(57;0.00342)|Ovarian(225;0.024)|Lung NSC(167;0.0259)|all_lung(232;0.0323)		Epithelial(69;1.47e-15)|COAD - Colon adenocarcinoma(37;0.0113)		ATTCTGTAGCTTTTGACAGAG	0.294																																					p.A393fs		Atlas-INDEL	.											.	SLCO6A1	153	.	0			c.1177delG						.						36.0	41.0	39.0					5																	101774421		2200	4291	6491	SO:0001589	frameshift_variant	133482	exon7			.	AF505657	CCDS34206.1, CCDS75282.1	5q21.2	2013-05-22			ENSG00000205359	ENSG00000205359		"""Solute carriers"""	23613	protein-coding gene	gene with protein product	"""cancer/testis antigen 48"""	613365					Standard	XM_005271874		Approved	OATP6A1, OATPY, MGC26949, CT48	uc003knp.3	Q86UG4	OTTHUMG00000162759	ENST00000506729.1:c.1176delA	chr5.hg19:g.101774421delT	ENSP00000421339:p.Lys392fs	123.0	0.0		143.0	11.0	NM_173488	A6NHC1|Q6ZMY5|Q86UV2|Q8IYU5	Frame_Shift_Del	DEL	ENST00000506729.1	hg19	CCDS34206.1																																																																																			.	.		0.294	SLCO6A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370335.1	NM_173488	
PIK3CB	5291	hgsc.bcm.edu	37	3	138461437	138461437	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:138461437delC	ENST00000477593.1	-	4	657	c.584delG	c.(583-585)ggafs	p.G195fs	PIK3CB_ENST00000289153.2_Frame_Shift_Del_p.G195fs			P42338	PK3CB_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit beta	195	PI3K-RBD. {ECO:0000255|PROSITE- ProRule:PRU00879}.				activation of MAPK activity (GO:0000187)|autophagy (GO:0006914)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|cellular calcium ion homeostasis (GO:0006874)|chemotaxis (GO:0006935)|embryonic cleavage (GO:0040016)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|positive regulation of autophagy (GO:0010508)|regulation of cell-matrix adhesion (GO:0001952)|regulation of clathrin-mediated endocytosis (GO:2000369)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytosol (GO:0005829)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)			NS(1)|breast(3)|endometrium(5)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(4)	41					Caffeine(DB00201)	GATGAGCTTTCCCCCATAAAG	0.353																																					p.G195fs		Atlas-INDEL	.											.	PIK3CB	103	.	0			c.585delA						.						99.0	94.0	96.0					3																	138461437		2203	4300	6503	SO:0001589	frameshift_variant	5291	exon3			.		CCDS3104.1	3q22.3	2013-09-19	2012-07-13		ENSG00000051382	ENSG00000051382	2.7.1.153		8976	protein-coding gene	gene with protein product		602925	"""phosphoinositide-3-kinase, catalytic, beta polypeptide"""	PIK3C1		8246984	Standard	NM_006219		Approved		uc011bmq.3	P42338	OTTHUMG00000159893	ENST00000477593.1:c.584delG	chr3.hg19:g.138461437delC	ENSP00000418143:p.Gly195fs	134.0	0.0		146.0	10.0	NM_006219	D3DNF0|Q24JU2	Frame_Shift_Del	DEL	ENST00000477593.1	hg19	CCDS3104.1																																																																																			.	.		0.353	PIK3CB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358019.1		
RAG2	5897	hgsc.bcm.edu	37	11	36614735	36614735	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:36614735delA	ENST00000311485.3	-	2	1145	c.984delT	c.(982-984)tttfs	p.F328fs	C11orf74_ENST00000446510.2_5'Flank|RAG2_ENST00000528428.1_5'Flank|C11orf74_ENST00000534635.1_5'Flank|C11orf74_ENST00000334307.5_5'Flank|C11orf74_ENST00000347206.4_5'Flank	NM_000536.3|NM_001243785.1|NM_001243786.1	NP_000527.2|NP_001230714.1|NP_001230715.1	P55895	RAG2_HUMAN	recombination activating gene 2	328					B cell differentiation (GO:0030183)|chromatin modification (GO:0016568)|pre-B cell allelic exclusion (GO:0002331)|T cell differentiation in thymus (GO:0033077)|V(D)J recombination (GO:0033151)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|methylated histone binding (GO:0035064)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(18)|ovary(1)|pancreas(2)|prostate(1)|skin(4)	32	all_lung(20;0.226)	all_hematologic(20;0.00756)				GTATGCCAAGAAAAACAGTTC	0.388									Familial Hemophagocytic Lymphohistiocytosis																												p.L329fs		Atlas-INDEL	.											.	RAG2	92	.	0			c.985delC						.						223.0	215.0	218.0					11																	36614735		2202	4298	6500	SO:0001589	frameshift_variant	5897	exon3	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	.	AF080577	CCDS7903.1	11p13	2014-09-17				ENSG00000175097			9832	protein-coding gene	gene with protein product		179616				1283330	Standard	NM_000536		Approved		uc001mwv.4	P55895		ENST00000311485.3:c.984delT	chr11.hg19:g.36614735delA	ENSP00000308620:p.Phe328fs	187.0	0.0		310.0	20.0	NM_001243785	A8K9E9|Q8TBL4	Frame_Shift_Del	DEL	ENST00000311485.3	hg19	CCDS7903.1																																																																																			.	.		0.388	RAG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389536.1	NM_000536	
SLIT3	6586	hgsc.bcm.edu	37	5	168100194	168100194	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:168100194delG	ENST00000519560.1	-	33	4248	c.3829delC	c.(3829-3831)ctcfs	p.L1277fs	SLIT3_ENST00000404867.3_Frame_Shift_Del_p.L1277fs|SLIT3_ENST00000332966.8_Frame_Shift_Del_p.L1284fs	NM_001271946.1|NM_003062.2	NP_001258875.1|NP_003053	O75094	SLIT3_HUMAN	slit homolog 3 (Drosophila)	1277	Laminin G-like. {ECO:0000255|PROSITE- ProRule:PRU00122}.				apoptotic process involved in luteolysis (GO:0061364)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|cellular response to hormone stimulus (GO:0032870)|negative chemotaxis (GO:0050919)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of gene expression (GO:0010629)|organ morphogenesis (GO:0009887)|response to cortisol (GO:0051414)|Roundabout signaling pathway (GO:0035385)	extracellular space (GO:0005615)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|Roundabout binding (GO:0048495)			endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(15)|liver(2)|lung(48)|ovary(4)|prostate(7)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	100	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CCAAGGTAGAGGGGGCTGTTG	0.567																																					p.L1284fs	Ovarian(29;311 847 10864 17279 24903)	Atlas-INDEL	.											.	SLIT3	224	.	0			c.3851delT						.						158.0	156.0	156.0					5																	168100194		2203	4300	6503	SO:0001589	frameshift_variant	6586	exon33			.	AB011538	CCDS4369.1, CCDS64311.1	5q35	2008-07-18	2001-11-28		ENSG00000184347	ENSG00000184347			11087	protein-coding gene	gene with protein product		603745	"""slit (Drosophila) homolog 3"""	SLIL2		9693030, 9813312	Standard	NM_001271946		Approved	slit2, MEGF5, SLIT1, Slit-3	uc010jjg.4	O75094	OTTHUMG00000130409	ENST00000519560.1:c.3829delC	chr5.hg19:g.168100194delG	ENSP00000430333:p.Leu1277fs	162.0	0.0		151.0	11.0	NM_001271946	A6H8U9|J3KNP3|O95804|Q9UFH5	Frame_Shift_Del	DEL	ENST00000519560.1	hg19	CCDS4369.1																																																																																			.	.		0.567	SLIT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252792.4	NM_003062	
TMEM104	54868	hgsc.bcm.edu	37	17	72791152	72791152	+	Splice_Site	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:72791152delG	ENST00000335464.5	+	7	591	c.429delG	c.(427-429)gtg>gt	p.V143fs	TMEM104_ENST00000582330.1_Splice_Site_p.V143fs|TMEM104_ENST00000582773.1_Splice_Site_p.V143fs|TMEM104_ENST00000417024.2_Splice_Site_p.V156fs	NM_017728.3	NP_060198.3	Q8NE00	TM104_HUMAN	transmembrane protein 104	143						integral component of membrane (GO:0016021)				NS(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|lung(5)|ovary(1)	19	all_lung(278;0.23)					TCCTTTCAGTGGGGGTCAACT	0.463																																					p.V143fs		Atlas-INDEL	.											.	TMEM104	49	.	0			c.428delT						.						178.0	149.0	159.0					17																	72791152		2203	4300	6503	SO:0001630	splice_region_variant	54868	exon7			.	AK074029	CCDS32723.1	17q25.1	2005-12-19				ENSG00000109066			25984	protein-coding gene	gene with protein product							Standard	NM_017728		Approved	FLJ20255, FLJ00021	uc002jls.4	Q8NE00		ENST00000335464.5:c.428-1G>-	chr17.hg19:g.72791152delG		147.0	0.0		131.0	10.0	NM_017728	Q8TEU1|Q9NT56|Q9NXH1	Frame_Shift_Del	DEL	ENST00000335464.5	hg19	CCDS32723.1																																																																																			.	.		0.463	TMEM104-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444442.1	NM_017728	Frame_Shift_Del
HSP90AB1	3326	hgsc.bcm.edu	37	6	44218079	44218079	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:44218079delA	ENST00000371554.1	+	6	914	c.700delA	c.(700-702)aaafs	p.K234fs	HSP90AB1_ENST00000371646.5_Frame_Shift_Del_p.K234fs|HSP90AB1_ENST00000353801.3_Frame_Shift_Del_p.K234fs			P08238	HS90B_HUMAN	heat shock protein 90kDa alpha (cytosolic), class B member 1	234					axon guidance (GO:0007411)|cellular response to interleukin-4 (GO:0071353)|cellular response to organic cyclic compound (GO:0071407)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|placenta development (GO:0001890)|positive regulation of cell size (GO:0045793)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of protein binding (GO:0032092)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|protein folding (GO:0006457)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to salt stress (GO:0009651)|response to unfolded protein (GO:0006986)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|inclusion body (GO:0016234)|membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|CTP binding (GO:0002135)|dATP binding (GO:0032564)|double-stranded RNA binding (GO:0003725)|GTP binding (GO:0005525)|MHC class II protein complex binding (GO:0023026)|nitric-oxide synthase regulator activity (GO:0030235)|poly(A) RNA binding (GO:0044822)|TPR domain binding (GO:0030911)|UTP binding (GO:0002134)			NS(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(12)|prostate(2)|skin(2)|urinary_tract(2)	33	all_cancers(18;1.7e-05)|all_lung(25;0.00747)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			agaggaagagaaaggtgagaa	0.413																																					p.E233fs		Atlas-INDEL	.											.	HSP90AB1	83	.	0			c.699delG						.						56.0	58.0	57.0					6																	44218079		2203	4299	6502	SO:0001589	frameshift_variant	3326	exon6			.	AF275719	CCDS4909.1	6p12	2011-09-02	2006-02-24	2006-02-24	ENSG00000096384	ENSG00000096384		"""Heat shock proteins / HSPC"""	5258	protein-coding gene	gene with protein product		140572	"""heat shock 90kD protein 1, beta"", ""heat shock 90kDa protein 1, beta"""	HSPC2, HSPCB		2768249, 16269234	Standard	NM_001271969		Approved		uc031sor.1	P08238	OTTHUMG00000014761	ENST00000371554.1:c.700delA	chr6.hg19:g.44218079delA	ENSP00000360609:p.Lys234fs	102.0	0.0		165.0	10.0	NM_007355	B2R5P0|Q5T9W7|Q9NQW0|Q9NTK6	Frame_Shift_Del	DEL	ENST00000371554.1	hg19	CCDS4909.1																																																																																			.	.		0.413	HSP90AB1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040730.1	NM_007355	
LTK	4058	hgsc.bcm.edu	37	15	41797198	41797198	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:41797198delC	ENST00000263800.6	-	16	2086	c.1990delG	c.(1990-1992)gacfs	p.D664fs	LTK_ENST00000561619.1_Frame_Shift_Del_p.D362fs|LTK_ENST00000453182.2_Frame_Shift_Del_p.D534fs|LTK_ENST00000355166.5_Frame_Shift_Del_p.D603fs	NM_002344.5	NP_002335.2	P29376	LTK_HUMAN	leukocyte receptor tyrosine kinase	664	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell proliferation (GO:0008283)|cellular response to retinoic acid (GO:0071300)|negative regulation of apoptotic process (GO:0043066)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol 3-kinase signaling (GO:0014065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of neuron projection development (GO:0010976)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(16)|skin(3)|urinary_tract(1)	26		all_cancers(109;1.89e-19)|all_epithelial(112;2.28e-16)|Lung NSC(122;5.34e-11)|all_lung(180;1.33e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.172)		OV - Ovarian serous cystadenocarcinoma(18;2.1e-17)|GBM - Glioblastoma multiforme(113;1.34e-06)|Colorectal(105;0.0148)|BRCA - Breast invasive adenocarcinoma(123;0.113)		ATCCCAAAGTCCCCAATCTTG	0.572										TSP Lung(18;0.14)																											p.D664fs		Atlas-INDEL	.											.	LTK	117	.	0			c.1991delA						.						45.0	45.0	45.0					15																	41797198		2203	4300	6503	SO:0001589	frameshift_variant	4058	exon16			.	D16105	CCDS10077.1, CCDS10078.1, CCDS45237.1	15q15.1-q21.1	2009-07-10	2008-01-23		ENSG00000062524	ENSG00000062524	2.7.10.1		6721	protein-coding gene	gene with protein product		151520	"""leukocyte tyrosine kinase"""			2320375	Standard	NM_206961		Approved	TYK1	uc001zoa.3	P29376	OTTHUMG00000130339	ENST00000263800.6:c.1990delG	chr15.hg19:g.41797198delC	ENSP00000263800:p.Asp664fs	127.0	0.0		140.0	10.0	NM_002344	A6NNJ8|B4DL89|E9PFX4	Frame_Shift_Del	DEL	ENST00000263800.6	hg19	CCDS10077.1																																																																																			.	.		0.572	LTK-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252690.2		
ATG2B	55102	hgsc.bcm.edu	37	14	96807965	96807965	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr14:96807965delT	ENST00000359933.4	-	6	1711	c.818delA	c.(817-819)aatfs	p.N273fs		NM_018036.5	NP_060506	Q96BY7	ATG2B_HUMAN	autophagy related 2B	273					autophagic vacuole assembly (GO:0000045)|cellular response to nitrogen starvation (GO:0006995)|mitochondrion degradation (GO:0000422)|nucleophagy (GO:0044804)	extrinsic component of membrane (GO:0019898)|lipid particle (GO:0005811)|pre-autophagosomal structure (GO:0000407)				breast(3)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(11)|liver(1)|lung(26)|ovary(1)|prostate(1)|skin(1)|urinary_tract(7)	64		all_cancers(154;0.0462)|all_epithelial(191;0.123)|Melanoma(154;0.155)		Epithelial(152;0.21)|COAD - Colon adenocarcinoma(157;0.244)		CTCTGGTAAATTTCTAGTTAG	0.418																																					p.N273fs		Atlas-INDEL	.											.	ATG2B	169	.	0			c.819delT						.						135.0	129.0	131.0					14																	96807965		1883	4109	5992	SO:0001589	frameshift_variant	55102	exon6			.	AK001104	CCDS9944.2	14q32.31	2014-02-12	2012-06-06	2007-07-31	ENSG00000066739	ENSG00000066739			20187	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 103"", ""ATG2 autophagy related 2 homolog B (S. cerevisiae)"""	C14orf103		22350415	Standard	NM_018036		Approved	FLJ10242	uc001yfi.3	Q96BY7	OTTHUMG00000149933	ENST00000359933.4:c.818delA	chr14.hg19:g.96807965delT	ENSP00000353010:p.Asn273fs	95.0	0.0		103.0	10.0	NM_018036	Q6ZRE7|Q96DQ3|Q9NW80	Frame_Shift_Del	DEL	ENST00000359933.4	hg19	CCDS9944.2																																																																																			.	.		0.418	ATG2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314037.1	NM_018036	
C5orf51	285636	hgsc.bcm.edu	37	5	41909898	41909898	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:41909898delT	ENST00000381647.2	+	3	277	c.258delT	c.(256-258)gatfs	p.D86fs	C5orf51_ENST00000505931.2_3'UTR	NM_175921.4	NP_787117.3	A6NDU8	CE051_HUMAN	chromosome 5 open reading frame 51	86										endometrium(1)|large_intestine(5)|lung(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	11						TAGATGAAGATTTTCCTGAAG	0.279																																					p.D86fs		Atlas-INDEL	.											.	C5orf51	28	.	0			c.257delA						.						45.0	49.0	48.0					5																	41909898		2198	4286	6484	SO:0001589	frameshift_variant	285636	exon3			.	AL833916, AK094002	CCDS34151.1	5p13.1	2008-07-18			ENSG00000205765	ENSG00000205765			27750	protein-coding gene	gene with protein product						14702039	Standard	NM_175921		Approved	LOC285636	uc003jmo.3	A6NDU8	OTTHUMG00000162084	ENST00000381647.2:c.258delT	chr5.hg19:g.41909898delT	ENSP00000371061:p.Asp86fs	129.0	0.0		172.0	13.0	NM_175921	A2RRM9	Frame_Shift_Del	DEL	ENST00000381647.2	hg19	CCDS34151.1																																																																																			.	.		0.279	C5orf51-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367144.1	NM_175921	
DACH1	1602	hgsc.bcm.edu	37	13	72440861	72440861	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr13:72440861delG	ENST00000359684.2	-	1	46	c.47delC	c.(46-48)cctfs	p.P16fs	DACH1_ENST00000305425.4_Frame_Shift_Del_p.P16fs|DACH1_ENST00000313174.7_Frame_Shift_Del_p.P16fs|DACH1_ENST00000354591.4_Frame_Shift_Del_p.P16fs			Q9UI36	DACH1_HUMAN	dachshund family transcription factor 1	16					cell proliferation (GO:0008283)|development of primary female sexual characteristics (GO:0046545)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation involved in contact inhibition (GO:0060244)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of transcription by competitive promoter binding (GO:0010944)|respiratory gaseous exchange (GO:0007585)|suckling behavior (GO:0001967)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity involved in preinitiation complex assembly (GO:0001075)	p.P16fs*180(1)		NS(1)|breast(2)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(23)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	41		Acute lymphoblastic leukemia(28;0.0503)|Breast(118;0.198)		GBM - Glioblastoma multiforme(99;0.00032)		TGGGGGTTGAGGGGGGACCAG	0.622																																					p.P16fs		Atlas-INDEL	.											.	DACH1	123	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.48delT						.						22.0	29.0	27.0					13																	72440861		2017	4176	6193	SO:0001589	frameshift_variant	1602	exon1			.	AJ005670	CCDS41899.1, CCDS53874.1, CCDS53873.1	13q22	2014-02-03	2014-02-03	2004-04-02	ENSG00000165659	ENSG00000276644			2663	protein-coding gene	gene with protein product		603803	"""dachshund homolog (Drosophila)"", ""dachshund homolog 1 (Drosophila)"""	DACH		9933575, 10395809, 15057823	Standard	NM_004392		Approved		uc021rkj.1	Q9UI36	OTTHUMG00000017063	ENST00000359684.2:c.47delC	chr13.hg19:g.72440861delG	ENSP00000352712:p.Pro16fs	182.0	0.0		179.0	11.0	NM_080759	D0FY35|D0FY36|O75523|O75687|Q5VYY3|Q5VYY4|Q96SG3|Q96SG4|Q9H524|Q9UMH4	Frame_Shift_Del	DEL	ENST00000359684.2	hg19																																																																																				.	.		0.622	DACH1-002	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000045240.1	NM_004392	
MYH3	4621	hgsc.bcm.edu	37	17	10535885	10535885	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:10535885delC	ENST00000583535.1	-	34	4951	c.4864delG	c.(4864-4866)gacfs	p.D1622fs	MYH3_ENST00000226209.7_Frame_Shift_Del_p.D1622fs	NM_002470.3	NP_002461.2	P11055	MYH3_HUMAN	myosin, heavy chain 3, skeletal muscle, embryonic	1622			D -> A (in DA2B). {ECO:0000269|PubMed:16642020}.		actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|embryonic limb morphogenesis (GO:0030326)|face morphogenesis (GO:0060325)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|sarcomere organization (GO:0045214)|skeletal muscle contraction (GO:0003009)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)	p.D1622N(1)		breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(5)|large_intestine(18)|lung(30)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	83						TCATTCAGGTCCCCCTCCATC	0.587																																					p.D1622fs		Atlas-INDEL	.											.	MYH3	227	.	1	Substitution - Missense(1)	lung(1)	c.4865delA						.						210.0	206.0	207.0					17																	10535885		2203	4300	6503	SO:0001589	frameshift_variant	4621	exon34			.		CCDS11157.1	17p13.1	2013-09-19	2006-09-29		ENSG00000109063	ENSG00000109063		"""Myosins / Myosin superfamily : Class II"""	7573	protein-coding gene	gene with protein product	"""myosin, skeletal, heavy chain, embryonic 1"", ""muscle embryonic myosin heavy chain 3"""	160720	"""myosin, heavy polypeptide 3, skeletal muscle, embryonic"""			2726495	Standard	NM_002470		Approved	MYHC-EMB, MYHSE1, HEMHC, SMHCE	uc002gmq.2	P11055	OTTHUMG00000130367	ENST00000583535.1:c.4864delG	chr17.hg19:g.10535885delC	ENSP00000464317:p.Asp1622fs	123.0	0.0		135.0	10.0	NM_002470	Q15492	Frame_Shift_Del	DEL	ENST00000583535.1	hg19	CCDS11157.1																																																																																			.	.		0.587	MYH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252734.2	NM_002470	
COL11A2	1302	hgsc.bcm.edu	37	6	33139837	33139837	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:33139837delG	ENST00000374708.4	-	39	3032	c.2774delC	c.(2773-2775)cctfs	p.P925fs	COL11A2_ENST00000374713.1_Frame_Shift_Del_p.P964fs|COL11A2_ENST00000361917.1_Frame_Shift_Del_p.P904fs|COL11A2_ENST00000374714.1_Frame_Shift_Del_p.P985fs|COL11A2_ENST00000357486.1_Frame_Shift_Del_p.P990fs|COL11A2_ENST00000341947.2_Frame_Shift_Del_p.P1011fs|COL11A2_ENST00000395197.1_Frame_Shift_Del_p.P951fs|COL11A2_ENST00000477772.1_Intron|COL11A2_ENST00000374712.1_Frame_Shift_Del_p.P930fs	NM_080681.2	NP_542412.2	P13942	COBA2_HUMAN	collagen, type XI, alpha 2	1011	Triple-helical region.				cartilage development (GO:0051216)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|palate development (GO:0060021)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|soft palate development (GO:0060023)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)			biliary_tract(1)|breast(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|liver(1)|lung(27)|ovary(5)|prostate(5)|skin(6)	68						TGCAGGGCCAGGGGGGCCAGA	0.582																																					p.P1011fs	Melanoma(1;90 116 3946 5341 17093)	Atlas-INDEL	.											.	COL11A2	124	.	0			c.3033delT						.						128.0	161.0	149.0					6																	33139837		1508	2706	4214	SO:0001589	frameshift_variant	1302	exon41			.	U32169	CCDS43452.1, CCDS54992.1	6p21.3	2013-01-16			ENSG00000204248	ENSG00000204248		"""Collagens"""	2187	protein-coding gene	gene with protein product		120290		DFNA13, DFNB53		7559422, 10581026	Standard	NM_080679		Approved	HKE5	uc003ocx.1	P13942	OTTHUMG00000031036	ENST00000374708.4:c.2774delC	chr6.hg19:g.33139837delG	ENSP00000363840:p.Pro925fs	96.0	0.0		199.0	12.0	NM_080680	A6NLX2|E7ER90|Q07751|Q13271|Q13272|Q13273|Q5JP94|Q5SUI8|Q7Z6C3|Q99866|Q9UIP9	Frame_Shift_Del	DEL	ENST00000374708.4	hg19	CCDS43452.1																																																																																			.	.		0.582	COL11A2-001	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076032.2		
CHPF2	54480	hgsc.bcm.edu	37	7	150932436	150932436	+	Frame_Shift_Del	DEL	C	C	-	rs146139489	byFrequency	TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:150932436delC	ENST00000035307.2	+	2	2079	c.566delC	c.(565-567)gccfs	p.A189fs	CHPF2_ENST00000495645.1_Frame_Shift_Del_p.A181fs	NM_019015.1	NP_061888.1	Q9P2E5	CHPF2_HUMAN	chondroitin polymerizing factor 2	189					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	acetylgalactosaminyltransferase activity (GO:0008376)|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity (GO:0050510)			breast(1)|endometrium(2)|large_intestine(3)|lung(3)|ovary(4)|prostate(1)|skin(3)	17						TATGTGCAGGCCCCCCGCCTG	0.617																																					p.A189fs		Atlas-INDEL	.											.	CHPF2	52	.	0			c.565delG						.						90.0	93.0	92.0					7																	150932436		2203	4300	6503	SO:0001589	frameshift_variant	54480	exon2			.	AB037823	CCDS34779.1, CCDS64803.1	7q36.1	2013-02-19			ENSG00000033100	ENSG00000033100	2.4.1.226	"""Beta 3-glycosyltransferases"", ""Beta 4-glycosyltransferases"""	29270	protein-coding gene	gene with protein product		608037				10718198, 12145278, 18316376	Standard	NM_019015		Approved	KIAA1402, ChSy-3, CSGlcA-T	uc003wjr.1	Q9P2E5	OTTHUMG00000157380	ENST00000035307.2:c.566delC	chr7.hg19:g.150932436delC	ENSP00000035307:p.Ala189fs	94.0	0.0		107.0	10.0	NM_019015	B2DBD8|Q6P2I4|Q6UXD2	Frame_Shift_Del	DEL	ENST00000035307.2	hg19	CCDS34779.1																																																																																			.	.		0.617	CHPF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348648.2	NM_019015	
MTOR	2475	hgsc.bcm.edu	37	1	11292498	11292498	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:11292498delT	ENST00000361445.4	-	16	2585	c.2509delA	c.(2509-2511)aggfs	p.R837fs		NM_004958.3	NP_004949.1	P42345	MTOR_HUMAN	mechanistic target of rapamycin (serine/threonine kinase)	837					cell growth (GO:0016049)|cellular response to hypoxia (GO:0071456)|cellular response to nutrient levels (GO:0031669)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell development (GO:0007281)|growth (GO:0040007)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|negative regulation of autophagy (GO:0010507)|negative regulation of cell size (GO:0045792)|negative regulation of macroautophagy (GO:0016242)|negative regulation of NFAT protein import into nucleus (GO:0051534)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|phosphatidylinositol-mediated signaling (GO:0048015)|phosphorylation (GO:0016310)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of gene expression (GO:0010628)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of myotube differentiation (GO:0010831)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein catabolic process (GO:0030163)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of carbohydrate utilization (GO:0043610)|regulation of fatty acid beta-oxidation (GO:0031998)|regulation of glycogen biosynthetic process (GO:0005979)|regulation of protein kinase activity (GO:0045859)|regulation of Rac GTPase activity (GO:0032314)|regulation of response to food (GO:0032095)|response to amino acid (GO:0043200)|response to nutrient (GO:0007584)|response to stress (GO:0006950)|ruffle organization (GO:0031529)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endomembrane system (GO:0012505)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|phosphatidylinositol 3-kinase complex (GO:0005942)|PML body (GO:0016605)|TORC1 complex (GO:0031931)|TORC2 complex (GO:0031932)	ATP binding (GO:0005524)|drug binding (GO:0008144)|kinase activity (GO:0016301)|phosphoprotein binding (GO:0051219)|protein serine/threonine kinase activity (GO:0004674)|ribosome binding (GO:0043022)|RNA polymerase III type 1 promoter DNA binding (GO:0001030)|RNA polymerase III type 2 promoter DNA binding (GO:0001031)|RNA polymerase III type 3 promoter DNA binding (GO:0001032)|TFIIIC-class transcription factor binding (GO:0001156)			breast(5)|central_nervous_system(7)|endometrium(20)|kidney(34)|large_intestine(21)|lung(43)|ovary(9)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	149					Everolimus(DB01590)|Pimecrolimus(DB00337)|Sirolimus(DB00877)|Temsirolimus(DB06287)	CTCACCTGCCTTTTGGCCAAC	0.448																																					p.R837fs		Atlas-INDEL	.											.	MTOR	327	.	0			c.2510delG						.						135.0	127.0	129.0					1																	11292498		2203	4300	6503	SO:0001589	frameshift_variant	2475	exon16			.	L34075	CCDS127.1	1p36	2014-09-17	2009-05-29	2009-05-29	ENSG00000198793	ENSG00000198793			3942	protein-coding gene	gene with protein product	"""FK506 binding protein 12-rapamycin associated protein 2"", ""rapamycin target protein"", ""FKBP12-rapamycin complex-associated protein 1"", ""FKBP-rapamycin associated protein"", ""rapamycin associated protein FRAP2"", ""dJ576K7.1 (FK506 binding protein 12-rapamycin associated protein 1)"", ""rapamycin and FKBP12 target 1"", ""mammalian target of rapamycin"""	601231	"""FK506 binding protein 12-rapamycin associated protein 1"""	FRAP, FRAP2, FRAP1		8008069, 8660990	Standard	NM_004958		Approved	RAFT1, RAPT1, FLJ44809	uc001asd.3	P42345	OTTHUMG00000002001	ENST00000361445.4:c.2509delA	chr1.hg19:g.11292498delT	ENSP00000354558:p.Arg837fs	138.0	0.0		138.0	11.0	NM_004958	Q4LE76|Q5TER1|Q6LE87|Q96QG3|Q9Y4I3	Frame_Shift_Del	DEL	ENST00000361445.4	hg19	CCDS127.1																																																																																			.	.		0.448	MTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005558.1	NM_004958	
CP	1356	hgsc.bcm.edu	37	3	148927955	148927955	+	Splice_Site	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:148927955delT	ENST00000264613.6	-	3	868	c.606delA	c.(604-606)aaa>aa	p.K202fs		NM_000096.3	NP_000087	P00450	CERU_HUMAN	ceruloplasmin (ferroxidase)	202	F5/8 type A 1.				cellular iron ion homeostasis (GO:0006879)|copper ion transport (GO:0006825)|transmembrane transport (GO:0055085)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)	chaperone binding (GO:0051087)|copper ion binding (GO:0005507)|ferroxidase activity (GO:0004322)			breast(6)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|prostate(1)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	44		Prostate(884;0.00217)|Hepatocellular(537;0.00826)|Myeloproliferative disorder(1037;0.0122)|all_neural(597;0.0189)|Melanoma(1037;0.152)	LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)		Drotrecogin alfa(DB00055)	AAGATGTACCTTTTTTACAGA	0.398																																					p.D203fs		Atlas-INDEL	.											.	CP	112	.	0			c.607delG						.						132.0	119.0	124.0					3																	148927955		2203	4300	6503	SO:0001630	splice_region_variant	1356	exon3			.	M13536	CCDS3141.1	3q23-q25	2010-07-01			ENSG00000047457	ENSG00000047457	1.16.3.1		2295	protein-coding gene	gene with protein product		117700					Standard	NM_000096		Approved		uc003ewy.4	P00450	OTTHUMG00000159563	ENST00000264613.6:c.607+1A>-	chr3.hg19:g.148927955delT		112.0	0.0		139.0	10.0	NM_000096	Q14063|Q2PP18|Q9UKS4	Frame_Shift_Del	DEL	ENST00000264613.6	hg19	CCDS3141.1																																																																																			.	.		0.398	CP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317498.1	NM_000096	Frame_Shift_Del
TBCCD1	55171	hgsc.bcm.edu	37	3	186272330	186272330	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:186272330delA	ENST00000424280.1	-	6	1736	c.1257delT	c.(1255-1257)tttfs	p.F419fs	TBCCD1_ENST00000338733.5_Frame_Shift_Del_p.F419fs|TBCCD1_ENST00000446782.1_Frame_Shift_Del_p.F323fs|TBCCD1_ENST00000479590.1_5'Flank	NM_001134415.1	NP_001127887.1	Q9NVR7	TBCC1_HUMAN	TBCC domain containing 1	419	C-CAP/cofactor C-like. {ECO:0000255|PROSITE-ProRule:PRU00659}.				cell morphogenesis (GO:0000902)|cytoskeleton organization (GO:0007010)|maintenance of centrosome location (GO:0051661)|maintenance of Golgi location (GO:0051684)|regulation of cell migration (GO:0030334)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|spindle pole centrosome (GO:0031616)				breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(4)|ovary(1)|skin(1)	17	all_cancers(143;3.75e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;4.3e-21)	GBM - Glioblastoma multiforme(93;0.0474)		AATGTGTATGAAAAGGGGCAA	0.463																																					p.H420fs		Atlas-INDEL	.											.	TBCCD1	42	.	0			c.1258delC						.						98.0	93.0	95.0					3																	186272330		2203	4300	6503	SO:0001589	frameshift_variant	55171	exon6			.	BC025748	CCDS3276.1, CCDS75061.1	3q27.3	2006-03-09			ENSG00000113838	ENSG00000113838			25546	protein-coding gene	gene with protein product						12477932	Standard	NM_001134415		Approved	FLJ10560	uc003fqg.3	Q9NVR7	OTTHUMG00000156613	ENST00000424280.1:c.1257delT	chr3.hg19:g.186272330delA	ENSP00000411253:p.Phe419fs	85.0	0.0		113.0	10.0	NM_001134415	B3KW69|D3DNU6|G5E9J4	Frame_Shift_Del	DEL	ENST00000424280.1	hg19	CCDS3276.1																																																																																			.	.		0.463	TBCCD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344774.1	NM_018138	
CSPG4	1464	hgsc.bcm.edu	37	15	75980311	75980311	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:75980311delC	ENST00000308508.5	-	3	3187	c.3095delG	c.(3094-3096)ggtfs	p.G1033fs		NM_001897.4	NP_001888.2	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4	1033	Gly/Ser-rich (glycosaminoglycan attachment domain).|Interaction with COL5A1. {ECO:0000250}.|Interaction with COL6A2. {ECO:0000250}.				activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|carbohydrate metabolic process (GO:0005975)|cell proliferation (GO:0008283)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|intracellular signal transduction (GO:0035556)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|small molecule metabolic process (GO:0044281)|tissue remodeling (GO:0048771)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell projection (GO:0042995)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			breast(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(3)|liver(2)|lung(18)|ovary(2)|pancreas(2)|prostate(4)|skin(4)	48						CCGCCGCCCACCCCGGGCCAC	0.647																																					p.G1032fs		Atlas-INDEL	.											.	CSPG4	175	.	0			c.3096delT						.						34.0	39.0	38.0					15																	75980311		2197	4293	6490	SO:0001589	frameshift_variant	1464	exon3			.	X96753, AY359468	CCDS10284.1	15q24.2	2010-04-19	2007-02-16		ENSG00000173546	ENSG00000173546		"""Proteoglycans / Cell surface : Other"""	2466	protein-coding gene	gene with protein product	"""melanoma-associated chondroitin sulfate proteoglycan"""	601172	"""chondroitin sulfate proteoglycan 4 (melanoma-associated)"""			8790396, 16407841	Standard	NM_001897		Approved	MCSPG, MEL-CSPG, MSK16, NG2, MCSP, HMW-MAA	uc002baw.3	Q6UVK1	OTTHUMG00000142836	ENST00000308508.5:c.3095delG	chr15.hg19:g.75980311delC	ENSP00000312506:p.Gly1033fs	114.0	0.0		130.0	10.0	NM_001897	D3DW77|Q92675	Frame_Shift_Del	DEL	ENST00000308508.5	hg19	CCDS10284.1																																																																																			.	.		0.647	CSPG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286472.1	NM_001897	
TPM3	7170	hgsc.bcm.edu	37	1	154148611	154148611	+	Frame_Shift_Del	DEL	T	T	-	rs35013279		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:154148611delT	ENST00000368530.2	-	3	549	c.357delA	c.(355-357)aaafs	p.K119fs	TPM3_ENST00000302206.5_5'UTR|TPM3_ENST00000368531.2_Frame_Shift_Del_p.K82fs|TPM3_ENST00000469717.1_Intron|TPM3_ENST00000271850.7_Frame_Shift_Del_p.K119fs|TPM3_ENST00000341372.3_Frame_Shift_Del_p.K57fs|TPM3_ENST00000328159.4_Frame_Shift_Del_p.K82fs|TPM3_ENST00000368533.3_Frame_Shift_Del_p.K82fs|TPM3_ENST00000341485.5_Frame_Shift_Del_p.K82fs|TPM3_ENST00000323144.7_Frame_Shift_Del_p.K82fs|TPM3_ENST00000330188.9_Frame_Shift_Del_p.K82fs	NM_152263.2	NP_689476.2	P06753	TPM3_HUMAN	tropomyosin 3	119					cellular component movement (GO:0006928)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle thin filament tropomyosin (GO:0005862)|stress fiber (GO:0001725)			TPM3/NTRK1_ENST00000392302(70)|TPM3/ALK(33)	breast(1)|endometrium(1)|large_intestine(2)|lung(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11	all_lung(78;9.35e-31)|Lung NSC(65;1.33e-28)|Hepatocellular(266;0.0877)|Melanoma(130;0.128)					CATCAGCAGCTTTTTCAGCTT	0.483			T	"""NTRK1, ALK, ROS1"""	"""papillary thyroid, ALCL, NSCLC"""																																p.A120fs		Atlas-INDEL	.		Dom	yes		1	1q22-q23	7170	tropomyosin 3		"""E, L"""	.	TPM3	46	.	0			c.358delG						.						133.0	125.0	127.0					1																	154148611		2203	4300	6503	SO:0001589	frameshift_variant	7170	exon3			.	BC008425	CCDS1060.1, CCDS41400.1, CCDS41401.1, CCDS41402.1, CCDS41403.1, CCDS60274.1, CCDS60275.1, CCDS72922.1	1q21.2	2014-09-17			ENSG00000143549	ENSG00000143549		"""Tropomyosins"""	12012	protein-coding gene	gene with protein product		191030		NEM1		1829807	Standard	NM_153649		Approved	TRK	uc001fec.2	P06753	OTTHUMG00000035853	ENST00000368530.2:c.357delA	chr1.hg19:g.154148611delT	ENSP00000357516:p.Lys119fs	148.0	0.0		247.0	16.0	NM_152263	D3DV71|P12324|Q2QD06|Q5VU58|Q5VU63|Q5VU66|Q5VU71|Q5VU72|Q8TCG3|Q969Q2|Q9NQH8	Frame_Shift_Del	DEL	ENST00000368530.2	hg19	CCDS41403.1																																																																																			.	.		0.483	TPM3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000087271.2	NM_152263	
MAP2K6	5608	hgsc.bcm.edu	37	17	67537867	67537867	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:67537867delT	ENST00000590474.1	+	12	1265	c.978delT	c.(976-978)tctfs	p.S326fs	MAP2K6_ENST00000589647.1_Frame_Shift_Del_p.S270fs	NM_002758.3	NP_002749.2	P52564	MP2K6_HUMAN	mitogen-activated protein kinase kinase 6	326	DVD domain.				activation of MAPK activity (GO:0000187)|apoptotic process (GO:0006915)|cardiac muscle contraction (GO:0060048)|cell cycle arrest (GO:0007050)|cellular response to sorbitol (GO:0072709)|DNA damage induced protein phosphorylation (GO:0006975)|innate immune response (GO:0045087)|muscle cell differentiation (GO:0042692)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of apoptotic process (GO:0043065)|positive regulation of muscle cell differentiation (GO:0051149)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)|response to ischemia (GO:0002931)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription, DNA-templated (GO:0006351)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|MAP kinase kinase activity (GO:0004708)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)			central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|stomach(1)	20	Breast(10;6.05e-10)					ATGTGGCATCTTTTGTAAAAC	0.393																																					p.S326fs		Atlas-INDEL	.											.	MAP2K6	41	.	0			c.977delC						.						122.0	114.0	117.0					17																	67537867		2203	4300	6503	SO:0001589	frameshift_variant	5608	exon12			.	U39064	CCDS11686.1	17q	2011-06-09						"""Mitogen-activated protein kinase cascade / Kinase kinases"""	6846	protein-coding gene	gene with protein product	"""protein kinase, mitogen-activated, kinase 6 (MAP kinase kinase 6)"""	601254		PRKMK6		8621675	Standard	XM_005257515		Approved	MEK6, MKK6, SAPKK3, MAPKK6	uc002jij.3	P52564		ENST00000590474.1:c.978delT	chr17.hg19:g.67537867delT	ENSP00000468348:p.Ser326fs	163.0	0.0		171.0	11.0	NM_002758		Frame_Shift_Del	DEL	ENST00000590474.1	hg19	CCDS11686.1																																																																																			.	.		0.393	MAP2K6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450689.1	NM_002758	
NYAP2	57624	hgsc.bcm.edu	37	2	226491650	226491650	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:226491650delA	ENST00000272907.6	+	5	2049	c.1636delA	c.(1636-1638)aaafs	p.K546fs	NYAP2_ENST00000409269.2_Frame_Shift_Del_p.E80fs	NM_020864.1	NP_065915.1	Q9P242	NYAP2_HUMAN	neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 2	546					neuron projection morphogenesis (GO:0048812)|phosphatidylinositol 3-kinase signaling (GO:0014065)												AGAGGAACTGAAAGTCCGAAG	0.423																																					p.L545fs		Atlas-INDEL	.											.	.	.	.	0			c.1635delG						.						23.0	24.0	24.0					2																	226491650		1874	4099	5973	SO:0001589	frameshift_variant	57624	exon5			.	AB040919	CCDS46529.1	2q36.3	2011-11-30	2011-11-30	2011-11-30	ENSG00000144460	ENSG00000144460			29291	protein-coding gene	gene with protein product		615478	"""KIAA1486"""	KIAA1486		10819331, 21946561	Standard	NM_020864		Approved		uc002voe.2	Q9P242	OTTHUMG00000153450	ENST00000272907.6:c.1636delA	chr2.hg19:g.226491650delA	ENSP00000272907:p.Lys546fs	104.0	0.0		148.0	10.0	NM_020864	A2RRN4|Q96NL2	Frame_Shift_Del	DEL	ENST00000272907.6	hg19	CCDS46529.1																																																																																			.	.		0.423	NYAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331258.1	NM_020864	
MEF2A	4205	hgsc.bcm.edu	37	15	100252908	100252908	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:100252908delC	ENST00000557785.1	+	11	1775	c.1426delC	c.(1426-1428)cccfs	p.P477fs	MEF2A_ENST00000453228.2_Frame_Shift_Del_p.P477fs|MEF2A_ENST00000338042.6_Frame_Shift_Del_p.P486fs|MEF2A_ENST00000557942.1_Frame_Shift_Del_p.P485fs|MEF2A_ENST00000354410.5_Frame_Shift_Del_p.P479fs|LYSMD4_ENST00000604213.1_5'Flank|MEF2A_ENST00000449277.2_Frame_Shift_Del_p.P409fs|MEF2A_ENST00000558812.1_Frame_Shift_Del_p.P417fs	NM_001171894.1	NP_001165365.1	Q02078	MEF2A_HUMAN	myocyte enhancer factor 2A	487					apoptotic process (GO:0006915)|cardiac conduction (GO:0061337)|cellular response to calcium ion (GO:0071277)|dendrite morphogenesis (GO:0048813)|ERK5 cascade (GO:0070375)|heart development (GO:0007507)|innate immune response (GO:0045087)|MAPK cascade (GO:0000165)|mitochondrial genome maintenance (GO:0000002)|mitochondrion distribution (GO:0048311)|muscle cell differentiation (GO:0042692)|muscle organ development (GO:0007517)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|ventricular cardiac myofibril assembly (GO:0055005)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|histone acetyltransferase binding (GO:0035035)|histone deacetylase binding (GO:0042826)|protein heterodimerization activity (GO:0046982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|SMAD binding (GO:0046332)			endometrium(2)|large_intestine(2)|lung(7)|ovary(1)	12	Lung NSC(78;0.00335)|all_lung(78;0.00659)|Melanoma(26;0.00778)|Medulloblastoma(229;0.163)		OV - Ovarian serous cystadenocarcinoma(32;0.00085)			GCTTGGCCGACCCCCAAACAC	0.532																																					p.R477fs		Atlas-INDEL	.											.	MEF2A	138	.	0			c.1431delA						.						37.0	40.0	39.0					15																	100252908		2046	4187	6233	SO:0001589	frameshift_variant	4205	exon11			.		CCDS45362.1, CCDS45363.1, CCDS53978.1, CCDS58401.1	15q26	2008-02-05	2007-04-24			ENSG00000068305		"""Myocyte enhancer factors"""	6993	protein-coding gene	gene with protein product		600660				1516833	Standard	NM_005587		Approved	RSRFC4, RSRFC9	uc002bvf.3	Q02078		ENST00000557785.1:c.1426delC	chr15.hg19:g.100252908delC	ENSP00000453441:p.Pro477fs	193.0	0.0		195.0	12.0	NM_005587	B4DFQ7|F6XG23|O43814|Q14223|Q14224|Q59GX4|Q7Z6C9|Q96D14	Frame_Shift_Del	DEL	ENST00000557785.1	hg19	CCDS53978.1																																																																																			.	.		0.532	MEF2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415985.1		
