#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
TAS1R3	83756	hgsc.bcm.edu	37	1	1267320	1267320	+	Splice_Site	SNP	T	T	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:1267320T>G	ENST00000339381.5	+	2	524		c.e2+2			NM_152228.1	NP_689414	Q7RTX0	TS1R3_HUMAN	taste receptor, type 1, member 3						detection of chemical stimulus involved in sensory perception of sweet taste (GO:0001582)|G-protein coupled receptor signaling pathway (GO:0007186)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein heterodimerization activity (GO:0046982)|taste receptor activity (GO:0008527)			kidney(2)|lung(8)|upper_aerodigestive_tract(1)|urinary_tract(1)	12	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;3.01e-35)|OV - Ovarian serous cystadenocarcinoma(86;3.88e-21)|Colorectal(212;0.000157)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00229)|BRCA - Breast invasive adenocarcinoma(365;0.00251)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.034)|Lung(427;0.146)		ATGCCCCAGGTGGGCGCCCCC	0.662																																					.		Atlas-SNP	.											.	TAS1R3	39	.	0			c.492+2T>G						.						25.0	31.0	29.0					1																	1267320		2190	4264	6454	SO:0001630	splice_region_variant	83756	exon2			CCCAGGTGGGCGC	AC026283	CCDS30556.1	1p36	2012-08-22			ENSG00000169962	ENSG00000169962		"""Taste receptors / Type 1"", ""GPCR / Unclassified : Taste receptors"""	15661	protein-coding gene	gene with protein product		605865				11319557	Standard	XM_006710939		Approved	T1R3	uc010nyk.2	Q7RTX0	OTTHUMG00000003071	ENST00000339381.5:c.492+2T>G	chr1.hg19:g.1267320T>G		325.0	0.0		206.0	9.0	NM_152228	Q5TA49|Q8NGW9	Splice_Site	SNP	ENST00000339381.5	hg19	CCDS30556.1	.	.	.	.	.	.	.	.	.	.	T	9.811	1.183254	0.21870	.	.	ENSG00000169962	ENST00000339381	.	.	.	4.75	4.75	0.60458	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.429	0.44395	0.0:0.0:0.1637:0.8363	.	.	.	.	.	-1	.	.	.	+	.	.	TAS1R3	1257183	1.000000	0.71417	0.949000	0.38748	0.337000	0.28794	7.860000	0.86993	1.790000	0.52503	0.459000	0.35465	.	.	.		0.662	TAS1R3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008493.1		Intron
PANK4	55229	hgsc.bcm.edu	37	1	2441359	2441359	+	Missense_Mutation	SNP	G	G	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:2441359G>C	ENST00000378466.3	-	18	2062	c.2050C>G	c.(2050-2052)Cag>Gag	p.Q684E	PANK4_ENST00000435556.3_Missense_Mutation_p.Q645E	NM_018216.1	NP_060686.1	Q9NVE7	PANK4_HUMAN	pantothenate kinase 4	684			Q -> R (in dbSNP:rs2494620). {ECO:0000269|Ref.2}.		coenzyme A biosynthetic process (GO:0015937)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|pantothenate kinase activity (GO:0004594)			breast(2)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(4)	23	all_cancers(77;0.000158)|all_epithelial(69;8.01e-05)|all_lung(157;0.0212)|Lung NSC(156;0.0376)|Ovarian(185;0.0634)	all_epithelial(116;3.18e-20)|all_lung(118;1.67e-08)|Lung NSC(185;2.69e-06)|Breast(487;0.00147)|Renal(390;0.00183)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.0847)|Medulloblastoma(700;0.123)		Epithelial(90;1.54e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.95e-23)|GBM - Glioblastoma multiforme(42;2.81e-08)|Colorectal(212;4.25e-05)|COAD - Colon adenocarcinoma(227;0.000196)|Kidney(185;0.000342)|BRCA - Breast invasive adenocarcinoma(365;0.00445)|KIRC - Kidney renal clear cell carcinoma(229;0.00549)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.201)		CTCTCTTCCTGGAGCGCAGAG	0.657																																					p.Q684E		Atlas-SNP	.											PANK4,NS,lymphoid_neoplasm,+1,1	PANK4	64	.	0			c.C2050G						.						46.0	54.0	52.0					1																	2441359		2198	4296	6494	SO:0001583	missense	55229	exon18			CTTCCTGGAGCGC	AK001644	CCDS42.1	1p36.32	2008-02-05			ENSG00000157881	ENSG00000157881			19366	protein-coding gene	gene with protein product		606162				11479594	Standard	XR_241034		Approved	FLJ10782	uc001ajm.1	Q9NVE7	OTTHUMG00000000791	ENST00000378466.3:c.2050C>G	chr1.hg19:g.2441359G>C	ENSP00000367727:p.Gln684Glu	231.0	0.0		189.0	0.0	NM_018216	B9DI84|Q53EU3|Q5TA84|Q7RTX3|Q9H3X5	Missense_Mutation	SNP	ENST00000378466.3	hg19	CCDS42.1	.	.	.	.	.	.	.	.	.	.	G	0.133	-1.111755	0.01813	.	.	ENSG00000157881	ENST00000378466;ENST00000435556	T;T	0.06068	3.35;3.35	5.03	-5.43	0.02632	Domain of unknown function DUF89 (2);	0.544208	0.20048	N	0.100373	T	0.01661	0.0053	N	0.03050	-0.425	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.38156	-0.9674	10	0.02654	T	1	-0.009	8.3957	0.32555	0.0:0.2361:0.5253:0.2386	.	645;684	E9PHT6;Q9NVE7	.;PANK4_HUMAN	E	684;645	ENSP00000367727:Q684E;ENSP00000421433:Q645E	ENSP00000367727:Q684E	Q	-	1	0	PANK4	2431219	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	0.211000	0.17474	-1.004000	0.03421	-0.397000	0.06425	CAG	.	.		0.657	PANK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002082.1		
ICMT	23463	hgsc.bcm.edu	37	1	6293699	6293699	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:6293699T>C	ENST00000343813.5	-	3	317	c.289A>G	c.(289-291)Atg>Gtg	p.M97V	LINC00337_ENST00000441724.1_RNA	NM_012405.3	NP_036537.1	O60725	ICMT_HUMAN	isoprenylcysteine carboxyl methyltransferase	97					C-terminal protein methylation (GO:0006481)|cellular protein modification process (GO:0006464)|in utero embryonic development (GO:0001701)|liver development (GO:0001889)|multicellular organism growth (GO:0035264)|positive regulation of cell proliferation (GO:0008284)|protein targeting to membrane (GO:0006612)|regulation of Ras protein signal transduction (GO:0046578)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	cAMP response element binding protein binding (GO:0008140)|protein C-terminal carboxyl O-methyltransferase activity (GO:0003880)|protein C-terminal S-isoprenylcysteine carboxyl O-methyltransferase activity (GO:0004671)			NS(1)|endometrium(2)	3	Ovarian(185;0.0634)	all_cancers(23;5.85e-39)|all_epithelial(116;2.4e-22)|all_lung(118;2.65e-08)|Lung NSC(185;6.45e-07)|all_neural(13;3.18e-06)|all_hematologic(16;8.99e-06)|Acute lymphoblastic leukemia(12;0.000365)|Breast(487;0.000688)|Renal(390;0.0007)|Colorectal(325;0.00104)|Glioma(11;0.00203)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0392)|Medulloblastoma(700;0.211)		Epithelial(90;5.52e-38)|GBM - Glioblastoma multiforme(13;6.51e-32)|OV - Ovarian serous cystadenocarcinoma(86;3.03e-19)|Colorectal(212;7.08e-08)|COAD - Colon adenocarcinoma(227;8.35e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|BRCA - Breast invasive adenocarcinoma(365;0.00109)|STAD - Stomach adenocarcinoma(132;0.00313)|READ - Rectum adenocarcinoma(331;0.0642)|Lung(427;0.182)		AGGGAGCACATGTACCTATTT	0.423																																					p.M97V		Atlas-SNP	.											.	ICMT	13	.	0			c.A289G						.						77.0	74.0	75.0					1																	6293699		2203	4300	6503	SO:0001583	missense	23463	exon3			AGCACATGTACCT	AF064084	CCDS61.1	1p36	2010-04-29			ENSG00000116237	ENSG00000116237	2.1.1.100		5350	protein-coding gene	gene with protein product	"""protein-S-isoprenylcysteine O-methyltransferase"""	605851				9614111, 10441503	Standard	XM_005263437		Approved	PCCMT, HSTE14, PPMT	uc001amk.3	O60725	OTTHUMG00000001254	ENST00000343813.5:c.289A>G	chr1.hg19:g.6293699T>C	ENSP00000343552:p.Met97Val	120.0	0.0		95.0	4.0	NM_012405	Q6FHT0	Missense_Mutation	SNP	ENST00000343813.5	hg19	CCDS61.1	.	.	.	.	.	.	.	.	.	.	T	3.940	-0.014327	0.07681	.	.	ENSG00000116237	ENST00000343813;ENST00000535068	.	.	.	5.83	4.69	0.59074	.	0.090275	0.85682	N	0.000000	T	0.39145	0.1067	L	0.31926	0.97	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.15178	-1.0446	9	0.10636	T	0.68	.	6.0053	0.19542	0.0:0.2443:0.0:0.7557	.	97	O60725	ICMT_HUMAN	V	97;1	.	ENSP00000343552:M97V	M	-	1	0	ICMT	6216286	1.000000	0.71417	0.983000	0.44433	0.968000	0.65278	3.181000	0.50903	1.013000	0.39391	0.533000	0.62120	ATG	.	.		0.423	ICMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000003681.1	NM_012405	
PLEKHG5	57449	hgsc.bcm.edu	37	1	6536010	6536010	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:6536010T>C	ENST00000400915.3	-	4	364	c.298A>G	c.(298-300)Agc>Ggc	p.S100G	PLEKHG5_ENST00000377740.3_Missense_Mutation_p.S121G|PLEKHG5_ENST00000535355.1_Missense_Mutation_p.S113G|PLEKHG5_ENST00000377748.1_Missense_Mutation_p.S121G|PLEKHG5_ENST00000537245.1_Missense_Mutation_p.S123G|PLEKHG5_ENST00000400913.1_Missense_Mutation_p.S44G|PLEKHG5_ENST00000377728.3_Missense_Mutation_p.S44G|PLEKHG5_ENST00000377725.1_Missense_Mutation_p.S44G|PLEKHG5_ENST00000340850.5_Missense_Mutation_p.S44G|PLEKHG5_ENST00000377737.2_Missense_Mutation_p.S44G|PLEKHG5_ENST00000544978.1_Missense_Mutation_p.S44G|PLEKHG5_ENST00000377732.1_Missense_Mutation_p.S81G	NM_001042663.1	NP_001036128.1	O94827	PKHG5_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 5	100					apoptotic signaling pathway (GO:0097190)|endothelial cell chemotaxis (GO:0035767)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)|signal transducer activity (GO:0004871)			liver(1)	1	Ovarian(185;0.02)|all_lung(157;0.154)	all_cancers(23;1.7e-35)|all_epithelial(116;2.78e-22)|all_lung(118;7.57e-07)|Lung NSC(185;4.26e-06)|Colorectal(325;4.47e-05)|all_hematologic(16;0.00014)|Breast(487;0.000688)|Renal(390;0.0007)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0448)		Epithelial(90;5.51e-35)|GBM - Glioblastoma multiforme(13;3.57e-27)|Colorectal(212;6.23e-08)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000894)|BRCA - Breast invasive adenocarcinoma(365;0.00107)|STAD - Stomach adenocarcinoma(132;0.00159)|READ - Rectum adenocarcinoma(331;0.0419)		TCCACAGAGCTCTCCTCCTCC	0.632											OREG0013041	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S123G		Atlas-SNP	.											.,1	PLEKHG5	66	.	0			c.A367G						.						108.0	107.0	107.0					1																	6536010		2203	4300	6503	SO:0001583	missense	57449	exon4			CAGAGCTCTCCTC	AK024676	CCDS79.1, CCDS41240.1, CCDS41241.1, CCDS57967.1, CCDS57968.1, CCDS57969.1	1p36.31	2014-09-17		2005-08-09	ENSG00000171680	ENSG00000171680		"""Pleckstrin homology (PH) domain containing"""	29105	protein-coding gene	gene with protein product	"""synectin-binding guanine exchange factor"""	611101				17564964	Standard	NM_001042663		Approved	KIAA0720, Syx, GEF720, Tech	uc010nzr.1	O94827	OTTHUMG00000000905	ENST00000400915.3:c.298A>G	chr1.hg19:g.6536010T>C	ENSP00000383706:p.Ser100Gly	167.0	0.0	634	93.0	4.0	NM_001265592	B3KU07|B7Z2M3|B7Z5X2|F5GZ21|F5H1I0|Q5SY17|Q5T8W5|Q5T8W9|Q6ZNM0|Q7Z436|Q86YD8|Q96BS1	Missense_Mutation	SNP	ENST00000400915.3	hg19	CCDS41241.1	.	.	.	.	.	.	.	.	.	.	T	2.162	-0.391982	0.04932	.	.	ENSG00000171680	ENST00000377748;ENST00000340850;ENST00000400913;ENST00000400915;ENST00000377740;ENST00000377732;ENST00000377728;ENST00000377725;ENST00000535355;ENST00000377737;ENST00000537245;ENST00000544978	T;T;T;T;T;T;T;T;T;T;T;T	0.70045	-0.43;-0.43;-0.43;-0.4;-0.37;-0.39;-0.43;-0.41;-0.39;-0.43;-0.45;-0.41	4.44	-1.08	0.09936	.	0.345630	0.27060	N	0.021124	T	0.30135	0.0755	N	0.01482	-0.84	0.09310	N	1	B;B;B;B;B	0.06786	0.001;0.0;0.0;0.001;0.0	B;B;B;B;B	0.04013	0.001;0.0;0.001;0.001;0.0	T	0.21211	-1.0252	10	0.25751	T	0.34	-9.0471	5.98	0.19401	0.1808:0.6279:0.0:0.1913	.	113;44;121;121;100	F5GZ21;O94827-4;Q5SY18;O94827-2;O94827	.;.;.;.;PKHG5_HUMAN	G	121;44;44;100;121;81;44;44;113;44;123;44	ENSP00000366977:S121G;ENSP00000344570:S44G;ENSP00000383704:S44G;ENSP00000383706:S100G;ENSP00000366969:S121G;ENSP00000366961:S81G;ENSP00000366957:S44G;ENSP00000366954:S44G;ENSP00000441445:S113G;ENSP00000366966:S44G;ENSP00000439625:S123G;ENSP00000437710:S44G	ENSP00000344570:S44G	S	-	1	0	PLEKHG5	6458597	0.012000	0.17670	0.002000	0.10522	0.079000	0.17450	0.231000	0.17872	-0.311000	0.08754	0.260000	0.18958	AGC	.	.		0.632	PLEKHG5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000002631.1	NM_020631	
CLSTN1	22883	hgsc.bcm.edu	37	1	9790636	9790636	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:9790636T>C	ENST00000377298.4	-	19	3668	c.2876A>G	c.(2875-2877)gAg>gGg	p.E959G	CLSTN1_ENST00000377288.3_Missense_Mutation_p.E940G|CLSTN1_ENST00000361311.4_Missense_Mutation_p.E949G|CLSTN1_ENST00000477264.1_5'UTR	NM_001009566.1	NP_001009566.1	O94985	CSTN1_HUMAN	calsyntenin 1	959	Glu-rich (highly acidic).				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)	cell junction (GO:0030054)|cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	beta-amyloid binding (GO:0001540)|calcium ion binding (GO:0005509)|kinesin binding (GO:0019894)|X11-like protein binding (GO:0042988)			breast(1)|endometrium(5)|kidney(2)|large_intestine(7)|liver(1)|lung(9)|prostate(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	36	all_lung(157;0.222)	all_lung(284;4.03e-05)|Lung NSC(185;6.93e-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;0.0234)|Colorectal(212;8.36e-08)|COAD - Colon adenocarcinoma(227;1.93e-05)|Kidney(185;0.000342)|BRCA - Breast invasive adenocarcinoma(304;0.000949)|KIRC - Kidney renal clear cell carcinoma(229;0.00122)|STAD - Stomach adenocarcinoma(132;0.00644)|READ - Rectum adenocarcinoma(331;0.0419)		GTCGCCCTGCTCCCCCTCCTC	0.647																																					p.E959G		Atlas-SNP	.											.	CLSTN1	88	.	0			c.A2876G						.						98.0	81.0	87.0					1																	9790636		2203	4300	6503	SO:0001583	missense	22883	exon19			CCCTGCTCCCCCT	AB020718	CCDS105.1, CCDS30580.1	1p36.22	2011-07-01			ENSG00000171603	ENSG00000171603		"""Cadherins / Cadherin-related"""	17447	protein-coding gene	gene with protein product	"""cadherin-related family member 12"""	611321				10048485	Standard	XM_005263432		Approved	CSTN1, KIAA0911, CDHR12	uc001aqh.3	O94985	OTTHUMG00000001451	ENST00000377298.4:c.2876A>G	chr1.hg19:g.9790636T>C	ENSP00000366513:p.Glu959Gly	83.0	0.0		93.0	4.0	NM_001009566	A8K183|Q5SR52|Q5UE58|Q71MN0|Q8N4K9	Missense_Mutation	SNP	ENST00000377298.4	hg19	CCDS30580.1	.	.	.	.	.	.	.	.	.	.	T	9.798	1.179632	0.21787	.	.	ENSG00000171603	ENST00000377298;ENST00000361311;ENST00000435891;ENST00000377288;ENST00000539822	T;T;T;T	0.05649	3.41;3.41;3.41;3.41	5.19	-1.11	0.09840	.	0.347275	0.28706	N	0.014410	T	0.03434	0.0099	N	0.24115	0.695	0.44619	D	0.997595	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.47724	-0.9095	10	0.24483	T	0.36	-10.8934	5.5378	0.17021	0.0:0.3988:0.1509:0.4503	.	940;949;959;314	B4E3Q1;O94985-2;O94985;B3KMD3	.;.;CSTN1_HUMAN;.	G	959;949;760;940;940	ENSP00000366513:E959G;ENSP00000354997:E949G;ENSP00000401934:E760G;ENSP00000366502:E940G	ENSP00000354997:E949G	E	-	2	0	CLSTN1	9713223	0.998000	0.40836	0.067000	0.19924	0.690000	0.40134	0.820000	0.27323	-0.157000	0.11059	0.533000	0.62120	GAG	.	.		0.647	CLSTN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000004239.1		
ZBTB17	7709	hgsc.bcm.edu	37	1	16270914	16270914	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:16270914A>G	ENST00000375743.4	-	9	1484	c.1252T>C	c.(1252-1254)Tac>Cac	p.Y418H	ZBTB17_ENST00000375733.2_Missense_Mutation_p.Y418H|ZBTB17_ENST00000448462.2_Missense_Mutation_p.Y355H|ZBTB17_ENST00000537142.1_Missense_Mutation_p.Y336H|ZBTB17_ENST00000479282.1_5'Flank	NM_003443.2	NP_003434.2	Q13105	ZBT17_HUMAN	zinc finger and BTB domain containing 17	418					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|ectoderm development (GO:0007398)|endoplasmic reticulum unfolded protein response (GO:0030968)|gastrulation with mouth forming second (GO:0001702)|negative regulation of cell cycle (GO:0045786)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(4)|large_intestine(1)|lung(4)|ovary(2)|prostate(2)	15		Colorectal(325;0.000257)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|Colorectal(212;4.12e-07)|COAD - Colon adenocarcinoma(227;2.43e-05)|BRCA - Breast invasive adenocarcinoma(304;9.97e-05)|Kidney(64;0.000182)|KIRC - Kidney renal clear cell carcinoma(64;0.00269)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0649)		TCGCACTGGTAGGGCTTCTCG	0.662																																					p.Y418H		Atlas-SNP	.											.	ZBTB17	45	.	0			c.T1252C						.						57.0	52.0	54.0					1																	16270914		2191	4290	6481	SO:0001583	missense	7709	exon9			ACTGGTAGGGCTT	U20647	CCDS165.1, CCDS55576.1, CCDS72712.1	1p36.13	2013-01-08	2004-07-16	2004-07-16	ENSG00000116809	ENSG00000116809		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	12936	protein-coding gene	gene with protein product		604084	"""zinc finger protein 151 (pHZ-67)"", ""zinc finger protein 60"""	ZNF151, ZNF60			Standard	NM_003443		Approved	MIZ1, pHZ-67	uc001axl.4	Q13105	OTTHUMG00000009377	ENST00000375743.4:c.1252T>C	chr1.hg19:g.16270914A>G	ENSP00000364895:p.Tyr418His	183.0	0.0		146.0	6.0	NM_003443	A0AV07|B4DXB4|B7ZLQ9|F5H411|Q15932|Q5JYB2|Q9NUC9	Missense_Mutation	SNP	ENST00000375743.4	hg19	CCDS165.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	23.9|23.9	4.468063|4.468063	0.84533|0.84533	.|.	.|.	ENSG00000116809|ENSG00000116809	ENST00000375729|ENST00000375743;ENST00000375733;ENST00000444654;ENST00000537142;ENST00000444358;ENST00000448462	.|T;T;T;T	.|0.21734	.|1.99;1.99;1.99;1.99	5.46|5.46	5.46|5.46	0.80206|0.80206	.|Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.|0.000000	.|0.64402	.|D	.|0.000001	T|T	0.41994|0.41994	0.1183|0.1183	L|L	0.49455|0.49455	1.56|1.56	0.58432|0.58432	D|D	0.999997|0.999997	.|D;D;D;D;D	.|0.89917	.|0.999;0.999;1.0;1.0;1.0	.|D;D;D;D;D	.|0.91635	.|0.992;0.997;0.997;0.999;0.99	T|T	0.29579|0.29579	-1.0007|-1.0007	6|10	0.87932|0.87932	D|D	0|0	.|.	15.5311|15.5311	0.75964|0.75964	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|374;355;418;336;418	.|B4DYU5;E7EPQ4;Q13105-2;F5H411;Q13105	.|.;.;.;.;ZBT17_HUMAN	P|H	3|418;418;337;336;4;355	.|ENSP00000364895:Y418H;ENSP00000364885:Y418H;ENSP00000438529:Y336H;ENSP00000391002:Y355H	ENSP00000364881:L3P|ENSP00000364885:Y418H	L|Y	-|-	2|1	0|0	ZBTB17|ZBTB17	16143501|16143501	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.605000|0.605000	0.37080|0.37080	9.232000|9.232000	0.95325|0.95325	2.064000|2.064000	0.61679|0.61679	0.533000|0.533000	0.62120|0.62120	CTA|TAC	.	.		0.662	ZBTB17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025998.1	NM_003443	
ATP13A2	23400	hgsc.bcm.edu	37	1	17314703	17314703	+	Nonsense_Mutation	SNP	G	G	T			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:17314703G>T	ENST00000326735.8	-	25	2822	c.2789C>A	c.(2788-2790)tCg>tAg	p.S930*	ATP13A2_ENST00000341676.5_Nonsense_Mutation_p.S886*|RP1-37C10.3_ENST00000446261.1_RNA|ATP13A2_ENST00000452699.1_Nonsense_Mutation_p.S925*			Q9NQ11	AT132_HUMAN	ATPase type 13A2	930					cell death (GO:0008219)|cellular response to manganese ion (GO:0071287)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(11)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		Colorectal(325;0.000147)|Breast(348;0.00104)|Renal(390;0.00145)|Lung NSC(340;0.00566)|all_lung(284;0.00797)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|COAD - Colon adenocarcinoma(227;1.11e-05)|BRCA - Breast invasive adenocarcinoma(304;1.99e-05)|Kidney(64;0.000171)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00645)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.182)		GACGCTGAACGAAGTGTCAAG	0.607																																					p.S930X		Atlas-SNP	.											ATP13A2,NS,carcinoma,0,1	ATP13A2	85	.	0			c.C2789A						.						140.0	125.0	130.0					1																	17314703		2203	4300	6503	SO:0001587	stop_gained	23400	exon25			CTGAACGAAGTGT	AL354615	CCDS175.1, CCDS44072.1, CCDS44073.1	1p36	2014-09-17			ENSG00000159363	ENSG00000159363		"""ATPases / P-type"", ""Parkinson disease"""	30213	protein-coding gene	gene with protein product		610513	"""Parkinson disease (autosomal recessive) 9 (Kufor-Rakeb syndrome)"""	PARK9		15381061, 16964263	Standard	XM_005245809		Approved	HSA9947, CLN12	uc001baa.2	Q9NQ11	OTTHUMG00000002293	ENST00000326735.8:c.2789C>A	chr1.hg19:g.17314703G>T	ENSP00000327214:p.Ser930*	260.0	0.0		198.0	0.0	NM_022089	O75700|Q5JXY1|Q5JXY2|Q6S9Z9	Nonsense_Mutation	SNP	ENST00000326735.8	hg19	CCDS175.1	.	.	.	.	.	.	.	.	.	.	G	29.7	5.026541	0.93518	.	.	ENSG00000159363	ENST00000326735;ENST00000341676;ENST00000452699;ENST00000502418	.	.	.	5.51	4.59	0.56863	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-17.1612	10.0451	0.42182	0.0932:0.0:0.9068:0.0	.	.	.	.	X	930;886;925;126	.	ENSP00000327214:S930X	S	-	2	0	ATP13A2	17187290	1.000000	0.71417	0.185000	0.23176	0.726000	0.41606	9.375000	0.97178	1.326000	0.45319	0.561000	0.74099	TCG	.	.		0.607	ATP13A2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000006617.1	NM_022089	
PLA2G2D	26279	hgsc.bcm.edu	37	1	20442055	20442055	+	Missense_Mutation	SNP	G	G	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:20442055G>C	ENST00000375105.3	-	3	295	c.237C>G	c.(235-237)tgC>tgG	p.C79W		NM_012400.2	NP_036532.1	Q9UNK4	PA2GD_HUMAN	phospholipase A2, group IID	79					glycerophospholipid biosynthetic process (GO:0046474)|inflammatory response (GO:0006954)|lipid catabolic process (GO:0016042)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|phospholipase A2 activity (GO:0004623)	p.C79C(1)		endometrium(1)|lung(2)	3		Colorectal(325;0.000147)|Renal(390;0.000469)|Lung NSC(340;0.00412)|all_lung(284;0.00419)|Breast(348;0.00526)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0427)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|COAD - Colon adenocarcinoma(152;1.15e-05)|BRCA - Breast invasive adenocarcinoma(304;8.01e-05)|Kidney(64;0.000175)|GBM - Glioblastoma multiforme(114;0.000798)|KIRC - Kidney renal clear cell carcinoma(64;0.00261)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		TGTAGATGCTGCACCCCTGGG	0.582										Multiple Myeloma(11;0.12)																											p.C79W	Melanoma(60;742 1548 31762 39240)	Atlas-SNP	.											PLA2G2D,NS,carcinoma,0,1	PLA2G2D	7	.	1	Substitution - coding silent(1)	lung(1)	c.C237G						.																																			SO:0001583	missense	26279	exon3			GATGCTGCACCCC	AF112982	CCDS203.1, CCDS72721.1	1p36.12	2008-09-19			ENSG00000117215	ENSG00000117215	3.1.1.4		9033	protein-coding gene	gene with protein product		605630				10455175	Standard	NM_012400		Approved	sPLA2S	uc001bcz.4	Q9UNK4	OTTHUMG00000002701	ENST00000375105.3:c.237C>G	chr1.hg19:g.20442055G>C	ENSP00000364246:p.Cys79Trp	234.0	0.0		225.0	0.0	NM_012400	A8K2Z1|B1AEL9|Q9UK01	Missense_Mutation	SNP	ENST00000375105.3	hg19	CCDS203.1	.	.	.	.	.	.	.	.	.	.	G	13.45	2.239625	0.39598	.	.	ENSG00000117215	ENST00000375105	T	0.37584	1.19	5.6	-0.0442	0.13856	Phospholipase A2 (3);	0.000000	0.64402	D	0.000008	T	0.63165	0.2488	M	0.93720	3.45	0.25014	N	0.99139	D	0.89917	1.0	D	0.97110	1.0	T	0.55885	-0.8070	10	0.87932	D	0	-26.6937	8.4483	0.32856	0.4766:0.0:0.5234:0.0	.	79	Q9UNK4	PA2GD_HUMAN	W	79	ENSP00000364246:C79W	ENSP00000364246:C79W	C	-	3	2	PLA2G2D	20314642	0.138000	0.22547	0.008000	0.14137	0.002000	0.02628	0.124000	0.15728	-0.023000	0.13963	-0.234000	0.12200	TGC	.	.		0.582	PLA2G2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007683.1		
ECE1	1889	hgsc.bcm.edu	37	1	21564732	21564732	+	Silent	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:21564732A>G	ENST00000374893.6	-	11	1358	c.1284T>C	c.(1282-1284)tgT>tgC	p.C428C	ECE1_ENST00000264205.6_Silent_p.C425C|ECE1_ENST00000436918.2_Silent_p.C428C|ECE1_ENST00000528294.1_5'UTR|ECE1_ENST00000415912.2_Silent_p.C412C|ECE1_ENST00000357071.4_Silent_p.C416C	NM_001397.2	NP_001388.1	P42892	ECE1_HUMAN	endothelin converting enzyme 1	428					bradykinin catabolic process (GO:0010815)|calcitonin catabolic process (GO:0010816)|ear development (GO:0043583)|embryonic digit morphogenesis (GO:0042733)|endothelin maturation (GO:0034959)|heart development (GO:0007507)|hormone catabolic process (GO:0042447)|peptide hormone processing (GO:0016486)|pharyngeal system development (GO:0060037)|positive regulation of receptor recycling (GO:0001921)|protein processing (GO:0016485)|regulation of systemic arterial blood pressure by endothelin (GO:0003100)|regulation of vasoconstriction (GO:0019229)|substance P catabolic process (GO:0010814)	early endosome (GO:0005769)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intrinsic component of endosome membrane (GO:0031302)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|vesicle (GO:0031982)|Weibel-Palade body (GO:0033093)	endopeptidase activity (GO:0004175)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|peptide hormone binding (GO:0017046)|protein homodimerization activity (GO:0042803)			endometrium(5)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|skin(1)	25		Lung NSC(340;1.14e-05)|all_lung(284;1.23e-05)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00147)|Ovarian(437;0.00432)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0183)|OV - Ovarian serous cystadenocarcinoma(117;4.83e-27)|COAD - Colon adenocarcinoma(152;1.36e-06)|GBM - Glioblastoma multiforme(114;1.47e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000162)|STAD - Stomach adenocarcinoma(196;0.00326)|KIRC - Kidney renal clear cell carcinoma(1967;0.00755)|READ - Rectum adenocarcinoma(331;0.0678)|Lung(427;0.206)		AGCGAGGAAGACAGGTCTGGA	0.562																																					p.C428C		Atlas-SNP	.											.	ECE1	76	.	0			c.T1284C						.						55.0	50.0	52.0					1																	21564732		2203	4300	6503	SO:0001819	synonymous_variant	1889	exon11			AGGAAGACAGGTC	D49471	CCDS215.1, CCDS44081.1, CCDS44082.1, CCDS44083.1	1p36.1	2008-02-05			ENSG00000117298	ENSG00000117298			3146	protein-coding gene	gene with protein product		600423		ECE		7805846, 7864876, 17592116	Standard	NM_001397		Approved		uc001bei.2	P42892	OTTHUMG00000002625	ENST00000374893.6:c.1284T>C	chr1.hg19:g.21564732A>G		107.0	0.0		67.0	4.0	NM_001397	A8K3P1|B4E291|Q14217|Q17RN5|Q2Z2K8|Q58GE7|Q5THM5|Q5THM7|Q5THM8|Q9UJQ6|Q9UPF4|Q9UPM4|Q9Y501	Silent	SNP	ENST00000374893.6	hg19	CCDS215.1																																																																																			.	.		0.562	ECE1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000007470.2	NM_001397	
PPT1	5538	hgsc.bcm.edu	37	1	40555118	40555118	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:40555118A>G	ENST00000433473.3	-	5	964	c.500T>C	c.(499-501)cTg>cCg	p.L167P	PPT1_ENST00000449045.2_Missense_Mutation_p.L64P	NM_000310.3	NP_000301.1	P50897	PPT1_HUMAN	palmitoyl-protein thioesterase 1	167					adult locomotory behavior (GO:0008344)|associative learning (GO:0008306)|brain development (GO:0007420)|cell death (GO:0008219)|cellular protein catabolic process (GO:0044257)|cofactor metabolic process (GO:0051186)|cofactor transport (GO:0051181)|grooming behavior (GO:0007625)|lipid catabolic process (GO:0016042)|lysosomal lumen acidification (GO:0007042)|membrane raft organization (GO:0031579)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of neuron apoptotic process (GO:0043524)|nervous system development (GO:0007399)|neuron development (GO:0048666)|neurotransmitter secretion (GO:0007269)|pinocytosis (GO:0006907)|positive regulation of pinocytosis (GO:0048549)|positive regulation of receptor-mediated endocytosis (GO:0048260)|protein catabolic process (GO:0030163)|protein depalmitoylation (GO:0002084)|protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)|regulation of phospholipase A2 activity (GO:0032429)|regulation of synapse structure and activity (GO:0050803)|sphingolipid catabolic process (GO:0030149)|visual perception (GO:0007601)	axon (GO:0030424)|cytosol (GO:0005829)|dendrite (GO:0030425)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|lysosome (GO:0005764)|membrane (GO:0016020)|membrane raft (GO:0045121)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|synaptic vesicle (GO:0008021)	palmitoyl-(protein) hydrolase activity (GO:0008474)|palmitoyl-CoA hydrolase activity (GO:0016290)			endometrium(5)|large_intestine(1)|lung(3)|ovary(1)|stomach(1)	11	Lung NSC(20;3.43e-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;1e-18)|Epithelial(16;3.6e-17)|all cancers(16;1.1e-15)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			CCCAGCATTCAGTGTTTTTCG	0.453																																					p.L167P		Atlas-SNP	.											.	PPT1	18	.	0			c.T500C						.						146.0	133.0	138.0					1																	40555118		2203	4300	6503	SO:0001583	missense	5538	exon5			GCATTCAGTGTTT	U44772	CCDS447.1, CCDS44119.1	1p32	2014-09-17	2008-07-31		ENSG00000131238	ENSG00000131238	3.1.2.22		9325	protein-coding gene	gene with protein product	"""ceroid-lipofuscinosis, neuronal 1, infantile"""	600722		PPT		7637805, 8325646	Standard	NM_000310		Approved	CLN1, INCL	uc001cfb.2	P50897	OTTHUMG00000004495	ENST00000433473.3:c.500T>C	chr1.hg19:g.40555118A>G	ENSP00000394863:p.Leu167Pro	171.0	0.0		146.0	6.0	NM_000310	B4DY24|Q6FGQ4	Missense_Mutation	SNP	ENST00000433473.3	hg19	CCDS447.1	.	.	.	.	.	.	.	.	.	.	A	22.8	4.332784	0.81801	.	.	ENSG00000131238	ENST00000433473;ENST00000449045;ENST00000439754;ENST00000372779	D;D;D;D	0.97831	-4.56;-4.56;-4.56;-4.56	4.82	4.82	0.62117	.	0.000000	0.85682	D	0.000000	D	0.98991	0.9656	H	0.94964	3.605	0.80722	D	1	D;D;D	0.89917	1.0;0.998;1.0	D;D;D	0.97110	1.0;0.98;0.975	D	0.99474	1.0946	10	0.87932	D	0	-14.266	13.3546	0.60621	1.0:0.0:0.0:0.0	.	64;117;167	P50897-2;B4DWU3;P50897	.;.;PPT1_HUMAN	P	167;64;62;196	ENSP00000394863:L167P;ENSP00000392293:L64P;ENSP00000403207:L62P;ENSP00000361865:L196P	ENSP00000361865:L196P	L	-	2	0	PPT1	40327705	1.000000	0.71417	0.943000	0.38184	0.973000	0.67179	8.254000	0.89844	2.019000	0.59389	0.528000	0.53228	CTG	.	.		0.453	PPT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000013126.2	NM_000310	
SZT2	23334	hgsc.bcm.edu	37	1	43893038	43893038	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:43893038A>G	ENST00000562955.1	+	24	3349	c.3349A>G	c.(3349-3351)Agt>Ggt	p.S1117G	SZT2_ENST00000372442.1_Missense_Mutation_p.S275G	NM_015284.3	NP_056099.3	Q5T011	SZT2_HUMAN	seizure threshold 2 homolog (mouse)	1174					central nervous system development (GO:0007417)|corpus callosum morphogenesis (GO:0021540)|embryo development (GO:0009790)|pigmentation (GO:0043473)|post-embryonic development (GO:0009791)|regulation of superoxide dismutase activity (GO:1901668)	extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)				NS(2)|breast(9)|central_nervous_system(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(19)|lung(39)|ovary(4)|pancreas(3)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	113						TGGGGCTCCCAGTCTGAAAGA	0.567																																					p.S1117G		Atlas-SNP	.											.	SZT2	383	.	0			c.A3349G						.						63.0	65.0	64.0					1																	43893038		2203	4300	6503	SO:0001583	missense	23334	exon24			GCTCCCAGTCTGA	AB007936	CCDS30694.1, CCDS30694.2	1p34.2	2012-11-19	2011-06-10	2011-06-10	ENSG00000198198	ENSG00000198198			29040	protein-coding gene	gene with protein product	"""seizure threshold 2 homolog A (mouse)"", ""seizure threshold 2 homolog B (mouse)"""	615463	"""chromosome 1 open reading frame 84"", ""KIAA0467"""	C1orf84, KIAA0467		9455484	Standard	NM_015284		Approved	FLJ10387, SZT2B, RP11-506B15.1, FLJ34502, SZT2A	uc001cjk.3	Q5T011	OTTHUMG00000007423	ENST00000562955.1:c.3349A>G	chr1.hg19:g.43893038A>G	ENSP00000457168:p.Ser1117Gly	125.0	0.0		98.0	4.0	NM_015284	A0PJK5|A7E2X4|O75055|Q5JUY7|Q5T012|Q5XKC7|Q6ZNI8|Q6ZT24|Q7Z636|Q8NAY9|Q9H5H7|Q9UFQ8	Missense_Mutation	SNP	ENST00000562955.1	hg19	CCDS30694.2	.	.	.	.	.	.	.	.	.	.	A	10.96	1.499087	0.26861	.	.	ENSG00000198198	ENST00000372442	.	.	.	5.79	5.79	0.91817	.	0.505466	0.22867	N	0.054669	T	0.45094	0.1325	L	0.54323	1.7	0.09310	N	1	B	0.18741	0.03	B	0.21917	0.037	T	0.38757	-0.9646	9	0.44086	T	0.13	.	12.5272	0.56093	1.0:0.0:0.0:0.0	.	1117	Q5T011-5	.	G	275	.	ENSP00000361519:S275G	S	+	1	0	SZT2	43665625	0.254000	0.23992	0.063000	0.19743	0.295000	0.27426	1.297000	0.33400	2.207000	0.71202	0.533000	0.62120	AGT	.	.		0.567	SZT2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019517.3	NM_015284	
KIF2C	11004	hgsc.bcm.edu	37	1	45226265	45226265	+	Splice_Site	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:45226265A>G	ENST00000372224.4	+	16	1687	c.1574A>G	c.(1573-1575)gAg>gGg	p.E525G	RP11-269F19.2_ENST00000440985.1_RNA|RP11-269F19.2_ENST00000428791.1_RNA|KIF2C_ENST00000372222.3_Splice_Site_p.E412G|KIF2C_ENST00000372218.4_Splice_Site_p.E484G|KIF2C_ENST00000372217.1_Splice_Site_p.E471G	NM_006845.3	NP_006836.2	Q99661	KIF2C_HUMAN	kinesin family member 2C	525	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|establishment or maintenance of microtubule cytoskeleton polarity (GO:0030951)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|regulation of chromosome segregation (GO:0051983)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|centromeric DNA binding (GO:0019237)|microtubule motor activity (GO:0003777)|microtubule plus-end binding (GO:0051010)			breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(16)|ovary(1)|skin(1)|urinary_tract(1)	34	Acute lymphoblastic leukemia(166;0.155)					CCCCCACAGGAGTGCATCAGG	0.597																																					p.E525G		Atlas-SNP	.											.	KIF2C	68	.	0			c.A1574G						.						81.0	73.0	75.0					1																	45226265		2203	4300	6503	SO:0001630	splice_region_variant	11004	exon16			CACAGGAGTGCAT	U63743	CCDS512.1, CCDS72774.1	1p34.1	2014-01-21	2003-01-13	2003-01-17	ENSG00000142945	ENSG00000142945		"""Kinesins"""	6393	protein-coding gene	gene with protein product		604538	"""kinesin-like 6 (mitotic centromere-associated kinesin)"""	KNSL6		9434124	Standard	NM_006845		Approved	MCAK, CT139	uc001cmg.4	Q99661	OTTHUMG00000008416	ENST00000372224.4:c.1573-1A>G	chr1.hg19:g.45226265A>G		87.0	0.0		80.0	4.0	NM_006845	B3ITR9|Q5JR88|Q6ICU1|Q96C18|Q96HB8|Q9BWV8	Missense_Mutation	SNP	ENST00000372224.4	hg19	CCDS512.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	21.3|21.3	4.131478|4.131478	0.77549|0.77549	.|.	.|.	ENSG00000142945|ENSG00000142945	ENST00000372224;ENST00000372218;ENST00000372222;ENST00000372217|ENST00000423289	T;T;T;T|.	0.17370|.	2.28;2.28;2.28;2.28|.	5.66|5.66	5.66|5.66	0.87406|0.87406	Kinesin, motor domain (3);|.	0.118870|.	0.64402|.	D|.	0.000011|.	T|T	0.80417|0.80417	0.4619|0.4619	M|M	0.87617|0.87617	2.895|2.895	0.80722|0.80722	D|D	1|1	P;D;P|.	0.54772|.	0.949;0.968;0.949|.	D;P;D|.	0.66497|.	0.944;0.801;0.944|.	T|T	0.83227|0.83227	-0.0065|-0.0065	10|5	0.87932|.	D|.	0|.	.|.	16.1884|16.1884	0.81971|0.81971	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	484;471;525|.	B7Z6Q6;Q99661-2;Q99661|.	.;.;KIF2C_HUMAN|.	G|G	525;484;412;471|3	ENSP00000361298:E525G;ENSP00000361292:E484G;ENSP00000361296:E412G;ENSP00000361291:E471G|.	ENSP00000361291:E471G|.	E|S	+|+	2|1	0|0	KIF2C|KIF2C	44998852|44998852	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.495000|0.495000	0.33615|0.33615	9.267000|9.267000	0.95665|0.95665	2.285000|2.285000	0.76669|0.76669	0.528000|0.528000	0.53228|0.53228	GAG|AGT	.	.		0.597	KIF2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023180.1	NM_006845	Missense_Mutation
MAST2	23139	hgsc.bcm.edu	37	1	46290243	46290243	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:46290243T>C	ENST00000361297.2	+	2	599	c.316T>C	c.(316-318)Tct>Cct	p.S106P	MAST2_ENST00000372009.2_Missense_Mutation_p.S106P	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)					CCTGGCCAGCTCTCTATCGGG	0.368																																					p.S106P		Atlas-SNP	.											.	MAST2	136	.	0			c.T316C						.						145.0	130.0	135.0					1																	46290243		1851	4093	5944	SO:0001583	missense	23139	exon2			GCCAGCTCTCTAT	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.316T>C	chr1.hg19:g.46290243T>C	ENSP00000354671:p.Ser106Pro	165.0	0.0		95.0	4.0	NM_015112		Missense_Mutation	SNP	ENST00000361297.2	hg19	CCDS41326.1	.	.	.	.	.	.	.	.	.	.	T	15.60	2.882221	0.51908	.	.	ENSG00000086015	ENST00000361297;ENST00000372009	T;T	0.66099	-0.15;-0.19	5.39	4.2	0.49525	.	0.000000	0.45126	D	0.000394	T	0.56499	0.1989	L	0.38175	1.15	0.34464	D	0.702027	D;D	0.56035	0.974;0.974	P;P	0.45913	0.497;0.497	T	0.72040	-0.4410	10	0.66056	D	0.02	-0.4891	13.6487	0.62297	0.0:0.0:0.1375:0.8625	.	106;106	E7ERL6;Q6P0Q8	.;MAST2_HUMAN	P	106	ENSP00000354671:S106P;ENSP00000361079:S106P	ENSP00000354671:S106P	S	+	1	0	MAST2	46062830	1.000000	0.71417	0.993000	0.49108	0.934000	0.57294	3.754000	0.55189	2.048000	0.60808	0.533000	0.62120	TCT	.	.		0.368	MAST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021977.1	NM_015112	
PDE4B	5142	hgsc.bcm.edu	37	1	66458806	66458806	+	Intron	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:66458806T>C	ENST00000329654.4	+	3	468				PDE4B_ENST00000423207.2_Missense_Mutation_p.F73L|PDE4B_ENST00000371049.3_Intron	NM_001037341.1	NP_001032418.1	Q07343	PDE4B_HUMAN	phosphodiesterase 4B, cAMP-specific						cAMP catabolic process (GO:0006198)|cellular response to drug (GO:0035690)|cellular response to epinephrine stimulus (GO:0071872)|cellular response to lipopolysaccharide (GO:0071222)|leukocyte migration (GO:0050900)|negative regulation of relaxation of cardiac muscle (GO:1901898)|neutrophil chemotaxis (GO:0030593)|neutrophil homeostasis (GO:0001780)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-2 production (GO:0032743)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of high voltage-gated calcium channel activity (GO:1901841)|T cell receptor signaling pathway (GO:0050852)	cell periphery (GO:0071944)|cytosol (GO:0005829)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|Z disc (GO:0030018)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cAMP binding (GO:0030552)|ion channel binding (GO:0044325)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(14)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)	37					Adenosine monophosphate(DB00131)|Amrinone(DB01427)|Caffeine(DB00201)|Dyphylline(DB00651)|Enprofylline(DB00824)|Ibudilast(DB05266)|Iloprost(DB01088)|Ketotifen(DB00920)|Papaverine(DB01113)|Pentoxifylline(DB00806)|Roflumilast(DB01656)|Theobromine(DB01412)|Theophylline(DB00277)	GCGTCGTCGCTTCACTGTGGC	0.438																																					p.F73L		Atlas-SNP	.											.	PDE4B	231	.	0			c.T217C						.						68.0	64.0	66.0					1																	66458806		2203	4300	6503	SO:0001627	intron_variant	5142	exon1			CGTCGCTTCACTG	L20971	CCDS632.1, CCDS30742.1, CCDS30743.1, CCDS72802.1	1p31	2010-06-24	2010-06-24		ENSG00000184588	ENSG00000184588		"""Phosphodiesterases"""	8781	protein-coding gene	gene with protein product	"""phosphodiesterase E4 dunce homolog (Drosophila)"""	600127	"""phosphodiesterase 4B, cAMP-specific (dunce (Drosophila)-homolog phosphodiesterase E4)"", ""phosphodiesterase 4B, cAMP-specific (phosphodiesterase E4 dunce homolog, Drosophila)"""	DPDE4			Standard	XM_005270925		Approved		uc001dco.3	Q07343	OTTHUMG00000009088	ENST00000329654.4:c.281+74288T>C	chr1.hg19:g.66458806T>C		142.0	0.0		89.0	4.0	NM_001037340	A5YW33|O15443|Q13945|Q5TEK4|Q5TEK5|Q5TEK6	Missense_Mutation	SNP	ENST00000329654.4	hg19	CCDS632.1	.	.	.	.	.	.	.	.	.	.	T	14.81	2.646020	0.47258	.	.	ENSG00000184588	ENST00000423207	T	0.68025	-0.3	5.52	5.52	0.82312	.	.	.	.	.	T	0.67468	0.2896	M	0.61703	1.905	0.80722	D	1	P	0.49447	0.924	P	0.60682	0.878	T	0.65467	-0.6161	9	0.11182	T	0.66	.	15.8108	0.78561	0.0:0.0:0.0:1.0	.	78	Q59GM8	.	L	73	ENSP00000392947:F73L	ENSP00000392947:F73L	F	+	1	0	PDE4B	66231394	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.471000	0.80985	2.320000	0.78422	0.528000	0.53228	TTC	.	.		0.438	PDE4B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000025188.3	NM_002600	
PDE4B	5142	hgsc.bcm.edu	37	1	66831430	66831430	+	Silent	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:66831430T>C	ENST00000329654.4	+	13	1552	c.1365T>C	c.(1363-1365)aaT>aaC	p.N455N	PDE4B_ENST00000480109.2_Silent_p.N222N|PDE4B_ENST00000371045.5_Silent_p.N283N|PDE4B_ENST00000423207.2_Silent_p.N440N|PDE4B_ENST00000371049.3_Silent_p.N455N	NM_001037341.1	NP_001032418.1	Q07343	PDE4B_HUMAN	phosphodiesterase 4B, cAMP-specific	455					cAMP catabolic process (GO:0006198)|cellular response to drug (GO:0035690)|cellular response to epinephrine stimulus (GO:0071872)|cellular response to lipopolysaccharide (GO:0071222)|leukocyte migration (GO:0050900)|negative regulation of relaxation of cardiac muscle (GO:1901898)|neutrophil chemotaxis (GO:0030593)|neutrophil homeostasis (GO:0001780)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-2 production (GO:0032743)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of high voltage-gated calcium channel activity (GO:1901841)|T cell receptor signaling pathway (GO:0050852)	cell periphery (GO:0071944)|cytosol (GO:0005829)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|Z disc (GO:0030018)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cAMP binding (GO:0030552)|ion channel binding (GO:0044325)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(14)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)	37					Adenosine monophosphate(DB00131)|Amrinone(DB01427)|Caffeine(DB00201)|Dyphylline(DB00651)|Enprofylline(DB00824)|Ibudilast(DB05266)|Iloprost(DB01088)|Ketotifen(DB00920)|Papaverine(DB01113)|Pentoxifylline(DB00806)|Roflumilast(DB01656)|Theobromine(DB01412)|Theophylline(DB00277)	GAGTCTCCAATCAGTTTCTCA	0.413																																					p.N455N		Atlas-SNP	.											.	PDE4B	231	.	0			c.T1365C						.						105.0	98.0	100.0					1																	66831430		2203	4300	6503	SO:0001819	synonymous_variant	5142	exon13			CTCCAATCAGTTT	L20971	CCDS632.1, CCDS30742.1, CCDS30743.1, CCDS72802.1	1p31	2010-06-24	2010-06-24		ENSG00000184588	ENSG00000184588		"""Phosphodiesterases"""	8781	protein-coding gene	gene with protein product	"""phosphodiesterase E4 dunce homolog (Drosophila)"""	600127	"""phosphodiesterase 4B, cAMP-specific (dunce (Drosophila)-homolog phosphodiesterase E4)"", ""phosphodiesterase 4B, cAMP-specific (phosphodiesterase E4 dunce homolog, Drosophila)"""	DPDE4			Standard	XM_005270925		Approved		uc001dco.3	Q07343	OTTHUMG00000009088	ENST00000329654.4:c.1365T>C	chr1.hg19:g.66831430T>C		106.0	0.0		96.0	5.0	NM_001037341	A5YW33|O15443|Q13945|Q5TEK4|Q5TEK5|Q5TEK6	Silent	SNP	ENST00000329654.4	hg19	CCDS632.1																																																																																			.	.		0.413	PDE4B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000025188.3	NM_002600	
TCTEX1D1	200132	hgsc.bcm.edu	37	1	67236141	67236141	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:67236141T>C	ENST00000282670.2	+	3	319	c.191T>C	c.(190-192)aTg>aCg	p.M64T	TCTEX1D1_ENST00000491611.1_3'UTR	NM_152665.2	NP_689878.2	Q8N7M0	TC1D1_HUMAN	Tctex1 domain containing 1	64										large_intestine(2)|lung(10)|skin(1)	13						ACAGTTCAGATGGAAAACACC	0.348																																					p.M64T		Atlas-SNP	.											.	TCTEX1D1	27	.	0			c.T191C						.						186.0	179.0	182.0					1																	67236141		2203	4300	6503	SO:0001583	missense	200132	exon3			TTCAGATGGAAAA	AK098192	CCDS633.1	1p31.2	2008-02-05			ENSG00000152760	ENSG00000152760			26882	protein-coding gene	gene with protein product							Standard	NM_152665		Approved	FLJ40873	uc001dcv.3	Q8N7M0	OTTHUMG00000009162	ENST00000282670.2:c.191T>C	chr1.hg19:g.67236141T>C	ENSP00000282670:p.Met64Thr	111.0	0.0		97.0	4.0	NM_152665	Q06YR9|Q5VYE1	Missense_Mutation	SNP	ENST00000282670.2	hg19	CCDS633.1	.	.	.	.	.	.	.	.	.	.	T	16.75	3.210431	0.58343	.	.	ENSG00000152760	ENST00000282670	T	0.14516	2.5	6.06	6.06	0.98353	.	0.120357	0.85682	D	0.000000	T	0.08802	0.0218	M	0.70275	2.135	0.58432	D	0.999999	P	0.36683	0.565	B	0.29440	0.102	T	0.05162	-1.0902	10	0.33141	T	0.24	0.0027	15.6071	0.76682	0.0:0.0:0.0:1.0	.	64	Q8N7M0	TC1D1_HUMAN	T	64	ENSP00000282670:M64T	ENSP00000282670:M64T	M	+	2	0	TCTEX1D1	67008729	1.000000	0.71417	1.000000	0.80357	0.911000	0.54048	6.361000	0.73070	2.323000	0.78572	0.528000	0.53228	ATG	.	.		0.348	TCTEX1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025399.2	NM_152665	
SYDE2	84144	hgsc.bcm.edu	37	1	85648623	85648623	+	Missense_Mutation	SNP	C	C	T			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:85648623C>T	ENST00000341460.5	-	3	1751	c.1702G>A	c.(1702-1704)Gaa>Aaa	p.E568K		NM_032184.1	NP_115560.1	Q5VT97	SYDE2_HUMAN	synapse defective 1, Rho GTPase, homolog 2 (C. elegans)	568					activation of Rho GTPase activity (GO:0032862)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho GTPase activator activity (GO:0005100)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|ovary(1)	20				all cancers(265;0.0126)|Epithelial(280;0.0336)		TGATGAACTTCTCGGCAGTTA	0.403																																					p.E568K		Atlas-SNP	.											.	SYDE2	135	.	0			c.G1702A						.						165.0	162.0	163.0					1																	85648623		1843	4098	5941	SO:0001583	missense	84144	exon3			GAACTTCTCGGCA	AL834286	CCDS44169.1	1p22.3	2008-02-05		2005-08-09	ENSG00000097096	ENSG00000097096			25841	protein-coding gene	gene with protein product							Standard	NM_032184		Approved	FLJ13815	uc009wcm.3	Q5VT97	OTTHUMG00000009956	ENST00000341460.5:c.1702G>A	chr1.hg19:g.85648623C>T	ENSP00000340594:p.Glu568Lys	183.0	0.0		122.0	5.0	NM_032184	Q5VT96|Q8NDB8|Q9H8A6	Missense_Mutation	SNP	ENST00000341460.5	hg19	CCDS44169.1	.	.	.	.	.	.	.	.	.	.	C	11.51	1.660920	0.29515	.	.	ENSG00000097096	ENST00000341460	T	0.08984	3.03	5.41	4.5	0.54988	.	0.288725	0.37136	N	0.002222	T	0.03477	0.0100	L	0.51422	1.61	0.23016	N	0.998423	B;B	0.33379	0.41;0.002	B;B	0.26614	0.071;0.005	T	0.19484	-1.0304	10	0.52906	T	0.07	.	13.9668	0.64213	0.0:0.9269:0.0:0.0731	.	568;568	Q5VT97;Q5VT97-2	SYDE2_HUMAN;.	K	568	ENSP00000340594:E568K	ENSP00000340594:E568K	E	-	1	0	SYDE2	85421211	0.979000	0.34478	0.985000	0.45067	0.416000	0.31233	2.532000	0.45659	1.306000	0.44926	0.650000	0.86243	GAA	.	.		0.403	SYDE2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127989.2		
PALMD	54873	hgsc.bcm.edu	37	1	100154982	100154982	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:100154982A>G	ENST00000263174.4	+	7	1541	c.1166A>G	c.(1165-1167)cAg>cGg	p.Q389R	PALMD_ENST00000605497.1_Missense_Mutation_p.Q389R	NM_017734.4	NP_060204.1	Q9NP74	PALMD_HUMAN	palmdelphin	389					regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|membrane (GO:0016020)				central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(8)|ovary(6)|pancreas(1)|prostate(2)	31		all_epithelial(167;0.000813)|all_lung(203;0.0214)|Lung NSC(277;0.0216)		Epithelial(280;0.067)|all cancers(265;0.117)|COAD - Colon adenocarcinoma(174;0.142)|Lung(183;0.201)		CCCACTTGTCAGGAGGACGAG	0.463																																					p.Q389R		Atlas-SNP	.											PALMD,colon,carcinoma,0,1	PALMD	64	.	0			c.A1166G						.						57.0	49.0	52.0					1																	100154982		2203	4299	6502	SO:0001583	missense	54873	exon7			CTTGTCAGGAGGA	AJ312214	CCDS758.1	1p22-p21	2008-07-18			ENSG00000099260	ENSG00000099260			15846	protein-coding gene	gene with protein product		610182		C1orf11		11478809	Standard	NM_017734		Approved	FLJ20271, PALML	uc001dsg.3	Q9NP74	OTTHUMG00000010764	ENST00000263174.4:c.1166A>G	chr1.hg19:g.100154982A>G	ENSP00000263174:p.Gln389Arg	181.0	0.0		120.0	5.0	NM_017734	Q9H7E6|Q9NPM5|Q9NPM6|Q9NPS0	Missense_Mutation	SNP	ENST00000263174.4	hg19	CCDS758.1	.	.	.	.	.	.	.	.	.	.	A	5.924	0.354610	0.11239	.	.	ENSG00000099260	ENST00000263174	T	0.18016	2.24	5.56	4.44	0.53790	.	0.803312	0.11781	N	0.530179	T	0.05090	0.0136	M	0.63428	1.95	0.26273	N	0.978398	B;P	0.41848	0.351;0.763	B;B	0.35182	0.197;0.165	T	0.38156	-0.9674	10	0.27082	T	0.32	-6.4421	2.0465	0.03561	0.5408:0.1453:0.0783:0.2356	.	389;309	Q9NP74;Q9NP74-2	PALMD_HUMAN;.	R	389	ENSP00000263174:Q389R	ENSP00000263174:Q389R	Q	+	2	0	PALMD	99927570	0.174000	0.23070	0.998000	0.56505	0.299000	0.27559	0.882000	0.28186	0.946000	0.37632	0.460000	0.39030	CAG	.	.		0.463	PALMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029672.1	NM_017734	
AKNAD1	254268	hgsc.bcm.edu	37	1	109369920	109369920	+	Missense_Mutation	SNP	G	G	T			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:109369920G>T	ENST00000370001.3	-	11	2111	c.1843C>A	c.(1843-1845)Caa>Aaa	p.Q615K	AKNAD1_ENST00000369995.3_Missense_Mutation_p.Q615K|AKNAD1_ENST00000369994.1_Missense_Mutation_p.Q585K|AKNAD1_ENST00000357393.4_Missense_Mutation_p.Q322K	NM_152763.4	NP_689976.2	Q5T1N1	AKND1_HUMAN	AKNA domain containing 1	615						cytoplasm (GO:0005737)				breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(10)|ovary(3)|prostate(6)|skin(3)|stomach(2)	32						TCCACGTTTTGCTTCCTAAAA	0.363																																					p.Q615K		Atlas-SNP	.											.	AKNAD1	83	.	0			c.C1843A						.						144.0	149.0	148.0					1																	109369920		2203	4299	6502	SO:0001583	missense	254268	exon11			CGTTTTGCTTCCT	AK095517	CCDS791.2	1p13.3	2009-10-29	2009-10-29	2009-10-29	ENSG00000162641	ENSG00000162641			28398	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 62"""	C1orf62			Standard	NM_152763		Approved	MGC26989	uc001dwa.4	Q5T1N1	OTTHUMG00000011231	ENST00000370001.3:c.1843C>A	chr1.hg19:g.109369920G>T	ENSP00000359018:p.Gln615Lys	70.0	0.0		61.0	4.0	NM_152763	B9EK62|Q5T1N0|Q8N990|Q8NCN9	Missense_Mutation	SNP	ENST00000370001.3	hg19	CCDS791.2	.	.	.	.	.	.	.	.	.	.	G	10.91	1.483286	0.26598	.	.	ENSG00000162641	ENST00000370001;ENST00000357393;ENST00000369994;ENST00000369995	T;T;T;T	0.20069	2.1;2.1;2.1;2.1	5.0	3.12	0.35913	.	0.665053	0.13262	N	0.401240	T	0.07098	0.0180	L	0.46157	1.445	0.09310	N	1	B;B	0.26635	0.155;0.084	B;B	0.22386	0.039;0.039	T	0.27297	-1.0078	10	0.52906	T	0.07	-2.3218	6.9745	0.24666	0.0941:0.1884:0.7175:0.0	.	322;615	B4DET8;Q5T1N1	.;AKND1_HUMAN	K	615;322;585;615	ENSP00000359018:Q615K;ENSP00000349968:Q322K;ENSP00000359011:Q585K;ENSP00000359012:Q615K	ENSP00000349968:Q322K	Q	-	1	0	AKNAD1	109171443	1.000000	0.71417	0.170000	0.22879	0.000000	0.00434	2.655000	0.46707	0.807000	0.34208	-0.258000	0.10820	CAA	.	.		0.363	AKNAD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030923.2	NM_152763	
DDX20	11218	hgsc.bcm.edu	37	1	112305374	112305374	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:112305374A>G	ENST00000369702.4	+	9	1800	c.1180A>G	c.(1180-1182)Atg>Gtg	p.M394V	DDX20_ENST00000475700.1_5'UTR|DDX20_ENST00000536167.1_3'UTR	NM_007204.4	NP_009135.4	Q9UHI6	DDX20_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 20	394	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP catabolic process (GO:0006200)|gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|oogenesis (GO:0048477)|positive regulation of apoptotic process (GO:0043065)|regulation of steroid biosynthetic process (GO:0050810)|RNA metabolic process (GO:0016070)|RNA processing (GO:0006396)|spliceosomal snRNP assembly (GO:0000387)|spliceosomal tri-snRNP complex assembly (GO:0000244)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)|transcriptional repressor complex (GO:0017053)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|DNA binding (GO:0003677)			endometrium(3)|kidney(7)|large_intestine(6)|lung(3)|pancreas(1)|prostate(1)	21		all_cancers(81;1.06e-05)|all_epithelial(167;7.36e-06)|all_lung(203;2.44e-05)|Lung NSC(69;4.15e-05)		Lung(183;0.0234)|Colorectal(144;0.0282)|all cancers(265;0.0614)|Epithelial(280;0.0999)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		GGAGACATACATGCATCGGAT	0.403																																					p.M394V		Atlas-SNP	.											.	DDX20	50	.	0			c.A1180G						.						160.0	159.0	159.0					1																	112305374		2203	4300	6503	SO:0001583	missense	11218	exon9			ACATACATGCATC	AF106019	CCDS842.1	1p21.1-p13.2	2008-02-05	2003-06-13		ENSG00000064703	ENSG00000064703		"""DEAD-boxes"""	2743	protein-coding gene	gene with protein product		606168	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 20, 103kD"""			10383418	Standard	NM_007204		Approved	DP103, GEMIN3	uc001ebs.3	Q9UHI6	OTTHUMG00000011956	ENST00000369702.4:c.1180A>G	chr1.hg19:g.112305374A>G	ENSP00000358716:p.Met394Val	103.0	0.0		79.0	4.0	NM_007204	B4DWV7|Q96F72|Q9NVM3|Q9UF59|Q9UIY0|Q9Y659	Missense_Mutation	SNP	ENST00000369702.4	hg19	CCDS842.1	.	.	.	.	.	.	.	.	.	.	A	20.3	3.975185	0.74360	.	.	ENSG00000064703	ENST00000369702	T	0.73681	-0.77	5.64	5.64	0.86602	Helicase, C-terminal (3);	0.037568	0.85682	D	0.000000	T	0.41465	0.1160	N	0.00471	-1.455	0.80722	D	1	B	0.29766	0.256	B	0.42112	0.376	T	0.64453	-0.6404	10	0.87932	D	0	-24.0728	15.5302	0.75952	1.0:0.0:0.0:0.0	.	394	Q9UHI6	DDX20_HUMAN	V	394	ENSP00000358716:M394V	ENSP00000358716:M394V	M	+	1	0	DDX20	112106897	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	7.154000	0.77437	2.145000	0.66743	0.533000	0.62120	ATG	.	.		0.403	DDX20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033063.2	NM_007204	
NBPF7	343505	hgsc.bcm.edu	37	1	120378829	120378829	+	IGR	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:120378829T>C								REG4 (24546 upstream) : ADAM30 (57326 downstream)																							CTCCTGCAGCTTCCTGATGAG	0.493																																					p.K306R		Atlas-SNP	.											.	NBPF7	46	.	0			c.A917G						.						46.0	47.0	46.0					1																	120378829		1970	4183	6153	SO:0001628	intergenic_variant	343505	exon7			TGCAGCTTCCTGA																													chr1.hg19:g.120378829T>C		106.0	0.0		81.0	4.0	NM_001047980		Missense_Mutation	SNP		hg19																																																																																				.	.	0	0.493								
HIST2H2AC	8338	hgsc.bcm.edu	37	1	149858905	149858905	+	Silent	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:149858905A>G	ENST00000331380.2	+	1	381	c.381A>G	c.(379-381)aaA>aaG	p.K127K	BOLA1_ENST00000369153.2_5'Flank|HIST2H2BE_ENST00000369155.2_5'Flank	NM_003517.2	NP_003508.1	Q16777	H2A2C_HUMAN	histone cluster 2, H2ac	127						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|breast(3)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(11)|ovary(1)|skin(1)	20	Breast(34;0.0124)|all_hematologic(923;0.127)		STAD - Stomach adenocarcinoma(528;0.133)|LUSC - Lung squamous cell carcinoma(543;0.221)			ACAAAGCCAAAAGCAAATAAA	0.463																																					p.K127K		Atlas-SNP	.											.	HIST2H2AC	75	.	0			c.A381G						.						67.0	71.0	70.0					1																	149858905		2203	4300	6503	SO:0001819	synonymous_variant	8338	exon1			AGCCAAAAGCAAA	AY131973	CCDS937.1	1q21.2	2011-01-27	2006-10-11	2003-02-21	ENSG00000184260	ENSG00000184260		"""Histones / Replication-dependent"""	4738	protein-coding gene	gene with protein product		602797	"""H2A histone family, member Q"", ""histone 2, H2ac"""	H2A, H2AFQ		1469070, 9439656, 12408966	Standard	NM_003517		Approved	H2A/q	uc001etd.3	Q16777	OTTHUMG00000035825	ENST00000331380.2:c.381A>G	chr1.hg19:g.149858905A>G		281.0	0.0		394.0	78.0	NM_003517	Q6DRA7|Q8IUE5	Silent	SNP	ENST00000331380.2	hg19	CCDS937.1																																																																																			.	.		0.463	HIST2H2AC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087128.1	NM_003517	
OTUD7B	56957	hgsc.bcm.edu	37	1	149936173	149936173	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:149936173A>G	ENST00000369135.4	-	6	1000	c.706T>C	c.(706-708)Tgg>Cgg	p.W236R	OTUD7B_ENST00000479905.1_5'UTR	NM_020205.2	NP_064590.2	Q6GQQ9	OTU7B_HUMAN	OTU deubiquitinase 7B	236	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)			GTCTGCTGCCACCTCCAGCGC	0.532																																					p.W236R		Atlas-SNP	.											.	OTUD7B	76	.	0			c.T706C						.						108.0	119.0	115.0					1																	149936173		2108	4247	6355	SO:0001583	missense	56957	exon6			GCTGCCACCTCCA	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.706T>C	chr1.hg19:g.149936173A>G	ENSP00000358131:p.Trp236Arg	70.0	0.0		94.0	4.0	NM_020205	B7Z643|D3DUZ8|Q5SZ60|Q8WWA7|Q9NQ53|Q9UFF4	Missense_Mutation	SNP	ENST00000369135.4	hg19	CCDS41389.1	.	.	.	.	.	.	.	.	.	.	A	19.56	3.850341	0.71719	.	.	ENSG00000163113	ENST00000369135;ENST00000543330;ENST00000417191	T;T	0.33438	1.41;1.5	4.87	4.87	0.63330	Ovarian tumour, otubain (2);	0.119404	0.64402	D	0.000009	T	0.39036	0.1063	L	0.56340	1.77	0.80722	D	1	D;D	0.76494	0.999;0.994	D;D	0.72982	0.979;0.968	T	0.13442	-1.0509	9	.	.	.	-8.913	13.7243	0.62748	1.0:0.0:0.0:0.0	.	236;236	B7Z643;Q6GQQ9	.;OTU7B_HUMAN	R	236	ENSP00000358131:W236R;ENSP00000408231:W236R	.	W	-	1	0	OTUD7B	148202797	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	8.654000	0.91092	2.178000	0.69098	0.533000	0.62120	TGG	.	.		0.532	OTUD7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034146.3	NM_020205	
MEF2D	4209	hgsc.bcm.edu	37	1	156446904	156446904	+	Missense_Mutation	SNP	G	G	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:156446904G>C	ENST00000348159.4	-	7	1235	c.755C>G	c.(754-756)cCa>cGa	p.P252R	MEF2D_ENST00000353795.3_Missense_Mutation_p.P206R|MEF2D_ENST00000340875.5_Missense_Mutation_p.P251R|MEF2D_ENST00000360595.3_Missense_Mutation_p.P252R|MEF2D_ENST00000368240.2_Missense_Mutation_p.P252R|MEF2D_ENST00000464356.2_Missense_Mutation_p.P251R	NM_005920.2	NP_005911.1	Q14814	MEF2D_HUMAN	myocyte enhancer factor 2D	252	Poly-Pro.				adult heart development (GO:0007512)|apoptotic process (GO:0006915)|chondrocyte differentiation (GO:0002062)|endochondral ossification (GO:0001958)|muscle organ development (GO:0007517)|nervous system development (GO:0007399)|osteoblast differentiation (GO:0001649)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal muscle cell differentiation (GO:0035914)|transcription from RNA polymerase II promoter (GO:0006366)	intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	activating transcription factor binding (GO:0033613)|histone deacetylase binding (GO:0042826)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(4)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|urinary_tract(1)	15	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					AGGTGGGGGTGGAGACTTGGC	0.607																																					p.P252R		Atlas-SNP	.											MEF2D,colon,adenoma,0,1	MEF2D	43	.	0			c.C755G						.						83.0	76.0	78.0					1																	156446904		2203	4300	6503	SO:0001583	missense	4209	exon7			GGGGGTGGAGACT	BC054520	CCDS1143.1, CCDS60304.1	1q12-q23	2008-02-05	2007-04-24		ENSG00000116604	ENSG00000116604		"""Myocyte enhancer factors"""	6997	protein-coding gene	gene with protein product		600663				8269842	Standard	NM_005920		Approved		uc001fpb.4	Q14814	OTTHUMG00000033095	ENST00000348159.4:c.755C>G	chr1.hg19:g.156446904G>C	ENSP00000271555:p.Pro252Arg	185.0	0.0		351.0	0.0	NM_005920	D3DVC0|Q14815|Q5T9U5|Q5T9U6	Missense_Mutation	SNP	ENST00000348159.4	hg19	CCDS1143.1	.	.	.	.	.	.	.	.	.	.	G	29.4	5.004510	0.93287	.	.	ENSG00000116604	ENST00000348159;ENST00000340875;ENST00000368240;ENST00000353795;ENST00000360595;ENST00000454816	T;T;T;T;T;T	0.34667	1.35;1.35;1.35;1.35;1.35;1.35	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	T	0.57227	0.2039	M	0.81497	2.545	0.80722	D	1	D;D;D	0.76494	0.999;0.997;0.995	D;D;D	0.71870	0.968;0.909;0.975	T	0.61941	-0.6959	10	0.72032	D	0.01	-12.8772	18.1525	0.89678	0.0:0.0:1.0:0.0	.	257;252;252	Q4LE66;Q14814;Q14814-4	.;MEF2D_HUMAN;.	R	252;251;252;206;252;251	ENSP00000271555:P252R;ENSP00000343159:P251R;ENSP00000357223:P252R;ENSP00000344705:P206R;ENSP00000353803:P252R;ENSP00000388505:P251R	ENSP00000343159:P251R	P	-	2	0	MEF2D	154713528	1.000000	0.71417	0.994000	0.49952	0.982000	0.71751	9.238000	0.95380	2.626000	0.88956	0.655000	0.94253	CCA	.	.		0.607	MEF2D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080562.2	NM_005920	
METTL18	92342	hgsc.bcm.edu	37	1	169762228	169762228	+	Silent	SNP	T	T	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:169762228T>G	ENST00000310392.4	-	2	962	c.609A>C	c.(607-609)atA>atC	p.I203I	METTL18_ENST00000303469.2_Silent_p.I203I|C1orf112_ENST00000359326.4_5'Flank|C1orf112_ENST00000286031.6_5'Flank|C1orf112_ENST00000456684.1_5'Flank|C1orf112_ENST00000413811.2_5'Flank|C1orf112_ENST00000498289.1_Intron	NM_033418.2	NP_219486.1	O95568	MET18_HUMAN	methyltransferase like 18	203						cytoplasm (GO:0005737)	protein methyltransferase activity (GO:0008276)			kidney(1)|large_intestine(3)|lung(4)	8						TGAATGCAGTTATACCTAGTA	0.383																																					p.I203I		Atlas-SNP	.											.	METTL18	23	.	0			c.A609C						.						126.0	129.0	128.0					1																	169762228		2203	4299	6502	SO:0001819	synonymous_variant	92342	exon2			TGCAGTTATACCT	AL035369	CCDS1284.1	1q24.2	2013-10-11	2011-03-02	2011-03-02	ENSG00000171806	ENSG00000171806			28793	protein-coding gene	gene with protein product	"""histidine protein methyltransferase 1"""	615255	"""chromosome 1 open reading frame 156"""	C1orf156		20864530	Standard	NM_033418		Approved	MGC9084, AsTP2, HPM1	uc001ggn.4	O95568	OTTHUMG00000035813	ENST00000310392.4:c.609A>C	chr1.hg19:g.169762228T>G		208.0	0.0		291.0	54.0	NM_033418	B2R9T5	Silent	SNP	ENST00000310392.4	hg19	CCDS1284.1																																																																																			.	.		0.383	METTL18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087109.1	NM_033418	
RGSL1	353299	hgsc.bcm.edu	37	1	182442764	182442764	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:182442764A>G	ENST00000294854.8	+	6	538	c.518A>G	c.(517-519)gAg>gGg	p.E173G	RGSL1_ENST00000542961.1_Missense_Mutation_p.E208G	NM_001137669.1	NP_001131141.1	A5PLK6	RGSL_HUMAN	regulator of G-protein signaling like 1	173					termination of G-protein coupled receptor signaling pathway (GO:0038032)	integral component of membrane (GO:0016021)				central_nervous_system(2)|skin(4)	6						ACTAGGAGGGAGATCCTGAGC	0.483																																					p.E173G	Ovarian(71;11 616 11292 12944 18021 32289 33994 41738 46526)	Atlas-SNP	.											.	RGSL1	111	.	0			c.A518G						.						98.0	78.0	84.0					1																	182442764		692	1591	2283	SO:0001583	missense	353299	exon6			GGAGGGAGATCCT	AF510428	CCDS58049.1	1q25	2013-04-02	2007-08-14		ENSG00000121446	ENSG00000121446			18636	protein-coding gene	gene with protein product		611012	"""regulator of G-protein signalling like 1"", ""regulator of G-protein signaling like 2"", ""regulator of G-protein signalling like 2"""	RGSL2		12801632	Standard	NM_001137669		Approved		uc009wxw.3	A5PLK6	OTTHUMG00000035217	ENST00000294854.8:c.518A>G	chr1.hg19:g.182442764A>G	ENSP00000457748:p.Glu173Gly	146.0	0.0		177.0	8.0	NM_001137669	A2A2Z0|A6PVM2|A6PVM3|Q0VAJ4|Q0VAJ5|Q6ZRL0|Q86UV0|Q9H084	Missense_Mutation	SNP	ENST00000294854.8	hg19	CCDS58049.1																																																																																			.	.		0.483	RGSL1-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320710.3	NM_181572	
ASPM	259266	hgsc.bcm.edu	37	1	197056087	197056087	+	Missense_Mutation	SNP	A	A	G	rs200083138		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:197056087A>G	ENST00000367409.4	-	27	10433	c.10177T>C	c.(10177-10179)Tcc>Ccc	p.S3393P	ASPM_ENST00000367408.1_Missense_Mutation_p.S1058P|ASPM_ENST00000294732.7_Missense_Mutation_p.S1808P	NM_018136.4	NP_060606.3	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle) homolog, microcephaly associated (Drosophila)	3393					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						ACAACTTTGGACCTACTTCGT	0.269																																					p.S3393P		Atlas-SNP	.											ASPM,caecum,carcinoma,0,1	ASPM	444	.	0			c.T10177C						.						63.0	63.0	63.0					1																	197056087		2203	4297	6500	SO:0001583	missense	259266	exon27			CTTTGGACCTACT	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.10177T>C	chr1.hg19:g.197056087A>G	ENSP00000356379:p.Ser3393Pro	82.0	0.0		100.0	4.0	NM_018136	Q4G1H1|Q5VYL3|Q86UX4|Q8IUL2|Q8IZJ7|Q8IZJ8|Q8IZJ9|Q8N4D1|Q9NVS1|Q9NVT6	Missense_Mutation	SNP	ENST00000367409.4	hg19	CCDS1389.1	.	.	.	.	.	.	.	.	.	.	A	13.40	2.226779	0.39399	.	.	ENSG00000066279	ENST00000367409;ENST00000294732;ENST00000367408	T;T;T	0.56103	0.48;1.73;1.41	5.76	0.131	0.14755	.	0.110888	0.64402	N	0.000008	T	0.22322	0.0538	N	0.03608	-0.345	0.23425	N	0.997702	B;B	0.12630	0.001;0.006	B;B	0.12837	0.002;0.008	T	0.11941	-1.0567	10	0.30078	T	0.28	.	5.2057	0.15289	0.3084:0.1907:0.5009:0.0	.	1808;3393	Q4G1H1;Q8IZT6	.;ASPM_HUMAN	P	3393;1808;1058	ENSP00000356379:S3393P;ENSP00000294732:S1808P;ENSP00000356378:S1058P	ENSP00000294732:S1808P	S	-	1	0	ASPM	195322710	0.643000	0.27269	0.954000	0.39281	0.607000	0.37147	0.998000	0.29744	0.041000	0.15688	0.533000	0.62120	TCC	.	A|1.000;C|0.000		0.269	ASPM-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000088256.1	NM_018136	
DSTYK	25778	hgsc.bcm.edu	37	1	205180473	205180473	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:205180473A>G	ENST00000367162.3	-	1	221	c.191T>C	c.(190-192)cTc>cCc	p.L64P	DSTYK_ENST00000367160.4_Missense_Mutation_p.L64P|DSTYK_ENST00000367161.3_Missense_Mutation_p.L64P	NM_015375.2	NP_056190.1	Q6XUX3	DUSTY_HUMAN	dual serine/threonine and tyrosine protein kinase	64					cellular response to fibroblast growth factor stimulus (GO:0044344)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of kinase activity (GO:0033674)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)	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)			breast(2)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)|skin(2)	14						GAGGGAGGAGAGACAAGTGTG	0.692																																					p.L64P		Atlas-SNP	.											.	DSTYK	87	.	0			c.T191C						.						28.0	26.0	27.0					1																	205180473		2202	4300	6502	SO:0001583	missense	25778	exon1			GAGGAGAGACAAG	AF068286	CCDS1451.1, CCDS1452.1	1q32	2008-12-18	2008-12-18	2008-12-18	ENSG00000133059	ENSG00000133059			29043	protein-coding gene	gene with protein product		612666	"""receptor interacting protein kinase 5"""	RIPK5		15178406	Standard	NM_015375		Approved	KIAA0472, DustyPK, RIP5	uc001hbw.3	Q6XUX3	OTTHUMG00000037102	ENST00000367162.3:c.191T>C	chr1.hg19:g.205180473A>G	ENSP00000356130:p.Leu64Pro	67.0	0.0		54.0	4.0	NM_199462	B7ZL64|O75060|Q17R94|Q5RKT0|Q6IN87|Q6P997|Q86Y03|Q9P1S5	Missense_Mutation	SNP	ENST00000367162.3	hg19	CCDS1451.1	.	.	.	.	.	.	.	.	.	.	A	0.965	-0.702055	0.03255	.	.	ENSG00000133059	ENST00000367160;ENST00000367161;ENST00000367162	T;T;T	0.78126	-0.66;-1.08;-1.15	4.42	3.51	0.40186	.	0.329127	0.25887	N	0.027644	T	0.43277	0.1240	N	0.00707	-1.245	0.40637	D	0.981912	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.28839	-1.0031	10	0.18276	T	0.48	-6.8449	8.2263	0.31570	0.1914:0.0:0.8086:0.0	.	64;64	Q6XUX3-2;Q6XUX3	.;DUSTY_HUMAN	P	64	ENSP00000356128:L64P;ENSP00000356129:L64P;ENSP00000356130:L64P	ENSP00000356128:L64P	L	-	2	0	DSTYK	203447096	0.995000	0.38212	0.982000	0.44146	0.567000	0.35839	1.630000	0.37081	1.094000	0.41399	-0.232000	0.12228	CTC	.	.		0.692	DSTYK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090345.1	NM_015375	
FLVCR1	28982	hgsc.bcm.edu	37	1	213068596	213068596	+	Silent	SNP	G	G	T			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:213068596G>T	ENST00000366971.4	+	10	1830	c.1632G>T	c.(1630-1632)acG>acT	p.T544T	FLVCR1_ENST00000483790.1_3'UTR	NM_014053.3	NP_054772.1	Q9Y5Y0	FLVC1_HUMAN	feline leukemia virus subgroup C cellular receptor 1	544			T -> M (in dbSNP:rs3207090). {ECO:0000269|PubMed:15489334}.		blood vessel development (GO:0001568)|cell death (GO:0008219)|cellular iron ion homeostasis (GO:0006879)|embryonic digit morphogenesis (GO:0042733)|embryonic skeletal system morphogenesis (GO:0048704)|erythrocyte differentiation (GO:0030218)|erythrocyte maturation (GO:0043249)|head morphogenesis (GO:0060323)|heme export (GO:0097037)|heme transport (GO:0015886)|in utero embryonic development (GO:0001701)|mitochondrial transport (GO:0006839)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|regulation of organ growth (GO:0046620)|spleen development (GO:0048536)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	heme transporter activity (GO:0015232)|transporter activity (GO:0005215)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(1)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(2)	12				OV - Ovarian serous cystadenocarcinoma(81;0.00733)|all cancers(67;0.013)|GBM - Glioblastoma multiforme(131;0.0845)|Epithelial(68;0.11)		AACCAAAAACGGTTATGTTGT	0.383																																					p.T544T	Esophageal Squamous(199;2235 2952 19233 26256)	Atlas-SNP	.											FLVCR1,rectum,carcinoma,+1,1	FLVCR1	31	.	0			c.G1632T						.						119.0	109.0	113.0					1																	213068596		2203	4300	6503	SO:0001819	synonymous_variant	28982	exon10			AAAAACGGTTATG	AF118637	CCDS1510.1	1q32.3	2014-05-30			ENSG00000162769	ENSG00000162769		"""Solute carriers"""	24682	protein-coding gene	gene with protein product		609144	"""ataxia, posterior column 1, with retinitis pigmentosa"""	AXPC1		10400745, 10648427, 21070897	Standard	NM_014053		Approved	FLVCR, MFSD7B, PCA	uc001hjt.3	Q9Y5Y0	OTTHUMG00000036924	ENST00000366971.4:c.1632G>T	chr1.hg19:g.213068596G>T		216.0	0.0		246.0	0.0	NM_014053	Q1HE16|Q86XY9|Q9NVR9	Silent	SNP	ENST00000366971.4	hg19	CCDS1510.1	.	.	.	.	.	.	.	.	.	.	G	0.014	-1.571189	0.00895	.	.	ENSG00000162769	ENST00000419102	.	.	.	4.7	-9.39	0.00619	.	.	.	.	.	T	0.14270	0.0345	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.13335	-1.0513	4	.	.	.	-16.4378	0.9914	0.01458	0.4041:0.1528:0.2673:0.1757	.	.	.	.	L	343	.	.	R	+	2	0	FLVCR1	211135219	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	-2.028000	0.01431	-2.726000	0.00386	-2.213000	0.00299	CGG	.	.		0.383	FLVCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089678.2	NM_014053	
KCNK2	3776	hgsc.bcm.edu	37	1	215297991	215297991	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:215297991A>G	ENST00000444842.2	+	3	523	c.373A>G	c.(373-375)Ata>Gta	p.I125V	KCNK2_ENST00000391895.2_Missense_Mutation_p.I121V|KCNK2_ENST00000391894.2_Missense_Mutation_p.I110V	NM_001017425.2|NM_014217.3	NP_001017425.2|NP_055032.1	O95069	KCNK2_HUMAN	potassium channel, subfamily K, member 2	125					G-protein coupled receptor signaling pathway (GO:0007186)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	endoplasmic reticulum (GO:0005783)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	outward rectifier potassium channel activity (GO:0015271)|potassium channel inhibitor activity (GO:0019870)|potassium ion leak channel activity (GO:0022841)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(15)|upper_aerodigestive_tract(1)	30				OV - Ovarian serous cystadenocarcinoma(81;0.0399)|all cancers(67;0.0556)|GBM - Glioblastoma multiforme(131;0.068)	Dofetilide(DB00204)|Dronedarone(DB04855)	AGTGGCAGCAATAAATGCAGG	0.388																																					p.I125V		Atlas-SNP	.											.	KCNK2	135	.	0			c.A373G						.						138.0	136.0	137.0					1																	215297991		2203	4300	6503	SO:0001583	missense	3776	exon3			GCAGCAATAAATG	AF004711	CCDS31024.1, CCDS41466.1, CCDS41467.1	1q41	2012-03-07			ENSG00000082482	ENSG00000082482		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Two-P"""	6277	protein-coding gene	gene with protein product		603219				9721223, 16382106	Standard	NM_001017424		Approved	K2p2.1, TREK-1	uc001hkr.4	O95069	OTTHUMG00000037017	ENST00000444842.2:c.373A>G	chr1.hg19:g.215297991A>G	ENSP00000394033:p.Ile125Val	310.0	0.0		389.0	106.0	NM_001017425	A1Z1V3|A8K618|B2RCS4|B7ZL56|D3DTA5|Q5DP47|Q5DP48|Q9NRT2|Q9UNE3	Missense_Mutation	SNP	ENST00000444842.2	hg19	CCDS41467.1	.	.	.	.	.	.	.	.	.	.	A	7.878	0.729600	0.15507	.	.	ENSG00000082482	ENST00000391895;ENST00000478774;ENST00000391894;ENST00000444842;ENST00000457122	T;T;T;T;T	0.20069	2.1;2.29;2.11;2.1;2.55	5.91	3.6	0.41247	Ion transport 2 (1);	0.140469	0.64402	N	0.000005	T	0.11623	0.0283	N	0.17278	0.47	0.42989	D	0.994483	B;B;B	0.14012	0.001;0.009;0.003	B;B;B	0.14023	0.006;0.01;0.006	T	0.13737	-1.0498	10	0.14252	T	0.57	.	10.2248	0.43218	0.8663:0.0:0.1337:0.0	.	110;125;121	O95069-2;O95069;O95069-3	.;KCNK2_HUMAN;.	V	121;69;110;125;69	ENSP00000375765:I121V;ENSP00000420569:I69V;ENSP00000375764:I110V;ENSP00000394033:I125V;ENSP00000413460:I69V	ENSP00000375764:I110V	I	+	1	0	KCNK2	213364614	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.845000	0.55880	0.502000	0.28037	0.524000	0.50904	ATA	.	.		0.388	KCNK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089856.2	NM_014217	
MARC1	64757	hgsc.bcm.edu	37	1	220960447	220960447	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:220960447A>G	ENST00000366910.5	+	1	347	c.161A>G	c.(160-162)cAg>cGg	p.Q54R		NM_022746.3	NP_073583.3	Q5VT66	MARC1_HUMAN	mitochondrial amidoxime reducing component 1	54					detoxification of nitrogen compound (GO:0051410)|nitrate metabolic process (GO:0042126)|oxidation-reduction process (GO:0055114)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	molybdenum ion binding (GO:0030151)|molybdopterin cofactor binding (GO:0043546)|nitrate reductase activity (GO:0008940)|pyridoxal phosphate binding (GO:0030170)										CTGCTGCAGCAGGTGGGCACA	0.751																																					p.Q54R		Atlas-SNP	.											.	.	.	.	0			c.A161G						.						7.0	7.0	7.0					1																	220960447		2015	4019	6034	SO:0001583	missense	64757	exon1			TGCAGCAGGTGGG	AK026043	CCDS1526.1	1q41	2011-11-02	2011-11-02	2011-11-02	ENSG00000186205	ENSG00000186205			26189	protein-coding gene	gene with protein product		614126	"""MOCO sulphurase C-terminal domain containing 1"""	MOSC1		11886751	Standard	NM_022746		Approved	FLJ22390	uc001hms.3	Q5VT66	OTTHUMG00000037353	ENST00000366910.5:c.161A>G	chr1.hg19:g.220960447A>G	ENSP00000355877:p.Gln54Arg	52.0	0.0		50.0	5.0	NM_022746	A8K447|B2D078|Q5VVS9|Q5VVT0|Q5VVT1|Q8N9P5|Q96FN8|Q9H6C7	Missense_Mutation	SNP	ENST00000366910.5	hg19	CCDS1526.1	.	.	.	.	.	.	.	.	.	.	A	7.969	0.748572	0.15710	.	.	ENSG00000186205	ENST00000366910	T	0.22134	1.97	4.13	4.13	0.48395	Pyruvate kinase-like, insert domain (1);	0.409866	0.19939	N	0.102686	T	0.08758	0.0217	N	0.08118	0	0.29995	N	0.816538	B;B	0.26081	0.141;0.031	B;B	0.21151	0.033;0.022	T	0.21042	-1.0257	10	0.15066	T	0.55	-15.0579	6.8898	0.24222	0.8435:0.0:0.1565:0.0	.	54;54	Q5VT66-2;Q5VT66	.;MOSC1_HUMAN	R	54	ENSP00000355877:Q54R	ENSP00000355877:Q54R	Q	+	2	0	MOSC1	219027070	1.000000	0.71417	1.000000	0.80357	0.394000	0.30568	1.491000	0.35583	1.490000	0.48466	0.254000	0.18369	CAG	.	.		0.751	MARC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090904.1	NM_022746	
PARP1	142	hgsc.bcm.edu	37	1	226570841	226570841	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	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	129.0	0.0		191.0	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	
PSEN2	5664	hgsc.bcm.edu	37	1	227073343	227073343	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:227073343T>C	ENST00000366783.3	+	6	897	c.461T>C	c.(460-462)aTc>aCc	p.I154T	PSEN2_ENST00000472139.2_Missense_Mutation_p.I10T|PSEN2_ENST00000391872.2_Missense_Mutation_p.I187T|PSEN2_ENST00000366782.1_Missense_Mutation_p.I187T|PSEN2_ENST00000340188.4_Missense_Mutation_p.I154T|PSEN2_ENST00000422240.2_Missense_Mutation_p.I154T	NM_000447.2|NM_012486.2	NP_000438.2|NP_036618.2	P49810	PSN2_HUMAN	presenilin 2	154					amyloid precursor protein catabolic process (GO:0042987)|anagen (GO:0042640)|apoptotic signaling pathway (GO:0097190)|beta-amyloid metabolic process (GO:0050435)|brain morphogenesis (GO:0048854)|calcium ion transport (GO:0006816)|cardiac muscle contraction (GO:0060048)|cell fate specification (GO:0001708)|dorsal/ventral neural tube patterning (GO:0021904)|embryonic limb morphogenesis (GO:0030326)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|forebrain development (GO:0030900)|hematopoietic progenitor cell differentiation (GO:0002244)|intracellular signal transduction (GO:0035556)|locomotion (GO:0040011)|lung alveolus development (GO:0048286)|membrane protein ectodomain proteolysis (GO:0006509)|membrane protein intracellular domain proteolysis (GO:0031293)|memory (GO:0007613)|myeloid leukocyte differentiation (GO:0002573)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of protein binding (GO:0032091)|negative regulation of protein complex assembly (GO:0031333)|negative regulation of protein phosphorylation (GO:0001933)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of apoptotic process (GO:0043065)|positive regulation of catalytic activity (GO:0043085)|positive regulation of coagulation (GO:0050820)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|protein processing (GO:0016485)|protein transport (GO:0015031)|regulation of epidermal growth factor-activated receptor activity (GO:0007176)|regulation of synaptic plasticity (GO:0048167)|response to hypoxia (GO:0001666)|somitogenesis (GO:0001756)|T cell activation involved in immune response (GO:0002286)|T cell receptor signaling pathway (GO:0050852)|thymus development (GO:0048538)	apical plasma membrane (GO:0016324)|axon (GO:0030424)|cell cortex (GO:0005938)|cell surface (GO:0009986)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|ciliary rootlet (GO:0035253)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|kinetochore (GO:0000776)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrial inner membrane (GO:0005743)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|nuclear inner membrane (GO:0005637)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|Z disc (GO:0030018)	aspartic-type endopeptidase activity (GO:0004190)|endopeptidase activity (GO:0004175)			cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(8)|urinary_tract(1)	20		Prostate(94;0.0771)				GTTATGACCATCTTCTTGGTG	0.602																																					p.I154T		Atlas-SNP	.											.	PSEN2	55	.	0			c.T461C						.						213.0	141.0	165.0					1																	227073343		2203	4300	6503	SO:0001583	missense	5664	exon6			TGACCATCTTCTT	BC006365	CCDS1556.1, CCDS44324.1	1q42.13	2014-09-17	2014-02-24		ENSG00000143801	ENSG00000143801			9509	protein-coding gene	gene with protein product		600759	"""Alzheimer disease 4"""	AD4		7638621	Standard	NM_000447		Approved	AD3L, STM2, PS2	uc009xeo.1	P49810	OTTHUMG00000037563	ENST00000366783.3:c.461T>C	chr1.hg19:g.227073343T>C	ENSP00000355747:p.Ile154Thr	93.0	0.0		142.0	6.0	NM_012486	A8K8D4|B1AP21|Q96P32	Missense_Mutation	SNP	ENST00000366783.3	hg19	CCDS1556.1	.	.	.	.	.	.	.	.	.	.	T	24.0	4.478244	0.84747	.	.	ENSG00000143801	ENST00000366783;ENST00000340188;ENST00000422240;ENST00000366782;ENST00000391872;ENST00000472139	D;D;D;D;D;D	0.99552	-6.15;-6.15;-6.15;-6.15;-6.15;-6.15	5.27	5.27	0.74061	.	0.106621	0.64402	D	0.000007	D	0.99211	0.9726	L	0.56124	1.755	0.58432	D	0.999999	B;D	0.57571	0.11;0.98	B;P	0.55260	0.215;0.772	D	0.99047	1.0826	10	0.87932	D	0	.	15.1959	0.73088	0.0:0.0:0.0:1.0	.	154;154	A8K8D4;P49810	.;PSN2_HUMAN	T	154;154;154;187;187;10	ENSP00000355747:I154T;ENSP00000339860:I154T;ENSP00000403737:I154T;ENSP00000355746:I187T;ENSP00000375745:I187T;ENSP00000427806:I10T	ENSP00000339860:I154T	I	+	2	0	PSEN2	225139966	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.007000	0.70731	2.011000	0.59026	0.454000	0.30748	ATC	.	.		0.602	PSEN2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000091539.1	NM_000447	
OBSCN	84033	hgsc.bcm.edu	37	1	228434468	228434468	+	Missense_Mutation	SNP	G	G	C	rs372487722		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:228434468G>C	ENST00000422127.1	+	13	4041	c.3997G>C	c.(3997-3999)Ggg>Cgg	p.G1333R	OBSCN_ENST00000366709.4_5'UTR|OBSCN_ENST00000570156.2_Missense_Mutation_p.G1425R|OBSCN_ENST00000366707.4_5'UTR|OBSCN_ENST00000284548.11_Missense_Mutation_p.G1333R	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	1333	Ig-like 13.				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)	p.G1334fs*37(2)		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)				CTGTGAGGCTGGGGGCCAGCG	0.592																																					p.G1425R		Atlas-SNP	.											.,2	OBSCN	2142	.	2	Deletion - Frameshift(2)	large_intestine(2)	c.G4273C						.						71.0	80.0	77.0					1																	228434468		2004	4180	6184	SO:0001583	missense	84033	exon14			GAGGCTGGGGGCC	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.3997G>C	chr1.hg19:g.228434468G>C	ENSP00000409493:p.Gly1333Arg	339.0	1.0		371.0	0.0	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	hg19	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	.	7.104	0.574764	0.13623	.	.	ENSG00000154358	ENST00000284548;ENST00000422127	T;T	0.11930	2.73;2.73	5.07	4.15	0.48705	Immunoglobulin subtype (1);	0.070770	0.53938	D	0.000044	T	0.17408	0.0418	L	0.49256	1.55	0.80722	D	1	P;D	0.54964	0.536;0.969	B;P	0.46796	0.398;0.527	T	0.01162	-1.1432	10	0.48119	T	0.1	.	11.4416	0.50100	0.1512:0.0:0.8488:0.0	.	1333;1333	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	R	1333	ENSP00000284548:G1333R;ENSP00000409493:G1333R	ENSP00000284548:G1333R	G	+	1	0	OBSCN	226501091	1.000000	0.71417	0.896000	0.35187	0.062000	0.15995	5.366000	0.66122	1.115000	0.41800	0.557000	0.71058	GGG	.	.		0.592	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
OBSCN	84033	hgsc.bcm.edu	37	1	228560756	228560756	+	Missense_Mutation	SNP	C	C	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:228560756C>G	ENST00000422127.1	+	94	22321	c.22277C>G	c.(22276-22278)tCc>tGc	p.S7426C	OBSCN_ENST00000570156.2_Missense_Mutation_p.S8383C|OBSCN_ENST00000366707.4_Missense_Mutation_p.S5060C	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	7426					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)				GAGCACATCTCCCGGATCCTG	0.637																																					p.S8383C		Atlas-SNP	.											.	OBSCN	2142	.	0			c.C25148G						.						21.0	25.0	23.0					1																	228560756		2070	4184	6254	SO:0001583	missense	84033	exon105			ACATCTCCCGGAT	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.22277C>G	chr1.hg19:g.228560756C>G	ENSP00000409493:p.Ser7426Cys	125.0	0.0		183.0	40.0	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	hg19	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	C	27.1	4.799630	0.90538	.	.	ENSG00000154358	ENST00000422127;ENST00000366707	T;T	0.79033	-1.14;-1.23	5.44	5.44	0.79542	.	.	.	.	.	D	0.82388	0.5026	L	0.32530	0.975	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.81618	-0.0851	9	0.39692	T	0.17	.	16.4183	0.83750	0.0:1.0:0.0:0.0	.	7426	Q5VST9	OBSCN_HUMAN	C	7426;5060	ENSP00000409493:S7426C;ENSP00000355668:S5060C	ENSP00000355668:S5060C	S	+	2	0	OBSCN	226627379	1.000000	0.71417	1.000000	0.80357	0.769000	0.43574	4.248000	0.58760	2.550000	0.86006	0.462000	0.41574	TCC	.	.		0.637	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
PCNXL2	80003	hgsc.bcm.edu	37	1	233334767	233334767	+	Missense_Mutation	SNP	C	C	A			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:233334767C>A	ENST00000258229.9	-	15	3218	c.2984G>T	c.(2983-2985)gGg>gTg	p.G995V	PCNXL2_ENST00000488780.2_Missense_Mutation_p.G128V	NM_014801.3	NP_055616.3	A6NKB5	PCX2_HUMAN	pecanex-like 2 (Drosophila)	995						integral component of membrane (GO:0016021)				NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(7)|large_intestine(19)|lung(30)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	86		all_cancers(173;0.0347)|Prostate(94;0.137)				CGAGGTTATCCCAGACACAGC	0.502																																					p.G995V		Atlas-SNP	.											.	PCNXL2	204	.	0			c.G2984T						.						18.0	19.0	18.0					1																	233334767		1969	4160	6129	SO:0001583	missense	80003	exon15			GTTATCCCAGACA	AK055374	CCDS44335.1	1q42.2	2008-02-05	2001-11-28		ENSG00000135749	ENSG00000135749			8736	protein-coding gene	gene with protein product			"""pecanex (Drosophila)-like 2"""			12477932	Standard	NM_014801		Approved	KIAA0435, FLJ11383	uc001hvl.2	A6NKB5	OTTHUMG00000037824	ENST00000258229.9:c.2984G>T	chr1.hg19:g.233334767C>A	ENSP00000258229:p.Gly995Val	399.0	0.0		468.0	304.0	NM_014801	O43162|Q5T9Z8|Q5TDF1|Q8TEP4|Q96HP9|Q9HAL8	Missense_Mutation	SNP	ENST00000258229.9	hg19	CCDS44335.1	.	.	.	.	.	.	.	.	.	.	C	17.36	3.368733	0.61624	.	.	ENSG00000135749	ENST00000258229;ENST00000488780;ENST00000518351	T;T	0.46819	2.95;0.86	5.33	5.33	0.75918	.	.	.	.	.	T	0.66973	0.2844	M	0.64997	1.995	0.80722	D	1	D	0.71674	0.998	D	0.68621	0.959	T	0.68447	-0.5406	9	0.59425	D	0.04	.	19.0247	0.92927	0.0:1.0:0.0:0.0	.	995	A6NKB5	PCX2_HUMAN	V	995;128;164	ENSP00000258229:G995V;ENSP00000429231:G164V	ENSP00000258229:G995V	G	-	2	0	PCNXL2	231401390	0.998000	0.40836	0.912000	0.35992	0.178000	0.23041	6.539000	0.73856	2.512000	0.84698	0.591000	0.81541	GGG	.	.		0.502	PCNXL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092480.3	NM_014801	