TUBA3E	112714	hgsc.bcm.edu	37	2	130951451	130951451	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:130951451delC	ENST00000312988.7	-	4	1064	c.964delG	c.(964-966)gacfs	p.D322fs		NM_207312.2	NP_997195	Q6PEY2	TBA3E_HUMAN	tubulin, alpha 3e	322					microtubule-based process (GO:0007017)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			endometrium(4)|kidney(7)|large_intestine(6)|lung(9)|skin(2)	28	Colorectal(110;0.1)					GGGACCACGTCCCCCCTGTAC	0.557																																					p.D322fs		Atlas-INDEL	.											.	TUBA3E	73	.	0			c.965delA						.						154.0	134.0	141.0					2																	130951451		2203	4300	6503	SO:0001589	frameshift_variant	112714	exon4			.	BC057811	CCDS2158.1	2q21.1	2007-03-16			ENSG00000152086	ENSG00000152086		"""Tubulins"""	20765	protein-coding gene	gene with protein product							Standard	NM_207312		Approved		uc002tqv.3	Q6PEY2	OTTHUMG00000131626	ENST00000312988.7:c.964delG	chr2.hg19:g.130951451delC	ENSP00000318197:p.Asp322fs	169.0	0.0		231.0	14.0	NM_207312		Frame_Shift_Del	DEL	ENST00000312988.7	hg19	CCDS2158.1																																																																																			.	.		0.557	TUBA3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254519.1	NM_207312	
ABCC5	10057	hgsc.bcm.edu	37	3	183699624	183699624	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:183699624delT	ENST00000334444.6	-	8	1278	c.1038delA	c.(1036-1038)aaafs	p.K346fs	ABCC5_ENST00000492216.1_5'UTR|ABCC5_ENST00000265586.6_Frame_Shift_Del_p.K346fs	NM_005688.2	NP_005679.2	O15440	MRP5_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 5	346	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan biosynthetic process (GO:0030213)|hyaluronan metabolic process (GO:0030212)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(32)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	62	all_cancers(143;1.85e-10)|Ovarian(172;0.0303)		Epithelial(37;1.74e-35)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)		Adefovir Dipivoxil(DB00718)|Alprostadil(DB00770)|Atorvastatin(DB01076)|Cisplatin(DB00515)|Dinoprostone(DB00917)|Dipyridamole(DB00975)|Fluorouracil(DB00544)|Glutathione(DB00143)|Mercaptopurine(DB01033)|Probenecid(DB01032)|Rifampicin(DB01045)|Sildenafil(DB00203)|Sulfinpyrazone(DB01138)|Zidovudine(DB00495)	CGGCCACGCATTTTCTCCTGA	0.408																																					p.C347fs		Atlas-INDEL	.											.	ABCC5	142	.	0			c.1039delT						.						52.0	51.0	51.0					3																	183699624		1882	4111	5993	SO:0001589	frameshift_variant	10057	exon8			.	AF104942	CCDS33898.1, CCDS43176.1	3q27	2012-03-14			ENSG00000114770	ENSG00000114770		"""ATP binding cassette transporters / subfamily C"""	56	protein-coding gene	gene with protein product		605251				8894702, 9827529	Standard	XM_005247058		Approved	MRP5, SMRP, EST277145, MOAT-C	uc003fmg.3	O15440	OTTHUMG00000156871	ENST00000334444.6:c.1038delA	chr3.hg19:g.183699624delT	ENSP00000333926:p.Lys346fs	106.0	0.0		165.0	12.0	NM_005688	B9EIQ2|O14517|Q29ZA9|Q29ZB1|Q86UX3|Q86W30|Q9UN85|Q9UNP5|Q9UQC3	Frame_Shift_Del	DEL	ENST00000334444.6	hg19	CCDS43176.1																																																																																			.	.		0.408	ABCC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346350.1	NM_005688	
CNOT11	55571	hgsc.bcm.edu	37	2	101885729	101885729	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:101885729delA	ENST00000289382.3	+	7	1550	c.1387delA	c.(1387-1389)aaafs	p.K463fs	RNF149_ENST00000485752.1_5'Flank	NM_017546.4	NP_060016.3	Q9UKZ1	CNO11_HUMAN	CCR4-NOT transcription complex, subunit 11	463					cell proliferation (GO:0008283)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|transcription, DNA-templated (GO:0006351)	CCR4-NOT complex (GO:0030014)|cytosol (GO:0005829)|nucleus (GO:0005634)											GATCCGTAACAAAATTATTAA	0.393																																					p.N462fs		Atlas-INDEL	.											.	.	.	.	0			c.1386delC						.						79.0	83.0	81.0					2																	101885729		2203	4300	6503	SO:0001589	frameshift_variant	55571	exon7			.	AF103798	CCDS2050.1	2q12.1	2013-01-24	2013-01-24	2013-01-24	ENSG00000158435	ENSG00000158435			25217	protein-coding gene	gene with protein product			"""chromosome 2 open reading frame 29"""	C2orf29		10497265, 23232451, 23303381	Standard	NM_017546		Approved	C40	uc002taw.4	Q9UKZ1	OTTHUMG00000130686	ENST00000289382.3:c.1387delA	chr2.hg19:g.101885729delA	ENSP00000289382:p.Lys463fs	130.0	0.0		161.0	10.0	NM_017546	Q6P2M9|Q8N681	Frame_Shift_Del	DEL	ENST00000289382.3	hg19	CCDS2050.1																																																																																			.	.		0.393	CNOT11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253181.1	NM_017546	
IDH1	3417	hgsc.bcm.edu	37	2	209110110	209110110	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:209110110delT	ENST00000415913.1	-	5	834	c.453delA	c.(451-453)aaafs	p.K151fs	IDH1_ENST00000345146.2_Frame_Shift_Del_p.K151fs|IDH1_ENST00000446179.1_Frame_Shift_Del_p.K151fs	NM_001282387.1	NP_001269316.1	O75874	IDHC_HUMAN	isocitrate dehydrogenase 1 (NADP+), soluble	151					2-oxoglutarate metabolic process (GO:0006103)|cellular lipid metabolic process (GO:0044255)|female gonad development (GO:0008585)|glutathione metabolic process (GO:0006749)|glyoxylate cycle (GO:0006097)|isocitrate metabolic process (GO:0006102)|NADPH regeneration (GO:0006740)|response to oxidative stress (GO:0006979)|response to steroid hormone (GO:0048545)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	isocitrate dehydrogenase (NADP+) activity (GO:0004450)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)			NS(1)|autonomic_ganglia(2)|biliary_tract(24)|bone(237)|central_nervous_system(3764)|endometrium(3)|haematopoietic_and_lymphoid_tissue(794)|kidney(2)|large_intestine(7)|lung(7)|prostate(6)|skin(5)|soft_tissue(12)|thyroid(22)|urinary_tract(1)	4887				Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)		TTATCTCTACTTTTCCAGGCC	0.388			Mis		gliobastoma																																p.V152X	Pancreas(158;264 1958 3300 35450 36047)	Atlas-INDEL	.		Dom	yes		2	2q33.3	3417	"""isocitrate dehydrogenase 1 (NADP+), soluble"""		O	.	IDH1	6310	.	0			c.454delG						.						152.0	137.0	142.0					2																	209110110		2203	4300	6503	SO:0001589	frameshift_variant	3417	exon5			.		CCDS2381.1	2q34	2014-09-17			ENSG00000138413	ENSG00000138413	1.1.1.42		5382	protein-coding gene	gene with protein product		147700					Standard	NM_005896		Approved		uc002vcu.3	O75874	OTTHUMG00000132943	ENST00000415913.1:c.453delA	chr2.hg19:g.209110110delT	ENSP00000390265:p.Lys151fs	147.0	0.0		208.0	13.0	NM_005896	Q567U4|Q6FHQ6|Q7Z3V0|Q93090|Q9NTJ9|Q9UKW8	Frame_Shift_Del	DEL	ENST00000415913.1	hg19	CCDS2381.1																																																																																			.	.		0.388	IDH1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336672.1		
C2orf71	388939	hgsc.bcm.edu	37	2	29294038	29294038	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:29294038delG	ENST00000331664.5	-	1	3089	c.3090delC	c.(3088-3090)cccfs	p.P1030fs		NM_001029883.2	NP_001025054.1	A6NGG8	CB071_HUMAN	chromosome 2 open reading frame 71	1030	Pro-rich.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	primary cilium (GO:0072372)				NS(2)|breast(5)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(11)|lung(20)|ovary(2)|prostate(6)|skin(3)|stomach(1)	60						CAGGTGGGCTGGGGGGCGTCT	0.667																																					p.S1031fs		Atlas-INDEL	.											.	C2orf71	146	.	0			c.3091delA						.						29.0	35.0	33.0					2																	29294038		1942	4118	6060	SO:0001589	frameshift_variant	388939	exon1			.		CCDS42669.1	2p23.2	2014-01-28			ENSG00000179270	ENSG00000179270			34383	protein-coding gene	gene with protein product		613425				20398886	Standard	NM_001029883		Approved	FLJ34931, RP54	uc002rmt.2	A6NGG8	OTTHUMG00000152024	ENST00000331664.5:c.3090delC	chr2.hg19:g.29294038delG	ENSP00000332809:p.Pro1030fs	128.0	0.0		190.0	12.0	NM_001029883		Frame_Shift_Del	DEL	ENST00000331664.5	hg19	CCDS42669.1																																																																																			.	.		0.667	C2orf71-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000324924.3	NM_001029883	
SEC14L4	284904	hgsc.bcm.edu	37	22	30890192	30890192	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr22:30890192delA	ENST00000255858.7	-	7	608	c.525delT	c.(523-525)tttfs	p.F175fs	SEC14L4_ENST00000392772.2_Frame_Shift_Del_p.F121fs|SEC14L4_ENST00000381982.3_Frame_Shift_Del_p.F175fs|SEC14L4_ENST00000540456.1_Frame_Shift_Del_p.F160fs|RP4-539M6.14_ENST00000442126.1_RNA|RP4-539M6.14_ENST00000610156.1_RNA	NM_001161368.1|NM_174977.3	NP_001154840.1|NP_777637.1	Q9UDX3	S14L4_HUMAN	SEC14-like 4 (S. cerevisiae)	175	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.					integral component of membrane (GO:0016021)|intracellular (GO:0005622)	lipid binding (GO:0008289)|transporter activity (GO:0005215)			breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(5)|pancreas(1)|skin(1)	21					Vitamin E(DB00163)	CCAGGATGCTAAAAAACTGTG	0.517																																					p.S176fs		Atlas-INDEL	.											.	SEC14L4	43	.	0			c.526delA						.						112.0	116.0	114.0					22																	30890192		2203	4300	6503	SO:0001589	frameshift_variant	284904	exon7			.	AY158085	CCDS13878.1, CCDS54517.1	22q12.1	2003-03-10			ENSG00000133488	ENSG00000133488			20627	protein-coding gene	gene with protein product		612825					Standard	NM_174977		Approved	TAP3, dJ130H16.5	uc003aid.2	Q9UDX3	OTTHUMG00000151258	ENST00000255858.7:c.525delT	chr22.hg19:g.30890192delA	ENSP00000255858:p.Phe175fs	145.0	0.0		199.0	12.0	NM_001161368	A5D6W7|A6NCV4	Frame_Shift_Del	DEL	ENST00000255858.7	hg19	CCDS13878.1																																																																																			.	.		0.517	SEC14L4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321946.1	NM_174977	
SYTL2	54843	hgsc.bcm.edu	37	11	85435856	85435856	+	Intron	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:85435856delT	ENST00000528231.1	-	7	1737				SYTL2_ENST00000316356.4_Intron|SYTL2_ENST00000525423.1_Frame_Shift_Del_p.K548fs|SYTL2_ENST00000527523.1_Intron|SYTL2_ENST00000524452.1_Intron|SYTL2_ENST00000354566.3_Frame_Shift_Del_p.K548fs|SYTL2_ENST00000389960.4_Intron|SYTL2_ENST00000359152.5_Frame_Shift_Del_p.K1072fs	NM_001162951.1|NM_001162953.1	NP_001156423.1|NP_001156425.1	Q9HCH5	SYTL2_HUMAN	synaptotagmin-like 2						exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of mucus secretion (GO:0070257)|vesicle docking involved in exocytosis (GO:0006904)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|exocytic vesicle (GO:0070382)|extrinsic component of plasma membrane (GO:0019897)|Golgi apparatus (GO:0005794)|melanosome (GO:0042470)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	neurexin family protein binding (GO:0042043)|phosphatase binding (GO:0019902)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(22)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	52		Acute lymphoblastic leukemia(157;4.19e-06)|all_hematologic(158;0.0033)		KIRC - Kidney renal clear cell carcinoma(183;0.202)|Kidney(183;0.237)		CACTTTCATATTTTGAGGGGA	0.418																																					p.Y549fs		Atlas-INDEL	.											.	SYTL2	231	.	0			c.1645delT						.						104.0	102.0	102.0					11																	85435856		2203	4299	6502	SO:0001627	intron_variant	54843	exon1			.	AJ303364	CCDS31649.1, CCDS31652.1, CCDS41698.1, CCDS53687.1, CCDS53688.1, CCDS53689.1	11q14.1	2014-06-13			ENSG00000137501	ENSG00000137501			15585	protein-coding gene	gene with protein product	"""chromosome 11 synaptotagmin"", ""breast cancer-associated antigen SGA-72M"", ""protein phosphatase 1, regulatory subunit 151"""	612880				10997877	Standard	XM_005274057		Approved	FLJ20163, FLJ21219, KIAA1597, exophilin-4, CHR11SYT, SLP2, SGA72M, MGC102768, PPP1R151	uc001pbb.3	Q9HCH5	OTTHUMG00000166977	ENST00000528231.1:c.1459+3082A>-	chr11.hg19:g.85435856delT		103.0	0.0		153.0	10.0	NM_206927	B3KRS3|B4DJT5|B4DKW3|B4DQ26|B7SA85|B7ZLX6|B7ZLX7|Q2YDA7|Q6TV07|Q6ZN59|Q6ZVC5|Q8ND34|Q96BJ2|Q9H768|Q9NXM1	Frame_Shift_Del	DEL	ENST00000528231.1	hg19	CCDS53688.1																																																																																			.	.		0.418	SYTL2-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000392192.1	NM_206927	
OGT	8473	hgsc.bcm.edu	37	X	70783055	70783055	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:70783055delA	ENST00000373719.3	+	17	2441	c.2224delA	c.(2224-2226)aaafs	p.K742fs	OGT_ENST00000373701.3_Frame_Shift_Del_p.K732fs	NM_181672.2|NM_181673.2	NP_858058.1|NP_858059.1	O15294	OGT1_HUMAN	O-linked N-acetylglucosamine (GlcNAc) transferase	742					apoptotic process (GO:0006915)|cellular response to retinoic acid (GO:0071300)|chromatin organization (GO:0006325)|circadian regulation of gene expression (GO:0032922)|histone H3-K4 trimethylation (GO:0080182)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|negative regulation of protein ubiquitination (GO:0031397)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of catalytic activity (GO:0043085)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of histone H3-K27 methylation (GO:0061087)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of proteolysis (GO:0045862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein O-linked glycosylation (GO:0006493)|regulation of gluconeogenesis involved in cellular glucose homeostasis (GO:0090526)|regulation of glycolytic process (GO:0006110)|regulation of insulin receptor signaling pathway (GO:0046626)|regulation of Rac protein signal transduction (GO:0035020)|response to insulin (GO:0032868)|response to nutrient (GO:0007584)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone acetyltransferase complex (GO:0000123)|microtubule organizing center (GO:0005815)|mitochondrion (GO:0005739)|MLL5-L complex (GO:0070688)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	acetylglucosaminyltransferase activity (GO:0008375)|enzyme activator activity (GO:0008047)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|protein N-acetylglucosaminyltransferase activity (GO:0016262)|protein O-GlcNAc transferase activity (GO:0097363)			breast(6)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(5)|liver(3)|lung(9)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Renal(35;0.156)					CATCGACCTCAAAGCATTTCT	0.358																																					p.L741fs		Atlas-INDEL	.											.	OGT	207	.	0			c.2223delC						.						132.0	116.0	121.0					X																	70783055		2203	4300	6503	SO:0001589	frameshift_variant	8473	exon17			.	U77413	CCDS14414.1, CCDS35502.1	Xq13	2013-07-24	2012-05-04		ENSG00000147162	ENSG00000147162	2.4.1.255	"""Tetratricopeptide (TTC) repeat domain containing"""	8127	protein-coding gene	gene with protein product	"""UDP-N-acetylglucosamine:polypeptide-N-acetylglucosaminyl transferase"""	300255	"""O-linked N-acetylglucosamine (GlcNAc) transferase (UDP-N-acetylglucosamine:polypeptide-N-acetylglucosaminyl transferase)"""			9083068	Standard	NM_181672		Approved	O-GLCNAC, HRNT1, MGC22921, FLJ23071	uc004eaa.2	O15294	OTTHUMG00000033316	ENST00000373719.3:c.2224delA	chrX.hg19:g.70783055delA	ENSP00000362824:p.Lys742fs	115.0	0.0		174.0	11.0	NM_181672	Q7Z3K0|Q8WWM8|Q96CC1|Q9UG57	Frame_Shift_Del	DEL	ENST00000373719.3	hg19	CCDS14414.1																																																																																			.	.		0.358	OGT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000081829.3	NM_003605, NM_181672	
HMGXB3	22993	hgsc.bcm.edu	37	5	149386090	149386090	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:149386090delC	ENST00000502717.1	+	3	656	c.192delC	c.(190-192)ctcfs	p.L64fs	HMGXB3_ENST00000503427.1_Frame_Shift_Del_p.L64fs	NM_014983.2	NP_055798	Q12766	HMGX3_HUMAN	HMG box domain containing 3	310	Arg-rich.				phosphorylation (GO:0016310)	nucleus (GO:0005634)	DNA binding (GO:0003677)|kinase activity (GO:0016301)			central_nervous_system(1)|endometrium(3)|kidney(3)|skin(2)	9						AGCAGGAGCTCCCCCACCTCC	0.488																																					p.L64fs		Atlas-INDEL	.											.	HMGXB3	31	.	0			c.191delT						.						60.0	58.0	59.0					5																	149386090		692	1591	2283	SO:0001589	frameshift_variant	22993	exon3			.	D83778	CCDS54935.1	5q33.1	2011-07-01		2009-01-05	ENSG00000113716	ENSG00000113716		"""High mobility group / Non-canonical"""	28982	protein-coding gene	gene with protein product				HMGX3		8724849	Standard	NM_014983		Approved	SMF, KIAA0194	uc003lrk.4	Q12766	OTTHUMG00000163493	ENST00000502717.1:c.192delC	chr5.hg19:g.149386090delC	ENSP00000421917:p.Leu64fs	101.0	0.0		123.0	11.0	NM_014983	G5E9Y4|Q86UG3|Q9UMF4	Frame_Shift_Del	DEL	ENST00000502717.1	hg19	CCDS54935.1																																																																																			.	.		0.488	HMGXB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373771.1	XM_001717202	
GK	2710	hgsc.bcm.edu	37	X	30719015	30719015	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:30719015delA	ENST00000378943.3	+	10	1005	c.826delA	c.(826-828)aaafs	p.K276fs	GK-AS1_ENST00000464659.1_RNA|GK_ENST00000378946.3_Frame_Shift_Del_p.K282fs|GK_ENST00000427190.1_Frame_Shift_Del_p.K77fs|RP11-242C19.2_ENST00000497961.1_RNA|GK_ENST00000378945.3_Frame_Shift_Del_p.K276fs	NM_001128127.2	NP_001121599.1	P32189	GLPK_HUMAN	glycerol kinase	282					cellular lipid metabolic process (GO:0044255)|glucose homeostasis (GO:0042593)|glycerol catabolic process (GO:0019563)|glycerol metabolic process (GO:0006071)|glycerol-3-phosphate biosynthetic process (GO:0046167)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|triglyceride metabolic process (GO:0006641)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrial outer membrane (GO:0005741)|nucleus (GO:0005634)	ATP binding (GO:0005524)|glycerol kinase activity (GO:0004370)			central_nervous_system(1)|large_intestine(3)	4						TGGACAAGCCAAAAATACGTG	0.368																																					p.A281fs		Atlas-INDEL	.											.	GK	95	.	0			c.843delC						.						82.0	76.0	78.0					X																	30719015		2202	4300	6502	SO:0001589	frameshift_variant	2710	exon11			.	X78711	CCDS14225.1, CCDS35224.1, CCDS48090.1, CCDS75963.1	Xp21.3	2014-09-17			ENSG00000198814	ENSG00000198814	2.7.1.30	"""Glycerol kinases"""	4289	protein-coding gene	gene with protein product		300474				7987308	Standard	NM_203391		Approved	GK1, GKD	uc022buj.1	P32189	OTTHUMG00000021328	ENST00000378943.3:c.826delA	chrX.hg19:g.30719015delA	ENSP00000368226:p.Lys276fs	98.0	0.0		142.0	10.0	NM_203391	A6NJP5|B2R833|Q6IQ27|Q8IVR5|Q9UMP0|Q9UMP1	Frame_Shift_Del	DEL	ENST00000378943.3	hg19	CCDS48090.1																																																																																			.	.		0.368	GK-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056170.1	NM_000167	
OBSCN	84033	hgsc.bcm.edu	37	1	228564975	228564975	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:228564975delC	ENST00000422127.1	+	101	23306	c.23262delC	c.(23260-23262)ctcfs	p.L7754fs	OBSCN_ENST00000570156.2_Frame_Shift_Del_p.L8711fs|OBSCN_ENST00000366707.4_Frame_Shift_Del_p.L5388fs	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	7754	Protein kinase 2. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				CCGAGCTGCTCCCCTGCCTGG	0.692																																					p.L8711fs		Atlas-INDEL	.											.	OBSCN	2142	.	0			c.26132delT						.						11.0	15.0	13.0					1																	228564975		1939	3919	5858	SO:0001589	frameshift_variant	84033	exon112			.	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.23262delC	chr1.hg19:g.228564975delC	ENSP00000409493:p.Leu7754fs	55.0	0.0		115.0	10.0	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Frame_Shift_Del	DEL	ENST00000422127.1	hg19	CCDS58065.1																																																																																			.	.		0.692	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
NPAT	4863	hgsc.bcm.edu	37	11	108043363	108043363	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:108043363delT	ENST00000278612.8	-	13	2453	c.2348delA	c.(2347-2349)aatfs	p.N783fs	NPAT_ENST00000610253.1_5'UTR	NM_002519.2	NP_002510.2	Q14207	NPAT_HUMAN	nuclear protein, ataxia-telangiectasia locus	783					positive regulation of transcription, DNA-templated (GO:0045893)|regulation of gene expression (GO:0010468)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|transcription, DNA-templated (GO:0006351)	Cajal body (GO:0015030)|cytoplasm (GO:0005737)|Gemini of coiled bodies (GO:0097504)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(21)|ovary(2)|prostate(2)|skin(5)	46		all_cancers(61;2.31e-10)|all_epithelial(67;1.11e-06)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		BRCA - Breast invasive adenocarcinoma(274;1.05e-05)|Epithelial(105;3.01e-05)|all cancers(92;0.000816)|Colorectal(284;0.116)		TAGTTCTGCATTTTTAGTAGG	0.383																																					p.N783fs		Atlas-INDEL	.											.	NPAT	124	.	0			c.2349delT						.						71.0	67.0	68.0					11																	108043363		1836	4096	5932	SO:0001589	frameshift_variant	4863	exon13			.	X97186	CCDS41710.1	11q22-q23	2008-02-01			ENSG00000149308	ENSG00000149308			7896	protein-coding gene	gene with protein product		601448				9205109	Standard	NM_002519		Approved	E14	uc001pjz.4	Q14207	OTTHUMG00000166385	ENST00000278612.8:c.2348delA	chr11.hg19:g.108043363delT	ENSP00000278612:p.Asn783fs	131.0	0.0		191.0	13.0	NM_002519	A8K1V5|A8K6M2|Q13632|Q14967|Q16580|Q86W55|Q8IWE9	Frame_Shift_Del	DEL	ENST00000278612.8	hg19	CCDS41710.1																																																																																			.	.		0.383	NPAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389506.2	NM_002519	
APAF1	317	hgsc.bcm.edu	37	12	99119233	99119233	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:99119233delG	ENST00000551964.1	+	25	4107	c.3371delG	c.(3370-3372)aggfs	p.R1124fs	APAF1_ENST00000547045.1_Frame_Shift_Del_p.R1081fs|APAF1_ENST00000333991.1_Intron|APAF1_ENST00000552268.1_Intron|APAF1_ENST00000339433.3_Intron|APAF1_ENST00000549007.1_Intron|APAF1_ENST00000550527.1_Frame_Shift_Del_p.R1113fs|APAF1_ENST00000359972.2_Frame_Shift_Del_p.R1070fs|APAF1_ENST00000357310.1_Frame_Shift_Del_p.R1081fs	NM_181861.1	NP_863651.1	O14727	APAF_HUMAN	apoptotic peptidase activating factor 1	1124					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c (GO:0008635)|apoptotic process (GO:0006915)|forebrain development (GO:0030900)|intrinsic apoptotic signaling pathway (GO:0097193)|nervous system development (GO:0007399)|neural tube closure (GO:0001843)|neuron apoptotic process (GO:0051402)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|regulation of apoptotic DNA fragmentation (GO:1902510)|regulation of apoptotic process (GO:0042981)|response to G1 DNA damage checkpoint signaling (GO:0072432)	apoptosome (GO:0043293)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|nucleotide binding (GO:0000166)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(13)|liver(1)|lung(15)|ovary(2)|prostate(2)|skin(1)	42					Adenosine triphosphate(DB00171)	CATGAATTGAGGGGCCACAAC	0.478																																					p.R1124fs		Atlas-INDEL	.											.	APAF1	111	.	0			c.3370delA						.						131.0	114.0	120.0					12																	99119233		2203	4300	6503	SO:0001589	frameshift_variant	317	exon25			.	AF013263	CCDS9069.1, CCDS9070.1, CCDS9071.1, CCDS55862.1, CCDS55863.1	12q23	2013-01-10	2006-10-23			ENSG00000120868		"""WD repeat domain containing"""	576	protein-coding gene	gene with protein product		602233	"""apoptotic protease activating factor"", ""apoptotic peptidase activating factor"""			9267021, 10702682	Standard	NM_181861		Approved	CED4, APAF-1	uc001tfz.3	O14727	OTTHUMG00000170214	ENST00000551964.1:c.3371delG	chr12.hg19:g.99119233delG	ENSP00000448165:p.Arg1124fs	129.0	0.0		167.0	11.0	NM_181861	B2RMX8|O43297|Q7Z438|Q9BXZ6|Q9UBZ5|Q9UGN8|Q9UGN9|Q9UGP0|Q9UJ58|Q9UJ59|Q9UJ60|Q9UJ61|Q9UJ62|Q9UJ63|Q9UJ64|Q9UJ65|Q9UJ66|Q9UJ67|Q9UNC9	Frame_Shift_Del	DEL	ENST00000551964.1	hg19	CCDS9069.1																																																																																			.	.		0.478	APAF1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408006.1	NM_181861.1	
ZAK	51776	hgsc.bcm.edu	37	2	174130888	174130888	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:174130888delT	ENST00000375213.3	+	20	1891	c.1813delT	c.(1813-1815)tttfs	p.F605fs	MLK7-AS1_ENST00000422703.1_RNA|MLK7-AS1_ENST00000423106.2_RNA|MLTK_ENST00000409176.2_Frame_Shift_Del_p.F605fs	NM_016653.2	NP_057737.2	Q9NYL2	MLTK_HUMAN		605					activation of JUN kinase activity (GO:0007257)|activation of MAPKK activity (GO:0000186)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell death (GO:0008219)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|DNA damage checkpoint (GO:0000077)|intracellular signal transduction (GO:0035556)|positive regulation of apoptotic process (GO:0043065)|protein phosphorylation (GO:0006468)|response to radiation (GO:0009314)|response to stress (GO:0006950)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|MAP kinase kinase kinase activity (GO:0004709)|poly(A) RNA binding (GO:0044822)|protein serine/threonine kinase activity (GO:0004674)										CTTCTCACACTTTGATGGCCA	0.517																																					p.H604fs		Atlas-INDEL	.											.	ZAK	62	.	0			c.1812delC						.						63.0	59.0	60.0					2																	174130888		2005	4193	6198	SO:0001589	frameshift_variant	0	exon20			.																												ENST00000375213.3:c.1813delT	chr2.hg19:g.174130888delT	ENSP00000364361:p.Phe605fs	202.0	0.0		233.0	14.0	NM_016653	B3KPG2|Q53SX1|Q580W8|Q59GY5|Q86YW8|Q9HCC4|Q9HCC5|Q9HDD2|Q9NYE9	Frame_Shift_Del	DEL	ENST00000375213.3	hg19	CCDS42777.1																																																																																			.	.		0.517	MLTK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255401.1		
COL11A2	1302	hgsc.bcm.edu	37	6	33132109	33132109	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:33132109delC	ENST00000374708.4	-	63	5005	c.4747delG	c.(4747-4749)gccfs	p.A1583fs	COL11A2_ENST00000374713.1_Frame_Shift_Del_p.A1622fs|COL11A2_ENST00000361917.1_Frame_Shift_Del_p.A1562fs|COL11A2_ENST00000374714.1_Frame_Shift_Del_p.A1643fs|COL11A2_ENST00000357486.1_Frame_Shift_Del_p.A1648fs|COL11A2_ENST00000341947.2_Frame_Shift_Del_p.A1669fs|COL11A2_ENST00000395197.1_Frame_Shift_Del_p.A1609fs|COL11A2_ENST00000477772.1_5'UTR|COL11A2_ENST00000374712.1_Frame_Shift_Del_p.A1588fs	NM_080681.2	NP_542412.2	P13942	COBA2_HUMAN	collagen, type XI, alpha 2	1669	Fibrillar collagen NC1. {ECO:0000255|PROSITE-ProRule:PRU00793}.				cartilage development (GO:0051216)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|palate development (GO:0060021)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|soft palate development (GO:0060023)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)			biliary_tract(1)|breast(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|liver(1)|lung(27)|ovary(5)|prostate(5)|skin(6)	68						TCCTCATTGGCCCCACGGAGT	0.622																																					p.A1669fs	Melanoma(1;90 116 3946 5341 17093)	Atlas-INDEL	.											.	COL11A2	124	.	0			c.5006delC						.						35.0	33.0	34.0					6																	33132109		1511	2708	4219	SO:0001589	frameshift_variant	1302	exon65			.	U32169	CCDS43452.1, CCDS54992.1	6p21.3	2013-01-16			ENSG00000204248	ENSG00000204248		"""Collagens"""	2187	protein-coding gene	gene with protein product		120290		DFNA13, DFNB53		7559422, 10581026	Standard	NM_080679		Approved	HKE5	uc003ocx.1	P13942	OTTHUMG00000031036	ENST00000374708.4:c.4747delG	chr6.hg19:g.33132109delC	ENSP00000363840:p.Ala1583fs	127.0	0.0		177.0	13.0	NM_080680	A6NLX2|E7ER90|Q07751|Q13271|Q13272|Q13273|Q5JP94|Q5SUI8|Q7Z6C3|Q99866|Q9UIP9	Frame_Shift_Del	DEL	ENST00000374708.4	hg19	CCDS43452.1																																																																																			.	.		0.622	COL11A2-001	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076032.2		
TNFSF8	944	hgsc.bcm.edu	37	9	117666406	117666406	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:117666406delT	ENST00000223795.2	-	4	623	c.510delA	c.(508-510)aaafs	p.K170fs	TNFSF8_ENST00000474301.1_Intron	NM_001244.3	NP_001235.1	P32971	TNFL8_HUMAN	tumor necrosis factor (ligand) superfamily, member 8	170					apoptotic process (GO:0006915)|CD8-positive, alpha-beta T cell differentiation (GO:0043374)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|defense response to Gram-positive bacterium (GO:0050830)|immune response (GO:0006955)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)	receptor binding (GO:0005102)			endometrium(1)|large_intestine(2)|lung(4)|ovary(1)|skin(3)|urinary_tract(1)	12						CCAGGGCCTGTTTTTTGATAT	0.428																																					p.Q171fs		Atlas-INDEL	.											.	TNFSF8	34	.	0			c.511delC						.						205.0	180.0	189.0					9																	117666406		2203	4300	6503	SO:0001589	frameshift_variant	944	exon4			.	L09753	CCDS6810.1, CCDS75884.1	9q33	2008-02-05			ENSG00000106952	ENSG00000106952		"""Tumor necrosis factor (ligand) superfamily"", ""CD molecules"""	11938	protein-coding gene	gene with protein product		603875		CD30LG		8391931, 9349718	Standard	NM_001244		Approved	CD153	uc004bji.2	P32971	OTTHUMG00000021025	ENST00000223795.2:c.510delA	chr9.hg19:g.117666406delT	ENSP00000223795:p.Lys170fs	255.0	0.0		255.0	16.0	NM_001244	O43404	Frame_Shift_Del	DEL	ENST00000223795.2	hg19	CCDS6810.1																																																																																			.	.		0.428	TNFSF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055464.1		
MAPT	4137	hgsc.bcm.edu	37	17	44060593	44060593	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:44060593delC	ENST00000571987.1	+	5	423	c.423delC	c.(421-423)ggcfs	p.G141fs	MAPT_ENST00000347967.5_Intron|MAPT_ENST00000535772.1_Intron|MAPT_ENST00000420682.2_Intron|MAPT_ENST00000415613.2_Frame_Shift_Del_p.G141fs|MAPT_ENST00000574436.1_Intron|MAPT_ENST00000446361.3_Intron|MAPT_ENST00000576518.1_Intron|MAPT_ENST00000334239.8_Intron|MAPT_ENST00000351559.5_Intron|MAPT_ENST00000431008.3_Intron|MAPT_ENST00000344290.5_Frame_Shift_Del_p.G141fs|MAPT_ENST00000340799.5_Intron|MAPT_ENST00000570299.1_Intron|MAPT_ENST00000262410.5_Frame_Shift_Del_p.G141fs			P10636	TAU_HUMAN	microtubule-associated protein tau	141					adult walking behavior (GO:0007628)|apoptotic process (GO:0006915)|axon cargo transport (GO:0008088)|axon extension (GO:0048675)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|generation of neurons (GO:0048699)|microtubule cytoskeleton organization (GO:0000226)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|neuron migration (GO:0001764)|positive regulation of axon extension (GO:0045773)|positive regulation of microtubule polymerization (GO:0031116)|regulation of autophagy (GO:0010506)|regulation of microtubule polymerization (GO:0031113)|regulation of microtubule-based movement (GO:0060632)	axon (GO:0030424)|axoneme (GO:0005930)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|growth cone (GO:0030426)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nuclear periphery (GO:0034399)|plasma membrane (GO:0005886)|tubulin complex (GO:0045298)	apolipoprotein binding (GO:0034185)|enzyme binding (GO:0019899)|lipoprotein particle binding (GO:0071813)|microtubule binding (GO:0008017)|SH3 domain binding (GO:0017124)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	38		Melanoma(429;0.216)			Docetaxel(DB01248)|Paclitaxel(DB01229)	GAGAGCCAGGCCCCCCAGGTC	0.657																																					p.G141fs		Atlas-INDEL	.											.	MAPT	135	.	0			c.422delG						.						20.0	18.0	19.0					17																	44060593		2203	4298	6501	SO:0001589	frameshift_variant	4137	exon6			.	J03778	CCDS11499.1, CCDS11500.1, CCDS11501.1, CCDS11502.1, CCDS45715.1, CCDS45716.1, CCDS56033.1	17q21	2014-09-17			ENSG00000186868	ENSG00000186868			6893	protein-coding gene	gene with protein product	"""G protein beta1/gamma2 subunit-interacting factor 1"", ""microtubule-associated protein tau, isoform 4"", ""protein phosphatase 1, regulatory subunit 103"""	157140		DDPAC, MAPTL		7936241, 3131773	Standard	NM_001123067		Approved	MTBT1, tau, PPND, FTDP-17, TAU, MSTD, MTBT2, FLJ31424, MGC138549, PPP1R103	uc010dau.3	P10636	OTTHUMG00000168833	ENST00000571987.1:c.423delC	chr17.hg19:g.44060593delC	ENSP00000458742:p.Gly141fs	169.0	0.0		163.0	10.0	NM_001123066	P18518|Q14799|Q15549|Q15550|Q15551|Q1RMF6|Q53YB1|Q5CZI7|Q5XWF0|Q6QT54|Q9UDJ3|Q9UMH0|Q9UQ96	Frame_Shift_Del	DEL	ENST00000571987.1	hg19	CCDS11501.1																																																																																			.	.		0.657	MAPT-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000440133.1	NM_016835	
RCCD1	91433	hgsc.bcm.edu	37	15	91500927	91500927	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:91500927delG	ENST00000394258.2	+	4	853	c.651delG	c.(649-651)gcgfs	p.A217fs	RCCD1_ENST00000556618.1_Frame_Shift_Del_p.A217fs|AC068831.6_ENST00000553321.1_RNA|RCCD1_ENST00000555155.1_Frame_Shift_Del_p.A217fs|RCCD1_ENST00000556774.1_Intron	NM_001017919.1|NM_033544.2	NP_001017919.1|NP_291022.2	A6NED2	RCCD1_HUMAN	RCC1 domain containing 1	217						cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				breast(1)|kidney(1)|large_intestine(2)	4	Lung NSC(78;0.0987)|all_lung(78;0.175)		Lung(145;0.189)			AGGTGGCCGCGGGGGGCTGGC	0.597																																					p.A217fs		Atlas-INDEL	.											.	RCCD1	9	.	0			c.650delC						.						109.0	107.0	108.0					15																	91500927		2198	4298	6496	SO:0001589	frameshift_variant	91433	exon4			.		CCDS32333.1	15q26.1	2005-10-21	2005-10-21			ENSG00000166965			30457	protein-coding gene	gene with protein product						12477932	Standard	XM_006720763		Approved	MGC14386	uc002bqk.3	A6NED2		ENST00000394258.2:c.651delG	chr15.hg19:g.91500927delG	ENSP00000377801:p.Ala217fs	136.0	0.0		174.0	16.0	NM_001017919	B2RTP9|Q29RX6	Frame_Shift_Del	DEL	ENST00000394258.2	hg19	CCDS32333.1																																																																																			.	.		0.597	RCCD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000414748.1	NM_033544	
AKAP7	9465	hgsc.bcm.edu	37	6	131481221	131481221	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:131481221delT	ENST00000431975.2	+	3	272	c.174delT	c.(172-174)aatfs	p.N58fs	AKAP7_ENST00000368123.4_Frame_Shift_Del_p.N36fs|AKAP7_ENST00000366358.2_3'UTR|AKAP7_ENST00000541650.1_Frame_Shift_Del_p.N57fs	NM_016377.3	NP_057461.2	Q9P0M2	AKA7G_HUMAN	A kinase (PRKA) anchor protein 7	58						cytosol (GO:0005829)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|nucleotide binding (GO:0000166)|protein kinase A binding (GO:0051018)			endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(2)|prostate(1)|stomach(1)	13	Breast(56;0.152)			GBM - Glioblastoma multiforme(226;0.0184)|OV - Ovarian serous cystadenocarcinoma(155;0.0345)		CTCAAATAAATTTGAAGAGAA	0.303																																					p.N58fs		Atlas-INDEL	.											.	AKAP7	61	.	0			c.173delA						.						51.0	50.0	50.0					6																	131481221		2203	4295	6498	SO:0001589	frameshift_variant	9465	exon3			.	AF047715	CCDS5142.1, CCDS5143.1, CCDS5144.1, CCDS5142.2	6q23.2	2012-10-24			ENSG00000118507	ENSG00000118507		"""A-kinase anchor proteins"""	377	protein-coding gene	gene with protein product		604693				9545239	Standard	NM_016377		Approved	AKAP18, AKAP15	uc003qck.4	O43687	OTTHUMG00000015563	ENST00000431975.2:c.174delT	chr6.hg19:g.131481221delT	ENSP00000405252:p.Asn58fs	145.0	0.0		163.0	10.0	NM_016377	B4DUC3|Q9HCZ8	Frame_Shift_Del	DEL	ENST00000431975.2	hg19	CCDS5142.2																																																																																			.	.		0.303	AKAP7-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042209.2	NM_004842	
DENND4A	10260	hgsc.bcm.edu	37	15	65983623	65983623	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:65983623delT	ENST00000431932.2	-	22	3385	c.3177delA	c.(3175-3177)aaafs	p.K1059fs	DENND4A_ENST00000567323.1_5'Flank|DENND4A_ENST00000443035.3_Frame_Shift_Del_p.K1102fs	NM_005848.3	NP_005839.3	Q7Z401	MYCPP_HUMAN	DENN/MADD domain containing 4A	1059					positive regulation of Rab GTPase activity (GO:0032851)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(17)|lung(11)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	51						CAGCTCCCAATTTTTCAACTA	0.383																																					p.L1103fs		Atlas-INDEL	.											.	DENND4A	217	.	0			c.3307delT						.						49.0	45.0	47.0					15																	65983623		1811	4062	5873	SO:0001589	frameshift_variant	10260	exon23			.	AF534403	CCDS45285.1, CCDS53949.1	15q22.31	2012-10-03	2006-01-27	2006-01-27				"""DENN/MADD domain containing"""	24321	protein-coding gene	gene with protein product		600382	"""c-myc promoter binding protein"""	MYCPBP		8056341, 12906859	Standard	NM_005848		Approved	IRLB	uc002api.3	Q7Z401		ENST00000431932.2:c.3177delA	chr15.hg19:g.65983623delT	ENSP00000396830:p.Lys1059fs	119.0	0.0		118.0	10.0	NM_001144823	E7EPL3|Q14655|Q86T77|Q8IVX2|Q8NB93	Frame_Shift_Del	DEL	ENST00000431932.2	hg19	CCDS45285.1																																																																																			.	.		0.383	DENND4A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419611.1	NM_005848	
SLC35A3	23443	hgsc.bcm.edu	37	1	100483342	100483342	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:100483342delT	ENST00000370155.3	+	7	1250	c.858delT	c.(856-858)tatfs	p.Y286fs	SLC35A3_ENST00000427993.2_Frame_Shift_Del_p.Y286fs|SLC35A3_ENST00000370156.3_3'UTR|SLC35A3_ENST00000465289.1_Intron|SLC35A3_ENST00000370153.1_Frame_Shift_Del_p.Y328fs	NM_012243.1	NP_036375.1	Q9Y2D2	S35A3_HUMAN	solute carrier family 35 (UDP-N-acetylglucosamine (UDP-GlcNAc) transporter), member A3	286					transmembrane transport (GO:0055085)|UDP-N-acetylglucosamine metabolic process (GO:0006047)|UDP-N-acetylglucosamine transport (GO:0015788)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	sugar:proton symporter activity (GO:0005351)|UDP-N-acetylglucosamine transmembrane transporter activity (GO:0005462)			biliary_tract(1)|kidney(1)|large_intestine(2)|lung(5)|skin(1)|urinary_tract(1)	11		all_epithelial(167;0.000686)|all_lung(203;0.0154)|Lung NSC(277;0.0155)		Epithelial(280;0.124)|all cancers(265;0.198)|Lung(183;0.199)		TGATCTCCTATTTTTGGCTTC	0.299																																					p.Y328fs	Ovarian(7;298 356 944 2149 6911)	Atlas-INDEL	.											.	SLC35A3	25	.	0			c.983delA						.						65.0	67.0	66.0					1																	100483342		2202	4288	6490	SO:0001589	frameshift_variant	23443	exon7			.	AB021981	CCDS762.1, CCDS60204.1, CCDS60205.1	1p21	2013-05-22			ENSG00000117620	ENSG00000117620		"""Solute carriers"""	11023	protein-coding gene	gene with protein product		605632	"""solute carrier family 35 (UDP-N-acetylglucosamine (UDP-GlcNAc) transporter), member 3"""			10393322	Standard	NM_001271685		Approved		uc001dsr.2	Q9Y2D2	OTTHUMG00000010805	ENST00000370155.3:c.858delT	chr1.hg19:g.100483342delT	ENSP00000359174:p.Tyr286fs	194.0	0.0		186.0	12.0	NM_001271685	A8K3F8|D3DT54|Q68CR2|Q9BSB7	Frame_Shift_Del	DEL	ENST00000370155.3	hg19	CCDS762.1																																																																																			.	.		0.299	SLC35A3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000029783.1	NM_012243	