KIF26B	55083	hgsc.bcm.edu	37	1	245849535	245849535	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:245849535T>C	ENST00000407071.2	+	12	3690	c.3250T>C	c.(3250-3252)Tct>Cct	p.S1084P	KIF26B_ENST00000366518.4_Missense_Mutation_p.S703P	NM_018012.3	NP_060482.2	Q2KJY2	KI26B_HUMAN	kinesin family member 26B	1084					establishment of cell polarity (GO:0030010)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|ureteric bud invasion (GO:0072092)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(21)|ovary(4)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	51	all_cancers(71;3.86e-05)|all_epithelial(71;0.000121)|Ovarian(71;0.0412)|all_lung(81;0.0498)|Lung NSC(105;0.0708)|Breast(184;0.127)		OV - Ovarian serous cystadenocarcinoma(106;0.022)			GCCACCCAGCTCTCCTTCCCA	0.657																																					p.S1084P		Atlas-SNP	.											.	KIF26B	343	.	0			c.T3250C						.						46.0	53.0	51.0					1																	245849535		1957	4157	6114	SO:0001583	missense	55083	exon12			CCCAGCTCTCCTT	AK001019	CCDS44342.1	1q44	2008-02-05			ENSG00000162849	ENSG00000162849		"""Kinesins"""	25484	protein-coding gene	gene with protein product		614026					Standard	NM_018012		Approved	FLJ10157	uc001ibf.1	Q2KJY2	OTTHUMG00000040079	ENST00000407071.2:c.3250T>C	chr1.hg19:g.245849535T>C	ENSP00000385545:p.Ser1084Pro	245.0	0.0		326.0	16.0	NM_018012	Q6ZQR9|Q6ZUZ0|Q8IUN3|Q8IVR1|Q9NWB4	Missense_Mutation	SNP	ENST00000407071.2	hg19	CCDS44342.1	.	.	.	.	.	.	.	.	.	.	T	16.31	3.088282	0.55968	.	.	ENSG00000162849	ENST00000407071;ENST00000366518;ENST00000413001	T;T	0.80480	-1.38;-1.37	5.77	5.77	0.91146	.	.	.	.	.	T	0.81508	0.4837	M	0.77616	2.38	0.58432	D	0.999999	P;P	0.42409	0.779;0.779	B;B	0.39805	0.141;0.31	T	0.82194	-0.0578	9	0.38643	T	0.18	.	16.0977	0.81139	0.0:0.0:0.0:1.0	.	703;1084	B7WPD9;Q2KJY2	.;KI26B_HUMAN	P	1084;703;700	ENSP00000385545:S1084P;ENSP00000355475:S703P	ENSP00000355475:S703P	S	+	1	0	KIF26B	243916158	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	7.794000	0.85869	2.215000	0.71742	0.459000	0.35465	TCT	.	.		0.657	KIF26B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381037.1	XM_371354	
OR2C3	81472	hgsc.bcm.edu	37	1	247695757	247695757	+	Silent	SNP	G	G	C	rs61746303|rs386641879	byFrequency	TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:247695757G>C	ENST00000366487.3	-	2	418	c.57C>G	c.(55-57)tcC>tcG	p.S19S	GCSAML_ENST00000366491.2_Intron|GCSAML_ENST00000366489.1_Intron|GCSAML_ENST00000527541.1_Intron|GCSAML_ENST00000527084.1_Intron|GCSAML_ENST00000366490.3_Intron|GCSAML_ENST00000463359.1_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		235.0	0.0		280.0	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	
OR2T4	127074	hgsc.bcm.edu	37	1	248525054	248525054	+	Silent	SNP	C	C	T			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:248525054C>T	ENST00000366475.1	+	1	172	c.172C>T	c.(172-174)Cta>Tta	p.L58L		NM_001004696.1	NP_001004696.1	Q8NH00	OR2T4_HUMAN	olfactory receptor, family 2, subfamily T, member 4	58						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|liver(2)|lung(47)	56	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			ACATCCAGCACTACTTTGTGT	0.488																																					p.L58L		Atlas-SNP	.											OR2T4,NS,carcinoma,0,1	OR2T4	126	.	0			c.C172T						.						174.0	171.0	172.0					1																	248525054		2203	4300	6503	SO:0001819	synonymous_variant	127074	exon1			CCAGCACTACTTT	BK004464	CCDS31113.1	1q44	2012-08-09			ENSG00000196944	ENSG00000196944		"""GPCR / Class A : Olfactory receptors"""	15016	protein-coding gene	gene with protein product							Standard	NM_001004696		Approved	OR2T4Q	uc001ieh.1	Q8NH00	OTTHUMG00000040453	ENST00000366475.1:c.172C>T	chr1.hg19:g.248525054C>T		437.0	0.0		535.0	0.0	NM_001004696	Q6IEZ8	Silent	SNP	ENST00000366475.1	hg19	CCDS31113.1																																																																																			.	.		0.488	OR2T4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097349.2	NM_001004696	
TAF1B	9014	hgsc.bcm.edu	37	2	10045015	10045015	+	Nonsense_Mutation	SNP	A	A	T			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	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*	85.0	0.0		83.0	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	
APOB	338	hgsc.bcm.edu	37	2	21235238	21235238	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:21235238T>C	ENST00000233242.1	-	26	4629	c.4502A>G	c.(4501-4503)tAt>tGt	p.Y1501C		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	1501					artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AGACAGGCCATATGTGCCTTT	0.458																																					p.Y1501C		Atlas-SNP	.											.	APOB	761	.	0			c.A4502G						.						144.0	137.0	140.0					2																	21235238		2203	4300	6503	SO:0001583	missense	338	exon26			AGGCCATATGTGC	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"""Apolipoproteins"""	603	protein-coding gene	gene with protein product		107730	"""apolipoprotein B (including Ag(x) antigen)"""				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.4502A>G	chr2.hg19:g.21235238T>C	ENSP00000233242:p.Tyr1501Cys	260.0	0.0		190.0	77.0	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Missense_Mutation	SNP	ENST00000233242.1	hg19	CCDS1703.1	.	.	.	.	.	.	.	.	.	.	T	10.21	1.286329	0.23478	.	.	ENSG00000084674	ENST00000233242;ENST00000535079	T	0.00840	5.63	5.88	3.47	0.39725	.	0.243265	0.29139	N	0.013031	T	0.02727	0.0082	L	0.56769	1.78	0.26805	N	0.969117	D	0.71674	0.998	P	0.60173	0.87	T	0.31724	-0.9933	10	0.72032	D	0.01	.	7.505	0.27540	0.1345:0.0681:0.0:0.7974	.	1501	P04114	APOB_HUMAN	C	1501	ENSP00000233242:Y1501C	ENSP00000233242:Y1501C	Y	-	2	0	APOB	21088743	0.677000	0.27577	0.007000	0.13788	0.036000	0.12997	1.291000	0.33330	0.458000	0.26988	0.533000	0.62120	TAT	.	.		0.458	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1		
PFN4	375189	hgsc.bcm.edu	37	2	24345390	24345390	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:24345390T>C	ENST00000313213.4	-	2	387	c.16A>G	c.(16-18)Agc>Ggc	p.S6G	FAM228B_ENST00000407625.1_5'Flank|PFN4_ENST00000465360.1_Intron|FAM228B_ENST00000420135.2_5'Flank|RP11-507M3.1_ENST00000584973.1_5'Flank	NM_199346.1	NP_955378.1	Q8NHR9	PROF4_HUMAN	profilin family, member 4	6					actin cytoskeleton organization (GO:0030036)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	lipid binding (GO:0008289)			breast(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)|pancreas(1)	6	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AACAATAAGCTCTGCAAATGG	0.463																																					p.S6G		Atlas-SNP	.											.	PFN4	16	.	0			c.A16G						.						140.0	140.0	140.0					2																	24345390		2203	4300	6503	SO:0001583	missense	375189	exon2			ATAAGCTCTGCAA	BC029523	CCDS1709.1	2p24.1	2008-02-05			ENSG00000176732	ENSG00000176732			31103	protein-coding gene	gene with protein product							Standard	NM_199346		Approved		uc002rfa.1	Q8NHR9	OTTHUMG00000090816	ENST00000313213.4:c.16A>G	chr2.hg19:g.24345390T>C	ENSP00000322170:p.Ser6Gly	234.0	0.0		164.0	8.0	NM_199346	Q53TL9	Missense_Mutation	SNP	ENST00000313213.4	hg19	CCDS1709.1	.	.	.	.	.	.	.	.	.	.	T	10.82	1.459562	0.26248	.	.	ENSG00000176732	ENST00000313213;ENST00000436622	.	.	.	5.05	5.05	0.67936	.	0.551999	0.17529	N	0.170944	T	0.29321	0.0730	N	0.22421	0.69	0.21762	N	0.999558	B	0.13145	0.007	B	0.14578	0.011	T	0.12192	-1.0557	9	0.30078	T	0.28	-2.0685	11.5184	0.50536	0.0:0.0:0.0:1.0	.	6	Q8NHR9	PROF4_HUMAN	G	6	.	ENSP00000322170:S6G	S	-	1	0	PFN4	24198894	0.105000	0.21958	0.900000	0.35374	0.746000	0.42486	2.027000	0.41078	2.043000	0.60533	0.459000	0.35465	AGC	.	.		0.463	PFN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207617.2	NM_199346	
DNMT3A	1788	hgsc.bcm.edu	37	2	25467083	25467083	+	Silent	SNP	G	G	T	rs568207978		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:25467083G>T	ENST00000264709.3	-	15	2129	c.1792C>A	c.(1792-1794)Cga>Aga	p.R598R	DNMT3A_ENST00000402667.1_Silent_p.R375R|DNMT3A_ENST00000380746.4_Silent_p.R409R|DNMT3A_ENST00000321117.5_Silent_p.R598R|DNMT3A_ENST00000474887.1_5'UTR	NM_175629.2	NP_783328.1	Q9Y6K1	DNM3A_HUMAN	DNA (cytosine-5-)-methyltransferase 3 alpha	598	ADD. {ECO:0000255|PROSITE- ProRule:PRU00865}.				C-5 methylation of cytosine (GO:0090116)|cellular response to amino acid stimulus (GO:0071230)|DNA methylation (GO:0006306)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation involved in gamete generation (GO:0043046)|DNA methylation on cytosine within a CG sequence (GO:0010424)|hypermethylation of CpG island (GO:0044027)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of gene expression by genetic imprinting (GO:0006349)|S-adenosylhomocysteine metabolic process (GO:0046498)|S-adenosylmethioninamine metabolic process (GO:0046499)|spermatogenesis (GO:0007283)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|euchromatin (GO:0000791)|nuclear heterochromatin (GO:0005720)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates (GO:0051718)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|unmethylated CpG binding (GO:0045322)	p.R598*(2)		breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(964)|kidney(3)|large_intestine(10)|lung(29)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	1021	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CAGTCCTCTCGCCGCCGCAGC	0.647			"""Mis, F, N, S"""		AML																																p.R598R		Atlas-SNP	.		Rec	yes		2	2p23	1788	DNA (cytosine-5-)-methyltransferase 3 alpha		L	DNMT3A,NS,haematopoietic_neoplasm,0,4	DNMT3A	1807	.	2	Substitution - Nonsense(2)	haematopoietic_and_lymphoid_tissue(2)	c.C1792A						.						29.0	34.0	33.0					2																	25467083		2203	4299	6502	SO:0001819	synonymous_variant	1788	exon15			CCTCTCGCCGCCG		CCDS1718.2, CCDS33157.1, CCDS46232.1	2p23	2014-09-17			ENSG00000119772	ENSG00000119772			2978	protein-coding gene	gene with protein product		602769				9662389, 10433969	Standard	NM_175630		Approved		uc002rgc.4	Q9Y6K1	OTTHUMG00000094777	ENST00000264709.3:c.1792C>A	chr2.hg19:g.25467083G>T		217.0	1.0		189.0	0.0	NM_175629	E9PEB8|Q86TE8|Q86XF5|Q8IZV0|Q8WXU9	Silent	SNP	ENST00000264709.3	hg19	CCDS33157.1																																																																																			.	.		0.647	DNMT3A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000211587.1	NM_022552	
ASXL2	55252	hgsc.bcm.edu	37	2	26029194	26029194	+	Silent	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:26029194A>G	ENST00000435504.4	-	4	449	c.156T>C	c.(154-156)ccT>ccC	p.P52P	ASXL2_ENST00000272341.4_5'UTR|ASXL2_ENST00000497092.1_5'UTR|ASXL2_ENST00000336112.4_Silent_p.P24P			Q76L83	ASXL2_HUMAN	additional sex combs like transcriptional regulator 2	52					adult heart development (GO:0007512)|embryonic skeletal system morphogenesis (GO:0048704)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of bone mineralization involved in bone maturation (GO:1900159)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of histone H3-K27 trimethylation (GO:1902466)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035360)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|peroxisome proliferator activated receptor binding (GO:0042975)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(7)|pancreas(1)|prostate(4)|skin(3)|urinary_tract(3)	33	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GGCATGCAAGAGGAGAAGTCC	0.373																																					p.P52P		Atlas-SNP	.											.	ASXL2	217	.	0			c.T156C						.						45.0	43.0	44.0					2																	26029194		1899	4122	6021	SO:0001819	synonymous_variant	55252	exon3			TGCAAGAGGAGAA			2p24.1	2014-06-17	2014-06-17		ENSG00000143970	ENSG00000143970			23805	protein-coding gene	gene with protein product		612991	"""additional sex combs like 2 (Drosophila)"""			12888926	Standard	NM_018263		Approved	ASXH2, FLJ10898, KIAA1685	uc002rgs.2	Q76L83	OTTHUMG00000152176	ENST00000435504.4:c.156T>C	chr2.hg19:g.26029194A>G		159.0	0.0		107.0	6.0	NM_018263	Q53TC9|Q5H9U4|Q76L81|Q86XM1|Q9C0H8|Q9NV67	Silent	SNP	ENST00000435504.4	hg19																																																																																				.	.		0.373	ASXL2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000325593.3	NM_018263	
ZNF513	130557	hgsc.bcm.edu	37	2	27603076	27603076	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:27603076A>G	ENST00000323703.6	-	2	293	c.95T>C	c.(94-96)cTg>cCg	p.L32P	ZNF513_ENST00000491924.1_5'Flank|ZNF513_ENST00000407879.1_5'UTR	NM_144631.5	NP_653232.3	Q8N8E2	ZN513_HUMAN	zinc finger protein 513	32					regulation of transcription, DNA-templated (GO:0006355)|response to stimulus (GO:0050896)|retina development in camera-type eye (GO:0060041)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|transcription regulatory region DNA binding (GO:0044212)			endometrium(5)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)	17	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CTCCAATACCAGGGCCCCGGG	0.577																																					p.L32P		Atlas-SNP	.											.	ZNF513	45	.	0			c.T95C						.						85.0	92.0	90.0					2																	27603076		2203	4300	6503	SO:0001583	missense	130557	exon2			AATACCAGGGCCC	AL833946	CCDS1751.1, CCDS56114.1	2p23.3	2014-01-28			ENSG00000163795	ENSG00000163795		"""Zinc fingers, C2H2-type"""	26498	protein-coding gene	gene with protein product		613598				12477932	Standard	NM_001201459		Approved	FLJ32203, RP58	uc002rkk.3	Q8N8E2	OTTHUMG00000097783	ENST00000323703.6:c.95T>C	chr2.hg19:g.27603076A>G	ENSP00000318373:p.Leu32Pro	121.0	0.0		101.0	5.0	NM_144631	A8K3S5|B7WP71|Q3ZCU1|Q68CJ1|Q86UZ3|Q8NDL8|Q96ML3	Missense_Mutation	SNP	ENST00000323703.6	hg19	CCDS1751.1	.	.	.	.	.	.	.	.	.	.	A	19.79	3.893132	0.72524	.	.	ENSG00000163795	ENST00000323703	T	0.19669	2.13	3.84	3.84	0.44239	.	0.000000	0.34088	N	0.004275	T	0.30230	0.0758	L	0.29908	0.895	0.80722	D	1	D	0.71674	0.998	D	0.79784	0.993	T	0.03193	-1.1062	10	0.56958	D	0.05	-3.2129	9.2058	0.37289	1.0:0.0:0.0:0.0	.	32	Q8N8E2	ZN513_HUMAN	P	32	ENSP00000318373:L32P	ENSP00000318373:L32P	L	-	2	0	ZNF513	27456580	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.946000	0.75953	1.746000	0.51805	0.413000	0.27773	CTG	.	.		0.577	ZNF513-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215026.2	NM_144631	
C2orf16	84226	hgsc.bcm.edu	37	2	27800546	27800546	+	Silent	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:27800546A>G	ENST00000408964.2	+	1	1158	c.1107A>G	c.(1105-1107)ggA>ggG	p.G369G		NM_032266.3	NP_115642.3	Q68DN1	CB016_HUMAN	chromosome 2 open reading frame 16	369						extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(33)|urinary_tract(1)	47	Acute lymphoblastic leukemia(172;0.155)					CTAAGTCAGGAGTGCAGGTAG	0.463																																					p.G369G		Atlas-SNP	.											.	C2orf16	357	.	0			c.A1107G						.						67.0	65.0	66.0					2																	27800546		1912	4123	6035	SO:0001819	synonymous_variant	84226	exon1			GTCAGGAGTGCAG	AL136898	CCDS42666.1	2p23.3	2013-09-20			ENSG00000221843	ENSG00000221843			25275	protein-coding gene	gene with protein product	"""P-S-E-R-S-H-H-S repeats containing"""						Standard	NM_032266		Approved	DKFZp434G118	uc002rkz.4	Q68DN1	OTTHUMG00000159099	ENST00000408964.2:c.1107A>G	chr2.hg19:g.27800546A>G		82.0	0.0		75.0	4.0	NM_032266	B9EIQ4|Q53S01|Q8ND64|Q9H088	Silent	SNP	ENST00000408964.2	hg19	CCDS42666.1																																																																																			.	.		0.463	C2orf16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353292.1	NM_032266	
CAPN13	92291	hgsc.bcm.edu	37	2	30987138	30987138	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:30987138A>G	ENST00000295055.8	-	6	735	c.559T>C	c.(559-561)Ttc>Ctc	p.F187L	CAPN13_ENST00000465960.2_5'UTR|CAPN13_ENST00000534090.2_Missense_Mutation_p.F187L	NM_144575.2	NP_653176.2	Q6MZZ7	CAN13_HUMAN	calpain 13	187	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.				proteolysis (GO:0006508)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(5)|large_intestine(5)|lung(11)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(1)	30	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.155)					TCCTCGAGGAAGCCATAGTGC	0.582																																					p.F187L		Atlas-SNP	.											.	CAPN13	70	.	0			c.T559C						.						53.0	55.0	54.0					2																	30987138		2092	4212	6304	SO:0001583	missense	92291	exon6			CGAGGAAGCCATA		CCDS46252.1	2p22-p21	2008-02-05			ENSG00000162949	ENSG00000162949			16663	protein-coding gene	gene with protein product		610228				11675017	Standard	NM_144575		Approved	FLJ23523	uc021vfm.1	Q6MZZ7	OTTHUMG00000152053	ENST00000295055.8:c.559T>C	chr2.hg19:g.30987138A>G	ENSP00000295055:p.Phe187Leu	168.0	0.0		96.0	5.0	NM_144575	Q17RF0|Q580X1|Q8TE80	Missense_Mutation	SNP	ENST00000295055.8	hg19	CCDS46252.1	.	.	.	.	.	.	.	.	.	.	A	11.72	1.722535	0.30503	.	.	ENSG00000162949	ENST00000295055;ENST00000534090	T;T	0.15256	2.44;2.44	5.22	-0.408	0.12381	Peptidase C2, calpain, catalytic domain (3);	0.812208	0.11609	N	0.546995	T	0.08980	0.0222	N	0.21583	0.68	0.19300	N	0.999976	B	0.31351	0.32	B	0.31390	0.129	T	0.38693	-0.9649	10	0.17369	T	0.5	.	5.478	0.16706	0.6284:0.0:0.2399:0.1317	.	187	Q6MZZ7	CAN13_HUMAN	L	187	ENSP00000295055:F187L;ENSP00000431298:F187L	ENSP00000295055:F187L	F	-	1	0	CAPN13	30840642	0.243000	0.23878	0.988000	0.46212	0.208000	0.24298	0.287000	0.18920	0.301000	0.22738	0.379000	0.24179	TTC	.	.		0.582	CAPN13-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325101.2	NM_144575	
ARHGEF33	100271715	hgsc.bcm.edu	37	2	39181520	39181521	+	Missense_Mutation	DNP	GA	GA	AT			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G|A	G|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:39181520_39181521GA>AT	ENST00000536934.1	+	11	1229_1230	c.1144_1145GA>AT	c.(1144-1146)GAa>ATa	p.E382I	ARHGEF33_ENST00000398800.4_Missense_Mutation_p.E382I|ARHGEF33_ENST00000409978.1_Missense_Mutation_p.E382I			A8MVX0	ARG33_HUMAN	Rho guanine nucleotide exchange factor (GEF) 33	382	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.						Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(3)|pancreas(1)|prostate(1)	5						TCAGGGTGATGAAGAGATTAAA	0.475																																					p.E382K|p.E382V		Atlas-SNP	.											.	ARHGEF33	34	.	0			c.G1144A|c.A1145T						.																																			SO:0001583	missense	100271715	exon11			GGTGATGAAGAGA|GTGATGAAGAGAT		CCDS46263.1, CCDS46263.2	2p22.1	2012-07-24			ENSG00000214694	ENSG00000214694		"""Rho guanine nucleotide exchange factors"""	37252	protein-coding gene	gene with protein product							Standard	NM_001145451		Approved		uc021vgd.1	A8MVX0	OTTHUMG00000153540	Exception_encountered	chr2.hg19:g.39181520_39181521delinsAT	ENSP00000445586:p.Glu382Ile	201.0|203.0	0.0		120.0|119.0	38.0|36.0	NM_001145451	J3KPX2	Missense_Mutation	SNP	ENST00000536934.1	hg19																																																																																				.	.		0.475	ARHGEF33-202	KNOWN	basic	protein_coding	protein_coding		NM_001145451	
SLC3A1	6519	hgsc.bcm.edu	37	2	44513251	44513251	+	Silent	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:44513251A>G	ENST00000260649.6	+	4	922	c.846A>G	c.(844-846)caA>caG	p.Q282Q	SLC3A1_ENST00000409380.1_Silent_p.Q4Q|SLC3A1_ENST00000409387.1_Silent_p.Q282Q|SLC3A1_ENST00000409741.1_Silent_p.Q282Q|SLC3A1_ENST00000410056.3_Silent_p.Q282Q|SLC3A1_ENST00000409229.3_Silent_p.Q282Q	NM_000341.3	NP_000332.2	Q07837	SLC31_HUMAN	solute carrier family 3 (amino acid transporter heavy chain), member 1	282					amino acid transmembrane transport (GO:0003333)|amino acid transport (GO:0006865)|basic amino acid transport (GO:0015802)|carbohydrate metabolic process (GO:0005975)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|L-cystine transport (GO:0015811)|transmembrane transport (GO:0055085)	brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)|vacuolar membrane (GO:0005774)	amino acid transmembrane transporter activity (GO:0015171)|basic amino acid transmembrane transporter activity (GO:0015174)|catalytic activity (GO:0003824)|cation binding (GO:0043169)|L-cystine transmembrane transporter activity (GO:0015184)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(11)|prostate(1)|skin(3)	26		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)			L-Cystine(DB00138)	TGAAAGAGCAACCTGATTTAA	0.358																																					p.Q282Q		Atlas-SNP	.											.	SLC3A1	62	.	0			c.A846G						.						128.0	127.0	127.0					2																	44513251		2203	4300	6503	SO:0001819	synonymous_variant	6519	exon4			AGAGCAACCTGAT		CCDS1819.1	2p16.3	2013-07-19	2013-07-19		ENSG00000138079	ENSG00000138079		"""Solute carriers"""	11025	protein-coding gene	gene with protein product		104614	"""solute carrier family 3 (cystine, dibasic and neutral amino acid transporters, activator of cystine, dibasic and neutral amino acid transport), member 1"""			8486766, 9186880	Standard	NM_000341		Approved	CSNU1, D2H, RBAT, ATR1, NBAT	uc002ruc.4	Q07837	OTTHUMG00000128759	ENST00000260649.6:c.846A>G	chr2.hg19:g.44513251A>G		128.0	0.0		99.0	4.0	NM_000341	A8K0S1|O00658|Q15295|Q4J6B4|Q4J6B5|Q4J6B6|Q4J6B7|Q4J6B8|Q4J6B9|Q52M92|Q52M94	Silent	SNP	ENST00000260649.6	hg19	CCDS1819.1																																																																																			.	.		0.358	SLC3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250676.1	NM_000341	
FBXO11	80204	hgsc.bcm.edu	37	2	48066902	48066902	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:48066902T>C	ENST00000403359.3	-	2	311	c.239A>G	c.(238-240)gAt>gGt	p.D80G	FBXO11_ENST00000480038.1_5'UTR|FBXO11_ENST00000316377.4_5'UTR|FBXO11_ENST00000378314.3_5'UTR|FBXO11_ENST00000402508.1_5'UTR	NM_001190274.1	NP_001177203.1	Q86XK2	FBX11_HUMAN	F-box protein 11	80					cellular protein modification process (GO:0006464)|peptidyl-arginine N-methylation (GO:0035246)|protein ubiquitination (GO:0016567)|sensory perception of sound (GO:0007605)|ubiquitin-dependent protein catabolic process (GO:0006511)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	protein-arginine N-methyltransferase activity (GO:0016274)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.0?(2)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	26		Acute lymphoblastic leukemia(82;0.0299)|all_hematologic(82;0.0358)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			TGCAGGCACATCATCATCTGT	0.353			"""Mis, F, D"""		DLBCL																																p.D80G		Atlas-SNP	.		Rec	yes		2	2p16.3	80204	F-box protein 11		L	.	FBXO11	127	.	2	Whole gene deletion(2)	haematopoietic_and_lymphoid_tissue(2)	c.A239G						.						94.0	87.0	90.0					2																	48066902		2203	4300	6503	SO:0001583	missense	80204	exon2			GGCACATCATCAT	AF174599	CCDS1837.1, CCDS54357.1	2p16.3	2014-01-29	2008-06-23	2008-06-23	ENSG00000138081	ENSG00000138081		"""Ubiquitin protein ligase E3 component n-recognins"", ""F-boxes /  ""other"""""	13590	protein-coding gene	gene with protein product	"""ubiquitin protein ligase E3 component n-recognin 6"""	607871	"""F-box only protein 11"""			10531035, 16487488, 18162545	Standard	NM_025133		Approved	FBX11, UBR6	uc002rwe.3	Q86XK2	OTTHUMG00000129130	ENST00000403359.3:c.239A>G	chr2.hg19:g.48066902T>C	ENSP00000384823:p.Asp80Gly	123.0	0.0		79.0	4.0	NM_001190274	A1L491|Q52ZP1|Q53EP7|Q53RT5|Q8IXG3|Q96E90|Q9H6V8|Q9H9L1|Q9NR14|Q9UFK1|Q9UHI1|Q9UKC2	Missense_Mutation	SNP	ENST00000403359.3	hg19	CCDS54357.1	.	.	.	.	.	.	.	.	.	.	T	12.89	2.072929	0.36566	.	.	ENSG00000138081	ENST00000403359	T	0.49139	0.79	5.34	4.15	0.48705	.	.	.	.	.	T	0.29423	0.0733	N	0.08118	0	0.80722	D	1	.	.	.	.	.	.	T	0.06954	-1.0798	7	0.20519	T	0.43	-24.1546	10.2135	0.43156	0.1528:0.0:0.0:0.8472	.	.	.	.	G	80	ENSP00000384823:D80G	ENSP00000384823:D80G	D	-	2	0	FBXO11	47920406	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.012000	0.76366	0.925000	0.37094	0.455000	0.32223	GAT	.	.		0.353	FBXO11-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251181.3	NM_012167, NM_018693, NM_025133	
PSME4	23198	hgsc.bcm.edu	37	2	54197809	54197809	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:54197809A>G	ENST00000404125.1	-	1	168	c.113T>C	c.(112-114)cTg>cCg	p.L38P	ACYP2_ENST00000607452.1_5'Flank|ACYP2_ENST00000422521.2_5'Flank|ACYP2_ENST00000606082.1_5'Flank	NM_014614.2	NP_055429.2	Q14997	PSME4_HUMAN	proteasome (prosome, macropain) activator subunit 4	38					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to DNA damage stimulus (GO:0006974)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|spermatogenesis, exchange of chromosomal proteins (GO:0035093)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)|spermatoproteasome complex (GO:1990111)	lysine-acetylated histone binding (GO:0070577)|peptidase activator activity (GO:0016504)			breast(5)|endometrium(8)|kidney(1)|large_intestine(11)|lung(26)|ovary(4)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(2)	60			Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181)			CGCGTAGGGCAGCAGCTTGTT	0.716																																					p.L38P		Atlas-SNP	.											.	PSME4	247	.	0			c.T113C						.						9.0	11.0	11.0					2																	54197809		690	1586	2276	SO:0001583	missense	23198	exon1			TAGGGCAGCAGCT	D38521	CCDS33197.2	2p16.1	2003-04-14			ENSG00000068878	ENSG00000068878		"""Proteasome (prosome, macropain) subunits"""	20635	protein-coding gene	gene with protein product		607705				7584044, 12093752	Standard	NM_014614		Approved	PA200, KIAA0077	uc002rxp.2	Q14997	OTTHUMG00000151852	ENST00000404125.1:c.113T>C	chr2.hg19:g.54197809A>G	ENSP00000384211:p.Leu38Pro	126.0	0.0		94.0	6.0	NM_014614	Q1XBG4|Q1XBG5|Q1XBG6|Q2M1Z0|Q6IPR2|Q86XF8	Missense_Mutation	SNP	ENST00000404125.1	hg19	CCDS33197.2	.	.	.	.	.	.	.	.	.	.	a	26.7	4.762560	0.89932	.	.	ENSG00000068878	ENST00000404125	T	0.61742	0.08	3.55	3.55	0.40652	.	.	.	.	.	T	0.75598	0.3871	M	0.84219	2.685	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.79586	-0.1742	9	0.87932	D	0	.	11.9294	0.52837	1.0:0.0:0.0:0.0	.	38	Q14997	PSME4_HUMAN	P	38	ENSP00000384211:L38P	ENSP00000374643:L38P	L	-	2	0	PSME4	54051313	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.361000	0.90098	1.469000	0.48083	0.451000	0.29950	CTG	.	.		0.716	PSME4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324163.1	XM_040158	
SPTBN1	6711	hgsc.bcm.edu	37	2	54858486	54858486	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:54858486T>C	ENST00000356805.4	+	16	3583	c.3302T>C	c.(3301-3303)cTc>cCc	p.L1101P	SPTBN1_ENST00000333896.5_Missense_Mutation_p.L1088P	NM_003128.2	NP_003119.2	Q01082	SPTB2_HUMAN	spectrin, beta, non-erythrocytic 1	1101					actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi to plasma membrane protein transport (GO:0043001)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|plasma membrane organization (GO:0007009)|protein targeting to plasma membrane (GO:0072661)	axolemma (GO:0030673)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|ankyrin binding (GO:0030506)|phospholipid binding (GO:0005543)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(8)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(27)|ovary(4)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	82			Lung(47;0.24)			GAGAAGCTGCTCACGCAGCAC	0.582																																					p.L1101P		Atlas-SNP	.											.	SPTBN1	378	.	0			c.T3302C						.						146.0	121.0	130.0					2																	54858486		2203	4300	6503	SO:0001583	missense	6711	exon16			AGCTGCTCACGCA		CCDS33198.1, CCDS33199.1	2p21	2013-01-10			ENSG00000115306	ENSG00000115306		"""Pleckstrin homology (PH) domain containing"""	11275	protein-coding gene	gene with protein product		182790					Standard	NM_003128		Approved		uc002rxu.3	Q01082	OTTHUMG00000133746	ENST00000356805.4:c.3302T>C	chr2.hg19:g.54858486T>C	ENSP00000349259:p.Leu1101Pro	205.0	0.0		138.0	6.0	NM_003128	B2RP63|O60837|Q16057|Q53R99|Q59ER3|Q8IX99	Missense_Mutation	SNP	ENST00000356805.4	hg19	CCDS33198.1	.	.	.	.	.	.	.	.	.	.	T	16.82	3.227677	0.58668	.	.	ENSG00000115306	ENST00000356805;ENST00000333896	T;T	0.50277	0.75;0.75	5.56	5.56	0.83823	.	0.134965	0.52532	D	0.000079	T	0.70570	0.3239	M	0.80616	2.505	0.80722	D	1	D;D	0.89917	0.998;1.0	D;D	0.81914	0.985;0.995	T	0.75473	-0.3305	10	0.87932	D	0	.	15.727	0.77770	0.0:0.0:0.0:1.0	.	1088;1101	Q01082-3;Q01082	.;SPTB2_HUMAN	P	1101;1088	ENSP00000349259:L1101P;ENSP00000334156:L1088P	ENSP00000334156:L1088P	L	+	2	0	SPTBN1	54711990	1.000000	0.71417	0.996000	0.52242	0.225000	0.24961	7.991000	0.88244	2.118000	0.64928	0.533000	0.62120	CTC	.	.		0.582	SPTBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258115.3		
CCDC88A	55704	hgsc.bcm.edu	37	2	55536323	55536323	+	Missense_Mutation	SNP	A	A	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:55536323A>C	ENST00000436346.1	-	24	4988	c.4147T>G	c.(4147-4149)Ttt>Gtt	p.F1383V	CCDC88A_ENST00000413716.2_Missense_Mutation_p.F1382V|AC012358.8_ENST00000366287.4_RNA|CCDC88A_ENST00000263630.8_Missense_Mutation_p.F1383V|CCDC88A_ENST00000336838.6_Missense_Mutation_p.F1382V|CCDC88A_ENST00000422883.2_Missense_Mutation_p.F6V	NM_001135597.1|NM_001254943.1	NP_001129069.1|NP_001241872.1	Q3V6T2	GRDN_HUMAN	coiled-coil domain containing 88A	1383					activation of protein kinase B activity (GO:0032148)|cell migration (GO:0016477)|DNA replication (GO:0006260)|lamellipodium assembly (GO:0030032)|membrane organization (GO:0061024)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell proliferation (GO:0042127)|regulation of DNA replication (GO:0006275)|regulation of neuron projection development (GO:0010975)|regulation of protein phosphorylation (GO:0001932)|TOR signaling (GO:0031929)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|membrane (GO:0016020)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|microtubule binding (GO:0008017)|phosphatidylinositol binding (GO:0035091)|protein homodimerization activity (GO:0042803)|protein kinase B binding (GO:0043422)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(22)|lung(23)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|urinary_tract(1)	69						GGGTCATAAAATTTGTATTGA	0.289																																					p.F1383V		Atlas-SNP	.											.	CCDC88A	336	.	0			c.T4147G						.						46.0	47.0	47.0					2																	55536323		2197	4283	6480	SO:0001583	missense	55704	exon24			CATAAAATTTGTA	AB033038, AF112218	CCDS33203.1, CCDS46288.1, CCDS58710.1	2p16.3	2013-03-13	2007-05-31	2007-05-31	ENSG00000115355	ENSG00000115355			25523	protein-coding gene	gene with protein product	"""Galpha-interacting vesicle-associated protein"", ""Akt-phosphorylation enhancer"", ""girdin"", ""girders of actin filaments"""	609736	"""KIAA1212"""	KIAA1212		15749703, 15753085	Standard	NM_001135597		Approved	FLJ10392, APE, GIV, HkRP1, GRDN	uc002ryv.2	Q3V6T2	OTTHUMG00000151915	ENST00000436346.1:c.4147T>G	chr2.hg19:g.55536323A>C	ENSP00000410608:p.Phe1383Val	187.0	0.0		195.0	83.0	NM_018084	A1IGE7|B7ZM78|C9JG83|Q53SF1|Q581G3|Q5HYD0|Q7Z339|Q7Z3C5	Missense_Mutation	SNP	ENST00000436346.1	hg19		.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	A|A|A	24.0|24.0|24.0	4.481486|4.481486|4.481486	0.84747|0.84747|0.84747	.|.|.	.|.|.	ENSG00000115355|ENSG00000115355|ENSG00000115355	ENST00000336838;ENST00000263630;ENST00000436346;ENST00000422883;ENST00000412148;ENST00000413716;ENST00000426576|ENST00000456975|ENST00000444458	T;T;T;T;T;T|.|.	0.58210|.|.	0.35;0.35;0.35;0.35;0.35;0.35|.|.	5.84|5.84|5.84	5.84|5.84|5.84	0.93424|0.93424|0.93424	.|.|.	0.000000|.|.	0.49916|.|.	U|.|.	0.000140|.|.	T|T|T	0.76248|0.76248|0.76248	0.3961|0.3961|0.3961	M|M|M	0.76838|0.76838|0.76838	2.35|2.35|2.35	0.37274|0.37274|0.37274	D|D|D	0.907559|0.907559|0.907559	D;D;D;D;P;D;D|.|.	0.89917|.|.	0.987;0.997;0.992;1.0;0.931;0.992;0.99|.|.	P;D;P;D;P;D;P|.|.	0.85130|.|.	0.893;0.99;0.844;0.997;0.782;0.925;0.897|.|.	T|T|T	0.80329|0.80329|0.80329	-0.1428|-0.1428|-0.1428	10|5|5	0.31617|.|.	T|.|.	0.26|.|.	-17.7153|-17.7153|-17.7153	16.2055|16.2055|16.2055	0.82126|0.82126|0.82126	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.|.	1382;1383;1328;6;1383;1382;1382|.|.	B7ZM78;Q3V6T2-2;D6W5D1;B3KW94;Q3V6T2;Q3V6T2-3;Q3V6T2-4|.|.	.;.;.;.;GRDN_HUMAN;.;.|.|.	V|S|K	1382;1383;1383;6;428;1382;558|363|7	ENSP00000338728:F1382V;ENSP00000263630:F1383V;ENSP00000410608:F1383V;ENSP00000390012:F428V;ENSP00000404431:F1382V;ENSP00000405080:F558V|.|.	ENSP00000263630:F1383V|.|.	F|I|N	-|-|-	1|2|3	0|0|2	CCDC88A|CCDC88A|CCDC88A	55389827|55389827|55389827	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.991000|0.991000|0.991000	0.79684|0.79684|0.79684	9.210000|9.210000|9.210000	0.95106|0.95106|0.95106	2.226000|2.226000|2.226000	0.72624|0.72624|0.72624	0.482000|0.482000|0.482000	0.46254|0.46254|0.46254	TTT|ATT|AAT	.	.		0.289	CCDC88A-203	KNOWN	basic	protein_coding	protein_coding		NM_017571	
IMMT	10989	hgsc.bcm.edu	37	2	86385804	86385804	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:86385804T>C	ENST00000410111.3	-	10	1460	c.1073A>G	c.(1072-1074)tAt>tGt	p.Y358C	IMMT_ENST00000254636.5_Missense_Mutation_p.Y259C|IMMT_ENST00000409051.2_Missense_Mutation_p.Y311C|IMMT_ENST00000449247.2_Missense_Mutation_p.Y347C|IMMT_ENST00000442664.2_Missense_Mutation_p.Y357C|Y_RNA_ENST00000363371.1_RNA|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	358					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						CAGCTCATGATACTGAGATAC	0.438																																					p.Y358C		Atlas-SNP	.											.	IMMT	65	.	0			c.A1073G						.						60.0	55.0	57.0					2																	86385804		1879	4124	6003	SO:0001583	missense	10989	exon10			TCATGATACTGAG	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.1073A>G	chr2.hg19:g.86385804T>C	ENSP00000387262:p.Tyr358Cys	173.0	0.0		136.0	58.0	NM_006839	B1H0U5|B2R5N6|Q14539|Q15092|Q68D41|Q69HW5|Q6IBL0|Q7Z3X1|Q8TAJ5|Q9P0V2	Missense_Mutation	SNP	ENST00000410111.3	hg19	CCDS46355.1	.	.	.	.	.	.	.	.	.	.	T	26.2	4.715540	0.89112	.	.	ENSG00000132305	ENST00000254636;ENST00000449247;ENST00000410111;ENST00000442664;ENST00000409051;ENST00000545283;ENST00000377310	T;T;T;T;T	0.36520	1.25;1.25;1.25;1.25;1.25	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.63153	0.2487	M	0.81341	2.54	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;1.0;1.0;1.0;1.0;1.0;1.0	T	0.66122	-0.6002	10	0.51188	T	0.08	-11.236	16.0709	0.80928	0.0:0.0:0.0:1.0	.	311;346;326;260;347;326;358	B9A067;B4DKR1;F8W9I1;B4DS66;Q16891-2;Q16891-3;Q16891	.;.;.;.;.;.;IMMT_HUMAN	C	259;347;358;357;311;347;326	ENSP00000254636:Y259C;ENSP00000396899:Y347C;ENSP00000387262:Y358C;ENSP00000407788:Y357C;ENSP00000387227:Y311C	ENSP00000254636:Y259C	Y	-	2	0	IMMT	86239315	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.519000	0.81809	2.198000	0.70561	0.528000	0.53228	TAT	.	.		0.438	IMMT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000329909.2	NM_006839	
VWA3B	200403	hgsc.bcm.edu	37	2	98828460	98828460	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:98828460T>C	ENST00000477737.1	+	13	2009	c.1805T>C	c.(1804-1806)aTc>aCc	p.I602T	VWA3B_ENST00000435344.1_Missense_Mutation_p.I602T|VWA3B_ENST00000451075.2_Missense_Mutation_p.I452T	NM_144992.4	NP_659429.4	Q502W6	VWA3B_HUMAN	von Willebrand factor A domain containing 3B	602	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.									NS(3)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	70						ACACAGGCAATCTACCTTCTG	0.478																																					p.I602T		Atlas-SNP	.											.	VWA3B	138	.	0			c.T1805C						.						100.0	99.0	99.0					2																	98828460		1871	4111	5982	SO:0001583	missense	200403	exon13			AGGCAATCTACCT	AL832761	CCDS42718.1	2q11.2	2008-02-05			ENSG00000168658	ENSG00000168658			28385	protein-coding gene	gene with protein product						12477932	Standard	NM_144992		Approved	DKFZp686F2227, MGC26733	uc002syo.3	Q502W6	OTTHUMG00000153104	ENST00000477737.1:c.1805T>C	chr2.hg19:g.98828460T>C	ENSP00000417955:p.Ile602Thr	148.0	0.0		111.0	5.0	NM_144992	B9EK71|Q86T73|Q8N2D0|Q8N770|Q8NA79|Q8ND63|Q8ND65|Q8WW02	Missense_Mutation	SNP	ENST00000477737.1	hg19	CCDS42718.1	.	.	.	.	.	.	.	.	.	.	T	15.66	2.898203	0.52227	.	.	ENSG00000168658	ENST00000435344;ENST00000477737;ENST00000451075	T;T;T	0.80994	-1.44;1.66;-1.44	5.4	5.4	0.78164	von Willebrand factor, type A (3);	0.000000	0.85682	D	0.000000	D	0.89733	0.6800	M	0.83312	2.635	0.32177	N	0.580877	D;D;D;D	0.89917	0.999;1.0;1.0;0.999	D;D;D;D	0.87578	0.996;0.997;0.992;0.998	D	0.92042	0.5641	10	0.87932	D	0	.	13.3675	0.60694	0.0:0.0:0.0:1.0	.	452;602;602;602	B7Z7Q7;Q502W6;Q502W6-8;Q502W6-6	.;VWA3B_HUMAN;.;.	T	602;602;452	ENSP00000401959:I602T;ENSP00000417955:I602T;ENSP00000389463:I452T	ENSP00000388158:I602T	I	+	2	0	VWA3B	98194892	1.000000	0.71417	0.994000	0.49952	0.235000	0.25334	5.137000	0.64789	2.212000	0.71576	0.391000	0.25812	ATC	.	.		0.478	VWA3B-020	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353469.2	NM_144992	
SLC35F5	80255	hgsc.bcm.edu	37	2	114512776	114512776	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:114512776T>C	ENST00000245680.2	-	3	652	c.239A>G	c.(238-240)gAt>gGt	p.D80G	SLC35F5_ENST00000409342.1_Missense_Mutation_p.D74G	NM_025181.2	NP_079457.2	Q8WV83	S35F5_HUMAN	solute carrier family 35, member F5	80					transport (GO:0006810)	integral component of membrane (GO:0016021)				endometrium(1)|kidney(4)|large_intestine(2)|lung(7)|ovary(2)|prostate(3)|skin(1)	20						CCATATCACATCAACAAGCAG	0.423																																					p.D80G		Atlas-SNP	.											.	SLC35F5	60	.	0			c.A239G						.						87.0	83.0	84.0					2																	114512776		2203	4300	6503	SO:0001583	missense	80255	exon3			ATCACATCAACAA	AF529364	CCDS2119.1	2q14.1	2013-05-22			ENSG00000115084	ENSG00000115084		"""Solute carriers"""	23617	protein-coding gene	gene with protein product							Standard	XM_005263799		Approved	FLJ22004	uc002tku.1	Q8WV83	OTTHUMG00000131361	ENST00000245680.2:c.239A>G	chr2.hg19:g.114512776T>C	ENSP00000245680:p.Asp80Gly	129.0	0.0		95.0	4.0	NM_025181	Q9H6P8|Q9H7D8	Missense_Mutation	SNP	ENST00000245680.2	hg19	CCDS2119.1	.	.	.	.	.	.	.	.	.	.	T	23.4	4.411181	0.83340	.	.	ENSG00000115084	ENST00000245680;ENST00000409106;ENST00000409342	T;T	0.48201	0.82;0.83	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	T	0.63733	0.2536	L	0.56199	1.76	0.58432	D	0.999998	D;D;D	0.89917	1.0;1.0;0.993	D;D;D	0.85130	0.996;0.997;0.984	T	0.66380	-0.5938	10	0.72032	D	0.01	-17.5576	13.9127	0.63878	0.0:0.0:0.0:1.0	.	80;74;80	B2RDY0;B8ZZV6;Q8WV83	.;.;S35F5_HUMAN	G	80;74;74	ENSP00000245680:D80G;ENSP00000386754:D74G	ENSP00000245680:D80G	D	-	2	0	SLC35F5	114229246	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.978000	0.76147	2.209000	0.71365	0.533000	0.62120	GAT	.	.		0.423	SLC35F5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254150.1	NM_025181	
MYO7B	4648	hgsc.bcm.edu	37	2	128345986	128345986	+	Silent	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:128345986A>G	ENST00000409816.2	+	14	1742	c.1710A>G	c.(1708-1710)cgA>cgG	p.R570R	MYO7B_ENST00000389524.4_Silent_p.R570R|MYO7B_ENST00000428314.1_Silent_p.R570R			Q6PIF6	MYO7B_HUMAN	myosin VIIB	570	Myosin motor.					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)		AGAAGAACCGAGACGTGCTGA	0.557																																					p.R570R		Atlas-SNP	.											.	MYO7B	359	.	0			c.A1710G						.						49.0	54.0	53.0					2																	128345986		1975	4152	6127	SO:0001819	synonymous_variant	4648	exon15			GAACCGAGACGTG		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.1710A>G	chr2.hg19:g.128345986A>G		81.0	0.0		75.0	4.0	NM_001080527	Q14786|Q8TEE1	Silent	SNP	ENST00000409816.2	hg19	CCDS46405.1																																																																																			.	.		0.557	MYO7B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000331124.3	XM_291001	
PLEKHB2	55041	hgsc.bcm.edu	37	2	131884342	131884342	+	Silent	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:131884342A>G	ENST00000403716.1	+	4	836	c.276A>G	c.(274-276)gaA>gaG	p.E92E	PLEKHB2_ENST00000303908.3_Silent_p.E92E|PLEKHB2_ENST00000409279.1_Silent_p.E92E|PLEKHB2_ENST00000234115.6_Silent_p.E92E|PLEKHB2_ENST00000439822.2_Silent_p.E92E|PLEKHB2_ENST00000409612.1_Silent_p.E92E|PLEKHB2_ENST00000404460.1_Silent_p.E92E|PLEKHB2_ENST00000438882.2_Silent_p.E92E|PLEKHB2_ENST00000409158.1_Silent_p.E92E|PLEKHB2_ENST00000538982.1_Silent_p.E44E	NM_001100623.1|NM_001267062.1|NM_001267063.1|NM_001267064.1|NM_001267065.1|NM_001267066.1|NM_017958.2	NP_001094093.1|NP_001253991.1|NP_001253992.1|NP_001253993.1|NP_001253994.1|NP_001253995.1|NP_060428.2	Q96CS7	PKHB2_HUMAN	pleckstrin homology domain containing, family B (evectins) member 2	92	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.					endosome (GO:0005768)|membrane (GO:0016020)				large_intestine(1)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	9				BRCA - Breast invasive adenocarcinoma(221;0.0828)		TTTGTGCAGAAAGCACAGATG	0.343																																					p.E92E		Atlas-SNP	.											.	PLEKHB2	47	.	0			c.A276G						.						109.0	108.0	108.0					2																	131884342		2203	4300	6503	SO:0001819	synonymous_variant	55041	exon4			TGCAGAAAGCACA		CCDS2166.1, CCDS46413.1, CCDS58729.1, CCDS58730.1, CCDS74576.1, CCDS74577.1	2q22.1	2013-01-10			ENSG00000115762	ENSG00000115762		"""Pleckstrin homology (PH) domain containing"""	19236	protein-coding gene	gene with protein product						10200314	Standard	NM_017958		Approved	EVT2, FLJ20783	uc031rpd.1	Q96CS7	OTTHUMG00000131656	ENST00000403716.1:c.276A>G	chr2.hg19:g.131884342A>G		102.0	0.0		93.0	36.0	NM_001267062	B4DF08|B4DZ66|B8ZZN1|Q53FF1|Q53TH7|Q86W37|Q9BV75|Q9NWK1	Silent	SNP	ENST00000403716.1	hg19	CCDS46413.1																																																																																			.	.		0.343	PLEKHB2-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331304.2	NM_017958	