TSPO	706	hgsc.bcm.edu	37	22	43557161	43557161	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr22:43557161delC	ENST00000396265.3	+	2	180	c.5delC	c.(4-6)gccfs	p.A2fs	TSPO_ENST00000583777.1_5'UTR|TSPO_ENST00000329563.4_Frame_Shift_Del_p.P97fs|TSPO_ENST00000337554.3_Frame_Shift_Del_p.P97fs			B1AH88	TSPOB_HUMAN	translocator protein (18kDa)	2					adrenal gland development (GO:0030325)|aging (GO:0007568)|behavioral response to pain (GO:0048266)|cellular hypotonic response (GO:0071476)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to zinc ion (GO:0071294)|chloride transport (GO:0006821)|contact inhibition (GO:0060242)|glial cell migration (GO:0008347)|negative regulation of glial cell proliferation (GO:0060253)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|negative regulation of tumor necrosis factor production (GO:0032720)|peripheral nervous system axon regeneration (GO:0014012)|positive regulation of apoptotic process (GO:0043065)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of glial cell proliferation (GO:0060252)|positive regulation of mitochondrial depolarization (GO:0051901)|positive regulation of necrotic cell death (GO:0010940)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|regulation of steroid biosynthetic process (GO:0050810)|response to drug (GO:0042493)|response to manganese ion (GO:0010042)|response to progesterone (GO:0032570)|response to testosterone (GO:0033574)|response to vitamin B1 (GO:0010266)|steroid biosynthetic process (GO:0006694)	mitochondrial outer membrane (GO:0005741)	androgen binding (GO:0005497)|benzodiazepine receptor activity (GO:0008503)			endometrium(1)|prostate(1)	2		Ovarian(80;0.0694)				CTGGGCATGGCCCCCCATCTT	0.617																																					p.W95fs		Atlas-INDEL	.											.	TSPO	6	.	0			c.285delG						.						76.0	66.0	70.0					22																	43557161		2203	4300	6503	SO:0001589	frameshift_variant	706	exon3			.	AF075589	CCDS33661.1	22q13.3	2006-07-12	2006-07-12	2006-07-12	ENSG00000100300	ENSG00000100300			1158	protein-coding gene	gene with protein product	"""peripheral-type benzodiazepine receptor/recognition site"""	109610	"""benzodiazapine receptor (peripheral)"""	BZRP		1326278, 1847678, 16822554	Standard	NM_000714		Approved	PBR, MBR, PKBS, mDRC, DBI, IBP, pk18	uc003bdo.4	B1AH88	OTTHUMG00000150573	ENST00000396265.3:c.5delC	chr22.hg19:g.43557161delC	ENSP00000379563:p.Ala2fs	173.0	0.0		195.0	15.0	NM_001256531	Q13849|Q6IAZ7	Frame_Shift_Del	DEL	ENST00000396265.3	hg19																																																																																				.	.		0.617	TSPO-201	KNOWN	basic	protein_coding	protein_coding		NM_007311	
FLOT1	10211	hgsc.bcm.edu	37	6	30698207	30698207	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:30698207delG	ENST00000376389.3	-	11	1307	c.1087delC	c.(1087-1089)cagfs	p.Q363fs	FLOT1_ENST00000456573.2_Frame_Shift_Del_p.Q315fs	NM_005803.2	NP_005794.1	P41440	S19A1_HUMAN	flotillin 1	0					folic acid metabolic process (GO:0046655)|folic acid transport (GO:0015884)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	folic acid binding (GO:0005542)|folic acid transporter activity (GO:0008517)|methotrexate transporter activity (GO:0015350)	p.Q363K(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(6)|prostate(1)	13					Methotrexate(DB00563)|Pralatrexate(DB06813)	CTCCAGACCTGGGGCAGCTTC	0.592																																					p.Q363fs		Atlas-INDEL	.											.	FLOT1	28	.	1	Substitution - Missense(1)	lung(1)	c.1088delA						.						140.0	152.0	148.0					6																	30698207		2203	4299	6502	SO:0001589	frameshift_variant	10211	exon11			.	AF089750	CCDS4688.1	6p21.3	2010-02-17			ENSG00000137312	ENSG00000137312			3757	protein-coding gene	gene with protein product		606998					Standard	XM_005248780		Approved		uc003nrm.3	O75955	OTTHUMG00000031151	ENST00000376389.3:c.1087delC	chr6.hg19:g.30698207delG	ENSP00000365569:p.Gln363fs	122.0	0.0		210.0	14.0	NM_005803	B2R7U8|B7Z8C3|E9PFY4|O00553|O60227|Q13026|Q9BTX8	Frame_Shift_Del	DEL	ENST00000376389.3	hg19	CCDS4688.1																																																																																			.	.		0.592	FLOT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076276.2		
ANKMY1	51281	hgsc.bcm.edu	37	2	241465814	241465814	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:241465814delC	ENST00000272972.3	-	5	949	c.735delG	c.(733-735)gggfs	p.G245fs	ANKMY1_ENST00000403283.1_Intron|ANKMY1_ENST00000405002.1_Intron|ANKMY1_ENST00000401804.1_Frame_Shift_Del_p.G334fs|ANKMY1_ENST00000373320.4_Intron|ANKMY1_ENST00000361678.4_Intron|ANKMY1_ENST00000391987.1_Frame_Shift_Del_p.G245fs|ANKMY1_ENST00000462004.1_5'UTR|ANKMY1_ENST00000406958.1_Intron|ANKMY1_ENST00000536462.1_Intron|ANKMY1_ENST00000373318.2_Intron|ANKMY1_ENST00000405523.3_Intron	NM_016552.2	NP_057636.2	Q9P2S6	ANKY1_HUMAN	ankyrin repeat and MYND domain containing 1	245							metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(5)|large_intestine(4)|lung(14)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	30		all_epithelial(40;2.79e-15)|Breast(86;2.41e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0335)|Lung NSC(271;0.106)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;1.03e-30)|all cancers(36;4.78e-28)|OV - Ovarian serous cystadenocarcinoma(60;1.45e-14)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;7.8e-06)|Lung(119;0.00271)|LUSC - Lung squamous cell carcinoma(224;0.01)|Colorectal(34;0.0101)|COAD - Colon adenocarcinoma(134;0.0476)		CACTGCGCTTCCCCTCCAGGA	0.552																																					p.K246fs		Atlas-INDEL	.											.	ANKMY1	112	.	0			c.736delA						.						115.0	97.0	103.0					2																	241465814		2203	4300	6503	SO:0001589	frameshift_variant	51281	exon5			.	AB034636	CCDS2535.1, CCDS2536.1, CCDS63184.1, CCDS63185.1, CCDS74681.1	2q37.3	2013-01-10			ENSG00000144504	ENSG00000144504		"""Zinc fingers, MYND-type"", ""Ankyrin repeat domain containing"""	20987	protein-coding gene	gene with protein product							Standard	XM_005247020		Approved	FLJ20499, ZMYND13	uc002vyz.1	Q9P2S6	OTTHUMG00000133355	ENST00000272972.3:c.735delG	chr2.hg19:g.241465814delC	ENSP00000272972:p.Gly245fs	169.0	0.0		183.0	11.0	NM_016552	B2RB78|Q4ZFV3|Q8IYX5|Q8NDK5|Q9H0V8|Q9NX10	Frame_Shift_Del	DEL	ENST00000272972.3	hg19	CCDS2536.1																																																																																			.	.		0.552	ANKMY1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257187.2	NM_017844	
KLHDC7B	113730	hgsc.bcm.edu	37	22	50988068	50988068	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr22:50988068delG	ENST00000395676.2	+	1	1607	c.1473delG	c.(1471-1473)ctgfs	p.L491fs	CTA-384D8.31_ENST00000434237.1_RNA	NM_138433.3	NP_612442.2	Q96G42	KLD7B_HUMAN	kelch domain containing 7B	491										central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	14		all_cancers(38;1.53e-10)|all_epithelial(38;1.82e-09)|Breast(42;0.000448)|all_lung(38;0.000665)|Lung NSC(38;0.0104)|Ovarian(80;0.104)|Lung SC(80;0.162)|Hepatocellular(38;0.178)		OV - Ovarian serous cystadenocarcinoma(4;7.49e-69)|all cancers(3;9.79e-66)|Epithelial(4;1.3e-63)|GBM - Glioblastoma multiforme(4;0.000399)|Lung(4;0.125)|BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		TCGTGGCACTGGGGGGCTTCC	0.667																																					p.L491fs		Atlas-INDEL	.											.	KLHDC7B	39	.	0			c.1472delT						.						47.0	53.0	51.0					22																	50988068		2202	4296	6498	SO:0001589	frameshift_variant	113730	exon1			.	BC009980	CCDS14097.2	22q13.33	2006-11-29		2005-12-13	ENSG00000130487	ENSG00000130487			25145	protein-coding gene	gene with protein product							Standard	NM_138433		Approved	MGC16635	uc003bmi.3	Q96G42	OTTHUMG00000150250	ENST00000395676.2:c.1473delG	chr22.hg19:g.50988068delG	ENSP00000379034:p.Leu491fs	78.0	0.0		105.0	10.0	NM_138433		Frame_Shift_Del	DEL	ENST00000395676.2	hg19	CCDS14097.2																																																																																			.	.		0.667	KLHDC7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317089.2	NM_138433	
PRB4	5545	hgsc.bcm.edu	37	12	11461606	11461606	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:11461606delG	ENST00000535904.1	-	3	344	c.311delC	c.(310-312)ccafs	p.P104fs	PRB4_ENST00000279575.1_Frame_Shift_Del_p.P104fs|PRB4_ENST00000445719.2_Frame_Shift_Del_p.P104fs			P10163	PRB4_HUMAN	proline-rich protein BstNI subfamily 4	125	9.5 X 21 AA tandem repeats of K-P-[EQ]- [GR]-[PR]-[PR]-P-Q-G-G-N-Q-[PS]-[QH]- [RG]-[PT]-P-P-[PH]-P-G.					extracellular region (GO:0005576)				breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(12)|ovary(1)|skin(4)|upper_aerodigestive_tract(3)	30						TCCTCCTTGTGGGGGTGGTCT	0.622										HNSCC(22;0.051)																											p.P104fs		Atlas-INDEL	.											.	PRB4	59	.	0			c.312delA						.						226.0	237.0	233.0					12																	11461606		2202	4299	6501	SO:0001589	frameshift_variant	5545	exon3			.		CCDS8641.1, CCDS58208.1	12p13.2	2012-10-02			ENSG00000230657	ENSG00000230657			9340	protein-coding gene	gene with protein product		180990					Standard	NM_002723		Approved		uc001qzt.4	P10163	OTTHUMG00000169116	ENST00000535904.1:c.311delC	chr12.hg19:g.11461606delG	ENSP00000442834:p.Pro104fs	83.0	0.0		131.0	11.0	NM_001261399	A1L439|O00600|P02813|P10161|P10162|P81489	Frame_Shift_Del	DEL	ENST00000535904.1	hg19	CCDS8641.1																																																																																			.	.		0.622	PRB4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402308.1	NM_002723	
GBP7	388646	hgsc.bcm.edu	37	1	89613446	89613446	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:89613446delT	ENST00000294671.2	-	8	1307	c.1169delA	c.(1168-1170)aagfs	p.K391fs		NM_207398.2	NP_997281.2	Q8N8V2	GBP7_HUMAN	guanylate binding protein 7	391						membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		Lung NSC(277;0.0908)		all cancers(265;0.00835)|Epithelial(280;0.0322)		GTCTTCCTTCTTTTTCTCCAT	0.438																																					p.K390fs		Atlas-INDEL	.											GBP7,NS,carcinoma,-1,1	GBP7	57	.	0			c.1170delG						.						115.0	113.0	113.0					1																	89613446		2203	4300	6503	SO:0001589	frameshift_variant	388646	exon8			.	AK096141	CCDS720.1	1p22.2	2008-02-05			ENSG00000213512	ENSG00000213512			29606	protein-coding gene	gene with protein product		612468					Standard	NM_207398		Approved	FLJ38822, GBP4L	uc001dna.2	Q8N8V2	OTTHUMG00000010659	ENST00000294671.2:c.1169delA	chr1.hg19:g.89613446delT	ENSP00000294671:p.Lys391fs	122.0	0.0		183.0	11.0	NM_207398		Frame_Shift_Del	DEL	ENST00000294671.2	hg19	CCDS720.1																																																																																			.	.		0.438	GBP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029401.1	NM_207398	
GMCL1	64395	hgsc.bcm.edu	37	2	70076825	70076825	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:70076825delA	ENST00000282570.3	+	8	1136	c.885delA	c.(883-885)ttafs	p.L295fs		NM_178439.3	NP_848526.1	Q96IK5	GMCL1_HUMAN	germ cell-less, spermatogenesis associated 1	295					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)	nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)				endometrium(2)|kidney(1)|large_intestine(3)|lung(4)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	15						ATGGATCTTTAAAACAGCTTT	0.289																																					p.L295X		Atlas-INDEL	.											.	GMCL1	50	.	0			c.884delT						.						86.0	88.0	87.0					2																	70076825		2203	4298	6501	SO:0001589	frameshift_variant	64395	exon8			.	AK023119	CCDS1895.1	2p13.3	2013-01-09	2012-08-20		ENSG00000087338	ENSG00000087338		"""BTB/POZ domain containing"""	23843	protein-coding gene	gene with protein product	"""spermatogenesis associated 29"""		"""germ cell-less homolog 1 (Drosophila)"""				Standard	NM_178439		Approved	FLJ13057, BTBD13, GCL1, SPATA29	uc002sfu.3	Q96IK5	OTTHUMG00000129643	ENST00000282570.3:c.885delA	chr2.hg19:g.70076825delA	ENSP00000282570:p.Leu295fs	175.0	0.0		221.0	14.0	NM_178439	Q9H826|Q9H8V7|Q9H927	Frame_Shift_Del	DEL	ENST00000282570.3	hg19	CCDS1895.1																																																																																			.	.		0.289	GMCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251841.2	NM_178439	
HFM1	164045	hgsc.bcm.edu	37	1	91846518	91846518	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:91846518delA	ENST00000370425.3	-	7	922	c.824delT	c.(823-825)ttcfs	p.F275fs	HFM1_ENST00000370424.3_Intron|HFM1_ENST00000294696.5_5'UTR	NM_001017975.3	NP_001017975.3	A2PYH4	HFM1_HUMAN	HFM1, ATP-dependent DNA helicase homolog (S. cerevisiae)	275					resolution of meiotic recombination intermediates (GO:0000712)		ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(17)|lung(33)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	75		all_lung(203;0.00961)|Lung NSC(277;0.0351)		all cancers(265;0.000481)|Epithelial(280;0.00863)|OV - Ovarian serous cystadenocarcinoma(397;0.126)|KIRC - Kidney renal clear cell carcinoma(1967;0.171)		AAATTCTTTGAAAATACTTCT	0.234																																					p.F275fs		Atlas-INDEL	.											.	HFM1	188	.	0			c.825delC						.						56.0	67.0	63.0					1																	91846518		2198	4293	6491	SO:0001589	frameshift_variant	164045	exon7			.	AB204867	CCDS30769.2	1p22.2	2008-03-26			ENSG00000162669	ENSG00000162669			20193	protein-coding gene	gene with protein product		615684	"""SEC63 domain containing 1"""	SEC63D1		14702039, 17286053	Standard	XM_006710395		Approved	MER3, FLJ39011, FLJ36760	uc001doa.4	A2PYH4	OTTHUMG00000010093	ENST00000370425.3:c.824delT	chr1.hg19:g.91846518delA	ENSP00000359454:p.Phe275fs	150.0	0.0		170.0	11.0	NM_001017975	B1B0B6|Q8N9Q0	Frame_Shift_Del	DEL	ENST00000370425.3	hg19	CCDS30769.2																																																																																			.	.		0.234	HFM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316716.2	NM_001017975	
KLHL5	51088	hgsc.bcm.edu	37	4	39064232	39064232	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:39064232delT	ENST00000504108.1	+	1	381	c.98delT	c.(97-99)cttfs	p.L33fs	KLHL5_ENST00000508137.2_Intron|KLHL5_ENST00000359687.2_Frame_Shift_Del_p.L33fs|KLHL5_ENST00000381930.3_Frame_Shift_Del_p.L33fs|KLHL5_ENST00000261425.3_5'UTR|KLHL5_ENST00000261426.5_Frame_Shift_Del_p.L33fs	NM_015990.4	NP_057074.3	Q96PQ7	KLHL5_HUMAN	kelch-like family member 5	33						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				endometrium(3)|kidney(1)|large_intestine(11)|lung(9)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	29						TGTGCAGTGCTTTTTGCCCGT	0.393																																					p.L33fs		Atlas-INDEL	.											.	KLHL5	75	.	0			c.97delC						.						233.0	219.0	224.0					4																	39064232		2203	4300	6503	SO:0001589	frameshift_variant	51088	exon1			.	AF272976	CCDS3449.1, CCDS33974.1, CCDS33975.1, CCDS54756.1	4p15.1	2013-01-30	2013-01-30		ENSG00000109790	ENSG00000109790		"""Kelch-like"", ""BTB/POZ domain containing"""	6356	protein-coding gene	gene with protein product		608064	"""kelch (Drosophila)-like 5"", ""kelch-like 5 (Drosophila)"""			11590829, 14672410	Standard	NM_001007075		Approved		uc003gtp.3	Q96PQ7	OTTHUMG00000097819	ENST00000504108.1:c.98delT	chr4.hg19:g.39064232delT	ENSP00000423897:p.Leu33fs	203.0	0.0		260.0	16.0	NM_015990	A8K170|B7WP68|E9PCF4|F8WAE7|G3XA92|Q6Y881|Q86XW0|Q9NUK3|Q9NV27|Q9NVA9|Q9Y2X2	Frame_Shift_Del	DEL	ENST00000504108.1	hg19	CCDS33974.1																																																																																			.	.		0.393	KLHL5-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000360604.1		
SRGAP1	57522	hgsc.bcm.edu	37	12	64536183	64536183	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:64536183delA	ENST00000355086.3	+	22	3513	c.2989delA	c.(2989-2991)aaafs	p.K997fs	SRGAP1_ENST00000357825.3_Frame_Shift_Del_p.K974fs|SRGAP1_ENST00000543397.1_Frame_Shift_Del_p.K934fs	NM_020762.2	NP_065813.1	Q7Z6B7	SRGP1_HUMAN	SLIT-ROBO Rho GTPase activating protein 1	997					axon guidance (GO:0007411)|cell migration (GO:0016477)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho GTPase activator activity (GO:0005100)			breast(4)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(26)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	65			GBM - Glioblastoma multiforme(3;0.000139)|BRCA - Breast invasive adenocarcinoma(9;0.225)	GBM - Glioblastoma multiforme(28;0.0608)		GGAGCAAGTGAAAAACTCTCC	0.542																																					p.V996fs		Atlas-INDEL	.											.	SRGAP1	146	.	0			c.2988delG						.						114.0	87.0	96.0					12																	64536183		2203	4300	6503	SO:0001589	frameshift_variant	57522	exon22			.	AB037725	CCDS8967.1	12q13.13	2011-07-04			ENSG00000196935	ENSG00000196935		"""Rho GTPase activating proteins"""	17382	protein-coding gene	gene with protein product		606523				11672528	Standard	NM_020762		Approved	KIAA1304, ARHGAP13	uc010ssp.1	Q7Z6B7	OTTHUMG00000168750	ENST00000355086.3:c.2989delA	chr12.hg19:g.64536183delA	ENSP00000347198:p.Lys997fs	112.0	0.0		136.0	10.0	NM_020762	Q9H8A3|Q9P2P2	Frame_Shift_Del	DEL	ENST00000355086.3	hg19	CCDS8967.1																																																																																			.	.		0.542	SRGAP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400896.1		
TRIM31	11074	hgsc.bcm.edu	37	6	30075888	30075888	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:30075888delT	ENST00000376734.3	-	6	950	c.825delA	c.(823-825)aaafs	p.K275fs	TRIM31_ENST00000540829.1_Frame_Shift_Del_p.K275fs|TRIM31_ENST00000485864.1_5'UTR|TRIM31-AS1_ENST00000440874.1_RNA	NM_007028.3	NP_008959.3	Q9BZY9	TRI31_HUMAN	tripartite motif containing 31	275					innate immune response (GO:0045087)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral transcription (GO:0032897)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein ubiquitination (GO:0016567)|regulation of viral release from host cell (GO:1902186)	mitochondrion (GO:0005739)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(5)|ovary(2)|prostate(2)|skin(2)	15						CTTCACTGAGTTTTTTCTCCA	0.438																																					p.L276fs		Atlas-INDEL	.											.	TRIM31	40	.	0			c.826delC						.						82.0	82.0	82.0					6																	30075888		1511	2709	4220	SO:0001589	frameshift_variant	11074	exon6			.	AF230386	CCDS34374.1	6p21.3	2013-01-09	2011-01-25		ENSG00000204616	ENSG00000204616		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	16289	protein-coding gene	gene with protein product		609316	"""tripartite motif-containing 31"""			11331580	Standard	XM_006714977		Approved	RNF, HCGI, C6orf13, HCG1	uc003npg.1	Q9BZY9	OTTHUMG00000031064	ENST00000376734.3:c.825delA	chr6.hg19:g.30075888delT	ENSP00000365924:p.Lys275fs	139.0	0.0		264.0	16.0	NM_007028	A6NLX6|A9R9Q4|Q53H52|Q5RI37|Q5SRJ7|Q5SRJ8|Q5SS28|Q96AK4|Q96AP8|Q99579|Q9BZY8	Frame_Shift_Del	DEL	ENST00000376734.3	hg19	CCDS34374.1																																																																																			.	.		0.438	TRIM31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076081.2		
EIF3M	10480	hgsc.bcm.edu	37	11	32610663	32610663	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:32610663delC	ENST00000531120.1	+	4	483	c.420delC	c.(418-420)atcfs	p.I140fs	EIF3M_ENST00000524896.1_Intron	NM_006360.4	NP_006351.2			eukaryotic translation initiation factor 3, subunit M											breast(3)|endometrium(4)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	16	Breast(20;0.109)					TCCAGTACATCCCAACTGAGC	0.413																																					p.I140fs		Atlas-INDEL	.											.	EIF3M	37	.	0			c.419delT						.						117.0	100.0	106.0					11																	32610663		2202	4299	6501	SO:0001589	frameshift_variant	10480	exon4			.	AK131064	CCDS7880.1	11p13	2012-12-13	2007-07-27	2007-07-27	ENSG00000149100	ENSG00000149100			24460	protein-coding gene	gene with protein product	"""transport and golgi organization 7 homolog (Drosophila)"""	609641	"""PCI domain containing 1 (herpesvirus entry mediator)"""	PCID1		15919898, 15919899	Standard	NM_006360		Approved	hfl-B5, FLJ29030, GA17, eIF3m, TANGO7	uc001mtu.4	Q7L2H7	OTTHUMG00000166258	ENST00000531120.1:c.420delC	chr11.hg19:g.32610663delC	ENSP00000436049:p.Ile140fs	95.0	0.0		108.0	10.0	NM_006360		Frame_Shift_Del	DEL	ENST00000531120.1	hg19	CCDS7880.1																																																																																			.	.		0.413	EIF3M-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388762.2	NM_006360	
FANCI	55215	hgsc.bcm.edu	37	15	89837107	89837107	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:89837107delA	ENST00000310775.7	+	23	2421	c.2335delA	c.(2335-2337)aaafs	p.K780fs	FANCI_ENST00000300027.8_Frame_Shift_Del_p.K780fs	NM_001113378.1	NP_001106849.1	Q9NVI1	FANCI_HUMAN	Fanconi anemia, complementation group I	780					cell cycle (GO:0007049)|DNA repair (GO:0006281)|positive regulation of protein ubiquitination (GO:0031398)	membrane (GO:0016020)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|DNA polymerase binding (GO:0070182)			breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	Lung NSC(78;0.0472)|all_lung(78;0.089)					TATGTGTTACAAAAAACTCTC	0.343								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.Y778X		Atlas-INDEL	.											.	FANCI	129	.	0			c.2334delC						.						100.0	100.0	100.0					15																	89837107		2199	4299	6498	SO:0001589	frameshift_variant	55215	exon23	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	.	BC004277	CCDS10349.2, CCDS45346.1	15q26.1	2014-09-17	2007-05-03	2007-05-03	ENSG00000140525	ENSG00000140525		"""Fanconi anemia, complementation groups"""	25568	protein-coding gene	gene with protein product		611360	"""KIAA1794"""	KIAA1794		14630800, 17460694, 17412408	Standard	NM_001113378		Approved	FLJ10719	uc010bnp.1	Q9NVI1	OTTHUMG00000132993	ENST00000310775.7:c.2335delA	chr15.hg19:g.89837107delA	ENSP00000310842:p.Lys780fs	102.0	0.0		180.0	11.0	NM_001113378	A4ZVE4|A5YMH4|A6NJZ0|Q96JN1|Q96ST0|Q9BT96	Frame_Shift_Del	DEL	ENST00000310775.7	hg19	CCDS45346.1																																																																																			.	.		0.343	FANCI-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421140.1	NM_018193	
FAM187B	148109	hgsc.bcm.edu	37	19	35715793	35715793	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:35715793delC	ENST00000324675.3	-	2	1093	c.1045delG	c.(1045-1047)gcgfs	p.A349fs		NM_152481.1	NP_689694.1	Q17R55	F187B_HUMAN	family with sequence similarity 187, member B	349						integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|large_intestine(2)|lung(3)|ovary(2)	9						TTGAGCAGCGCCCCCAGCAGG	0.687																																					p.A349fs		Atlas-INDEL	.											FAM187B,NS,carcinoma,0,1	FAM187B	28	.	0			c.1046delC						.						29.0	31.0	30.0					19																	35715793		2203	4300	6503	SO:0001589	frameshift_variant	148109	exon2			.	AK098526	CCDS12448.1	19q13.12	2008-10-16	2008-10-16	2008-10-16	ENSG00000177558	ENSG00000177558			26366	protein-coding gene	gene with protein product			"""transmembrane protein 162"""	TMEM162			Standard	NM_152481		Approved	FLJ25660	uc002nyk.1	Q17R55	OTTHUMG00000164450	ENST00000324675.3:c.1045delG	chr19.hg19:g.35715793delC	ENSP00000323355:p.Ala349fs	145.0	0.0		189.0	12.0	NM_152481	Q8N7G6	Frame_Shift_Del	DEL	ENST00000324675.3	hg19	CCDS12448.1																																																																																			.	.		0.687	FAM187B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378854.1	NM_152481	
ATG9A	79065	hgsc.bcm.edu	37	2	220088847	220088847	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:220088847delC	ENST00000409618.1	-	8	1685	c.1246delG	c.(1246-1248)gtcfs	p.V416fs	ATG9A_ENST00000409422.1_Frame_Shift_Del_p.V355fs|ATG9A_ENST00000396761.2_Frame_Shift_Del_p.V416fs|ATG9A_ENST00000488833.1_5'Flank|ATG9A_ENST00000361242.4_Frame_Shift_Del_p.V416fs|AC068946.1_ENST00000408417.1_RNA			Q7Z3C6	ATG9A_HUMAN	autophagy related 9A	416					autophagic vacuole assembly (GO:0000045)|late nucleophagy (GO:0044805)|mitochondrion degradation (GO:0000422)|piecemeal microautophagy of nucleus (GO:0034727)|protein localization to pre-autophagosomal structure (GO:0034497)|protein transport (GO:0015031)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)|pre-autophagosomal structure (GO:0000407)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)				endometrium(2)|large_intestine(5)|lung(3)|prostate(1)|skin(1)|stomach(1)	13		Renal(207;0.0474)		Epithelial(149;1.37e-06)|all cancers(144;0.000222)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GTCACGGTGACCCCCAGGAGT	0.582																																					p.V416fs		Atlas-INDEL	.											.	ATG9A	50	.	0			c.1247delT						.						107.0	116.0	113.0					2																	220088847		2124	4227	6351	SO:0001589	frameshift_variant	79065	exon8			.	AK021732	CCDS42820.1	2q35	2014-02-12	2012-06-06	2005-09-11	ENSG00000198925	ENSG00000198925			22408	protein-coding gene	gene with protein product		612204	"""APG9 autophagy 9-like 1 (S. cerevisiae)"", ""ATG9 autophagy related 9 homolog A (S. cerevisiae)"""	APG9L1			Standard	NM_024085		Approved	FLJ22169	uc002vkf.1	Q7Z3C6	OTTHUMG00000154557	ENST00000409618.1:c.1246delG	chr2.hg19:g.220088847delC	ENSP00000386710:p.Val416fs	138.0	0.0		171.0	11.0	NM_001077198	Q3ZAQ6|Q6P0N7|Q7Z317|Q7Z320|Q8NDK6|Q8WU65|Q9BVL5|Q9H6L1|Q9HAG7	Frame_Shift_Del	DEL	ENST00000409618.1	hg19	CCDS42820.1																																																																																			.	.		0.582	ATG9A-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335930.1	NM_024085	
NUP153	9972	hgsc.bcm.edu	37	6	17665533	17665533	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:17665533delT	ENST00000262077.2	-	9	1151	c.1152delA	c.(1150-1152)aaafs	p.K384fs	NUP153_ENST00000537253.1_Frame_Shift_Del_p.K384fs	NM_005124.2	NP_005115.2	P49790	NU153_HUMAN	nucleoporin 153kDa	384					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of RNA export from nucleus (GO:0046832)|nuclear pore complex assembly (GO:0051292)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral entry into host cell (GO:0046718)|viral penetration into host nucleus (GO:0075732)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|nucleocytoplasmic transporter activity (GO:0005487)|protein anchor (GO:0043495)|structural constituent of nuclear pore (GO:0017056)|transporter activity (GO:0005215)|zinc ion binding (GO:0008270)			NS(2)|breast(6)|endometrium(4)|kidney(3)|large_intestine(7)|lung(23)|ovary(3)|skin(3)|urinary_tract(2)	53	Breast(50;0.0259)|Ovarian(93;0.0584)	all_hematologic(90;0.125)	all cancers(50;0.0981)|Epithelial(50;0.112)			TCAGAGATGGTTTAAAATAAA	0.363																																					p.P385fs		Atlas-INDEL	.											.	NUP153	116	.	0			c.1153delC						.						113.0	109.0	111.0					6																	17665533		2203	4300	6503	SO:0001589	frameshift_variant	9972	exon9			.	Z25535	CCDS4541.1, CCDS64359.1, CCDS75407.1	6p22.3	2008-07-29	2002-08-29		ENSG00000124789	ENSG00000124789			8062	protein-coding gene	gene with protein product		603948	"""nucleoporin 153kD"""			8110839	Standard	NM_001278209		Approved	HNUP153	uc003ncd.2	P49790	OTTHUMG00000014312	ENST00000262077.2:c.1152delA	chr6.hg19:g.17665533delT	ENSP00000262077:p.Lys384fs	108.0	0.0		163.0	10.0	NM_005124	B4DIK2|E7EPX5|F6QR24|Q4LE47|Q5T9I7|Q7Z743	Frame_Shift_Del	DEL	ENST00000262077.2	hg19	CCDS4541.1																																																																																			.	.		0.363	NUP153-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039953.1		
AIM1	202	hgsc.bcm.edu	37	6	106973032	106973032	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:106973032delA	ENST00000369066.3	+	3	3533	c.3046delA	c.(3046-3048)aaafs	p.K1016fs		NM_001624.2	NP_001615	Q9UMX9	S45A2_HUMAN	absent in melanoma 1	0					developmental pigmentation (GO:0048066)|melanin biosynthetic process (GO:0042438)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)				breast(8)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(7)|large_intestine(13)|lung(20)|ovary(5)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	69	Breast(9;0.0138)|all_epithelial(6;0.169)	all_cancers(87;4.67e-25)|all_epithelial(87;5.46e-21)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|Colorectal(196;3.46e-05)|all_lung(197;5.94e-05)|Lung NSC(302;7.26e-05)|Ovarian(999;0.00473)	Epithelial(6;0.00114)|all cancers(7;0.00726)|BRCA - Breast invasive adenocarcinoma(8;0.0114)|OV - Ovarian serous cystadenocarcinoma(5;0.0305)	all cancers(137;1.73e-50)|Epithelial(106;2.42e-48)|OV - Ovarian serous cystadenocarcinoma(136;1.51e-27)|BRCA - Breast invasive adenocarcinoma(108;0.00104)|GBM - Glioblastoma multiforme(226;0.00858)		TGTCCAAAATAAACTCAATCC	0.378																																					p.N1015fs		Atlas-INDEL	.											.	AIM1	161	.	0			c.3045delT						.						177.0	172.0	174.0					6																	106973032		2203	4300	6503	SO:0001589	frameshift_variant	202	exon3			.	U83115	CCDS34506.1	6q21	2014-01-29			ENSG00000112297	ENSG00000112297			356	protein-coding gene	gene with protein product	"""suppression of tumorigenicity 4"", ""beta-gamma crystallin domain containing 1"""	601797	"""suppression of tumorigenicity 4 (malignant melanoma)"""	ST4		1680551, 12693952	Standard	NM_001624		Approved	CRYBG1	uc003prh.3	Q9Y4K1	OTTHUMG00000015302	ENST00000369066.3:c.3046delA	chr6.hg19:g.106973032delA	ENSP00000358062:p.Lys1016fs	168.0	0.0		199.0	12.0	NM_001624	Q6P2P0|Q9BTM3	Frame_Shift_Del	DEL	ENST00000369066.3	hg19	CCDS34506.1																																																																																			.	.		0.378	AIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041669.1		
IKZF5	64376	hgsc.bcm.edu	37	10	124753859	124753859	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:124753859delT	ENST00000368886.5	-	5	1017	c.697delA	c.(697-699)accfs	p.T234fs	PSTK_ENST00000497219.1_Intron	NM_001271840.1	NP_001258769.1	Q9H5V7	IKZF5_HUMAN	IKAROS family zinc finger 5 (Pegasus)	234					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|lung(3)|prostate(1)	6		all_neural(114;0.169)|Colorectal(57;0.178)|Glioma(114;0.222)		Colorectal(40;0.0701)|COAD - Colon adenocarcinoma(40;0.0754)		GTTGGTGTGGTTTTTGCCATA	0.483																																					p.T233fs		Atlas-INDEL	.											.	IKZF5	26	.	0			c.698delC						.						160.0	158.0	159.0					10																	124753859		1966	4147	6113	SO:0001589	frameshift_variant	64376	exon5			.	AF230808	CCDS41574.1	10q26	2011-05-31	2006-08-25	2006-08-25	ENSG00000095574	ENSG00000095574		"""Zinc fingers, C2H2-type"", ""IKAROS zinc fingers"""	14283	protein-coding gene	gene with protein product		606238	"""zinc finger protein, subfamily 1A, 5"", ""zinc finger protein, subfamily 1A, 5 (Pegasus)"""	ZNFN1A5		10978333	Standard	NM_001271840		Approved	Pegasus, FLJ22973	uc021qaj.2	Q9H5V7	OTTHUMG00000019192	ENST00000368886.5:c.697delA	chr10.hg19:g.124753859delT	ENSP00000357881:p.Thr234fs	208.0	0.0		246.0	17.0	NM_001271840	B3KVH7|D3DRE7|Q9H2T0	Frame_Shift_Del	DEL	ENST00000368886.5	hg19	CCDS41574.1																																																																																			.	.		0.483	IKZF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050820.2	NM_022466	
BBS2	583	hgsc.bcm.edu	37	16	56534909	56534909	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:56534909delA	ENST00000245157.5	-	11	1674	c.1254delT	c.(1252-1254)tttfs	p.F418fs	BBS2_ENST00000568104.1_Frame_Shift_Del_p.F418fs|BBS2_ENST00000561951.1_5'Flank	NM_031885.3	NP_114091	Q9BXC9	BBS2_HUMAN	Bardet-Biedl syndrome 2	418					adult behavior (GO:0030534)|artery smooth muscle contraction (GO:0014824)|brain morphogenesis (GO:0048854)|cartilage development (GO:0051216)|cerebral cortex development (GO:0021987)|cilium morphogenesis (GO:0060271)|fat cell differentiation (GO:0045444)|Golgi to plasma membrane protein transport (GO:0043001)|hippocampus development (GO:0021766)|melanosome transport (GO:0032402)|negative regulation of appetite by leptin-mediated signaling pathway (GO:0038108)|negative regulation of gene expression (GO:0010629)|negative regulation of multicellular organism growth (GO:0040015)|nonmotile primary cilium assembly (GO:0035058)|photoreceptor cell maintenance (GO:0045494)|positive regulation of multicellular organism growth (GO:0040018)|protein localization (GO:0008104)|protein localization to organelle (GO:0033365)|regulation of cilium beat frequency involved in ciliary motility (GO:0060296)|sperm axoneme assembly (GO:0007288)|striatum development (GO:0021756)|vasodilation (GO:0042311)|visual perception (GO:0007601)	BBSome (GO:0034464)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	RNA polymerase II repressing transcription factor binding (GO:0001103)			breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)|skin(3)	26						TTCCTTCTGCAAAAATCAATA	0.468									Bardet-Biedl syndrome																												p.A419fs		Atlas-INDEL	.											.	BBS2	67	.	0			c.1255delG						.						140.0	137.0	138.0					16																	56534909		2198	4300	6498	SO:0001589	frameshift_variant	583	exon11	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	.	AF342736	CCDS32451.1	16q21	2013-01-08				ENSG00000125124			967	protein-coding gene	gene with protein product		606151		BBS		11285252	Standard	NM_031885		Approved		uc002ejd.2	Q9BXC9		ENST00000245157.5:c.1254delT	chr16.hg19:g.56534909delA	ENSP00000245157:p.Phe418fs	191.0	0.0		212.0	14.0	NM_031885	Q96CM0|Q96SN9	Frame_Shift_Del	DEL	ENST00000245157.5	hg19	CCDS32451.1																																																																																			.	.		0.468	BBS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434386.2	NM_031885	
SETD2	29072	hgsc.bcm.edu	37	3	47143007	47143007	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:47143007delG	ENST00000409792.3	-	8	4998	c.4956delC	c.(4954-4956)accfs	p.T1653fs		NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	1653	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)			breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		CCAGTTTGGTGGTAAAAAACC	0.398			"""N, F, S, Mis"""		clear cell renal carcinoma																																p.T1653fs		Atlas-INDEL	.		Rec	yes		3	3p21.31	29072	SET domain containing 2		E	.	SETD2	721	.	0			c.4957delA						.						159.0	159.0	159.0					3																	47143007		2203	4300	6503	SO:0001589	frameshift_variant	29072	exon8			.	AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"""Chromatin-modifying enzymes / K-methyltransferases"""	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.4956delC	chr3.hg19:g.47143007delG	ENSP00000386759:p.Thr1653fs	126.0	0.0		160.0	10.0	NM_014159	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Frame_Shift_Del	DEL	ENST00000409792.3	hg19	CCDS2749.2																																																																																			.	.		0.398	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159	
SHANK3	85358	hgsc.bcm.edu	37	22	51160703	51160703	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr22:51160703delG	ENST00000414786.2	+	21	4627	c.4400delG	c.(4399-4401)cggfs	p.R1467fs	SHANK3_ENST00000262795.3_Frame_Shift_Del_p.R1497fs|SHANK3_ENST00000445220.2_Frame_Shift_Del_p.R1483fs			Q9BYB0	SHAN3_HUMAN	SH3 and multiple ankyrin repeat domains 3	1481					adult behavior (GO:0030534)|alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor clustering (GO:0097113)|brain morphogenesis (GO:0048854)|dendritic spine morphogenesis (GO:0060997)|guanylate kinase-associated protein clustering (GO:0097117)|learning (GO:0007612)|MAPK cascade (GO:0000165)|memory (GO:0007613)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of actin filament bundle assembly (GO:0032232)|negative regulation of cell volume (GO:0045794)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of glutamate receptor signaling pathway (GO:1900451)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of synapse structural plasticity (GO:0051835)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density assembly (GO:0097107)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of long term synaptic depression (GO:1900452)|regulation of long-term synaptic potentiation (GO:1900271)|social behavior (GO:0035176)|striatal medium spiny neuron differentiation (GO:0021773)|synapse assembly (GO:0007416)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|ciliary membrane (GO:0060170)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)|neuron spine (GO:0044309)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	GKAP/Homer scaffold activity (GO:0030160)|identical protein binding (GO:0042802)|ionotropic glutamate receptor binding (GO:0035255)|protein C-terminus binding (GO:0008022)|scaffold protein binding (GO:0097110)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(5)	8		all_cancers(38;3.75e-11)|all_epithelial(38;1.82e-09)|Breast(42;0.000448)|all_lung(38;0.000665)|Lung NSC(38;0.0104)|Ovarian(80;0.104)|Lung SC(80;0.162)|Hepatocellular(38;0.178)		BRCA - Breast invasive adenocarcinoma(115;0.22)		GTGGAGAGCCGGGGGCTCCCT	0.677																																					p.R1467fs		Atlas-INDEL	.											.	SHANK3	96	.	0			c.4399delC						.						24.0	28.0	27.0					22																	51160703		1843	3976	5819	SO:0001589	frameshift_variant	85358	exon21			.	AB051437		22q13.3	2013-11-14			ENSG00000251322	ENSG00000251322		"""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	14294	protein-coding gene	gene with protein product	"""proline rich synapse associated protein 2"", ""shank postsynaptic density protein"""	606230				11258795, 11431708, 10806096, 17173049	Standard	NM_033517		Approved	SPANK-2, prosap2, KIAA1650, PSAP2	uc031ryd.1	Q9BYB0	OTTHUMG00000150169	ENST00000414786.2:c.4400delG	chr22.hg19:g.51160703delG	ENSP00000464552:p.Arg1467fs	177.0	0.0		214.0	13.0	NM_033517	D7UT47|Q8TET3	Frame_Shift_Del	DEL	ENST00000414786.2	hg19																																																																																				.	.		0.677	SHANK3-001	KNOWN	non_canonical_polymorphism|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000316674.2	NM_001080420	
MAPK15	225689	hgsc.bcm.edu	37	8	144802914	144802914	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr8:144802914delC	ENST00000338033.4	+	9	940	c.821delC	c.(820-822)tccfs	p.S274fs	RP11-429J17.5_ENST00000527908.1_RNA	NM_139021.2	NP_620590.2	Q8TD08	MK15_HUMAN	mitogen-activated protein kinase 15	274	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				MAPK cascade (GO:0000165)|negative regulation of DNA replication (GO:0008156)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|protein autophosphorylation (GO:0046777)|response to estradiol (GO:0032355)	extracellular region (GO:0005576)|intracellular (GO:0005622)|nucleus (GO:0005634)	ATP binding (GO:0005524)|MAP kinase activity (GO:0004707)|SH3 domain binding (GO:0017124)			endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)|skin(1)|stomach(1)	12	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.38e-41)|Epithelial(56;6.8e-40)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.146)			CCAGACACCTCCCCAGAGGCC	0.667																																					p.S274fs		Atlas-INDEL	.											.	MAPK15	32	.	0			c.820delT						.						33.0	46.0	41.0					8																	144802914		2145	4246	6391	SO:0001589	frameshift_variant	225689	exon9			.	AY065978	CCDS6409.2	8q24.3	2011-06-09			ENSG00000181085	ENSG00000181085		"""Mitogen-activated protein kinase cascade / Kinases"""	24667	protein-coding gene	gene with protein product	"""extracellular signal regulated kinase 8"""					11875070	Standard	XM_006716528		Approved	ERK8, ERK7	uc003yzj.3	Q8TD08	OTTHUMG00000146450	ENST00000338033.4:c.821delC	chr8.hg19:g.144802914delC	ENSP00000337691:p.Ser274fs	60.0	0.0		198.0	13.0	NM_139021	Q2TCF9|Q8N362	Frame_Shift_Del	DEL	ENST00000338033.4	hg19	CCDS6409.2																																																																																			.	.		0.667	MAPK15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000300348.1	NM_139021	
DSG4	147409	hgsc.bcm.edu	37	18	28986275	28986275	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr18:28986275delA	ENST00000308128.4	+	12	2007	c.1872delA	c.(1870-1872)tcafs	p.S624fs	DSG4_ENST00000359747.4_Frame_Shift_Del_p.S624fs|RP11-534N16.1_ENST00000581856.1_RNA|RP11-534N16.1_ENST00000578477.1_RNA	NM_177986.3	NP_817123.1	Q86SJ6	DSG4_HUMAN	desmoglein 4	624					anagen (GO:0042640)|BMP signaling pathway (GO:0030509)|homophilic cell adhesion (GO:0007156)|keratinocyte differentiation (GO:0030216)|single organismal cell-cell adhesion (GO:0016337)	desmosome (GO:0030057)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(6)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(11)|liver(2)|lung(35)|ovary(4)|skin(1)|stomach(1)|urinary_tract(1)	70			OV - Ovarian serous cystadenocarcinoma(10;0.00504)			CTGGAGTTTCAAATGTTGGTC	0.478																																					p.S624X		Atlas-INDEL	.											.	DSG4	343	.	0			c.1871delC						.						99.0	99.0	99.0					18																	28986275		2203	4300	6503	SO:0001589	frameshift_variant	147409	exon12			.	AY177664, AY168788	CCDS11897.1, CCDS45845.1	18q12.1	2010-01-26			ENSG00000175065	ENSG00000175065		"""Cadherins / Major cadherins"""	21307	protein-coding gene	gene with protein product		607892				12648213	Standard	NM_001134453		Approved	CDHF13, LAH	uc002kwq.2	Q86SJ6	OTTHUMG00000131979	ENST00000308128.4:c.1872delA	chr18.hg19:g.28986275delA	ENSP00000311859:p.Ser624fs	157.0	0.0		180.0	12.0	NM_001134453	A2RUI1|Q6Y9L9|Q8IXV4	Frame_Shift_Del	DEL	ENST00000308128.4	hg19	CCDS11897.1																																																																																			.	.		0.478	DSG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254941.1	NM_177986	
HNRNPDL	9987	hgsc.bcm.edu	37	4	83348625	83348625	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:83348625delT	ENST00000295470.5	-	4	1042	c.867delA	c.(865-867)aaafs	p.K289fs	HNRNPDL_ENST00000602300.1_Frame_Shift_Del_p.K170fs|HNRNPDL_ENST00000502762.1_Frame_Shift_Del_p.K289fs|HNRNPDL_ENST00000514511.1_5'UTR|HNRNPDL_ENST00000349655.4_Frame_Shift_Del_p.K170fs	NM_001207000.1|NM_031372.3	NP_001193929.1|NP_112740.1	O14979	HNRDL_HUMAN	heterogeneous nuclear ribonucleoprotein D-like	289	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				regulation of gene expression (GO:0010468)|regulation of transcription, DNA-templated (GO:0006355)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|poly(G) binding (GO:0034046)|single-stranded DNA binding (GO:0003697)										TTTCTAACAATTTTTTTACTG	0.289																																					p.L290fs		Atlas-INDEL	.											.	HNRPDL	35	.	0			c.868delT						.						74.0	75.0	75.0					4																	83348625		2202	4299	6501	SO:0001589	frameshift_variant	9987	exon4			.	D89092	CCDS3593.1, CCDS75153.1	4q21.22	2013-06-12		2013-06-12	ENSG00000152795	ENSG00000152795		"""RNA binding motif (RRM) containing"""	5037	protein-coding gene	gene with protein product		607137		HNRPDL		10072754, 9524220	Standard	NM_001207000		Approved	JKTBP, laAUF1	uc003hmr.3	O14979	OTTHUMG00000130299	ENST00000295470.5:c.867delA	chr4.hg19:g.83348625delT	ENSP00000295470:p.Lys289fs	135.0	0.0		125.0	11.0	NM_031372	Q6SPF2|Q7KZ74|Q7KZ75|Q96IM0|Q96S43	Frame_Shift_Del	DEL	ENST00000295470.5	hg19	CCDS3593.1																																																																																			.	.		0.289	HNRNPDL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252644.1	NM_005463	
MYO1H	283446	hgsc.bcm.edu	37	12	109879445	109879445	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:109879445delA	ENST00000431443.2	+	25	2546	c.2546delA	c.(2545-2547)gaafs	p.E849fs	MYO1H_ENST00000310903.5_Frame_Shift_Del_p.E839fs	NM_001101421.3	NP_001094891.3	Q8N1T3	MYO1H_HUMAN	myosin IH	849	Myosin tail. {ECO:0000255}.					myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(17)|prostate(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	47						GTTACAAGTGAAATCTTCAGG	0.408																																					p.E839fs		Atlas-INDEL	.											.	MYO1H	98	.	0			c.2515delG						.						93.0	82.0	85.0					12																	109879445		1861	4101	5962	SO:0001589	frameshift_variant	283446	exon25			.		CCDS53826.1	12q24.11	2011-09-27			ENSG00000174527	ENSG00000174527		"""Myosins / Myosin superfamily : Class I"""	13879	protein-coding gene	gene with protein product		614636					Standard	NM_001101421		Approved	FLJ37587	uc010sxn.1	Q8N1T3	OTTHUMG00000169252	ENST00000431443.2:c.2546delA	chr12.hg19:g.109879445delA	ENSP00000444076:p.Glu849fs	171.0	0.0		204.0	14.0	NM_001101421	F5H3C6	Frame_Shift_Del	DEL	ENST00000431443.2	hg19																																																																																				.	.		0.408	MYO1H-201	KNOWN	basic	protein_coding	protein_coding		NM_173597	
GABRA4	2557	hgsc.bcm.edu	37	4	46979532	46979532	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:46979532delG	ENST00000264318.3	-	4	1371	c.389delC	c.(388-390)cctfs	p.P130fs		NM_000809.3|NM_001204266.1|NM_001204267.1	NP_000800.2|NP_001191195.1|NP_001191196.1	P48169	GBRA4_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 4	130					central nervous system development (GO:0007417)|gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|regulation of response to drug (GO:2001023)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(17)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	45					Acamprosate(DB00659)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)	GAAAGTATCAGGGGTCCACAC	0.348																																					p.P130fs	Ovarian(6;283 369 8234 12290 33402)	Atlas-INDEL	.											.	GABRA4	129	.	0			c.390delT						.						99.0	98.0	98.0					4																	46979532		2202	4300	6502	SO:0001589	frameshift_variant	2557	exon4			.		CCDS3473.1	4p12	2012-06-22			ENSG00000109158	ENSG00000109158		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4078	protein-coding gene	gene with protein product	"""GABA(A) receptor, alpha 4"""	137141				7607683	Standard	NM_000809		Approved		uc021xnz.1	P48169	OTTHUMG00000099431	ENST00000264318.3:c.389delC	chr4.hg19:g.46979532delG	ENSP00000264318:p.Pro130fs	182.0	0.0		192.0	12.0	NM_000809	Q8IYR7	Frame_Shift_Del	DEL	ENST00000264318.3	hg19	CCDS3473.1																																																																																			.	.		0.348	GABRA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216893.1		
ZMAT1	84460	hgsc.bcm.edu	37	X	101138606	101138606	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:101138606delT	ENST00000372782.3	-	7	1840	c.1793delA	c.(1792-1794)aagfs	p.K600fs	ZMAT1_ENST00000494068.1_5'UTR|ZMAT1_ENST00000458570.1_Frame_Shift_Del_p.K429fs|ZMAT1_ENST00000540921.1_Frame_Shift_Del_p.K600fs	NM_001011657.3	NP_001011657	Q5H9K5	ZMAT1_HUMAN	zinc finger, matrin-type 1	600						nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			endometrium(3)|kidney(2)|large_intestine(6)|lung(6)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	22						GCTTTTTTTCTTTTTTCGATG	0.388																																					p.K598fs		Atlas-INDEL	.											.	ZMAT1	143	.	0			c.1794delG						.						178.0	153.0	161.0					X																	101138606		2203	4300	6503	SO:0001589	frameshift_variant	84460	exon7			.	Z69304	CCDS35348.1	Xq21	2012-10-05	2010-09-15		ENSG00000166432	ENSG00000166432		"""Zinc fingers, matrin-type"""	29377	protein-coding gene	gene with protein product							Standard	NM_001011657		Approved	KIAA1789	uc011mrl.2	Q5H9K5	OTTHUMG00000022044	ENST00000372782.3:c.1793delA	chrX.hg19:g.101138606delT	ENSP00000361868:p.Lys600fs	119.0	0.0		141.0	10.0	NM_001011657	Q8NDS3|Q96JN6	Frame_Shift_Del	DEL	ENST00000372782.3	hg19	CCDS35348.1																																																																																			.	.		0.388	ZMAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057598.1		
SLC36A4	120103	hgsc.bcm.edu	37	11	92901154	92901154	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:92901154delA	ENST00000326402.4	-	7	854	c.724delT	c.(724-726)tccfs	p.S242fs	SLC36A4_ENST00000529184.1_Frame_Shift_Del_p.S107fs	NM_152313.2	NP_689526.2	Q6YBV0	S36A4_HUMAN	solute carrier family 36 (proton/amino acid symporter), member 4	242					L-alanine transport (GO:0015808)|proline transport (GO:0015824)|tryptophan transport (GO:0015827)	integral component of membrane (GO:0016021)	symporter activity (GO:0015293)			breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(11)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	25		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				ACAGCCATGGAAACGTTGGCA	0.303																																					p.S242fs		Atlas-INDEL	.											.	SLC36A4	61	.	0			c.725delC						.						101.0	100.0	101.0					11																	92901154		2201	4295	6496	SO:0001589	frameshift_variant	120103	exon7			.	AY162216	CCDS8291.1, CCDS66202.1	11q21	2013-05-22			ENSG00000180773	ENSG00000180773		"""Solute carriers"""	19660	protein-coding gene	gene with protein product		613760					Standard	XM_005273758		Approved	PAT4, FLJ38932	uc001pdn.3	Q6YBV0	OTTHUMG00000167368	ENST00000326402.4:c.724delT	chr11.hg19:g.92901154delA	ENSP00000317382:p.Ser242fs	114.0	0.0		185.0	12.0	NM_152313	Q86X30|Q8IVM5|Q8N8S6	Frame_Shift_Del	DEL	ENST00000326402.4	hg19	CCDS8291.1																																																																																			.	.		0.303	SLC36A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394329.2		
HLA-DOA	3111	hgsc.bcm.edu	37	6	32974621	32974621	+	Intron	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:32974621delA	ENST00000229829.5	-	5	825				HLA-DOA_ENST00000495532.1_5'Flank|HLA-DOA_ENST00000450833.2_Intron	NM_002119.3	NP_002110.1	P06340	DOA_HUMAN	major histocompatibility complex, class II, DO alpha						antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|immune response (GO:0006955)|negative regulation of antigen processing and presentation of peptide antigen via MHC class II (GO:0002587)|regulation of T cell differentiation (GO:0045580)|signal transduction (GO:0007165)	endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)	MHC class II protein complex binding (GO:0023026)|MHC class II receptor activity (GO:0032395)			NS(1)|breast(1)|central_nervous_system(1)|large_intestine(2)|lung(3)|prostate(1)	9						ATCATTACCTAAAATAGCAGA	0.493																																					.		Atlas-INDEL	.											.	HLA-DOA	22	.	0			c.750-2T>-						.						89.0	85.0	86.0					6																	32974621		1511	2709	4220	SO:0001627	intron_variant	3111	exon6			.	M31525	CCDS4763.1	6p21.3	2013-01-11		2001-10-05	ENSG00000204252	ENSG00000204252		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4936	protein-coding gene	gene with protein product		142930		HLA-DZA, HLA-DNA		2370084	Standard	XM_005272804		Approved	HLA-D0-alpha	uc003ocr.3	P06340	OTTHUMG00000031211	ENST00000229829.5:c.750-3T>-	chr6.hg19:g.32974621delA		99.0	0.0		152.0	10.0	NM_002119	Q58HU0|Q58HU1|Q5STC7|Q9TQC6|Q9TQC7|Q9TQC8|Q9TQC9|Q9TQD0|Q9TQD1|Q9TQD2|Q9TQD3	Splice_Site	DEL	ENST00000229829.5	hg19	CCDS4763.1																																																																																			.	.		0.493	HLA-DOA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076426.2	NM_002119	
ARHGEF1	9138	hgsc.bcm.edu	37	19	42407036	42407036	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:42407036delG	ENST00000354532.3	+	18	1874	c.1726delG	c.(1726-1728)gggfs	p.G576fs	ARHGEF1_ENST00000337665.4_Frame_Shift_Del_p.G591fs|ARHGEF1_ENST00000347545.4_Frame_Shift_Del_p.G543fs|ARHGEF1_ENST00000378152.4_Frame_Shift_Del_p.G558fs|ARHGEF1_ENST00000599846.1_Frame_Shift_Del_p.G632fs	NM_004706.3	NP_004697.2	Q92888	ARHG1_HUMAN	Rho guanine nucleotide exchange factor (GEF) 1	576	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				cell proliferation (GO:0008283)|negative regulation of axonogenesis (GO:0050771)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of axonogenesis (GO:0050770)|Rho protein signal transduction (GO:0007266)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|poly(A) RNA binding (GO:0044822)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|endometrium(8)|large_intestine(6)|lung(9)|ovary(3)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	37		Renal(1328;0.000518)|Hepatocellular(1079;0.0046)|Medulloblastoma(540;0.0425)		Epithelial(262;5.89e-46)|GBM - Glioblastoma multiforme(1328;2.49e-12)|STAD - Stomach adenocarcinoma(1328;0.00644)		GCAGAGCATCGGGCAGAACAC	0.567																																					p.I590fs		Atlas-INDEL	.											.	ARHGEF1	95	.	0			c.1770delC						.						30.0	32.0	31.0					19																	42407036		2203	4300	6503	SO:0001589	frameshift_variant	9138	exon18			.	U64105	CCDS12590.1, CCDS12591.1, CCDS12592.1	19q13.13	2014-06-19			ENSG00000076928	ENSG00000076928		"""Rho guanine nucleotide exchange factors"""	681	protein-coding gene	gene with protein product		601855				8810315, 9135076	Standard	NM_004706		Approved	P115-RHOGEF, SUB1.5, LBCL2	uc002osa.3	Q92888	OTTHUMG00000182679	ENST00000354532.3:c.1726delG	chr19.hg19:g.42407036delG	ENSP00000346532:p.Gly576fs	99.0	0.0		108.0	10.0	NM_199002	O00513|Q8N4J4|Q96BF4|Q96F17|Q9BSB1	Frame_Shift_Del	DEL	ENST00000354532.3	hg19	CCDS12591.1																																																																																			.	.		0.567	ARHGEF1-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000463360.1	NM_199002	
TAF2	6873	hgsc.bcm.edu	37	8	120774703	120774703	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr8:120774703delA	ENST00000378164.2	-	19	2808	c.2510delT	c.(2509-2511)ttgfs	p.L837fs	TAF2_ENST00000519355.1_5'UTR	NM_003184.3	NP_003175	Q6P1X5	TAF2_HUMAN	TAF2 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 150kDa	837					G2/M transition of mitotic cell cycle (GO:0000086)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to organic cyclic compound (GO:0014070)|transcription initiation from RNA polymerase II promoter (GO:0006367)	transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	metallopeptidase activity (GO:0008237)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(2)|breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(21)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	49	Lung NSC(37;9.35e-07)|Ovarian(258;0.011)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)			TTCCATATTCAAAAATCTGGT	0.333																																					p.L837fs		Atlas-INDEL	.											.	TAF2	204	.	0			c.2511delG						.						69.0	69.0	69.0					8																	120774703		2203	4300	6503	SO:0001589	frameshift_variant	6873	exon19			.	AF040701	CCDS34937.1	8q24	2012-07-18	2002-08-29	2001-12-07	ENSG00000064313	ENSG00000064313			11536	protein-coding gene	gene with protein product		604912	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, B, 150kD"""	TAF2B		9774672, 9418870	Standard	NM_003184		Approved	TAFII150, CIF150	uc003you.3	Q6P1X5	OTTHUMG00000165009	ENST00000378164.2:c.2510delT	chr8.hg19:g.120774703delA	ENSP00000367406:p.Leu837fs	96.0	0.0		184.0	12.0	NM_003184	B2RE82|O43487|O43604|O60668|Q86WW7|Q8IWK4	Frame_Shift_Del	DEL	ENST00000378164.2	hg19	CCDS34937.1																																																																																			.	.		0.333	TAF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381436.1	NM_003184	
GPR155	151556	hgsc.bcm.edu	37	2	175326315	175326315	+	Splice_Site	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:175326315delC	ENST00000392552.2	-	8	1708		c.e8+1		GPR155_ENST00000392551.2_Splice_Site|GPR155_ENST00000295500.4_Splice_Site	NM_001267051.1|NM_152529.6	NP_001253980.1|NP_689742.4	Q7Z3F1	GP155_HUMAN	G protein-coupled receptor 155						cognition (GO:0050890)|intracellular signal transduction (GO:0035556)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(2)|endometrium(5)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(2)	26						TACCAACTTACCCCCAGCCAG	0.363																																					.		Atlas-INDEL	.											.	GPR155	76	.	0			c.1385+2G>-						.						121.0	131.0	128.0					2																	175326315		2203	4300	6503	SO:0001630	splice_region_variant	151556	exon8			.	AY255528	CCDS2259.1, CCDS74605.1	2q31.1	2012-04-10			ENSG00000163328	ENSG00000163328			22951	protein-coding gene	gene with protein product						12679517	Standard	NM_001033045		Approved	DEPDC3, DEP.7, FLJ31819, PGR22	uc002uiu.4	Q7Z3F1	OTTHUMG00000132336	ENST00000392552.2:c.1469+1G>-	chr2.hg19:g.175326315delC		135.0	0.0		178.0	13.0	NM_001267051	B2RCI2|D3DPE2|Q4G0Y6|Q53SJ3|Q53TA8|Q69YG8|Q86SP9|Q8N261|Q8N639|Q8N8K3|Q96MV6	Splice_Site	DEL	ENST00000392552.2	hg19	CCDS2259.1																																																																																			.	.		0.363	GPR155-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255455.1	NM_152529	Intron
ZNF181	339318	hgsc.bcm.edu	37	19	35230499	35230499	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:35230499delA	ENST00000492450.1	+	3	291	c.202delA	c.(202-204)aaafs	p.K69fs	ZNF181_ENST00000392232.3_Frame_Shift_Del_p.K113fs|ZNF181_ENST00000459757.2_Frame_Shift_Del_p.K68fs			Q2M3W8	ZN181_HUMAN	zinc finger protein 181	69	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(6)|kidney(2)|large_intestine(1)|lung(7)|ovary(2)|prostate(3)|skin(1)	22	all_lung(56;1.13e-07)|Lung NSC(56;1.81e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.138)			GATGATGGAGAAAAAACTGTC	0.383																																					p.E67fs		Atlas-INDEL	.											.	ZNF181	65	.	0			c.201delG						.						146.0	142.0	143.0					19																	35230499		2203	4300	6503	SO:0001589	frameshift_variant	339318	exon3			.	BC104759, H54888	CCDS32990.2, CCDS46043.1	19q13.13	2013-01-08	2006-04-27		ENSG00000197841	ENSG00000197841		"""Zinc fingers, C2H2-type"", ""-"""	12971	protein-coding gene	gene with protein product		606741	"""zinc finger protein 181 (HHZ181)"""				Standard	NM_001029997		Approved	HHZ181, MGC44316	uc002nvu.3	Q2M3W8	OTTHUMG00000157508	ENST00000492450.1:c.202delA	chr19.hg19:g.35230499delA	ENSP00000420727:p.Lys69fs	131.0	0.0		169.0	12.0	NM_001029997	B7ZKX3|Q49A75	Frame_Shift_Del	DEL	ENST00000492450.1	hg19	CCDS32990.2																																																																																			.	.		0.383	ZNF181-002	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349005.3	NM_001029997	
NSD1	64324	hgsc.bcm.edu	37	5	176638499	176638499	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:176638499delT	ENST00000439151.2	+	5	3144	c.3099delT	c.(3097-3099)gctfs	p.A1033fs	NSD1_ENST00000354179.4_Frame_Shift_Del_p.A764fs|NSD1_ENST00000361032.4_Frame_Shift_Del_p.A930fs|NSD1_ENST00000347982.4_Frame_Shift_Del_p.A764fs	NM_022455.4	NP_071900.2	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	1033					gastrulation with mouth forming second (GO:0001702)|histone H3-K36 methylation (GO:0010452)|histone H4-K20 methylation (GO:0034770)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|estrogen receptor binding (GO:0030331)|histone methyltransferase activity (H3-K36 specific) (GO:0046975)|histone methyltransferase activity (H4-K20 specific) (GO:0042799)|retinoic acid receptor binding (GO:0042974)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(18)|lung(24)|ovary(2)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(3)	96	all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.198)	Kidney(146;0.235)		TGCGAGATGCTTTTTCAGCCC	0.463			T	NUP98	AML		Sotos Syndrome		Weaver syndrome;Sotos syndrome;Beckwith-Wiedemann syndrome	HNSCC(47;0.14)																											p.A1033fs		Atlas-INDEL	.		Dom	yes		5	5q35	64324	nuclear receptor binding SET domain protein 1	yes	L	.	NSD1	416	.	0			c.3098delC						.						126.0	124.0	125.0					5																	176638499		2203	4300	6503	SO:0001589	frameshift_variant	64324	exon5	Familial Cancer Database	Weaver-Smith syndrome;Cerebral Gigantism;BWS, Exomphalos-Macroglossia-Gigantism (EMG) syndrome, Wiedemann-Beckwith syndrome, WBS	.	AK026066	CCDS4412.1, CCDS4413.1	5q35	2014-09-17	2003-03-12		ENSG00000165671	ENSG00000165671		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	14234	protein-coding gene	gene with protein product		606681	"""Sotos syndrome"""	STO		9628876, 11896389	Standard	NM_022455		Approved	ARA267, FLJ22263, KMT3B	uc003mfr.4	Q96L73	OTTHUMG00000130846	ENST00000439151.2:c.3099delT	chr5.hg19:g.176638499delT	ENSP00000395929:p.Ala1033fs	120.0	0.0		166.0	12.0	NM_022455	Q96PD8|Q96RN7	Frame_Shift_Del	DEL	ENST00000439151.2	hg19	CCDS4412.1																																																																																			.	.		0.463	NSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253412.2	NM_172349	
ATG2A	23130	hgsc.bcm.edu	37	11	64665805	64665805	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:64665805delG	ENST00000377264.3	-	33	4813	c.4701delC	c.(4699-4701)cccfs	p.P1567fs	ATG2A_ENST00000421419.2_Frame_Shift_Del_p.P1569fs	NM_015104.2	NP_055919.2	Q2TAZ0	ATG2A_HUMAN	autophagy related 2A	1567					autophagic vacuole assembly (GO:0000045)|cellular response to nitrogen starvation (GO:0006995)|mitochondrion degradation (GO:0000422)|nucleophagy (GO:0044804)	extrinsic component of membrane (GO:0019898)|lipid particle (GO:0005811)|pre-autophagosomal structure (GO:0000407)				breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(19)|ovary(3)|prostate(5)|skin(1)|stomach(1)|urinary_tract(3)	55						GGTTGGTAGTGGGGGCCACAT	0.637											OREG0004029	type=REGULATORY REGION|Gene=BC033850|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.T1568fs		Atlas-INDEL	.											.	ATG2A	133	.	0			c.4702delA						.						50.0	52.0	51.0					11																	64665805		2201	4297	6498	SO:0001589	frameshift_variant	23130	exon33			.		CCDS31602.1	11q13.1	2014-02-12	2012-06-06		ENSG00000110046	ENSG00000110046			29028	protein-coding gene	gene with protein product			"""ATG2 autophagy related 2 homolog A (S. cerevisiae)"""			21887408	Standard	NM_015104		Approved	KIAA0404	uc001obx.3	Q2TAZ0	OTTHUMG00000066831	ENST00000377264.3:c.4701delC	chr11.hg19:g.64665805delG	ENSP00000366475:p.Pro1567fs	101.0	0.0	1078	141.0	11.0	NM_015104	O43154|Q14DM2|Q6ZTV2|Q7Z6K8|Q8IVY5|Q8TAI8|Q96HH7	Frame_Shift_Del	DEL	ENST00000377264.3	hg19	CCDS31602.1																																																																																			.	.		0.637	ATG2A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000143224.1	NM_015104	
SRPR	6734	hgsc.bcm.edu	37	11	126136482	126136482	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:126136482delT	ENST00000332118.6	-	6	883	c.729delA	c.(727-729)aaafs	p.K243fs	SRPR_ENST00000532259.1_Frame_Shift_Del_p.K215fs|FOXRED1_ENST00000532125.1_5'Flank|SRPR_ENST00000530680.1_5'Flank|FOXRED1_ENST00000263578.5_5'Flank|FOXRED1_ENST00000442061.2_5'Flank	NM_003139.3	NP_003130.2	P08240	SRPR_HUMAN	signal recognition particle receptor (docking protein)	243					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|cotranslational protein targeting to membrane (GO:0006613)|endoplasmic reticulum unfolded protein response (GO:0030968)|gene expression (GO:0010467)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|signal recognition particle receptor complex (GO:0005785)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|signal recognition particle binding (GO:0005047)			endometrium(7)|large_intestine(2)|lung(9)|ovary(2)|prostate(1)	21	all_hematologic(175;0.145)			BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0736)		CCCGGGGTGCTTTTTTGCCCT	0.502																																					p.A244fs		Atlas-INDEL	.											.	SRPR	60	.	0			c.730delG						.						109.0	109.0	109.0					11																	126136482		2201	4299	6500	SO:0001589	frameshift_variant	6734	exon6			.	BC001162	CCDS31717.1, CCDS53722.1	11q24-q25	2012-10-02	2008-10-29		ENSG00000182934	ENSG00000182934			11307	protein-coding gene	gene with protein product		182180	"""signal recognition particle receptor ('docking protein')"""			3340536, 1312991	Standard	NM_001177842		Approved	SRP-alpha, Sralpha	uc001qdh.3	P08240	OTTHUMG00000165826	ENST00000332118.6:c.729delA	chr11.hg19:g.126136482delT	ENSP00000328023:p.Lys243fs	193.0	0.0		230.0	14.0	NM_003139	A6NIB3|B2R5Z8|B4E0H3|E9PJS4|Q9BVJ4	Frame_Shift_Del	DEL	ENST00000332118.6	hg19	CCDS31717.1																																																																																			.	.		0.502	SRPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386425.2	NM_003139	
SYNE1	23345	hgsc.bcm.edu	37	6	152553297	152553297	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:152553297delT	ENST00000367255.5	-	113	21417	c.20816delA	c.(20815-20817)aatfs	p.N6939fs	SYNE1_ENST00000356820.4_Frame_Shift_Del_p.N1463fs|SYNE1_ENST00000265368.4_Frame_Shift_Del_p.N6939fs|SYNE1_ENST00000448038.1_Frame_Shift_Del_p.N6868fs|SYNE1_ENST00000341594.5_Frame_Shift_Del_p.N6551fs|SYNE1_ENST00000423061.1_Frame_Shift_Del_p.N6868fs	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	6939					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		ACCTATGGAATTTTTAATATT	0.299										HNSCC(10;0.0054)																											p.N6939fs		Atlas-INDEL	.											.	SYNE1	3227	.	0			c.20817delT						.						55.0	62.0	60.0					6																	152553297		2203	4299	6502	SO:0001589	frameshift_variant	23345	exon113			.	AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"""myocyte nuclear envelope protein 1"", ""nuclear envelope spectrin repeat-1"""	608441	"""chromosome 6 open reading frame 98"""	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.20816delA	chr6.hg19:g.152553297delT	ENSP00000356224:p.Asn6939fs	183.0	0.0		180.0	13.0	NM_182961	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Frame_Shift_Del	DEL	ENST00000367255.5	hg19	CCDS5236.2																																																																																			.	.		0.299	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961	
STAP1	26228	hgsc.bcm.edu	37	4	68472044	68472044	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:68472044delA	ENST00000265404.2	+	9	939	c.857delA	c.(856-858)gaafs	p.E286fs	STAP1_ENST00000396225.1_Frame_Shift_Del_p.E286fs	NM_012108.2	NP_036240.1	Q9ULZ2	STAP1_HUMAN	signal transducing adaptor family member 1	286					intracellular protein transport (GO:0006886)|membrane fusion (GO:0061025)|positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)				NS(1)|large_intestine(1)|liver(1)|lung(7)|skin(1)|urinary_tract(1)	12						GGGAGAAGTGAAAAGTTGAAG	0.318																																					p.E286fs		Atlas-INDEL	.											.	STAP1	46	.	0			c.856delG						.						102.0	109.0	106.0					4																	68472044		2203	4300	6503	SO:0001589	frameshift_variant	26228	exon9			.	AB023483	CCDS3515.1	4q13.2	2013-02-14	2007-08-09		ENSG00000035720	ENSG00000035720		"""SH2 domain containing"""	24133	protein-coding gene	gene with protein product	"""BCR downstream signaling 1"""	604298				10518561, 10679268	Standard	NM_012108		Approved	STAP-1, BRDG1	uc003hde.4	Q9ULZ2	OTTHUMG00000129304	ENST00000265404.2:c.857delA	chr4.hg19:g.68472044delA	ENSP00000265404:p.Glu286fs	176.0	0.0		165.0	11.0	NM_012108	B2R980	Frame_Shift_Del	DEL	ENST00000265404.2	hg19	CCDS3515.1																																																																																			.	.		0.318	STAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251434.1	NM_012108	
LILRA2	11027	hgsc.bcm.edu	37	19	55098671	55098671	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:55098671delC	ENST00000251377.3	+	9	1443	c.1310delC	c.(1309-1311)tccfs	p.S437fs	LILRA2_ENST00000251376.3_Frame_Shift_Del_p.S420fs|LILRB1_ENST00000418536.2_Intron|LILRB1_ENST00000448689.1_Intron|LILRB1_ENST00000396321.2_Intron|CTB-83J4.2_ENST00000596330.1_lincRNA|LILRA2_ENST00000391738.3_Frame_Shift_Del_p.S437fs|LILRA2_ENST00000391737.1_Frame_Shift_Del_p.S408fs			Q8N149	LIRA2_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 2	437					defense response (GO:0006952)|immune system process (GO:0002376)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	antigen binding (GO:0003823)|receptor activity (GO:0004872)			breast(1)|endometrium(2)|kidney(4)|large_intestine(2)|lung(33)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	50				GBM - Glioblastoma multiforme(193;0.0963)		TGTCCAGCATCCCTAGGCCAA	0.582																																					p.S437fs		Atlas-INDEL	.											.	LILRA2	99	.	0			c.1309delT						.						134.0	113.0	120.0					19																	55098671		2203	4300	6503	SO:0001589	frameshift_variant	11027	exon8			.	U82275	CCDS12900.1, CCDS46179.1, CCDS74453.1	19q13.4	2013-01-11			ENSG00000239998	ENSG00000239998		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6603	protein-coding gene	gene with protein product		604812				9079806, 9548455	Standard	XM_005258452		Approved	LIR-7, ILT1, CD85h, LIR7		Q8N149	OTTHUMG00000065703	ENST00000251377.3:c.1310delC	chr19.hg19:g.55098671delC	ENSP00000251377:p.Ser437fs	198.0	0.0		205.0	13.0	NM_001130917	O75020	Frame_Shift_Del	DEL	ENST00000251377.3	hg19	CCDS46179.1																																																																																			.	.		0.582	LILRA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140813.2		
MICAL3	57553	hgsc.bcm.edu	37	22	18387542	18387542	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr22:18387542delC	ENST00000441493.2	-	3	680	c.328delG	c.(328-330)gccfs	p.A110fs	MICAL3_ENST00000383094.3_Frame_Shift_Del_p.A110fs|MICAL3_ENST00000207726.7_Frame_Shift_Del_p.A110fs|MICAL3_ENST00000400561.2_Frame_Shift_Del_p.A110fs|MICAL3_ENST00000444520.1_Frame_Shift_Del_p.A110fs|MICAL3_ENST00000429452.1_Frame_Shift_Del_p.A110fs|MICAL3_ENST00000414725.2_Frame_Shift_Del_p.A110fs|MICAL3_ENST00000585038.1_Frame_Shift_Del_p.A110fs	NM_015241.2	NP_056056.2	Q7RTP6	MICA3_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 3	110	Monooxygenase domain. {ECO:0000250}.				actin filament depolymerization (GO:0030042)|cytoskeleton organization (GO:0007010)|exocytosis (GO:0006887)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	actin binding (GO:0003779)|FAD binding (GO:0071949)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	4		all_epithelial(15;0.198)		Lung(27;0.0427)		ACCACCTTGGCCCCCAGTAAG	0.532																																					p.A110fs		Atlas-INDEL	.											.	MICAL3	53	.	0			c.329delC						.						106.0	96.0	99.0					22																	18387542		1568	3582	5150	SO:0001589	frameshift_variant	57553	exon3			.	AB037785	CCDS46659.1, CCDS46660.1, CCDS46661.1	22q11.21	2013-03-26	2013-03-26		ENSG00000243156	ENSG00000243156			24694	protein-coding gene	gene with protein product		608882				12110185	Standard	NM_015241		Approved	KIAA0819	uc002zng.4	Q7RTP6	OTTHUMG00000150067	ENST00000441493.2:c.328delG	chr22.hg19:g.18387542delC	ENSP00000416015:p.Ala110fs	156.0	0.0		164.0	12.0	NM_015241	B2RXJ5|E9PEF0|O94909|Q5U4P4|Q6ICK4|Q96DF2|Q9P2I3	Frame_Shift_Del	DEL	ENST00000441493.2	hg19	CCDS46659.1																																																																																			.	.		0.532	MICAL3-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447351.1		
CDKL2	8999	hgsc.bcm.edu	37	4	76551036	76551036	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:76551036delT	ENST00000429927.2	-	2	840	c.137delA	c.(136-138)aagfs	p.K46fs	CDKL2_ENST00000307465.4_Frame_Shift_Del_p.K46fs	NM_003948.3	NP_003939.1	Q92772	CDKL2_HUMAN	cyclin-dependent kinase-like 2 (CDC2-related kinase)	46	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				sex differentiation (GO:0007548)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)			breast(3)|endometrium(1)|large_intestine(4)|lung(6)|ovary(2)|prostate(2)|skin(2)|stomach(2)	22			Lung(101;0.0973)|LUSC - Lung squamous cell carcinoma(112;0.122)			CATTGCAATCTTTTTAACCAT	0.313																																					p.K46fs		Atlas-INDEL	.											.	CDKL2	58	.	0			c.138delG						.						176.0	166.0	169.0					4																	76551036		2202	4299	6501	SO:0001589	frameshift_variant	8999	exon2			.	U35146	CCDS3570.1	4q21.21	2011-11-04			ENSG00000138769	ENSG00000138769		"""Cyclin-dependent kinases"""	1782	protein-coding gene	gene with protein product		603442				9000130	Standard	NM_003948		Approved	P56, KKIAMRE	uc003hiq.3	Q92772	OTTHUMG00000130103	ENST00000429927.2:c.137delA	chr4.hg19:g.76551036delT	ENSP00000412365:p.Lys46fs	103.0	0.0		127.0	11.0	NM_003948	B2R695	Frame_Shift_Del	DEL	ENST00000429927.2	hg19	CCDS3570.1																																																																																			.	.		0.313	CDKL2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252409.2	NM_003948	
RXRB	6257	hgsc.bcm.edu	37	6	33164342	33164342	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:33164342delC	ENST00000374680.3	-	5	1073	c.862delG	c.(862-864)gatfs	p.D288fs	RXRB_ENST00000544186.1_Frame_Shift_Del_p.D98fs|RXRB_ENST00000413614.2_Frame_Shift_Del_p.D192fs|RXRB_ENST00000374685.4_Frame_Shift_Del_p.D288fs	NM_001270401.1|NM_021976.4	NP_001257330.1|NP_068811.1	P28702	RXRB_HUMAN	retinoid X receptor, beta	288	Hinge.				cardiac muscle cell proliferation (GO:0060038)|cellular response to retinoic acid (GO:0071300)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|maternal placenta development (GO:0001893)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)|ventricular cardiac muscle cell differentiation (GO:0055012)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	9-cis retinoic acid receptor activity (GO:0004886)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(3)|lung(3)|ovary(3)|prostate(1)|skin(2)	15					Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Bexarotene(DB00307)|Tazarotene(DB00799)|Tretinoin(DB00755)	CCCTCCCCATCCCCATCCTTG	0.622																																					p.D288fs		Atlas-INDEL	.											.	RXRB	34	.	0			c.863delA						.						51.0	66.0	61.0					6																	33164342		1508	2705	4213	SO:0001589	frameshift_variant	6257	exon5			.	M84820	CCDS4768.1, CCDS59007.1	6p21.3	2013-01-16			ENSG00000204231	ENSG00000204231		"""Nuclear hormone receptors"""	10478	protein-coding gene	gene with protein product	"""nuclear receptor subfamily 2 group B member 2"""	180246				8257090	Standard	NM_021976		Approved	NR2B2, H-2RIIBP, RCoR-1	uc003odc.4	P28702	OTTHUMG00000031298	ENST00000374680.3:c.862delG	chr6.hg19:g.33164342delC	ENSP00000363812:p.Asp288fs	86.0	0.0		152.0	10.0	NM_021976	P28703|Q59G65|Q5JP92|Q5STQ1	Frame_Shift_Del	DEL	ENST00000374680.3	hg19	CCDS4768.1																																																																																			.	.		0.622	RXRB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076642.2	NM_021976	
CSF1	1435	hgsc.bcm.edu	37	1	110466713	110466713	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:110466713delC	ENST00000329608.6	+	6	1861	c.1470delC	c.(1468-1470)agcfs	p.S490fs	CSF1_ENST00000369802.3_Frame_Shift_Del_p.S490fs|CSF1_ENST00000344188.5_Frame_Shift_Del_p.S374fs|CSF1_ENST00000369801.1_Frame_Shift_Del_p.S374fs|CSF1_ENST00000420111.2_Frame_Shift_Del_p.S192fs	NM_000757.5|NM_172211.3	NP_000748|NP_757350.1	P09603	CSF1_HUMAN	colony stimulating factor 1 (macrophage)	490					branching involved in mammary gland duct morphogenesis (GO:0060444)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|developmental process involved in reproduction (GO:0003006)|hemopoiesis (GO:0030097)|homeostasis of number of cells within a tissue (GO:0048873)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|macrophage differentiation (GO:0030225)|mammary duct terminal end bud growth (GO:0060763)|mammary gland fat development (GO:0060611)|monocyte activation (GO:0042117)|odontogenesis (GO:0042476)|ossification (GO:0001503)|osteoclast differentiation (GO:0030316)|osteoclast proliferation (GO:0002158)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of gene expression (GO:0010628)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of monocyte differentiation (GO:0045657)|positive regulation of mononuclear cell proliferation (GO:0032946)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of odontogenesis of dentin-containing tooth (GO:0042488)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of Ras protein signal transduction (GO:0046579)|regulation of macrophage derived foam cell differentiation (GO:0010743)|regulation of ossification (GO:0030278)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	cytokine activity (GO:0005125)|growth factor activity (GO:0008083)|macrophage colony-stimulating factor receptor binding (GO:0005157)|protein homodimerization activity (GO:0042803)			breast(1)|endometrium(3)|large_intestine(3)|liver(1)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	20		all_epithelial(167;3.58e-05)|all_lung(203;0.000116)|Lung NSC(277;0.000233)|Acute lymphoblastic leukemia(138;0.204)		Lung(183;0.0238)|Colorectal(144;0.112)|all cancers(265;0.117)|Epithelial(280;0.127)|LUSC - Lung squamous cell carcinoma(189;0.135)		GATCCTTCAGCCCGCAGCTCC	0.627																																					p.S490fs		Atlas-INDEL	.											.	CSF1	40	.	0			c.1469delG						.						53.0	56.0	55.0					1																	110466713		2203	4300	6503	SO:0001589	frameshift_variant	1435	exon6			.	BC021117	CCDS816.1, CCDS817.1, CCDS30797.1	1p13.3	2012-09-20			ENSG00000184371	ENSG00000184371			2432	protein-coding gene	gene with protein product		120420				1540160	Standard	NM_172210		Approved	M-CSF, MCSF, MGC31930	uc001dyw.4	P09603	OTTHUMG00000011646	ENST00000329608.6:c.1470delC	chr1.hg19:g.110466713delC	ENSP00000327513:p.Ser490fs	135.0	0.0		177.0	11.0	NM_000757	A8K6J5|Q13130|Q14086|Q14806|Q5VVF3|Q5VVF4|Q9UQR8	Frame_Shift_Del	DEL	ENST00000329608.6	hg19	CCDS816.1																																																																																			.	.		0.627	CSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032208.1	NM_000757	
CS	1431	hgsc.bcm.edu	37	12	56676682	56676682	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:56676682delA	ENST00000351328.3	-	5	551	c.361delT	c.(361-363)tggfs	p.W121fs	CS_ENST00000548567.1_Frame_Shift_Del_p.W55fs|CS_ENST00000542324.2_Frame_Shift_Del_p.W108fs	NM_004077.2	NP_004068.2	O75390	CISY_HUMAN	citrate synthase	121					carbohydrate metabolic process (GO:0005975)|cellular carbohydrate metabolic process (GO:0044262)|cellular metabolic process (GO:0044237)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	citrate (Si)-synthase activity (GO:0004108)|poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(2)|lung(4)|ovary(1)|skin(1)	17		Myeloproliferative disorder(1001;0.000374)		BRCA - Breast invasive adenocarcinoma(357;6.17e-07)		ACCAGCAGCCAAAATAAGCCC	0.478																																					p.W121fs		Atlas-INDEL	.											.	CS	44	.	0			c.362delG						.						109.0	111.0	110.0					12																	56676682		2203	4300	6503	SO:0001589	frameshift_variant	1431	exon5			.		CCDS8913.1	12q13.2	2012-10-02				ENSG00000062485	2.3.3.1		2422	protein-coding gene	gene with protein product		118950					Standard	NM_004077		Approved		uc001sks.1	O75390	OTTHUMG00000170344	ENST00000351328.3:c.361delT	chr12.hg19:g.56676682delA	ENSP00000342056:p.Trp121fs	103.0	0.0		134.0	10.0	NM_004077	Q71UT9|Q7KZH0|Q96FZ8|Q9BWN8	Frame_Shift_Del	DEL	ENST00000351328.3	hg19	CCDS8913.1																																																																																			.	.		0.478	CS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408588.2	NM_004077	
LYPD3	27076	hgsc.bcm.edu	37	19	43968611	43968611	+	Intron	DEL	G	G	-	rs200281794		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:43968611delG	ENST00000244333.3	-	2	168					NM_014400.2	NP_055215.2	O95274	LYPD3_HUMAN	LY6/PLAUR domain containing 3						cell-matrix adhesion (GO:0007160)|cellular component movement (GO:0006928)	anchored component of plasma membrane (GO:0046658)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)				cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(1)|pancreas(1)|upper_aerodigestive_tract(2)	11		Prostate(69;0.0153)				CTGCGCTCCTGGGGGAGCGGA	0.607																																					.		Atlas-INDEL	.											.	LYPD3	24	.	0			c.80-2C>-						.						49.0	44.0	46.0					19																	43968611		2203	4300	6503	SO:0001627	intron_variant	27076	exon3			.	AF082889	CCDS12620.1	19q13.31	2008-02-05				ENSG00000124466			24880	protein-coding gene	gene with protein product		609484				11179665, 11245483	Standard	NM_014400		Approved	C4.4A	uc002owl.1	O95274		ENST00000244333.3:c.80-3C>-	chr19.hg19:g.43968611delG		104.0	0.0		183.0	11.0	NM_014400	Q9UJ74	Splice_Site	DEL	ENST00000244333.3	hg19	CCDS12620.1																																																																																			.	.		0.607	LYPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463177.1	NM_014400	
KDM4C	23081	hgsc.bcm.edu	37	9	7169999	7169999	+	Intron	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:7169999delA	ENST00000381309.3	+	21	3559				KDM4C_ENST00000381306.3_Frame_Shift_Del_p.K1036fs|KDM4C_ENST00000428870.2_Intron|KDM4C_ENST00000442236.2_Intron	NM_015061.3	NP_055876.2	Q9H3R0	KDM4C_HUMAN	lysine (K)-specific demethylase 4C						histone H3-K9 demethylation (GO:0033169)|positive regulation of cell proliferation (GO:0008284)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)	androgen receptor binding (GO:0050681)|dioxygenase activity (GO:0051213)|enzyme binding (GO:0019899)|histone demethylase activity (H3-K9 specific) (GO:0032454)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(8)|lung(14)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	43						GATTAATTCTAAAAAAAGCCA	0.408																																					p.S1034fs		Atlas-INDEL	.											.	KDM4C	186	.	0			c.3102delT						.						45.0	40.0	42.0					9																	7169999		692	1591	2283	SO:0001627	intron_variant	23081	exon21			.	AB018323	CCDS6471.1, CCDS55285.1, CCDS55286.1, CCDS55287.1	9p24-p23	2013-01-23	2009-04-06	2009-04-06	ENSG00000107077	ENSG00000107077		"""Chromatin-modifying enzymes / K-demethylases"", ""Tudor domain containing"""	17071	protein-coding gene	gene with protein product	"""tudor domain containing 14C"""	605469	"""jumonji domain containing 2C"""	JMJD2C		9872452, 15138608	Standard	NM_015061		Approved	GASC1, KIAA0780, TDRD14C	uc003zkh.3	Q9H3R0	OTTHUMG00000019536	ENST00000381309.3:c.2994+109A>-	chr9.hg19:g.7169999delA		100.0	0.0		134.0	11.0	NM_001146694	B4E1Y4|B7ZL46|F5H347|F5H7P0|O94877|Q2M3M0|Q5JUC9|Q5VYJ2|Q5VYJ3	Frame_Shift_Del	DEL	ENST00000381309.3	hg19	CCDS6471.1																																																																																			.	.		0.408	KDM4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051692.1	NM_015061	