ZRANB3	84083	hgsc.bcm.edu	37	2	135985575	135985575	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:135985575T>C	ENST00000264159.6	-	14	2081	c.1965A>G	c.(1963-1965)atA>atG	p.I655M	ZRANB3_ENST00000412849.1_5'UTR|ZRANB3_ENST00000401392.1_Missense_Mutation_p.I655M|ZRANB3_ENST00000536680.1_Missense_Mutation_p.I655M	NM_032143.2	NP_115519.2	Q5FWF4	ZRAB3_HUMAN	zinc finger, RAN-binding domain containing 3	655					cellular response to DNA damage stimulus (GO:0006974)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|DNA rewinding (GO:0036292)|DNA strand renaturation (GO:0000733)|negative regulation of DNA recombination (GO:0045910)|replication fork processing (GO:0031297)|replication fork protection (GO:0048478)|response to UV (GO:0009411)	nuclear replication fork (GO:0043596)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|endodeoxyribonuclease activity (GO:0004520)|helicase activity (GO:0004386)|K63-linked polyubiquitin binding (GO:0070530)|zinc ion binding (GO:0008270)			NS(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(10)|upper_aerodigestive_tract(1)	20				BRCA - Breast invasive adenocarcinoma(221;0.135)		TGAGGCTATCTATTTGCATAA	0.284																																					p.I655M		Atlas-SNP	.											.	ZRANB3	109	.	0			c.A1965G						.						45.0	35.0	38.0					2																	135985575		1576	3543	5119	SO:0001583	missense	84083	exon14			GCTATCTATTTGC	AL136824	CCDS46419.1, CCDS67963.1, CCDS74580.1	2q21.3	2013-05-13			ENSG00000121988	ENSG00000121988		"""Zinc fingers, RAN-binding domain containing"""	25249	protein-coding gene	gene with protein product						11230166	Standard	XM_005263809		Approved	DKFZP434B1727	uc002tum.3	Q5FWF4	OTTHUMG00000150475	ENST00000264159.6:c.1965A>G	chr2.hg19:g.135985575T>C	ENSP00000264159:p.Ile655Met	92.0	0.0		104.0	37.0	NM_032143	B3KYA1|B4E375|B5MDI3|D3DP76|E9PBP0|Q53SM1|Q6P2C4|Q8N1P4|Q9H0E8	Missense_Mutation	SNP	ENST00000264159.6	hg19	CCDS46419.1	.	.	.	.	.	.	.	.	.	.	T	7.579	0.668435	0.14776	.	.	ENSG00000121988	ENST00000538542;ENST00000283060;ENST00000401392;ENST00000264159;ENST00000536680	D;D;D	0.90676	-2.71;-2.71;-2.7	4.45	4.45	0.53987	.	0.393053	0.24568	N	0.037409	T	0.77363	0.4119	N	0.08118	0	0.22571	N	0.998979	P;P	0.41345	0.63;0.746	B;B	0.33196	0.076;0.159	T	0.72057	-0.4405	10	0.48119	T	0.1	-8.633	10.2931	0.43608	0.0:0.0:0.0:1.0	.	655;655	Q5FWF4;Q5FWF4-3	ZRAB3_HUMAN;.	M	120;120;655;655;655	ENSP00000383979:I655M;ENSP00000264159:I655M;ENSP00000441320:I655M	ENSP00000264159:I655M	I	-	3	3	ZRANB3	135702045	0.802000	0.28943	0.359000	0.25824	0.351000	0.29236	1.326000	0.33735	1.987000	0.57996	0.454000	0.30748	ATA	.	.		0.284	ZRANB3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318254.1	NM_032143	
RBM43	375287	hgsc.bcm.edu	37	2	152107693	152107693	+	Silent	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:152107693A>G	ENST00000331426.5	-	4	952	c.801T>C	c.(799-801)ggT>ggC	p.G267G		NM_198557.2	NP_940959.1	Q6ZSC3	RBM43_HUMAN	RNA binding motif protein 43	267							nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			endometrium(2)|large_intestine(3)|lung(2)|ovary(1)	8				BRCA - Breast invasive adenocarcinoma(221;0.131)		TTGGCTGAGAACCAACTTGAA	0.363																																					p.G267G		Atlas-SNP	.											.	RBM43	35	.	0			c.T801C						.						85.0	81.0	83.0					2																	152107693		2203	4300	6503	SO:0001819	synonymous_variant	375287	exon4			CTGAGAACCAACT	AK127552	CCDS2191.1	2q23.3	2007-01-30	2007-01-30	2007-01-30	ENSG00000184898	ENSG00000184898		"""RNA binding motif (RRM) containing"""	24790	protein-coding gene	gene with protein product			"""chromosome 2 open reading frame 38"""	C2orf38			Standard	NM_198557		Approved	FLJ45645	uc002txh.3	Q6ZSC3	OTTHUMG00000131866	ENST00000331426.5:c.801T>C	chr2.hg19:g.152107693A>G		152.0	0.0		96.0	4.0	NM_198557	B2RMT5	Silent	SNP	ENST00000331426.5	hg19	CCDS2191.1																																																																																			.	.		0.363	RBM43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254816.2	NM_198557	
PKP4	8502	hgsc.bcm.edu	37	2	159499020	159499020	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:159499020A>G	ENST00000389759.3	+	11	1830	c.1718A>G	c.(1717-1719)aAg>aGg	p.K573R	PKP4_ENST00000389757.3_Missense_Mutation_p.K573R	NM_003628.3	NP_003619.2	Q99569	PKP4_HUMAN	plakophilin 4	573					cell-cell junction assembly (GO:0007043)|cell-cell signaling (GO:0007267)|positive regulation of cytokinesis (GO:0032467)|positive regulation of gene expression (GO:0010628)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell adhesion (GO:0030155)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)|desmosome (GO:0030057)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|spindle midzone (GO:0051233)|spindle pole (GO:0000922)				breast(2)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(9)|lung(21)|ovary(6)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1)	61						GGGGGAATCAAGCATCTGGTT	0.418										HNSCC(62;0.18)																											p.K573R		Atlas-SNP	.											.	PKP4	133	.	0			c.A1718G						.						110.0	112.0	111.0					2																	159499020		2203	4300	6503	SO:0001583	missense	8502	exon11			GAATCAAGCATCT	X81889	CCDS33305.1, CCDS33306.1	2q24.1	2013-02-14			ENSG00000144283	ENSG00000144283		"""Armadillo repeat containing"""	9026	protein-coding gene	gene with protein product		604276				9342840, 8937994	Standard	NM_003628		Approved	p0071	uc002tzv.3	Q99569	OTTHUMG00000153969	ENST00000389759.3:c.1718A>G	chr2.hg19:g.159499020A>G	ENSP00000374409:p.Lys573Arg	130.0	0.0		123.0	42.0	NM_001005476	Q86W91	Missense_Mutation	SNP	ENST00000389759.3	hg19	CCDS33305.1	.	.	.	.	.	.	.	.	.	.	A	14.97	2.693650	0.48202	.	.	ENSG00000144283	ENST00000428353;ENST00000389757;ENST00000389759;ENST00000389756	T;T	0.68765	-0.35;-0.35	5.87	5.87	0.94306	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.55705	0.1937	N	0.12182	0.205	0.49299	D	0.999776	B;B;B;B;B	0.32302	0.363;0.107;0.073;0.053;0.313	B;B;B;B;B	0.38194	0.267;0.078;0.031;0.039;0.137	T	0.60434	-0.7264	10	0.56958	D	0.05	-16.9594	16.2813	0.82687	1.0:0.0:0.0:0.0	.	425;528;573;573;424	Q6LCG8;Q4W5T8;Q99569-2;Q99569;F8W7E2	.;.;.;PKP4_HUMAN;.	R	424;573;573;61	ENSP00000374407:K573R;ENSP00000374409:K573R	ENSP00000374406:K61R	K	+	2	0	PKP4	159207266	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.100000	0.71473	2.244000	0.73946	0.533000	0.62120	AAG	.	.		0.418	PKP4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333250.1		
XIRP2	129446	hgsc.bcm.edu	37	2	168103504	168103504	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:168103504A>G	ENST00000409195.1	+	9	5691	c.5602A>G	c.(5602-5604)Atg>Gtg	p.M1868V	XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409273.1_Missense_Mutation_p.M1646V|XIRP2_ENST00000295237.9_Missense_Mutation_p.M1868V|XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000409043.1_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	1693					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						AAAAGGTAACATGCTAGCCAC	0.378																																					p.M1868V		Atlas-SNP	.											.	XIRP2	914	.	0			c.A5602G						.						74.0	67.0	69.0					2																	168103504		1873	4107	5980	SO:0001583	missense	129446	exon9			GGTAACATGCTAG	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.5602A>G	chr2.hg19:g.168103504A>G	ENSP00000386840:p.Met1868Val	77.0	0.0		87.0	4.0	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	2.510	-0.313082	0.05422	.	.	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273	T;T;T	0.02301	4.35;4.35;4.36	5.46	4.27	0.50696	.	0.520995	0.23169	N	0.051148	T	0.02807	0.0084	L	0.57536	1.79	0.24198	N	0.995521	B;B;B	0.24920	0.07;0.114;0.003	B;B;B	0.20955	0.014;0.032;0.009	T	0.43589	-0.9382	10	0.19590	T	0.45	-0.0097	7.2509	0.26148	0.7042:0.151:0.0:0.1447	.	1693;1693;1646	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	V	1868;1868;1646	ENSP00000386840:M1868V;ENSP00000295237:M1868V;ENSP00000387255:M1646V	ENSP00000295237:M1868V	M	+	1	0	XIRP2	167811750	0.918000	0.31147	0.480000	0.27341	0.287000	0.27160	2.351000	0.44071	0.963000	0.38082	0.528000	0.53228	ATG	.	.		0.378	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381	
CHN1	1123	hgsc.bcm.edu	37	2	175666522	175666522	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:175666522T>C	ENST00000409900.3	-	12	1434	c.1121A>G	c.(1120-1122)gAg>gGg	p.E374G	CHN1_ENST00000409597.1_Missense_Mutation_p.E190G|CHN1_ENST00000488080.1_5'UTR|CHN1_ENST00000409156.3_Missense_Mutation_p.E348G|CHN1_ENST00000295497.7_Missense_Mutation_p.E249G	NM_001822.5	NP_001813.1	P15882	CHIN_HUMAN	chimerin 1	374	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				ephrin receptor signaling pathway (GO:0048013)|motor neuron axon guidance (GO:0008045)|positive regulation of signal transduction (GO:0009967)|regulation of axonogenesis (GO:0050770)|regulation of Rac GTPase activity (GO:0032314)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)|SH3/SH2 adaptor activity (GO:0005070)			NS(1)|breast(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	18			OV - Ovarian serous cystadenocarcinoma(117;0.226)			TTCCAATTGCTCATCCGGATC	0.408			T	TAF15	extraskeletal myxoid chondrosarcoma																																p.E374G		Atlas-SNP	.		Dom	yes		2	2q31-q32.1	1123	chimerin (chimaerin) 1		M	.	CHN1	67	.	0			c.A1121G						.						177.0	175.0	176.0					2																	175666522		1933	4142	6075	SO:0001583	missense	1123	exon12			AATTGCTCATCCG		CCDS46454.1, CCDS46455.1, CCDS56147.1	2q31-q32.1	2013-02-14	2012-10-17		ENSG00000128656	ENSG00000128656		"""Rho GTPase activating proteins"", ""SH2 domain containing"""	1943	protein-coding gene	gene with protein product	"""Chimerin 1 (GTPase-activating protein, rho, 2)"", ""chimaerin 1"""	118423	"""Duane retraction syndrome 2"", ""chimerin (chimaerin) 1"""	CHN, DURS2		2299665, 15013773, 18653847	Standard	NM_001822		Approved	RhoGAP2, ARHGAP2, n-chimerin	uc002uji.3	P15882	OTTHUMG00000154225	ENST00000409900.3:c.1121A>G	chr2.hg19:g.175666522T>C	ENSP00000386741:p.Glu374Gly	151.0	0.0		131.0	7.0	NM_001822	A8K1M6|B3KNU6|B4DV19|Q53SD6|Q53SH5|Q96FB0	Missense_Mutation	SNP	ENST00000409900.3	hg19	CCDS46455.1	.	.	.	.	.	.	.	.	.	.	T	18.55	3.648972	0.67358	.	.	ENSG00000128656	ENST00000409900;ENST00000295497;ENST00000409597;ENST00000409156;ENST00000409089;ENST00000444394	T;T;T;T;T;T	0.22945	1.93;1.93;1.93;1.93;1.93;1.93	5.42	5.42	0.78866	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.094279	0.64402	D	0.000001	T	0.28034	0.0691	M	0.63208	1.945	0.80722	D	1	B;B;B	0.15930	0.015;0.009;0.007	B;B;B	0.17979	0.02;0.012;0.007	T	0.06698	-1.0812	10	0.56958	D	0.05	.	11.0068	0.47639	0.0:0.0:0.1558:0.8442	.	348;374;249	B4DV19;P15882;P15882-2	.;CHIN_HUMAN;.	G	374;249;190;348;166;149	ENSP00000386741:E374G;ENSP00000295497:E249G;ENSP00000386469:E190G;ENSP00000386470:E348G;ENSP00000386322:E166G;ENSP00000411911:E149G	ENSP00000295497:E249G	E	-	2	0	CHN1	175374768	1.000000	0.71417	0.991000	0.47740	0.996000	0.88848	6.193000	0.72075	2.173000	0.68751	0.482000	0.46254	GAG	.	.		0.408	CHN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334453.1	NM_001822	
TTN	7273	hgsc.bcm.edu	37	2	179600364	179600364	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:179600364A>G	ENST00000591111.1	-	48	14082	c.13858T>C	c.(13858-13860)Tgt>Cgt	p.C4620R	TTN_ENST00000342992.6_Missense_Mutation_p.C3693R|TTN-AS1_ENST00000582847.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000359218.5_Intron|TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000460472.2_Intron|TTN_ENST00000589042.1_Missense_Mutation_p.C4937R|TTN_ENST00000342175.6_Intron			Q8WZ42	TITIN_HUMAN	titin	12372	Ig-like 26.				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)			TCTTCAAAACAGATCTTATAA	0.433																																					p.C4937R		Atlas-SNP	.											.	TTN	18412	.	0			c.T14809C						.						73.0	71.0	72.0					2																	179600364		1838	4081	5919	SO:0001583	missense	7273	exon50			CAAAACAGATCTT	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.13858T>C	chr2.hg19:g.179600364A>G	ENSP00000465570:p.Cys4620Arg	116.0	0.0		121.0	6.0	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		.	.	.	.	.	.	.	.	.	.	A	9.169	1.020586	0.19433	.	.	ENSG00000155657	ENST00000342992	T	0.64803	-0.12	5.77	4.55	0.56014	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.60919	0.2306	M	0.66939	2.045	0.80722	D	1	B	0.13145	0.007	B	0.21151	0.033	T	0.63571	-0.6607	9	0.87932	D	0	.	12.1032	0.53796	0.8715:0.0:0.0:0.1285	.	4620	Q8WZ42	TITIN_HUMAN	R	3693	ENSP00000343764:C3693R	ENSP00000343764:C3693R	C	-	1	0	TTN	179308609	1.000000	0.71417	0.998000	0.56505	0.930000	0.56654	3.947000	0.56652	2.326000	0.78906	0.533000	0.62120	TGT	.	.		0.433	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
CCDC141	285025	hgsc.bcm.edu	37	2	179839801	179839801	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:179839801T>C	ENST00000409284.1	-	4	626	c.509A>G	c.(508-510)cAt>cGt	p.H170R	CCDC141_ENST00000420890.2_Missense_Mutation_p.H170R			Q6ZP82	CC141_HUMAN	coiled-coil domain containing 141	170										NS(2)|breast(1)|endometrium(5)|kidney(1)|large_intestine(17)|lung(37)|ovary(8)|pancreas(2)|skin(4)|upper_aerodigestive_tract(1)	78			OV - Ovarian serous cystadenocarcinoma(117;0.0274)|Epithelial(96;0.0531)|all cancers(119;0.147)			ATGATGTTCATGAAGCTGAAG	0.328																																					p.H170R		Atlas-SNP	.											.	CCDC141	362	.	0			c.A509G						.																																			SO:0001583	missense	285025	exon4			TGTTCATGAAGCT	AK096821		2q31.2	2013-01-14			ENSG00000163492	ENSG00000163492		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	26821	protein-coding gene	gene with protein product	"""coiled-coil protein associated with myosin II and DISC1"""					20956536	Standard	NM_173648		Approved	FLJ39502, CAMDI	uc002une.2	Q6ZP82	OTTHUMG00000132578	ENST00000409284.1:c.509A>G	chr2.hg19:g.179839801T>C	ENSP00000386503:p.His170Arg	107.0	0.0		69.0	4.0	NM_173648	H7C0P1|J3KNW6|Q8N8H3	Missense_Mutation	SNP	ENST00000409284.1	hg19		.	.	.	.	.	.	.	.	.	.	T	19.54	3.846174	0.71603	.	.	ENSG00000163492	ENST00000420890;ENST00000443758;ENST00000446116;ENST00000409284	T;T	0.42131	0.98;1.21	5.51	5.51	0.81932	.	.	.	.	.	T	0.57140	0.2033	M	0.64997	1.995	0.80722	D	1	D	0.69078	0.997	P	0.58520	0.84	T	0.57294	-0.7836	8	.	.	.	.	15.6278	0.76874	0.0:0.0:0.0:1.0	.	170	B8ZZB3	.	R	170	ENSP00000395995:H170R;ENSP00000390190:H170R	.	H	-	2	0	CCDC141	179548046	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.518000	0.67068	2.096000	0.63516	0.533000	0.62120	CAT	.	.		0.328	CCDC141-003	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000335873.1	NM_173648	
ANKAR	150709	hgsc.bcm.edu	37	2	190585478	190585478	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:190585478T>C	ENST00000520309.1	+	12	2688	c.2600T>C	c.(2599-2601)cTc>cCc	p.L867P	ANKAR_ENST00000431575.2_Missense_Mutation_p.L796P|ANKAR_ENST00000281412.6_Missense_Mutation_p.L631P|ANKAR_ENST00000313581.4_Missense_Mutation_p.L867P|ANKAR_ENST00000438402.2_Missense_Mutation_p.L867P	NM_144708.3	NP_653309.3	Q7Z5J8	ANKAR_HUMAN	ankyrin and armadillo repeat containing	867						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)			CATAAAGGCCTCCCATATCTT	0.328																																					p.L867P		Atlas-SNP	.											.	ANKAR	184	.	0			c.T2600C						.						194.0	216.0	208.0					2																	190585478		2203	4300	6503	SO:0001583	missense	150709	exon12			AAGGCCTCCCATA	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.2600T>C	chr2.hg19:g.190585478T>C	ENSP00000427882:p.Leu867Pro	75.0	0.0		69.0	5.0	NM_144708	Q3ZCS6|Q4G0M2|Q6ZU02	Missense_Mutation	SNP	ENST00000520309.1	hg19	CCDS33351.2	.	.	.	.	.	.	.	.	.	.	T	14.97	2.694602	0.48202	.	.	ENSG00000151687	ENST00000520309;ENST00000313581;ENST00000438402;ENST00000431575;ENST00000281412	T;T;T;T;T	0.38722	1.12;1.12;1.12;1.12;1.12	4.84	4.84	0.62591	.	0.360162	0.25275	N	0.031844	T	0.39436	0.1078	N	0.19112	0.55	0.53688	D	0.99997	.	.	.	.	.	.	T	0.40421	-0.9564	8	0.66056	D	0.02	-3.9671	13.541	0.61674	0.0:0.0:0.0:1.0	.	.	.	.	P	867;867;867;796;631	ENSP00000427882:L867P;ENSP00000313513:L867P;ENSP00000397243:L867P;ENSP00000393043:L796P;ENSP00000281412:L631P	ENSP00000281412:L631P	L	+	2	0	ANKAR	190293723	1.000000	0.71417	0.920000	0.36463	0.223000	0.24884	3.763000	0.55257	2.054000	0.61138	0.533000	0.62120	CTC	.	.		0.328	ANKAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335045.3	NM_144708	
STAT1	6772	hgsc.bcm.edu	37	2	191862950	191862950	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:191862950T>C	ENST00000361099.3	-	8	1013	c.626A>G	c.(625-627)aAg>aGg	p.K209R	STAT1_ENST00000409465.1_Missense_Mutation_p.K209R|STAT1_ENST00000392322.3_Missense_Mutation_p.K209R|STAT1_ENST00000540176.1_Intron|STAT1_ENST00000392323.2_Missense_Mutation_p.K211R	NM_007315.3	NP_009330.1	P42224	STAT1_HUMAN	signal transducer and activator of transcription 1, 91kDa	209					apoptotic process (GO:0006915)|blood circulation (GO:0008015)|cellular response to insulin stimulus (GO:0032869)|cellular response to interferon-beta (GO:0035458)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|metanephric mesenchymal cell differentiation (GO:0072162)|metanephric mesenchymal cell proliferation involved in metanephros development (GO:0072136)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of macrophage fusion (GO:0034240)|negative regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003340)|negative regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072308)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of apoptotic process (GO:0042981)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|renal tubule development (GO:0061326)|response to cAMP (GO:0051591)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to exogenous dsRNA (GO:0043330)|response to hydrogen peroxide (GO:0042542)|response to mechanical stimulus (GO:0009612)|response to nutrient (GO:0007584)|response to peptide hormone (GO:0043434)|transcription from RNA polymerase II promoter (GO:0006366)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity (GO:0000983)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|tumor necrosis factor receptor binding (GO:0005164)			autonomic_ganglia(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(2)|large_intestine(6)|lung(13)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	39			OV - Ovarian serous cystadenocarcinoma(117;0.00434)|Epithelial(96;0.0555)|all cancers(119;0.141)			TACCTTTCTCTTATTGTCAAG	0.348																																					p.K209R		Atlas-SNP	.											.	STAT1	93	.	0			c.A626G						.						139.0	132.0	134.0					2																	191862950		2202	4297	6499	SO:0001583	missense	6772	exon8			TTTCTCTTATTGT		CCDS2309.1, CCDS42793.1	2q32.2-q32.3	2014-09-17	2002-08-29		ENSG00000115415	ENSG00000115415		"""SH2 domain containing"""	11362	protein-coding gene	gene with protein product	"""transcription factor ISGF-3 components p91/p84"""	600555	"""signal transducer and activator of transcription 1, 91kD"""			7885841	Standard	NM_139266		Approved	STAT91, ISGF-3	uc002usj.2	P42224	OTTHUMG00000132699	ENST00000361099.3:c.626A>G	chr2.hg19:g.191862950T>C	ENSP00000354394:p.Lys209Arg	128.0	0.0		69.0	4.0	NM_007315	A8K989|B2RCA0|D2KFR8|D3DPI7|Q53S88|Q53XW4|Q68D00|Q9UDL5	Missense_Mutation	SNP	ENST00000361099.3	hg19	CCDS2309.1	.	.	.	.	.	.	.	.	.	.	T	10.06	1.247059	0.22796	.	.	ENSG00000115415	ENST00000361099;ENST00000409465;ENST00000392322;ENST00000392323;ENST00000544783	T;T;T;T	0.61274	0.12;0.12;0.12;0.12	4.89	4.89	0.63831	STAT transcription factor, all-alpha (2);STAT transcription factor, coiled coil (1);	0.043563	0.85682	D	0.000000	T	0.47893	0.1470	L	0.58354	1.805	0.80722	D	1	B;B	0.14805	0.011;0.009	B;B	0.21151	0.033;0.02	T	0.39583	-0.9607	10	0.15066	T	0.55	-38.7538	6.6173	0.22784	0.1386:0.077:0.0:0.7844	.	209;209	P42224-2;P42224	.;STAT1_HUMAN	R	209;209;209;211;117	ENSP00000354394:K209R;ENSP00000386244:K209R;ENSP00000376136:K209R;ENSP00000376137:K211R	ENSP00000354394:K209R	K	-	2	0	STAT1	191571195	1.000000	0.71417	0.992000	0.48379	0.679000	0.39708	3.548000	0.53670	2.052000	0.61016	0.533000	0.62120	AAG	.	.		0.348	STAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255997.3	NM_007315	
TMEM237	65062	hgsc.bcm.edu	37	2	202501540	202501540	+	Missense_Mutation	SNP	T	T	A	rs376226585		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:202501540T>A	ENST00000409883.2	-	5	321	c.205A>T	c.(205-207)Act>Tct	p.T69S	TMEM237_ENST00000409444.2_Missense_Mutation_p.T61S	NM_001044385.2	NP_001037850.1	Q96Q45	TM237_HUMAN	transmembrane protein 237	69					cilium assembly (GO:0042384)|regulation of Wnt signaling pathway (GO:0030111)	ciliary transition zone (GO:0035869)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				endometrium(2)|kidney(1)|large_intestine(1)|lung(3)	7						AGTTCTTTAGTTGATGGCTCA	0.438																																					p.T69S		Atlas-SNP	.											.	TMEM237	21	.	0			c.A205T						.	T	SER/THR,SER/THR	0,3676		0,0,1838	63.0	59.0	60.0		181,205	0.4	0.5	2		60	1,8177		0,1,4088	no	missense,missense	TMEM237	NM_152388.2,NM_001044385.1	58,58	0,1,5926	AA,AT,TT		0.0122,0.0,0.0084	benign,benign	61/401,69/409	202501540	1,11853	1838	4089	5927	SO:0001583	missense	65062	exon4			CTTTAGTTGATGG	AB053301	CCDS46489.1, CCDS46490.1	2q33	2012-05-08	2011-05-20	2011-05-20	ENSG00000155755	ENSG00000155755			14432	protein-coding gene	gene with protein product		614423	"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 4"""	ALS2CR4		11586298, 20375344	Standard	NM_001044385		Approved	JBTS14	uc021vvg.2	Q96Q45	OTTHUMG00000154526	ENST00000409883.2:c.205A>T	chr2.hg19:g.202501540T>A	ENSP00000386264:p.Thr69Ser	53.0	0.0		44.0	19.0	NM_001044385	B4E1R8|B4E2R8|E9PAR8|E9PBF8|E9PG24|E9PGX0|Q53TS9|Q53TT2|Q7Z3B6|Q8IZ18|Q8NBF8|Q96CY1	Missense_Mutation	SNP	ENST00000409883.2	hg19	CCDS46489.1	.	.	.	.	.	.	.	.	.	.	T	8.241	0.806894	0.16467	0.0	1.22E-4	ENSG00000155755	ENST00000409444;ENST00000409883;ENST00000435876;ENST00000426684	T;T	0.44083	0.93;0.93	5.27	0.376	0.16193	.	0.122859	0.53938	N	0.000044	T	0.26557	0.0649	L	0.39397	1.21	0.09310	N	1	B;B	0.12013	0.005;0.0	B;B	0.09377	0.004;0.003	T	0.11348	-1.0591	10	0.33141	T	0.24	-3.1583	4.4306	0.11525	0.1405:0.3118:0.0:0.5477	.	69;93	E9PAR8;Q96Q45	.;TM237_HUMAN	S	61;69;69;91	ENSP00000387203:T61S;ENSP00000386264:T69S	ENSP00000387203:T61S	T	-	1	0	TMEM237	202209785	0.966000	0.33281	0.460000	0.27093	0.309000	0.27889	0.146000	0.16180	-0.071000	0.12886	0.528000	0.53228	ACT	.	.		0.438	TMEM237-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000335753.1	NM_152388	
MAP2	4133	hgsc.bcm.edu	37	2	210543360	210543360	+	Silent	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:210543360A>G	ENST00000360351.4	+	5	833	c.327A>G	c.(325-327)gaA>gaG	p.E109E	MAP2_ENST00000392194.1_Silent_p.E109E|MAP2_ENST00000361559.4_Silent_p.E109E|MAP2_ENST00000447185.1_Silent_p.E109E|MAP2_ENST00000199940.6_Silent_p.E109E	NM_002374.3	NP_002365.3	P11137	MTAP2_HUMAN	microtubule-associated protein 2	109					axonogenesis (GO:0007409)|cellular response to organic substance (GO:0071310)|central nervous system neuron development (GO:0021954)|dendrite morphogenesis (GO:0048813)|microtubule bundle formation (GO:0001578)|neuron projection development (GO:0031175)	cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|neuronal cell body (GO:0043025)|nuclear periphery (GO:0034399)	dystroglycan binding (GO:0002162)|structural molecule activity (GO:0005198)			breast(7)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(36)|liver(2)|lung(42)|ovary(11)|pancreas(2)|prostate(2)|skin(2)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	124		Hepatocellular(293;0.137)|Lung NSC(271;0.163)|Renal(323;0.202)		UCEC - Uterine corpus endometrioid carcinoma (47;6.64e-05)|Epithelial(149;3.12e-100)|all cancers(144;6.88e-91)|Lung(261;0.0624)|LUSC - Lung squamous cell carcinoma(261;0.0662)|STAD - Stomach adenocarcinoma(1183;0.18)	Docetaxel(DB01248)|Estramustine(DB01196)|Paclitaxel(DB01229)	TGAAAGGTGAACAAGAGAAAG	0.423																																					p.E109E	Pancreas(27;423 979 28787 29963)	Atlas-SNP	.											.	MAP2	372	.	0			c.A327G						.						121.0	114.0	116.0					2																	210543360		2203	4300	6503	SO:0001819	synonymous_variant	4133	exon6			AGGTGAACAAGAG		CCDS2384.1, CCDS2385.1, CCDS33369.1	2q34-q35	2008-05-27			ENSG00000078018	ENSG00000078018		"""A-kinase anchor proteins"""	6839	protein-coding gene	gene with protein product		157130				3103857, 7479905	Standard	XM_005246554		Approved	MAP2A, MAP2B, MAP2C	uc002vde.1	P11137	OTTHUMG00000132962	ENST00000360351.4:c.327A>G	chr2.hg19:g.210543360A>G		127.0	0.0		80.0	4.0	NM_001039538	Q17S04|Q8IUX2|Q99975|Q99976	Silent	SNP	ENST00000360351.4	hg19	CCDS2384.1																																																																																			.	.		0.423	MAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256521.2	NM_001039538	
TTLL4	9654	hgsc.bcm.edu	37	2	219617891	219617891	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:219617891T>C	ENST00000392102.1	+	18	3581	c.3241T>C	c.(3241-3243)Tct>Cct	p.S1081P	TTLL4_ENST00000457313.1_Missense_Mutation_p.S916P|TTLL4_ENST00000442769.1_Missense_Mutation_p.S1017P|TTLL4_ENST00000258398.4_Missense_Mutation_p.S1081P	NM_014640.4	NP_055455.3	Q14679	TTLL4_HUMAN	tubulin tyrosine ligase-like family, member 4	1081					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)		GGGAGTTGTCTCTGATTCTGC	0.527																																					p.S1081P	GBM(172;1818 2053 15407 20943 49753)	Atlas-SNP	.											.	TTLL4	96	.	0			c.T3241C						.						227.0	214.0	218.0					2																	219617891		2203	4300	6503	SO:0001583	missense	9654	exon18			GTTGTCTCTGATT		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.3241T>C	chr2.hg19:g.219617891T>C	ENSP00000375951:p.Ser1081Pro	268.0	0.0		195.0	8.0	NM_014640	A8K6V5|Q8WW29	Missense_Mutation	SNP	ENST00000392102.1	hg19	CCDS2422.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.96|14.96	2.691596|2.691596	0.48097|0.48097	.|.	.|.	ENSG00000135912|ENSG00000135912	ENST00000436668|ENST00000457313;ENST00000392102;ENST00000442769;ENST00000258398	.|T;T;T;T	.|0.04502	.|3.82;4.05;3.61;4.05	5.17|5.17	2.78|2.78	0.32641|0.32641	.|.	.|0.558082	.|0.18504	.|N	.|0.139256	T|T	0.05640|0.05640	0.0148|0.0148	M|M	0.68952|0.68952	2.095|2.095	0.26038|0.26038	N|N	0.981642|0.981642	.|B;D;B	.|0.54601	.|0.337;0.967;0.026	.|B;B;B	.|0.40329	.|0.133;0.326;0.008	T|T	0.35251|0.35251	-0.9796|-0.9796	5|10	.|0.39692	.|T	.|0.17	.|.	4.1007|4.1007	0.10012|0.10012	0.3445:0.0872:0.0:0.5683|0.3445:0.0872:0.0:0.5683	.|.	.|916;1017;1081	.|E9PH58;E7EX20;Q14679	.|.;.;TTLL4_HUMAN	P|P	183|916;1081;1017;1081	.|ENSP00000393332:S916P;ENSP00000375951:S1081P;ENSP00000396555:S1017P;ENSP00000258398:S1081P	.|ENSP00000258398:S1081P	L|S	+|+	2|1	0|0	TTLL4|TTLL4	219326135|219326135	0.122000|0.122000	0.22280|0.22280	0.992000|0.992000	0.48379|0.48379	0.996000|0.996000	0.88848|0.88848	0.705000|0.705000	0.25675|0.25675	0.420000|0.420000	0.25954|0.25954	0.533000|0.533000	0.62120|0.62120	CTC|TCT	.	.		0.527	TTLL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256726.1	NM_014640	
TM4SF20	79853	hgsc.bcm.edu	37	2	228243963	228243963	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:228243963T>C	ENST00000304568.3	-	1	59	c.22A>G	c.(22-24)Aca>Gca	p.T8A		NM_024795.3	NP_079071.2	Q53R12	T4S20_HUMAN	transmembrane 4 L six family member 20	8						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|kidney(2)|large_intestine(1)|lung(4)|stomach(2)	10		Renal(207;0.025)|all_lung(227;0.123)|Esophageal squamous(248;0.23)|all_hematologic(139;0.248)		Epithelial(121;3.8e-11)|all cancers(144;2.57e-08)|Lung(261;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.0115)		TTGCAGGATGTCCATCCTTCG	0.468																																					p.T8A		Atlas-SNP	.											.	TM4SF20	24	.	0			c.A22G						.						111.0	109.0	110.0					2																	228243963		2203	4300	6503	SO:0001583	missense	79853	exon1			AGGATGTCCATCC	AK026453	CCDS2466.1	2q36.3	2008-02-05			ENSG00000168955	ENSG00000168955			26230	protein-coding gene	gene with protein product		615404				12975309	Standard	NM_024795		Approved	FLJ22800, TCCE518	uc002vpb.2	Q53R12	OTTHUMG00000133187	ENST00000304568.3:c.22A>G	chr2.hg19:g.228243963T>C	ENSP00000303028:p.Thr8Ala	157.0	0.0		115.0	5.0	NM_024795	B2RP42|Q5U609|Q6UWS1|Q9H5X9	Missense_Mutation	SNP	ENST00000304568.3	hg19	CCDS2466.1	.	.	.	.	.	.	.	.	.	.	T	15.42	2.827170	0.50739	.	.	ENSG00000168955	ENST00000304568;ENST00000449706	T	0.27402	1.67	5.77	5.77	0.91146	.	0.083182	0.51477	D	0.000093	T	0.34687	0.0906	L	0.28556	0.865	0.36193	D	0.850231	D	0.76494	0.999	D	0.79784	0.993	T	0.35699	-0.9778	10	0.02654	T	1	-21.5116	9.352	0.38145	0.1595:0.0:0.0:0.8405	.	8	Q53R12	T4S20_HUMAN	A	8	ENSP00000303028:T8A	ENSP00000303028:T8A	T	-	1	0	TM4SF20	227952207	1.000000	0.71417	0.999000	0.59377	0.905000	0.53344	2.974000	0.49272	2.194000	0.70268	0.482000	0.46254	ACA	.	.		0.468	TM4SF20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256896.2	NM_024795	
DGKD	8527	hgsc.bcm.edu	37	2	234368500	234368500	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:234368500T>C	ENST00000264057.2	+	23	2804	c.2792T>C	c.(2791-2793)gTc>gCc	p.V931A	DGKD_ENST00000409813.3_Missense_Mutation_p.V887A	NM_152879.2	NP_690618.2	Q16760	DGKD_HUMAN	diacylglycerol kinase, delta 130kDa	931					blood coagulation (GO:0007596)|cell growth (GO:0016049)|diacylglycerol metabolic process (GO:0046339)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|multicellular organismal development (GO:0007275)|platelet activation (GO:0030168)|protein homooligomerization (GO:0051260)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein transport (GO:0015031)|response to organic substance (GO:0010033)|second-messenger-mediated signaling (GO:0019932)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol binding (GO:0019992)|diacylglycerol kinase activity (GO:0004143)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			central_nervous_system(2)|endometrium(4)|kidney(1)|large_intestine(13)|lung(15)|ovary(1)|pancreas(1)|skin(1)	38		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0538)		Epithelial(121;1.31e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000416)|Lung(119;0.00285)|LUSC - Lung squamous cell carcinoma(224;0.00655)	Phosphatidylserine(DB00144)	ATTCGGATTGTCCACAAGAAC	0.632																																					p.V931A		Atlas-SNP	.											.	DGKD	106	.	0			c.T2792C						.						68.0	60.0	63.0					2																	234368500		2203	4300	6503	SO:0001583	missense	8527	exon23			GGATTGTCCACAA	D63479	CCDS2504.1, CCDS46546.1	2q37	2013-01-10	2002-08-29		ENSG00000077044	ENSG00000077044		"""Sterile alpha motif (SAM) domain containing"", ""Pleckstrin homology (PH) domain containing"""	2851	protein-coding gene	gene with protein product	"""diglyceride kinase"""	601826	"""diacylglycerol kinase, delta (130kD)"""			8626538, 12810723	Standard	NM_003648		Approved	KIAA0145, DGKdelta	uc002vui.1	Q16760	OTTHUMG00000133290	ENST00000264057.2:c.2792T>C	chr2.hg19:g.234368500T>C	ENSP00000264057:p.Val931Ala	163.0	0.0		117.0	5.0	NM_152879	Q14158|Q6PK55|Q8NG53	Missense_Mutation	SNP	ENST00000264057.2	hg19	CCDS2504.1	.	.	.	.	.	.	.	.	.	.	T	13.04	2.118733	0.37436	.	.	ENSG00000077044	ENST00000264057;ENST00000409813	T;T	0.42513	0.97;0.97	4.35	3.15	0.36227	.	0.802743	0.11222	N	0.586553	T	0.44603	0.1301	M	0.73962	2.25	0.09310	N	1	B;B	0.22146	0.029;0.065	B;B	0.28991	0.068;0.097	T	0.40905	-0.9538	10	0.18710	T	0.47	.	11.1441	0.48419	0.0:0.0:0.1548:0.8452	.	887;931	Q16760-2;Q16760	.;DGKD_HUMAN	A	931;887	ENSP00000264057:V931A;ENSP00000386455:V887A	ENSP00000264057:V931A	V	+	2	0	DGKD	234033239	0.989000	0.36119	0.088000	0.20740	0.949000	0.60115	3.992000	0.56980	0.786000	0.33708	0.379000	0.24179	GTC	.	.		0.632	DGKD-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257072.2	NM_003648	
COL6A3	1293	hgsc.bcm.edu	37	2	238273019	238273019	+	Missense_Mutation	SNP	C	C	T			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:238273019C>T	ENST00000295550.4	-	13	6343	c.5891G>A	c.(5890-5892)aGa>aAa	p.R1964K	COL6A3_ENST00000347401.3_Missense_Mutation_p.R1763K|COL6A3_ENST00000409809.1_Missense_Mutation_p.R1758K|COL6A3_ENST00000346358.4_Missense_Mutation_p.R1764K|COL6A3_ENST00000353578.4_Missense_Mutation_p.R1758K|COL6A3_ENST00000472056.1_Missense_Mutation_p.R1357K	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	1964	Nonhelical region.|VWFA 10. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		CTCAGATGCTCTGTGTAAATC	0.473																																					p.R1964K		Atlas-SNP	.											.	COL6A3	608	.	0			c.G5891A						.						121.0	108.0	112.0					2																	238273019		2203	4300	6503	SO:0001583	missense	1293	exon13			GATGCTCTGTGTA	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.5891G>A	chr2.hg19:g.238273019C>T	ENSP00000295550:p.Arg1964Lys	120.0	0.0		91.0	4.0	NM_004369	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Missense_Mutation	SNP	ENST00000295550.4	hg19	CCDS33412.1	.	.	.	.	.	.	.	.	.	.	C	11.48	1.650292	0.29336	.	.	ENSG00000163359	ENST00000295550;ENST00000347401;ENST00000353578;ENST00000472056;ENST00000409809;ENST00000346358	T;T;T;T;T;T	0.36878	1.23;1.23;1.23;1.23;1.23;1.23	5.62	-2.49	0.06403	von Willebrand factor, type A (2);	0.738576	0.11875	N	0.521021	T	0.21267	0.0512	L	0.41710	1.295	0.09310	N	1	B;B;B	0.24721	0.11;0.035;0.0	B;B;B	0.19666	0.026;0.018;0.0	T	0.34650	-0.9820	10	0.08837	T	0.75	.	7.5818	0.27970	0.0:0.3077:0.1993:0.493	.	1357;1758;1964	E9PFQ6;P12111-2;P12111	.;.;CO6A3_HUMAN	K	1964;1763;1758;1357;1758;1764	ENSP00000295550:R1964K;ENSP00000315609:R1763K;ENSP00000315873:R1758K;ENSP00000418285:R1357K;ENSP00000386844:R1758K;ENSP00000295546:R1764K	ENSP00000295550:R1964K	R	-	2	0	COL6A3	237937758	0.000000	0.05858	0.079000	0.20413	0.696000	0.40369	-1.679000	0.01940	-0.193000	0.10415	0.650000	0.86243	AGA	.	.		0.473	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369	
CNTN6	27255	hgsc.bcm.edu	37	3	1414128	1414128	+	Silent	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:1414128A>G	ENST00000446702.2	+	13	2265	c.1638A>G	c.(1636-1638)aaA>aaG	p.K546K	CNTN6_ENST00000350110.2_Silent_p.K546K|CNTN6_ENST00000539053.1_Silent_p.K474K			Q9UQ52	CNTN6_HUMAN	contactin 6	546	Ig-like C2-type 6.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|central nervous system development (GO:0007417)|Notch signaling pathway (GO:0007219)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				breast(6)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(34)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	90		all_cancers(2;0.000164)|all_epithelial(2;0.107)		Epithelial(13;0.000233)|all cancers(10;0.0013)|OV - Ovarian serous cystadenocarcinoma(96;0.0139)		ACTTAAAAAAAGGAGTGGCTC	0.368																																					p.K546K		Atlas-SNP	.											.	CNTN6	245	.	0			c.A1638G						.						106.0	107.0	107.0					3																	1414128		2203	4300	6503	SO:0001819	synonymous_variant	27255	exon13			AAAAAAAGGAGTG	AB003592	CCDS2557.1	3p26-p25	2013-02-11			ENSG00000134115	ENSG00000134115		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	2176	protein-coding gene	gene with protein product	"""neural adhesion molecule"""	607220				9486763	Standard	NM_014461		Approved	NB-3	uc003bpa.3	Q9UQ52	OTTHUMG00000119030	ENST00000446702.2:c.1638A>G	chr3.hg19:g.1414128A>G		99.0	0.0		74.0	4.0	NM_014461	Q2KHM2	Silent	SNP	ENST00000446702.2	hg19	CCDS2557.1																																																																																			.	.		0.368	CNTN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239235.2	NM_014461	
SUMF1	285362	hgsc.bcm.edu	37	3	4403894	4403894	+	Silent	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:4403894T>C	ENST00000272902.5	-	9	1094	c.1059A>G	c.(1057-1059)acA>acG	p.T353T	SUMF1_ENST00000534863.1_Intron|SUMF1_ENST00000458465.2_Silent_p.T221T|SUMF1_ENST00000405420.2_Silent_p.T333T|SUMF1_ENST00000383843.5_Silent_p.T328T	NM_182760.3	NP_877437.2	Q8NBK3	SUMF1_HUMAN	sulfatase modifying factor 1	353	Interaction with sulfatases.				cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)	metal ion binding (GO:0046872)|oxidoreductase activity (GO:0016491)			breast(1)|endometrium(1)|large_intestine(2)|lung(5)|prostate(1)|upper_aerodigestive_tract(3)	13		Melanoma(143;0.068)|Colorectal(144;0.233)		Epithelial(13;0.0147)|OV - Ovarian serous cystadenocarcinoma(96;0.0444)|all cancers(10;0.0549)		AGCTATCAGGTGTGTTCTGGC	0.532																																					p.T353T		Atlas-SNP	.											.	SUMF1	23	.	0			c.A1059G						.						89.0	81.0	84.0					3																	4403894		2203	4300	6503	SO:0001819	synonymous_variant	285362	exon9			ATCAGGTGTGTTC	BC017005	CCDS2564.1, CCDS54548.1, CCDS54549.1	3p26.1	2009-07-23			ENSG00000144455	ENSG00000144455			20376	protein-coding gene	gene with protein product		607939				12757705, 12757706	Standard	NM_182760		Approved	FGE, UNQ3037	uc003bpz.2	Q8NBK3	OTTHUMG00000090269	ENST00000272902.5:c.1059A>G	chr3.hg19:g.4403894T>C		131.0	0.0		96.0	4.0	NM_182760	B4DXK5|B7XD05|E9PGL0|G5E9B0|Q0VAC6|Q0VAC7|Q2NL78|Q53ZE4|Q6UY39|Q96AK5|Q96DK8	Silent	SNP	ENST00000272902.5	hg19	CCDS2564.1																																																																																			.	.		0.532	SUMF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206591.2	NM_182760	
TADA3	10474	hgsc.bcm.edu	37	3	9827071	9827071	+	Silent	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:9827071A>G	ENST00000301964.2	-	7	1407	c.849T>C	c.(847-849)ccT>ccC	p.P283P	TADA3_ENST00000343450.2_Silent_p.P283P|TADA3_ENST00000440161.1_Silent_p.P283P	NM_006354.2	NP_006345.1	O75528	TADA3_HUMAN	transcriptional adaptor 3	283					chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|intracellular estrogen receptor signaling pathway (GO:0030520)|mitotic nuclear division (GO:0007067)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of histone deacetylation (GO:0031063)|regulation of protein phosphorylation (GO:0001932)|regulation of protein stability (GO:0031647)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of tubulin deacetylation (GO:0090043)|transcription, DNA-templated (GO:0006351)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|intracellular (GO:0005622)|mitotic spindle (GO:0072686)|nucleus (GO:0005634)|STAGA complex (GO:0030914)|transcription factor TFTC complex (GO:0033276)	ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|protein domain specific binding (GO:0019904)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(4)|skin(2)|upper_aerodigestive_tract(1)	16						CAGACATGTCAGGAATAGGAG	0.483																																					p.P283P		Atlas-SNP	.											.	TADA3	36	.	0			c.T849C						.						88.0	86.0	87.0					3																	9827071		2203	4300	6503	SO:0001819	synonymous_variant	10474	exon7			CATGTCAGGAATA	AF069733	CCDS2583.1, CCDS2584.1	3p25.3	2010-08-13	2009-10-02	2009-10-02	ENSG00000171148	ENSG00000171148			19422	protein-coding gene	gene with protein product		602945	"""transcriptional adaptor 3 (NGG1 homolog, yeast)-like"""	TADA3L		9674425, 11707411	Standard	NM_006354		Approved	FLJ20221, FLJ21329, ADA3, hADA3, NGG1	uc010hcn.2	O75528	OTTHUMG00000128440	ENST00000301964.2:c.849T>C	chr3.hg19:g.9827071A>G		155.0	0.0		123.0	5.0	NM_133480	Q6FI83|Q9UFS2	Silent	SNP	ENST00000301964.2	hg19	CCDS2583.1																																																																																			.	.		0.483	TADA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250236.1		
CRELD1	78987	hgsc.bcm.edu	37	3	9984844	9984844	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:9984844T>C	ENST00000383811.3	+	8	1500	c.901T>C	c.(901-903)Tcc>Ccc	p.S301P	CRELD1_ENST00000489674.1_3'UTR|CRELD1_ENST00000397170.3_Missense_Mutation_p.S301P|CRELD1_ENST00000326434.5_Missense_Mutation_p.S301P|CRELD1_ENST00000452070.1_Missense_Mutation_p.S301P	NM_015513.4	NP_056328	Q96HD1	CREL1_HUMAN	cysteine-rich with EGF-like domains 1	301					cardiac septum development (GO:0003279)|endocardial cushion development (GO:0003197)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|stomach(1)|urinary_tract(1)	14						GCAGGTGGGCTCCAAGTGTCT	0.607																																					p.S301P		Atlas-SNP	.											.	CRELD1	48	.	0			c.T901C						.						50.0	50.0	50.0					3																	9984844		2203	4300	6503	SO:0001583	missense	78987	exon9			GTGGGCTCCAAGT	AF452623	CCDS2593.1, CCDS33693.1	3p25.3	2005-12-08	2004-02-13		ENSG00000163703	ENSG00000163703			14630	protein-coding gene	gene with protein product		607170	"""atrioventricular septal defect 2"""	AVSD2		10922384, 12137942	Standard	NM_015513		Approved		uc003buf.3	Q96HD1	OTTHUMG00000128653	ENST00000383811.3:c.901T>C	chr3.hg19:g.9984844T>C	ENSP00000373322:p.Ser301Pro	204.0	0.0		157.0	7.0	NM_001077415	A8MX90|B2RAA9|Q6I9X5|Q8NFT4|Q9Y409	Missense_Mutation	SNP	ENST00000383811.3	hg19	CCDS2593.1	.	.	.	.	.	.	.	.	.	.	T	17.45	3.392787	0.62066	.	.	ENSG00000163703	ENST00000397170;ENST00000383811;ENST00000452070;ENST00000326434	D;D;D;D	0.87966	-2.32;-2.32;-2.32;-2.32	4.67	3.56	0.40772	Growth factor, receptor (1);	0.244831	0.39834	N	0.001255	T	0.80369	0.4610	N	0.21240	0.645	0.33581	D	0.599836	P;P	0.51933	0.855;0.949	B;P	0.48454	0.36;0.578	T	0.82384	-0.0484	9	.	.	.	.	8.403	0.32597	0.0:0.0:0.3872:0.6128	.	301;301	Q96HD1;Q96HD1-2	CREL1_HUMAN;.	P	301	ENSP00000380355:S301P;ENSP00000373322:S301P;ENSP00000393643:S301P;ENSP00000321856:S301P	.	S	+	1	0	CRELD1	9959844	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	5.774000	0.68906	1.734000	0.51633	0.459000	0.35465	TCC	.	.		0.607	CRELD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250533.1	NM_015513	