MFN1	55669	hgsc.bcm.edu	37	3	179082955	179082955	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:179082955delT	ENST00000471841.1	+	7	821	c.695delT	c.(694-696)attfs	p.I232fs	MFN1_ENST00000263969.5_Frame_Shift_Del_p.I232fs|MFN1_ENST00000280653.7_Frame_Shift_Del_p.I232fs	NM_033540.2	NP_284941	Q8IWA4	MFN1_HUMAN	mitofusin 1	232	Dynamin-type G.				mitochondrial fusion (GO:0008053)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(14)|ovary(3)|prostate(1)|urinary_tract(1)	31	all_cancers(143;1.67e-16)|Ovarian(172;0.0172)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;5.78e-26)|GBM - Glioblastoma multiforme(14;0.00225)|BRCA - Breast invasive adenocarcinoma(182;0.0923)			AAGCCTAATATTTTCATTCTC	0.328																																					p.I232fs		Atlas-INDEL	.											.	MFN1	72	.	0			c.694delA						.						57.0	62.0	60.0					3																	179082955		2203	4299	6502	SO:0001589	frameshift_variant	55669	exon7			.	AF054986	CCDS3228.1	3q26.32	2006-12-13			ENSG00000171109	ENSG00000171109			18262	protein-coding gene	gene with protein product		608506				8358434, 11181170	Standard	NM_033540		Approved	FLJ20693	uc003fjs.3	Q8IWA4	OTTHUMG00000157385	ENST00000471841.1:c.695delT	chr3.hg19:g.179082955delT	ENSP00000420617:p.Ile232fs	153.0	0.0		155.0	11.0	NM_033540	B2RAR1|D3DNR6|O15323|O60639|Q9BZB5|Q9NWQ2	Frame_Shift_Del	DEL	ENST00000471841.1	hg19	CCDS3228.1																																																																																			.	.		0.328	MFN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348654.2	NM_017927	
NEK5	341676	hgsc.bcm.edu	37	13	52650224	52650224	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr13:52650224delT	ENST00000355568.4	-	19	1842	c.1703delA	c.(1702-1704)aatfs	p.N568fs		NM_199289.1	NP_954983.1	Q6P3R8	NEK5_HUMAN	NIMA-related kinase 5	568					positive regulation of cysteine-type endopeptidase activity (GO:2001056)|positive regulation of striated muscle cell differentiation (GO:0051155)		ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			breast(5)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(8)|lung(11)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	39		Breast(56;0.00173)|Lung NSC(96;0.0168)|Prostate(109;0.0412)|Hepatocellular(98;0.152)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;3.7e-08)		CTGTTCTGGATTTTTACTTTC	0.358																																					p.N568fs		Atlas-INDEL	.											.	NEK5	189	.	0			c.1704delT						.						141.0	137.0	139.0					13																	52650224		2203	4299	6502	SO:0001589	frameshift_variant	341676	exon19			.	BC063885	CCDS31979.1	13q14.2	2012-11-15	2012-11-15		ENSG00000197168	ENSG00000197168			7748	protein-coding gene	gene with protein product			"""NIMA (never in mitosis gene a)-related kinase 5"""			9552363	Standard	XM_006719807		Approved		uc001vge.3	Q6P3R8	OTTHUMG00000016957	ENST00000355568.4:c.1703delA	chr13.hg19:g.52650224delT	ENSP00000347767:p.Asn568fs	96.0	0.0		131.0	10.0	NM_199289	Q5TAP5	Frame_Shift_Del	DEL	ENST00000355568.4	hg19	CCDS31979.1																																																																																			.	.		0.358	NEK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045045.3	NM_199289	
RALY	22913	hgsc.bcm.edu	37	20	32664985	32664985	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr20:32664985delG	ENST00000246194.3	+	8	1312	c.810delG	c.(808-810)cagfs	p.Q270fs	RALY_ENST00000375114.3_Frame_Shift_Del_p.Q254fs	NM_016732.2	NP_057951.1	Q9UKM9	RALY_HUMAN	RALY heterogeneous nuclear ribonucleoprotein	270					mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			kidney(2)|large_intestine(3)|lung(2)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	12						GCCTGCCCCAGGGGGAAGCAC	0.697																																					p.Q270fs		Atlas-INDEL	.											.	RALY	44	.	0			c.809delA						.						26.0	28.0	27.0					20																	32664985		2199	4298	6497	SO:0001589	frameshift_variant	22913	exon8			.	AF148457	CCDS13229.1, CCDS13230.1	20q11.21-q11.23	2013-08-06	2013-08-06		ENSG00000125970	ENSG00000125970		"""RNA binding motif (RRM) containing"""	15921	protein-coding gene	gene with protein product		614663	"""RNA-binding protein (autoantigenic, hnRNP-associated with lethal yellow)"", ""RNA binding protein, autoantigenic (hnRNP-associated with lethal yellow homolog (mouse))"""			10500250, 23614458	Standard	NM_016732		Approved	P542, HNRPCL2	uc002xab.3	Q9UKM9	OTTHUMG00000032283	ENST00000246194.3:c.810delG	chr20.hg19:g.32664985delG	ENSP00000246194:p.Gln270fs	157.0	0.0		197.0	12.0	NM_016732	Q14621|Q2M365|Q5QPL8|Q9BQX6|Q9UJE3	Frame_Shift_Del	DEL	ENST00000246194.3	hg19	CCDS13230.1																																																																																			.	.		0.697	RALY-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078753.1		
SORBS2	8470	hgsc.bcm.edu	37	4	186570678	186570678	+	Frame_Shift_Del	DEL	G	G	-	rs113864748		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:186570678delG	ENST00000284776.7	-	9	1021	c.512delC	c.(511-513)ccafs	p.P171fs	SORBS2_ENST00000448662.2_Frame_Shift_Del_p.P240fs|SORBS2_ENST00000431808.1_Frame_Shift_Del_p.P171fs|SORBS2_ENST00000319471.9_Frame_Shift_Del_p.P257fs|SORBS2_ENST00000498125.1_5'UTR|SORBS2_ENST00000437304.2_Frame_Shift_Del_p.P350fs|SORBS2_ENST00000355634.5_Frame_Shift_Del_p.P271fs|SORBS2_ENST00000418609.1_Frame_Shift_Del_p.P75fs|SORBS2_ENST00000393528.3_Frame_Shift_Del_p.P217fs|SORBS2_ENST00000449407.2_Frame_Shift_Del_p.P242fs	NM_021069.4	NP_066547.1	O94875	SRBS2_HUMAN	sorbin and SH3 domain containing 2	171	Pro-rich.				actin filament organization (GO:0007015)|cell adhesion (GO:0007155)|cell migration (GO:0016477)	actin cytoskeleton (GO:0015629)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	cytoskeletal adaptor activity (GO:0008093)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)			endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(9)|lung(21)|ovary(2)|prostate(2)|skin(4)|urinary_tract(1)	53		all_cancers(14;4.27e-52)|all_epithelial(14;6.58e-39)|all_lung(41;1.42e-13)|Lung NSC(41;3.73e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.00692)|Hepatocellular(41;0.00826)|Renal(120;0.00994)|Prostate(90;0.0101)|all_hematologic(60;0.0174)|all_neural(102;0.244)		OV - Ovarian serous cystadenocarcinoma(60;1.54e-09)|BRCA - Breast invasive adenocarcinoma(30;0.000232)|GBM - Glioblastoma multiforme(59;0.000385)|STAD - Stomach adenocarcinoma(60;0.00109)|LUSC - Lung squamous cell carcinoma(40;0.0205)		TGGAACATGTGGGGGAGGCAC	0.552																																					p.P350fs	Esophageal Squamous(153;41 2433 9491 36028)	Atlas-INDEL	.											.	SORBS2	300	.	0			c.1050delA						.						106.0	106.0	106.0					4																	186570678		2203	4300	6503	SO:0001589	frameshift_variant	8470	exon10			.		CCDS3845.1, CCDS43289.2, CCDS47173.1, CCDS47174.1, CCDS47175.1, CCDS47176.1, CCDS54825.1, CCDS59482.1	4q35.1	2008-02-05			ENSG00000154556	ENSG00000154556			24098	protein-coding gene	gene with protein product	"""Arg/Abl interacting protein"""					9211900, 9872452	Standard	NM_021069		Approved	ARGBP2, KIAA0777	uc003iym.3	O94875	OTTHUMG00000157215	ENST00000284776.7:c.512delC	chr4.hg19:g.186570678delG	ENSP00000284776:p.Pro171fs	230.0	0.0		192.0	12.0	NM_001145673	A6NEK9|B3KPQ7|B7Z1G5|B7Z3X6|C9JKV9|D3DP62|D3DP63|E9PAS5|E9PAW4|G3XAI0|H7BXR4|J3KNZ5|O60592|O60593|Q96EX0	Frame_Shift_Del	DEL	ENST00000284776.7	hg19	CCDS3845.1																																																																																			.	.		0.552	SORBS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347944.3	NM_003603	
FAM71B	153745	hgsc.bcm.edu	37	5	156592606	156592606	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:156592606delC	ENST00000302938.4	-	1	669	c.574delG	c.(574-576)gacfs	p.D192fs		NM_130899.2	NP_570969.2	Q8TC56	FA71B_HUMAN	family with sequence similarity 71, member B	192						nucleus (GO:0005634)				NS(3)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(10)|lung(32)|ovary(4)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	68	Renal(175;0.00212)	Medulloblastoma(196;0.0523)|all_neural(177;0.21)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			GGTGGTGCGTCCCCAGATAGA	0.507																																					p.D192fs		Atlas-INDEL	.											.	FAM71B	145	.	0			c.575delA						.						200.0	201.0	200.0					5																	156592606		2203	4300	6503	SO:0001589	frameshift_variant	153745	exon1			.		CCDS4335.1	5q33.3	2005-08-09			ENSG00000170613	ENSG00000170613			28397	protein-coding gene	gene with protein product						12477932	Standard	NM_130899		Approved	MGC26988	uc003lwn.3	Q8TC56	OTTHUMG00000130246	ENST00000302938.4:c.574delG	chr5.hg19:g.156592606delC	ENSP00000305596:p.Asp192fs	208.0	0.0		265.0	17.0	NM_130899	Q1EDD9|Q8TC64|Q96LY8	Frame_Shift_Del	DEL	ENST00000302938.4	hg19	CCDS4335.1																																																																																			.	.		0.507	FAM71B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252570.2	NM_130899	
OR14J1	442191	hgsc.bcm.edu	37	6	29274914	29274914	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:29274914delG	ENST00000377160.2	+	1	512	c.448delG	c.(448-450)gggfs	p.G151fs		NM_030946.1	NP_112208.1	Q9UGF5	O14J1_HUMAN	olfactory receptor, family 14, subfamily J, member 1	151						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(3)|lung(8)|ovary(2)|upper_aerodigestive_tract(2)	17						GTGGATTGCTGGGGGCCTCTC	0.488																																					p.A149fs		Atlas-INDEL	.											.	OR14J1	43	.	0			c.447delT						.						154.0	156.0	155.0					6																	29274914		1511	2709	4220	SO:0001589	frameshift_variant	442191	exon1			.		CCDS34362.1	6p21.3	2012-08-09	2008-04-02	2008-04-02	ENSG00000204695	ENSG00000204695		"""GPCR / Class A : Olfactory receptors"""	13971	protein-coding gene	gene with protein product			"""olfactory receptor, family 5, subfamily U, member 1"""	OR5U1			Standard	NM_030946		Approved	hs6M1-28	uc011dln.2	Q9UGF5	OTTHUMG00000031184	ENST00000377160.2:c.448delG	chr6.hg19:g.29274914delG	ENSP00000366365:p.Gly151fs	116.0	0.0		252.0	16.0	NM_030946	A2BEC2|B0V078|Q5ST27	Frame_Shift_Del	DEL	ENST00000377160.2	hg19	CCDS34362.1																																																																																			.	.		0.488	OR14J1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076362.2		
DNAH10	196385	hgsc.bcm.edu	37	12	124289391	124289391	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:124289391delT	ENST00000409039.3	+	17	2462	c.2437delT	c.(2437-2439)tttfs	p.F814fs		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	814	Stem. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		CGTGAAGGAATTTTTTGAACA	0.507																																					p.E812fs		Atlas-INDEL	.											.	DNAH10	888	.	0			c.2436delA						.						118.0	121.0	120.0					12																	124289391		2203	4300	6503	SO:0001589	frameshift_variant	196385	exon17			.	AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"""Axonemal dyneins"""	2941	protein-coding gene	gene with protein product		605884	"""dynein, axonemal, heavy polypeptide 10"""				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.2437delT	chr12.hg19:g.124289391delT	ENSP00000386770:p.Phe814fs	148.0	0.0		159.0	10.0	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Frame_Shift_Del	DEL	ENST00000409039.3	hg19	CCDS9255.2																																																																																			.	.		0.507	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3		
RB1CC1	9821	hgsc.bcm.edu	37	8	53569774	53569774	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr8:53569774delT	ENST00000025008.5	-	15	3138	c.2615delA	c.(2614-2616)aatfs	p.N872fs	RB1CC1_ENST00000435644.2_Frame_Shift_Del_p.N872fs|RB1CC1_ENST00000521611.1_Intron|RB1CC1_ENST00000539297.1_Frame_Shift_Del_p.N872fs	NM_014781.4	NP_055596.3	Q8TDY2	RBCC1_HUMAN	RB1-inducible coiled-coil 1	872					autophagic vacuole assembly (GO:0000045)|cell cycle (GO:0007049)|heart development (GO:0007507)|JNK cascade (GO:0007254)|liver development (GO:0001889)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell size (GO:0045793)|positive regulation of protein phosphorylation (GO:0001934)|regulation of autophagy (GO:0010506)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|pre-autophagosomal structure membrane (GO:0034045)|ULK1-ATG13-FIP200 complex (GO:0070969)				NS(2)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(19)|ovary(8)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	60		all_cancers(86;0.137)|all_epithelial(80;0.00494)|Lung NSC(129;0.011)|all_lung(136;0.023)				TTCATATTCATTTTTTAAAGA	0.289																																					p.N872fs	GBM(180;1701 2102 13475 42023 52570)	Atlas-INDEL	.											.,1	RB1CC1	163	.	0			c.2616delT						.						31.0	34.0	33.0					8																	53569774		2176	4252	6428	SO:0001589	frameshift_variant	9821	exon15			.	AB059622	CCDS34892.1, CCDS47856.1	8q11	2014-06-13				ENSG00000023287			15574	protein-coding gene	gene with protein product	"""200 kDa FAK family kinase-interacting protein"", ""phosphatase 1, regulatory subunit 131"""	606837				11850849, 7724523, 18443221	Standard	NM_014781		Approved	KIAA0203, Cc1, DRAGOU14, FIP200, ATG17, PPP1R131	uc003xre.4	Q8TDY2		ENST00000025008.5:c.2615delA	chr8.hg19:g.53569774delT	ENSP00000025008:p.Asn872fs	54.0	0.0		159.0	10.0	NM_001083617	Q86YR4|Q8WVU9|Q92601	Frame_Shift_Del	DEL	ENST00000025008.5	hg19	CCDS34892.1																																																																																			.	.		0.289	RB1CC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000378011.1	NM_014781	
CCDC14	64770	hgsc.bcm.edu	37	3	123675247	123675247	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:123675247delA	ENST00000488653.2	-	3	348	c.258delT	c.(256-258)tttfs	p.F86fs	CCDC14_ENST00000483247.1_Intron|CCDC14_ENST00000433542.2_Frame_Shift_Del_p.F86fs|CCDC14_ENST00000489746.1_5'UTR|CCDC14_ENST00000485727.1_5'UTR			Q49A88	CCD14_HUMAN	coiled-coil domain containing 14	86					substantia nigra development (GO:0021762)	centrosome (GO:0005813)				NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(10)	21		Lung NSC(201;0.0371)|Prostate(884;0.0405)|Myeloproliferative disorder(1037;0.205)		Lung(219;0.00942)|GBM - Glioblastoma multiforme(114;0.159)		AATCTGCATTAAAACGTGGTA	0.279																																					p.N87fs		Atlas-INDEL	.											.	CCDC14	97	.	0			c.259delA						.						64.0	61.0	62.0					3																	123675247		692	1585	2277	SO:0001589	frameshift_variant	64770	exon3			.	AL122079	CCDS3025.2	3q21.1	2014-03-20			ENSG00000175455	ENSG00000175455			25766	protein-coding gene	gene with protein product						12477932	Standard	NM_022757		Approved	FLJ12892, DKFZp434L1050	uc010hrt.3	Q49A88	OTTHUMG00000153005	ENST00000488653.2:c.258delT	chr3.hg19:g.123675247delA	ENSP00000420180:p.Phe86fs	96.0	0.0		189.0	12.0	NM_022757	B7Z2T2|B8ZZ41|B8ZZ58|D3DN98|Q7Z3N3|Q86T30|Q8IWF8|Q8WUJ8|Q96K47|Q9H9A3|Q9UFH0	Frame_Shift_Del	DEL	ENST00000488653.2	hg19																																																																																				.	.		0.279	CCDC14-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_022757	
SPATA31A1	647060	hgsc.bcm.edu	37	9	39358166	39358166	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:39358166delC	ENST00000377647.3	+	4	433	c.404delC	c.(403-405)tccfs	p.S135fs	SPATA31A1_ENST00000473440.1_3'UTR	NM_001085452.1	NP_001078921.1	Q5TZJ5	S31A1_HUMAN	SPATA31 subfamily A, member 1	135	Pro-rich.				cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											GATGGAGCCTCCCAGTCCTCT	0.597																																					p.S135fs		Atlas-INDEL	.											.	.	.	.	0			c.403delT						.						1.0	1.0	1.0					9																	39358166		51	27	78	SO:0001589	frameshift_variant	647060	exon4			.		CCDS43808.1	9p12	2012-10-15	2012-10-12	2012-10-12	ENSG00000204849	ENSG00000204849			23394	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 36"", ""family with sequence similarity 75, member A1"""	C9orf36, FAM75A1		20850414	Standard	XM_006716851		Approved	DKFZP434B204, C9orf36A, OTTHUMG00000013156		Q5TZJ5	OTTHUMG00000013156	ENST00000377647.3:c.404delC	chr9.hg19:g.39358166delC	ENSP00000366875:p.Ser135fs	135.0	0.0		157.0	10.0	NM_001085452		Frame_Shift_Del	DEL	ENST00000377647.3	hg19	CCDS43808.1																																																																																			.	.		0.597	SPATA31A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036910.1	NM_001085452	
HGD	3081	hgsc.bcm.edu	37	3	120352071	120352071	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:120352071delG	ENST00000283871.5	-	13	1570	c.1111delC	c.(1111-1113)catfs	p.H371fs		NM_000187.3	NP_000178.2	Q93099	HGD_HUMAN	homogentisate 1,2-dioxygenase	371			H -> R (in AKU). {ECO:0000269|PubMed:10594001}.		cellular nitrogen compound metabolic process (GO:0034641)|L-phenylalanine catabolic process (GO:0006559)|small molecule metabolic process (GO:0044281)|tyrosine catabolic process (GO:0006572)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	homogentisate 1,2-dioxygenase activity (GO:0004411)|metal ion binding (GO:0046872)			cervix(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(11)|ovary(1)|prostate(1)|skin(2)	25				GBM - Glioblastoma multiforme(114;0.158)		TCAGGTCCATGGGGGGTCATT	0.542																																					p.H371fs		Atlas-INDEL	.											.	HGD	65	.	0			c.1112delA						.						132.0	105.0	114.0					3																	120352071		2203	4296	6499	SO:0001589	frameshift_variant	3081	exon13			.		CCDS3000.1	3q	2010-04-27	2010-04-27		ENSG00000113924	ENSG00000113924	1.13.11.5		4892	protein-coding gene	gene with protein product	"""homogentisate oxidase"""	607474	"""homogentisate 1,2-dioxygenase (homogentisate oxidase)"""	AKU		8188241	Standard	NM_000187		Approved	HGO	uc003edw.3	Q93099	OTTHUMG00000159441	ENST00000283871.5:c.1111delC	chr3.hg19:g.120352071delG	ENSP00000283871:p.His371fs	119.0	0.0		182.0	15.0	NM_000187	A8K417|B2R8Z0	Frame_Shift_Del	DEL	ENST00000283871.5	hg19	CCDS3000.1																																																																																			.	.		0.542	HGD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355410.1		
STXBP5L	9515	hgsc.bcm.edu	37	3	121001118	121001118	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:121001118delT	ENST00000273666.6	+	20	2387	c.2116delT	c.(2116-2118)tttfs	p.F706fs	STXBP5L_ENST00000492541.1_Frame_Shift_Del_p.F706fs|STXBP5L_ENST00000497029.1_Frame_Shift_Del_p.F706fs|STXBP5L_ENST00000472879.1_Intron|STXBP5L_ENST00000471454.1_Intron	NM_014980.2	NP_055795.1	Q9Y2K9	STB5L_HUMAN	syntaxin binding protein 5-like	706					exocytosis (GO:0006887)|glucose homeostasis (GO:0042593)|negative regulation of insulin secretion (GO:0046676)|positive regulation of protein secretion (GO:0050714)|protein transport (GO:0015031)|regulation of exocytosis (GO:0017157)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(3)|endometrium(3)|kidney(3)|large_intestine(12)|lung(28)|ovary(7)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	68				GBM - Glioblastoma multiforme(114;0.0694)		CAAAGACAACTTTTGCATGCG	0.393																																					p.N705fs		Atlas-INDEL	.											.	STXBP5L	159	.	0			c.2115delC						.						101.0	90.0	93.0					3																	121001118		1956	4168	6124	SO:0001589	frameshift_variant	9515	exon20			.	AB023223	CCDS43137.1	3q13.33-q21.1	2013-01-10			ENSG00000145087	ENSG00000145087		"""WD repeat domain containing"""	30757	protein-coding gene	gene with protein product		609381				10231032, 14767561	Standard	NM_014980		Approved	KIAA1006, LLGL4	uc003eec.4	Q9Y2K9	OTTHUMG00000159426	ENST00000273666.6:c.2116delT	chr3.hg19:g.121001118delT	ENSP00000273666:p.Phe706fs	103.0	0.0		138.0	11.0	NM_014980	Q4G1B4|Q6PIC3	Frame_Shift_Del	DEL	ENST00000273666.6	hg19	CCDS43137.1																																																																																			.	.		0.393	STXBP5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355256.3		
SHROOM1	134549	hgsc.bcm.edu	37	5	132159877	132159877	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:132159877delG	ENST00000378679.3	-	7	2280	c.1476delC	c.(1474-1476)cccfs	p.P492fs	SHROOM1_ENST00000378676.1_Frame_Shift_Del_p.P423fs|SHROOM1_ENST00000488072.1_5'Flank|SHROOM1_ENST00000319854.3_Frame_Shift_Del_p.P492fs	NM_001172700.1	NP_001166171.1	Q2M3G4	SHRM1_HUMAN	shroom family member 1	492					actin filament bundle assembly (GO:0051017)|cell morphogenesis (GO:0000902)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|myosin II complex (GO:0016460)	actin filament binding (GO:0051015)			endometrium(1)|kidney(4)|large_intestine(2)|lung(4)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	17			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			CTGCAGCTGTGGGGGGATTGG	0.542																																					p.T493fs		Atlas-INDEL	.											.	SHROOM1	35	.	0			c.1477delA						.						102.0	94.0	97.0					5																	132159877		2203	4300	6503	SO:0001589	frameshift_variant	134549	exon4			.	AF314142	CCDS4161.1, CCDS54902.1	5q31.1	2007-05-03			ENSG00000164403	ENSG00000164403			24084	protein-coding gene	gene with protein product		611179				11853319, 16615870	Standard	NM_133456		Approved	APXL2, KIAA1960	uc003kxy.2	Q2M3G4	OTTHUMG00000059835	ENST00000378679.3:c.1476delC	chr5.hg19:g.132159877delG	ENSP00000367950:p.Pro492fs	269.0	0.0		294.0	18.0	NM_133456	B7WP40|B7ZL01|Q8TDP0|Q8TF41	Frame_Shift_Del	DEL	ENST00000378679.3	hg19	CCDS54902.1																																																																																			.	.		0.542	SHROOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000133033.1	NM_133456	
FANCI	55215	hgsc.bcm.edu	37	15	89803947	89803947	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:89803947delC	ENST00000310775.7	+	4	247	c.161delC	c.(160-162)tccfs	p.S54fs	FANCI_ENST00000451393.2_5'UTR|FANCI_ENST00000300027.8_Frame_Shift_Del_p.S54fs|FANCI_ENST00000567996.1_Frame_Shift_Del_p.S54fs	NM_001113378.1	NP_001106849.1	Q9NVI1	FANCI_HUMAN	Fanconi anemia, complementation group I	54					cell cycle (GO:0007049)|DNA repair (GO:0006281)|positive regulation of protein ubiquitination (GO:0031398)	membrane (GO:0016020)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|DNA polymerase binding (GO:0070182)			breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	Lung NSC(78;0.0472)|all_lung(78;0.089)					CAATAAGGTTCCCCCTGCTCT	0.398								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.S54fs		Atlas-INDEL	.											.	FANCI	129	.	0			c.160delT						.		,	14,4250		6,2,2124	93.0	89.0	91.0		,	5.6	1.0	15		90	46,8208		23,0,4104	no	frameshift,frameshift	FANCI	NM_018193.2,NM_001113378.1	,	29,2,6228	A1A1,A1R,RR		0.5573,0.3283,0.4793	,	,	89803947	60,12458	2200	4299	6499	SO:0001589	frameshift_variant	55215	exon4	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	.	BC004277	CCDS10349.2, CCDS45346.1	15q26.1	2014-09-17	2007-05-03	2007-05-03	ENSG00000140525	ENSG00000140525		"""Fanconi anemia, complementation groups"""	25568	protein-coding gene	gene with protein product		611360	"""KIAA1794"""	KIAA1794		14630800, 17460694, 17412408	Standard	NM_001113378		Approved	FLJ10719	uc010bnp.1	Q9NVI1	OTTHUMG00000132993	ENST00000310775.7:c.161delC	chr15.hg19:g.89803947delC	ENSP00000310842:p.Ser54fs	93.0	0.0		149.0	10.0	NM_001113378	A4ZVE4|A5YMH4|A6NJZ0|Q96JN1|Q96ST0|Q9BT96	Frame_Shift_Del	DEL	ENST00000310775.7	hg19	CCDS45346.1																																																																																			.	.		0.398	FANCI-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421140.1	NM_018193	
ZCCHC9	84240	hgsc.bcm.edu	37	5	80608454	80608454	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:80608454delA	ENST00000254037.2	+	5	3944	c.789delA	c.(787-789)acafs	p.T263fs	ZCCHC9_ENST00000380199.5_Frame_Shift_Del_p.T263fs|ZCCHC9_ENST00000506458.1_3'UTR|ZCCHC9_ENST00000407610.3_Frame_Shift_Del_p.T263fs|ZCCHC9_ENST00000438268.2_Frame_Shift_Del_p.T263fs			Q8N567	ZCHC9_HUMAN	zinc finger, CCHC domain containing 9	263					negative regulation of phosphatase activity (GO:0010923)		poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)	13		Lung NSC(167;0.0427)|all_lung(232;0.0464)|Ovarian(174;0.135)		OV - Ovarian serous cystadenocarcinoma(54;8.18e-45)|Epithelial(54;2.72e-39)|all cancers(79;7.33e-34)		AACCCAAAACAAAAATACCTA	0.403																																					p.T263fs		Atlas-INDEL	.											.	ZCCHC9	26	.	0			c.788delC						.						88.0	83.0	85.0					5																	80608454		2203	4300	6503	SO:0001589	frameshift_variant	84240	exon6			.	BC014841	CCDS4054.1	5q14.1	2013-01-09			ENSG00000131732	ENSG00000131732		"""Zinc fingers, CCHC domain containing"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	25424	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 41"""					12477932	Standard	NM_032280		Approved	DKFZp761J139, PPP1R41	uc003khi.3	Q8N567	OTTHUMG00000119014	ENST00000254037.2:c.789delA	chr5.hg19:g.80608454delA	ENSP00000254037:p.Thr263fs	122.0	0.0		165.0	10.0	NM_001131036	B2RAE7|Q9H027	Frame_Shift_Del	DEL	ENST00000254037.2	hg19	CCDS4054.1																																																																																			.	.		0.403	ZCCHC9-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239213.1	NM_032280	
KALRN	8997	hgsc.bcm.edu	37	3	124210257	124210257	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:124210257delA	ENST00000240874.3	+	31	4826	c.4669delA	c.(4669-4671)aaafs	p.K1557fs	KALRN_ENST00000460856.1_Frame_Shift_Del_p.K1548fs|KALRN_ENST00000360013.3_Frame_Shift_Del_p.K1557fs	NM_003947.4	NP_003938.1	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase	1557	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.				apoptotic signaling pathway (GO:0097190)|intracellular signal transduction (GO:0035556)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|protein phosphorylation (GO:0006468)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(21)|lung(28)|ovary(4)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	83						CTCAGACAATAAAACAGTGCT	0.542																																					p.N1556fs		Atlas-INDEL	.											.	KALRN	556	.	0			c.4668delT						.						77.0	69.0	72.0					3																	124210257		2203	4300	6503	SO:0001589	frameshift_variant	8997	exon31			.	U94190	CCDS3027.1, CCDS3028.1	3q21.2	2013-02-11	2005-03-11	2005-03-12	ENSG00000160145	ENSG00000160145		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	4814	protein-coding gene	gene with protein product	"""serine/threonine kinase with Dbl and pleckstrin homology domains"""	604605	"""huntingtin-associated protein interacting protein (duo)"""	HAPIP		9285789, 10023074	Standard	NM_001024660		Approved	duo, Hs.8004, TRAD, DUET, Kalirin, ARHGEF24	uc003ehd.3	O60229	OTTHUMG00000125545	ENST00000240874.3:c.4669delA	chr3.hg19:g.124210257delA	ENSP00000240874:p.Lys1557fs	74.0	0.0		103.0	10.0	NM_003947	A8MSI4|C9JQ37|Q6ZN45|Q8TBQ5|Q9NSZ4|Q9Y2A5	Frame_Shift_Del	DEL	ENST00000240874.3	hg19	CCDS3027.1																																																																																			.	.		0.542	KALRN-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000258843.4	NM_003947	
ADH1B	125	hgsc.bcm.edu	37	4	100231959	100231959	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:100231959delT	ENST00000305046.8	-	8	1133	c.1066delA	c.(1066-1068)atafs	p.I356fs	ADH1B_ENST00000394887.3_Frame_Shift_Del_p.I316fs			P00325	ADH1B_HUMAN	alcohol dehydrogenase 1B (class I), beta polypeptide	356					ethanol oxidation (GO:0006069)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	alcohol dehydrogenase activity, zinc-dependent (GO:0004024)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(12)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	33				OV - Ovarian serous cystadenocarcinoma(123;1.02e-07)	Ethanol(DB00898)|Fomepizole(DB01213)	CCTTCATTTATTTTTTCAAAA	0.348																																					p.I356fs		Atlas-INDEL	.											.	ADH1B	68	.	0			c.1067delT						.						96.0	96.0	96.0					4																	100231959		2203	4300	6503	SO:0001589	frameshift_variant	125	exon8			.	AF153821	CCDS34033.1, CCDS68761.1	4q23	2008-02-05	2007-11-06		ENSG00000196616	ENSG00000196616	1.1.1.1	"""Alcohol dehydrogenases"""	250	protein-coding gene	gene with protein product		103720		ADH2		3006456	Standard	NM_000668		Approved		uc003hus.4	P00325	OTTHUMG00000161413	ENST00000305046.8:c.1066delA	chr4.hg19:g.100231959delT	ENSP00000306606:p.Ile356fs	166.0	0.0		202.0	14.0	NM_000668	A8MYN5|B4DRS9|B4DVC3|Q13711|Q4ZGI9|Q96KI7	Frame_Shift_Del	DEL	ENST00000305046.8	hg19	CCDS34033.1																																																																																			.	.		0.348	ADH1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364853.1	NM_000668	
FPGT-TNNI3K	100526835	hgsc.bcm.edu	37	1	74930379	74930379	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:74930379delA	ENST00000370899.3	+	24	2522	c.2485delA	c.(2485-2487)aaafs	p.K829fs	TNNI3K_ENST00000326637.3_Intron|FPGT-TNNI3K_ENST00000557284.2_Intron|TNNI3K_ENST00000370891.2_Intron	NM_001199327.1	NP_001186256			FPGT-TNNI3K readthrough																		TCTTAAGAAGAAAAATGAAGA	0.353																																					p.K828fs		Atlas-INDEL	.											.	.	.	.	0			c.2484delG						.						19.0	18.0	18.0					1																	74930379		876	1990	2866	SO:0001589	frameshift_variant	100526835	exon24			.			1p31.3	2014-03-14			ENSG00000259030	ENSG00000259030			42952	other	readthrough							Standard	NM_001112808		Approved		uc001dge.2		OTTHUMG00000166281	ENST00000370899.3:c.2485delA	chr1.hg19:g.74930379delA	ENSP00000359936:p.Lys829fs	127.0	0.0		144.0	10.0	NM_001199327		Frame_Shift_Del	DEL	ENST00000370899.3	hg19																																																																																				.	.		0.353	FPGT-TNNI3K-003	NOVEL	basic|appris_candidate|readthrough_transcript|exp_conf	protein_coding	protein_coding	OTTHUMT00000026438.3		
CCDC60	160777	hgsc.bcm.edu	37	12	119968734	119968734	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:119968734delA	ENST00000327554.2	+	13	1882	c.1417delA	c.(1417-1419)aaafs	p.K474fs	RP11-768F21.1_ENST00000509470.2_lincRNA	NM_178499.3	NP_848594.2	Q8IWA6	CCD60_HUMAN	coiled-coil domain containing 60	474										endometrium(4)|kidney(3)|large_intestine(8)|lung(15)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	40	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.207)		CCGCCCCGCCAAAAAGATCCT	0.488																																					p.A472fs		Atlas-INDEL	.											.	CCDC60	84	.	0			c.1416delC						.						88.0	85.0	86.0					12																	119968734		2203	4300	6503	SO:0001589	frameshift_variant	160777	exon13			.	BC040553	CCDS9190.1	12q24.23	2006-02-03			ENSG00000183273	ENSG00000183273			28610	protein-coding gene	gene with protein product						12477932	Standard	NM_178499		Approved	MGC39827	uc001txe.3	Q8IWA6	OTTHUMG00000168943	ENST00000327554.2:c.1417delA	chr12.hg19:g.119968734delA	ENSP00000333374:p.Lys474fs	148.0	0.0		162.0	10.0	NM_178499		Frame_Shift_Del	DEL	ENST00000327554.2	hg19	CCDS9190.1																																																																																			.	.		0.488	CCDC60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401680.1	NM_178499	
OIT3	170392	hgsc.bcm.edu	37	10	74673122	74673122	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:74673122delG	ENST00000334011.5	+	6	1065	c.847delG	c.(847-849)ggtfs	p.G284fs		NM_152635.1	NP_689848.1	Q8WWZ8	OIT3_HUMAN	oncoprotein induced transcript 3	284	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.					nucleus (GO:0005634)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|liver(2)|lung(14)|ovary(2)|prostate(1)|skin(2)	35	Prostate(51;0.0198)					GGAGCTGGTTGGTGGCCTGGA	0.527																																					p.V282fs	Colon(7;19 345 13446 17537)	Atlas-INDEL	.											.	OIT3	62	.	0			c.846delT						.						167.0	156.0	160.0					10																	74673122		2203	4300	6503	SO:0001589	frameshift_variant	170392	exon6			.		CCDS7318.1	10q22.2-q22.3	2004-04-21			ENSG00000138315	ENSG00000138315			29953	protein-coding gene	gene with protein product		609330				12975309, 12939600	Standard	NM_152635		Approved	LZP, FLJ39116	uc001jte.1	Q8WWZ8	OTTHUMG00000018444	ENST00000334011.5:c.847delG	chr10.hg19:g.74673122delG	ENSP00000333900:p.Gly284fs	114.0	0.0		157.0	11.0	NM_152635	A0AVP3|Q8N1M8	Frame_Shift_Del	DEL	ENST00000334011.5	hg19	CCDS7318.1																																																																																			.	.		0.527	OIT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048596.1	NM_152635	
SLC17A9	63910	hgsc.bcm.edu	37	20	61588797	61588797	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr20:61588797delG	ENST00000370351.4	+	3	393	c.262delG	c.(262-264)gggfs	p.G89fs	SLC17A9_ENST00000370349.3_Frame_Shift_Del_p.G83fs|SLC17A9_ENST00000488738.1_3'UTR	NM_022082.3	NP_071365	Q9BYT1	S17A9_HUMAN	solute carrier family 17 (vesicular nucleotide transporter), member 9	89					exocytosis (GO:0006887)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)	transporter activity (GO:0005215)			endometrium(2)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	23						CTCCAGGATTGGGGGTGAGAA	0.642																																					p.I87fs		Atlas-INDEL	.											.	SLC17A9	54	.	0			c.261delT						.						74.0	81.0	78.0					20																	61588797		2175	4259	6434	SO:0001589	frameshift_variant	63910	exon3			.	AK027065	CCDS42901.1	20q13.33	2013-07-18	2013-07-18	2009-01-22	ENSG00000101194	ENSG00000101194		"""Solute carriers"""	16192	protein-coding gene	gene with protein product		612107	"""chromosome 20 open reading frame 59"", ""solute carrier family 17, member 9"""	C20orf59		18375752	Standard	NM_022082		Approved	FLJ23412, VNUT	uc002yea.4	Q9BYT1	OTTHUMG00000032951	ENST00000370351.4:c.262delG	chr20.hg19:g.61588797delG	ENSP00000359376:p.Gly89fs	113.0	0.0		153.0	10.0	NM_022082	B3KTF2|Q5W198|Q8TB07|Q8TBP4|Q8TEL5|Q9BYT0|Q9BYT2	Frame_Shift_Del	DEL	ENST00000370351.4	hg19	CCDS42901.1																																																																																			.	.		0.642	SLC17A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080100.1	NM_022082	
HTT	3064	hgsc.bcm.edu	37	4	3129309	3129309	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:3129309delC	ENST00000355072.5	+	12	1866	c.1721delC	c.(1720-1722)accfs	p.T574fs		NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	574					anterior/posterior pattern specification (GO:0009952)|axon cargo transport (GO:0008088)|cell aging (GO:0007569)|citrulline metabolic process (GO:0000052)|determination of adult lifespan (GO:0008340)|dopamine receptor signaling pathway (GO:0007212)|endoplasmic reticulum organization (GO:0007029)|endosomal transport (GO:0016197)|ER to Golgi vesicle-mediated transport (GO:0006888)|establishment of mitotic spindle orientation (GO:0000132)|Golgi organization (GO:0007030)|grooming behavior (GO:0007625)|hormone metabolic process (GO:0042445)|insulin secretion (GO:0030073)|iron ion homeostasis (GO:0055072)|L-glutamate import (GO:0051938)|lactate biosynthetic process from pyruvate (GO:0019244)|locomotory behavior (GO:0007626)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|neural plate formation (GO:0021990)|neuron apoptotic process (GO:0051402)|neuron development (GO:0048666)|olfactory lobe development (GO:0021988)|organ development (GO:0048513)|paraxial mesoderm formation (GO:0048341)|positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031587)|protein import into nucleus (GO:0006606)|quinolinate biosynthetic process (GO:0019805)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of protein phosphatase type 2A activity (GO:0034047)|regulation of synaptic plasticity (GO:0048167)|response to calcium ion (GO:0051592)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|social behavior (GO:0035176)|spermatogenesis (GO:0007283)|striatum development (GO:0021756)|urea cycle (GO:0000050)|vesicle transport along microtubule (GO:0047496)|visual learning (GO:0008542)	autophagic vacuole (GO:0005776)|axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|late endosome (GO:0005770)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	beta-tubulin binding (GO:0048487)|diazepam binding (GO:0050809)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|p53 binding (GO:0002039)|transcription factor binding (GO:0008134)			breast(1)|cervix(2)|endometrium(14)|kidney(5)|large_intestine(23)|lung(28)|ovary(4)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	87		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)		TCAGCTGTTACCCCTTCAGAC	0.517																																					p.T574fs		Atlas-INDEL	.											.	HTT	221	.	0			c.1720delA						.						49.0	51.0	50.0					4																	3129309		1960	4139	6099	SO:0001589	frameshift_variant	3064	exon12			.	L12392	CCDS43206.1	4p16.3	2014-09-17	2007-12-04	2007-12-04	ENSG00000197386	ENSG00000197386		"""Endogenous ligands"""	4851	protein-coding gene	gene with protein product		613004	"""huntingtin (Huntington disease)"""	HD		8458085	Standard	NM_002111		Approved	IT15	uc021xkv.1	P42858	OTTHUMG00000159916	ENST00000355072.5:c.1721delC	chr4.hg19:g.3129309delC	ENSP00000347184:p.Thr574fs	225.0	0.0		253.0	17.0	NM_002111	Q9UQB7	Frame_Shift_Del	DEL	ENST00000355072.5	hg19	CCDS43206.1																																																																																			.	.		0.517	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111	
IQGAP1	8826	hgsc.bcm.edu	37	15	91009653	91009653	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:91009653delA	ENST00000268182.5	+	17	2144	c.2020delA	c.(2020-2022)aaafs	p.K675fs	IQGAP1_ENST00000560738.1_Frame_Shift_Del_p.K103fs	NM_003870.3	NP_003861.1	P46940	IQGA1_HUMAN	IQ motif containing GTPase activating protein 1	675					cellular response to calcium ion (GO:0071277)|cellular response to epidermal growth factor stimulus (GO:0071364)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|glomerular visceral epithelial cell development (GO:0072015)|negative regulation of catalytic activity (GO:0043086)|negative regulation of dephosphorylation (GO:0035305)|neuron projection extension (GO:1990138)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|regulation of cytokine production (GO:0001817)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	actin filament (GO:0005884)|axon (GO:0030424)|cell junction (GO:0030054)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|extracellular vesicular exosome (GO:0070062)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|lateral plasma membrane (GO:0016328)|microtubule (GO:0005874)|midbody (GO:0030496)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|slit diaphragm (GO:0036057)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|GTPase activator activity (GO:0005096)|GTPase inhibitor activity (GO:0005095)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|protein serine/threonine kinase activator activity (GO:0043539)|Ras GTPase activator activity (GO:0005099)			breast(2)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(14)|liver(1)|lung(18)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	59	Melanoma(11;0.00551)|Lung NSC(78;0.0237)|all_lung(78;0.0488)		BRCA - Breast invasive adenocarcinoma(143;0.0745)|KIRC - Kidney renal clear cell carcinoma(17;0.138)|Kidney(142;0.194)			AGCCAAGAAGAAAAAACTGGC	0.463																																					p.K673fs		Atlas-INDEL	.											.	IQGAP1	140	.	0			c.2019delG						.						75.0	64.0	68.0					15																	91009653		2198	4298	6496	SO:0001589	frameshift_variant	8826	exon17			.	D29640	CCDS10362.1	15q26.1	2008-07-18			ENSG00000140575	ENSG00000140575			6110	protein-coding gene	gene with protein product	"""RasGAP-like with IQ motifs"""	603379				8051149, 8670801	Standard	XM_005254984		Approved	p195, KIAA0051, SAR1, HUMORFA01	uc002bpl.1	P46940	OTTHUMG00000149832	ENST00000268182.5:c.2020delA	chr15.hg19:g.91009653delA	ENSP00000268182:p.Lys675fs	95.0	0.0		144.0	11.0	NM_003870	A7MBM3	Frame_Shift_Del	DEL	ENST00000268182.5	hg19	CCDS10362.1																																																																																			.	.		0.463	IQGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313493.1	NM_003870	