TMEM43	79188	hgsc.bcm.edu	37	3	14174380	14174380	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:14174380T>C	ENST00000306077.4	+	6	711	c.457T>C	c.(457-459)Tca>Cca	p.S153P	RP11-434D12.1_ENST00000608606.1_5'Flank	NM_024334.2	NP_077310.1	Q9BTV4	TMM43_HUMAN	transmembrane protein 43	153					nuclear membrane organization (GO:0071763)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(1)|cervix(3)|endometrium(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|skin(2)	19						TGAATGGAGGTCAGAAATCAT	0.562																																					p.S153P		Atlas-SNP	.											.	TMEM43	33	.	0			c.T457C						.						85.0	87.0	86.0					3																	14174380		2203	4300	6503	SO:0001583	missense	79188	exon6			TGGAGGTCAGAAA	BC008054	CCDS2618.1	3p25.1	2014-09-17			ENSG00000170876	ENSG00000170876			28472	protein-coding gene	gene with protein product		612048	"""arrhythmogenic right ventricular dysplasia 5"""	ARVD5		11230166, 18313022	Standard	NM_024334		Approved	MGC3222, DKFZp586G1919, LUMA	uc003byk.2	Q9BTV4	OTTHUMG00000129802	ENST00000306077.4:c.457T>C	chr3.hg19:g.14174380T>C	ENSP00000303992:p.Ser153Pro	228.0	0.0		138.0	8.0	NM_024334	Q7L4N5|Q8NC30|Q96A63|Q96F19|Q96JX0|Q9H076	Missense_Mutation	SNP	ENST00000306077.4	hg19	CCDS2618.1	.	.	.	.	.	.	.	.	.	.	T	17.50	3.405530	0.62288	.	.	ENSG00000170876	ENST00000306077	T	0.40476	1.03	5.08	3.84	0.44239	.	0.138505	0.50627	D	0.000118	T	0.32164	0.0820	L	0.39898	1.24	0.47778	D	0.99951	P;P	0.39326	0.668;0.473	B;B	0.38712	0.233;0.28	T	0.14671	-1.0464	10	0.54805	T	0.06	-10.7548	7.6526	0.28356	0.0:0.0761:0.1408:0.7832	.	83;153	Q8TEP9;Q9BTV4	.;TMM43_HUMAN	P	153	ENSP00000303992:S153P	ENSP00000303992:S153P	S	+	1	0	TMEM43	14149381	1.000000	0.71417	0.997000	0.53966	0.922000	0.55478	3.222000	0.51223	1.900000	0.55004	0.482000	0.46254	TCA	.	.		0.562	TMEM43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252030.2	NM_024334	
SH3BP5	9467	hgsc.bcm.edu	37	3	15311265	15311265	+	Silent	SNP	C	C	T			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:15311265C>T	ENST00000383791.3	-	4	670	c.450G>A	c.(448-450)caG>caA	p.Q150Q	SH3BP5_ENST00000465894.2_5'Flank|SH3BP5_ENST00000253688.5_5'UTR|SH3BP5_ENST00000426925.1_5'UTR|SH3BP5_ENST00000408919.3_5'UTR	NM_004844.4	NP_004835.2	O60239	3BP5_HUMAN	SH3-domain binding protein 5 (BTK-associated)	150					intracellular signal transduction (GO:0035556)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	protein kinase inhibitor activity (GO:0004860)			NS(1)|endometrium(3)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)	12						CGGAGTCGAACTGCCGCTTGT	0.652																																					p.Q150Q		Atlas-SNP	.											.	SH3BP5	32	.	0			c.G450A						.						88.0	88.0	88.0					3																	15311265		2203	4300	6503	SO:0001819	synonymous_variant	9467	exon4			GTCGAACTGCCGC	AB005047	CCDS2625.2, CCDS43055.1	3p24.3	2008-07-10			ENSG00000131370	ENSG00000131370			10827	protein-coding gene	gene with protein product	"""SH3 binding protein"""	605612				9571151, 10339589	Standard	NM_004844		Approved	Sab	uc003bzp.2	O60239	OTTHUMG00000129859	ENST00000383791.3:c.450G>A	chr3.hg19:g.15311265C>T		166.0	0.0		135.0	6.0	NM_004844	B3KQW6|Q5JWV9	Silent	SNP	ENST00000383791.3	hg19	CCDS2625.2																																																																																			.	.		0.652	SH3BP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340740.2	NM_004844	
CTNNB1	1499	hgsc.bcm.edu	37	3	41266104	41266104	+	Missense_Mutation	SNP	G	G	T	rs28931589|rs121913416		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:41266104G>T	ENST00000349496.5	+	3	381	c.101G>T	c.(100-102)gGa>gTa	p.G34V	CTNNB1_ENST00000396185.3_Missense_Mutation_p.G34V|CTNNB1_ENST00000405570.1_Missense_Mutation_p.G34V|CTNNB1_ENST00000453024.1_Missense_Mutation_p.G27V|CTNNB1_ENST00000396183.3_Missense_Mutation_p.G34V	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	34			G -> E (in PTR). {ECO:0000269|PubMed:10192393}.|G -> R (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|G -> V (in hepatoblastoma; dbSNP:rs28931589). {ECO:0000269|PubMed:9927029}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|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)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.G34E(73)|p.G34V(72)|p.A5_A80del(53)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.?(4)|p.V22_G38del(3)|p.W25_I140del(3)|p.T3_A126del(2)|p.A5fs*7(2)|p.D32_S47del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.A13_R151del(1)|p.D32_H36>D(1)|p.M14_S45del(1)|p.A20_N141del(1)|p.M1_A87del(1)|p.D11_Y142>H(1)|p.H24_G38del(1)|p.S23_I35del(1)|p.Y30_A97del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.Q28_A43del(1)|p.A5_T59del(1)|p.A20_I35del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.S23_A39del(1)|p.H24_M131del(1)|p.A21_A80del(1)|p.D32fs*9(1)|p.A5_T40del(1)|p.S29_H36del(1)|p.A5_E54del(1)|p.W25_I35del(1)|p.S33_S37del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.Q28_Q61del(1)|p.A20_S111del(1)|p.Y30_T40del(1)|p.GIHS34?(1)|p.A5_I35del(1)|p.D32_H36del(1)|p.Y30_A80del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		CTGGACTCTGGAATCCATTCT	0.488	G34E(AGS_STOMACH)	15	"""H, Mis, T"""	PLAG1	"""colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"""				Pilomatrixoma, Familial Clustering of																												p.G34V	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"""catenin (cadherin-associated protein), beta 1"""		"""E, M, O"""	CTNNB1,gallbladder,other,0,161	CTNNB1	4904	.	276	Substitution - Missense(145)|Deletion - In frame(105)|Complex - deletion inframe(16)|Unknown(7)|Deletion - Frameshift(3)	liver(146)|endometrium(30)|large_intestine(27)|stomach(21)|central_nervous_system(20)|skin(8)|pancreas(8)|ovary(6)|small_intestine(2)|lung(2)|adrenal_gland(1)|haematopoietic_and_lymphoid_tissue(1)|biliary_tract(1)|pituitary(1)|prostate(1)|bone(1)	c.G101T						.						93.0	78.0	83.0					3																	41266104		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	ACTCTGGAATCCA	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"""Armadillo repeat containing"""	2514	protein-coding gene	gene with protein product		116806	"""catenin (cadherin-associated protein), beta 1 (88kD)"""	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.101G>T	chr3.hg19:g.41266104G>T	ENSP00000344456:p.Gly34Val	491.0	0.0		299.0	112.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	G	23.7	4.450603	0.84101	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.53206	0.63;0.63;0.63;0.63;0.63;0.63;0.63;0.63;0.63	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.72053	0.3413	M	0.79258	2.445	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.74188	-0.3746	10	0.87932	D	0	-31.2232	19.9596	0.97236	0.0:0.0:1.0:0.0	rs28931589	34	P35222	CTNB1_HUMAN	V	27;34;34;34;34;27;34;34;34	ENSP00000400508:G27V;ENSP00000385604:G34V;ENSP00000412219:G34V;ENSP00000379486:G34V;ENSP00000344456:G34V;ENSP00000411226:G27V;ENSP00000379488:G34V;ENSP00000409302:G34V;ENSP00000401599:G34V	ENSP00000344456:G34V	G	+	2	0	CTNNB1	41241108	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.869000	0.99810	2.726000	0.93360	0.655000	0.94253	GGA	.	.		0.488	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210	
CCR5	1234	hgsc.bcm.edu	37	3	46414409	46414409	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:46414409T>C	ENST00000292303.4	+	2	162	c.16T>C	c.(16-18)Tca>Cca	p.S6P	RP11-24F11.2_ENST00000451485.1_RNA|CCR5_ENST00000343801.4_Missense_Mutation_p.S6P|CCR5_ENST00000445772.1_Missense_Mutation_p.S6P	NM_001100168.1	NP_001093638.1	P51681	CCR5_HUMAN	chemokine (C-C motif) receptor 5 (gene/pseudogene)	6					calcium ion transport (GO:0006816)|calcium-mediated signaling (GO:0019722)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular defense response (GO:0006968)|cellular response to lipopolysaccharide (GO:0071222)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|dendritic cell chemotaxis (GO:0002407)|entry into host cell (GO:0030260)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|MAPK cascade (GO:0000165)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to cholesterol (GO:0070723)|signaling (GO:0023052)|viral process (GO:0016032)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|C-C chemokine binding (GO:0019957)|C-C chemokine receptor activity (GO:0016493)|chemokine (C-C motif) ligand 5 binding (GO:0071791)|chemokine receptor activity (GO:0004950)|coreceptor activity (GO:0015026)|phosphatidylinositol phospholipase C activity (GO:0004435)			central_nervous_system(1)|large_intestine(2)|lung(13)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	20				BRCA - Breast invasive adenocarcinoma(193;0.00112)|KIRC - Kidney renal clear cell carcinoma(197;0.017)|Kidney(197;0.02)	Maraviroc(DB04835)	TTATCAAGTGTCAAGTCCAAT	0.408																																					p.S6P		Atlas-SNP	.											.	CCR5	128	.	0			c.T16C						.						108.0	116.0	113.0					3																	46414409		2203	4296	6499	SO:0001583	missense	1234	exon3			CAAGTGTCAAGTC		CCDS2739.1	3p21	2012-08-08	2012-01-23		ENSG00000160791	ENSG00000160791		"""GPCR / Class A : Chemokine receptors : C-C motif"", ""CD molecules"""	1606	protein-coding gene	gene with protein product		601373	"""chemokine (C-C motif) receptor 5"""	CMKBR5		8639485	Standard	NM_001100168		Approved	CKR-5, CC-CKR-5, CKR5, CD195, IDDM22	uc003cpo.4	P51681	OTTHUMG00000133481	ENST00000292303.4:c.16T>C	chr3.hg19:g.46414409T>C	ENSP00000292303:p.Ser6Pro	107.0	0.0		83.0	5.0	NM_000579	O14692|O14693|O14695|O14696|O14697|O14698|O14699|O14700|O14701|O14702|O14703|O14704|O14705|O14706|O14707|O14708|O15538|Q9UPA4	Missense_Mutation	SNP	ENST00000292303.4	hg19	CCDS2739.1	.	.	.	.	.	.	.	.	.	.	T	17.55	3.417258	0.62622	.	.	ENSG00000160791	ENST00000343801;ENST00000292303;ENST00000445772	T;T;T	0.71222	-0.55;-0.55;-0.55	5.16	-10.3	0.00346	.	0.662303	0.12189	U	0.491419	T	0.42268	0.1195	N	0.20401	0.57	0.09310	N	1	B	0.34226	0.443	B	0.34301	0.179	T	0.35871	-0.9771	10	0.31617	T	0.26	.	3.9897	0.09532	0.141:0.0818:0.1953:0.5819	.	6	P51681	CCR5_HUMAN	P	6	ENSP00000343985:S6P;ENSP00000292303:S6P;ENSP00000404881:S6P	ENSP00000292303:S6P	S	+	1	0	CCR5	46389413	0.000000	0.05858	0.000000	0.03702	0.866000	0.49608	-4.085000	0.00298	-3.515000	0.00149	0.459000	0.35465	TCA	.	.		0.408	CCR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257377.2	NM_000579	
SCAP	22937	hgsc.bcm.edu	37	3	47459317	47459317	+	Splice_Site	SNP	C	C	T			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:47459317C>T	ENST00000265565.5	-	17	2860		c.e17-1		SCAP_ENST00000545718.1_Intron|SCAP_ENST00000465628.1_5'Flank|SCAP_ENST00000441517.2_Intron	NM_012235.2	NP_036367.2	Q12770	SCAP_HUMAN	SREBF chaperone						aging (GO:0007568)|cholesterol metabolic process (GO:0008203)|negative regulation of cholesterol biosynthetic process (GO:0045541)|positive regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045716)|regulation of fatty acid biosynthetic process (GO:0042304)|response to hypoxia (GO:0001666)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)|SREBP signaling pathway (GO:0032933)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|protein complex (GO:0043234)	unfolded protein binding (GO:0051082)			endometrium(4)|kidney(1)|large_intestine(4)|liver(1)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	26				BRCA - Breast invasive adenocarcinoma(193;0.000278)|KIRC - Kidney renal clear cell carcinoma(197;0.00592)|Kidney(197;0.00679)		GCGCTGCCTGCTGGGGGCCAg	0.716																																					.	Pancreas(149;978 1908 29304 37806 46700)	Atlas-SNP	.											.	SCAP	88	.	0			c.2448-1G>A						.						12.0	14.0	14.0					3																	47459317		1788	3567	5355	SO:0001630	splice_region_variant	22937	exon18			TGCCTGCTGGGGG	BC020987	CCDS2755.2	3p21.31	2013-01-10			ENSG00000114650	ENSG00000114650		"""WD repeat domain containing"""	30634	protein-coding gene	gene with protein product	"""SREBP cleavage activating protein"""	601510				8898195, 8724849, 10570913	Standard	XM_005264967		Approved	KIAA0199	uc003crh.1	Q12770	OTTHUMG00000125539	ENST00000265565.5:c.2448-1G>A	chr3.hg19:g.47459317C>T		102.0	0.0		85.0	4.0	NM_012235	Q8N2E0|Q8WUA1	Splice_Site	SNP	ENST00000265565.5	hg19	CCDS2755.2	.	.	.	.	.	.	.	.	.	.	C	18.66	3.671428	0.67814	.	.	ENSG00000114650	ENST00000265565;ENST00000383739	.	.	.	4.62	-0.573	0.11742	.	.	.	.	.	.	.	.	.	.	.	0.36060	D	0.841372	.	.	.	.	.	.	.	.	.	.	.	.	.	.	1.7192	0.02908	0.1395:0.2827:0.3706:0.2073	.	.	.	.	.	-1	.	.	.	-	.	.	SCAP	47434321	0.270000	0.24152	0.199000	0.23439	0.951000	0.60555	0.542000	0.23222	0.195000	0.20347	0.550000	0.68814	.	.	.		0.716	SCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246872.2	NM_012235	Intron
SMARCC1	6599	hgsc.bcm.edu	37	3	47727630	47727630	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:47727630T>C	ENST00000254480.5	-	14	1413	c.1294A>G	c.(1294-1296)Agt>Ggt	p.S432G	SMARCC1_ENST00000425518.1_5'UTR	NM_003074.3	NP_003065.3	Q92922	SMRC1_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 1	432					ATP-dependent chromatin remodeling (GO:0043044)|chromatin remodeling (GO:0006338)|insulin receptor signaling pathway (GO:0008286)|nervous system development (GO:0007399)|nucleosome disassembly (GO:0006337)|organ morphogenesis (GO:0009887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)|XY body (GO:0001741)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|protein N-terminus binding (GO:0047485)|transcription coactivator activity (GO:0003713)			breast(1)|endometrium(5)|kidney(2)|large_intestine(3)|lung(15)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	33				BRCA - Breast invasive adenocarcinoma(193;7.47e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00862)|Kidney(197;0.01)		ACTGATCGACTCTGATCACCT	0.368																																					p.S432G		Atlas-SNP	.											.	SMARCC1	85	.	0			c.A1294G						.						150.0	129.0	136.0					3																	47727630		2203	4300	6503	SO:0001583	missense	6599	exon14			ATCGACTCTGATC	U66615	CCDS2758.1	3p21.31	2008-05-15			ENSG00000173473	ENSG00000173473			11104	protein-coding gene	gene with protein product		601732				8804307	Standard	NM_003074		Approved	BAF155, SRG3, Rsc8, CRACC1	uc003crq.2	Q92922	OTTHUMG00000133519	ENST00000254480.5:c.1294A>G	chr3.hg19:g.47727630T>C	ENSP00000254480:p.Ser432Gly	119.0	0.0		133.0	6.0	NM_003074	Q17RS0|Q6P172|Q8IWH2	Missense_Mutation	SNP	ENST00000254480.5	hg19	CCDS2758.1	.	.	.	.	.	.	.	.	.	.	T	11.85	1.761401	0.31228	.	.	ENSG00000173473	ENST00000254480	T	0.46451	0.87	5.84	5.84	0.93424	.	0.115587	0.85682	N	0.000000	T	0.32315	0.0825	N	0.25332	0.735	0.44352	D	0.997241	B	0.02656	0.0	B	0.04013	0.001	T	0.06058	-1.0848	10	0.32370	T	0.25	-9.119	15.1063	0.72324	0.0:0.0:0.0:1.0	.	432	Q92922	SMRC1_HUMAN	G	432	ENSP00000254480:S432G	ENSP00000254480:S432G	S	-	1	0	SMARCC1	47702634	0.998000	0.40836	0.996000	0.52242	0.390000	0.30446	2.761000	0.47589	2.240000	0.73641	0.514000	0.50259	AGT	.	.		0.368	SMARCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257491.1		
COL7A1	1294	hgsc.bcm.edu	37	3	48608294	48608294	+	Splice_Site	SNP	C	C	T			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:48608294C>T	ENST00000328333.8	-	94	7379	c.7272G>A	c.(7270-7272)cgG>cgA	p.R2424R	COL7A1_ENST00000454817.1_Splice_Site_p.R2392R	NM_000094.3	NP_000085.1	Q02388	CO7A1_HUMAN	collagen, type VII, alpha 1	2424	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)		AGCCCCTCACCCGCTCTCCAC	0.662																																					p.R2424R		Atlas-SNP	.											.	COL7A1	320	.	0			c.G7272A						.						34.0	28.0	30.0					3																	48608294		2202	4300	6502	SO:0001630	splice_region_variant	1294	exon94			CCTCACCCGCTCT	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.7272+1G>A	chr3.hg19:g.48608294C>T		210.0	0.0		173.0	74.0	NM_000094	Q14054|Q16507	Silent	SNP	ENST00000328333.8	hg19	CCDS2773.1																																																																																			.	.		0.662	COL7A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257519.1	NM_000094	Silent
APEH	327	hgsc.bcm.edu	37	3	49722913	49722913	+	IGR	SNP	C	C	T			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:49722913C>T	ENST00000296456.5	+	0	3220				MST1_ENST00000494828.2_5'Flank|MST1_ENST00000383728.3_3'UTR|MST1_ENST00000449682.2_Missense_Mutation_p.D472N|AC099668.5_ENST00000563780.1_RNA	NM_001640.3	NP_001631.3	P13798	ACPH_HUMAN	acylaminoacyl-peptide hydrolase						beta-amyloid metabolic process (GO:0050435)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear membrane (GO:0031965)	omega peptidase activity (GO:0008242)|poly(A) RNA binding (GO:0044822)|serine-type endopeptidase activity (GO:0004252)			endometrium(3)|large_intestine(1)|lung(6)|ovary(1)|skin(1)|stomach(2)|urinary_tract(1)	15				BRCA - Breast invasive adenocarcinoma(193;4.53e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		CCTGGGGGGTCCAGGATTGAT	0.592																																					p.D472N		Atlas-SNP	.											.	MST1	84	.	0			c.G1414A						.						29.0	32.0	31.0					3																	49722913		2202	4299	6501	SO:0001628	intergenic_variant	4485	exon12			GGGGGTCCAGGAT	D38441	CCDS2801.1	3p21	2013-05-29	2013-05-29		ENSG00000164062	ENSG00000164062	3.4.19.1		586	protein-coding gene	gene with protein product	"""acylaminoacyl-peptidase"""	102645	"""N-acylaminoacyl-peptide hydrolase"""	D3F15S2, DNF15S2, D3S48E		2392324	Standard	NM_001640		Approved		uc003cxf.3	P13798	OTTHUMG00000156882		chr3.hg19:g.49722913C>T		366.0	0.0		421.0	22.0	NM_020998	Q9BQ33|Q9P0Y2	Missense_Mutation	SNP	ENST00000296456.5	hg19	CCDS2801.1	.	.	.	.	.	.	.	.	.	.	C	10.90	1.481708	0.26598	.	.	ENSG00000173531	ENST00000449682	T	0.79940	-1.32	4.78	2.98	0.34508	.	0.707688	0.11995	N	0.509451	T	0.60392	0.2265	N	0.08118	0	0.80722	D	1	B	0.21753	0.06	B	0.26094	0.066	T	0.44436	-0.9328	10	0.10636	T	0.68	.	8.1354	0.31052	0.0:0.8059:0.0:0.1941	.	472	G3XAK1	.	N	472	ENSP00000414287:D472N	ENSP00000414287:D472N	D	-	1	0	MST1	49697917	1.000000	0.71417	0.995000	0.50966	0.784000	0.44337	3.079000	0.50104	0.689000	0.31550	0.655000	0.94253	GAC	.	.		0.592	APEH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346415.2		
DNAH1	25981	hgsc.bcm.edu	37	3	52430409	52430409	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:52430409T>C	ENST00000420323.2	+	71	11546	c.11285T>C	c.(11284-11286)cTc>cCc	p.L3762P		NM_015512.4	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	3827	AAA 6. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|response to mechanical stimulus (GO:0009612)	axonemal dynein complex (GO:0005858)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			cervix(2)|endometrium(18)|kidney(6)|large_intestine(3)|lung(31)|prostate(1)|urinary_tract(1)	62				BRCA - Breast invasive adenocarcinoma(193;2.02e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000207)|Kidney(197;0.0022)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		CGCCTCTGGCTCACCAGCCTG	0.622																																					p.L3762P		Atlas-SNP	.											.	DNAH1	534	.	0			c.T11285C						.						27.0	31.0	30.0					3																	52430409		2092	4214	6306	SO:0001583	missense	25981	exon71			TCTGGCTCACCAG	U61738	CCDS46842.1	3p21-p14	2008-02-05	2006-09-04		ENSG00000114841	ENSG00000114841		"""Axonemal dyneins"""	2940	protein-coding gene	gene with protein product		603332	"""dynein, axonemal, heavy polypeptide 1"""			8812413, 9256245	Standard	NM_015512		Approved	XLHSRF-1, DNAHC1, HDHC7, HL-11, HL11	uc011bef.2	Q9P2D7	OTTHUMG00000158378	ENST00000420323.2:c.11285T>C	chr3.hg19:g.52430409T>C	ENSP00000401514:p.Leu3762Pro	120.0	0.0		76.0	5.0	NM_015512	B0I1R6|O00436|O15435|O95491|Q6ZU48|Q86YK7|Q8TEJ4|Q92863|Q9H8E6|Q9UFW6|Q9Y4Z7	Missense_Mutation	SNP	ENST00000420323.2	hg19	CCDS46842.1	.	.	.	.	.	.	.	.	.	.	T	18.28	3.588217	0.66105	.	.	ENSG00000114841	ENST00000420323;ENST00000273600	T	0.20069	2.1	4.35	4.35	0.52113	.	0.000000	0.64402	D	0.000011	T	0.64692	0.2621	H	0.99104	4.43	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.80487	-0.1361	10	0.87932	D	0	.	13.7114	0.62670	0.0:0.0:0.0:1.0	.	3762;3827	C9JXH6;Q9P2D7-2	.;.	P	3762;515	ENSP00000401514:L3762P	ENSP00000273600:L515P	L	+	2	0	DNAH1	52405449	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	5.757000	0.68766	1.831000	0.53308	0.402000	0.26972	CTC	.	.		0.622	DNAH1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350816.1	NM_015512	
NISCH	11188	hgsc.bcm.edu	37	3	52524124	52524124	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:52524124T>C	ENST00000479054.1	+	19	3562	c.3490T>C	c.(3490-3492)Tcc>Ccc	p.S1164P	NISCH_ENST00000345716.4_Missense_Mutation_p.S1164P			Q9Y2I1	NISCH_HUMAN	nischarin	1164					actin cytoskeleton organization (GO:0030036)|apoptotic process (GO:0006915)|glucose metabolic process (GO:0006006)|negative regulation of cell migration (GO:0030336)|norepinephrine secretion (GO:0048243)|Rac protein signal transduction (GO:0016601)|regulation of blood pressure (GO:0008217)|regulation of synaptic transmission, GABAergic (GO:0032228)	cytosol (GO:0005829)|endosome (GO:0005768)|membrane (GO:0016020)|plasma membrane (GO:0005886)	G-protein coupled amine receptor activity (GO:0008227)|identical protein binding (GO:0042802)|phosphatidylinositol binding (GO:0035091)			NS(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(9)|ovary(4)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	33				BRCA - Breast invasive adenocarcinoma(193;1.93e-05)|Kidney(197;0.00216)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)|OV - Ovarian serous cystadenocarcinoma(275;0.0577)	Tizanidine(DB00697)	CCTCATGTGGTCCTCGGTGGT	0.622																																					p.S1164P		Atlas-SNP	.											.	NISCH	97	.	0			c.T3490C						.						76.0	60.0	65.0					3																	52524124		2203	4300	6503	SO:0001583	missense	11188	exon18			ATGTGGTCCTCGG	AF082516	CCDS33767.1, CCDS63651.1, CCDS63652.1	3p21.1	2008-07-18			ENSG00000010322	ENSG00000010322			18006	protein-coding gene	gene with protein product	"""imidazoline receptor candidate"", ""I-1 receptor candidate protein"", ""imidazoline receptor antisera selected"""	615507				11912194, 10882231	Standard	NM_007184		Approved	KIAA0975, I-1, IRAS	uc003ded.4	Q9Y2I1	OTTHUMG00000158571	ENST00000479054.1:c.3490T>C	chr3.hg19:g.52524124T>C	ENSP00000418232:p.Ser1164Pro	173.0	0.0		124.0	5.0	NM_007184	C9J245|Q6PGP3|Q6PIB4|Q7L8M3|Q7Z2X6|Q9UES6|Q9UEU4|Q9UFW3	Missense_Mutation	SNP	ENST00000479054.1	hg19	CCDS33767.1	.	.	.	.	.	.	.	.	.	.	T	21.6	4.170001	0.78452	.	.	ENSG00000010322	ENST00000479054;ENST00000345716;ENST00000414197	T;T	0.10382	2.88;2.88	5.18	5.18	0.71444	.	0.248715	0.36740	N	0.002423	T	0.09202	0.0227	L	0.27053	0.805	0.31244	N	0.694856	P	0.36789	0.57	B	0.36959	0.237	T	0.04946	-1.0916	10	0.72032	D	0.01	-15.1695	11.088	0.48099	0.0:0.0:0.1549:0.8451	.	1164	Q9Y2I1	NISCH_HUMAN	P	1164;1164;508	ENSP00000418232:S1164P;ENSP00000339958:S1164P	ENSP00000339958:S1164P	S	+	1	0	NISCH	52499164	1.000000	0.71417	0.999000	0.59377	0.970000	0.65996	3.096000	0.50243	1.969000	0.57287	0.459000	0.35465	TCC	.	.		0.622	NISCH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351357.1	NM_007184	
CHDH	55349	hgsc.bcm.edu	37	3	53855776	53855776	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:53855776T>C	ENST00000315251.6	-	5	1320	c.883A>G	c.(883-885)Agt>Ggt	p.S295G		NM_018397.4	NP_060867.2	Q8NE62	CHDH_HUMAN	choline dehydrogenase	295					glycine betaine biosynthetic process from choline (GO:0019285)	mitochondrial inner membrane (GO:0005743)	choline dehydrogenase activity (GO:0008812)|flavin adenine dinucleotide binding (GO:0050660)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(2)|prostate(1)	17		Hepatocellular(537;0.152)		BRCA - Breast invasive adenocarcinoma(193;0.000158)|KIRC - Kidney renal clear cell carcinoma(284;0.00588)|Kidney(284;0.00673)|OV - Ovarian serous cystadenocarcinoma(275;0.118)	Choline(DB00122)	GCACCTCCACTCAGAATCACC	0.567																																					p.S295G		Atlas-SNP	.											.	CHDH	34	.	0			c.A883G						.						116.0	107.0	110.0					3																	53855776		2203	4300	6503	SO:0001583	missense	55349	exon5			CTCCACTCAGAAT	AJ272267	CCDS2873.1	3p21	2004-11-24			ENSG00000016391	ENSG00000016391	1.1.99.1		24288	protein-coding gene	gene with protein product							Standard	NM_018397		Approved		uc003dgz.3	Q8NE62	OTTHUMG00000158281	ENST00000315251.6:c.883A>G	chr3.hg19:g.53855776T>C	ENSP00000319851:p.Ser295Gly	133.0	0.0		92.0	4.0	NM_018397	Q9NY17	Missense_Mutation	SNP	ENST00000315251.6	hg19	CCDS2873.1	.	.	.	.	.	.	.	.	.	.	T	28.2	4.900201	0.92035	.	.	ENSG00000016391	ENST00000315251	T	0.69040	-0.37	5.6	5.6	0.85130	Glucose-methanol-choline oxidoreductase, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.83691	0.5309	M	0.90870	3.155	0.80722	D	1	D	0.56035	0.974	P	0.61070	0.883	D	0.86520	0.1815	10	0.49607	T	0.09	-24.8983	15.8023	0.78463	0.0:0.0:0.0:1.0	.	295	Q8NE62	CHDH_HUMAN	G	295	ENSP00000319851:S295G	ENSP00000319851:S295G	S	-	1	0	CHDH	53830816	1.000000	0.71417	0.998000	0.56505	0.989000	0.77384	3.748000	0.55142	2.137000	0.66172	0.533000	0.62120	AGT	.	.		0.567	CHDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350567.2	NM_018397	
SPATA12	353324	hgsc.bcm.edu	37	3	57107744	57107744	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:57107744T>C	ENST00000334325.1	+	2	697	c.22T>C	c.(22-24)Tgt>Cgt	p.C8R	ARHGEF3_ENST00000338458.4_Intron	NM_181727.1	NP_859078.1	Q7Z6I5	SPT12_HUMAN	spermatogenesis associated 12	8										large_intestine(2)|lung(1)	3				KIRC - Kidney renal clear cell carcinoma(284;0.0111)|Kidney(284;0.0129)		TGCTCTGACTTGTGGGTCCAC	0.547																																					p.C8R		Atlas-SNP	.											.	SPATA12	9	.	0			c.T22C						.						43.0	43.0	43.0					3																	57107744		2203	4300	6503	SO:0001583	missense	353324	exon2			CTGACTTGTGGGT	AY221117	CCDS2879.1	3p21.2	2012-09-19			ENSG00000186451	ENSG00000186451			23221	protein-coding gene	gene with protein product		609869				22981541, 17251597	Standard	NM_181727		Approved		uc003dij.1	Q7Z6I5	OTTHUMG00000158862	ENST00000334325.1:c.22T>C	chr3.hg19:g.57107744T>C	ENSP00000335392:p.Cys8Arg	108.0	0.0		59.0	4.0	NM_181727	A0AVA8|B2RMW1	Missense_Mutation	SNP	ENST00000334325.1	hg19	CCDS2879.1	.	.	.	.	.	.	.	.	.	.	T	8.868	0.948493	0.18356	.	.	ENSG00000186451	ENST00000334325	.	.	.	3.11	0.529	0.17095	.	.	.	.	.	T	0.25644	0.0624	N	0.08118	0	0.09310	N	1	D	0.69078	0.997	P	0.62184	0.899	T	0.10636	-1.0621	8	0.87932	D	0	.	3.678	0.08299	0.2232:0.0:0.2312:0.5455	.	8	Q7Z6I5	SPT12_HUMAN	R	8	.	ENSP00000335392:C8R	C	+	1	0	SPATA12	57082784	0.004000	0.15560	0.006000	0.13384	0.165000	0.22458	0.158000	0.16422	0.106000	0.17784	-0.460000	0.05396	TGT	.	.		0.547	SPATA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352457.2	NM_181727	
ADAMTS9	56999	hgsc.bcm.edu	37	3	64619493	64619493	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:64619493T>C	ENST00000498707.1	-	13	2261	c.1919A>G	c.(1918-1920)gAg>gGg	p.E640G	ADAMTS9_ENST00000295903.4_Missense_Mutation_p.E612G	NM_182920.1	NP_891550.1	Q9P2N4	ATS9_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 9	640	TSP type-1 1. {ECO:0000255|PROSITE- ProRule:PRU00210}.				glycoprotein catabolic process (GO:0006516)|multicellular organismal development (GO:0007275)|positive regulation of melanocyte differentiation (GO:0045636)|protein transport (GO:0015031)|proteolysis (GO:0006508)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(9)|kidney(4)|large_intestine(17)|liver(4)|lung(43)|ovary(3)|prostate(3)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	100		Lung NSC(201;0.00682)		BRCA - Breast invasive adenocarcinoma(55;0.00142)|Kidney(15;0.00202)|KIRC - Kidney renal clear cell carcinoma(15;0.00221)		GAGACATGGCTCCGTGTTGCA	0.438																																					p.E640G		Atlas-SNP	.											.	ADAMTS9	206	.	0			c.A1919G						.						131.0	114.0	120.0					3																	64619493		2203	4300	6503	SO:0001583	missense	56999	exon13			CATGGCTCCGTGT	AF261918	CCDS2903.1	3p14.1	2008-05-15	2005-08-19		ENSG00000163638	ENSG00000163638		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	13202	protein-coding gene	gene with protein product		605421	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 9"""			10936055	Standard	NM_182920		Approved	KIAA1312	uc003dmg.3	Q9P2N4	OTTHUMG00000158722	ENST00000498707.1:c.1919A>G	chr3.hg19:g.64619493T>C	ENSP00000418735:p.Glu640Gly	138.0	0.0		106.0	5.0	NM_182920	A1L4L0|B7ZVX9|B9ZVN0|Q9NR29	Missense_Mutation	SNP	ENST00000498707.1	hg19	CCDS2903.1	.	.	.	.	.	.	.	.	.	.	T	32	5.119479	0.94385	.	.	ENSG00000163638	ENST00000295903;ENST00000498707	T;T	0.03745	3.82;3.82	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	T	0.13756	0.0333	L	0.47078	1.49	0.80722	D	1	D;D;D;D	0.89917	0.994;0.995;1.0;0.987	D;D;D;P	0.91635	0.96;0.948;0.999;0.867	T	0.00505	-1.1700	10	0.66056	D	0.02	.	15.6399	0.76989	0.0:0.0:0.0:1.0	.	612;640;640;640	B7ZVX9;Q9P2N4-2;Q9P2N4-1;Q9P2N4	.;.;.;ATS9_HUMAN	G	612;640	ENSP00000295903:E612G;ENSP00000418735:E640G	ENSP00000295903:E612G	E	-	2	0	ADAMTS9	64594533	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	7.698000	0.84413	2.103000	0.63969	0.533000	0.62120	GAG	.	.		0.438	ADAMTS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351891.1		
LMOD3	56203	hgsc.bcm.edu	37	3	69171278	69171278	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:69171278T>C	ENST00000420581.2	-	1	439	c.260A>G	c.(259-261)gAg>gGg	p.E87G	LMOD3_ENST00000489031.1_Missense_Mutation_p.E87G|LMOD3_ENST00000475434.1_Missense_Mutation_p.E87G	NM_198271.3	NP_938012.2	Q0VAK6	LMOD3_HUMAN	leiomodin 3 (fetal)	87	Glu-rich.					cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(3)|ovary(1)	13		Lung NSC(201;0.0193)|Prostate(884;0.174)		BRCA - Breast invasive adenocarcinoma(55;7.88e-05)|Epithelial(33;0.000839)|LUSC - Lung squamous cell carcinoma(21;0.0119)|Lung(16;0.0191)|KIRC - Kidney renal clear cell carcinoma(39;0.205)|Kidney(39;0.24)		AACTCGTTCCTCTTCCAGCAT	0.458																																					p.E87G		Atlas-SNP	.											.	LMOD3	92	.	0			c.A260G						.						74.0	70.0	71.0					3																	69171278		1895	4115	6010	SO:0001583	missense	56203	exon1			CGTTCCTCTTCCA	AK096900	CCDS46862.1	3p14.1	2003-03-07			ENSG00000163380	ENSG00000163380			6649	protein-coding gene	gene with protein product							Standard	NM_198271		Approved		uc003dns.2	Q0VAK6	OTTHUMG00000158774	ENST00000420581.2:c.260A>G	chr3.hg19:g.69171278T>C	ENSP00000414670:p.Glu87Gly	183.0	0.0		98.0	4.0	NM_198271	B4DT85|Q0JTT2|Q5JPG6|Q8IUK4|Q96LS4	Missense_Mutation	SNP	ENST00000420581.2	hg19	CCDS46862.1	.	.	.	.	.	.	.	.	.	.	T	14.70	2.613497	0.46631	.	.	ENSG00000163380	ENST00000420581;ENST00000489031;ENST00000475434	T;T;T	0.36157	1.27;1.27;1.27	5.69	5.69	0.88448	.	0.047464	0.85682	D	0.000000	T	0.30355	0.0762	N	0.17082	0.46	0.40794	D	0.98328	P	0.43938	0.822	P	0.44477	0.451	T	0.11817	-1.0572	10	0.45353	T	0.12	-22.6551	15.9428	0.79771	0.0:0.0:0.0:1.0	.	87	Q0VAK6	LMOD3_HUMAN	G	87	ENSP00000414670:E87G;ENSP00000417210:E87G;ENSP00000418645:E87G	ENSP00000414670:E87G	E	-	2	0	LMOD3	69253968	1.000000	0.71417	0.930000	0.37139	0.228000	0.25075	8.040000	0.89188	2.182000	0.69389	0.482000	0.46254	GAG	.	.		0.458	LMOD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352138.1	XM_067529	
MINA	84864	hgsc.bcm.edu	37	3	97666254	97666254	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:97666254T>C	ENST00000333396.7	-	8	1682	c.1100A>G	c.(1099-1101)cAg>cGg	p.Q367R	MINA_ENST00000394198.2_Missense_Mutation_p.Q367R|MINA_ENST00000360258.4_Missense_Mutation_p.Q366R	NM_001042533.2|NM_032778.5	NP_001035998.1|NP_116167.3			MYC induced nuclear antigen											breast(2)|endometrium(1)|large_intestine(1)|lung(8)|ovary(1)	13						GTCTTTAAACTGCAGTCTCAC	0.448																																					p.Q367R		Atlas-SNP	.											.	MINA	39	.	0			c.A1100G						.						148.0	140.0	143.0					3																	97666254		2203	4300	6503	SO:0001583	missense	84864	exon8			TTAAACTGCAGTC	AB083189	CCDS2929.1, CCDS43114.1	3q22.1	2005-07-22			ENSG00000170854	ENSG00000170854			19441	protein-coding gene	gene with protein product		612049				12091391	Standard	NM_001042533		Approved	MINA53, FLJ14393, mdig	uc003dsb.1	Q8IUF8	OTTHUMG00000160107	ENST00000333396.7:c.1100A>G	chr3.hg19:g.97666254T>C	ENSP00000328251:p.Gln367Arg	113.0	0.0		107.0	5.0	NM_001042533		Missense_Mutation	SNP	ENST00000333396.7	hg19	CCDS43114.1	.	.	.	.	.	.	.	.	.	.	T	1.645	-0.515518	0.04200	.	.	ENSG00000170854	ENST00000442492;ENST00000333396;ENST00000394198;ENST00000360258	T;T;T	0.10860	2.83;2.83;2.84	5.92	0.536	0.17138	.	0.635091	0.16760	N	0.200679	T	0.08582	0.0213	L	0.45228	1.405	0.42485	D	0.992872	B;B	0.06786	0.001;0.001	B;B	0.06405	0.002;0.001	T	0.24764	-1.0151	10	0.15952	T	0.53	-8.4277	9.9583	0.41680	0.0:0.373:0.0:0.627	.	366;367	Q8IUF8-4;Q8IUF8	.;MINA_HUMAN	R	113;367;367;366	ENSP00000328251:Q367R;ENSP00000377748:Q367R;ENSP00000353395:Q366R	ENSP00000328251:Q367R	Q	-	2	0	MINA	99148944	0.779000	0.28652	0.246000	0.24233	0.130000	0.20726	0.988000	0.29616	0.165000	0.19558	0.533000	0.62120	CAG	.	.		0.448	MINA-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359244.3	NM_032778	
PVRL3	25945	hgsc.bcm.edu	37	3	110841052	110841052	+	Missense_Mutation	SNP	C	C	A			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:110841052C>A	ENST00000485303.1	+	4	1159	c.884C>A	c.(883-885)gCa>gAa	p.A295E	PVRL3_ENST00000493615.1_Missense_Mutation_p.A272E|PVRL3_ENST00000319792.3_Missense_Mutation_p.A295E	NM_001243286.1|NM_015480.2	NP_001230215.1|NP_056295.1	Q9NQS3	PVRL3_HUMAN	poliovirus receptor-related 3	295	Ig-like C2-type 2.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|fertilization (GO:0009566)|homophilic cell adhesion (GO:0007156)|lens morphogenesis in camera-type eye (GO:0002089)|retina morphogenesis in camera-type eye (GO:0060042)|single organismal cell-cell adhesion (GO:0016337)	apical junction complex (GO:0043296)|cell-cell adherens junction (GO:0005913)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	cell adhesion molecule binding (GO:0050839)|protein homodimerization activity (GO:0042803)			breast(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(7)|upper_aerodigestive_tract(3)	19						AATGCTGATGCAAATCCACCA	0.343																																					p.A295E		Atlas-SNP	.											.	PVRL3	78	.	0			c.C884A						.						85.0	83.0	84.0					3																	110841052		2203	4300	6503	SO:0001583	missense	25945	exon4			CTGATGCAAATCC	AF282874	CCDS2957.1, CCDS58842.1, CCDS58843.1	3q13	2013-01-29			ENSG00000177707	ENSG00000177707		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	17664	protein-coding gene	gene with protein product		607147				11024295	Standard	NM_015480		Approved	nectin-3, PPR3, PVRR3, DKFZP566B0846, CDw113, CD113	uc003dxt.2	Q9NQS3	OTTHUMG00000159239	ENST00000485303.1:c.884C>A	chr3.hg19:g.110841052C>A	ENSP00000418070:p.Ala295Glu	183.0	0.0		117.0	6.0	NM_001243286	E9PFR0|Q6NVZ3|Q8NC05|Q8WVU4|Q9BVA9|Q9Y412	Missense_Mutation	SNP	ENST00000485303.1	hg19	CCDS2957.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	25.1|25.1	4.603856|4.603856	0.87157|0.87157	.|.	.|.	ENSG00000177707|ENSG00000177707	ENST00000485303;ENST00000319792;ENST00000493615|ENST00000486596	T;T;T|.	0.15603|.	2.41;2.41;2.41|.	5.67|5.67	5.67|5.67	0.87782|0.87782	Immunoglobulin-like (1);Immunoglobulin-like fold (1);|.	0.145674|.	0.64402|.	D|.	0.000011|.	T|.	0.77260|.	0.4104|.	M|M	0.78223|0.78223	2.4|2.4	0.58432|0.58432	D|D	0.999999|0.999999	D;D|.	0.89917|.	1.0;0.998|.	D;D|.	0.75020|.	0.985;0.93|.	T|.	0.77008|.	-0.2747|.	10|.	0.72032|.	D|.	0.01|.	.|.	17.2528|17.2528	0.87047|0.87047	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	272;295|.	E9PFR0;Q9NQS3|.	.;PVRL3_HUMAN|.	E|X	295;295;272|195	ENSP00000418070:A295E;ENSP00000321514:A295E;ENSP00000420579:A272E|.	ENSP00000321514:A295E|.	A|C	+|+	2|3	0|2	PVRL3|PVRL3	112323742|112323742	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	6.778000|6.778000	0.75043|0.75043	2.680000|2.680000	0.91292|0.91292	0.484000|0.484000	0.47621|0.47621	GCA|TGC	.	.		0.343	PVRL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354045.1	NM_015480	
FBXO40	51725	hgsc.bcm.edu	37	3	121341494	121341494	+	Silent	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:121341494A>G	ENST00000338040.4	+	3	1632	c.1218A>G	c.(1216-1218)agA>agG	p.R406R		NM_016298.3	NP_057382.2	Q9UH90	FBX40_HUMAN	F-box protein 40	406					muscle cell differentiation (GO:0042692)	cytoplasm (GO:0005737)	ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|kidney(1)|large_intestine(11)|lung(19)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	46				GBM - Glioblastoma multiforme(114;0.189)		CTTTGGAAAGAGAACTCAAAG	0.463																																					p.R406R		Atlas-SNP	.											.	FBXO40	108	.	0			c.A1218G						.						116.0	112.0	113.0					3																	121341494		2203	4300	6503	SO:0001819	synonymous_variant	51725	exon3			GGAAAGAGAACTC	AF204674	CCDS33835.1	3q21.1	2004-08-24			ENSG00000163833	ENSG00000163833		"""F-boxes /  ""other"""""	29816	protein-coding gene	gene with protein product		609107				10574462	Standard	NM_016298		Approved	KIAA1195, Fbx40	uc003eeg.2	Q9UH90	OTTHUMG00000159410	ENST00000338040.4:c.1218A>G	chr3.hg19:g.121341494A>G		178.0	0.0		123.0	5.0	NM_016298	B2RAX7|Q32M70|Q9ULM5	Silent	SNP	ENST00000338040.4	hg19	CCDS33835.1																																																																																			.	.		0.463	FBXO40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355158.1	NM_016298	
DIRC2	84925	hgsc.bcm.edu	37	3	122514376	122514376	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:122514376A>G	ENST00000261038.5	+	1	735	c.337A>G	c.(337-339)Aag>Gag	p.K113E	HSPBAP1_ENST00000383659.1_5'Flank|HSPBAP1_ENST00000465044.1_5'Flank|HSPBAP1_ENST00000306103.2_5'Flank	NM_032839.2	NP_116228.1	Q96SL1	DIRC2_HUMAN	disrupted in renal carcinoma 2	113					transport (GO:0006810)	integral component of membrane (GO:0016021)|lysosome (GO:0005764)				endometrium(2)|large_intestine(1)|lung(14)|prostate(1)	18				GBM - Glioblastoma multiforme(114;0.0614)		GCTCCTGGACAAGAGAGGTGA	0.721																																					p.K113E		Atlas-SNP	.											.	DIRC2	25	.	0			c.A337G						.						14.0	16.0	16.0					3																	122514376		2201	4297	6498	SO:0001583	missense	84925	exon1			CTGGACAAGAGAG	AK027690	CCDS3018.1	3q21.1	2013-05-22			ENSG00000138463	ENSG00000138463		"""Solute carriers"""	16628	protein-coding gene	gene with protein product	"""renal cell carcinoma 4"", ""disrupted in renal cancer protein 2"""	602773				11912179	Standard	NM_032839		Approved	FLJ14784, RCC4	uc003efw.4	Q96SL1	OTTHUMG00000159553	ENST00000261038.5:c.337A>G	chr3.hg19:g.122514376A>G	ENSP00000261038:p.Lys113Glu	54.0	0.0		35.0	4.0	NM_032839	A8K561|Q8NBX9	Missense_Mutation	SNP	ENST00000261038.5	hg19	CCDS3018.1	.	.	.	.	.	.	.	.	.	.	A	18.73	3.685459	0.68157	.	.	ENSG00000138463	ENST00000261038	T	0.61510	0.1	4.63	3.43	0.39272	Major facilitator superfamily domain, general substrate transporter (1);	0.107793	0.64402	D	0.000007	T	0.42086	0.1187	L	0.46157	1.445	0.58432	D	0.999998	B	0.29988	0.264	B	0.20184	0.028	T	0.22556	-1.0213	10	0.14656	T	0.56	.	8.4917	0.33104	0.9085:0.0:0.0915:0.0	.	113	Q96SL1	DIRC2_HUMAN	E	113	ENSP00000261038:K113E	ENSP00000261038:K113E	K	+	1	0	DIRC2	123997066	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.281000	0.72632	1.931000	0.55961	0.454000	0.30748	AAG	.	.		0.721	DIRC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356180.2	NM_032839	
PTPLB	201562	hgsc.bcm.edu	37	3	123219490	123219490	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:123219490A>G	ENST00000383657.5	-	6	711	c.554T>C	c.(553-555)cTc>cCc	p.L185P		NM_198402.3	NP_940684.1	Q6Y1H2	HACD2_HUMAN	protein tyrosine phosphatase-like (proline instead of catalytic arginine), member b	185					fatty acid biosynthetic process (GO:0006633)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	lyase activity (GO:0016829)			kidney(2)	2				GBM - Glioblastoma multiforme(114;0.1)		ATATATTGTGAGCAGTTCTCC	0.393																																					p.L185P		Atlas-SNP	.											.	PTPLB	11	.	0			c.T554C						.						107.0	107.0	107.0					3																	123219490		1896	4120	6016	SO:0001583	missense	201562	exon6			ATTGTGAGCAGTT	AK074605	CCDS46895.1	3q21.1	2010-04-30			ENSG00000206527	ENSG00000206527			9640	protein-coding gene	gene with protein product		615939				15024066	Standard	NM_198402		Approved		uc003egj.2	Q6Y1H2	OTTHUMG00000159529	ENST00000383657.5:c.554T>C	chr3.hg19:g.123219490A>G	ENSP00000373153:p.Leu185Pro	150.0	0.0		131.0	6.0	NM_198402		Missense_Mutation	SNP	ENST00000383657.5	hg19	CCDS46895.1	.	.	.	.	.	.	.	.	.	.	A	23.3	4.404168	0.83230	.	.	ENSG00000206527	ENST00000383657;ENST00000469317	T;T	0.33865	1.39;1.39	5.91	5.91	0.95273	.	0.126462	0.53938	D	0.000044	T	0.59238	0.2179	M	0.68593	2.085	0.80722	D	1	D	0.76494	0.999	D	0.77557	0.99	T	0.59392	-0.7463	10	0.49607	T	0.09	-17.1207	16.3483	0.83171	1.0:0.0:0.0:0.0	.	185	Q6Y1H2	HACD2_HUMAN	P	185;74	ENSP00000373153:L185P;ENSP00000419237:L74P	ENSP00000373153:L185P	L	-	2	0	PTPLB	124702180	1.000000	0.71417	0.943000	0.38184	0.896000	0.52359	9.339000	0.96797	2.254000	0.74563	0.533000	0.62120	CTC	.	.		0.393	PTPLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356021.3	NM_198402	