SWT1	54823	hgsc.bcm.edu	37	1	185135718	185135718	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:185135718delA	ENST00000367500.4	+	3	264	c.99delA	c.(97-99)agafs	p.R33fs	SWT1_ENST00000367501.3_Frame_Shift_Del_p.R33fs	NM_017673.6	NP_060143.4	Q5T5J6	SWT1_HUMAN	SWT1 RNA endoribonuclease homolog (S. cerevisiae)	33										breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(11)|liver(1)|lung(16)|ovary(1)|prostate(1)|urinary_tract(1)	41						AGAAAGAGAGAAAAACCCCAG	0.289																																					p.R33fs		Atlas-INDEL	.											.	SWT1	88	.	0			c.98delG						.						59.0	65.0	63.0					1																	185135718		2201	4292	6493	SO:0001589	frameshift_variant	54823	exon3			.	AF288392	CCDS1367.1	1q25	2013-08-29	2011-01-24	2011-01-24	ENSG00000116668	ENSG00000116668			16785	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 26"""	C1orf26		11318611, 19127978, 23768067	Standard	NM_017673		Approved	FLJ20121, HsSwt1	uc001grg.4	Q5T5J6	OTTHUMG00000035390	ENST00000367500.4:c.99delA	chr1.hg19:g.185135718delA	ENSP00000356470:p.Arg33fs	123.0	0.0		180.0	11.0	NM_017673	Q8NEK9|Q9BZQ7|Q9NXQ0	Frame_Shift_Del	DEL	ENST00000367500.4	hg19	CCDS1367.1																																																																																			.	.		0.289	SWT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085790.1	NM_017673	
COL12A1	1303	hgsc.bcm.edu	37	6	75818818	75818818	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:75818818delT	ENST00000322507.8	-	52	8325	c.8016delA	c.(8014-8016)aaafs	p.K2672fs	COL12A1_ENST00000483888.2_Frame_Shift_Del_p.K2672fs|COL12A1_ENST00000345356.6_Frame_Shift_Del_p.K1508fs|COL12A1_ENST00000416123.2_Intron	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	2672	Laminin G-like.|Nonhelical region (NC3).				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type XII trimer (GO:0005595)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			breast(7)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(44)|liver(1)|lung(77)|ovary(7)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	169						CCTTGATGTCTTTTTCTATAA	0.308																																					p.D2673fs		Atlas-INDEL	.											.	COL12A1	385	.	0			c.8017delG						.						83.0	81.0	81.0					6																	75818818		1799	4070	5869	SO:0001589	frameshift_variant	1303	exon52			.	U73779	CCDS43481.1, CCDS43482.1	6q12-q13	2013-02-11	2003-07-24		ENSG00000111799	ENSG00000111799		"""Proteoglycans / Extracellular Matrix : Collagen proteoglycans"", ""Collagens"", ""Fibronectin type III domain containing"""	2188	protein-coding gene	gene with protein product	"""collagen type XII proteoglycan"""	120320	"""collagen, type XII, alpha 1-like"""	COL12A1L		9143499	Standard	XM_006715334		Approved		uc003phs.3	Q99715	OTTHUMG00000015051	ENST00000322507.8:c.8016delA	chr6.hg19:g.75818818delT	ENSP00000325146:p.Lys2672fs	175.0	0.0		173.0	11.0	NM_004370	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Frame_Shift_Del	DEL	ENST00000322507.8	hg19	CCDS43482.1																																																																																			.	.		0.308	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370	
PLOD2	5352	hgsc.bcm.edu	37	3	145794581	145794581	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:145794581delA	ENST00000360060.3	-	14	1779	c.1602delT	c.(1600-1602)tttfs	p.F534fs	PLOD2_ENST00000494950.1_Frame_Shift_Del_p.F500fs|PLOD2_ENST00000282903.5_Frame_Shift_Del_p.F555fs|PLOD2_ENST00000461497.1_Frame_Shift_Del_p.F215fs|RP11-274H2.2_ENST00000480247.1_RNA	NM_000935.2	NP_000926.2	O00469	PLOD2_HUMAN	procollagen-lysine, 2-oxoglutarate 5-dioxygenase 2	534					cellular protein modification process (GO:0006464)|extracellular matrix organization (GO:0030198)|response to hypoxia (GO:0001666)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|procollagen-lysine 5-dioxygenase activity (GO:0008475)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29					Vitamin C(DB00126)	CAGGATTTTCAAAAATCTGCC	0.294																																					p.E556fs		Atlas-INDEL	.											.	PLOD2	81	.	0			c.1666delG						.						78.0	86.0	83.0					3																	145794581		2202	4285	6487	SO:0001589	frameshift_variant	5352	exon15			.	U84573	CCDS3131.1, CCDS3132.1	3q24	2011-08-24	2005-01-04		ENSG00000152952	ENSG00000152952			9082	protein-coding gene	gene with protein product	"""lysyl hydroxlase 2"""	601865	"""procollagen-lysine, 2-oxoglutarate 5-dioxygenase (lysine hydroxylase) 2"""			9054364	Standard	XM_005247535		Approved	LH2	uc003evr.1	O00469	OTTHUMG00000159417	ENST00000360060.3:c.1602delT	chr3.hg19:g.145794581delA	ENSP00000353170:p.Phe534fs	126.0	0.0		161.0	12.0	NM_182943	B3KWS3|Q59ED2|Q8N170	Frame_Shift_Del	DEL	ENST00000360060.3	hg19	CCDS3131.1																																																																																			.	.		0.294	PLOD2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355185.1	NM_000935	
DNAH6	1768	hgsc.bcm.edu	37	2	84861633	84861633	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:84861633delG	ENST00000237449.6	+	29	4529	c.4521delG	c.(4519-4521)atgfs	p.M1507fs	DNAH6_ENST00000389394.3_Frame_Shift_Del_p.M1507fs|DNAH6_ENST00000398278.2_Frame_Shift_Del_p.M1507fs			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	1507	AAA 1. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(9)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	57						TTCAGATGATGGGGCGCTTCT	0.408																																					p.M1507fs		Atlas-INDEL	.											.	DNAH6	194	.	0			c.4520delT						.						44.0	42.0	43.0					2																	84861633		692	1591	2283	SO:0001589	frameshift_variant	1768	exon30			.	U61736	CCDS46348.1	2p11.2	2011-05-24	2006-09-04		ENSG00000115423	ENSG00000115423		"""Axonemal dyneins"""	2951	protein-coding gene	gene with protein product		603336	"""dynein, axonemal, heavy polypeptide 6"", ""dynein heavy chain-like 1"""	DNHL1		8812413	Standard	NM_001370		Approved	Dnahc6, HL-2, FLJ37357	uc010fgb.3	Q9C0G6	OTTHUMG00000128957	ENST00000237449.6:c.4521delG	chr2.hg19:g.84861633delG	ENSP00000237449:p.Met1507fs	101.0	0.0		144.0	10.0	NM_001370	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Frame_Shift_Del	DEL	ENST00000237449.6	hg19	CCDS46348.1																																																																																			.	.		0.408	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370	
DMXL2	23312	hgsc.bcm.edu	37	15	51914662	51914662	+	Frame_Shift_Del	DEL	G	G	-	rs2278990	byFrequency	TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:51914662delG	ENST00000251076.5	-	1	368	c.81delC	c.(79-81)cccfs	p.P27fs	DMXL2_ENST00000449909.3_Frame_Shift_Del_p.P27fs|DMXL2_ENST00000543779.2_Frame_Shift_Del_p.P27fs	NM_001174116.1|NM_015263.3	NP_001167587.1|NP_056078.2	Q8TDJ6	DMXL2_HUMAN	Dmx-like 2	27						cell junction (GO:0030054)|extracellular space (GO:0005615)|membrane (GO:0016020)|synaptic vesicle (GO:0008021)	Rab GTPase binding (GO:0017137)			breast(4)|central_nervous_system(1)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(26)|liver(1)|lung(28)|ovary(7)|prostate(7)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	101				all cancers(107;0.00494)		TCACCGTGAAGGGGACATCCC	0.687																																					p.F28fs		Atlas-INDEL	.											.	DMXL2	262	.	0			c.82delT						.						22.0	19.0	20.0					15																	51914662		2177	4261	6438	SO:0001589	frameshift_variant	23312	exon1			.	AB020663	CCDS10141.1, CCDS53945.1, CCDS53946.1	15q21.2	2013-01-10			ENSG00000104093	ENSG00000104093		"""WD repeat domain containing"""	2938	protein-coding gene	gene with protein product	"""rabconnectin 3"""	612186					Standard	NM_001174116		Approved	RC3, KIAA0856	uc010ufy.2	Q8TDJ6	OTTHUMG00000131749	ENST00000251076.5:c.81delC	chr15.hg19:g.51914662delG	ENSP00000251076:p.Pro27fs	128.0	0.0		156.0	10.0	NM_001174117	B2RTR3|B7ZMH3|F5GWF1|O94938	Frame_Shift_Del	DEL	ENST00000251076.5	hg19	CCDS10141.1																																																																																			.	.		0.687	DMXL2-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254671.2	NM_015263	
GHRHR	2692	hgsc.bcm.edu	37	7	31015405	31015405	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:31015405delT	ENST00000326139.2	+	10	942	c.896delT	c.(895-897)cttfs	p.L299fs	GHRHR_ENST00000461424.1_3'UTR|GHRHR_ENST00000409904.3_Frame_Shift_Del_p.L235fs|GHRHR_ENST00000409316.1_Frame_Shift_Del_p.A65fs	NM_000823.3	NP_000814.2	Q02643	GHRHR_HUMAN	growth hormone releasing hormone receptor	299					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|cAMP-mediated signaling (GO:0019933)|cell maturation (GO:0048469)|cellular response to insulin stimulus (GO:0032869)|determination of adult lifespan (GO:0008340)|growth hormone secretion (GO:0030252)|hormone metabolic process (GO:0042445)|lactation (GO:0007595)|multicellular organismal reproductive process (GO:0048609)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cell proliferation (GO:0008284)|positive regulation of growth hormone secretion (GO:0060124)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of multicellular organism growth (GO:0040018)|regulation of intracellular steroid hormone receptor signaling pathway (GO:0033143)|regulation of protein metabolic process (GO:0051246)|response to estrogen (GO:0043627)|response to glucocorticoid (GO:0051384)|response to insulin (GO:0032868)|somatotropin secreting cell development (GO:0060133)|water homeostasis (GO:0030104)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nuclear inner membrane (GO:0005637)|nuclear matrix (GO:0016363)|nuclear outer membrane (GO:0005640)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)	G-protein coupled receptor activity (GO:0004930)|growth factor binding (GO:0019838)|growth hormone-releasing hormone receptor activity (GO:0016520)|peptide hormone binding (GO:0017046)			biliary_tract(1)|breast(3)|endometrium(2)|kidney(1)|large_intestine(3)|lung(18)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	35					Sermorelin(DB00010)|Tesamorelin(DB08869)	AACTTTGGGCTTTTTCTCAAT	0.542																																					p.L299fs		Atlas-INDEL	.											.	GHRHR	55	.	0			c.895delC						.						112.0	96.0	101.0					7																	31015405		2203	4300	6503	SO:0001589	frameshift_variant	2692	exon10			.		CCDS5432.1	7p14	2012-08-10			ENSG00000106128	ENSG00000106128		"""GPCR / Class B : Glucagon receptors"""	4266	protein-coding gene	gene with protein product		139191				7680413, 7514564	Standard	NM_000823		Approved		uc003tbx.3	Q02643	OTTHUMG00000152801	ENST00000326139.2:c.896delT	chr7.hg19:g.31015405delT	ENSP00000320180:p.Leu299fs	129.0	0.0		183.0	12.0	NM_000823	Q99863	Frame_Shift_Del	DEL	ENST00000326139.2	hg19	CCDS5432.1																																																																																			.	.		0.542	GHRHR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327967.2		
KATNAL1	84056	hgsc.bcm.edu	37	13	30815176	30815176	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr13:30815176delT	ENST00000380615.3	-	5	707	c.540delA	c.(538-540)aaafs	p.K180fs	KATNAL1_ENST00000380617.3_Frame_Shift_Del_p.K180fs	NM_032116.4	NP_115492.1			katanin p60 subunit A-like 1											autonomic_ganglia(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(5)|skin(1)|urinary_tract(3)	19		Lung SC(185;0.0257)		all cancers(112;0.114)|OV - Ovarian serous cystadenocarcinoma(117;0.213)		CACCATCAAATTTTGGCATTT	0.368																																					p.F181fs		Atlas-INDEL	.											.	KATNAL1	53	.	0			c.541delT						.						205.0	186.0	192.0					13																	30815176		2203	4300	6503	SO:0001589	frameshift_variant	84056	exon5			.	AK097423	CCDS31956.1	13q12.3	2010-04-21			ENSG00000102781	ENSG00000102781		"""ATPases / AAA-type"""	28361	protein-coding gene	gene with protein product		614764				12477932	Standard	NM_001014380		Approved	MGC2599	uc001uss.4	Q9BW62	OTTHUMG00000016665	ENST00000380615.3:c.540delA	chr13.hg19:g.30815176delT	ENSP00000369989:p.Lys180fs	70.0	0.0		146.0	10.0	NM_001014380		Frame_Shift_Del	DEL	ENST00000380615.3	hg19	CCDS31956.1																																																																																			.	.		0.368	KATNAL1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044346.2	NM_032116	
DSCAM	1826	hgsc.bcm.edu	37	21	41452224	41452224	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr21:41452224delC	ENST00000400454.1	-	25	4752	c.4275delG	c.(4273-4275)gggfs	p.G1425fs		NM_001271534.1|NM_001389.3	NP_001258463.1|NP_001380.2	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule	1425	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|dendrite morphogenesis (GO:0048813)|dendrite self-avoidance (GO:0070593)|locomotory behavior (GO:0007626)|negative regulation of cell adhesion (GO:0007162)|nervous system development (GO:0007399)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of phosphorylation (GO:0042327)|post-embryonic retina morphogenesis in camera-type eye (GO:0060060)	axon (GO:0030424)|extracellular region (GO:0005576)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)				NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(22)|lung(47)|ovary(7)|pancreas(2)|prostate(3)|skin(14)|upper_aerodigestive_tract(6)|urinary_tract(4)	142		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				TTGGAAAACTCCCCCACTGCT	0.478																																					p.S1426fs	Melanoma(134;970 1778 1785 21664 32388)	Atlas-INDEL	.											.	DSCAM	347	.	0			c.4276delA						.						106.0	99.0	101.0					21																	41452224		1904	4126	6030	SO:0001589	frameshift_variant	1826	exon25			.	AF023449	CCDS42929.1	21q22.2-q22.3	2013-02-11			ENSG00000171587	ENSG00000171587		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	3039	protein-coding gene	gene with protein product		602523				9426258	Standard	NM_001271534		Approved	CHD2-42, CHD2-52	uc002yyq.1	O60469	OTTHUMG00000086732	ENST00000400454.1:c.4275delG	chr21.hg19:g.41452224delC	ENSP00000383303:p.Gly1425fs	180.0	0.0		179.0	11.0	NM_001271534	O60468	Frame_Shift_Del	DEL	ENST00000400454.1	hg19	CCDS42929.1																																																																																			.	.		0.478	DSCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195029.1	NM_001389	
DDX52	11056	hgsc.bcm.edu	37	17	36002258	36002258	+	Frame_Shift_Del	DEL	G	G	-	rs139568647		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:36002258delG	ENST00000349699.2	-	2	210	c.167delC	c.(166-168)ccafs	p.P56fs	RP11-697E22.2_ENST00000586950.1_RNA|RP11-697E22.2_ENST00000586163.1_RNA|DDX52_ENST00000394367.3_5'UTR	NM_007010.3	NP_008941.2	Q9Y2R4	DDX52_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 52	56						membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			biliary_tract(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(5)|ovary(1)|skin(3)	17		Breast(25;0.00637)|Ovarian(249;0.15)				ACACACACCTGGGACAGACTT	0.408																																					p.P56fs		Atlas-INDEL	.											.	DDX52	40	.	0			c.168delA						.						116.0	116.0	116.0					17																	36002258		2203	4300	6503	SO:0001589	frameshift_variant	11056	exon2			.	AF077033	CCDS11323.1	17q21.1	2014-05-06			ENSG00000141141	ENSG00000278053		"""DEAD-boxes"""	20038	protein-coding gene	gene with protein product		612500				11124703	Standard	XM_006721650		Approved	ROK1	uc002hoi.2	Q9Y2R4	OTTHUMG00000188475	ENST00000349699.2:c.167delC	chr17.hg19:g.36002258delG	ENSP00000268854:p.Pro56fs	185.0	0.0		181.0	11.0	NM_007010	Q86YG1|Q8N213|Q9NVE0|Q9Y482	Frame_Shift_Del	DEL	ENST00000349699.2	hg19	CCDS11323.1																																																																																			.	.		0.408	DDX52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256795.1	NM_152300	
PC	5091	hgsc.bcm.edu	37	11	66638785	66638785	+	Splice_Site	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:66638785delC	ENST00000393958.2	-	5	581		c.e5+1		PC_ENST00000524491.1_Splice_Site|PC_ENST00000393955.2_Splice_Site|PC_ENST00000355677.3_Splice_Site|PC_ENST00000393960.1_Splice_Site	NM_000920.3	NP_000911.2	P11498	PYC_HUMAN	pyruvate carboxylase						biotin metabolic process (GO:0006768)|carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|lipid metabolic process (GO:0006629)|oxaloacetate metabolic process (GO:0006107)|pyruvate metabolic process (GO:0006090)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|pyruvate carboxylase activity (GO:0004736)			cervix(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(12)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32		Melanoma(852;0.0525)		Lung(977;0.153)|LUSC - Lung squamous cell carcinoma(976;0.227)	Biotin(DB00121)|Pyruvic acid(DB00119)	GTTATATTCACCCGCAGCAAT	0.647																																					.		Atlas-INDEL	.											.	PC	116	.	0			c.487+2G>-						.						63.0	72.0	69.0					11																	66638785		2200	4295	6495	SO:0001630	splice_region_variant	5091	exon7			.	U04641	CCDS8152.1	11q13.4-q13.5	2012-07-11			ENSG00000173599	ENSG00000173599	6.4.1.1		8636	protein-coding gene	gene with protein product		608786				6548474	Standard	NM_022172		Approved	PCB	uc001ojn.1	P11498	OTTHUMG00000167099	ENST00000393958.2:c.487+1G>-	chr11.hg19:g.66638785delC		107.0	0.0		154.0	10.0	NM_001040716	B4DN00|Q16705	Splice_Site	DEL	ENST00000393958.2	hg19	CCDS8152.1																																																																																			.	.		0.647	PC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393115.1	NM_001040716	Intron
RBM12B	389677	hgsc.bcm.edu	37	8	94746698	94746698	+	Frame_Shift_Del	DEL	G	G	-	rs3133974	byFrequency	TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr8:94746698delG	ENST00000399300.2	-	3	2154	c.1941delC	c.(1939-1941)cccfs	p.P647fs	RBM12B_ENST00000520961.1_Intron|RBM12B_ENST00000517700.1_Intron|RP11-10N23.4_ENST00000517998.1_RNA	NM_203390.2	NP_976324.2	Q8IXT5	RB12B_HUMAN	RNA binding motif protein 12B	647							nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(7)|ovary(2)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	30	Breast(36;4.14e-07)		BRCA - Breast invasive adenocarcinoma(8;0.0168)			AGTCCTCCTCGGGGAGCTGCC	0.647																																					p.E648fs		Atlas-INDEL	.											.	RBM12B	78	.	0			c.1942delG						.						86.0	89.0	88.0					8																	94746698		1874	4107	5981	SO:0001589	frameshift_variant	389677	exon3			.		CCDS43755.1	8q22	2014-05-20			ENSG00000183808	ENSG00000183808		"""RNA binding motif (RRM) containing"""	32310	protein-coding gene	gene with protein product							Standard	NM_203390		Approved		uc003yfz.3	Q8IXT5	OTTHUMG00000164317	ENST00000399300.2:c.1941delC	chr8.hg19:g.94746698delG	ENSP00000382239:p.Pro647fs	75.0	0.0		159.0	10.0	NM_203390	A8MYB5	Frame_Shift_Del	DEL	ENST00000399300.2	hg19	CCDS43755.1																																																																																			.	.		0.647	RBM12B-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383603.1	NM_203390	
ADAMTSL4	54507	hgsc.bcm.edu	37	1	150532255	150532255	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:150532255delG	ENST00000369038.2	+	16	3163	c.2962delG	c.(2962-2964)gggfs	p.G989fs	RP11-54A4.2_ENST00000442435.2_RNA|ADAMTSL4_ENST00000369039.5_Frame_Shift_Del_p.G1012fs|ADAMTSL4_ENST00000271643.4_Frame_Shift_Del_p.G989fs			Q6UY14	ATL4_HUMAN	ADAMTS-like 4	989	TSP type-1 6. {ECO:0000255|PROSITE- ProRule:PRU00210}.				apoptotic process (GO:0006915)|extracellular matrix organization (GO:0030198)|positive regulation of apoptotic process (GO:0043065)	interstitial matrix (GO:0005614)	metalloendopeptidase activity (GO:0004222)|protease binding (GO:0002020)			breast(1)|cervix(1)|endometrium(6)|large_intestine(3)|lung(13)|ovary(2)|prostate(3)|skin(3)	32	all_cancers(9;3.13e-53)|all_epithelial(9;3.74e-43)|all_lung(15;2.43e-34)|Lung NSC(24;8.86e-31)|Breast(34;0.000326)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0241)|Epithelial(6;3.18e-23)|all cancers(9;1.79e-22)|OV - Ovarian serous cystadenocarcinoma(6;1.13e-14)|BRCA - Breast invasive adenocarcinoma(12;0.000503)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206)			CTCCTGCCAAGGGGGAACGCA	0.637											OREG0013787	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Q987fs		Atlas-INDEL	.											.	ADAMTSL4	101	.	0			c.2961delA						.						89.0	98.0	95.0					1																	150532255		2203	4300	6503	SO:0001589	frameshift_variant	54507	exon18			.	BC027478	CCDS955.1, CCDS30852.1, CCDS72908.1	1q21.2	2008-02-05	2005-12-01	2005-12-01	ENSG00000143382	ENSG00000143382			19706	protein-coding gene	gene with protein product		610113	"""thrombospondin repeat containing 1"""	TSRC1		12706885	Standard	NM_019032		Approved	DKFZP434K1772	uc001eux.3	Q6UY14	OTTHUMG00000034863	ENST00000369038.2:c.2962delG	chr1.hg19:g.150532255delG	ENSP00000358034:p.Gly989fs	72.0	0.0	1733	165.0	10.0	NM_019032	B2RTT0|F8WAD0|Q5T5F7|Q6IPM6|Q8N643|Q9HBS6	Frame_Shift_Del	DEL	ENST00000369038.2	hg19	CCDS955.1																																																																																			.	.		0.637	ADAMTSL4-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084395.4	NM_019032	
ZBED1	9189	hgsc.bcm.edu	37	X	2408092	2408092	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chrX:2408092delG	ENST00000381223.4	-	2	872	c.669delC	c.(667-669)cccfs	p.P223fs	ZBED1_ENST00000515319.1_5'Flank|ZBED1_ENST00000381218.3_Frame_Shift_Del_p.P223fs|DHRSX_ENST00000334651.5_Intron|ZBED1_ENST00000381222.2_Frame_Shift_Del_p.P223fs	NM_001171135.1|NM_001171136.1|NM_004729.3	NP_001164606.1|NP_001164607.1|NP_004720.1	O96006	ZBED1_HUMAN	zinc finger, BED-type containing 1	223					metabolic process (GO:0008152)	nuclear chromosome (GO:0000228)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|transposase activity (GO:0004803)			endometrium(8)|kidney(1)|large_intestine(3)|lung(11)|prostate(1)|upper_aerodigestive_tract(1)	25		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				ACAGGCAGTTGGGGGCGCCCA	0.637																																					p.N224fs		Atlas-INDEL	.											.	ZBED1	64	.	0			c.670delA						.						93.0	101.0	98.0					X																	2408092		2203	4296	6499	SO:0001589	frameshift_variant	9189	exon2			.	AB018328	CCDS14118.1	Xp22.33 and Yp11	2013-05-03	2004-01-14	2004-01-16	ENSG00000214717	ENSG00000214717		"""Pseudoautosomal regions / PAR1"", ""Zinc fingers, BED-type"""	447	protein-coding gene	gene with protein product		300178	"""Ac-like transposable element"""	ALTE		9872452, 9887332, 23533661	Standard	NM_001171135		Approved	TRAMP, KIAA0785, DREF, hDREF	uc004cqh.2	O96006	OTTHUMG00000021069	ENST00000381223.4:c.669delC	chrX.hg19:g.2408092delG	ENSP00000370621:p.Pro223fs	119.0	0.0		161.0	10.0	NM_001171135	Q96BY4	Frame_Shift_Del	DEL	ENST00000381223.4	hg19	CCDS14118.1																																																																																			.	.		0.637	ZBED1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000144310.3	NM_004729	
EP400	57634	hgsc.bcm.edu	37	12	132502833	132502833	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:132502833delA	ENST00000333577.4	+	22	4406	c.4297delA	c.(4297-4299)aaafs	p.K1434fs	EP400_ENST00000332482.4_Frame_Shift_Del_p.K1361fs|EP400_ENST00000330386.6_Frame_Shift_Del_p.K1398fs|EP400_ENST00000389561.2_Frame_Shift_Del_p.K1398fs|EP400_ENST00000389562.2_Frame_Shift_Del_p.K1397fs			Q96L91	EP400_HUMAN	E1A binding protein p400	1434					chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|Swr1 complex (GO:0000812)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(6)|central_nervous_system(10)|cervix(1)|endometrium(21)|kidney(13)|large_intestine(25)|lung(56)|ovary(5)|prostate(8)|skin(6)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	161	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.198)		OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06)		GCTGTCTAAGAAAAAGATACC	0.483																																					p.K1396fs		Atlas-INDEL	.											.	EP400	370	.	0			c.4188delG						.						55.0	58.0	57.0					12																	132502833		2203	4300	6503	SO:0001589	frameshift_variant	57634	exon21			.	U80743	CCDS31929.1, CCDS31929.2	12q24.33	2008-02-01	2002-02-05	2002-02-08		ENSG00000183495			11958	protein-coding gene	gene with protein product		606265	"""trinucleotide repeat containing 12"""	TNRC12		9225980, 11509179	Standard	NM_015409		Approved	CAGH32, KIAA1498, P400, KIAA1818, DKFZP434I225	uc001ujn.3	Q96L91		ENST00000333577.4:c.4297delA	chr12.hg19:g.132502833delA	ENSP00000333602:p.Lys1434fs	148.0	0.0		159.0	11.0	NM_015409	O15411|Q6P2F5|Q8N8Q7|Q8NE05|Q96JK7|Q9P230	Frame_Shift_Del	DEL	ENST00000333577.4	hg19																																																																																				.	.		0.483	EP400-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015409	
CEBPZ	10153	hgsc.bcm.edu	37	2	37449611	37449611	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:37449611delT	ENST00000234170.5	-	4	2122	c.1977delA	c.(1975-1977)aaafs	p.K659fs		NM_005760.2	NP_005751.2	Q03701	CEBPZ_HUMAN	CCAAT/enhancer binding protein (C/EBP), zeta	659					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(3)|endometrium(2)|large_intestine(7)|lung(12)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	28		all_hematologic(82;0.21)				CTGTCTCAAGTTTTTTCACTA	0.353																																					p.L660fs		Atlas-INDEL	.											.	CEBPZ	68	.	0			c.1978delC						.						142.0	134.0	137.0					2																	37449611		2203	4300	6503	SO:0001589	frameshift_variant	10153	exon4			.	M37197	CCDS1787.1	2p22.3	2008-09-03	2008-09-03		ENSG00000115816	ENSG00000115816			24218	protein-coding gene	gene with protein product		612828				2247079, 12534345	Standard	NM_005760		Approved	CBF2, CTF2	uc002rpz.3	Q03701	OTTHUMG00000100960	ENST00000234170.5:c.1977delA	chr2.hg19:g.37449611delT	ENSP00000234170:p.Lys659fs	150.0	0.0		188.0	12.0	NM_005760	Q8NE75	Frame_Shift_Del	DEL	ENST00000234170.5	hg19	CCDS1787.1																																																																																			.	.		0.353	CEBPZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218569.2	NM_005760	
ARHGAP22	58504	hgsc.bcm.edu	37	10	49661399	49661399	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:49661399delA	ENST00000249601.4	-	8	1232	c.936delT	c.(934-936)tttfs	p.F312fs	ARHGAP22_ENST00000374170.1_Frame_Shift_Del_p.F153fs|ARHGAP22_ENST00000417247.2_Frame_Shift_Del_p.F222fs|ARHGAP22_ENST00000435790.2_Frame_Shift_Del_p.F318fs|ARHGAP22_ENST00000477708.2_5'Flank|ARHGAP22_ENST00000374172.1_Frame_Shift_Del_p.F203fs|ARHGAP22_ENST00000417912.2_Frame_Shift_Del_p.F328fs	NM_001256024.1|NM_021226.3	NP_001242953.1|NP_067049.2	Q7Z5H3	RHG22_HUMAN	Rho GTPase activating protein 22	312	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|regulation of small GTPase mediated signal transduction (GO:0051056)|regulation of transcription, DNA-templated (GO:0006355)|small GTPase mediated signal transduction (GO:0007264)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)			endometrium(3)|large_intestine(3)|lung(7)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						TGTTAGGTCCAAAAACGGTTG	0.517																																					p.G329fs		Atlas-INDEL	.											.	ARHGAP22	94	.	0			c.985delG						.						158.0	135.0	143.0					10																	49661399		2202	4300	6502	SO:0001589	frameshift_variant	58504	exon8			.	AY324801	CCDS7227.1, CCDS58079.1, CCDS58080.1, CCDS58081.1	10q11.23	2013-01-10			ENSG00000128805	ENSG00000128805		"""Rho GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"""	30320	protein-coding gene	gene with protein product		610585				8619474	Standard	NM_021226		Approved	RhoGAP2	uc010qgm.3	Q7Z5H3	OTTHUMG00000018176	ENST00000249601.4:c.936delT	chr10.hg19:g.49661399delA	ENSP00000249601:p.Phe312fs	169.0	0.0		193.0	12.0	NM_001256024	A0AVP7|A5YM75|B4DED8|B9EGA0|C9JDM2|O00152|Q6ZSB0	Frame_Shift_Del	DEL	ENST00000249601.4	hg19	CCDS7227.1																																																																																			.	.		0.517	ARHGAP22-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000358767.1	NM_021226	
PPIL2	23759	hgsc.bcm.edu	37	22	22043036	22043036	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr22:22043036delG	ENST00000335025.8	+	15	1128	c.1037delG	c.(1036-1038)tggfs	p.W346fs	PPIL2_ENST00000446951.1_3'UTR|PPIL2_ENST00000492445.2_Frame_Shift_Del_p.W346fs|PPIL2_ENST00000456792.2_Frame_Shift_Del_p.W325fs|PPIL2_ENST00000412327.1_Frame_Shift_Del_p.W346fs|PPIL2_ENST00000398831.3_Frame_Shift_Del_p.W346fs|PPIL2_ENST00000406385.1_Frame_Shift_Del_p.W346fs					peptidylprolyl isomerase (cyclophilin)-like 2											endometrium(4)|kidney(2)|large_intestine(4)|lung(3)|ovary(2)|skin(2)	17	Colorectal(54;0.105)					GAGTCATACTGGGGGAAGCCC	0.622																																					p.W346fs		Atlas-INDEL	.											.	PPIL2	38	.	0			c.1036delT						.						67.0	66.0	66.0					22																	22043036		2203	4300	6503	SO:0001589	frameshift_variant	23759	exon15			.		CCDS13793.1	22q11.21	2013-01-29			ENSG00000100023	ENSG00000100023		"""U-box domain containing"""	9261	protein-coding gene	gene with protein product	"""U-box domain containing 7"""	607588				10591208	Standard	NM_014337		Approved	UBOX7, CYC4, Cyp-60	uc002zvh.4	Q13356	OTTHUMG00000030174	ENST00000335025.8:c.1037delG	chr22.hg19:g.22043036delG	ENSP00000334553:p.Trp346fs	125.0	0.0		183.0	11.0	NM_014337		Frame_Shift_Del	DEL	ENST00000335025.8	hg19	CCDS13793.1																																																																																			.	.		0.622	PPIL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075028.4		
CPNE7	27132	hgsc.bcm.edu	37	16	89649911	89649911	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:89649911delG	ENST00000268720.5	+	4	687	c.557delG	c.(556-558)aggfs	p.R186fs	CPNE7_ENST00000319518.8_Intron	NM_014427.4	NP_055242.1	Q9UBL6	CPNE7_HUMAN	copine VII	186					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)		TGGACGTGCAGGGGTGGCCAC	0.647																																					p.R186fs		Atlas-INDEL	.											.	CPNE7	56	.	0			c.556delA						.						24.0	17.0	20.0					16																	89649911		2127	4229	6356	SO:0001589	frameshift_variant	27132	exon4			.	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.557delG	chr16.hg19:g.89649911delG	ENSP00000268720:p.Arg186fs	136.0	0.0		146.0	10.0	NM_014427		Frame_Shift_Del	DEL	ENST00000268720.5	hg19	CCDS10980.1																																																																																			.	.		0.647	CPNE7-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000269929.2		
TUBGCP6	85378	hgsc.bcm.edu	37	22	50659190	50659190	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr22:50659190delC	ENST00000248846.5	-	16	3702	c.3598delG	c.(3598-3600)gagfs	p.E1200fs	TUBGCP6_ENST00000491449.1_5'UTR|TUBGCP6_ENST00000439308.2_Frame_Shift_Del_p.E1200fs			Q96RT7	GCP6_HUMAN	tubulin, gamma complex associated protein 6	1200	9 X 27 AA tandem repeats.				G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|gamma-tubulin ring complex (GO:0008274)|membrane (GO:0016020)|microtubule (GO:0005874)|spindle pole (GO:0000922)	microtubule binding (GO:0008017)			breast(4)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(13)|ovary(3)|prostate(2)|skin(2)	45		all_cancers(38;5.79e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		LUAD - Lung adenocarcinoma(64;0.109)|BRCA - Breast invasive adenocarcinoma(115;0.21)		GACACAGACTCCCCCAAGCTG	0.622																																					p.E1200fs		Atlas-INDEL	.											.	TUBGCP6	132	.	0			c.3599delA						.						75.0	68.0	70.0					22																	50659190		2203	4300	6503	SO:0001589	frameshift_variant	85378	exon16			.	AB051456	CCDS14087.1	22q13.31-q13.33	2008-07-01			ENSG00000128159	ENSG00000128159			18127	protein-coding gene	gene with protein product	"""gamma-tubulin complex component 6"""	610053				11694571, 11258795	Standard	XR_244458		Approved	GCP6, KIAA1669, DJ402G11.6	uc003bkb.1	Q96RT7	OTTHUMG00000030150	ENST00000248846.5:c.3598delG	chr22.hg19:g.50659190delC	ENSP00000248846:p.Glu1200fs	126.0	0.0		157.0	11.0	NM_020461	Q5JZ80|Q6PJ40|Q86YE9|Q9BY91|Q9UGX3|Q9UGX4	Frame_Shift_Del	DEL	ENST00000248846.5	hg19	CCDS14087.1																																																																																			.	.		0.622	TUBGCP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075004.3	NM_020461	
RABGEF1	27342	hgsc.bcm.edu	37	7	66270287	66270287	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:66270287delC	ENST00000284957.5	+	8	1058	c.981delC	c.(979-981)aacfs	p.N327fs	KCTD7_ENST00000451741.2_Frame_Shift_Del_p.N327fs|KCTD7_ENST00000380828.2_Frame_Shift_Del_p.N367fs|RABGEF1_ENST00000437078.2_Frame_Shift_Del_p.N341fs|RABGEF1_ENST00000484547.2_3'UTR|KCTD7_ENST00000510829.2_Frame_Shift_Del_p.N327fs|RABGEF1_ENST00000439720.2_Frame_Shift_Del_p.N340fs|RABGEF1_ENST00000450873.2_Frame_Shift_Del_p.N327fs			Q9UJ41	RABX5_HUMAN	RAB guanine nucleotide exchange factor (GEF) 1	544					endocytosis (GO:0006897)|positive regulation of Rab GTPase activity (GO:0032851)|protein targeting to membrane (GO:0006612)	early endosome (GO:0005769)	DNA binding (GO:0003677)|Rab GTPase binding (GO:0017137)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(5)|lung(9)|ovary(1)|stomach(1)	27						TGAAGGGCAACCCCCCACGCC	0.507																																					p.N327fs		Atlas-INDEL	.											.	RABGEF1	56	.	0			c.980delA						.						129.0	106.0	114.0					7																	66270287		2203	4300	6503	SO:0001589	frameshift_variant	27342	exon8			.	AJ250042	CCDS5535.1, CCDS69308.1, CCDS75610.1	7q11.21	2010-07-09			ENSG00000154710	ENSG00000154710			17676	protein-coding gene	gene with protein product		609700				12505986, 11098082	Standard	NM_014504		Approved	rabex-5, RABEX5	uc003tvh.3	Q9UJ41	OTTHUMG00000129547	ENST00000284957.5:c.981delC	chr7.hg19:g.66270287delC	ENSP00000284957:p.Asn327fs	115.0	0.0		162.0	10.0	NM_014504	B4DZM7|Q3HKR2|Q3HKR3|Q53FG0	Frame_Shift_Del	DEL	ENST00000284957.5	hg19	CCDS5535.1																																																																																			.	.		0.507	RABGEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251737.3	NM_014504	
FAM186A	121006	hgsc.bcm.edu	37	12	50748485	50748485	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:50748485delT	ENST00000327337.5	-	4	2129	c.2130delA	c.(2128-2130)aaafs	p.K710fs	FAM186A_ENST00000543111.1_Frame_Shift_Del_p.K710fs	NM_001145475.1	NP_001138947.1	A6NE01	F186A_HUMAN	family with sequence similarity 186, member A	710																	TGATTCCTAATTTTTCAGCTT	0.328																																					p.L711X	NSCLC(138;1796 1887 12511 19463 37884)	Atlas-INDEL	.											.	FAM186A	181	.	0			c.2131delT						.						85.0	63.0	70.0					12																	50748485		692	1591	2283	SO:0001589	frameshift_variant	121006	exon4			.		CCDS44878.1	12q13.13	2009-04-22			ENSG00000185958	ENSG00000185958			26980	protein-coding gene	gene with protein product							Standard	NM_001145475		Approved	LOC121006	uc001rwl.2	A6NE01	OTTHUMG00000167889	ENST00000327337.5:c.2130delA	chr12.hg19:g.50748485delT	ENSP00000329995:p.Lys710fs	114.0	0.0		147.0	10.0	NM_001145475		Frame_Shift_Del	DEL	ENST00000327337.5	hg19	CCDS44878.1																																																																																			.	.		0.328	FAM186A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396838.1	XM_001718353	
OR5M3	219482	hgsc.bcm.edu	37	11	56237709	56237709	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:56237709delT	ENST00000312240.2	-	1	305	c.265delA	c.(265-267)acafs	p.T89fs		NM_001004742.2	NP_001004742.2	Q8NGP4	OR5M3_HUMAN	olfactory receptor, family 5, subfamily M, member 3	89						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|central_nervous_system(2)|endometrium(2)|large_intestine(7)|lung(15)|ovary(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	37	Esophageal squamous(21;0.00448)					TAAGTAATTGTTTTTTTATCT	0.363																																					p.T89fs		Atlas-INDEL	.											.	OR5M3	103	.	0			c.266delC						.						87.0	80.0	83.0					11																	56237709		2201	4295	6496	SO:0001589	frameshift_variant	219482	exon1			.	AB065746	CCDS31532.1	11q11	2012-08-09			ENSG00000174937	ENSG00000174937		"""GPCR / Class A : Olfactory receptors"""	14806	protein-coding gene	gene with protein product							Standard	NM_001004742		Approved		uc010rjk.2	Q8NGP4	OTTHUMG00000166875	ENST00000312240.2:c.265delA	chr11.hg19:g.56237709delT	ENSP00000312208:p.Thr89fs	113.0	0.0		148.0	10.0	NM_001004742	B2RNM7|Q6IEW4|Q96RC0	Frame_Shift_Del	DEL	ENST00000312240.2	hg19	CCDS31532.1																																																																																			.	.		0.363	OR5M3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391639.1	NM_001004742	
IFT52	51098	hgsc.bcm.edu	37	20	42249541	42249541	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr20:42249541delC	ENST00000373030.3	+	9	874	c.744delC	c.(742-744)aacfs	p.N248fs	IFT52_ENST00000373039.4_Frame_Shift_Del_p.N248fs	NM_016004.2	NP_057088.2	Q9Y366	IFT52_HUMAN	intraflagellar transport 52	248					cilium morphogenesis (GO:0060271)|dorsal/ventral pattern formation (GO:0009953)|embryonic digit morphogenesis (GO:0042733)|heart looping (GO:0001947)|intraciliary transport (GO:0042073)|negative regulation of epithelial cell proliferation (GO:0050680)|neural tube formation (GO:0001841)|regulation of protein processing (GO:0070613)|smoothened signaling pathway (GO:0007224)	centriole (GO:0005814)|ciliary base (GO:0097546)|ciliary tip (GO:0097542)|cilium (GO:0005929)|dendrite terminus (GO:0044292)|intraciliary transport particle B (GO:0030992)|motile cilium (GO:0031514)|photoreceptor connecting cilium (GO:0032391)	protein C-terminus binding (GO:0008022)			endometrium(5)|kidney(1)|large_intestine(2)|lung(10)|ovary(2)|urinary_tract(1)	21		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.0031)			TCCACCTAAACCAGATTGATG	0.368																																					p.N248fs		Atlas-INDEL	.											.	IFT52	40	.	0			c.743delA						.						96.0	101.0	99.0					20																	42249541		2203	4300	6503	SO:0001589	frameshift_variant	51098	exon9			.	AF151811	CCDS33470.1	20q12-q13.1	2014-07-03	2014-07-03	2005-11-02	ENSG00000101052	ENSG00000101052		"""Intraflagellar transport homologs"""	15901	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 9"", ""intraflagellar transport 52 homolog (Chlamydomonas)"""	C20orf9		10810093	Standard	NM_016004		Approved	CGI-53, NGD5, dJ1028D15.1, NGD2	uc002xkw.3	Q9Y366	OTTHUMG00000032513	ENST00000373030.3:c.744delC	chr20.hg19:g.42249541delC	ENSP00000362121:p.Asn248fs	160.0	0.0		169.0	11.0	NM_016004	B3KMA1|E1P5W9|Q5H8Z0|Q9H1G3|Q9H1G4|Q9H1H2	Frame_Shift_Del	DEL	ENST00000373030.3	hg19	CCDS33470.1																																																																																			.	.		0.368	IFT52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079317.1	NM_016004	
HIAT1	64645	hgsc.bcm.edu	37	1	100525518	100525518	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:100525518delT	ENST00000370152.3	+	4	464	c.328delT	c.(328-330)tttfs	p.F111fs	RP4-714D9.2_ENST00000432294.1_RNA	NM_033055.2	NP_149044.2	Q96MC6	HIAT1_HUMAN	hippocampus abundant transcript 1	111					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(8)|skin(1)	16		all_epithelial(167;2.96e-06)|all_lung(203;0.00125)|Lung NSC(277;0.00131)		Epithelial(280;0.0832)|all cancers(265;0.136)|COAD - Colon adenocarcinoma(174;0.148)|Lung(183;0.195)		GCTAACGGTGTTTTTCACATG	0.383																																					p.V109fs		Atlas-INDEL	.											.	HIAT1	46	.	0			c.327delG						.						235.0	222.0	226.0					1																	100525518		2203	4300	6503	SO:0001589	frameshift_variant	64645	exon4			.	AK096669	CCDS763.1	1p21.3	2008-02-05			ENSG00000156875	ENSG00000156875			23363	protein-coding gene	gene with protein product						9299464	Standard	NM_033055		Approved	DKFZP564L0864	uc001dst.3	Q96MC6	OTTHUMG00000010755	ENST00000370152.3:c.328delT	chr1.hg19:g.100525518delT	ENSP00000359171:p.Phe111fs	177.0	0.0		194.0	12.0	NM_033055	Q6P2N7|Q8N8K2|Q8NBV3|Q96NY0|Q9NT25	Frame_Shift_Del	DEL	ENST00000370152.3	hg19	CCDS763.1																																																																																			.	.		0.383	HIAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029657.1	NM_033055	
SYCP1	6847	hgsc.bcm.edu	37	1	115487538	115487538	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:115487538delA	ENST00000369522.3	+	25	2329	c.2089delA	c.(2089-2091)aaafs	p.K697fs	SYCP1_ENST00000369518.1_Frame_Shift_Del_p.K697fs	NM_001282541.1|NM_003176.2	NP_001269470.1|NP_003167.2	Q15431	SYCP1_HUMAN	synaptonemal complex protein 1	697					chiasma assembly (GO:0051026)|lateral element assembly (GO:0051878)|meiotic DNA repair synthesis (GO:0000711)|reciprocal meiotic recombination (GO:0007131)|regulation of protein localization (GO:0032880)|sperm chromatin condensation (GO:0035092)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)	central element (GO:0000801)|male germ cell nucleus (GO:0001673)|transverse filament (GO:0000802)	DNA binding (GO:0003677)		RGS22/SYCP1(2)	NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(17)|lung(20)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	48	Lung SC(450;0.211)	all_cancers(81;8.65e-08)|all_epithelial(167;3.32e-07)|all_lung(203;6.55e-06)|Lung NSC(69;1.11e-05)|Acute lymphoblastic leukemia(138;0.221)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		AAAATTACAGAAAGAAATTGA	0.249																																					p.Q696fs		Atlas-INDEL	.											.	SYCP1	149	.	0			c.2088delG						.						37.0	39.0	38.0					1																	115487538		2198	4278	6476	SO:0001589	frameshift_variant	6847	exon25			.	D67035	CCDS879.1, CCDS72840.1	1p13-p12	2009-03-12			ENSG00000198765	ENSG00000198765			11487	protein-coding gene	gene with protein product	"""cancer/testis antigen 8"""	602162				9560255	Standard	XM_005271154		Approved	HOM-TES-14, SCP1, CT8	uc001efr.3	Q15431	OTTHUMG00000012057	ENST00000369522.3:c.2089delA	chr1.hg19:g.115487538delA	ENSP00000358535:p.Lys697fs	122.0	0.0		153.0	10.0	NM_003176	O14963|Q5VXJ6	Frame_Shift_Del	DEL	ENST00000369522.3	hg19	CCDS879.1																																																																																			.	.		0.249	SYCP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033386.1	NM_003176	