HEG1	57493	hgsc.bcm.edu	37	3	124746183	124746183	+	Missense_Mutation	SNP	G	G	A			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:124746183G>A	ENST00000311127.4	-	3	846	c.779C>T	c.(778-780)cCg>cTg	p.P260L		NM_020733.1	NP_065784.1	Q9ULI3	HEG1_HUMAN	heart development protein with EGF-like domains 1	260					cardiac atrium morphogenesis (GO:0003209)|cell-cell junction assembly (GO:0007043)|endothelial cell morphogenesis (GO:0001886)|in utero embryonic development (GO:0001701)|lung development (GO:0030324)|lymph circulation (GO:0003017)|lymph vessel development (GO:0001945)|multicellular organism growth (GO:0035264)|pericardium development (GO:0060039)|post-embryonic development (GO:0009791)|regulation of body fluid levels (GO:0050878)|vasculogenesis (GO:0001570)|venous blood vessel morphogenesis (GO:0048845)|ventricular septum development (GO:0003281)	cell-cell junction (GO:0005911)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(24)|ovary(2)|urinary_tract(4)	47						AAGAAAGGACGGGCTCCAAGC	0.552																																					p.P260L		Atlas-SNP	.											HEG1,NS,carcinoma,0,1	HEG1	109	.	0			c.C779T						.						61.0	65.0	64.0					3																	124746183		1997	4157	6154	SO:0001583	missense	57493	exon3			AAGGACGGGCTCC	AK074987	CCDS46898.1	3q21.2	2013-03-08	2013-03-08		ENSG00000173706	ENSG00000173706			29227	protein-coding gene	gene with protein product	"""heart of glass"""	614182	"""HEG homolog 1 (zebrafish)"""			10574462, 19151727, 23007647	Standard	NM_020733		Approved	KIAA1237, HEG	uc003ehs.4	Q9ULI3	OTTHUMG00000159486	ENST00000311127.4:c.779C>T	chr3.hg19:g.124746183G>A	ENSP00000311502:p.Pro260Leu	300.0	0.0		219.0	0.0	NM_020733	Q6NX66|Q8NC40|Q9BSV0	Missense_Mutation	SNP	ENST00000311127.4	hg19	CCDS46898.1	.	.	.	.	.	.	.	.	.	.	G	9.000	0.979900	0.18812	.	.	ENSG00000173706	ENST00000311127	T	0.42513	0.97	4.78	-0.6	0.11642	.	.	.	.	.	T	0.21145	0.0509	N	0.22421	0.69	0.09310	N	1	P;B	0.36660	0.564;0.429	B;B	0.26770	0.073;0.024	T	0.10222	-1.0639	9	0.59425	D	0.04	.	4.7733	0.13166	0.0:0.1765:0.3183:0.5051	.	260;260	Q9ULI3-2;Q9ULI3	.;HEG1_HUMAN	L	260	ENSP00000311502:P260L	ENSP00000311502:P260L	P	-	2	0	HEG1	126228873	0.013000	0.17824	0.000000	0.03702	0.002000	0.02628	0.444000	0.21661	-0.166000	0.10890	-1.036000	0.02392	CCG	.	.		0.552	HEG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355732.2	XM_087386	
PIK3R4	30849	hgsc.bcm.edu	37	3	130435361	130435361	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:130435361T>C	ENST00000356763.3	-	9	2767	c.2210A>G	c.(2209-2211)gAt>gGt	p.D737G		NM_014602.2	NP_055417.1	Q99570	PI3R4_HUMAN	phosphoinositide-3-kinase, regulatory subunit 4	737					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						GCTAGTAATATCTTTAGACCT	0.393																																					p.D737G		Atlas-SNP	.											.	PIK3R4	145	.	0			c.A2210G						.						74.0	75.0	74.0					3																	130435361		2203	4300	6503	SO:0001583	missense	30849	exon9			GTAATATCTTTAG	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.2210A>G	chr3.hg19:g.130435361T>C	ENSP00000349205:p.Asp737Gly	143.0	0.0		116.0	5.0	NM_014602	Q2TBF4	Missense_Mutation	SNP	ENST00000356763.3	hg19	CCDS3067.1	.	.	.	.	.	.	.	.	.	.	T	18.92	3.726274	0.69074	.	.	ENSG00000196455	ENST00000356763;ENST00000508273;ENST00000507330;ENST00000512430	T;T;T;T	0.46819	0.86;0.86;0.86;0.86	5.11	5.11	0.69529	.	0.000000	0.85682	D	0.000000	T	0.59676	0.2211	L	0.56769	1.78	0.80722	D	1	D	0.62365	0.991	P	0.59546	0.859	T	0.57021	-0.7882	10	0.28530	T	0.3	-27.2617	14.9134	0.70776	0.0:0.0:0.0:1.0	.	737	Q99570	PI3R4_HUMAN	G	737;96;96;96	ENSP00000349205:D737G;ENSP00000427302:D96G;ENSP00000424274:D96G;ENSP00000422767:D96G	ENSP00000349205:D737G	D	-	2	0	PIK3R4	131918051	1.000000	0.71417	0.996000	0.52242	0.958000	0.62258	7.698000	0.84413	1.929000	0.55896	0.533000	0.62120	GAT	.	.		0.393	PIK3R4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356668.1	NM_014602	
SLCO2A1	6578	hgsc.bcm.edu	37	3	133672591	133672591	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:133672591T>C	ENST00000310926.4	-	5	913	c.640A>G	c.(640-642)Atc>Gtc	p.I214V	SLCO2A1_ENST00000493729.1_Missense_Mutation_p.I138V|SLCO2A1_ENST00000478651.1_5'Flank	NM_005630.2	NP_005621.2	Q92959	SO2A1_HUMAN	solute carrier organic anion transporter family, member 2A1	214					lipid transport (GO:0006869)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	lipid transporter activity (GO:0005319)|prostaglandin transmembrane transporter activity (GO:0015132)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)|skin(2)|stomach(2)	30					Alprostadil(DB00770)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Furosemide(DB00695)|Iloprost(DB01088)|Phenobarbital(DB01174)|Pyruvic acid(DB00119)	AATACAGAGATGGCAAATAAG	0.517																																					p.I214V		Atlas-SNP	.											.	SLCO2A1	72	.	0			c.A640G						.						89.0	87.0	88.0					3																	133672591		2203	4300	6503	SO:0001583	missense	6578	exon5			CAGAGATGGCAAA		CCDS3084.1	3q21	2013-05-22	2003-11-25	2003-11-26	ENSG00000174640	ENSG00000174640		"""Solute carriers"""	10955	protein-coding gene	gene with protein product		601460	"""solute carrier family 21 (prostaglandin transporter), member 2"", ""matrin F/G 1"""	SLC21A2, MATR1		8787677, 9618293	Standard	NM_005630		Approved	PGT, OATP2A1	uc003eqa.4	Q92959	OTTHUMG00000159745	ENST00000310926.4:c.640A>G	chr3.hg19:g.133672591T>C	ENSP00000311291:p.Ile214Val	160.0	0.0		98.0	4.0	NM_005630	Q86V98|Q8IUN2	Missense_Mutation	SNP	ENST00000310926.4	hg19	CCDS3084.1	.	.	.	.	.	.	.	.	.	.	T	5.812	0.334093	0.11013	.	.	ENSG00000174640	ENST00000310926;ENST00000493729	T;T	0.58060	0.36;0.36	5.52	5.52	0.82312	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.057645	0.64402	D	0.000002	T	0.29491	0.0735	N	0.11201	0.11	0.46185	D	0.998915	B;B;B	0.31640	0.088;0.333;0.057	B;B;B	0.34991	0.086;0.193;0.045	T	0.24404	-1.0161	10	0.02654	T	1	.	10.0564	0.42248	0.0:0.0749:0.0:0.9251	.	214;138;214	F8W9W8;E7EU40;Q92959	.;.;SO2A1_HUMAN	V	214;138	ENSP00000311291:I214V;ENSP00000418893:I138V	ENSP00000311291:I214V	I	-	1	0	SLCO2A1	135155281	1.000000	0.71417	0.996000	0.52242	0.987000	0.75469	3.583000	0.53928	2.091000	0.63221	0.459000	0.35465	ATC	.	.		0.517	SLCO2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357131.1	NM_005630	
PPP2R3A	5523	hgsc.bcm.edu	37	3	135720746	135720746	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:135720746A>G	ENST00000264977.3	+	2	1023	c.406A>G	c.(406-408)Aac>Gac	p.N136D	PPP2R3A_ENST00000490467.1_Intron	NM_001190447.1|NM_002718.4	NP_001177376.1|NP_002709.2	Q06190	P2R3A_HUMAN	protein phosphatase 2, regulatory subunit B'', alpha	136					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						CAAAAACTCTAACCATGCAGC	0.363																																					p.N136D		Atlas-SNP	.											.	PPP2R3A	114	.	0			c.A406G						.						62.0	63.0	62.0					3																	135720746		2203	4300	6503	SO:0001583	missense	5523	exon2			AACTCTAACCATG	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.406A>G	chr3.hg19:g.135720746A>G	ENSP00000264977:p.Asn136Asp	98.0	0.0		71.0	4.0	NM_002718	A8KAE7|B4DNU1|B7ZAE3|Q06189|Q9NPQ5	Missense_Mutation	SNP	ENST00000264977.3	hg19	CCDS3087.1	.	.	.	.	.	.	.	.	.	.	A	14.86	2.662071	0.47572	.	.	ENSG00000073711	ENST00000264977	T	0.13778	2.56	5.81	4.63	0.57726	.	0.118979	0.56097	D	0.000026	T	0.17492	0.0420	L	0.54323	1.7	0.80722	D	1	P	0.52842	0.956	P	0.45071	0.468	T	0.00920	-1.1514	10	0.72032	D	0.01	.	11.2123	0.48806	0.7066:0.2934:0.0:0.0	.	136	Q06190	P2R3A_HUMAN	D	136	ENSP00000264977:N136D	ENSP00000264977:N136D	N	+	1	0	PPP2R3A	137203436	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	6.963000	0.76055	0.992000	0.38840	0.533000	0.62120	AAC	.	.		0.363	PPP2R3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357232.1	NM_002718	
TFDP2	7029	hgsc.bcm.edu	37	3	141678659	141678659	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:141678659T>C	ENST00000489671.1	-	11	1338	c.908A>G	c.(907-909)gAc>gGc	p.D303G	TFDP2_ENST00000495310.1_Missense_Mutation_p.D206G|TFDP2_ENST00000499676.2_Missense_Mutation_p.D243G|TFDP2_ENST00000486111.1_Missense_Mutation_p.D243G|TFDP2_ENST00000317104.7_Missense_Mutation_p.D227G|TFDP2_ENST00000477292.1_Missense_Mutation_p.D167G|TFDP2_ENST00000397991.4_Missense_Mutation_p.D275G|TFDP2_ENST00000310282.6_Missense_Mutation_p.D243G|TFDP2_ENST00000467072.1_Missense_Mutation_p.D243G|TFDP2_ENST00000479040.1_Missense_Mutation_p.D242G			Q14188	TFDP2_HUMAN	transcription factor Dp-2 (E2F dimerization partner 2)	303	DCB2.				gene expression (GO:0010467)|heart development (GO:0007507)|mitotic cell cycle (GO:0000278)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription cofactor activity (GO:0003712)|transcription factor binding (GO:0008134)			kidney(1)|upper_aerodigestive_tract(2)	3						AAAGGTGTTGTCAAAATTGAA	0.403																																					p.D303G		Atlas-SNP	.											.	TFDP2	44	.	0			c.A908G						.						101.0	95.0	97.0					3																	141678659		1943	4172	6115	SO:0001583	missense	7029	exon11			GTGTTGTCAAAAT	U18422	CCDS43159.1, CCDS54647.1, CCDS54648.1, CCDS54649.1, CCDS54650.1	3q23	2011-05-24			ENSG00000114126	ENSG00000114126			11751	protein-coding gene	gene with protein product		602160				7784053, 9027491	Standard	NM_001178138		Approved	Dp-2	uc003eun.4	Q14188	OTTHUMG00000164975	ENST00000489671.1:c.908A>G	chr3.hg19:g.141678659T>C	ENSP00000420616:p.Asp303Gly	163.0	0.0		114.0	5.0	NM_001178139	B7Z8C8|B7Z8L5|D3DNG1|E9PFC3|F8WAI2|Q13331|Q14187|Q6R754|Q8WU88|Q9UG28	Missense_Mutation	SNP	ENST00000489671.1	hg19	CCDS54650.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	29.5|29.5	5.009075|5.009075	0.93346|0.93346	.|.	.|.	ENSG00000114126|ENSG00000114126	ENST00000499676;ENST00000489671;ENST00000486111;ENST00000477292;ENST00000495310;ENST00000467072;ENST00000317104;ENST00000310282;ENST00000479040;ENST00000397991;ENST00000467667|ENST00000474279	T;T;T;T;T;T;T;T;T;T;T|.	0.49432|.	1.77;1.73;1.77;0.8;0.78;1.77;1.79;1.77;1.76;1.74;1.36|.	5.69|5.69	5.69|5.69	0.88448|0.88448	Transcription factor DP, C-terminal (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|.	0.83266|.	0.5217|.	M|M	0.89478|0.89478	3.035|3.035	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	0.999;1.0;0.999|.	D;D;D|.	0.97110|.	0.995;1.0;0.998|.	D|.	0.86263|.	0.1656|.	10|.	0.72032|.	D|.	0.01|.	-8.9532|-8.9532	15.944|15.944	0.79779|0.79779	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	206;303;243|.	B7Z8L5;Q14188;Q14188-5|.	.;TFDP2_HUMAN;.|.	G|W	243;303;243;167;206;243;227;243;242;275;243|16	ENSP00000439782:D243G;ENSP00000420616:D303G;ENSP00000420599:D243G;ENSP00000418971:D167G;ENSP00000419036:D206G;ENSP00000418590:D243G;ENSP00000315668:D227G;ENSP00000309622:D243G;ENSP00000417585:D242G;ENSP00000381078:D275G;ENSP00000417726:D243G|.	ENSP00000309622:D243G|.	D|X	-|-	2|3	0|0	TFDP2|TFDP2	143161349|143161349	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.973000|0.973000	0.67179|0.67179	7.539000|7.539000	0.82063|0.82063	2.170000|2.170000	0.68504|0.68504	0.379000|0.379000	0.24179|0.24179	GAC|TGA	.	.		0.403	TFDP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000353294.4	NM_006286	
MED12L	116931	hgsc.bcm.edu	37	3	151107817	151107817	+	Silent	SNP	C	C	A	rs541597798		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:151107817C>A	ENST00000474524.1	+	36	5435	c.5397C>A	c.(5395-5397)atC>atA	p.I1799I	MED12L_ENST00000273432.4_Silent_p.I1659I	NM_053002.4	NP_443728.3	Q86YW9	MD12L_HUMAN	mediator complex subunit 12-like	1799						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			NS(1)|breast(3)|central_nervous_system(3)|cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(27)|lung(50)|ovary(6)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	128			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			ACTCGCCTATCTCCTCCCAAA	0.463																																					p.I1799I		Atlas-SNP	.											.	MED12L	271	.	0			c.C5397A						.						175.0	171.0	172.0					3																	151107817		2203	4300	6503	SO:0001819	synonymous_variant	116931	exon36			GCCTATCTCCTCC	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.5397C>A	chr3.hg19:g.151107817C>A		166.0	0.0		86.0	32.0	NM_053002	Q96PC7|Q96PC8|Q9H9M5|Q9HCD7|Q9UI69	Silent	SNP	ENST00000474524.1	hg19	CCDS33876.1																																																																																			.	.		0.463	MED12L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357707.2	NM_053002	
IL12A	3592	hgsc.bcm.edu	37	3	159710910	159710910	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:159710910A>G	ENST00000305579.2	+	3	683	c.376A>G	c.(376-378)Aag>Gag	p.K126E	IL12A-AS1_ENST00000497452.1_RNA|IL12A_ENST00000480787.1_Intron|IL12A_ENST00000466512.1_Missense_Mutation_p.K126E	NM_000882.3	NP_000873.2	P29459	IL12A_HUMAN	interleukin 12A	92					cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|defense response to Gram-positive bacterium (GO:0050830)|defense response to protozoan (GO:0042832)|extrinsic apoptotic signaling pathway (GO:0097191)|immune response (GO:0006955)|negative regulation of interleukin-17 production (GO:0032700)|negative regulation of smooth muscle cell proliferation (GO:0048662)|positive regulation of cell adhesion (GO:0045785)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of lymphocyte proliferation (GO:0050671)|positive regulation of mononuclear cell proliferation (GO:0032946)|positive regulation of natural killer cell activation (GO:0032816)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target (GO:0002860)|positive regulation of NK T cell activation (GO:0051135)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|positive regulation of T cell differentiation (GO:0045582)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of tyrosine phosphorylation of Stat4 protein (GO:0042520)|response to lipopolysaccharide (GO:0032496)|response to UV-B (GO:0010224)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|interleukin-12 complex (GO:0043514)	interleukin-12 beta subunit binding (GO:0042163)|interleukin-12 receptor binding (GO:0005143)|interleukin-27 binding (GO:0045513)|protein heterodimerization activity (GO:0046982)			endometrium(3)|kidney(1)|large_intestine(1)|lung(4)	9			Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)			GGAATTAACCAAGGTATAAAG	0.383																																					p.K126E		Atlas-SNP	.											.	IL12A	23	.	0			c.A376G						.						62.0	68.0	66.0					3																	159710910		2202	4300	6502	SO:0001583	missense	3592	exon3			TTAACCAAGGTAT	M65271	CCDS3187.1	3q25.33	2014-04-04	2014-04-04		ENSG00000168811	ENSG00000168811		"""Interleukins and interleukin receptors"""	5969	protein-coding gene	gene with protein product	"""natural killer cell stimulatory factor 1, 35 kD subunit"", ""cytotoxic lymphocyte maturation factor 1, p35"", ""interleukin 12, p35"", ""IL-12, subunit p35"", ""NF cell stimulatory factor chain 1"", ""interleukin-12 alpha chain"", ""IL35 subunit"""	161560	"""interleukin 12A (natural killer cell stimulatory factor 1, cytotoxic lymphocyte maturation factor 1, p35)"""	NKSF1		1673147	Standard	NM_000882		Approved	CLMF, IL-12A, p35, NFSK	uc003fcx.3	P29459	OTTHUMG00000158942	ENST00000305579.2:c.376A>G	chr3.hg19:g.159710910A>G	ENSP00000303231:p.Lys126Glu	153.0	0.0		100.0	4.0	NM_000882	Q96QZ1	Missense_Mutation	SNP	ENST00000305579.2	hg19	CCDS3187.1	.	.	.	.	.	.	.	.	.	.	A	9.831	1.188533	0.21954	.	.	ENSG00000168811	ENST00000305579;ENST00000466512	.	.	.	5.66	0.495	0.16890	.	1.000120	0.08080	N	1.000000	T	0.34077	0.0885	L	0.47190	1.495	0.09310	N	1	B	0.21225	0.053	B	0.18871	0.023	T	0.33189	-0.9878	9	0.56958	D	0.05	-1.0851	5.5477	0.17073	0.5923:0.2909:0.1168:0.0	.	126	O60595	.	E	126	.	ENSP00000303231:K126E	K	+	1	0	IL12A	161193604	0.007000	0.16637	0.019000	0.16419	0.399000	0.30720	0.482000	0.22276	-0.134000	0.11516	0.460000	0.39030	AAG	.	.		0.383	IL12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352602.2	NM_000882	
ZBBX	79740	hgsc.bcm.edu	37	3	167006752	167006752	+	Intron	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:167006752T>C	ENST00000392766.2	-	19	2220				ZBBX_ENST00000392764.1_Intron|ZBBX_ENST00000392767.2_Intron|ZBBX_ENST00000455345.2_Silent_p.P633P|ZBBX_ENST00000307529.5_Silent_p.P633P	NM_001199201.1|NM_024687.3	NP_001186130.1|NP_078963.2	A8MT70	ZBBX_HUMAN	zinc finger, B-box domain containing							intracellular (GO:0005622)	zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(5)|kidney(5)|large_intestine(9)|liver(1)|lung(38)|ovary(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	70						AGCTATGGTCTGGAATCCATT	0.333																																					p.P633P		Atlas-SNP	.											.	ZBBX	299	.	0			c.A1899G						.																																			SO:0001627	intron_variant	79740	exon19			ATGGTCTGGAATC	AK026702	CCDS3199.2, CCDS56295.1, CCDS56296.1	3q26.1	2010-03-23			ENSG00000169064	ENSG00000169064			26245	protein-coding gene	gene with protein product						12477932	Standard	NM_024687		Approved	FLJ23049	uc011bpc.2	A8MT70	OTTHUMG00000133560	ENST00000392766.2:c.1880-6469A>G	chr3.hg19:g.167006752T>C		200.0	0.0		138.0	8.0	NM_001199201	A8MV69|B3KSC1|B5MDJ6|F2Z370|Q9H5T8	Silent	SNP	ENST00000392766.2	hg19	CCDS3199.2																																																																																			.	.		0.333	ZBBX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257657.3	NM_024687	
MFN1	55669	hgsc.bcm.edu	37	3	179085315	179085315	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:179085315T>C	ENST00000471841.1	+	8	968	c.842T>C	c.(841-843)tTc>tCc	p.F281S	MFN1_ENST00000263969.5_Missense_Mutation_p.F281S|MFN1_ENST00000280653.7_Missense_Mutation_p.F281S	NM_033540.2	NP_284941	Q8IWA4	MFN1_HUMAN	mitofusin 1	281	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)			AATCGTATCTTCTTTGTTTCA	0.398																																					p.F281S		Atlas-SNP	.											.	MFN1	72	.	0			c.T842C						.						73.0	72.0	72.0					3																	179085315		2203	4300	6503	SO:0001583	missense	55669	exon8			GTATCTTCTTTGT	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.842T>C	chr3.hg19:g.179085315T>C	ENSP00000420617:p.Phe281Ser	147.0	0.0		100.0	4.0	NM_033540	B2RAR1|D3DNR6|O15323|O60639|Q9BZB5|Q9NWQ2	Missense_Mutation	SNP	ENST00000471841.1	hg19	CCDS3228.1	.	.	.	.	.	.	.	.	.	.	T	20.6	4.015741	0.75161	.	.	ENSG00000171109	ENST00000471841;ENST00000280653;ENST00000539169;ENST00000263969;ENST00000474903	D;D;D;D	0.97256	-3.86;-3.86;-3.86;-4.31	5.44	5.44	0.79542	.	0.000000	0.85682	D	0.000000	D	0.98538	0.9512	M	0.87682	2.9	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.997;0.998;0.998	D	0.99751	1.1018	10	0.87932	D	0	-14.039	15.4952	0.75643	0.0:0.0:0.0:1.0	.	281;309;281	Q8IWA4-3;Q4AEJ4;Q8IWA4	.;.;MFN1_HUMAN	S	281;281;281;281;144	ENSP00000420617:F281S;ENSP00000280653:F281S;ENSP00000263969:F281S;ENSP00000419926:F144S	ENSP00000263969:F281S	F	+	2	0	MFN1	180568009	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.649000	0.83500	2.065000	0.61736	0.533000	0.62120	TTC	.	.		0.398	MFN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348654.2	NM_017927	
ATP13A3	79572	hgsc.bcm.edu	37	3	194175043	194175043	+	Missense_Mutation	SNP	C	C	T			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:194175043C>T	ENST00000439040.1	-	9	1500	c.709G>A	c.(709-711)Gct>Act	p.A237T	ATP13A3_ENST00000256031.4_Missense_Mutation_p.A237T			Q9H7F0	AT133_HUMAN	ATPase type 13A3	237						integral component of membrane (GO:0016021)|membrane (GO:0016020)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			NS(2)|endometrium(3)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	24	all_cancers(143;6.01e-09)|Ovarian(172;0.0634)	Melanoma(1037;0.211)	OV - Ovarian serous cystadenocarcinoma(49;3.83e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;5.98e-05)		ACCACAATAGCTAGAGCATAG	0.318																																					p.A237T		Atlas-SNP	.											.	ATP13A3	94	.	0			c.G709A						.						96.0	88.0	90.0					3																	194175043		1862	4099	5961	SO:0001583	missense	79572	exon8			CAATAGCTAGAGC	AJ306929	CCDS43187.1	3q29	2010-04-20			ENSG00000133657	ENSG00000133657		"""ATPases / P-type"""	24113	protein-coding gene	gene with protein product	"""ATPase family homolog up regulated in senescence cells"""	610232				11867234	Standard	NM_024524		Approved	AFURS1	uc003fty.4	Q9H7F0	OTTHUMG00000156034	ENST00000439040.1:c.709G>A	chr3.hg19:g.194175043C>T	ENSP00000416508:p.Ala237Thr	107.0	0.0		80.0	4.0	NM_024524	Q8NC11|Q96KS1	Missense_Mutation	SNP	ENST00000439040.1	hg19	CCDS43187.1	.	.	.	.	.	.	.	.	.	.	C	27.1	4.804402	0.90623	.	.	ENSG00000133657	ENST00000439040;ENST00000256031	D;D	0.89343	-2.5;-2.5	5.51	4.64	0.57946	.	0.114749	0.64402	D	0.000016	D	0.94820	0.8327	M	0.88105	2.93	0.53005	D	0.999965	D	0.63880	0.993	D	0.70487	0.969	D	0.94252	0.7494	10	0.31617	T	0.26	-7.8778	16.3875	0.83521	0.0:0.8681:0.1319:0.0	.	237	Q9H7F0	AT133_HUMAN	T	237	ENSP00000416508:A237T;ENSP00000256031:A237T	ENSP00000256031:A237T	A	-	1	0	ATP13A3	195656332	0.998000	0.40836	0.996000	0.52242	0.997000	0.91878	3.938000	0.56583	1.308000	0.44962	0.650000	0.86243	GCT	.	.		0.318	ATP13A3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342799.2	NM_024524	
NCBP2	22916	hgsc.bcm.edu	37	3	196664445	196664445	+	Missense_Mutation	SNP	C	C	T			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:196664445C>T	ENST00000321256.5	-	3	428	c.335G>A	c.(334-336)cGc>cAc	p.R112H	NCBP2_ENST00000452404.2_Missense_Mutation_p.R94H|NCBP2_ENST00000447325.1_Missense_Mutation_p.R42H|NCBP2_ENST00000467803.1_5'UTR|NCBP2_ENST00000427641.2_Missense_Mutation_p.R59H|NCBP2-AS1_ENST00000447775.1_RNA|NCBP2_ENST00000422610.1_Missense_Mutation_p.R42H	NM_007362.3	NP_031388.2	P52298	NCBP2_HUMAN	nuclear cap binding protein subunit 2, 20kDa	112	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.|mRNA cap-binding.				7-methylguanosine mRNA capping (GO:0006370)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|histone mRNA metabolic process (GO:0008334)|mRNA 3'-end processing (GO:0031124)|mRNA cis splicing, via spliceosome (GO:0045292)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|mRNA splicing, via spliceosome (GO:0000398)|ncRNA metabolic process (GO:0034660)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|positive regulation of RNA export from nucleus (GO:0046833)|positive regulation of viral transcription (GO:0050434)|regulation of translational initiation (GO:0006446)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|snRNA export from nucleus (GO:0006408)|spliceosomal snRNP assembly (GO:0000387)|termination of RNA polymerase II transcription (GO:0006369)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mRNA cap binding complex (GO:0005845)|nuclear cap binding complex (GO:0005846)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA 7-methylguanosine cap binding (GO:0000340)|RNA cap binding (GO:0000339)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)	5	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;3.42e-24)|all cancers(36;2.27e-22)|OV - Ovarian serous cystadenocarcinoma(49;4.13e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00551)		CCAGTCTGTGCGAATGATTCG	0.537																																					p.R112H		Atlas-SNP	.											.	NCBP2	12	.	0			c.G335A						.						119.0	106.0	110.0					3																	196664445		2203	4300	6503	SO:0001583	missense	22916	exon3			TCTGTGCGAATGA	D59253	CCDS3323.1, CCDS46986.1	3q29	2013-02-12	2002-08-29		ENSG00000114503	ENSG00000114503		"""RNA binding motif (RRM) containing"""	7659	protein-coding gene	gene with protein product		605133	"""nuclear cap binding protein subunit 2, 20kD"""			7478990, 7651522, 8682299	Standard	NM_001042540		Approved	NIP1, CBP20, Cbc2	uc003fxd.1	P52298	OTTHUMG00000155520	ENST00000321256.5:c.335G>A	chr3.hg19:g.196664445C>T	ENSP00000326806:p.Arg112His	99.0	0.0		73.0	4.0	NM_007362	B2RE91|B4DMK7|E9PAR5|Q14924|Q2TS50	Missense_Mutation	SNP	ENST00000321256.5	hg19	CCDS3323.1	.	.	.	.	.	.	.	.	.	.	C	33	5.260365	0.95368	.	.	ENSG00000114503	ENST00000447325;ENST00000321256;ENST00000427641;ENST00000452404;ENST00000422610;ENST00000411704	T;T;T;T;T;T	0.76448	-1.02;-1.02;-1.02;-1.02;-1.02;-1.02	4.96	4.96	0.65561	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	D	0.87281	0.6138	M	0.72576	2.205	0.80722	D	1	B;D;P	0.89917	0.226;1.0;0.654	B;D;B	0.97110	0.04;1.0;0.067	D	0.86708	0.1934	10	0.46703	T	0.11	.	17.7697	0.88487	0.0:1.0:0.0:0.0	.	94;59;112	P52298-2;E9PAR5;P52298	.;.;NCBP2_HUMAN	H	42;112;59;94;42;42	ENSP00000413518:R42H;ENSP00000326806:R112H;ENSP00000397619:R59H;ENSP00000412785:R94H;ENSP00000394105:R42H;ENSP00000389315:R42H	ENSP00000326806:R112H	R	-	2	0	NCBP2	198148842	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.518000	0.81795	2.767000	0.95098	0.655000	0.94253	CGC	.	.		0.537	NCBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340470.2	NM_007362	
FAM193A	8603	hgsc.bcm.edu	37	4	2659604	2659604	+	Silent	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:2659604A>G	ENST00000324666.5	+	6	864	c.513A>G	c.(511-513)gaA>gaG	p.E171E	FAM193A_ENST00000382839.3_Silent_p.E171E|FAM193A_ENST00000502458.1_Silent_p.E195E|FAM193A_ENST00000545951.1_Silent_p.E171E|FAM193A_ENST00000505311.1_Silent_p.E171E	NM_001256666.1	NP_001243595.1	P78312	F193A_HUMAN	family with sequence similarity 193, member A	171										NS(2)|breast(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(12)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	40						TCATTGAAGAACAGGTAAGCT	0.378																																					p.E195E		Atlas-SNP	.											.	FAM193A	103	.	0			c.A585G						.						120.0	130.0	126.0					4																	2659604		2203	4300	6503	SO:0001819	synonymous_variant	8603	exon7			TGAAGAACAGGTA	AB000459	CCDS33943.1, CCDS58874.1, CCDS58875.1, CCDS58876.1	4p16.3	2009-09-04	2009-09-04	2009-09-04					16822	protein-coding gene	gene with protein product			"""chromosome 4 open reading frame 8"""	C4orf8		9734812	Standard	NR_046335		Approved	RES4-22	uc010ick.3	P78312		ENST00000324666.5:c.513A>G	chr4.hg19:g.2659604A>G		93.0	0.0		71.0	4.0	NM_001256667	B7ZM85|B9EGR0|E9PFA1|O43607|P78311|P78313|Q9UEG8	Silent	SNP	ENST00000324666.5	hg19	CCDS58875.1																																																																																			.	.		0.378	FAM193A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000360903.1	NM_003704	
GPR125	166647	hgsc.bcm.edu	37	4	22439915	22439915	+	Missense_Mutation	SNP	G	G	C	rs147843055		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:22439915G>C	ENST00000334304.5	-	8	1318	c.1049C>G	c.(1048-1050)cCt>cGt	p.P350R	GPR125_ENST00000502482.1_Missense_Mutation_p.P350R|GPR125_ENST00000282943.5_5'UTR|GPR125_ENST00000508133.1_Missense_Mutation_p.P124R	NM_145290.3	NP_660333.2	Q8IWK6	GP125_HUMAN	G protein-coupled receptor 125	350					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)	G-protein coupled receptor activity (GO:0004930)			breast(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(33)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(1)	56		Breast(46;0.198)				CCTCTCTGGAGGACAGTACTG	0.448																																					p.P350R		Atlas-SNP	.											GPR125,colon,carcinoma,0,2	GPR125	118	.	0			c.C1049G						.						164.0	144.0	150.0					4																	22439915		2203	4300	6503	SO:0001583	missense	166647	exon8			TCTGGAGGACAGT	AK095866	CCDS33964.1	4p15.31	2014-08-08			ENSG00000152990	ENSG00000152990		"""-"", ""GPCR / Class B : Orphans"", ""Immunoglobulin superfamily / I-set domain containing"""	13839	protein-coding gene	gene with protein product		612303				12565841	Standard	NM_145290		Approved	FLJ38547, PGR21	uc003gqm.2	Q8IWK6	OTTHUMG00000160926	ENST00000334304.5:c.1049C>G	chr4.hg19:g.22439915G>C	ENSP00000334952:p.Pro350Arg	346.0	0.0		256.0	0.0	NM_145290	Q6UXK9|Q86SQ5|Q8TC55	Missense_Mutation	SNP	ENST00000334304.5	hg19	CCDS33964.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.150664	0.78001	.	.	ENSG00000152990	ENST00000334304;ENST00000508133;ENST00000502482;ENST00000514129	T;T;T	0.55413	0.52;0.52;0.52	5.6	5.6	0.85130	GPCR, family 2, extracellular hormone receptor domain (1);	0.054916	0.85682	D	0.000000	T	0.72415	0.3457	M	0.69823	2.125	0.54753	D	0.999983	D;D;D;P	0.65815	0.995;0.983;0.962;0.912	D;P;P;P	0.65443	0.935;0.905;0.605;0.611	T	0.74680	-0.3584	10	0.87932	D	0	-24.3783	19.618	0.95643	0.0:0.0:1.0:0.0	.	225;350;124;350	Q8IWK6-3;Q8IWK6-2;Q8IWK6-4;Q8IWK6	.;.;.;GP125_HUMAN	R	350;124;350;86	ENSP00000334952:P350R;ENSP00000422606:P124R;ENSP00000421006:P350R	ENSP00000334952:P350R	P	-	2	0	GPR125	22049013	1.000000	0.71417	0.991000	0.47740	0.989000	0.77384	4.196000	0.58407	2.635000	0.89317	0.650000	0.86243	CCT	.	.		0.448	GPR125-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362960.3		
ANAPC4	29945	hgsc.bcm.edu	37	4	25390352	25390352	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:25390352T>C	ENST00000315368.3	+	6	599	c.457T>C	c.(457-459)Tca>Cca	p.S153P	ANAPC4_ENST00000510092.1_Missense_Mutation_p.S153P	NM_013367.2	NP_037499.2	Q9UJX5	APC4_HUMAN	anaphase promoting complex subunit 4	153					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)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(2)|kidney(2)|large_intestine(9)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(2)	27		Breast(46;0.0503)				TAGCAACACCTCAAAAATATT	0.289																																					p.S153P		Atlas-SNP	.											.	ANAPC4	61	.	0			c.T457C						.						83.0	91.0	88.0					4																	25390352		2200	4290	6490	SO:0001583	missense	29945	exon6			AACACCTCAAAAA	AF191338	CCDS3434.1, CCDS68684.1	4p15.31	2011-06-15			ENSG00000053900	ENSG00000053900		"""Anaphase promoting complex subunits"""	19990	protein-coding gene	gene with protein product		606947				6180011	Standard	NM_013367		Approved	APC4	uc003gro.3	Q9UJX5	OTTHUMG00000097753	ENST00000315368.3:c.457T>C	chr4.hg19:g.25390352T>C	ENSP00000318775:p.Ser153Pro	128.0	0.0		100.0	5.0	NM_013367	A8K8H1|E9PCR4|Q6PCC6|Q9NSH6	Missense_Mutation	SNP	ENST00000315368.3	hg19	CCDS3434.1	.	.	.	.	.	.	.	.	.	.	T	15.58	2.875571	0.51695	.	.	ENSG00000053900	ENST00000315368;ENST00000510092;ENST00000505991	T;T	0.35605	1.3;1.3	5.8	4.68	0.58851	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.122787	0.56097	D	0.000037	T	0.33206	0.0855	L	0.38175	1.15	0.47621	D	0.999478	D	0.54397	0.966	P	0.47299	0.543	T	0.05037	-1.0910	10	0.42905	T	0.14	-15.9934	10.9841	0.47513	0.0:0.0:0.3892:0.6108	.	153	Q9UJX5	APC4_HUMAN	P	153	ENSP00000318775:S153P;ENSP00000426654:S153P	ENSP00000318775:S153P	S	+	1	0	ANAPC4	24999450	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	4.687000	0.61708	2.212000	0.71576	0.528000	0.53228	TCA	.	.		0.289	ANAPC4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000214986.1	NM_013367	
STIM2	57620	hgsc.bcm.edu	37	4	26997053	26997053	+	Silent	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:26997053A>G	ENST00000467011.1	+	4	875	c.450A>G	c.(448-450)gaA>gaG	p.E150E	STIM2_ENST00000465503.1_Silent_p.E150E|STIM2_ENST00000237364.5_Silent_p.E237E|STIM2_ENST00000467087.1_Silent_p.E150E|STIM2_ENST00000412829.2_Silent_p.E237E|STIM2_ENST00000382009.3_Silent_p.E237E	NM_001169117.1	NP_001162588	Q9P246	STIM2_HUMAN	stromal interaction molecule 2	150	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.				activation of store-operated calcium channel activity (GO:0032237)|calcium ion transmembrane transport (GO:0070588)|cellular calcium ion homeostasis (GO:0006874)|positive regulation of calcium ion transport (GO:0051928)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|store-operated calcium channel activity (GO:0015279)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(7)|prostate(1)|skin(2)|urinary_tract(1)	25		Breast(46;0.0503)				AGTTTGTTGAACTACCCCAAT	0.393																																					p.E150E		Atlas-SNP	.											.	STIM2	77	.	0			c.A450G						.						132.0	141.0	138.0					4																	26997053		2203	4300	6503	SO:0001819	synonymous_variant	57620	exon4			TGTTGAACTACCC	AB040915	CCDS3440.1, CCDS3440.2, CCDS54751.1, CCDS54752.1	4p15.2	2013-01-10			ENSG00000109689	ENSG00000109689		"""Sterile alpha motif (SAM) domain containing"""	19205	protein-coding gene	gene with protein product		610841				11463338	Standard	NM_020860		Approved		uc003gsh.4	Q9P246	OTTHUMG00000097805	ENST00000467011.1:c.450A>G	chr4.hg19:g.26997053A>G		145.0	0.0		95.0	4.0	NM_001169118	A6H8L7|B7ZVY0|Q96BF1|Q9BQH2|Q9H8R1	Silent	SNP	ENST00000467011.1	hg19	CCDS54752.1																																																																																			.	.		0.393	STIM2-003	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000356861.1	NM_020860	
TLR1	7096	hgsc.bcm.edu	37	4	38799868	38799868	+	Silent	SNP	C	C	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:38799868C>G	ENST00000502213.2	-	3	814	c.585G>C	c.(583-585)gtG>gtC	p.V195V	TLR1_ENST00000308979.2_Silent_p.V195V			Q15399	TLR1_HUMAN	toll-like receptor 1	195					cellular response to triacyl bacterial lipopeptide (GO:0071727)|detection of triacyl bacterial lipopeptide (GO:0042495)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|macrophage activation (GO:0042116)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of interleukin-6 biosynthetic process (GO:0045410)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|regulation of cytokine secretion (GO:0050707)|signal transduction (GO:0007165)|toll-like receptor 1 signaling pathway (GO:0034130)	cytoplasmic vesicle (GO:0031410)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|Toll-like receptor 1-Toll-like receptor 2 protein complex (GO:0035354)	protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(4)|stomach(2)	28						TTGTGGGGAACACAATGTGCA	0.398																																					p.V195V	GBM(5;216 373 40795 46382)	Atlas-SNP	.											.	TLR1	70	.	0			c.G585C						.						63.0	63.0	63.0					4																	38799868		2203	4300	6503	SO:0001819	synonymous_variant	7096	exon4			GGGGAACACAATG	U88540	CCDS33973.1	4p14	2008-02-05				ENSG00000174125		"""CD molecules"""	11847	protein-coding gene	gene with protein product		601194				9435236, 7584026	Standard	NM_003263		Approved	rsc786, KIAA0012, CD281	uc003gtl.3	Q15399		ENST00000502213.2:c.585G>C	chr4.hg19:g.38799868C>G		190.0	0.0		146.0	63.0	NM_003263	D1CS39|D1CS41|O15452|Q32MK3|Q32MK4|Q9UG90	Silent	SNP	ENST00000502213.2	hg19	CCDS33973.1																																																																																			.	.		0.398	TLR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360510.3		
TLR6	10333	hgsc.bcm.edu	37	4	38831040	38831040	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:38831040T>C	ENST00000381950.1	-	1	120	c.55A>G	c.(55-57)Atc>Gtc	p.I19V	TLR6_ENST00000436693.2_Missense_Mutation_p.I19V			Q9Y2C9	TLR6_HUMAN	toll-like receptor 6	19					activation of NF-kappaB-inducing kinase activity (GO:0007250)|cellular response to diacyl bacterial lipopeptide (GO:0071726)|defense response to bacterium (GO:0042742)|detection of diacyl bacterial lipopeptide (GO:0042496)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|nitric oxide metabolic process (GO:0046209)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-6 biosynthetic process (GO:0045410)|positive regulation of JUN kinase activity (GO:0043507)|regulation of cytokine secretion (GO:0050707)|signal transduction (GO:0007165)|T-helper 1 type immune response (GO:0042088)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 6 signaling pathway (GO:0034150)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)	cytoplasmic vesicle (GO:0031410)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|Toll-like receptor 2-Toll-like receptor 6 protein complex (GO:0035355)	diacyl lipopeptide binding (GO:0042498)|lipopeptide binding (GO:0071723)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						ACTATTATGATCATAAGGCAA	0.393																																					p.I19V		Atlas-SNP	.											.	TLR6	67	.	0			c.A55G						.						105.0	110.0	109.0					4																	38831040		2203	4300	6503	SO:0001583	missense	10333	exon2			TTATGATCATAAG		CCDS3446.1	4p16.1	2009-11-23			ENSG00000174130	ENSG00000174130		"""CD molecules"""	16711	protein-coding gene	gene with protein product		605403				10231569	Standard	NM_006068		Approved	CD286	uc010ifg.2	Q9Y2C9	OTTHUMG00000128579	ENST00000381950.1:c.55A>G	chr4.hg19:g.38831040T>C	ENSP00000371376:p.Ile19Val	100.0	0.0		74.0	4.0	NM_006068	B3Y640|B6CH35|B6RFS4|B6RFS5|Q2NKL3	Missense_Mutation	SNP	ENST00000381950.1	hg19	CCDS3446.1	.	.	.	.	.	.	.	.	.	.	T	0.406	-0.916001	0.02415	.	.	ENSG00000174130	ENST00000436693;ENST00000381950;ENST00000508542;ENST00000508254;ENST00000514655	T;T;T;T	0.28895	3.19;3.19;1.59;2.04	5.55	-1.15	0.09709	.	0.860892	0.10174	N	0.706691	T	0.13586	0.0329	N	0.20685	0.6	0.09310	N	1	B	0.09022	0.002	B	0.09377	0.004	T	0.35351	-0.9792	10	0.05351	T	0.99	.	5.8338	0.18594	0.1544:0.3217:0.0:0.5239	.	19	Q9Y2C9	TLR6_HUMAN	V	19	ENSP00000389600:I19V;ENSP00000371376:I19V;ENSP00000424718:I19V;ENSP00000423326:I19V	ENSP00000371376:I19V	I	-	1	0	TLR6	38507435	0.000000	0.05858	0.000000	0.03702	0.024000	0.10985	-0.268000	0.08607	-0.130000	0.11599	0.459000	0.35465	ATC	.	.		0.393	TLR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250431.1		
FIP1L1	81608	hgsc.bcm.edu	37	4	54319252	54319252	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:54319252A>G	ENST00000337488.6	+	16	1645	c.1451A>G	c.(1450-1452)gAg>gGg	p.E484G	FIP1L1_ENST00000507166.1_Intron|FIP1L1_ENST00000306932.6_Missense_Mutation_p.E410G|FIP1L1_ENST00000358575.5_Missense_Mutation_p.E478G	NM_030917.3	NP_112179.2	Q6UN15	FIP1_HUMAN	factor interacting with PAPOLA and CPSF1	484	Arg-rich.|Glu-rich.|Sufficient for interaction with CPSF1 and CSTF3.				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)			CGCACCAGAGAGAGAGAGAGG	0.458			T	PDGFRA	idiopathic hypereosinophilic syndrome																																p.E484G		Atlas-SNP	.		Dom	yes		4	4q12	81608	FIP1 like 1 (S. cerevisiae)		L	.	FIP1L1	60	.	0			c.A1451G						.						74.0	65.0	68.0					4																	54319252		2203	4300	6503	SO:0001583	missense	81608	exon16			CCAGAGAGAGAGA	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.1451A>G	chr4.hg19:g.54319252A>G	ENSP00000336752:p.Glu484Gly	171.0	0.0		82.0	4.0	NM_030917	B4DIR3|G3XAD6|Q0VGE0|Q499Y4|Q49AU3|Q7Z608|Q8WVN3|Q96F80|Q9H077	Missense_Mutation	SNP	ENST00000337488.6	hg19	CCDS3491.1	.	.	.	.	.	.	.	.	.	.	A	19.31	3.803115	0.70682	.	.	ENSG00000145216	ENST00000337488;ENST00000358575;ENST00000306932;ENST00000504094	T;T;T	0.07114	3.22;3.22;3.22	5.33	5.33	0.75918	.	0.085280	0.49916	D	0.000138	T	0.09024	0.0223	L	0.52573	1.65	0.80722	D	1	P;P;P;B	0.40731	0.59;0.608;0.728;0.231	B;B;B;B	0.36186	0.16;0.077;0.219;0.081	T	0.31194	-0.9952	10	0.14656	T	0.56	-17.5152	15.2591	0.73606	1.0:0.0:0.0:0.0	.	478;478;410;484	G3XAD6;B4DIR3;Q6UN15-3;Q6UN15	.;.;.;FIP1_HUMAN	G	484;478;410;141	ENSP00000336752:E484G;ENSP00000351383:E478G;ENSP00000302993:E410G	ENSP00000302993:E410G	E	+	2	0	FIP1L1	54014009	1.000000	0.71417	0.989000	0.46669	0.997000	0.91878	7.089000	0.76909	2.134000	0.65973	0.533000	0.62120	GAG	.	.		0.458	FIP1L1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250602.1	NM_030917	