PITRM1	10531	hgsc.bcm.edu	37	10	3207693	3207693	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:3207693delA	ENST00000224949.4	-	5	479	c.445delT	c.(445-447)tccfs	p.S149fs	PITRM1-AS1_ENST00000598280.1_RNA|PITRM1_ENST00000380989.2_Frame_Shift_Del_p.S149fs|PITRM1_ENST00000451104.2_Frame_Shift_Del_p.S117fs|PITRM1-AS1_ENST00000601046.1_RNA			Q5JRX3	PREP_HUMAN	pitrilysin metallopeptidase 1	149					positive regulation of catalytic activity (GO:0043085)|proteolysis (GO:0006508)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	enzyme activator activity (GO:0008047)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			breast(2)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(5)|liver(1)|lung(5)|ovary(1)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|urinary_tract(3)	33						TTTTGTGTGGAAAATGGATAC	0.363																																					p.S149fs		Atlas-INDEL	.											.	PITRM1	109	.	0			c.446delC						.						89.0	91.0	91.0					10																	3207693		1830	4086	5916	SO:0001589	frameshift_variant	10531	exon5			.	AB029027	CCDS55699.1, CCDS55700.1, CCDS59208.1	10p15.2	2008-07-30	2005-08-17		ENSG00000107959	ENSG00000107959			17663	protein-coding gene	gene with protein product	"""PreP peptidasome"""		"""pitrilysin metalloproteinase 1"""			1036083, 10470851, 16849325	Standard	NM_014889		Approved	MP1, KIAA1104, hMP1, PreP	uc009xhv.2	Q5JRX3	OTTHUMG00000017557	ENST00000224949.4:c.445delT	chr10.hg19:g.3207693delA	ENSP00000224949:p.Ser149fs	106.0	0.0		147.0	10.0	NM_014889	B3KMJ6|B4E0J8|C9JSL2|E7ES23|O95204|Q2M2G6|Q4VBR1|Q5JRW7|Q7L5Z7|Q9BSI6|Q9BVJ5|Q9UPP8	Frame_Shift_Del	DEL	ENST00000224949.4	hg19	CCDS59208.1																																																																																			.	.		0.363	PITRM1-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000046469.2		
ZNF804A	91752	hgsc.bcm.edu	37	2	185800708	185800708	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:185800708delA	ENST00000302277.6	+	4	1179	c.585delA	c.(583-585)gcafs	p.A195fs		NM_194250.1	NP_919226.1	Q7Z570	Z804A_HUMAN	zinc finger protein 804A	195							metal ion binding (GO:0046872)			NS(5)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(22)|liver(2)|lung(79)|ovary(7)|pancreas(1)|prostate(2)|skin(12)|urinary_tract(1)	146						ATTATACAGCAAAAAATAACC	0.388																																					p.A195fs		Atlas-INDEL	.											.	ZNF804A	322	.	0			c.584delC						.						62.0	65.0	64.0					2																	185800708		2203	4300	6503	SO:0001589	frameshift_variant	91752	exon4			.	AF052145	CCDS2291.1	2q32.1	2012-10-05	2006-10-27	2006-10-27	ENSG00000170396	ENSG00000170396			21711	protein-coding gene	gene with protein product		612282		C2orf10		12970790	Standard	NM_194250		Approved		uc002uph.3	Q7Z570	OTTHUMG00000132625	ENST00000302277.6:c.585delA	chr2.hg19:g.185800708delA	ENSP00000303252:p.Ala195fs	115.0	0.0		134.0	10.0	NM_194250	A7E253|Q6ZN26	Frame_Shift_Del	DEL	ENST00000302277.6	hg19	CCDS2291.1																																																																																			.	.		0.388	ZNF804A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255871.1	NM_194250	
DES	1674	hgsc.bcm.edu	37	2	220286238	220286238	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:220286238delG	ENST00000373960.3	+	6	1286	c.1200delG	c.(1198-1200)gtgfs	p.V400fs		NM_001927.3	NP_001918.3	P17661	DESM_HUMAN	desmin	400	Coil 2B.|Rod.				cytoskeleton organization (GO:0007010)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|regulation of heart contraction (GO:0008016)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intermediate filament (GO:0005882)|neuromuscular junction (GO:0031594)|sarcolemma (GO:0042383)|Z disc (GO:0030018)	cytoskeletal protein binding (GO:0008092)|identical protein binding (GO:0042802)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(2)|lung(10)|skin(1)	18		Renal(207;0.0183)		Epithelial(149;5.25e-07)|all cancers(144;0.000103)|Lung(261;0.00533)|LUSC - Lung squamous cell carcinoma(224;0.008)		CCCTGGATGTGGAGATTGCCA	0.642																																					p.V400fs		Atlas-INDEL	.											.	DES	53	.	0			c.1199delT						.						55.0	52.0	53.0					2																	220286238		2203	4300	6503	SO:0001589	frameshift_variant	1674	exon6			.	AF521879	CCDS33383.1	2q35	2014-09-17			ENSG00000175084	ENSG00000175084		"""Intermediate filaments type III"""	2770	protein-coding gene	gene with protein product	"""intermediate filament protein"""	125660				2673923, 9736733	Standard	NM_001927		Approved	CMD1I, CSM1, CSM2	uc002vll.3	P17661	OTTHUMG00000058924	ENST00000373960.3:c.1200delG	chr2.hg19:g.220286238delG	ENSP00000363071:p.Val400fs	91.0	0.0		106.0	10.0	NM_001927	Q15787|Q549R7|Q549R8|Q549R9|Q8IZR1|Q8IZR6|Q8NES2|Q8NEU6|Q8TAC4|Q8TCX2|Q8TD99|Q9UHN5|Q9UJ80	Frame_Shift_Del	DEL	ENST00000373960.3	hg19	CCDS33383.1																																																																																			.	.		0.642	DES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130240.1	NM_001927	
PSRC1	84722	hgsc.bcm.edu	37	1	109823600	109823600	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:109823600delG	ENST00000438534.2	-	5	931	c.793delC	c.(793-795)cggfs	p.R265fs	PSRC1_ENST00000369903.2_Frame_Shift_Del_p.R235fs|PSRC1_ENST00000409267.1_Frame_Shift_Del_p.R235fs|PSRC1_ENST00000369904.3_Intron|PSRC1_ENST00000369907.3_Frame_Shift_Del_p.R235fs|PSRC1_ENST00000369909.2_Frame_Shift_Del_p.R235fs|PSRC1_ENST00000409138.2_Frame_Shift_Del_p.R265fs	NM_001005290.3	NP_001005290.1	Q6PGN9	PSRC1_HUMAN	proline/serine-rich coiled-coil 1	265	Pro/Ser-rich.				microtubule bundle formation (GO:0001578)|mitotic metaphase plate congression (GO:0007080)|negative regulation of cell growth (GO:0030308)|positive regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045737)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of mitotic spindle organization (GO:0060236)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle (GO:0005819)	microtubule binding (GO:0008017)			endometrium(1)|large_intestine(1)|lung(2)|prostate(2)|skin(1)	7		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244)		Colorectal(144;0.0286)|Lung(183;0.0658)|COAD - Colon adenocarcinoma(174;0.112)|Epithelial(280;0.188)|all cancers(265;0.213)		CCCTGCGGCCGGGGCAGGCGT	0.642																																					p.R235fs		Atlas-INDEL	.											.	PSRC1	12	.	0			c.704delG						.						39.0	43.0	42.0					1																	109823600		2203	4300	6503	SO:0001589	frameshift_variant	84722	exon6			.		CCDS797.1, CCDS30791.1	1p13.3	2008-02-05			ENSG00000134222	ENSG00000134222			24472	protein-coding gene	gene with protein product	"""differential display and activated by p53"""	613126				12427559, 10618717	Standard	NM_001032291		Approved	DDA3	uc001dxd.3	Q6PGN9	OTTHUMG00000012000	ENST00000438534.2:c.793delC	chr1.hg19:g.109823600delG	ENSP00000413591:p.Arg265fs	132.0	0.0		163.0	10.0	NM_001032291	Q5T2Z3|Q6ZTI8|Q71MG3|Q9BV77	Frame_Shift_Del	DEL	ENST00000438534.2	hg19																																																																																				.	.		0.642	PSRC1-202	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000335567.3	NM_032636	
CRTAM	56253	hgsc.bcm.edu	37	11	122722405	122722405	+	Frame_Shift_Del	DEL	A	A	-	rs367891560		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:122722405delA	ENST00000227348.4	+	3	245	c.198delA	c.(196-198)ttafs	p.L66fs		NM_019604.2	NP_062550.2			cytotoxic and regulatory T cell molecule											breast(1)|endometrium(2)|large_intestine(5)|lung(7)|ovary(2)|pancreas(1)|prostate(1)	19		Breast(109;0.00249)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.28e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0308)		GTACAGCTTTAAAAAATTCCA	0.463																																					p.L66X		Atlas-INDEL	.											.	CRTAM	50	.	0			c.197delT						.						125.0	124.0	125.0					11																	122722405		2202	4299	6501	SO:0001589	frameshift_variant	56253	exon3			.	AF001622	CCDS8437.1	11q24.1	2013-01-11			ENSG00000109943	ENSG00000109943		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"""	24313	protein-coding gene	gene with protein product	"""class I MHC restricted T cell associated molecule"""	612597				10811014, 16300832	Standard	NM_019604		Approved	CD355	uc001pyj.3	O95727	OTTHUMG00000166026	ENST00000227348.4:c.198delA	chr11.hg19:g.122722405delA	ENSP00000227348:p.Leu66fs	137.0	0.0		186.0	15.0	NM_019604		Frame_Shift_Del	DEL	ENST00000227348.4	hg19	CCDS8437.1																																																																																			.	.		0.463	CRTAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387507.1	NM_019604	
LRRC34	151827	hgsc.bcm.edu	37	3	169514647	169514647	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:169514647delT	ENST00000316515.7	-	7	935	c.659delA	c.(658-660)aatfs	p.N220fs	RP11-362K14.6_ENST00000602835.1_RNA|RP11-362K14.7_ENST00000602913.1_RNA|LRRC34_ENST00000522526.2_Frame_Shift_Del_p.N233fs|LRRC34_ENST00000524327.1_5'UTR|LRRC34_ENST00000522830.1_Frame_Shift_Del_p.N204fs|LRRC34_ENST00000446859.1_Frame_Shift_Del_p.N265fs	NM_153353.4	NP_699184.2	Q8IZ02	LRC34_HUMAN	leucine rich repeat containing 34	220										breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|upper_aerodigestive_tract(2)	10	all_cancers(22;4.12e-22)|all_epithelial(15;7.54e-27)|all_lung(20;1.63e-16)|Lung NSC(18;6.92e-16)|Ovarian(172;0.000223)|Breast(254;0.197)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.00676)			AAGACAGTGATTTTCTTTCAA	0.348																																					p.N265fs		Atlas-INDEL	.											.	LRRC34	30	.	0			c.795delT						.						137.0	122.0	127.0					3																	169514647		2203	4300	6503	SO:0001589	frameshift_variant	151827	exon8			.	AK095125	CCDS3208.1, CCDS3208.2, CCDS54672.1	3q26.2	2014-03-18			ENSG00000171757	ENSG00000171757			28408	protein-coding gene	gene with protein product						12477932	Standard	NM_153353		Approved	MGC27085	uc003ffy.3	Q8IZ02	OTTHUMG00000164419	ENST00000316515.7:c.659delA	chr3.hg19:g.169514647delT	ENSP00000326150:p.Asn220fs	152.0	0.0		212.0	13.0	NM_001172779	B4DEJ7|E9PBH2|G5E9T7	Frame_Shift_Del	DEL	ENST00000316515.7	hg19																																																																																				.	.		0.348	LRRC34-201	KNOWN	basic	protein_coding	protein_coding		NM_153353	
KIFC2	90990	hgsc.bcm.edu	37	8	145693776	145693776	+	Frame_Shift_Del	DEL	C	C	-	rs144988968		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr8:145693776delC	ENST00000301332.2	+	8	1252	c.875delC	c.(874-876)gccfs	p.A292fs	CYHR1_ENST00000306145.5_5'Flank|CYHR1_ENST00000403000.2_5'Flank|KIFC2_ENST00000301331.5_Frame_Shift_Del_p.A40fs|CYHR1_ENST00000424149.2_5'Flank	NM_145754.2	NP_665697.1	Q96AC6	KIFC2_HUMAN	kinesin family member C2	292	Gln-rich.				ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(7)|ovary(3)|prostate(3)|skin(2)|urinary_tract(1)	19	all_cancers(97;4.61e-11)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.08e-41)|Epithelial(56;8.67e-41)|all cancers(56;1.1e-35)|BRCA - Breast invasive adenocarcinoma(115;0.035)|Colorectal(110;0.055)			ACCACAGAAGCCCTCCGAGCC	0.672																																					p.A292fs		Atlas-INDEL	.											.	KIFC2	53	.	0			c.874delG						.						20.0	25.0	23.0					8																	145693776		2200	4299	6499	SO:0001589	frameshift_variant	90990	exon8			.	AY007121	CCDS6427.1	8q24.3	2007-02-13			ENSG00000167702	ENSG00000167702		"""Kinesins"""	29530	protein-coding gene	gene with protein product						9115737	Standard	NM_145754		Approved		uc003zcz.3	Q96AC6	OTTHUMG00000165133	ENST00000301332.2:c.875delC	chr8.hg19:g.145693776delC	ENSP00000301332:p.Ala292fs	99.0	0.0		163.0	10.0	NM_145754	E9PHB2|Q96NN6	Frame_Shift_Del	DEL	ENST00000301332.2	hg19	CCDS6427.1																																																																																			.	.		0.672	KIFC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382052.2	NM_145754	
NPY4R	5540	hgsc.bcm.edu	37	10	47087668	47087668	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr10:47087668delC	ENST00000395716.1	+	2	970	c.885delC	c.(883-885)atcfs	p.I295fs	NPY4R_ENST00000374312.1_Frame_Shift_Del_p.I295fs			P50391	NPY4R_HUMAN	neuropeptide Y receptor Y4	295					blood circulation (GO:0008015)|digestion (GO:0007586)|feeding behavior (GO:0007631)|G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|pancreatic polypeptide receptor activity (GO:0001602)|peptide binding (GO:0042277)|peptide YY receptor activity (GO:0001601)										ATGAGGCCATCCCCATCTGCC	0.552																																					p.I295fs		Atlas-INDEL	.											.	PPYR1	54	.	0			c.884delT						.						176.0	145.0	156.0					10																	47087668		2203	4300	6503	SO:0001589	frameshift_variant	5540	exon3			.		CCDS73100.1	10q11.2	2013-03-26	2013-03-26	2013-03-26	ENSG00000204174	ENSG00000204174		"""GPCR / Class A : Neuropeptide receptors : Y"""	9329	protein-coding gene	gene with protein product		601790	"""pancreatic polypeptide receptor 1"""	PPYR1		9417917	Standard	NM_005972		Approved	Y4, PP1	uc001jee.3	P50391	OTTHUMG00000018108	ENST00000395716.1:c.885delC	chr10.hg19:g.47087668delC	ENSP00000379066:p.Ile295fs	155.0	0.0		152.0	11.0	NM_005972	Q13456|Q5ISU3|Q5T2X9|Q6FH06	Frame_Shift_Del	DEL	ENST00000395716.1	hg19	CCDS31193.1																																																																																			.	.		0.552	NPY4R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047837.1		
FIP1L1	81608	hgsc.bcm.edu	37	4	54265950	54265950	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr4:54265950delA	ENST00000337488.6	+	10	953	c.759delA	c.(757-759)acafs	p.T253fs	FIP1L1_ENST00000507922.1_Frame_Shift_Del_p.T238fs|FIP1L1_ENST00000358575.5_Frame_Shift_Del_p.T238fs|FIP1L1_ENST00000306932.6_Frame_Shift_Del_p.T215fs|FIP1L1_ENST00000507166.1_Frame_Shift_Del_p.T253fs	NM_030917.3	NP_112179.2	Q6UN15	FIP1_HUMAN	factor interacting with PAPOLA and CPSF1	253	Necessary for stimulating PAPOLA activity.				mRNA processing (GO:0006397)	mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			large_intestine(3)|liver(1)|ovary(1)|skin(1)	6			GBM - Glioblastoma multiforme(3;3.31e-36)|LUSC - Lung squamous cell carcinoma(32;0.0134)			TTCCATCTACAAAAGCTGAGT	0.383			T	PDGFRA	idiopathic hypereosinophilic syndrome																																p.T253fs		Atlas-INDEL	.		Dom	yes		4	4q12	81608	FIP1 like 1 (S. cerevisiae)		L	.	FIP1L1	60	.	0			c.758delC						.						167.0	164.0	165.0					4																	54265950		2203	4300	6503	SO:0001589	frameshift_variant	81608	exon10			.	AF161429	CCDS3491.1, CCDS47055.1, CCDS47056.1	4q12	2013-06-18	2013-06-18		ENSG00000145216	ENSG00000145216			19124	protein-coding gene	gene with protein product		607686	"""FIP1 like 1 (S. cerevisiae)"", ""FIP1L1 cleavage and polyadenylation specific factor subunit"""			11230166, 14749727	Standard	NM_030917		Approved	DKFZp586K0717, FIP1	uc003hae.3	Q6UN15	OTTHUMG00000128701	ENST00000337488.6:c.759delA	chr4.hg19:g.54265950delA	ENSP00000336752:p.Thr253fs	116.0	0.0		138.0	11.0	NM_030917	B4DIR3|G3XAD6|Q0VGE0|Q499Y4|Q49AU3|Q7Z608|Q8WVN3|Q96F80|Q9H077	Frame_Shift_Del	DEL	ENST00000337488.6	hg19	CCDS3491.1																																																																																			.	.		0.383	FIP1L1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250602.1	NM_030917	
TLE2	7089	hgsc.bcm.edu	37	19	3013796	3013796	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr19:3013796delG	ENST00000262953.6	-	11	1006	c.744delC	c.(742-744)cccfs	p.P248fs	TLE2_ENST00000426948.2_Frame_Shift_Del_p.P262fs|TLE2_ENST00000447365.2_5'UTR|TLE2_ENST00000455444.2_Frame_Shift_Del_p.P126fs|TLE2_ENST00000586422.1_Intron|TLE2_ENST00000590536.1_Frame_Shift_Del_p.P249fs|TLE2_ENST00000587217.1_5'UTR|TLE2_ENST00000591529.1_Frame_Shift_Del_p.P262fs|TLE2_ENST00000443826.3_Frame_Shift_Del_p.P126fs	NM_003260.4	NP_003251.2	Q04725	TLE2_HUMAN	transducin-like enhancer of split 2	248	CCN domain.				negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	extracellular space (GO:0005615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(6)|prostate(1)	13				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)		TAGCCGGGCTGGGGGGCTCTG	0.607																																					p.S263fs		Atlas-INDEL	.											.	TLE2	35	.	0			c.787delA						.						48.0	53.0	51.0					19																	3013796		1896	4104	6000	SO:0001589	frameshift_variant	7089	exon12			.	M99436	CCDS45911.1, CCDS45912.1, CCDS45913.1, CCDS74255.1	19p13.3	2014-03-07	2014-03-07					"""WD repeat domain containing"""	11838	protein-coding gene	gene with protein product	"""enhancer of split groucho 2"""	601041	"""transducin-like enhancer of split 2, homolog of Drosophila E(sp1)"", ""transducin-like enhancer of split 2 (E(sp1) homolog, Drosophila)"""			8808280	Standard	NM_003260		Approved	ESG2, GRG2, ESG, FLJ41188	uc002lww.3	Q04725		ENST00000262953.6:c.744delC	chr19.hg19:g.3013796delG	ENSP00000262953:p.Pro248fs	133.0	0.0		160.0	10.0	NM_001144761	B4DE03|E9PEV7|F8WCH2|Q8WVY0|Q9Y6S0	Frame_Shift_Del	DEL	ENST00000262953.6	hg19	CCDS45911.1																																																																																			.	.		0.607	TLE2-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000452194.2	NM_003260	
PYGO2	90780	hgsc.bcm.edu	37	1	154931663	154931663	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:154931663delA	ENST00000368457.2	-	3	984	c.813delT	c.(811-813)tttfs	p.F271fs	RP11-307C12.12_ENST00000605085.1_RNA|PYGO2_ENST00000483463.1_5'Flank|PYGO2_ENST00000368456.1_Frame_Shift_Del_p.F234fs	NM_138300.3	NP_612157.1	Q9BRQ0	PYGO2_HUMAN	pygopus family PHD finger 2	271	Pro-rich.				brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|developmental growth (GO:0048589)|in utero embryonic development (GO:0001701)|kidney development (GO:0001822)|lens development in camera-type eye (GO:0002088)|mammary gland development (GO:0030879)|palate development (GO:0060021)|positive regulation of chromatin binding (GO:0035563)|post-embryonic development (GO:0009791)|regulation of histone H3-K4 methylation (GO:0051569)|regulation of mammary gland epithelial cell proliferation (GO:0033599)|spermatid nucleus differentiation (GO:0007289)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone acetyltransferase regulator activity (GO:0035034)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(2)|lung(3)|skin(2)|urinary_tract(1)	10	all_epithelial(22;4.9e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			GCTCCTGGGGAAAAGCAGTAG	0.632																																					p.P272fs	NSCLC(87;357 1460 1955 21029 23522)	Atlas-INDEL	.											.	PYGO2	32	.	0			c.814delC						.						10.0	10.0	10.0					1																	154931663		2200	4295	6495	SO:0001589	frameshift_variant	90780	exon3			.	BC006132	CCDS1075.1	1q22	2013-10-09	2013-10-09		ENSG00000163348	ENSG00000163348		"""Zinc fingers, PHD-type"""	30257	protein-coding gene	gene with protein product		606903	"""pygopus homolog 2 (Drosophila)"""			11988739	Standard	NM_138300		Approved		uc001fft.3	Q9BRQ0	OTTHUMG00000037370	ENST00000368457.2:c.813delT	chr1.hg19:g.154931663delA	ENSP00000357442:p.Phe271fs	95.0	0.0		205.0	14.0	NM_138300	Q8WYZ4|Q96CY2	Frame_Shift_Del	DEL	ENST00000368457.2	hg19	CCDS1075.1																																																																																			.	.		0.632	PYGO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090949.1	NM_138300	
PCBD2	84105	hgsc.bcm.edu	37	5	134296318	134296318	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr5:134296318delA	ENST00000512783.1	+	4	360	c.340delA	c.(340-342)aaafs	p.K115fs	PCBD2_ENST00000254908.6_Frame_Shift_Del_p.K115fs			Q9H0N5	PHS2_HUMAN	pterin-4 alpha-carbinolamine dehydratase/dimerization cofactor of hepatocyte nuclear factor 1 alpha (TCF1) 2	115					positive regulation of transcription, DNA-templated (GO:0045893)|protein heterooligomerization (GO:0051291)|protein homotetramerization (GO:0051289)|tetrahydrobiopterin biosynthetic process (GO:0006729)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	4-alpha-hydroxytetrahydrobiopterin dehydratase activity (GO:0008124)|phenylalanine 4-monooxygenase activity (GO:0004505)			kidney(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			TGAACTGACCAAAAAAGATGT	0.368																																					p.T113fs		Atlas-INDEL	.											.	PCBD2	3	.	0			c.339delC						.						86.0	77.0	80.0					5																	134296318		1830	4098	5928	SO:0001589	frameshift_variant	84105	exon4			.	AF499009	CCDS43364.1	5q31.1	2008-02-05	2006-01-10			ENSG00000132570			24474	protein-coding gene	gene with protein product		609836	"""6-pyruvoyl-tetrahydropterin synthase/dimerization cofactor of hepatocyte nuclear factor 1 alpha (TCF1) 2"""			15182178, 11980910	Standard	NM_032151		Approved	DCOHM, DCOH2	uc010jdz.3	Q9H0N5		ENST00000512783.1:c.340delA	chr5.hg19:g.134296318delA	ENSP00000421544:p.Lys115fs	166.0	0.0		198.0	15.0	NM_032151	Q8TD40	Frame_Shift_Del	DEL	ENST00000512783.1	hg19	CCDS43364.1																																																																																			.	.		0.368	PCBD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371578.1	NM_032151	
CLCA2	9635	hgsc.bcm.edu	37	1	86916286	86916286	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:86916286delT	ENST00000370565.4	+	12	2187	c.2025delT	c.(2023-2025)tatfs	p.Y675fs	CLCA2_ENST00000498802.1_3'UTR	NM_006536.5	NP_006527.1	Q9UQC9	CLCA2_HUMAN	chloride channel accessory 2	675					cell adhesion (GO:0007155)|transport (GO:0006810)	cell junction (GO:0030054)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	chloride channel activity (GO:0005254)|ligand-gated ion channel activity (GO:0015276)			NS(2)|breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(18)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	42		Lung NSC(277;0.238)		all cancers(265;0.0233)|Epithelial(280;0.0452)		ACTCGAGGTATTTTTTCTCCT	0.358																																					p.Y675fs	Melanoma(157;1000 1898 5363 5664 48018)|Ovarian(88;135 1366 2838 28875 34642)	Atlas-INDEL	.											.	CLCA2	102	.	0			c.2024delA						.						102.0	104.0	103.0					1																	86916286		2203	4300	6503	SO:0001589	frameshift_variant	9635	exon12			.		CCDS708.1	1p22.3	2012-02-26	2009-01-29		ENSG00000137975	ENSG00000137975			2016	protein-coding gene	gene with protein product		604003	"""chloride channel, calcium activated, family member 2"", ""chloride channel regulator 2"""				Standard	NM_006536		Approved	CLCRG2	uc001dlr.4	Q9UQC9	OTTHUMG00000010256	ENST00000370565.4:c.2025delT	chr1.hg19:g.86916286delT	ENSP00000359596:p.Tyr675fs	78.0	0.0		128.0	11.0	NM_006536	A8K2T3|Q9Y6N2	Frame_Shift_Del	DEL	ENST00000370565.4	hg19	CCDS708.1																																																																																			.	.		0.358	CLCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028284.1	NM_006536	
ZNF629	23361	hgsc.bcm.edu	37	16	30795213	30795213	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:30795213delC	ENST00000262525.4	-	3	643	c.436delG	c.(436-438)gcgfs	p.A146fs		NM_001080417.1	NP_001073886.1	Q9UEG4	ZN629_HUMAN	zinc finger protein 629	146					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(3)|urinary_tract(1)	22			Colorectal(24;0.198)			GGCTTCTCCGCCCCCGCCGGG	0.697																																					p.A146fs		Atlas-INDEL	.											.	ZNF629	44	.	0			c.437delC						.						17.0	19.0	18.0					16																	30795213		2187	4293	6480	SO:0001589	frameshift_variant	23361	exon3			.	AB002324	CCDS45463.1	16p11.2	2013-01-08				ENSG00000102870		"""Zinc fingers, C2H2-type"""	29008	protein-coding gene	gene with protein product			"""zinc finger protein 65"""	ZNF65		9205841	Standard	NM_001080417		Approved	KIAA0326	uc002dzs.1	Q9UEG4		ENST00000262525.4:c.436delG	chr16.hg19:g.30795213delC	ENSP00000262525:p.Ala146fs	28.0	0.0		139.0	10.0	NM_001080417	Q15938	Frame_Shift_Del	DEL	ENST00000262525.4	hg19	CCDS45463.1																																																																																			.	.		0.697	ZNF629-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434291.1	NM_015309	
TMEM63A	9725	hgsc.bcm.edu	37	1	226055702	226055702	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:226055702delC	ENST00000366835.3	-	7	670	c.400delG	c.(400-402)gagfs	p.E134fs	TMEM63A_ENST00000537914.1_5'Flank|TMEM63A_ENST00000474478.1_5'Flank	NM_014698.2	NP_055513.2	O94886	CSCL1_HUMAN	transmembrane protein 63A	134					ion transport (GO:0006811)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	nucleotide binding (GO:0000166)			breast(2)|endometrium(3)|large_intestine(5)|lung(6)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	24	Breast(184;0.197)					ATGGCGTCCTCCCCACACCAT	0.532																																					p.E134fs		Atlas-INDEL	.											.	TMEM63A	75	.	0			c.401delA						.						166.0	122.0	137.0					1																	226055702		2203	4300	6503	SO:0001589	frameshift_variant	9725	exon7			.		CCDS31042.1	1q42.12	2008-02-05	2005-07-25	2005-07-25	ENSG00000196187	ENSG00000196187			29118	protein-coding gene	gene with protein product			"""KIAA0792"""	KIAA0792		9872452, 9455484	Standard	NM_014698		Approved		uc001hpm.2	O94886	OTTHUMG00000037442	ENST00000366835.3:c.400delG	chr1.hg19:g.226055702delC	ENSP00000355800:p.Glu134fs	73.0	0.0		178.0	11.0	NM_014698	Q53GI7|Q5TE96|Q8N2U2	Frame_Shift_Del	DEL	ENST00000366835.3	hg19	CCDS31042.1																																																																																			.	.		0.532	TMEM63A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091154.2	NM_014698	
UNC13C	440279	hgsc.bcm.edu	37	15	54860046	54860046	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:54860046delA	ENST00000260323.11	+	29	6007	c.6007delA	c.(6007-6009)aaafs	p.K2003fs	UNC13C_ENST00000537900.1_Frame_Shift_Del_p.K2001fs|UNC13C_ENST00000545554.1_Frame_Shift_Del_p.K2003fs	NM_001080534.1	NP_001074003.1	Q8NB66	UN13C_HUMAN	unc-13 homolog C (C. elegans)	2003	MHD2. {ECO:0000255|PROSITE- ProRule:PRU00588}.				exocytosis (GO:0006887)|intracellular signal transduction (GO:0035556)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)			breast(3)|endometrium(5)|kidney(5)|large_intestine(20)|lung(70)|ovary(6)|pancreas(2)|prostate(2)|upper_aerodigestive_tract(4)|urinary_tract(4)	121				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)		TTTCTTGGAGAAAAGCCCAGA	0.378																																					p.E2002fs		Atlas-INDEL	.											.	UNC13C	674	.	0			c.6006delG						.						68.0	64.0	65.0					15																	54860046		1797	4068	5865	SO:0001589	frameshift_variant	440279	exon28			.	AK091491	CCDS45264.1	15q21.3	2012-10-02			ENSG00000137766	ENSG00000137766			23149	protein-coding gene	gene with protein product		614568					Standard	NM_001080534		Approved	Munc13-3, DKFZp547H074	uc021smr.1	Q8NB66	OTTHUMG00000172542	ENST00000260323.11:c.6007delA	chr15.hg19:g.54860046delA	ENSP00000260323:p.Lys2003fs	137.0	0.0		160.0	10.0	NM_001080534	Q0P613|Q8ND48|Q96NP3	Frame_Shift_Del	DEL	ENST00000260323.11	hg19	CCDS45264.1																																																																																			.	.		0.378	UNC13C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419028.3	NM_173166	
MERTK	10461	hgsc.bcm.edu	37	2	112754915	112754915	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:112754915delC	ENST00000295408.4	+	10	1723	c.1466delC	c.(1465-1467)gccfs	p.A489fs	MERTK_ENST00000409780.1_Frame_Shift_Del_p.A313fs|MERTK_ENST00000421804.2_Frame_Shift_Del_p.A489fs			Q12866	MERTK_HUMAN	MER proto-oncogene, tyrosine kinase	489					apoptotic cell clearance (GO:0043277)|blood coagulation (GO:0007596)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|leukocyte migration (GO:0050900)|natural killer cell differentiation (GO:0001779)|negative regulation of lymphocyte activation (GO:0051250)|peptidyl-tyrosine phosphorylation (GO:0018108)|phagocytosis (GO:0006909)|platelet activation (GO:0030168)|positive regulation of phagocytosis (GO:0050766)|protein kinase B signaling (GO:0043491)|protein phosphorylation (GO:0006468)|retina development in camera-type eye (GO:0060041)|secretion by cell (GO:0032940)|spermatogenesis (GO:0007283)|substrate adhesion-dependent cell spreading (GO:0034446)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|rhabdomere (GO:0016028)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|endometrium(3)|kidney(2)|large_intestine(6)|liver(1)|lung(18)|pancreas(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(10)	46						GTAGATTATGCCCCCTCTTCA	0.438																																					p.A489fs		Atlas-INDEL	.											.	MERTK	112	.	0			c.1465delG						.						201.0	200.0	200.0					2																	112754915		2203	4300	6503	SO:0001589	frameshift_variant	10461	exon10			.	U08023	CCDS2094.1	2q14.1	2014-06-26	2014-06-26		ENSG00000153208	ENSG00000153208		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	7027	protein-coding gene	gene with protein product		604705	"""c-mer proto-oncogene tyrosine kinase"""			8086340, 10343112	Standard	XM_005263565		Approved	mer, RP38	uc002thk.1	Q12866	OTTHUMG00000131278	ENST00000295408.4:c.1466delC	chr2.hg19:g.112754915delC	ENSP00000295408:p.Ala489fs	117.0	0.0		172.0	11.0	NM_006343	Q9HBB4	Frame_Shift_Del	DEL	ENST00000295408.4	hg19	CCDS2094.1																																																																																			.	.		0.438	MERTK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254046.2		
FUS	2521	hgsc.bcm.edu	37	16	31202283	31202283	+	Splice_Site	DEL	G	G	-	rs35711706		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:31202283delG	ENST00000254108.7	+	14	1498		c.e14-1		FUS_ENST00000380244.3_Splice_Site|FUS_ENST00000474990.1_Splice_Site|FUS_ENST00000568685.1_Splice_Site	NM_001170634.1|NM_001170937.1|NM_004960.3	NP_001164105.1|NP_001164408.1|NP_004951.1	P35637	FUS_HUMAN	FUS RNA binding protein						cell death (GO:0008219)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)		FUS/ERG(167)|FUS/DDIT3(631)|FUS/FEV(2)|FUS/ATF1(4)|FUS/CREB3L1(6)|FUS/CREB3L2(158)	breast(3)|endometrium(5)|kidney(3)|large_intestine(1)|lung(5)|prostate(3)|skin(1)|urinary_tract(1)	22		Renal(780;0.000219)|Breast(268;0.00957)|Hepatocellular(780;0.121)		GBM - Glioblastoma multiforme(240;2.31e-05)|Kidney(780;0.000209)		TTTTGTCCTAGGGGGTAACTA	0.587			T	"""DDIT3, ERG, FEV, ATF1, CREB3L2, CREB3L1"""	"""liposarcoma, AML, Ewing sarcoma, angiomatoid fibrous histiocytoma, fibromyxoid sarcoma"""																																.		Atlas-INDEL	.		Dom	yes		16	16p11.2	2521	"""fusion, derived from t(12;16) malignant liposarcoma"""		"""M, L"""	.	FUS	52	.	0			c.1382-2G>-						.						64.0	76.0	72.0					16																	31202283		2197	4300	6497	SO:0001630	splice_region_variant	2521	exon14			.	AF071213	CCDS10707.1, CCDS58454.1	16p11.2	2014-09-17	2014-05-09		ENSG00000089280	ENSG00000089280		"""RNA binding motif (RRM) containing"""	4010	protein-coding gene	gene with protein product	"""heterogeneous nuclear ribonucleoprotein P2"", ""translocated in liposarcoma"""	137070	"""fusion, derived from t(12;16) malignant liposarcoma"", ""amyotrophic lateral sclerosis 6"", ""fusion (involved in t(12;16) in malignant liposarcoma)"", ""fused in sarcoma"""	ALS6		2372777, 7503811, 19251628, 19251627	Standard	NM_004960		Approved	TLS, FUS1, hnRNP-P2, HNRNPP2	uc002ebe.2	P35637	OTTHUMG00000132395	ENST00000254108.7:c.1394-1G>-	chr16.hg19:g.31202283delG		110.0	0.0		134.0	10.0	NM_001170937	Q9H4A8	Splice_Site	DEL	ENST00000254108.7	hg19	CCDS10707.1																																																																																			.	.		0.587	FUS-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255526.2	NM_004960	Intron
RBM24	221662	hgsc.bcm.edu	37	6	17281858	17281858	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:17281858delG	ENST00000379052.5	+	1	282	c.46delG	c.(46-48)gggfs	p.G17fs	RBM24_ENST00000318204.5_5'Flank|RBM24_ENST00000425446.2_5'Flank	NM_001143942.1	NP_001137414.1	Q9BX46	RBM24_HUMAN	RNA binding motif protein 24	17	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				cell differentiation (GO:0030154)|regulation of mRNA stability (GO:0043488)|regulation of myotube differentiation (GO:0010830)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	mRNA 3'-UTR binding (GO:0003730)|nucleotide binding (GO:0000166)			endometrium(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(2)|skin(1)	13	Breast(50;0.0615)|Ovarian(93;0.0733)	all_hematologic(90;0.062)	all cancers(50;0.131)|Epithelial(50;0.15)			GATCTTCGTCGGGGGGCTGCC	0.692																																					p.V15fs		Atlas-INDEL	.											.	RBM24	40	.	0			c.45delC						.						26.0	35.0	32.0					6																	17281858		692	1591	2283	SO:0001589	frameshift_variant	221662	exon1			.	BC040928	CCDS4538.1, CCDS47378.1, CCDS47379.1	6p22.3	2013-02-12	2004-04-23	2004-04-23	ENSG00000112183	ENSG00000112183		"""RNA binding motif (RRM) containing"""	21539	protein-coding gene	gene with protein product			"""RNA-binding region (RNP1, RRM) containing 6"""	RNPC6			Standard	NM_153020		Approved	FLJ30829, dJ259A10.1	uc003nbz.4	Q9BX46	OTTHUMG00000014306	ENST00000379052.5:c.46delG	chr6.hg19:g.17281858delG	ENSP00000368341:p.Gly17fs	167.0	0.0		282.0	19.0	NM_001143942	E9PAY4|Q6QDA4|Q8N9D3|Q96NI3	Frame_Shift_Del	DEL	ENST00000379052.5	hg19	CCDS47378.1																																																																																			.	.		0.692	RBM24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039946.2	NM_153020	
DCTN2	10540	hgsc.bcm.edu	37	12	57926541	57926541	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:57926541delA	ENST00000548249.1	-	10	1094	c.827delT	c.(826-828)ttgfs	p.L276fs	DCTN2_ENST00000543672.1_Frame_Shift_Del_p.L281fs|DCTN2_ENST00000537439.1_Frame_Shift_Del_p.L253fs|DCTN2_ENST00000434715.3_Frame_Shift_Del_p.L281fs|DCTN2_ENST00000551400.1_5'Flank	NM_001261412.1|NM_001261413.1	NP_001248341.1|NP_001248342.1	Q13561	DCTN2_HUMAN	dynactin 2 (p50)	276					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell proliferation (GO:0008283)|G2/M transition of mitotic cell cycle (GO:0000086)|melanosome transport (GO:0032402)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle organization (GO:0007052)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dynactin complex (GO:0005869)|dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|vesicle (GO:0031982)	motor activity (GO:0003774)|spectrin binding (GO:0030507)			endometrium(1)|large_intestine(4)|lung(2)|ovary(2)|upper_aerodigestive_tract(2)	11						CACTTGATCCAAAACTGCAAG	0.478																																					p.L278fs		Atlas-INDEL	.											.	DCTN2	51	.	0			c.834delG						.						83.0	80.0	81.0					12																	57926541		1909	4131	6040	SO:0001589	frameshift_variant	10540	exon10			.	U50733	CCDS44930.1, CCDS58245.1, CCDS73489.1	12q13.3	2008-05-14				ENSG00000175203			2712	protein-coding gene	gene with protein product		607376				8647893	Standard	NM_001261412		Approved	RBP50, DCTN-50	uc001som.2	Q13561	OTTHUMG00000170124	ENST00000548249.1:c.827delT	chr12.hg19:g.57926541delA	ENSP00000447824:p.Leu276fs	141.0	0.0		155.0	16.0	NM_001261412	B2RBK5|Q86YN2|Q9BW17	Frame_Shift_Del	DEL	ENST00000548249.1	hg19	CCDS58245.1																																																																																			.	.		0.478	DCTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407393.2	NM_006400	
PRDM15	63977	hgsc.bcm.edu	37	21	43256618	43256618	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr21:43256618delA	ENST00000269844.3	-	16	2350	c.2240delT	c.(2239-2241)ttcfs	p.F747fs	PRDM15_ENST00000398548.1_Frame_Shift_Del_p.F418fs|PRDM15_ENST00000447207.2_Frame_Shift_Del_p.F381fs|PRDM15_ENST00000538201.1_Frame_Shift_Del_p.F381fs|PRDM15_ENST00000422911.1_Frame_Shift_Del_p.F418fs	NM_022115.3	NP_071398.3	P57071	PRD15_HUMAN	PR domain containing 15	747					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(11)|ovary(3)|skin(2)|stomach(2)|urinary_tract(1)	43						GCTGTTCTGGAAGATCTTGCT	0.627																																					p.F747fs		Atlas-INDEL	.											.	PRDM15	110	.	0			c.2241delC						.						172.0	158.0	163.0					21																	43256618		2203	4300	6503	SO:0001589	frameshift_variant	63977	exon16			.	AF276513	CCDS13676.1, CCDS42932.1, CCDS63370.1	21q22.3	2013-01-08	2002-07-31		ENSG00000141956	ENSG00000141956		"""Zinc fingers, C2H2-type"""	13999	protein-coding gene	gene with protein product			"""chromosome 21 open reading frame 83"""	ZNF298, C21orf83		12036297, 12036298	Standard	NM_022115		Approved		uc002yzq.1	P57071	OTTHUMG00000086781	ENST00000269844.3:c.2240delT	chr21.hg19:g.43256618delA	ENSP00000269844:p.Phe747fs	179.0	0.0		204.0	14.0	NM_022115	E9PDJ6|E9PF37|E9PGL3|Q4W8S0|Q4W8S3|Q4W8S4|Q4W8S5|Q8N0X3|Q8NEX0|Q9NQV3	Frame_Shift_Del	DEL	ENST00000269844.3	hg19	CCDS13676.1																																																																																			.	.		0.627	PRDM15-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_022115	
BCL9	607	hgsc.bcm.edu	37	1	147084890	147084890	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:147084890delG	ENST00000234739.3	+	5	1002	c.262delG	c.(262-264)gggfs	p.G88fs	BCL9_ENST00000473292.1_Intron	NM_004326.2	NP_004317.2	O00512	BCL9_HUMAN	B-cell CLL/lymphoma 9	88					canonical Wnt signaling pathway (GO:0060070)|myotube differentiation involved in skeletal muscle regeneration (GO:0014908)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell maintenance (GO:0035019)	cis-Golgi network (GO:0005801)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)				breast(1)|large_intestine(2)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	7	all_hematologic(923;0.115)					GCTGAAGAATGGGGCTGGAAA	0.582			T	"""IGH@, IGL@"""	B-ALL																																p.N87fs		Atlas-INDEL	.		Dom	yes		1	1q21	607	B-cell CLL/lymphoma 9		L	.	BCL9	150	.	0			c.261delT						.						39.0	43.0	42.0					1																	147084890		2203	4300	6503	SO:0001589	frameshift_variant	607	exon5			.	Y13620	CCDS30833.1	1q21	2008-02-05			ENSG00000116128	ENSG00000116128			1008	protein-coding gene	gene with protein product		602597				9490669	Standard	NM_004326		Approved		uc001epq.3	O00512	OTTHUMG00000014031	ENST00000234739.3:c.262delG	chr1.hg19:g.147084890delG	ENSP00000234739:p.Gly88fs	108.0	0.0		244.0	16.0	NM_004326	Q5T489	Frame_Shift_Del	DEL	ENST00000234739.3	hg19	CCDS30833.1																																																																																			.	.		0.582	BCL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039468.1	NM_004326	
MMP27	64066	hgsc.bcm.edu	37	11	102564704	102564704	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:102564704delT	ENST00000260229.4	-	8	1217	c.1126delA	c.(1126-1128)atafs	p.I376fs		NM_022122.2	NP_071405.2	Q9H306	MMP27_HUMAN	matrix metallopeptidase 27	376					collagen catabolic process (GO:0030574)	proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(12)|ovary(2)|prostate(2)|skin(11)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	45	all_cancers(8;0.000843)|all_epithelial(12;0.00362)|Lung NSC(15;0.21)	all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	Epithelial(9;0.0509)|Lung(13;0.0696)|LUSC - Lung squamous cell carcinoma(19;0.13)|all cancers(10;0.176)	BRCA - Breast invasive adenocarcinoma(274;0.0151)	Marimastat(DB00786)	GCTGCATCTATTTTCTTCACA	0.403																																					p.I376fs		Atlas-INDEL	.											.	MMP27	84	.	0			c.1127delT						.						151.0	143.0	145.0					11																	102564704		2203	4299	6502	SO:0001589	frameshift_variant	64066	exon8			.	AF195192	CCDS8319.1	11q24	2008-07-18	2005-08-08		ENSG00000137675	ENSG00000137675			14250	protein-coding gene	gene with protein product	"""matrix metalloprotease 27"""		"""matrix metalloproteinase 27"""			10419448	Standard	NM_022122		Approved		uc001phd.1	Q9H306	OTTHUMG00000168099	ENST00000260229.4:c.1126delA	chr11.hg19:g.102564704delT	ENSP00000260229:p.Ile376fs	152.0	0.0		164.0	10.0	NM_022122	Q6UWK6	Frame_Shift_Del	DEL	ENST00000260229.4	hg19	CCDS8319.1																																																																																			.	.		0.403	MMP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398128.1	NM_022122	