KIT	3815	hgsc.bcm.edu	37	4	55594207	55594207	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:55594207T>C	ENST00000288135.5	+	13	2007	c.1910T>C	c.(1909-1911)cTc>cCc	p.L637P		NM_000222.2|NM_001093772.1	NP_000213.1|NP_001087241.1	P10721	KIT_HUMAN	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	637	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cellular response to thyroid hormone stimulus (GO:0097067)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell cytokine production (GO:0002371)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|digestive tract development (GO:0048565)|ectopic germ cell programmed cell death (GO:0035234)|embryonic hemopoiesis (GO:0035162)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation (GO:0050673)|erythrocyte differentiation (GO:0030218)|erythropoietin-mediated signaling pathway (GO:0038162)|Fc receptor signaling pathway (GO:0038093)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell migration (GO:0008354)|glycosphingolipid metabolic process (GO:0006687)|hemopoiesis (GO:0030097)|immature B cell differentiation (GO:0002327)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|Kit signaling pathway (GO:0038109)|lamellipodium assembly (GO:0030032)|lymphoid progenitor cell differentiation (GO:0002320)|male gonad development (GO:0008584)|mast cell chemotaxis (GO:0002551)|mast cell cytokine production (GO:0032762)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|mast cell proliferation (GO:0070662)|megakaryocyte development (GO:0035855)|melanocyte adhesion (GO:0097326)|melanocyte differentiation (GO:0030318)|melanocyte migration (GO:0097324)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of programmed cell death (GO:0043069)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|pigmentation (GO:0043473)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of developmental pigmentation (GO:0048070)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|stem cell differentiation (GO:0048863)|stem cell maintenance (GO:0019827)|T cell differentiation (GO:0030217)|visual learning (GO:0008542)	acrosomal vesicle (GO:0001669)|cell-cell junction (GO:0005911)|cytoplasmic side of plasma membrane (GO:0009898)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|stem cell factor receptor activity (GO:0005020)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(8)|autonomic_ganglia(1)|bone(21)|breast(2)|central_nervous_system(4)|endometrium(10)|eye(12)|genital_tract(18)|haematopoietic_and_lymphoid_tissue(1820)|kidney(17)|large_intestine(17)|lung(27)|ovary(23)|pancreas(4)|prostate(1)|salivary_gland(15)|skin(228)|soft_tissue(4117)|stomach(3)|testis(55)|thymus(7)|upper_aerodigestive_tract(1)	6411	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	CGGGAAGCCCTCATGTCTGAA	0.453		1	"""Mis, O"""		"""GIST, AML, TGCT, mastocytosis, mucosal melanoma"""	"""GIST, epithelioma"""	Piebald trait		Piebaldism;Mast Cell disease, Familial Clustering of;Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Gastrointestinal Stromal Tumors																												p.L637P		Atlas-SNP	.	yes	Dom	yes	Familial gastrointestinal stromal tumour	4	4q12	3815	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	yes	"""L, M, O, E"""	KIT,NS,carcinoma,0,1	KIT	7396	.	0			c.T1910C						.						139.0	127.0	131.0					4																	55594207		2203	4300	6503	SO:0001583	missense	3815	exon13	Familial Cancer Database	Piebald trait;incl.: Familial Cutaneous Mastocytosis (Urticaria Pigmentosum);Sporadic Multiple GIST;Familial GIST, incl. Multiple Familial Gastrointestinal Autonomic Nerve Tumors (GANT)	AAGCCCTCATGTC	S67773	CCDS3496.1, CCDS47058.1	4q12	2014-09-17			ENSG00000157404	ENSG00000157404		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6342	protein-coding gene	gene with protein product		164920	"""piebald trait"""	PBT		9027509	Standard	NM_001093772		Approved	CD117, SCFR, C-Kit	uc010igr.3	P10721	OTTHUMG00000128713	ENST00000288135.5:c.1910T>C	chr4.hg19:g.55594207T>C	ENSP00000288135:p.Leu637Pro	286.0	0.0		164.0	7.0	NM_000222	B5A956|D5LXN2|D5M931|F5H8F8|Q6IQ28|Q99662|Q9UM99	Missense_Mutation	SNP	ENST00000288135.5	hg19	CCDS3496.1	.	.	.	.	.	.	.	.	.	.	T	21.6	4.174152	0.78452	.	.	ENSG00000157404	ENST00000288135;ENST00000412167	D;D	0.85339	-1.97;-1.97	6.06	6.06	0.98353	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.48767	D	0.000173	D	0.93400	0.7895	M	0.86502	2.82	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	0.94277	0.7516	10	0.87932	D	0	.	16.6093	0.84858	0.0:0.0:0.0:1.0	.	144;633;637	D5MAV8;P10721-2;P10721	.;.;KIT_HUMAN	P	637;633	ENSP00000288135:L637P;ENSP00000390987:L633P	ENSP00000288135:L637P	L	+	2	0	KIT	55288964	1.000000	0.71417	0.983000	0.44433	0.651000	0.38670	7.963000	0.87922	2.324000	0.78689	0.533000	0.62120	CTC	.	.		0.453	KIT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250618.1		
POLR2B	5431	hgsc.bcm.edu	37	4	57871855	57871855	+	Missense_Mutation	SNP	C	C	T			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:57871855C>T	ENST00000381227.1	+	10	1600	c.1187C>T	c.(1186-1188)gCt>gTt	p.A396V	POLR2B_ENST00000431623.2_Missense_Mutation_p.A321V|RNU6-998P_ENST00000515894.1_RNA|POLR2B_ENST00000314595.5_Missense_Mutation_p.A396V|POLR2B_ENST00000441246.2_Missense_Mutation_p.A389V			P30876	RPB2_HUMAN	polymerase (RNA) II (DNA directed) polypeptide B, 140kDa	396					7-methylguanosine mRNA capping (GO:0006370)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|positive regulation of viral transcription (GO:0050434)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	DNA-directed RNA polymerase II, core complex (GO:0005665)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|ribonucleoside binding (GO:0032549)			breast(1)|central_nervous_system(2)|endometrium(6)|kidney(10)|large_intestine(9)|lung(17)|ovary(2)|prostate(4)|skin(1)	52	Glioma(25;0.08)|all_neural(26;0.181)					TTGGATCTTGCTGGGCCGCTG	0.373																																					p.A396V		Atlas-SNP	.											.	POLR2B	108	.	0			c.C1187T						.						90.0	90.0	90.0					4																	57871855		2203	4300	6503	SO:0001583	missense	5431	exon9			ATCTTGCTGGGCC		CCDS3511.1	4q12	2013-01-21	2002-08-29		ENSG00000047315	ENSG00000047315		"""RNA polymerase subunits"""	9188	protein-coding gene	gene with protein product		180661	"""polymerase (RNA) II (DNA directed) polypeptide B (140kD)"""			1518060, 8034326	Standard	NM_000938		Approved	RPB2	uc003hcl.1	P30876	OTTHUMG00000128771	ENST00000381227.1:c.1187C>T	chr4.hg19:g.57871855C>T	ENSP00000370625:p.Ala396Val	83.0	0.0		103.0	5.0	NM_000938	A8K1A8|Q8IZ61	Missense_Mutation	SNP	ENST00000381227.1	hg19	CCDS3511.1	.	.	.	.	.	.	.	.	.	.	C	36	5.645050	0.96704	.	.	ENSG00000047315	ENST00000381227;ENST00000431623;ENST00000441246;ENST00000314595	T;T;T;T	0.76578	-1.03;-1.03;-1.03;-1.03	5.46	5.46	0.80206	RNA polymerase, beta subunit, protrusion (1);	0.000000	0.85682	D	0.000000	D	0.88735	0.6517	M	0.83603	2.65	0.80722	D	1	P;P	0.46621	0.881;0.881	P;P	0.61003	0.882;0.882	D	0.89240	0.3583	10	0.66056	D	0.02	.	19.6697	0.95907	0.0:1.0:0.0:0.0	.	321;396	C9J4M6;P30876	.;RPB2_HUMAN	V	396;321;389;396	ENSP00000370625:A396V;ENSP00000391096:A321V;ENSP00000391452:A389V;ENSP00000312735:A396V	ENSP00000312735:A396V	A	+	2	0	POLR2B	57566612	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	7.776000	0.85560	2.724000	0.93272	0.650000	0.86243	GCT	.	.		0.373	POLR2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250692.1	NM_000938	
POLR2B	5431	hgsc.bcm.edu	37	4	57883331	57883331	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:57883331A>G	ENST00000381227.1	+	16	2491	c.2078A>G	c.(2077-2079)tAt>tGt	p.Y693C	POLR2B_ENST00000431623.2_Missense_Mutation_p.Y618C|POLR2B_ENST00000314595.5_Missense_Mutation_p.Y693C|POLR2B_ENST00000441246.2_Missense_Mutation_p.Y686C			P30876	RPB2_HUMAN	polymerase (RNA) II (DNA directed) polypeptide B, 140kDa	693					7-methylguanosine mRNA capping (GO:0006370)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|positive regulation of viral transcription (GO:0050434)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	DNA-directed RNA polymerase II, core complex (GO:0005665)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|ribonucleoside binding (GO:0032549)			breast(1)|central_nervous_system(2)|endometrium(6)|kidney(10)|large_intestine(9)|lung(17)|ovary(2)|prostate(4)|skin(1)	52	Glioma(25;0.08)|all_neural(26;0.181)					TGTTCCACATATACACACTGT	0.408																																					p.Y693C		Atlas-SNP	.											.	POLR2B	108	.	0			c.A2078G						.						324.0	298.0	307.0					4																	57883331		2203	4300	6503	SO:0001583	missense	5431	exon15			CCACATATACACA		CCDS3511.1	4q12	2013-01-21	2002-08-29		ENSG00000047315	ENSG00000047315		"""RNA polymerase subunits"""	9188	protein-coding gene	gene with protein product		180661	"""polymerase (RNA) II (DNA directed) polypeptide B (140kD)"""			1518060, 8034326	Standard	NM_000938		Approved	RPB2	uc003hcl.1	P30876	OTTHUMG00000128771	ENST00000381227.1:c.2078A>G	chr4.hg19:g.57883331A>G	ENSP00000370625:p.Tyr693Cys	440.0	1.0		357.0	154.0	NM_000938	A8K1A8|Q8IZ61	Missense_Mutation	SNP	ENST00000381227.1	hg19	CCDS3511.1	.	.	.	.	.	.	.	.	.	.	A	19.18	3.776910	0.70107	.	.	ENSG00000047315	ENST00000381227;ENST00000431623;ENST00000441246;ENST00000314595	T;T;T;T	0.78126	-1.15;-1.15;-1.15;-1.15	4.91	4.91	0.64330	RNA polymerase Rpb2, domain 5 (1);	0.000000	0.85682	D	0.000000	D	0.90473	0.7016	H	0.94345	3.525	0.80722	D	1	D;D	0.69078	0.993;0.997	D;D	0.66351	0.943;0.943	D	0.93205	0.6595	10	0.87932	D	0	.	14.828	0.70128	1.0:0.0:0.0:0.0	.	618;693	C9J4M6;P30876	.;RPB2_HUMAN	C	693;618;686;693	ENSP00000370625:Y693C;ENSP00000391096:Y618C;ENSP00000391452:Y686C;ENSP00000312735:Y693C	ENSP00000312735:Y693C	Y	+	2	0	POLR2B	57578088	1.000000	0.71417	0.151000	0.22473	0.886000	0.51366	9.283000	0.95860	1.956000	0.56807	0.379000	0.24179	TAT	.	.		0.408	POLR2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250692.1	NM_000938	
SLC4A4	8671	hgsc.bcm.edu	37	4	72102334	72102334	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:72102334T>C	ENST00000264485.5	+	2	158	c.41T>C	c.(40-42)cTc>cCc	p.L14P	SLC4A4_ENST00000351898.6_Missense_Mutation_p.L14P|SLC4A4_ENST00000425175.1_Missense_Mutation_p.L14P	NM_001098484.2	NP_001091954.1	Q9Y6R1	S4A4_HUMAN	solute carrier family 4 (sodium bicarbonate cotransporter), member 4	14					bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)	basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|sodium:bicarbonate symporter activity (GO:0008510)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(9)|liver(1)|lung(21)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	58			Lung(101;0.0739)|LUSC - Lung squamous cell carcinoma(112;0.225)		Sodium bicarbonate(DB01390)	GCTTCCTTCCTCAAGCATGTG	0.423																																					p.L14P		Atlas-SNP	.											.	SLC4A4	269	.	0			c.T41C						.						116.0	118.0	117.0					4																	72102334		1887	4108	5995	SO:0001583	missense	8671	exon2			CCTTCCTCAAGCA	AF007216	CCDS3549.1, CCDS43236.1, CCDS47071.1	4q13.3	2013-07-19	2013-07-19		ENSG00000080493	ENSG00000080493		"""Solute carriers"""	11030	protein-coding gene	gene with protein product		603345	"""solute carrier family 4, sodium bicarbonate cotransporter, member 4"""	SLC4A5		9235899, 9651366	Standard	NM_001098484		Approved	NBC1, HNBC1, NBC2, pNBC, hhNMC	uc010iic.3	Q9Y6R1	OTTHUMG00000129907	ENST00000264485.5:c.41T>C	chr4.hg19:g.72102334T>C	ENSP00000264485:p.Leu14Pro	127.0	0.0		91.0	4.0	NM_001098484	C4B714|O15153|Q8NEJ2|Q9H262|Q9NRZ1|Q9UIC0|Q9UIC1|Q9UP50	Missense_Mutation	SNP	ENST00000264485.5	hg19	CCDS43236.1	.	.	.	.	.	.	.	.	.	.	T	17.42	3.384766	0.61956	.	.	ENSG00000080493	ENST00000264485;ENST00000425175;ENST00000351898	T;T;T	0.78924	-1.22;-1.22;-0.85	5.82	5.82	0.92795	.	0.262393	0.39341	N	0.001382	D	0.85301	0.5665	M	0.74881	2.28	0.80722	D	1	P;D;P	0.59767	0.835;0.986;0.898	B;P;P	0.57152	0.445;0.814;0.451	D	0.86055	0.1528	10	0.49607	T	0.09	.	16.1832	0.81925	0.0:0.0:0.0:1.0	.	14;14;14	A5JJ20;Q9Y6R1-4;Q9Y6R1	.;.;S4A4_HUMAN	P	14	ENSP00000264485:L14P;ENSP00000393557:L14P;ENSP00000307349:L14P	ENSP00000264485:L14P	L	+	2	0	SLC4A4	72321198	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	6.002000	0.70693	2.228000	0.72767	0.533000	0.62120	CTC	.	.		0.423	SLC4A4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362090.1	NM_003759	
ALB	213	hgsc.bcm.edu	37	4	74282071	74282071	+	Splice_Site	SNP	G	G	A			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:74282071G>A	ENST00000503124.1	+	8	1046		c.e8+1		ALB_ENST00000295897.4_Splice_Site|ALB_ENST00000401494.3_Splice_Site|ALB_ENST00000509063.1_Splice_Site|ALB_ENST00000415165.2_Splice_Site|ALB_ENST00000505649.1_Splice_Site			Q8TES7	FBF1_HUMAN	albumin						apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				NS(1)|endometrium(4)|kidney(1)|large_intestine(6)|liver(9)|lung(16)|ovary(3)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	48	Breast(15;0.00102)		Epithelial(6;4.8e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000263)|all cancers(17;0.000472)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			TCCAGAATGCGTAAGTAATTT	0.294																																					.		Atlas-SNP	.											ALB,NS,carcinoma,+1,1	ALB	132	.	0			c.1289+1G>A						.						37.0	37.0	37.0					4																	74282071		2202	4298	6500	SO:0001630	splice_region_variant	213	exon10			GAATGCGTAAGTA	V00494	CCDS3555.1	4q13.3	2008-02-05	2006-06-30	2006-06-30	ENSG00000163631	ENSG00000163631			399	protein-coding gene	gene with protein product		103600				6292049, 6192711	Standard	NM_000477		Approved		uc003hgs.4	P02768	OTTHUMG00000129919	ENST00000503124.1:c.839+1G>A	chr4.hg19:g.74282071G>A		118.0	0.0		111.0	41.0	NM_000477	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Splice_Site	SNP	ENST00000503124.1	hg19		.	.	.	.	.	.	.	.	.	.	G	11.43	1.637194	0.29157	.	.	ENSG00000163631	ENST00000295897;ENST00000415165;ENST00000329326;ENST00000503124;ENST00000509063;ENST00000401494;ENST00000430202;ENST00000511370	.	.	.	5.74	4.89	0.63831	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.8057	0.69952	0.0:0.0:0.8546:0.1454	.	.	.	.	.	-1	.	.	.	+	.	.	ALB	74500935	1.000000	0.71417	0.547000	0.28179	0.272000	0.26649	3.923000	0.56469	1.414000	0.47017	0.591000	0.81541	.	.	.		0.294	ALB-011	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000365419.1	NM_000477	Intron
G3BP2	9908	hgsc.bcm.edu	37	4	76572284	76572284	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:76572284T>C	ENST00000359707.4	-	10	1771	c.986A>G	c.(985-987)gAt>gGt	p.D329G	G3BP2_ENST00000395719.3_Missense_Mutation_p.D329G|G3BP2_ENST00000357854.3_Missense_Mutation_p.D296G	NM_203505.2	NP_987101.1	Q9UN86	G3BP2_HUMAN	GTPase activating protein (SH3 domain) binding protein 2	329					cytoplasmic sequestering of NF-kappaB (GO:0007253)|mRNA transport (GO:0051028)|Ras protein signal transduction (GO:0007265)	cytoplasm (GO:0005737)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|receptor signaling complex scaffold activity (GO:0030159)			breast(3)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(6)|upper_aerodigestive_tract(3)|urinary_tract(2)	27			Lung(101;0.0973)|LUSC - Lung squamous cell carcinoma(112;0.122)			TTGATGACTATCTGGATAGCG	0.343																																					p.D329G		Atlas-SNP	.											.	G3BP2	52	.	0			c.A986G						.						101.0	100.0	101.0					4																	76572284		2203	4299	6502	SO:0001583	missense	9908	exon10			TGACTATCTGGAT	AB014560	CCDS3571.1, CCDS3572.1	4q21.1	2013-02-12	2006-11-01		ENSG00000138757	ENSG00000138757		"""RNA binding motif (RRM) containing"""	30291	protein-coding gene	gene with protein product	"""Ras-GTPase activating protein SH3 domain-binding protein 2"""					9734811, 9575347	Standard	NM_203504		Approved	KIAA0660	uc003his.3	Q9UN86	OTTHUMG00000130097	ENST00000359707.4:c.986A>G	chr4.hg19:g.76572284T>C	ENSP00000352738:p.Asp329Gly	137.0	0.0		118.0	5.0	NM_012297	A8K6X1|O60606|O75149|Q9UPA1	Missense_Mutation	SNP	ENST00000359707.4	hg19	CCDS3571.1	.	.	.	.	.	.	.	.	.	.	T	28.8	4.953458	0.92660	.	.	ENSG00000138757	ENST00000395719;ENST00000359707;ENST00000357854	T;T;T	0.74632	-0.86;-0.86;-0.86	6.04	6.04	0.98038	Nucleotide-binding, alpha-beta plait (1);	0.000000	0.85682	D	0.000000	D	0.85660	0.5748	M	0.71206	2.165	0.80722	D	1	D;D	0.67145	0.996;0.991	D;D	0.77557	0.99;0.979	D	0.86994	0.2112	10	0.87932	D	0	.	16.5763	0.84648	0.0:0.0:0.0:1.0	.	296;329	Q9UN86-2;Q9UN86	.;G3BP2_HUMAN	G	329;329;296	ENSP00000379069:D329G;ENSP00000352738:D329G;ENSP00000350518:D296G	ENSP00000350518:D296G	D	-	2	0	G3BP2	76791308	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.698000	0.84413	2.317000	0.78254	0.459000	0.35465	GAT	.	.		0.343	G3BP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252399.2	NM_012297	
CNOT6L	246175	hgsc.bcm.edu	37	4	78652675	78652675	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:78652675T>C	ENST00000504123.1	-	9	1020	c.890A>G	c.(889-891)aAg>aGg	p.K297R	CNOT6L_ENST00000264903.4_Missense_Mutation_p.K297R			Q96LI5	CNO6L_HUMAN	CCR4-NOT transcription complex, subunit 6-like	297	Nuclease domain.				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						CACTGTATGCTTCTGCACCAA	0.363																																					p.K297R		Atlas-SNP	.											.	CNOT6L	57	.	0			c.A890G						.						84.0	82.0	82.0					4																	78652675		2105	4268	6373	SO:0001583	missense	246175	exon9			GTATGCTTCTGCA	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.890A>G	chr4.hg19:g.78652675T>C	ENSP00000424896:p.Lys297Arg	144.0	0.0		96.0	4.0	NM_144571	Q9UF92	Missense_Mutation	SNP	ENST00000504123.1	hg19		.	.	.	.	.	.	.	.	.	.	T	19.25	3.790975	0.70452	.	.	ENSG00000138767	ENST00000504123;ENST00000264903;ENST00000512485;ENST00000505983	T;T;T;T	0.78595	-1.19;-1.19;-1.19;-1.19	5.86	5.86	0.93980	Endonuclease/exonuclease/phosphatase (2);	0.000000	0.85682	D	0.000000	T	0.75510	0.3859	L	0.42529	1.33	0.80722	D	1	P;B	0.40834	0.73;0.242	B;B	0.42555	0.391;0.16	T	0.77778	-0.2460	10	0.59425	D	0.04	-4.0875	16.2526	0.82494	0.0:0.0:0.0:1.0	.	270;297	Q96LI5-2;Q96LI5	.;CNO6L_HUMAN	R	297;297;304;72	ENSP00000424896:K297R;ENSP00000264903:K297R;ENSP00000425571:K304R;ENSP00000426320:K72R	ENSP00000264903:K297R	K	-	2	0	CNOT6L	78871699	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.040000	0.89188	2.241000	0.73720	0.482000	0.46254	AAG	.	.		0.363	CNOT6L-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000362515.1		
FRAS1	80144	hgsc.bcm.edu	37	4	79458204	79458204	+	Silent	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:79458204T>C	ENST00000264895.6	+	72	11588	c.11148T>C	c.(11146-11148)gcT>gcC	p.A3716A		NM_025074.6	NP_079350.5	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	3712					cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						TTAATTCTGCTTACAAACTCC	0.408																																					p.A3716A		Atlas-SNP	.											.	FRAS1	779	.	0			c.T11148C						.						134.0	133.0	133.0					4																	79458204		1825	4088	5913	SO:0001819	synonymous_variant	80144	exon72			TTCTGCTTACAAA	AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"""Fraser syndrome 1"""			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000264895.6:c.11148T>C	chr4.hg19:g.79458204T>C		149.0	0.0		96.0	4.0	NM_025074	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Silent	SNP	ENST00000264895.6	hg19	CCDS54771.1																																																																																			.	.		0.408	FRAS1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
PTPN13	5783	hgsc.bcm.edu	37	4	87735675	87735675	+	Missense_Mutation	SNP	C	C	A	rs373179030		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:87735675C>A	ENST00000411767.2	+	48	7492	c.7429C>A	c.(7429-7431)Caa>Aaa	p.Q2477K	PTPN13_ENST00000316707.6_Missense_Mutation_p.Q2286K|PTPN13_ENST00000427191.2_Missense_Mutation_p.Q2458K|PTPN13_ENST00000436978.1_Missense_Mutation_p.Q2482K|PTPN13_ENST00000511467.1_Missense_Mutation_p.Q2482K			Q12923	PTN13_HUMAN	protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase)	2477					peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein tyrosine phosphatase activity (GO:0004725)			NS(4)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(23)|lung(24)|ovary(4)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	93		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)		AGAAGAAGAGCAAAAACAGCA	0.413																																					p.Q2482K		Atlas-SNP	.											.	PTPN13	203	.	0			c.C7444A						.						90.0	84.0	86.0					4																	87735675		1880	4115	5995	SO:0001583	missense	5783	exon48			GAAGAGCAAAAAC		CCDS47093.1, CCDS47094.1, CCDS47095.1, CCDS47096.1	4q21.3	2011-06-09			ENSG00000163629	ENSG00000163629		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9646	protein-coding gene	gene with protein product		600267				8287977	Standard	NM_006264		Approved	PTP1E, PTP-BAS, PTPL1, PTP-BL	uc003hpy.3	Q12923	OTTHUMG00000160968	ENST00000411767.2:c.7429C>A	chr4.hg19:g.87735675C>A	ENSP00000407249:p.Gln2477Lys	565.0	0.0		397.0	185.0	NM_080685	B2RTR0|Q15159|Q15263|Q15264|Q15265|Q15674|Q16826|Q8IWH7|Q9NYN9|Q9UDA8	Missense_Mutation	SNP	ENST00000411767.2	hg19	CCDS47094.1	.	.	.	.	.	.	.	.	.	.	C	14.56	2.572041	0.45798	.	.	ENSG00000163629	ENST00000427191;ENST00000436978;ENST00000316707;ENST00000411767;ENST00000511467;ENST00000357349	T;T;T;T;T	0.52295	0.67;0.7;0.78;0.67;0.7	5.64	4.79	0.61399	.	0.353216	0.21743	N	0.069799	T	0.26666	0.0652	N	0.04508	-0.205	0.24922	N	0.991978	B;B;B;B	0.12630	0.006;0.006;0.004;0.006	B;B;B;B	0.10450	0.005;0.005;0.002;0.005	T	0.18116	-1.0347	10	0.46703	T	0.11	.	11.7022	0.51577	0.1389:0.7275:0.1336:0.0	.	2286;2458;2477;2482	Q12923-2;Q12923-3;Q12923;Q12923-4	.;.;PTN13_HUMAN;.	K	2458;2482;2286;2477;2482;2426	ENSP00000408368:Q2458K;ENSP00000394794:Q2482K;ENSP00000322675:Q2286K;ENSP00000407249:Q2477K;ENSP00000426626:Q2482K	ENSP00000322675:Q2286K	Q	+	1	0	PTPN13	87954699	0.945000	0.32115	0.339000	0.25562	0.917000	0.54804	2.537000	0.45702	1.510000	0.48803	0.563000	0.77884	CAA	.	.		0.413	PTPN13-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363191.1		
EGF	1950	hgsc.bcm.edu	37	4	110925702	110925702	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:110925702A>G	ENST00000265171.5	+	22	3660	c.3215A>G	c.(3214-3216)gAg>gGg	p.E1072G	EGF_ENST00000509793.1_Missense_Mutation_p.E1030G|EGF_ENST00000503392.1_Missense_Mutation_p.E1031G	NM_001178130.1|NM_001963.4	NP_001171601.1|NP_001954.2	P01133	EGF_HUMAN	epidermal growth factor	1072					activation of MAPKK activity (GO:0000186)|activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|branching morphogenesis of an epithelial tube (GO:0048754)|DNA replication (GO:0006260)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERK1 and ERK2 cascade (GO:0070371)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|mammary gland alveolus development (GO:0060749)|negative regulation of cholesterol efflux (GO:0090370)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of secretion (GO:0051048)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cerebellar granule cell precursor proliferation (GO:0021940)|positive regulation of DNA binding (GO:0043388)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of hyaluronan biosynthetic process (GO:1900127)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of calcium ion import (GO:0090279)|regulation of protein localization to cell surface (GO:2000008)|signal transduction (GO:0007165)|STAT protein import into nucleus (GO:0007262)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	calcium ion binding (GO:0005509)|epidermal growth factor receptor binding (GO:0005154)|growth factor activity (GO:0008083)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)			breast(1)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(19)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		Hepatocellular(203;0.0893)		OV - Ovarian serous cystadenocarcinoma(123;9.87e-06)	Sucralfate(DB00364)	AATCCTTATGAGGAGTCGAGC	0.468																																					p.E1072G		Atlas-SNP	.											.	EGF	113	.	0			c.A3215G						.						123.0	122.0	123.0					4																	110925702		2203	4300	6503	SO:0001583	missense	1950	exon22			CTTATGAGGAGTC	X04571	CCDS3689.1, CCDS54794.1, CCDS54795.1	4q25	2012-10-02	2010-05-11		ENSG00000138798	ENSG00000138798			3229	protein-coding gene	gene with protein product		131530	"""epidermal growth factor (beta-urogastrone)"""				Standard	NM_001963		Approved		uc003hzy.4	P01133	OTTHUMG00000132044	ENST00000265171.5:c.3215A>G	chr4.hg19:g.110925702A>G	ENSP00000265171:p.Glu1072Gly	117.0	0.0		73.0	4.0	NM_001963	B4DRK7|E7EVD2|E9PBF0|Q52LZ6	Missense_Mutation	SNP	ENST00000265171.5	hg19	CCDS3689.1	.	.	.	.	.	.	.	.	.	.	A	8.949	0.967629	0.18659	.	.	ENSG00000138798	ENST00000509793;ENST00000265171;ENST00000503392	D;D;D	0.89415	-2.51;-2.43;-2.13	4.2	4.2	0.49525	.	0.596165	0.15279	N	0.270820	T	0.79540	0.4463	L	0.32530	0.975	0.25845	N	0.984007	P;P;P	0.44734	0.842;0.763;0.651	B;B;B	0.30855	0.057;0.121;0.057	T	0.74705	-0.3575	10	0.72032	D	0.01	.	9.8422	0.41006	1.0:0.0:0.0:0.0	.	1031;1030;1072	E7EVD2;P01133-2;P01133	.;.;EGF_HUMAN	G	1030;1072;1031	ENSP00000424316:E1030G;ENSP00000265171:E1072G;ENSP00000421384:E1031G	ENSP00000265171:E1072G	E	+	2	0	EGF	111145151	0.993000	0.37304	0.924000	0.36721	0.002000	0.02628	2.581000	0.46077	1.874000	0.54306	0.528000	0.53228	GAG	.	.		0.468	EGF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255065.1		
ALPK1	80216	hgsc.bcm.edu	37	4	113353286	113353286	+	Missense_Mutation	SNP	G	G	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:113353286G>C	ENST00000458497.1	+	11	2862	c.2583G>C	c.(2581-2583)atG>atC	p.M861I	ALPK1_ENST00000504176.2_Missense_Mutation_p.M783I|ALPK1_ENST00000177648.9_Missense_Mutation_p.M861I	NM_001102406.1|NM_025144.3	NP_001095876.1|NP_079420.3	Q96QP1	ALPK1_HUMAN	alpha-kinase 1	861			M -> T (in dbSNP:rs11726117). {ECO:0000269|PubMed:10021370, ECO:0000269|PubMed:10819331, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17344846, ECO:0000269|Ref.5}.				ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.T861T(1)		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)		TCGACAGCATGGATGTTCCCT	0.572																																					p.M861I		Atlas-SNP	.											ALPK1,NS,carcinoma,0,1	ALPK1	125	.	1	Substitution - coding silent(1)	endometrium(1)	c.G2583C						.						55.0	52.0	53.0					4																	113353286		2203	4300	6503	SO:0001583	missense	80216	exon11			CAGCATGGATGTT	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.2583G>C	chr4.hg19:g.113353286G>C	ENSP00000398048:p.Met861Ile	198.0	0.0		128.0	0.0	NM_001102406	B4E3G1|F5H138|Q68CI9|Q6P9F9|Q6ZNK4|Q9P201	Missense_Mutation	SNP	ENST00000458497.1	hg19	CCDS3697.1	.	.	.	.	.	.	.	.	.	.	G	8.375	0.836138	0.16891	.	.	ENSG00000073331	ENST00000458497;ENST00000177648;ENST00000504176	T;T;T	0.02280	4.43;4.43;4.36	4.81	-5.27	0.02763	.	0.519792	0.18510	N	0.139088	T	0.01222	0.0040	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.42172	-0.9467	10	0.56958	D	0.05	0.2401	10.3661	0.44024	0.3425:0.0952:0.5623:0.0	.	783;861	F5H138;Q96QP1	.;ALPK1_HUMAN	I	861;861;783	ENSP00000398048:M861I;ENSP00000177648:M861I;ENSP00000426044:M783I	ENSP00000177648:M861I	M	+	3	0	ALPK1	113572735	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-0.844000	0.04345	-1.052000	0.03222	-0.150000	0.13652	ATG	.	.		0.572	ALPK1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256421.2	NM_025144	
SPRY1	10252	hgsc.bcm.edu	37	4	124323536	124323536	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:124323536T>C	ENST00000394339.2	+	2	1130	c.790T>C	c.(790-792)Tct>Cct	p.S264P	SPRY1_ENST00000339241.1_Missense_Mutation_p.S264P	NM_001258039.1|NM_005841.2	NP_001244968.1|NP_005832.1	O43609	SPY1_HUMAN	sprouty homolog 1, antagonist of FGF signaling (Drosophila)	264	Cys-rich.|SPR. {ECO:0000255|PROSITE- ProRule:PRU00572}.				epidermal growth factor receptor signaling pathway (GO:0007173)|multicellular organismal development (GO:0007275)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)	cytosol (GO:0005829)|plasma membrane (GO:0005886)				NS(1)|large_intestine(4)|lung(2)|ovary(1)|skin(3)	11						GGGAGCCATGTCTTTATTTTT	0.483																																					p.S264P		Atlas-SNP	.											.	SPRY1	28	.	0			c.T790C						.						239.0	203.0	215.0					4																	124323536		2203	4300	6503	SO:0001583	missense	10252	exon2			GCCATGTCTTTAT	AF041037	CCDS3731.1	4q	2009-04-17	2001-11-28		ENSG00000164056	ENSG00000164056			11269	protein-coding gene	gene with protein product		602465	"""sprouty (Drosophila) homolog 1 (antagonist of FGF signaling)"""			9458049, 15962011	Standard	NM_001258038		Approved	hSPRY1	uc003ifa.4	O43609	OTTHUMG00000133071	ENST00000394339.2:c.790T>C	chr4.hg19:g.124323536T>C	ENSP00000377871:p.Ser264Pro	155.0	0.0		98.0	4.0	NM_001258039	D3DNX6|Q6PNE0	Missense_Mutation	SNP	ENST00000394339.2	hg19	CCDS3731.1	.	.	.	.	.	.	.	.	.	.	T	15.57	2.873713	0.51695	.	.	ENSG00000164056	ENST00000339241;ENST00000394339	T;T	0.72282	-0.64;-0.64	4.61	0.355	0.16069	.	0.237030	0.35739	N	0.003003	T	0.74764	0.3759	M	0.80616	2.505	0.52501	D	0.999952	P	0.49783	0.928	P	0.49387	0.609	T	0.76537	-0.2923	9	.	.	.	-5.6009	12.2445	0.54561	0.0:0.0:0.3998:0.6002	.	264	O43609	SPY1_HUMAN	P	264	ENSP00000343785:S264P;ENSP00000377871:S264P	.	S	+	1	0	SPRY1	124542986	1.000000	0.71417	0.940000	0.37924	0.982000	0.71751	2.656000	0.46716	0.321000	0.23259	0.459000	0.35465	TCT	.	.		0.483	SPRY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256711.1		
FGA	2243	hgsc.bcm.edu	37	4	155511792	155511792	+	Silent	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:155511792T>C	ENST00000302053.3	-	1	126	c.48A>G	c.(46-48)acA>acG	p.T16T	FGA_ENST00000403106.3_Silent_p.T16T	NM_000508.3	NP_000499.1	P02671	FIBA_HUMAN	fibrinogen alpha chain	16					blood coagulation (GO:0007596)|blood coagulation, common pathway (GO:0072377)|cell-matrix adhesion (GO:0007160)|cellular protein complex assembly (GO:0043623)|extracellular matrix organization (GO:0030198)|negative regulation of blood coagulation, common pathway (GO:2000261)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of exocytosis (GO:0045921)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of peptide hormone secretion (GO:0090277)|positive regulation of protein secretion (GO:0050714)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of vasoconstriction (GO:0045907)|protein polymerization (GO:0051258)|response to calcium ion (GO:0051592)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|cell cortex (GO:0005938)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|plasma membrane (GO:0005886)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|vesicle (GO:0031982)	structural molecule activity (GO:0005198)			NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(14)|liver(2)|lung(20)|ovary(3)|pancreas(1)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	73	all_hematologic(180;0.215)	Renal(120;0.0458)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Sucralfate(DB00364)|Tenecteplase(DB00031)	ATACCCATGCTGTGCCCACCA	0.498																																					p.T16T	NSCLC(143;340 1922 20892 22370 48145)	Atlas-SNP	.											.	FGA	179	.	0			c.A48G						.						73.0	54.0	61.0					4																	155511792		2197	4278	6475	SO:0001819	synonymous_variant	2243	exon1			CCATGCTGTGCCC		CCDS3787.1, CCDS47152.1	4q28	2014-09-17			ENSG00000171560	ENSG00000171560		"""Fibrinogen C domain containing"", ""Endogenous ligands"""	3661	protein-coding gene	gene with protein product		134820	"""fibrinogen, A alpha polypeptide"""				Standard	NM_000508		Approved		uc003iod.1	P02671	OTTHUMG00000150330	ENST00000302053.3:c.48A>G	chr4.hg19:g.155511792T>C		119.0	0.0		100.0	4.0	NM_000508	A8K3E4|D3DP14|D3DP15|Q4QQH7|Q9BX62|Q9UCH2	Silent	SNP	ENST00000302053.3	hg19	CCDS3787.1																																																																																			.	.		0.498	FGA-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317593.1	NM_000508	
FASTKD3	79072	hgsc.bcm.edu	37	5	7868134	7868134	+	Silent	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:7868134A>G	ENST00000264669.5	-	2	199	c.63T>C	c.(61-63)gcT>gcC	p.A21A	FASTKD3_ENST00000513658.1_Intron|MTRR_ENST00000341013.6_5'Flank|MTRR_ENST00000440940.2_5'Flank|MTRR_ENST00000502509.1_Intron|MTRR_ENST00000264668.2_5'Flank	NM_024091.3	NP_076996.2	Q14CZ7	FAKD3_HUMAN	FAST kinase domains 3	21					cellular respiration (GO:0045333)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)			breast(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|liver(2)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39						AAGCAGCCAGAGCTCTATGCA	0.388																																					p.A21A		Atlas-SNP	.											.	FASTKD3	88	.	0			c.T63C						.						65.0	73.0	70.0					5																	7868134		2203	4300	6503	SO:0001819	synonymous_variant	79072	exon2			AGCCAGAGCTCTA	AK026927	CCDS3873.1	5p15.31	2008-02-05			ENSG00000124279	ENSG00000124279			28758	protein-coding gene	gene with protein product						12477932	Standard	NM_024091		Approved	MGC5297, FLJ23274	uc003jeb.3	Q14CZ7	OTTHUMG00000131029	ENST00000264669.5:c.63T>C	chr5.hg19:g.7868134A>G		103.0	0.0		98.0	4.0	NM_024091	Q9BVD3	Silent	SNP	ENST00000264669.5	hg19	CCDS3873.1																																																																																			.	.		0.388	FASTKD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253673.1	NM_024091	
FAM173B	134145	hgsc.bcm.edu	37	5	10236710	10236710	+	Silent	SNP	C	C	T			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:10236710C>T	ENST00000511437.1	-	3	336	c.324G>A	c.(322-324)aaG>aaA	p.K108K	FAM173B_ENST00000280330.8_5'UTR|FAM173B_ENST00000510052.1_5'UTR|FAM173B_ENST00000510047.1_Silent_p.K108K	NM_199133.3	NP_954584.2	Q6P4H8	F173B_HUMAN	family with sequence similarity 173, member B	108						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	16						TGAACCCTTTCTTCGCAGCCG	0.403																																					p.K108K		Atlas-SNP	.											.	FAM173B	24	.	0			c.G324A						.						80.0	78.0	78.0					5																	10236710		1856	4111	5967	SO:0001819	synonymous_variant	134145	exon3			CCCTTTCTTCGCA		CCDS43301.1, CCDS58942.1	5p15.2	2008-08-08			ENSG00000150756	ENSG00000150756			27029	protein-coding gene	gene with protein product						12477932	Standard	NM_199133		Approved		uc003jeo.3	Q6P4H8	OTTHUMG00000161771	ENST00000511437.1:c.324G>A	chr5.hg19:g.10236710C>T		101.0	0.0		91.0	4.0	NM_199133	B4DT41|B4DXK2|E9PBZ4	Silent	SNP	ENST00000511437.1	hg19	CCDS43301.1																																																																																			.	.		0.403	FAM173B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000366048.2	NM_199133	
TRIO	7204	hgsc.bcm.edu	37	5	14286982	14286982	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:14286982A>G	ENST00000344204.4	+	4	374	c.350A>G	c.(349-351)gAg>gGg	p.E117G	TRIO_ENST00000537187.1_Missense_Mutation_p.E117G|TRIO_ENST00000509967.2_Missense_Mutation_p.E68G	NM_007118.2	NP_009049.2	O75962	TRIO_HUMAN	trio Rho guanine nucleotide exchange factor	117	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.				apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	cytosol (GO:0005829)	ATP binding (GO:0005524)|guanyl-nucleotide exchange factor activity (GO:0005085)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(2)|breast(6)|central_nervous_system(4)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(21)|lung(34)|ovary(4)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	118	Lung NSC(4;0.000742)					CTCTGCAGCGAGGAGGTCTGC	0.587																																					p.E117G		Atlas-SNP	.											.	TRIO	305	.	0			c.A350G						.						97.0	82.0	87.0					5																	14286982		2203	4300	6503	SO:0001583	missense	7204	exon4			GCAGCGAGGAGGT	AF091395	CCDS3883.1	5p14-p15.1	2013-01-11	2012-07-12		ENSG00000038382	ENSG00000038382		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"""	12303	protein-coding gene	gene with protein product		601893	"""triple functional domain (PTPRF interacting)"""			8643598	Standard	NM_007118		Approved	ARHGEF23	uc003jff.3	O75962	OTTHUMG00000131057	ENST00000344204.4:c.350A>G	chr5.hg19:g.14286982A>G	ENSP00000339299:p.Glu117Gly	132.0	0.0		98.0	4.0	NM_007118	D3DTD1|Q13458|Q59EQ7|Q6PJC9|Q6ZN05|Q8IWK8	Missense_Mutation	SNP	ENST00000344204.4	hg19	CCDS3883.1	.	.	.	.	.	.	.	.	.	.	A	18.99	3.739618	0.69304	.	.	ENSG00000038382	ENST00000344204;ENST00000537187;ENST00000509967	T;T;T	0.65916	-0.18;-0.18;-0.18	5.56	5.56	0.83823	Cellular retinaldehyde-binding/triple function, C-terminal (4);	0.000000	0.85682	D	0.000000	T	0.79441	0.4446	M	0.79926	2.475	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.87578	0.998;0.995	T	0.78826	-0.2051	10	0.32370	T	0.25	.	15.711	0.77626	1.0:0.0:0.0:0.0	.	68;117	F5H228;O75962	.;TRIO_HUMAN	G	117;117;68	ENSP00000339299:E117G;ENSP00000446348:E117G;ENSP00000445592:E68G	ENSP00000339299:E117G	E	+	2	0	TRIO	14339982	1.000000	0.71417	0.995000	0.50966	0.652000	0.38707	9.339000	0.96797	2.118000	0.64928	0.482000	0.46254	GAG	.	.		0.587	TRIO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253711.2	NM_007118	
RAD17	5884	hgsc.bcm.edu	37	5	68687769	68687769	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:68687769T>C	ENST00000509734.1	+	12	1829	c.1151T>C	c.(1150-1152)gTc>gCc	p.V384A	RAD17_ENST00000504177.1_Intron|RAD17_ENST00000361732.2_Missense_Mutation_p.V373A|RAD17_ENST00000358030.2_Missense_Mutation_p.V208A|RAD17_ENST00000282891.6_Missense_Mutation_p.V287A|RAD17_ENST00000380774.3_Missense_Mutation_p.V384A|RAD17_ENST00000345306.6_Missense_Mutation_p.V373A|RAD17_ENST00000354312.3_Missense_Mutation_p.V373A|RAD17_ENST00000305138.4_Missense_Mutation_p.V373A|RAD17_ENST00000354868.5_Missense_Mutation_p.V373A|RAD17_ENST00000521422.1_Missense_Mutation_p.V208A			O75943	RAD17_HUMAN	RAD17 homolog (S. pombe)	384					cellular response to DNA damage stimulus (GO:0006974)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication checkpoint (GO:0000076)|mitotic cell cycle checkpoint (GO:0007093)|negative regulation of DNA replication (GO:0008156)|regulation of phosphorylation (GO:0042325)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)						Lung NSC(167;5.19e-05)|Prostate(74;0.0143)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;9.36e-57)|Epithelial(20;1.21e-52)|all cancers(19;3.34e-48)|Lung(70;0.0183)		AATCAAGAGGTCCAAGCTATT	0.333								Other conserved DNA damage response genes																													p.V384A		Atlas-SNP	.											.	RAD17	49	.	0			c.T1151C						.						64.0	74.0	71.0					5																	68687769		2203	4299	6502	SO:0001583	missense	5884	exon10			AAGAGGTCCAAGC	AF085736	CCDS4003.1, CCDS4004.1, CCDS4005.1, CCDS47226.1	5q13	2010-09-24	2001-11-28		ENSG00000152942	ENSG00000152942			9807	protein-coding gene	gene with protein product		603139	"""RAD1 (S. pombe) homolog"""			9869296, 9660800	Standard	NM_133343		Approved	Rad24, RAD17Sp, CCYC	uc003jwo.3	O75943	OTTHUMG00000099357	ENST00000509734.1:c.1151T>C	chr5.hg19:g.68687769T>C	ENSP00000426191:p.Val384Ala	233.0	0.0		184.0	8.0	NM_133339	A8K8X2|D3DWA5|O75714|Q7Z3S4|Q9UNK7|Q9UNR7|Q9UNR8|Q9UPF5	Missense_Mutation	SNP	ENST00000509734.1	hg19	CCDS4003.1	.	.	.	.	.	.	.	.	.	.	T	9.057	0.993456	0.19043	.	.	ENSG00000152942	ENST00000361732;ENST00000509734;ENST00000354868;ENST00000521422;ENST00000354312;ENST00000345306;ENST00000305138;ENST00000282891;ENST00000358030;ENST00000380774	T;T;T;T;T;T;T;T;T;T	0.23950	1.88;1.88;1.88;1.88;1.88;1.88;1.88;1.88;1.88;1.88	5.24	2.79	0.32731	.	0.791975	0.12301	N	0.481067	T	0.16128	0.0388	N	0.21097	0.63	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.002;0.001;0.001	T	0.31166	-0.9953	10	0.21540	T	0.41	-22.5517	8.9953	0.36048	0.0:0.1565:0.0:0.8435	.	384;287;373	O75943;O75943-4;O75943-2	RAD17_HUMAN;.;.	A	373;384;373;208;373;373;373;287;208;384	ENSP00000355226:V373A;ENSP00000426191:V384A;ENSP00000346938:V373A;ENSP00000427743:V208A;ENSP00000346271:V373A;ENSP00000311227:V373A;ENSP00000303134:V373A;ENSP00000282891:V287A;ENSP00000350725:V208A;ENSP00000370151:V384A	ENSP00000282891:V287A	V	+	2	0	RAD17	68723525	0.069000	0.21087	0.487000	0.27428	0.996000	0.88848	1.580000	0.36547	0.299000	0.22661	0.528000	0.53228	GTC	.	.		0.333	RAD17-008	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369171.1	NM_133344	
ACOT12	134526	hgsc.bcm.edu	37	5	80640756	80640756	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:80640756T>C	ENST00000307624.3	-	8	906	c.878A>G	c.(877-879)gAt>gGt	p.D293G	ACOT12_ENST00000508234.1_5'Flank	NM_130767.2	NP_570123.1	Q8WYK0	ACO12_HUMAN	acyl-CoA thioesterase 12	293	Acyl coenzyme A hydrolase 2.				acetyl-CoA metabolic process (GO:0006084)|acyl-CoA metabolic process (GO:0006637)|fatty acid metabolic process (GO:0006631)|pyruvate metabolic process (GO:0006090)	cytosol (GO:0005829)	acetyl-CoA hydrolase activity (GO:0003986)|ATP binding (GO:0005524)|carboxylic ester hydrolase activity (GO:0052689)|lipid binding (GO:0008289)			cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(7)|ovary(2)	23		Lung NSC(167;0.0176)|all_lung(232;0.0205)|Ovarian(174;0.135)		OV - Ovarian serous cystadenocarcinoma(54;1.37e-45)|Epithelial(54;1.25e-39)|all cancers(79;5.01e-34)		ATTTTCCTTATCATCAGCAGC	0.478																																					p.D293G		Atlas-SNP	.											.	ACOT12	57	.	0			c.A878G						.						137.0	133.0	134.0					5																	80640756		2203	4300	6503	SO:0001583	missense	134526	exon8			TCCTTATCATCAG	AB078619	CCDS4055.1	5q14.1	2011-09-13			ENSG00000172497	ENSG00000172497		"""Acyl CoA thioesterases"", ""StAR-related lipid transfer (START) domain containing"""	24436	protein-coding gene	gene with protein product	"""StAR-related lipid transfer (START) domain containing 15"""	614315				16103133, 16940157	Standard	NM_130767		Approved	Cach, THEAL, STARD15	uc003khl.4	Q8WYK0	OTTHUMG00000131305	ENST00000307624.3:c.878A>G	chr5.hg19:g.80640756T>C	ENSP00000303246:p.Asp293Gly	167.0	0.0		101.0	5.0	NM_130767	B3KVK9|Q5FWE9	Missense_Mutation	SNP	ENST00000307624.3	hg19	CCDS4055.1	.	.	.	.	.	.	.	.	.	.	T	8.370	0.835206	0.16820	.	.	ENSG00000172497	ENST00000307624	T	0.32515	1.45	5.46	4.27	0.50696	.	0.734758	0.13829	N	0.359880	T	0.29945	0.0749	M	0.67700	2.07	0.09310	N	0.999997	B	0.16396	0.017	B	0.13407	0.009	T	0.25047	-1.0143	10	0.34782	T	0.22	-0.9437	6.4229	0.21754	0.0:0.0809:0.1599:0.7592	.	293	Q8WYK0	ACO12_HUMAN	G	293	ENSP00000303246:D293G	ENSP00000303246:D293G	D	-	2	0	ACOT12	80676512	0.193000	0.23313	0.023000	0.16930	0.756000	0.42949	2.254000	0.43214	0.882000	0.36016	0.418000	0.28097	GAT	.	.		0.478	ACOT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254074.1	NM_130767	