SCN9A	6335	hgsc.bcm.edu	37	2	167094772	167094772	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:167094772delA	ENST00000409435.1	-	19	3632	c.3633delT	c.(3631-3633)tttfs	p.F1211fs	AC010127.3_ENST00000447809.2_RNA|SCN9A_ENST00000303354.6_Frame_Shift_Del_p.F1212fs|SCN9A_ENST00000409672.1_Frame_Shift_Del_p.F1200fs|SCN9A_ENST00000375387.4_Frame_Shift_Del_p.F1212fs			Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha subunit	1211					behavioral response to pain (GO:0048266)|inflammatory response (GO:0006954)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|post-embryonic development (GO:0009791)|response to toxic substance (GO:0009636)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	sodium ion binding (GO:0031402)|voltage-gated sodium channel activity (GO:0005248)			NS(1)|breast(5)|central_nervous_system(6)|endometrium(6)|kidney(3)|large_intestine(27)|lung(38)|ovary(6)|prostate(8)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	108					Lacosamide(DB06218)|Lidocaine(DB00281)|Ranolazine(DB00243)|Rufinamide(DB06201)|Valproic Acid(DB00313)|Zonisamide(DB00909)	AAATATCTTCAAAAGCCTGTG	0.294																																					p.E1201fs		Atlas-INDEL	.											.	SCN9A	296	.	0			c.3601delG	GRCh37	CD072484	SCN9A	D		.						19.0	18.0	18.0					2																	167094772		1862	4135	5997	SO:0001589	frameshift_variant	6335	exon20			.	X82835	CCDS46441.1	2q24	2014-09-17	2007-01-23		ENSG00000169432	ENSG00000169432		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10597	protein-coding gene	gene with protein product		603415	"""sodium channel, voltage-gated, type IX, alpha polypeptide"""			7720699, 10198179, 16382098	Standard	NM_002977		Approved	Nav1.7, PN1, NE-NA, NENA, ETHA	uc010fpl.3	Q15858	OTTHUMG00000154044	ENST00000409435.1:c.3633delT	chr2.hg19:g.167094772delA	ENSP00000386330:p.Phe1211fs	213.0	0.0		234.0	17.0	NM_002977	A1BUH5|Q6B4R9|Q6B4S0|Q6B4S1|Q70HX1|Q70HX2|Q8WTU1|Q8WWN4	Frame_Shift_Del	DEL	ENST00000409435.1	hg19	CCDS46441.1																																																																																			.	.		0.294	SCN9A-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333639.1	NM_002977	
FREM2	341640	hgsc.bcm.edu	37	13	39265691	39265691	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr13:39265691delC	ENST00000280481.7	+	1	4426	c.4210delC	c.(4210-4212)cccfs	p.P1404fs		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	1404					cell communication (GO:0007154)|homophilic cell adhesion (GO:0007156)|inner ear development (GO:0048839)|morphogenesis of an epithelium (GO:0002009)	basement membrane (GO:0005604)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(35)|lung(39)|ovary(9)|pancreas(2)|prostate(12)|skin(11)|upper_aerodigestive_tract(7)|urinary_tract(2)	148		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		TGGAATAAATCCCCTCATAGA	0.418																																					p.N1403fs		Atlas-INDEL	.											.	FREM2	385	.	0			c.4209delT						.						151.0	134.0	140.0					13																	39265691		2203	4300	6503	SO:0001589	frameshift_variant	341640	exon1			.	BX538150	CCDS31960.1	13q13.3	2004-12-15			ENSG00000150893	ENSG00000150893			25396	protein-coding gene	gene with protein product		608945				15345741	Standard	NM_207361		Approved	DKFZp686J0811	uc001uwv.3	Q5SZK8	OTTHUMG00000016759	ENST00000280481.7:c.4210delC	chr13.hg19:g.39265691delC	ENSP00000280481:p.Pro1404fs	89.0	0.0		157.0	10.0	NM_207361	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Frame_Shift_Del	DEL	ENST00000280481.7	hg19	CCDS31960.1																																																																																			.	.		0.418	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361	
CACNA2D1	781	hgsc.bcm.edu	37	7	81624216	81624216	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:81624216delT	ENST00000356253.5	-	21	2014	c.1759delA	c.(1759-1761)acafs	p.T587fs	CACNA2D1_ENST00000356860.3_Frame_Shift_Del_p.T568fs			P54289	CA2D1_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 1	587					calcium ion transport (GO:0006816)|regulation of calcium ion transport (GO:0051924)	extracellular vesicular exosome (GO:0070062)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(15)|liver(1)|lung(42)|ovary(6)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	81					Amlodipine(DB00381)|Cyclandelate(DB04838)|Felodipine(DB01023)|Gabapentin(DB00996)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)	GTTCTGAATGTTTTTTCTCCA	0.299																																					p.T568fs		Atlas-INDEL	.											.	CACNA2D1	191	.	0			c.1703delC						.						79.0	77.0	78.0					7																	81624216		2200	4292	6492	SO:0001589	frameshift_variant	781	exon20			.	M76559	CCDS5598.1	7q21-q22	2014-09-17			ENSG00000153956	ENSG00000153956		"""Calcium channel subunits"""	1399	protein-coding gene	gene with protein product		114204	"""long intergenic non-protein coding RNA 1112"""	CACNL2A, CACNA2, MHS3, LINC01112		8188232	Standard	XM_005250570		Approved	lncRNA-N3	uc003uhr.1	P54289	OTTHUMG00000023622	ENST00000356253.5:c.1759delA	chr7.hg19:g.81624216delT	ENSP00000348589:p.Thr587fs	216.0	0.0		240.0	16.0	NM_000722	Q17R45|Q9UD80|Q9UD81|Q9UD82	Frame_Shift_Del	DEL	ENST00000356253.5	hg19																																																																																				.	.		0.299	CACNA2D1-201	KNOWN	basic	protein_coding	protein_coding			
SECISBP2	79048	hgsc.bcm.edu	37	9	91943618	91943618	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:91943618delA	ENST00000375807.3	+	5	689	c.618delA	c.(616-618)gcafs	p.A206fs	SECISBP2_ENST00000470305.1_3'UTR|SECISBP2_ENST00000339901.4_Frame_Shift_Del_p.A133fs|SECISBP2_ENST00000534113.2_Frame_Shift_Del_p.A138fs	NM_001282688.1|NM_001282690.1|NM_024077.3	NP_001269617.1|NP_001269619.1|NP_076982.3	Q96T21	SEBP2_HUMAN	SECIS binding protein 2	206					translation (GO:0006412)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	mRNA 3'-UTR binding (GO:0003730)|poly(A) RNA binding (GO:0044822)|ribonucleoprotein complex binding (GO:0043021)|selenocysteine insertion sequence binding (GO:0035368)	p.N208fs*8(1)		breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(11)|ovary(3)|skin(2)	32						GAATCATTGCAAAAAATGTAT	0.358																																					p.A206fs		Atlas-INDEL	.											.,1	SECISBP2	64	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.617delC						.						82.0	75.0	78.0					9																	91943618		2203	4300	6503	SO:0001589	frameshift_variant	79048	exon5			.	AF380995	CCDS6683.1, CCDS65076.1, CCDS65077.1	9q22	2008-02-05			ENSG00000187742	ENSG00000187742			30972	protein-coding gene	gene with protein product		607693				11230166	Standard	XM_005252193		Approved		uc004aqj.1	Q96T21	OTTHUMG00000020182	ENST00000375807.3:c.618delA	chr9.hg19:g.91943618delA	ENSP00000364965:p.Ala206fs	165.0	0.0		186.0	12.0	NM_024077	F8W892|Q5HYY1|Q8IYC0|Q9H0A1	Frame_Shift_Del	DEL	ENST00000375807.3	hg19	CCDS6683.1																																																																																			.	.		0.358	SECISBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052990.3	NM_024077	
WDR45B	56270	hgsc.bcm.edu	37	17	80575188	80575188	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr17:80575188delT	ENST00000392325.4	-	8	984	c.790delA	c.(790-792)aggfs	p.R264fs	WDR45B_ENST00000571835.1_5'UTR	NM_019613.3	NP_062559.2	Q5MNZ6	WIPI3_HUMAN	WD repeat domain 45B	264																	TGTTTATTCCTTTTTGGATCT	0.532																																					p.R264fs		Atlas-INDEL	.											.	.	.	.	0			c.791delG						.						134.0	107.0	116.0					17																	80575188		2203	4300	6503	SO:0001589	frameshift_variant	56270	exon8			.	AF091083	CCDS11815.2	17q25.3	2013-01-11	2013-01-11	2013-01-11	ENSG00000141580	ENSG00000141580		"""WD repeat domain containing"""	25072	protein-coding gene	gene with protein product		609226	"""WDR45-like"""	WDR45L		12477932	Standard	NM_019613		Approved	WIPI3	uc002kfq.3	Q5MNZ6	OTTHUMG00000150146	ENST00000392325.4:c.790delA	chr17.hg19:g.80575188delT	ENSP00000376139:p.Arg264fs	150.0	0.0		148.0	11.0	NM_019613	O95328|Q2MCP6|Q6IBN2	Frame_Shift_Del	DEL	ENST00000392325.4	hg19	CCDS11815.2																																																																																			.	.		0.532	WDR45B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316536.1	NM_019613	
ZSWIM2	151112	hgsc.bcm.edu	37	2	187713741	187713741	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:187713741delG	ENST00000295131.2	-	1	156	c.117delC	c.(115-117)cccfs	p.P39fs		NM_182521.2	NP_872327.2	Q8NEG5	ZSWM2_HUMAN	zinc finger, SWIM-type containing 2	39					apoptotic process (GO:0006915)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|protein polyubiquitination (GO:0000209)		ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(28)|ovary(2)|prostate(4)|skin(6)|urinary_tract(1)	52			OV - Ovarian serous cystadenocarcinoma(117;0.0274)|Epithelial(96;0.164)			GGAAGCCAGTGGGGCCCATCT	0.602																																					p.T40fs		Atlas-INDEL	.											.	ZSWIM2	119	.	0			c.118delA						.						60.0	57.0	58.0					2																	187713741		2203	4300	6503	SO:0001589	frameshift_variant	151112	exon1			.	AK128006	CCDS33348.1	2q32.2	2008-02-05			ENSG00000163012	ENSG00000163012		"""Zinc fingers, SWIM-type"", ""Zinc fingers, ZZ-type"""	30990	protein-coding gene	gene with protein product						12477932	Standard	NM_182521		Approved	MGC33890, ZZZ2	uc002upu.1	Q8NEG5	OTTHUMG00000154259	ENST00000295131.2:c.117delC	chr2.hg19:g.187713741delG	ENSP00000295131:p.Pro39fs	193.0	0.0		244.0	16.0	NM_182521	B3KXV6|Q53SI3|Q57ZY3	Frame_Shift_Del	DEL	ENST00000295131.2	hg19	CCDS33348.1																																																																																			.	.		0.602	ZSWIM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334565.1	NM_182521	
COX5B	1329	hgsc.bcm.edu	37	2	98264520	98264520	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:98264520delC	ENST00000258424.2	+	4	386	c.339delC	c.(337-339)tgcfs	p.C113fs	COX5B_ENST00000464949.1_3'UTR	NM_001862.2	NP_001853.2	P10606	COX5B_HUMAN	cytochrome c oxidase subunit Vb	113					cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|respiratory electron transport chain (GO:0022904)|respiratory gaseous exchange (GO:0007585)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	cytochrome-c oxidase activity (GO:0004129)|metal ion binding (GO:0046872)			endometrium(1)|lung(1)|urinary_tract(1)	3						CCCAGCGATGCCCCCGCTGTG	0.507																																					p.C113fs		Atlas-INDEL	.											.	COX5B	9	.	0			c.338delG						.						49.0	48.0	49.0					2																	98264520		2203	4300	6503	SO:0001589	frameshift_variant	1329	exon4			.	BC006229	CCDS2032.1	2q11.2	2011-07-04			ENSG00000135940	ENSG00000135940	1.9.3.1	"""Mitochondrial respiratory chain complex / Complex IV"""	2269	protein-coding gene	gene with protein product		123866					Standard	NM_001862		Approved		uc002sya.3	P10606	OTTHUMG00000130548	ENST00000258424.2:c.339delC	chr2.hg19:g.98264520delC	ENSP00000258424:p.Cys113fs	183.0	0.0		215.0	13.0	NM_001862	Q53YB7|Q96J18|Q99610	Frame_Shift_Del	DEL	ENST00000258424.2	hg19	CCDS2032.1																																																																																			.	.		0.507	COX5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252972.2	NM_001862	
NRBP2	340371	hgsc.bcm.edu	37	8	144919257	144919257	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr8:144919257delT	ENST00000442628.2	-	14	1356	c.1217delA	c.(1216-1218)aagfs	p.K406fs	NRBP2_ENST00000327830.5_Frame_Shift_Del_p.K163fs	NM_178564.3	NP_848659.2			nuclear receptor binding protein 2											central_nervous_system(2)|kidney(1)|large_intestine(2)	5	all_cancers(97;2.31e-11)|all_epithelial(106;1.58e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;1.23e-39)|all cancers(56;6.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.18)			GGTCTTGGCCTTTTGGACCTC	0.612																																					p.K406fs		Atlas-INDEL	.											.	NRBP2	20	.	0			c.1218delG						.						46.0	52.0	50.0					8																	144919257		2203	4300	6503	SO:0001589	frameshift_variant	340371	exon14			.	BC037396	CCDS34959.1, CCDS34959.2	8q24.3	2005-01-24							19339	protein-coding gene	gene with protein product		615563				14702039	Standard	NM_178564		Approved	DKFZp434P086	uc011lkt.2	Q9NSY0		ENST00000442628.2:c.1217delA	chr8.hg19:g.144919257delT	ENSP00000414055:p.Lys406fs	146.0	0.0		231.0	14.0	NM_178564		Frame_Shift_Del	DEL	ENST00000442628.2	hg19	CCDS34959.2																																																																																			.	.		0.612	NRBP2-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382247.1	NM_178564	
CUL9	23113	hgsc.bcm.edu	37	6	43172517	43172517	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr6:43172517delC	ENST00000252050.4	+	22	4455	c.4371delC	c.(4369-4371)agcfs	p.S1457fs	CUL9_ENST00000354495.3_Frame_Shift_Del_p.S1347fs|CUL9_ENST00000372647.2_Frame_Shift_Del_p.S1457fs	NM_015089.2	NP_055904.1	Q8IWT3	CUL9_HUMAN	cullin 9	1457					microtubule cytoskeleton organization (GO:0000226)|protein ubiquitination (GO:0016567)|regulation of mitosis (GO:0007088)|ubiquitin-dependent protein catabolic process (GO:0006511)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|liver(1)|lung(30)|ovary(5)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(4)	92						GGGACCGGAGCCCGGCGCCTT	0.597																																					p.S1457fs		Atlas-INDEL	.											.	CUL9	248	.	0			c.4370delG						.						78.0	85.0	83.0					6																	43172517		2203	4300	6503	SO:0001589	frameshift_variant	23113	exon22			.	AB014608	CCDS4890.1	6p21.1	2011-05-24			ENSG00000112659	ENSG00000112659			15982	protein-coding gene	gene with protein product	"""parkin-like cytoplasmic p53 binding protein"", ""p53-associated parkin-like cytoplasmic protein"""	607489				17332328, 10521492, 12526791	Standard	NM_015089		Approved	H7AP1, KIAA0708, PARC	uc003ouk.3	Q8IWT3	OTTHUMG00000014723	ENST00000252050.4:c.4371delC	chr6.hg19:g.43172517delC	ENSP00000252050:p.Ser1457fs	99.0	0.0		172.0	11.0	NM_015089	O75188|Q5TCY3|Q68CP2|Q68D92|Q8N3W9|Q9BU56	Frame_Shift_Del	DEL	ENST00000252050.4	hg19	CCDS4890.1																																																																																			.	.		0.597	CUL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040582.2	NM_015089	
IFNAR1	3454	hgsc.bcm.edu	37	21	34707933	34707933	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr21:34707933delT	ENST00000270139.3	+	2	332	c.180delT	c.(178-180)actfs	p.T60fs	IFNAR1_ENST00000416947.2_5'UTR|IFNAR1_ENST00000442357.2_Frame_Shift_Del_p.T60fs	NM_000629.2	NP_000620.2	P17181	INAR1_HUMAN	interferon (alpha, beta and omega) receptor 1	60	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|JAK-STAT cascade (GO:0007259)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-1 beta secretion (GO:0050718)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to virus (GO:0009615)|T cell activation (GO:0042110)|type I interferon biosynthetic process (GO:0045351)|type I interferon signaling pathway (GO:0060337)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	type I interferon receptor activity (GO:0004905)			breast(2)|central_nervous_system(1)|cervix(1)|kidney(2)|large_intestine(3)|liver(1)|lung(2)|skin(2)	14					"""""""Interferon Alfa-2a(DB00034)|""""Interferon Alfa-2b(DB00105)|Interferon alfa-n1(DB00011)|Interferon alfa-n3(DB00018)|Interferon alfacon-1(DB00069)|Interferon beta-1a(DB00060)|Interferon beta-1b(DB00068)|Natural alpha interferon(DB05258)|Peginterferon alfa-2a(DB00008)|Peginterferon alfa-2b(DB00022)"""	GGAATGTGACTTTTTCATTCG	0.338																																					p.T60fs	Esophageal Squamous(73;817 1211 32990 35667 42746)	Atlas-INDEL	.											.	IFNAR1	44	.	0			c.179delC						.						132.0	119.0	124.0					21																	34707933		2203	4300	6503	SO:0001589	frameshift_variant	3454	exon2			.		CCDS13624.1	21q22.1	2008-05-02			ENSG00000142166	ENSG00000142166		"""Interferons"""	5432	protein-coding gene	gene with protein product		107450		IFNAR		8181059	Standard	NM_000629		Approved	IFRC	uc002yrn.3	P17181	OTTHUMG00000065126	ENST00000270139.3:c.180delT	chr21.hg19:g.34707933delT	ENSP00000270139:p.Thr60fs	99.0	0.0		116.0	11.0	NM_000629	B2R6L9|B4DNT3|D3DSF0|Q53GW9|Q53H11|Q6PKD7|Q7M4L2|Q8WTZ2	Frame_Shift_Del	DEL	ENST00000270139.3	hg19	CCDS13624.1																																																																																			.	.		0.338	IFNAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139823.4		
FN1	2335	hgsc.bcm.edu	37	2	216230250	216230250	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr2:216230250delT	ENST00000359671.1	-	42	7114	c.6849delA	c.(6847-6849)aaafs	p.K2283fs	FN1_ENST00000346544.3_Frame_Shift_Del_p.K2108fs|FN1_ENST00000443816.1_Frame_Shift_Del_p.K2162fs|FN1_ENST00000421182.1_Frame_Shift_Del_p.K2137fs|FN1_ENST00000446046.1_Frame_Shift_Del_p.K2227fs|FN1_ENST00000323926.6_Frame_Shift_Del_p.K2343fs|FN1_ENST00000345488.5_Frame_Shift_Del_p.K2081fs|FN1_ENST00000357867.4_Frame_Shift_Del_p.K2073fs|FN1_ENST00000357009.2_3'UTR|FN1_ENST00000356005.4_Frame_Shift_Del_p.K2193fs|FN1_ENST00000354785.4_Frame_Shift_Del_p.K2374fs|FN1_ENST00000432072.2_Frame_Shift_Del_p.K2164fs|FN1_ENST00000336916.4_Frame_Shift_Del_p.K2252fs			P02751	FINC_HUMAN	fibronectin 1	2283	Fibrin-binding 2.|Fibronectin type-I 11. {ECO:0000255|PROSITE-ProRule:PRU00478}.				acute-phase response (GO:0006953)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|calcium-independent cell-matrix adhesion (GO:0007161)|cell adhesion (GO:0007155)|cell-substrate junction assembly (GO:0007044)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|integrin activation (GO:0033622)|leukocyte migration (GO:0050900)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of axon extension (GO:0045773)|regulation of cell shape (GO:0008360)|response to wounding (GO:0009611)|substrate adhesion-dependent cell spreading (GO:0034446)	apical plasma membrane (GO:0016324)|basal lamina (GO:0005605)|blood microparticle (GO:0072562)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule lumen (GO:0031093)	collagen binding (GO:0005518)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|peptidase activator activity (GO:0016504)|protease binding (GO:0002020)		FN1/ALK(2)	NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(7)|endometrium(9)|kidney(8)|large_intestine(33)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	109		Renal(323;0.127)		Epithelial(149;9.59e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Ocriplasmin(DB08888)	TGAATTCTCCTTTTCCGTTCC	0.443																																					p.G2375fs		Atlas-INDEL	.											.	FN1	521	.	0			c.7123delG						.						324.0	278.0	293.0					2																	216230250		2203	4300	6503	SO:0001589	frameshift_variant	2335	exon43			.		CCDS2399.1, CCDS2400.1, CCDS42813.1, CCDS42814.1, CCDS46510.1, CCDS46512.1	2q34	2014-01-30			ENSG00000115414	ENSG00000115414		"""Fibronectin type III domain containing"", ""Endogenous ligands"""	3778	protein-coding gene	gene with protein product	"""migration-stimulating factor"", ""cold-insoluble globulin"""	135600				2992939, 3003095	Standard	NM_054034		Approved	MSF, CIG, LETS, GFND2, FINC	uc002vfa.3	P02751	OTTHUMG00000133054	ENST00000359671.1:c.6849delA	chr2.hg19:g.216230250delT	ENSP00000352696:p.Lys2283fs	163.0	0.0		151.0	11.0	NM_212482	B7ZLF0|E9PE77|E9PG29|O95609|O95610|Q14312|Q14325|Q14326|Q17RV7|Q564H7|Q585T2|Q59EH1|Q60FE4|Q68DP8|Q68DP9|Q68DT4|Q6LDP6|Q6MZS0|Q6MZU5|Q6N025|Q6N0A6|Q7Z391|Q86T27|Q8IVI8|Q96KP7|Q96KP8|Q96KP9|Q9H1B8|Q9HAP3|Q9UMK2	Frame_Shift_Del	DEL	ENST00000359671.1	hg19																																																																																				.	.		0.443	FN1-204	KNOWN	basic	protein_coding	protein_coding		NM_212476	
NDUFAF6	137682	hgsc.bcm.edu	37	8	96060727	96060727	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr8:96060727delA	ENST00000396124.4	+	7	780	c.757delA	c.(757-759)aaafs	p.K253fs	NDUFAF6_ENST00000396111.2_Frame_Shift_Del_p.K161fs|NDUFAF6_ENST00000286687.4_Frame_Shift_Del_p.K101fs|NDUFAF6_ENST00000396113.1_Frame_Shift_Del_p.K161fs|NDUFAF6_ENST00000542894.1_Frame_Shift_Del_p.K201fs	NM_152416.3	NP_689629.2	Q330K2	NDUF6_HUMAN	NADH dehydrogenase (ubiquinone) complex I, assembly factor 6	253					biosynthetic process (GO:0009058)|mitochondrial respiratory chain complex I assembly (GO:0032981)	cytoplasm (GO:0005737)|mitochondrial inner membrane (GO:0005743)|nucleus (GO:0005634)	transferase activity (GO:0016740)										GAACCAAGATAAAAATGTGAG	0.383																																					p.D252fs		Atlas-INDEL	.											.	.	.	.	0			c.756delT						.						120.0	110.0	113.0					8																	96060727		1850	4111	5961	SO:0001589	frameshift_variant	137682	exon7			.	BC028166	CCDS6266.2	8q22.1	2013-10-21	2012-05-08	2012-05-08	ENSG00000156170	ENSG00000156170		"""Mitochondrial respiratory chain complex assembly factors"""	28625	protein-coding gene	gene with protein product		612392	"""chromosome 8 open reading frame 38"""	C8orf38		22019594, 23509070	Standard	NM_152416		Approved	MGC40214	uc003yhj.3	Q330K2	OTTHUMG00000150173	ENST00000396124.4:c.757delA	chr8.hg19:g.96060727delA	ENSP00000379430:p.Lys253fs	69.0	0.0		178.0	11.0	NM_152416	A8MT28|A8MWF0|B4DQ45|Q8N6U6	Frame_Shift_Del	DEL	ENST00000396124.4	hg19	CCDS6266.2																																																																																			.	.		0.383	NDUFAF6-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316700.2	NM_152416	
COG2	22796	hgsc.bcm.edu	37	1	230800279	230800279	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:230800279delA	ENST00000366669.4	+	5	546	c.431delA	c.(430-432)gaafs	p.E144fs	COG2_ENST00000535166.1_Frame_Shift_Del_p.E28fs|COG2_ENST00000534989.1_Frame_Shift_Del_p.E85fs|COG2_ENST00000366668.3_Frame_Shift_Del_p.E144fs	NM_001145036.1|NM_007357.2	NP_001138508.1|NP_031383.1	Q14746	COG2_HUMAN	component of oligomeric golgi complex 2	144					Golgi organization (GO:0007030)|intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|oligosaccharide biosynthetic process (GO:0009312)|protein glycosylation (GO:0006486)	cytosol (GO:0005829)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|Golgi transport complex (GO:0017119)	protein transporter activity (GO:0008565)			NS(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(11)|prostate(2)|skin(2)|urinary_tract(3)	27	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.178)				GAGAAAATTGAAAAAATCTTA	0.269																																					p.E144fs		Atlas-INDEL	.											.	COG2	61	.	0			c.430delG						.						28.0	30.0	29.0					1																	230800279		2196	4274	6470	SO:0001589	frameshift_variant	22796	exon5			.	Z34975	CCDS1584.1, CCDS44329.1	1q42.2	2008-02-05	2002-05-28	2002-05-31	ENSG00000135775	ENSG00000135775		"""Components of oligomeric golgi complex"""	6546	protein-coding gene	gene with protein product		606974	"""low density lipoprotein receptor defect C complementing"""	LDLC		7962052	Standard	NM_007357		Approved		uc001htw.3	Q14746	OTTHUMG00000037753	ENST00000366669.4:c.431delA	chr1.hg19:g.230800279delA	ENSP00000355629:p.Glu144fs	86.0	0.0		178.0	11.0	NM_007357	Q86U99	Frame_Shift_Del	DEL	ENST00000366669.4	hg19	CCDS1584.1																																																																																			.	.		0.269	COG2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000092087.1	NM_007357	
SIN3A	25942	hgsc.bcm.edu	37	15	75693144	75693144	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:75693144delC	ENST00000394947.3	-	11	1978	c.1664delG	c.(1663-1665)ggcfs	p.G555fs	SIN3A_ENST00000394949.4_Frame_Shift_Del_p.G555fs|SIN3A_ENST00000360439.4_Frame_Shift_Del_p.G555fs	NM_001145358.1	NP_001138830.1			SIN3 transcription regulator family member A									p.G555V(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(15)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	63						ATAGCTGGAGCCCAATCGTTT	0.488																																					p.G555fs		Atlas-INDEL	.											.	SIN3A	152	.	1	Substitution - Missense(1)	endometrium(1)	c.1665delC						.						115.0	99.0	105.0					15																	75693144		2197	4294	6491	SO:0001589	frameshift_variant	25942	exon11			.	AK027559	CCDS10279.1	15q22.33	2013-08-21	2013-08-21		ENSG00000169375	ENSG00000169375			19353	protein-coding gene	gene with protein product		607776	"""SIN3 homolog A, transcription regulator (yeast)"", ""SIN3 transcription regulator homolog A (yeast)"""			10773092, 7601471	Standard	NM_001145357		Approved	KIAA0700, DKFZP434K2235	uc002bai.3	Q96ST3	OTTHUMG00000142834	ENST00000394947.3:c.1664delG	chr15.hg19:g.75693144delC	ENSP00000378402:p.Gly555fs	116.0	0.0		142.0	10.0	NM_001145358		Frame_Shift_Del	DEL	ENST00000394947.3	hg19	CCDS10279.1																																																																																			.	.		0.488	SIN3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286469.1	NM_015477	
ATP2C2	9914	hgsc.bcm.edu	37	16	84456800	84456800	+	Frame_Shift_Del	DEL	A	A	-	rs200531713	byFrequency	TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr16:84456800delA	ENST00000262429.4	+	10	939	c.850delA	c.(850-852)aaafs	p.K284fs	ATP2C2_ENST00000420010.2_3'UTR|ATP2C2_ENST00000416219.2_Frame_Shift_Del_p.K284fs	NM_014861.2	NP_055676.2	O75185	AT2C2_HUMAN	ATPase, Ca++ transporting, type 2C, member 2	284					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|prostate(3)|skin(5)|urinary_tract(1)	33						TCAGACACCTAAAACTCCTTT	0.458																																					p.P283fs		Atlas-INDEL	.											.	ATP2C2	75	.	0			c.849delT						.						112.0	106.0	108.0					16																	84456800		1975	4162	6137	SO:0001589	frameshift_variant	9914	exon10			.	AK091051	CCDS42207.1, CCDS67088.1	16q24.1	2010-04-20			ENSG00000064270	ENSG00000064270	3.6.3.8	"""ATPases / P-type"""	29103	protein-coding gene	gene with protein product	"""secretory pathway calcium ATPase 2"""	613082				9734811	Standard	XM_006721355		Approved	KIAA0703, SPCA2	uc002fhx.3	O75185		ENST00000262429.4:c.850delA	chr16.hg19:g.84456800delA	ENSP00000262429:p.Lys284fs	172.0	0.0		162.0	10.0	NM_014861	B4DU76|E7ES94|Q5HYC3|Q5S053|Q68CQ2	Frame_Shift_Del	DEL	ENST00000262429.4	hg19	CCDS42207.1																																																																																			.	.		0.458	ATP2C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433404.1	NM_014861	
NFE2	4778	hgsc.bcm.edu	37	12	54686722	54686722	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr12:54686722delG	ENST00000540264.2	-	2	1067	c.558delC	c.(556-558)cccfs	p.P186fs	NFE2_ENST00000312156.4_Frame_Shift_Del_p.P186fs|RP11-968A15.8_ENST00000553061.1_RNA|NFE2_ENST00000553070.1_Frame_Shift_Del_p.P186fs|NFE2_ENST00000435572.2_Frame_Shift_Del_p.P186fs			Q16621	NFE2_HUMAN	nuclear factor, erythroid 2	186	Transactivation domain.				blood circulation (GO:0008015)|blood coagulation (GO:0007596)|cell-cell signaling (GO:0007267)|hemostasis (GO:0007599)|labyrinthine layer blood vessel development (GO:0060716)|multicellular organismal development (GO:0007275)|negative regulation of bone mineralization (GO:0030502)|negative regulation of syncytium formation by plasma membrane fusion (GO:0034242)|nucleosome disassembly (GO:0006337)|positive regulation of peptidyl-lysine acetylation (GO:2000758)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein N-terminus binding (GO:0047485)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|WW domain binding (GO:0050699)			breast(1)|central_nervous_system(1)|large_intestine(5)|lung(7)|upper_aerodigestive_tract(2)	16						CCAAGGAGTTGGGCATGAGTG	0.607																																					p.N187fs		Atlas-INDEL	.											.	NFE2	28	.	0			c.559delA						.						89.0	84.0	86.0					12																	54686722		2203	4300	6503	SO:0001589	frameshift_variant	4778	exon4			.	BC005044	CCDS8876.1	12q13	2013-08-23	2013-08-23			ENSG00000123405		"""basic leucine zipper proteins"""	7780	protein-coding gene	gene with protein product		601490	"""nuclear factor (erythroid-derived 2), 45kD"", ""nuclear factor (erythroid-derived 2), 45kDa"""			8355703	Standard	NM_001136023		Approved	NF-E2	uc001sfr.5	Q16621		ENST00000540264.2:c.558delC	chr12.hg19:g.54686722delG	ENSP00000439120:p.Pro186fs	141.0	0.0		155.0	11.0	NM_001261461	Q07720|Q6ICV9	Frame_Shift_Del	DEL	ENST00000540264.2	hg19	CCDS8876.1																																																																																			.	.		0.607	NFE2-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405747.1	NM_006163	
DIEXF	27042	hgsc.bcm.edu	37	1	210010321	210010321	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr1:210010321delC	ENST00000491415.2	+	6	884	c.827delC	c.(826-828)accfs	p.T276fs		NM_014388.6	NP_055203.4	Q68CQ4	DIEXF_HUMAN	digestive organ expansion factor homolog (zebrafish)	276					multicellular organismal development (GO:0007275)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(6)|central_nervous_system(2)|cervix(2)|endometrium(2)|kidney(15)|large_intestine(7)|lung(12)|ovary(1)|skin(3)|stomach(1)|urinary_tract(2)	53						AGCCCATTCACCCCCCTCCAG	0.493																																					p.T276fs		Atlas-INDEL	.											.	DIEXF	97	.	0			c.826delA						.			5,4261		2,1,2130	119.0	128.0	125.0			4.7	0.8	1		126	6,8248		3,0,4124	no	frameshift	DIEXF	NM_014388.6		5,1,6254	A1A1,A1R,RR		0.0727,0.1172,0.0879			210010321	11,12509	2203	4300	6503	SO:0001589	frameshift_variant	27042	exon6			.	BC022964	CCDS1493.1	1q32.2	2011-08-12	2011-02-16	2011-02-16	ENSG00000117597	ENSG00000117597			28440	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 107"""	C1orf107		16322560	Standard	NM_014388		Approved	MGC29875, DEF, UTP25	uc001hhr.2	Q68CQ4	OTTHUMG00000036654	ENST00000491415.2:c.827delC	chr1.hg19:g.210010321delC	ENSP00000419005:p.Thr276fs	110.0	0.0		162.0	11.0	NM_014388	O75992|Q4VY00|Q63HL9	Frame_Shift_Del	DEL	ENST00000491415.2	hg19	CCDS1493.1																																																																																			.	.		0.493	DIEXF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089127.2	NM_014388	
NOM1	64434	hgsc.bcm.edu	37	7	156754952	156754952	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:156754952delT	ENST00000275820.3	+	5	1755	c.1740delT	c.(1738-1740)gctfs	p.A580fs		NM_138400.1	NP_612409.1	Q5C9Z4	NOM1_HUMAN	nucleolar protein with MIF4G domain 1	580						nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(5)|kidney(4)|large_intestine(9)|lung(7)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	31	Ovarian(565;0.218)	all_hematologic(28;0.0749)	OV - Ovarian serous cystadenocarcinoma(82;0.00301)	UCEC - Uterine corpus endometrioid carcinoma (81;0.169)		TGCAGAGAGCTTTGGTGAGTC	0.488																																					p.A580fs		Atlas-INDEL	.											.	NOM1	73	.	0			c.1739delC						.						130.0	121.0	124.0					7																	156754952		2203	4300	6503	SO:0001589	frameshift_variant	64434	exon5			.	AF107455	CCDS34787.1	7q36.3	2014-06-13	2005-03-30	2005-03-30	ENSG00000146909	ENSG00000146909			13244	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 113"""	611269	"""chromosome 7 open reading frame 3"""	C7orf3		10329000	Standard	XM_005249560		Approved	SGD1, PPP1R113	uc003wmy.3	Q5C9Z4	OTTHUMG00000152639	ENST00000275820.3:c.1740delT	chr7.hg19:g.156754952delT	ENSP00000275820:p.Ala580fs	174.0	0.0		228.0	14.0	NM_138400	Q96I08	Frame_Shift_Del	DEL	ENST00000275820.3	hg19	CCDS34787.1																																																																																			.	.		0.488	NOM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327098.1	NM_138400	
BSN	8927	hgsc.bcm.edu	37	3	49692373	49692373	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr3:49692373delG	ENST00000296452.4	+	5	5498	c.5384delG	c.(5383-5385)aggfs	p.R1795fs		NM_003458.3	NP_003449.2	Q9UPA5	BSN_HUMAN	bassoon presynaptic cytomatrix protein	1795					synaptic transmission (GO:0007268)	axon (GO:0030424)|cell junction (GO:0030054)|dendrite (GO:0030425)|neuron projection terminus (GO:0044306)|nucleus (GO:0005634)|presynaptic cytoskeletal matrix assembled at active zones (GO:0048788)	metal ion binding (GO:0046872)			breast(8)|central_nervous_system(2)|cervix(2)|endometrium(16)|kidney(3)|large_intestine(17)|lung(37)|ovary(7)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	106				BRCA - Breast invasive adenocarcinoma(193;6.66e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0032)|Kidney(197;0.00336)		GGAAGACCCAGGGAGGCCAAG	0.602																																					p.R1795fs		Atlas-INDEL	.											.	BSN	272	.	0			c.5383delA						.						71.0	76.0	74.0					3																	49692373		2203	4300	6503	SO:0001589	frameshift_variant	8927	exon5			.	AF052224	CCDS2800.1	3p21	2013-01-07	2013-01-07		ENSG00000164061	ENSG00000164061			1117	protein-coding gene	gene with protein product	"""zinc finger protein 231"", ""neuronal double zinc finger protein"""	604020	"""bassoon (presynaptic cytomatrix protein)"""	ZNF231		9806829, 10329005	Standard	NM_003458		Approved		uc003cxe.4	Q9UPA5	OTTHUMG00000133750	ENST00000296452.4:c.5384delG	chr3.hg19:g.49692373delG	ENSP00000296452:p.Arg1795fs	143.0	0.0		164.0	10.0	NM_003458	O43161|Q7LGH3	Frame_Shift_Del	DEL	ENST00000296452.4	hg19	CCDS2800.1																																																																																			.	.		0.602	BSN-001	KNOWN	NMD_exception|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000258164.1	NM_003458	
ARNT2	9915	hgsc.bcm.edu	37	15	80867380	80867380	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr15:80867380delA	ENST00000303329.4	+	14	1607	c.1442delA	c.(1441-1443)gaafs	p.E481fs	ARNT2_ENST00000527771.1_Frame_Shift_Del_p.E470fs|ARNT2_ENST00000533983.1_Frame_Shift_Del_p.E470fs	NM_014862.3	NP_055677.3	Q9HBZ2	ARNT2_HUMAN	aryl-hydrocarbon receptor nuclear translocator 2	481					central nervous system development (GO:0007417)|in utero embryonic development (GO:0001701)|negative regulation of apoptotic process (GO:0043066)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|response to estradiol (GO:0032355)|response to hypoxia (GO:0001666)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	aryl hydrocarbon receptor binding (GO:0017162)|DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			NS(1)|central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(16)|ovary(1)|pancreas(2)|prostate(2)|skin(1)	35			BRCA - Breast invasive adenocarcinoma(143;0.134)			AAGTCCGTGGAAAAGGCGGAT	0.478																																					p.E481fs		Atlas-INDEL	.											.	ARNT2	88	.	0			c.1441delG						.						177.0	171.0	173.0					15																	80867380		2203	4300	6503	SO:0001589	frameshift_variant	9915	exon14			.	AB002305	CCDS32307.1	15q25.1	2013-05-21			ENSG00000172379	ENSG00000172379		"""Basic helix-loop-helix proteins"""	16876	protein-coding gene	gene with protein product		606036				11247670	Standard	NM_014862		Approved	KIAA0307, bHLHe1	uc002bfr.3	Q9HBZ2	OTTHUMG00000165478	ENST00000303329.4:c.1442delA	chr15.hg19:g.80867380delA	ENSP00000307479:p.Glu481fs	124.0	0.0		165.0	10.0	NM_014862	B4DIS7|O15024|Q8IYC2	Frame_Shift_Del	DEL	ENST00000303329.4	hg19	CCDS32307.1																																																																																			.	.		0.478	ARNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384389.2		
DGKZ	8525	hgsc.bcm.edu	37	11	46396358	46396358	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr11:46396358delC	ENST00000454345.1	+	19	2256	c.2131delC	c.(2131-2133)cccfs	p.P711fs	MIR4688_ENST00000577966.1_RNA|DGKZ_ENST00000318201.8_Frame_Shift_Del_p.P500fs|DGKZ_ENST00000527911.1_Frame_Shift_Del_p.P523fs|DGKZ_ENST00000395574.3_Frame_Shift_Del_p.P489fs|DGKZ_ENST00000532868.2_Frame_Shift_Del_p.P527fs|DGKZ_ENST00000343674.6_Frame_Shift_Del_p.P539fs|DGKZ_ENST00000528615.1_Frame_Shift_Del_p.P301fs|DGKZ_ENST00000456247.2_Frame_Shift_Del_p.P522fs|DGKZ_ENST00000543978.1_Intron|DGKZ_ENST00000421244.2_Frame_Shift_Del_p.P523fs	NM_001105540.1	NP_001099010.1	Q13574	DGKZ_HUMAN	diacylglycerol kinase, zeta	711					blood coagulation (GO:0007596)|cell migration (GO:0016477)|intracellular signal transduction (GO:0035556)|lipid phosphorylation (GO:0046834)|mitotic G1 DNA damage checkpoint (GO:0031571)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of Ras protein signal transduction (GO:0046580)|phosphorylation (GO:0016310)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)	cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|enzyme inhibitor activity (GO:0004857)|lipid kinase activity (GO:0001727)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)|protein C-terminus binding (GO:0008022)			central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(5)|lung(12)|pancreas(1)|prostate(1)|skin(1)	25				GBM - Glioblastoma multiforme(35;0.0259)|Lung(87;0.141)		GGACCTGAAACCCCAGTGTGT	0.612																																					p.K710fs		Atlas-INDEL	.											.	DGKZ	199	.	0			c.2130delA						.						86.0	84.0	85.0					11																	46396358		2202	4299	6501	SO:0001589	frameshift_variant	8525	exon19			.	U51477	CCDS7918.1, CCDS41640.1, CCDS44579.1, CCDS44580.1, CCDS55757.1, CCDS55758.1, CCDS55759.1, CCDS44579.2	11p11.2	2010-11-24	2010-11-24		ENSG00000149091	ENSG00000149091	2.7.1.107		2857	protein-coding gene	gene with protein product		601441	"""diacylglycerol kinase, zeta 104kDa"""			8626588	Standard	NM_003646		Approved	DAGK5, hDGKzeta, DGK-ZETA, DAGK6	uc001ncn.1	Q13574	OTTHUMG00000166437	ENST00000454345.1:c.2131delC	chr11.hg19:g.46396358delC	ENSP00000412178:p.Pro711fs	96.0	0.0		161.0	10.0	NM_001105540	B7Z2M9|B7Z6M3|E9PPW4|F6UCU9|G3V0F6|J3KNJ6|O00542|Q6ZVG7|Q8IVW9	Frame_Shift_Del	DEL	ENST00000454345.1	hg19	CCDS41640.1																																																																																			.	.		0.612	DGKZ-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000389772.1	NM_001105540	
TNRC18	84629	hgsc.bcm.edu	37	7	5353050	5353050	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr7:5353050delC	ENST00000430969.1	-	27	7820	c.7472delG	c.(7471-7473)ggcfs	p.G2491fs	TNRC18_ENST00000399537.4_Frame_Shift_Del_p.G2491fs	NM_001080495.2	NP_001073964.2	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	2491							chromatin binding (GO:0003682)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)	11		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)		CTCCTGCCAGCCCCCCGCCCC	0.692																																					p.G2491fs		Atlas-INDEL	.											.	TNRC18	311	.	0			c.7473delC						.						10.0	11.0	11.0					7																	5353050		1563	3573	5136	SO:0001589	frameshift_variant	84629	exon27			.	U80753	CCDS47534.1	7p22.1	2012-04-17			ENSG00000182095	ENSG00000182095		"""Trinucleotide (CAG) repeat containing"""	11962	protein-coding gene	gene with protein product						9225980	Standard	NM_001080495		Approved	CAGL79, TNRC18A, KIAA1856	uc003soi.4	O15417	OTTHUMG00000151831	ENST00000430969.1:c.7472delG	chr7.hg19:g.5353050delC	ENSP00000395538:p.Gly2491fs	91.0	0.0		168.0	11.0	NM_001080495	A8MX41|Q96JH1|Q96K91	Frame_Shift_Del	DEL	ENST00000430969.1	hg19	CCDS47534.1																																																																																			.	.		0.692	TNRC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding			
UBAP2	55833	hgsc.bcm.edu	37	9	34017099	34017099	+	Frame_Shift_Del	DEL	T	T	-	rs566017101		TCGA-DD-A1EG-01A-11D-A20W-10	TCGA-DD-A1EG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	50ee360c-e3df-4888-9999-ebb88e271d08	636fb0c9-ce48-45f0-a066-45004952b47f	g.chr9:34017099delT	ENST00000379238.1	-	2	165	c.48delA	c.(46-48)aaafs	p.K16fs	UBAP2_ENST00000539807.1_5'UTR|UBAP2_ENST00000360802.1_Frame_Shift_Del_p.K16fs|RNU7-36P_ENST00000516597.1_RNA|UBAP2_ENST00000480885.1_5'UTR|UBAP2_ENST00000418786.2_Frame_Shift_Del_p.K16fs|UBAP2_ENST00000449054.1_Frame_Shift_Del_p.K16fs|UBAP2_ENST00000379239.4_Intron					ubiquitin associated protein 2											endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(13)|ovary(3)|stomach(1)	32			LUSC - Lung squamous cell carcinoma(29;0.00575)	GBM - Glioblastoma multiforme(74;0.168)		AAATCTGTGGTTTTTCCCGAG	0.343																																					p.P17fs		Pindel	.											.	UBAP2	82	.	0			c.49delC						.						140.0	120.0	127.0					9																	34017099		2203	4300	6503	SO:0001589	frameshift_variant	55833	exon2			.	AB040924	CCDS6547.1, CCDS75828.1	9p11.2	2008-02-05			ENSG00000137073	ENSG00000137073			14185	protein-coding gene	gene with protein product						8871400	Standard	NM_018449		Approved	KIAA1491, bA176F3.5, FLJ22435	uc003ztq.1	Q5T6F2	OTTHUMG00000000427	ENST00000379238.1:c.48delA	chr9.hg19:g.34017099delT	ENSP00000368540:p.Lys16fs	107.0	0.0		135.0	11.0	NM_018449		Frame_Shift_Del	DEL	ENST00000379238.1	hg19	CCDS6547.1																																																																																			.	.		0.343	UBAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001071.1	NM_018449	