MCTP1	79772	hgsc.bcm.edu	37	5	94353090	94353090	+	Silent	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:94353090T>C	ENST00000515393.1	-	2	818	c.819A>G	c.(817-819)ttA>ttG	p.L273L	MCTP1_ENST00000429576.2_Silent_p.L52L|MCTP1_ENST00000312216.8_Silent_p.L52L|MCTP1_ENST00000505208.1_Silent_p.L52L	NM_024717.4	NP_078993.4	Q6DN14	MCTP1_HUMAN	multiple C2 domains, transmembrane 1	273	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				calcium-mediated signaling (GO:0019722)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)			breast(1)|endometrium(3)|large_intestine(13)|liver(2)|lung(13)|ovary(2)|skin(4)|stomach(2)|urinary_tract(1)	41		all_cancers(142;1.68e-05)|all_epithelial(76;1.51e-07)|all_lung(232;0.0167)|Lung NSC(167;0.0207)|Ovarian(225;0.0218)|Colorectal(57;0.207)		all cancers(79;9.1e-17)		CTCGAGCAGCTAAACTTTGAC	0.418																																					p.L273L		Atlas-SNP	.											.	MCTP1	110	.	0			c.A819G						.						155.0	145.0	148.0					5																	94353090		2203	4300	6503	SO:0001819	synonymous_variant	79772	exon2			AGCAGCTAAACTT		CCDS34203.1, CCDS47247.1, CCDS75275.1	5q15	2008-02-05			ENSG00000175471	ENSG00000175471			26183	protein-coding gene	gene with protein product						15528213	Standard	XM_005272082		Approved	FLJ22344	uc003kkx.2	Q6DN14	OTTHUMG00000162742	ENST00000515393.1:c.819A>G	chr5.hg19:g.94353090T>C		107.0	0.0		109.0	5.0	NM_024717	Q6DN13|Q8N2W1|Q8NBA2|Q96LX0|Q9H6E8	Silent	SNP	ENST00000515393.1	hg19	CCDS34203.1	.	.	.	.	.	.	.	.	.	.	T	10.03	1.237812	0.22711	.	.	ENSG00000175471	ENST00000503301	.	.	.	5.79	5.79	0.91817	.	.	.	.	.	T	0.70395	0.3219	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.69544	-0.5117	4	.	.	.	-8.8561	13.651	0.62310	0.0:0.0:0.0:1.0	.	.	.	.	G	82	.	.	S	-	1	0	MCTP1	94378846	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.437000	0.59955	2.213000	0.71641	0.533000	0.62120	AGC	.	.		0.418	MCTP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000370280.3	NM_024717	
CAMK4	814	hgsc.bcm.edu	37	5	110820086	110820086	+	Silent	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:110820086A>G	ENST00000282356.4	+	11	1742	c.1344A>G	c.(1342-1344)gcA>gcG	p.A448A	CAMK4_ENST00000512890.1_3'UTR|CAMK4_ENST00000512453.1_Silent_p.A448A	NM_001744.4	NP_001735.1	Q16566	KCC4_HUMAN	calcium/calmodulin-dependent protein kinase IV	448					activation of phospholipase C activity (GO:0007202)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|long-term memory (GO:0007616)|myeloid dendritic cell differentiation (GO:0043011)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleocytoplasmic transport (GO:0006913)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of osteoclast differentiation (GO:0045670)|regulation of T cell differentiation in thymus (GO:0033081)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(13)|ovary(3)|prostate(2)|skin(1)|urinary_tract(1)	30		all_cancers(142;1.49e-05)|all_epithelial(76;1.82e-07)|Prostate(80;0.00964)|all_lung(232;0.0181)|Lung NSC(167;0.0298)|Ovarian(225;0.0446)|Colorectal(57;0.0478)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;3.79e-08)|Epithelial(69;5.29e-08)|all cancers(49;1.1e-05)|COAD - Colon adenocarcinoma(37;0.109)		AGGAGGCAGCAGCTCCCAGAG	0.532																																					p.A448A		Atlas-SNP	.											.	CAMK4	77	.	0			c.A1344G						.						53.0	53.0	53.0					5																	110820086		2202	4300	6502	SO:0001819	synonymous_variant	814	exon11			GGCAGCAGCTCCC	D30742	CCDS4103.1	5q22.1	2012-09-20			ENSG00000152495	ENSG00000152495	2.7.11.17		1464	protein-coding gene	gene with protein product	"""brain Ca++-calmodulin-dependent protein kinase type IV"", ""calcium/calmodulin-dependent protein kinase type IV catalytic chain"", ""CAM kinase IV"", ""CAM kinase- GR"""	114080				2536634	Standard	NM_001744		Approved	CaMK-GR	uc003kpf.3	Q16566	OTTHUMG00000128792	ENST00000282356.4:c.1344A>G	chr5.hg19:g.110820086A>G		107.0	0.0		80.0	4.0	NM_001744	D3DSZ7	Silent	SNP	ENST00000282356.4	hg19	CCDS4103.1																																																																																			.	.		0.532	CAMK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250719.2	NM_001744	
AP3S1	1176	hgsc.bcm.edu	37	5	115238635	115238635	+	Silent	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:115238635T>C	ENST00000316788.7	+	5	956	c.399T>C	c.(397-399)aaT>aaC	p.N133N	AP3S1_ENST00000505423.1_Intron	NM_001284.2	NP_001275.1	Q92572	AP3S1_HUMAN	adaptor-related protein complex 3, sigma 1 subunit	133					anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|insulin receptor signaling pathway (GO:0008286)|intracellular protein transport (GO:0006886)	AP-3 adaptor complex (GO:0030123)|AP-type membrane coat adaptor complex (GO:0030119)|Golgi apparatus (GO:0005794)|transport vesicle (GO:0030133)	protein transporter activity (GO:0008565)|transporter activity (GO:0005215)	p.N133N(1)		cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)|pancreas(1)|prostate(1)	12		all_cancers(142;0.00377)|all_epithelial(76;0.000129)|Prostate(80;0.0132)|Ovarian(225;0.0776)|Lung NSC(810;0.245)		OV - Ovarian serous cystadenocarcinoma(64;1.08e-07)|Epithelial(69;1.11e-06)|all cancers(49;5.2e-05)		TGGAGACAAATATGAATGAGA	0.328																																					p.N133N		Atlas-SNP	.											AP3S1,NS,carcinoma,0,2	AP3S1	25	.	1	Substitution - coding silent(1)	prostate(1)	c.T399C						.						91.0	88.0	89.0					5																	115238635		2202	4300	6502	SO:0001819	synonymous_variant	1176	exon5			GACAAATATGAAT	D63643	CCDS4123.1	5q22	2010-06-29			ENSG00000177879	ENSG00000177879			2013	protein-coding gene	gene with protein product		601507		CLAPS3		8697810, 9118953	Standard	NM_001284		Approved		uc003krl.3	Q92572	OTTHUMG00000128887	ENST00000316788.7:c.399T>C	chr5.hg19:g.115238635T>C		97.0	0.0		100.0	4.0	NM_001284	O00647|O00676|O00721|O00727|Q53XL4|Q6ICQ2	Silent	SNP	ENST00000316788.7	hg19	CCDS4123.1																																																																																			.	.		0.328	AP3S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250847.2		
MEGF10	84466	hgsc.bcm.edu	37	5	126792818	126792818	+	Splice_Site	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:126792818A>G	ENST00000274473.6	+	26	3499		c.e26-1		MEGF10_ENST00000503335.2_Splice_Site	NM_032446.2	NP_115822.1	Q96KG7	MEG10_HUMAN	multiple EGF-like-domains 10						homotypic cell-cell adhesion (GO:0034109)|muscle cell development (GO:0055001)|recognition of apoptotic cell (GO:0043654)|regulation of muscle cell differentiation (GO:0051147)|regulation of skeletal muscle tissue development (GO:0048641)|skeletal muscle satellite cell activation (GO:0014719)|skeletal muscle satellite cell differentiation (GO:0014816)|skeletal muscle satellite cell proliferation (GO:0014841)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)				breast(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(28)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	68		Prostate(80;0.165)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0657)|Epithelial(69;0.123)		TGGTTATCACAGAACCTACAG	0.383																																					.		Atlas-SNP	.											.	MEGF10	152	.	0			c.3233-2A>G						.						95.0	84.0	88.0					5																	126792818		2203	4300	6503	SO:0001630	splice_region_variant	84466	exon25			TATCACAGAACCT	AK021631	CCDS4142.1	5q33	2008-02-05			ENSG00000145794	ENSG00000145794			29634	protein-coding gene	gene with protein product		612453				11347906	Standard	NM_032446		Approved	KIAA1780	uc003kui.4	Q96KG7	OTTHUMG00000128984	ENST00000274473.6:c.3233-1A>G	chr5.hg19:g.126792818A>G		156.0	0.0		91.0	4.0	NM_001256545	Q68DE5|Q8WUL3	Splice_Site	SNP	ENST00000274473.6	hg19	CCDS4142.1	.	.	.	.	.	.	.	.	.	.	A	19.52	3.843575	0.71488	.	.	ENSG00000145794	ENST00000503335;ENST00000274473	.	.	.	5.77	5.77	0.91146	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.0879	0.81070	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	MEGF10	126820717	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	8.725000	0.91468	2.197000	0.70478	0.455000	0.32223	.	.	.		0.383	MEGF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250973.2	NM_032446	Intron
RAPGEF6	51735	hgsc.bcm.edu	37	5	130766663	130766663	+	Missense_Mutation	SNP	G	G	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:130766663G>C	ENST00000509018.1	-	26	4559	c.4354C>G	c.(4354-4356)Cag>Gag	p.Q1452E	RAPGEF6_ENST00000307984.5_Missense_Mutation_p.Q1465E|RAPGEF6_ENST00000296859.6_Missense_Mutation_p.Q1460E|RAPGEF6_ENST00000507093.1_Missense_Mutation_p.Q1460E|CTC-432M15.3_ENST00000514667.1_Missense_Mutation_p.Q1502E	NM_001164386.1|NM_016340.5	NP_001157858.1|NP_057424.3	Q8TEU7	RPGF6_HUMAN	Rap guanine nucleotide exchange factor (GEF) 6	1452			Q -> R (in dbSNP:rs1291602). {ECO:0000269|PubMed:11524421, ECO:0000269|PubMed:12581858, ECO:0000269|Ref.2}.		positive regulation of GTPase activity (GO:0043547)|Ras protein signal transduction (GO:0007265)|regulation of GTPase activity (GO:0043087)|regulation of small GTPase mediated signal transduction (GO:0051056)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	GTP-dependent protein binding (GO:0030742)|guanyl-nucleotide exchange factor activity (GO:0005085)|Ras GTPase binding (GO:0017016)	p.Q1452*(1)|p.Q1465*(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(7)|lung(10)|ovary(3)|skin(1)|stomach(1)	31			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0721)		AATACTCTCTGTTTAACTGTC	0.463																																					p.Q1465E	Melanoma(168;435 1955 13113 13877 23213)	Atlas-SNP	.											RAPGEF6_ENST00000509018,NS,carcinoma,0,2	RAPGEF6	361	.	2	Substitution - Nonsense(2)	prostate(2)	c.C4393G						.						145.0	151.0	149.0					5																	130766663		2203	4300	6503	SO:0001583	missense	51735	exon28			CTCTCTGTTTAAC	AF117947	CCDS34225.1, CCDS54897.1, CCDS54898.1, CCDS54899.1, CCDS54900.1	5q31.1	2008-02-05	2004-03-01	2004-03-02	ENSG00000158987	ENSG00000158987			20655	protein-coding gene	gene with protein product		610499	"""PDZ domain containing guanine nucleotide exchange factor (GEF) 2"""	PDZGEF2		11524421, 12095257	Standard	NM_016340		Approved	RA-GEF-2, PDZ-GEF2	uc010jdi.2	Q8TEU7	OTTHUMG00000162683	ENST00000509018.1:c.4354C>G	chr5.hg19:g.130766663G>C	ENSP00000421684:p.Gln1452Glu	270.0	0.0		197.0	0.0	NM_001164387	A3KN82|A5PLL6|B7ZML2|E9PDV7|Q8NI21|Q8TEU6|Q96PC1	Missense_Mutation	SNP	ENST00000509018.1	hg19	CCDS34225.1	.	.	.	.	.	.	.	.	.	.	G	13.17	2.158025	0.38119	.	.	ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000217128	ENST00000509018;ENST00000307984;ENST00000507093;ENST00000296859;ENST00000358714;ENST00000514667	T;T;T;T;T	0.23754	1.99;1.89;1.89;1.99;2.07	5.22	2.19	0.27852	.	0.112278	0.64402	D	0.000013	T	0.14700	0.0355	N	0.08118	0	0.80722	D	1	B;B;B;B;B	0.06786	0.001;0.0;0.0;0.0;0.0	B;B;B;B;B	0.10450	0.005;0.0;0.0;0.001;0.0	T	0.08186	-1.0734	10	0.72032	D	0.01	.	14.5329	0.67939	0.0:0.0:0.6233:0.3767	.	1460;1460;1502;1465;1452	A3KN82;B7ZML2;E9PCH4;Q8TEU7-3;Q8TEU7	.;.;.;.;RPGF6_HUMAN	E	1452;1465;1460;1460;1465;1502	ENSP00000421684:Q1452E;ENSP00000309298:Q1465E;ENSP00000426081:Q1460E;ENSP00000296859:Q1460E;ENSP00000426948:Q1502E	ENSP00000426948:Q1502E	Q	-	1	0	RAPGEF6;FNIP1	130794562	1.000000	0.71417	0.995000	0.50966	0.850000	0.48378	4.611000	0.61162	0.654000	0.30846	0.655000	0.94253	CAG	.	.		0.463	RAPGEF6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000370059.1	NM_016340	
HSPA4	3308	hgsc.bcm.edu	37	5	132432855	132432855	+	Silent	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:132432855T>C	ENST00000304858.2	+	15	2095	c.1806T>C	c.(1804-1806)ggT>ggC	p.G602G		NM_002154.3	NP_002145.3	P34932	HSP74_HUMAN	heat shock 70kDa protein 4	602					chaperone-mediated protein complex assembly (GO:0051131)|protein import into mitochondrial outer membrane (GO:0045040)|response to unfolded protein (GO:0006986)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(10)|stomach(1)	32			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			ATTCTCAGGGTAAGATGATCA	0.348																																					p.G602G	Colon(114;1299 1588 6063 12302 48757)	Atlas-SNP	.											.	HSPA4	68	.	0			c.T1806C						.						113.0	112.0	112.0					5																	132432855		2203	4300	6503	SO:0001819	synonymous_variant	3308	exon15			TCAGGGTAAGATG	AB023420	CCDS4166.1	5q31.1	2011-09-07	2002-08-29		ENSG00000170606	ENSG00000170606		"""Heat shock proteins / HSP70"""	5237	protein-coding gene	gene with protein product	"""hsp70 RY"""	601113	"""heat shock 70kD protein 4"""			8335910	Standard	NM_002154		Approved	HS24/P52, HSPH2	uc003kyj.3	P34932	OTTHUMG00000129012	ENST00000304858.2:c.1806T>C	chr5.hg19:g.132432855T>C		115.0	0.0		114.0	5.0	NM_002154	O95756|Q2TAL4|Q9BUK9	Silent	SNP	ENST00000304858.2	hg19	CCDS4166.1																																																																																			.	.		0.348	HSPA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251011.1	NM_002154, NM_198431	
ANKHD1	54882	hgsc.bcm.edu	37	5	139864753	139864753	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:139864753T>C	ENST00000360839.2	+	12	2072	c.1918T>C	c.(1918-1920)Tcg>Ccg	p.S640P	ANKHD1-EIF4EBP3_ENST00000532219.1_Missense_Mutation_p.S640P|ANKHD1_ENST00000297183.6_Missense_Mutation_p.S640P	NM_017747.2	NP_060217.1	Q8IWZ3	ANKH1_HUMAN	ankyrin repeat and KH domain containing 1	640						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(8)|kidney(6)|large_intestine(14)|lung(18)|ovary(5)|prostate(2)|skin(3)|urinary_tract(2)	60			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TACAGTAGTGTCGCTGGCATG	0.448																																					p.S640P		Atlas-SNP	.											.	ANKHD1	233	.	0			c.T1918C						.						102.0	92.0	95.0					5																	139864753		2203	4300	6503	SO:0001583	missense	54882	exon12			GTAGTGTCGCTGG	AF521882	CCDS4225.1, CCDS43371.1, CCDS43372.1, CCDS75319.1	5q31.3	2013-01-10			ENSG00000131503	ENSG00000131503		"""Ankyrin repeat domain containing"""	24714	protein-coding gene	gene with protein product		610500				10470851, 11230166, 16098192	Standard	NM_017747		Approved	MASK, FLJ20288, FLJ11979, FLJ10042, FLJ14127, KIAA1085		Q8IWZ3	OTTHUMG00000161610	ENST00000360839.2:c.1918T>C	chr5.hg19:g.139864753T>C	ENSP00000354085:p.Ser640Pro	166.0	0.0		140.0	8.0	NM_017747	A6NH85|Q149P2|Q8IWZ2|Q8WY90|Q96G77|Q96GK0|Q9H2U0|Q9HA95|Q9NWG4|Q9UPR7	Missense_Mutation	SNP	ENST00000360839.2	hg19	CCDS4225.1	.	.	.	.	.	.	.	.	.	.	T	28.3	4.908170	0.92107	.	.	ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000254996	ENST00000360839;ENST00000422011;ENST00000297183;ENST00000253810;ENST00000310356;ENST00000235510;ENST00000421134;ENST00000412116;ENST00000532219	T;T;T;T;T	0.65916	-0.01;-0.01;-0.18;-0.18;-0.01	5.17	5.17	0.71159	Ankyrin repeat-containing domain (4);	0.000000	0.85682	D	0.000000	T	0.77412	0.4126	M	0.66439	2.03	0.80722	D	1	D;D;D;D	0.76494	0.997;0.999;0.997;0.997	D;D;D;D	0.83275	0.991;0.996;0.995;0.995	T	0.80101	-0.1523	10	0.72032	D	0.01	.	15.2896	0.73857	0.0:0.0:0.0:1.0	.	640;659;640;640	Q8IWZ3-4;E9PDP5;Q8IWZ2;Q8IWZ3	.;.;.;ANKH1_HUMAN	P	640;673;640;640;174;120;659;46;640	ENSP00000354085:S640P;ENSP00000297183:S640P;ENSP00000394489:S659P;ENSP00000405602:S46P;ENSP00000432016:S640P	ENSP00000432016:S640P	S	+	1	0	ANKHD1-EIF4EBP3;ANKHD1	139844937	1.000000	0.71417	0.997000	0.53966	0.958000	0.62258	7.976000	0.88070	2.071000	0.62044	0.379000	0.24179	TCG	.	.		0.448	ANKHD1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000251672.1	NM_017747	
PCDHA6	56142	hgsc.bcm.edu	37	5	140209711	140209711	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:140209711T>C	ENST00000529310.1	+	1	2149	c.2035T>C	c.(2035-2037)Tca>Cca	p.S679P	PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron	NM_018909.2|NM_031848.2|NM_031849.1	NP_061732.1|NP_114036.1|NP_114037.1	Q9UN73	PCDA6_HUMAN	protocadherin alpha 6	679					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(42)|prostate(8)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	89			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCCAAAGGCGTCATCACGGGC	0.677																																					p.S679P		Atlas-SNP	.											.	PCDHA6	442	.	0			c.T2035C						.						38.0	44.0	42.0					5																	140209711		2199	4298	6497	SO:0001583	missense	56142	exon1			AAGGCGTCATCAC	AF152484	CCDS47281.1, CCDS47282.1	5q31	2010-11-26			ENSG00000081842	ENSG00000081842		"""Cadherins / Protocadherins : Clustered"""	8672	other	complex locus constituent	"""KIAA0345-like 8"""	606312		CNRS2		10380929, 10662547	Standard	NM_018909		Approved	CNR2, CRNR2, PCDH-ALPHA6		Q9UN73	OTTHUMG00000163353	ENST00000529310.1:c.2035T>C	chr5.hg19:g.140209711T>C	ENSP00000433378:p.Ser679Pro	233.0	0.0		133.0	6.0	NM_018909	O75283|Q9NRT8	Missense_Mutation	SNP	ENST00000529310.1	hg19	CCDS47281.1	.	.	.	.	.	.	.	.	.	.	T	8.428	0.847962	0.17034	.	.	ENSG00000081842	ENST00000529310	T	0.52754	0.65	3.98	3.98	0.46160	.	0.268055	0.19503	U	0.112681	T	0.40222	0.1108	L	0.58810	1.83	0.20821	N	0.999844	B;B	0.17667	0.023;0.005	B;B	0.25291	0.059;0.006	T	0.26189	-1.0110	10	0.36615	T	0.2	.	4.3124	0.10977	0.0:0.1066:0.2058:0.6876	.	679;679	Q9UN73-3;Q9UN73	.;PCDA6_HUMAN	P	679	ENSP00000433378:S679P	ENSP00000433378:S679P	S	+	1	0	PCDHA6	140189895	0.059000	0.20769	0.010000	0.14722	0.007000	0.05969	1.420000	0.34804	1.798000	0.52647	0.254000	0.18369	TCA	.	.		0.677	PCDHA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372829.3	NM_018909	
PCDHB1	29930	hgsc.bcm.edu	37	5	140433196	140433196	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:140433196T>C	ENST00000306549.3	+	1	2218	c.2141T>C	c.(2140-2142)gTc>gCc	p.V714A		NM_013340.2	NP_037472.2	Q9Y5F3	PCDB1_HUMAN	protocadherin beta 1	714					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(16)|liver(1)|lung(13)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	53			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			ATTATACATGTCTACCAAAAG	0.348																																					p.V714A		Atlas-SNP	.											.	PCDHB1	148	.	0			c.T2141C						.						104.0	108.0	106.0					5																	140433196		2203	4300	6503	SO:0001583	missense	29930	exon1			TACATGTCTACCA	AF152488	CCDS4243.1	5q31	2010-01-26			ENSG00000171815	ENSG00000171815		"""Cadherins / Protocadherins : Clustered"""	8680	other	protocadherin		606327				10380929	Standard	NM_013340		Approved	PCDH-BETA1	uc003lik.1	Q9Y5F3	OTTHUMG00000129627	ENST00000306549.3:c.2141T>C	chr5.hg19:g.140433196T>C	ENSP00000307234:p.Val714Ala	165.0	0.0		142.0	7.0	NM_013340	Q2M257	Missense_Mutation	SNP	ENST00000306549.3	hg19	CCDS4243.1	.	.	.	.	.	.	.	.	.	.	T	10.88	1.474182	0.26423	.	.	ENSG00000171815	ENST00000306549	T	0.14391	2.51	5.91	5.91	0.95273	.	0.461817	0.17620	N	0.167760	T	0.09024	0.0223	N	0.08118	0	0.20638	N	0.99987	B	0.16396	0.017	B	0.11329	0.006	T	0.26189	-1.0110	10	0.87932	D	0	.	13.7272	0.62765	0.0:0.0:0.0:1.0	.	714	Q9Y5F3	PCDB1_HUMAN	A	714	ENSP00000307234:V714A	ENSP00000307234:V714A	V	+	2	0	PCDHB1	140413380	0.922000	0.31269	0.996000	0.52242	0.876000	0.50452	2.997000	0.49457	2.269000	0.75478	0.533000	0.62120	GTC	.	.		0.348	PCDHB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251822.2	NM_013340	
PCDHGA2	56113	hgsc.bcm.edu	37	5	140720687	140720687	+	Missense_Mutation	SNP	C	C	T			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:140720687C>T	ENST00000394576.2	+	1	2149	c.2149C>T	c.(2149-2151)Cgg>Tgg	p.R717W	PCDHGA3_ENST00000253812.6_5'Flank|PCDHGA1_ENST00000517417.1_Intron	NM_018915.2	NP_061738.1	Q9Y5H1	PCDG2_HUMAN	protocadherin gamma subfamily A, 2	717					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(20)|lung(32)|ovary(1)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	77			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCACAGGCTGCGGCGCTGGCA	0.642																																					p.R717W		Atlas-SNP	.											.	PCDHGA2	205	.	0			c.C2149T						.						84.0	88.0	87.0					5																	140720687		2203	4300	6503	SO:0001583	missense	56113	exon1			AGGCTGCGGCGCT	AF152508	CCDS47289.1	5q31	2011-03-28			ENSG00000081853	ENSG00000081853		"""Cadherins / Protocadherins : Clustered"""	8700	other	protocadherin		606289				10380929	Standard	NM_018915		Approved	PCDH-GAMMA-A2		Q9Y5H1	OTTHUMG00000163679	ENST00000394576.2:c.2149C>T	chr5.hg19:g.140720687C>T	ENSP00000378077:p.Arg717Trp	399.0	0.0		342.0	132.0	NM_018915	Q52LL6|Q9Y5D5	Missense_Mutation	SNP	ENST00000394576.2	hg19	CCDS47289.1	.	.	.	.	.	.	.	.	.	.	.	11.29	1.594846	0.28445	.	.	ENSG00000081853	ENST00000394576	T	0.17054	2.3	4.88	-5.05	0.02955	.	0.000000	0.38548	U	0.001643	T	0.16685	0.0401	M	0.66560	2.04	0.19775	N	0.99995	B;B	0.31599	0.33;0.107	B;B	0.33750	0.169;0.03	T	0.19063	-1.0317	10	0.49607	T	0.09	.	12.2431	0.54555	0.4631:0.4704:0.0:0.0665	.	717;717	Q9Y5H1-2;Q9Y5H1	.;PCDG2_HUMAN	W	717	ENSP00000378077:R717W	ENSP00000378077:R717W	R	+	1	2	PCDHGA2	140700871	0.000000	0.05858	0.691000	0.30163	0.028000	0.11728	-0.359000	0.07632	-0.673000	0.05259	0.306000	0.20318	CGG	.	.		0.642	PCDHGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374738.1	NM_018915	
PCDHGB2	56103	hgsc.bcm.edu	37	5	140741739	140741739	+	Silent	SNP	G	G	C	rs576630104		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:140741739G>C	ENST00000522605.1	+	1	2037	c.2037G>C	c.(2035-2037)cgG>cgC	p.R679R	PCDHGA2_ENST00000394576.2_Intron|PCDHGA5_ENST00000518069.1_5'Flank|PCDHGA3_ENST00000253812.6_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_018923.2|NM_032096.1	NP_061746.1|NP_115267.1	Q9Y5G2	PCDGE_HUMAN	protocadherin gamma subfamily B, 2	679					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|large_intestine(5)|lung(3)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	14			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCGACCGCCGGGAGCCCTCTG	0.597																																					p.R679R		Atlas-SNP	.											PCDHGB2_ENST00000522605,NS,carcinoma,+1,1	PCDHGB2	196	.	0			c.G2037C						.						61.0	65.0	63.0					5																	140741739		2021	4177	6198	SO:0001819	synonymous_variant	56103	exon1			CCGCCGGGAGCCC	AF152331	CCDS54924.1, CCDS75332.1	5q31	2010-01-26				ENSG00000253910		"""Cadherins / Protocadherins : Clustered"""	8709	other	protocadherin		606300				10380929	Standard	NM_018923		Approved	PCDH-GAMMA-B2		Q9Y5G2		ENST00000522605.1:c.2037G>C	chr5.hg19:g.140741739G>C		257.0	1.0		183.0	0.0	NM_018923	Q3MIJ3|Q9UN65	Silent	SNP	ENST00000522605.1	hg19	CCDS54924.1																																																																																			.	.		0.597	PCDHGB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374741.1	NM_018923	
CAMK2A	815	hgsc.bcm.edu	37	5	149629865	149629865	+	Missense_Mutation	SNP	G	G	T			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:149629865G>T	ENST00000348628.6	-	11	1489	c.824C>A	c.(823-825)tCc>tAc	p.S275Y	CAMK2A_ENST00000398376.3_Missense_Mutation_p.S275Y	NM_015981.3|NM_171825.2	NP_057065.2|NP_741960.1	Q9UQM7	KCC2A_HUMAN	calcium/calmodulin-dependent protein kinase II alpha	275					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)			TGCCACGGTGGAGCGGTGCTG	0.587																																					p.S275Y		Atlas-SNP	.											.	CAMK2A	42	.	0			c.C824A						.						73.0	73.0	73.0					5																	149629865		2132	4259	6391	SO:0001583	missense	815	exon11			ACGGTGGAGCGGT	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.824C>A	chr5.hg19:g.149629865G>T	ENSP00000261793:p.Ser275Tyr	106.0	0.0		77.0	26.0	NM_171825	Q9UL21|Q9Y2H4|Q9Y352	Missense_Mutation	SNP	ENST00000348628.6	hg19	CCDS43386.1	.	.	.	.	.	.	.	.	.	.	G	33	5.201341	0.94997	.	.	ENSG00000070808	ENST00000348628;ENST00000398376	T;T	0.69306	-0.37;-0.39	5.38	5.38	0.77491	Protein kinase-like domain (1);	0.075620	0.53938	D	0.000047	T	0.81725	0.4883	M	0.82323	2.585	0.80722	D	1	D;D;D	0.58268	0.982;0.981;0.969	P;P;P	0.58331	0.837;0.822;0.692	D	0.84634	0.0691	10	0.87932	D	0	.	19.1203	0.93360	0.0:0.0:1.0:0.0	.	275;275;275	Q9UQM7-2;Q9UQM7;A8K161	.;KCC2A_HUMAN;.	Y	275	ENSP00000261793:S275Y;ENSP00000381412:S275Y	ENSP00000261793:S275Y	S	-	2	0	CAMK2A	149610058	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	9.750000	0.98875	2.539000	0.85634	0.655000	0.94253	TCC	.	.		0.587	CAMK2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258869.2	NM_015981	
CYFIP2	26999	hgsc.bcm.edu	37	5	156721858	156721858	+	Missense_Mutation	SNP	G	G	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:156721858G>C	ENST00000347377.6	+	4	705	c.274G>C	c.(274-276)Gcc>Ccc	p.A92P	CYFIP2_ENST00000377576.3_Missense_Mutation_p.A92P|CYFIP2_ENST00000521420.1_Intron|CYFIP2_ENST00000522463.1_Intron|CYFIP2_ENST00000541131.1_Intron|CYFIP2_ENST00000442283.2_5'UTR|CYFIP2_ENST00000318218.6_Missense_Mutation_p.A92P	NM_001037332.2	NP_001032409.2			cytoplasmic FMR1 interacting protein 2											breast(1)|endometrium(12)|kidney(2)|lung(23)	38	Renal(175;0.00212)	Medulloblastoma(196;0.0306)|all_neural(177;0.0897)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			CTGTTCCCGGGCCATTCCCAG	0.527																																					p.A92P		Atlas-SNP	.											.	CYFIP2	354	.	0			c.G274C						.						116.0	125.0	122.0					5																	156721858		2145	4280	6425	SO:0001583	missense	26999	exon4			TCCCGGGCCATTC	AF160973	CCDS75364.1	5q34	2008-07-18				ENSG00000055163			13760	protein-coding gene	gene with protein product	"""p53 inducible protein"""	606323				11438699	Standard	NM_001037333		Approved	PIR121	uc021ygm.1	Q96F07		ENST00000347377.6:c.274G>C	chr5.hg19:g.156721858G>C	ENSP00000313567:p.Ala92Pro	329.0	0.0		225.0	10.0	NM_001037332		Missense_Mutation	SNP	ENST00000347377.6	hg19		.	.	.	.	.	.	.	.	.	.	G	32	5.153806	0.94645	.	.	ENSG00000055163	ENST00000318218;ENST00000347377;ENST00000377576	T;T;T	0.44482	0.92;0.92;0.92	4.94	4.94	0.65067	.	0.000000	0.85682	D	0.000000	T	0.69958	0.3169	M	0.88310	2.945	0.80722	D	1	P;D;P	0.67145	0.943;0.996;0.909	P;D;P	0.67548	0.49;0.952;0.665	T	0.77552	-0.2545	10	0.72032	D	0.01	-10.9957	18.1684	0.89736	0.0:0.0:1.0:0.0	.	92;92;92	E7EVF4;Q96F07-2;Q96F07	.;.;CYFP2_HUMAN	P	92	ENSP00000325817:A92P;ENSP00000313567:A92P;ENSP00000366799:A92P	ENSP00000325817:A92P	A	+	1	0	CYFIP2	156654436	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.769000	0.98969	2.285000	0.76669	0.563000	0.77884	GCC	.	.		0.527	CYFIP2-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001037332	
GABRG2	2566	hgsc.bcm.edu	37	5	161569294	161569294	+	Silent	SNP	G	G	A			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:161569294G>A	ENST00000361925.4	+	7	1114	c.894G>A	c.(892-894)aaG>aaA	p.K298K	GABRG2_ENST00000356592.3_Silent_p.K298K|GABRG2_ENST00000393933.4_Silent_p.K203K|GABRG2_ENST00000414552.2_Silent_p.K338K			P18507	GBRG2_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 2	298					adult behavior (GO:0030534)|cellular response to histamine (GO:0071420)|chloride transmembrane transport (GO:1902476)|gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|post-embryonic development (GO:0009791)|synaptic transmission (GO:0007268)|synaptic transmission, GABAergic (GO:0051932)|transmembrane transport (GO:0055085)|transport (GO:0006810)	axon (GO:0030424)|cell junction (GO:0030054)|chloride channel complex (GO:0034707)|cytoplasm (GO:0005737)|dendrite membrane (GO:0032590)|GABA-A receptor complex (GO:1902711)|inhibitory synapse (GO:0060077)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			NS(1)|breast(1)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(15)|lung(24)|ovary(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	62	Renal(175;0.000319)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0734)|OV - Ovarian serous cystadenocarcinoma(192;0.135)|Epithelial(171;0.136)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Ginkgo biloba(DB01381)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	GGATCAATAAGGATGCTGTTC	0.403																																					p.K338K		Atlas-SNP	.											.	GABRG2	142	.	0			c.G1014A						.						218.0	183.0	195.0					5																	161569294		2203	4300	6503	SO:0001819	synonymous_variant	2566	exon8			CAATAAGGATGCT		CCDS4358.1, CCDS4359.1, CCDS47333.1	5q34	2012-06-22			ENSG00000113327	ENSG00000113327		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4087	protein-coding gene	gene with protein product	"""GABA(A) receptor, gamma 2"""	137164					Standard	NM_198904		Approved		uc010jjc.3	P18507	OTTHUMG00000130350	ENST00000361925.4:c.894G>A	chr5.hg19:g.161569294G>A		240.0	0.0		167.0	63.0	NM_198903	F5HB82|Q6GRL6|Q6PCC3|Q9UDB3|Q9UN15	Silent	SNP	ENST00000361925.4	hg19	CCDS4358.1																																																																																			.	.		0.403	GABRG2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252706.1		
KCNIP1	30820	hgsc.bcm.edu	37	5	170145819	170145819	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:170145819A>G	ENST00000411494.1	+	3	152	c.152A>G	c.(151-153)gAg>gGg	p.E51G	KCNIP1_ENST00000328939.4_Missense_Mutation_p.E40G|KCNIP1_ENST00000377360.4_Missense_Mutation_p.E49G|KCNIP1_ENST00000434108.1_Missense_Mutation_p.E40G|KCNIP1_ENST00000520740.1_Missense_Mutation_p.E12G|KCNIP1_ENST00000390656.4_Missense_Mutation_p.E40G			Q9NZI2	KCIP1_HUMAN	Kv channel interacting protein 1	51	EF-hand 1; degenerate. {ECO:0000255|PROSITE-ProRule:PRU00448}.				detection of calcium ion (GO:0005513)|positive regulation of action potential (GO:0045760)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|potassium channel complex (GO:0034705)	calcium ion binding (GO:0005509)|potassium channel activity (GO:0005267)|potassium channel regulator activity (GO:0015459)|voltage-gated ion channel activity (GO:0005244)			autonomic_ganglia(1)|large_intestine(7)|lung(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	18	Renal(175;0.000159)|Lung NSC(126;0.0191)|all_lung(126;0.0297)	Medulloblastoma(196;0.0109)|all_neural(177;0.0177)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			GAGGGACTGGAGCAGCTCGAG	0.552																																					p.E51G		Atlas-SNP	.											.	KCNIP1	66	.	0			c.A152G						.						61.0	57.0	59.0					5																	170145819		2203	4300	6503	SO:0001583	missense	30820	exon3			GACTGGAGCAGCT	AF199597	CCDS34285.1, CCDS34286.1, CCDS4374.1, CCDS64312.1, CCDS64313.1	5q35	2013-01-10			ENSG00000182132	ENSG00000182132		"""EF-hand domain containing"""	15521	protein-coding gene	gene with protein product		604660				10676964	Standard	NM_001278339		Approved	KCHIP1	uc003map.3	Q9NZI2	OTTHUMG00000130442	ENST00000411494.1:c.152A>G	chr5.hg19:g.170145819A>G	ENSP00000395323:p.Glu51Gly	190.0	0.0		144.0	6.0	NM_001034837	B7Z7B4|Q3YAD0|Q3YAD1|Q3YAD2|Q3YAD3|Q5U822	Missense_Mutation	SNP	ENST00000411494.1	hg19	CCDS34286.1	.	.	.	.	.	.	.	.	.	.	A	29.0	4.970494	0.92919	.	.	ENSG00000182132	ENST00000377360;ENST00000328939;ENST00000390656;ENST00000520740;ENST00000434108;ENST00000411494	T;T;T;T;T;T	0.24538	1.85;1.85;1.85;1.85;1.85;1.85	5.59	5.59	0.84812	EF-hand-like domain (1);	0.191271	0.56097	D	0.000039	T	0.45135	0.1327	M	0.88640	2.97	0.80722	D	1	P;P;P;P	0.49635	0.862;0.838;0.926;0.577	P;P;B;B	0.48400	0.576;0.519;0.393;0.305	T	0.54984	-0.8211	9	.	.	.	.	13.7125	0.62675	1.0:0.0:0.0:0.0	.	40;40;51;49	Q3YAD0;Q3YAD2;Q9NZI2;Q3YAD3	.;.;KCIP1_HUMAN;.	G	49;40;40;12;40;51	ENSP00000366577:E49G;ENSP00000329686:E40G;ENSP00000375071:E40G;ENSP00000431102:E12G;ENSP00000414886:E40G;ENSP00000395323:E51G	.	E	+	2	0	KCNIP1	170078397	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	8.904000	0.92590	2.117000	0.64856	0.533000	0.62120	GAG	.	.		0.552	KCNIP1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000371760.1		
GPRIN1	114787	hgsc.bcm.edu	37	5	176025442	176025442	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:176025442T>C	ENST00000303991.4	-	2	1571	c.1394A>G	c.(1393-1395)gAc>gGc	p.D465G		NM_052899.2	NP_443131.2	Q7Z2K8	GRIN1_HUMAN	G protein regulated inducer of neurite outgrowth 1	465					neuron projection development (GO:0031175)	cell projection (GO:0042995)|plasma membrane (GO:0005886)				NS(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(3)|liver(1)|lung(15)|ovary(2)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	all_cancers(89;0.00263)|Renal(175;0.000269)|Lung NSC(126;0.00902)|all_lung(126;0.0142)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			AGATATGGGGTCCTCCCTTCT	0.532																																					p.D465G		Atlas-SNP	.											.	GPRIN1	77	.	0			c.A1394G						.						94.0	105.0	101.0					5																	176025442		2201	4299	6500	SO:0001583	missense	114787	exon2			ATGGGGTCCTCCC	AB067480	CCDS4405.1	5q35.2	2008-02-05			ENSG00000169258	ENSG00000169258			24835	protein-coding gene	gene with protein product		611239				11572484	Standard	NM_052899		Approved	GRIN1, KIAA1893	uc003meo.1	Q7Z2K8	OTTHUMG00000130659	ENST00000303991.4:c.1394A>G	chr5.hg19:g.176025442T>C	ENSP00000305839:p.Asp465Gly	183.0	0.0		119.0	5.0	NM_052899	C9JM70|Q8ND74|Q96PZ4	Missense_Mutation	SNP	ENST00000303991.4	hg19	CCDS4405.1	.	.	.	.	.	.	.	.	.	.	T	15.11	2.736476	0.49045	.	.	ENSG00000169258	ENST00000303991;ENST00000335532	T	0.12774	2.65	5.04	2.61	0.31194	.	0.907068	0.09103	N	0.848199	T	0.14056	0.0340	M	0.64997	1.995	0.09310	N	1	B	0.21225	0.053	B	0.23419	0.046	T	0.40887	-0.9539	10	0.26408	T	0.33	0.1413	3.3295	0.07079	0.1702:0.1836:0.0:0.6462	.	465	Q7Z2K8	GRIN1_HUMAN	G	465	ENSP00000305839:D465G	ENSP00000305839:D465G	D	-	2	0	GPRIN1	175958048	0.001000	0.12720	0.020000	0.16555	0.273000	0.26683	0.917000	0.28665	0.262000	0.21774	0.374000	0.22700	GAC	.	.		0.532	GPRIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253149.1	NM_052899	
FGFR4	2264	hgsc.bcm.edu	37	5	176518005	176518005	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:176518005T>C	ENST00000292408.4	+	5	748	c.503T>C	c.(502-504)gTc>gCc	p.V168A	FGFR4_ENST00000393637.1_Missense_Mutation_p.V168A|FGFR4_ENST00000292410.3_Missense_Mutation_p.V168A|FGFR4_ENST00000393648.2_Missense_Mutation_p.V168A|FGFR4_ENST00000502906.1_Missense_Mutation_p.V168A	NM_002011.3|NM_213647.1	NP_002002.3|NP_998812.1	P22455	FGFR4_HUMAN	fibroblast growth factor receptor 4	168	Ig-like C2-type 2.				alveolar secondary septum development (GO:0061144)|cell migration (GO:0016477)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose homeostasis (GO:0042593)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ induction (GO:0001759)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphate ion homeostasis (GO:0055062)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of metalloenzyme activity (GO:0048554)|positive regulation of proteolysis (GO:0045862)|protein autophosphorylation (GO:0046777)|regulation of bile acid biosynthetic process (GO:0070857)|regulation of cholesterol homeostasis (GO:2000188)|regulation of extracellular matrix disassembly (GO:0010715)|regulation of lipid metabolic process (GO:0019216)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)|protein tyrosine kinase activity (GO:0004713)	p.V168D(2)		breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(16)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	34	all_cancers(89;5.93e-05)|Renal(175;0.000269)|Lung NSC(126;0.0088)|all_lung(126;0.0142)	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)		Palifermin(DB00039)|Ponatinib(DB08901)	GGGAACACCGTCAAGTTCCGC	0.612										TSP Lung(9;0.080)																											p.V168A		Atlas-SNP	.											FGFR4_ENST00000292408,bladder,carcinoma,0,2	FGFR4	174	.	2	Substitution - Missense(2)	urinary_tract(2)	c.T503C						.						95.0	76.0	82.0					5																	176518005		2203	4300	6503	SO:0001583	missense	2264	exon4			ACACCGTCAAGTT	AF202063	CCDS4410.1, CCDS4411.1	5q35.2	2013-09-19			ENSG00000160867	ENSG00000160867		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"""	3691	protein-coding gene	gene with protein product		134935					Standard	XM_005265837		Approved	JTK2, CD334	uc003mfm.3	P22455	OTTHUMG00000151523	ENST00000292408.4:c.503T>C	chr5.hg19:g.176518005T>C	ENSP00000292408:p.Val168Ala	126.0	1.0		98.0	4.0	NM_022963	G3JVM2|G3JVM5|G3JVM7|G3JVM9|O43785|Q14309|Q71TW8|Q8TDA0|Q96KE5	Missense_Mutation	SNP	ENST00000292408.4	hg19	CCDS4410.1	.	.	.	.	.	.	.	.	.	.	T	17.12	3.309399	0.60414	.	.	ENSG00000160867	ENST00000292408;ENST00000503708;ENST00000393648;ENST00000502906;ENST00000292410;ENST00000393637;ENST00000377207	T;T;T;T;T;T	0.67345	1.44;-0.26;1.44;1.44;1.44;1.44	4.74	4.74	0.60224	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.122935	0.53938	D	0.000046	T	0.72036	0.3411	L	0.31845	0.965	0.50171	D	0.999851	D;D;P;P	0.65815	0.994;0.995;0.604;0.942	D;D;B;P	0.66716	0.94;0.946;0.269;0.569	T	0.74601	-0.3611	10	0.56958	D	0.05	.	14.0727	0.64870	0.0:0.0:0.0:1.0	.	168;168;168;168	B5A965;B4DVP5;P22455-2;P22455	.;.;.;FGFR4_HUMAN	A	168;168;168;168;168;168;280	ENSP00000292408:V168A;ENSP00000424905:V168A;ENSP00000377259:V168A;ENSP00000424960:V168A;ENSP00000292410:V168A;ENSP00000377254:V168A	ENSP00000292408:V168A	V	+	2	0	FGFR4	176450611	1.000000	0.71417	0.804000	0.32291	0.776000	0.43924	7.825000	0.86693	1.999000	0.58509	0.459000	0.35465	GTC	.	.		0.612	FGFR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253410.1		
C5orf60	285679	hgsc.bcm.edu	37	5	179070461	179070461	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:179070461T>C	ENST00000448248.2	-	3	336	c.311A>G	c.(310-312)aAc>aGc	p.N104S	C5orf60_ENST00000506142.1_5'UTR	NM_001142306.1	NP_001135778.1	A6NFR6	CE060_HUMAN	chromosome 5 open reading frame 60	104						integral component of membrane (GO:0016021)				NS(1)|breast(1)|kidney(5)	7						GATCTCAAGGTTCTCCAGTTC	0.537																																					p.N104S		Atlas-SNP	.											.	C5orf60	24	.	0			c.A311G						.						79.0	75.0	76.0					5																	179070461		692	1591	2283	SO:0001583	missense	285679	exon3			TCAAGGTTCTCCA	BC043435	CCDS47353.1	5q35.3	2010-08-19			ENSG00000204661	ENSG00000204661			27753	protein-coding gene	gene with protein product						12477932	Standard	NM_001142306		Approved		uc003mki.3	A6NFR6	OTTHUMG00000163221	ENST00000448248.2:c.311A>G	chr5.hg19:g.179070461T>C	ENSP00000404583:p.Asn104Ser	117.0	0.0		74.0	4.0	NM_001142306	A1L488|B7ZM52|B7ZM53	Missense_Mutation	SNP	ENST00000448248.2	hg19	CCDS47353.1	.	.	.	.	.	.	.	.	.	.	t	6.002	0.368781	0.11352	.	.	ENSG00000204661	ENST00000448248	T	0.25749	1.78	0.742	0.742	0.18341	.	.	.	.	.	T	0.21674	0.0522	N	0.08118	0	0.09310	N	1	P;P	0.49696	0.927;0.927	P;P	0.56563	0.801;0.801	T	0.15292	-1.0442	8	0.62326	D	0.03	.	.	.	.	.	104;104	A6NFR6-2;A6NFR6-4	.;.	S	104	ENSP00000404583:N104S	ENSP00000404583:N104S	N	-	2	0	C5orf60	179003067	0.001000	0.12720	0.002000	0.10522	0.006000	0.05464	0.425000	0.21346	0.576000	0.29452	0.172000	0.16884	AAC	.	.		0.537	C5orf60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372148.2	NM_001142306	
RREB1	6239	hgsc.bcm.edu	37	6	7246876	7246876	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:7246876A>G	ENST00000349384.6	+	11	4342	c.4028A>G	c.(4027-4029)gAg>gGg	p.E1343G	RREB1_ENST00000379938.2_Missense_Mutation_p.E1398G|RREB1_ENST00000334984.6_Intron|RREB1_ENST00000379933.3_Missense_Mutation_p.E1343G	NM_001003698.3	NP_001003698.1	Q92766	RREB1_HUMAN	ras responsive element binding protein 1	1343					multicellular organismal development (GO:0007275)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|Ras protein signal transduction (GO:0007265)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear body (GO:0016604)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(18)|ovary(5)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58	Ovarian(93;0.0398)	all_hematologic(90;0.0384)|Prostate(151;0.191)				GGCACTGAGGAGAGCACTGGG	0.682																																					p.E1398G		Atlas-SNP	.											.	RREB1	242	.	0			c.A4193G						.						53.0	50.0	51.0					6																	7246876		2177	4273	6450	SO:0001583	missense	6239	exon12			CTGAGGAGAGCAC	U26914	CCDS34335.1, CCDS34336.1, CCDS54963.1	6p25	2013-01-08			ENSG00000124782	ENSG00000124782		"""Zinc fingers, C2H2-type"""	10449	protein-coding gene	gene with protein product	"""hindsight homolog (drosophila)"""	602209				9367691, 18394891	Standard	NM_001003698		Approved	HNT	uc003mxb.3	Q92766	OTTHUMG00000014201	ENST00000349384.6:c.4028A>G	chr6.hg19:g.7246876A>G	ENSP00000305560:p.Glu1343Gly	97.0	0.0		45.0	5.0	NM_001003699	A2RRF5|E2GM80|E2GM81|O75567|O75568|Q5VYB2|Q6BEP5|Q6BEP6|Q6BEP8|Q86SU2|Q9Y474	Missense_Mutation	SNP	ENST00000349384.6	hg19	CCDS34336.1	.	.	.	.	.	.	.	.	.	.	A	14.75	2.629142	0.46944	.	.	ENSG00000124782	ENST00000379933;ENST00000379938;ENST00000349384	T;T;T	0.11169	2.8;2.83;2.8	5.14	2.7	0.31948	.	.	.	.	.	T	0.05456	0.0144	M	0.68593	2.085	0.58432	D	0.999997	P;P	0.38504	0.501;0.634	B;B	0.36766	0.116;0.232	T	0.12993	-1.0526	9	0.72032	D	0.01	-4.7087	6.988	0.24739	0.7947:0.0:0.0726:0.1327	.	1343;1398	Q92766;Q92766-2	RREB1_HUMAN;.	G	1343;1398;1343	ENSP00000369265:E1343G;ENSP00000369270:E1398G;ENSP00000305560:E1343G	ENSP00000305560:E1343G	E	+	2	0	RREB1	7191875	0.979000	0.34478	0.378000	0.26068	0.088000	0.18126	2.496000	0.45346	0.281000	0.22233	0.459000	0.35465	GAG	.	.		0.682	RREB1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352985.1		
SYCP2L	221711	hgsc.bcm.edu	37	6	10942722	10942722	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:10942722T>C	ENST00000283141.6	+	22	2140	c.1844T>C	c.(1843-1845)cTc>cCc	p.L615P		NM_001040274.2	NP_001035364.2	Q5T4T6	SYC2L_HUMAN	synaptonemal complex protein 2-like	615						nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|kidney(4)|large_intestine(10)|lung(12)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	36	Breast(50;0.0838)|Ovarian(93;0.107)	all_hematologic(90;0.135)	Epithelial(50;0.239)			CTGAGTGAGCTCTCTTCCTTG	0.348																																					p.L615P		Atlas-SNP	.											.	SYCP2L	101	.	0			c.T1844C						.						47.0	43.0	44.0					6																	10942722		1834	4085	5919	SO:0001583	missense	221711	exon22			GTGAGCTCTCTTC	AK128130	CCDS43423.1	6p24.2	2008-11-06	2007-07-02	2007-07-02	ENSG00000153157	ENSG00000153157			21537	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 177"""	C6orf177			Standard	NM_001040274		Approved	dJ62D2.1, NO145	uc003mzo.3	Q5T4T6	OTTHUMG00000014250	ENST00000283141.6:c.1844T>C	chr6.hg19:g.10942722T>C	ENSP00000283141:p.Leu615Pro	95.0	0.0		74.0	4.0	NM_001040274	A6NDS5|Q08GK5|Q6ZRM2|Q96EJ2	Missense_Mutation	SNP	ENST00000283141.6	hg19	CCDS43423.1	.	.	.	.	.	.	.	.	.	.	T	10.04	1.242314	0.22796	.	.	ENSG00000153157	ENST00000283141	T	0.22134	1.97	4.27	-2.85	0.05734	.	1.111370	0.06908	N	0.807156	T	0.04048	0.0113	L	0.29908	0.895	0.09310	N	1	B	0.14805	0.011	B	0.14578	0.011	T	0.43653	-0.9378	10	0.34782	T	0.22	-1.4292	4.4828	0.11774	0.0:0.282:0.322:0.396	.	615	Q5T4T6	SYC2L_HUMAN	P	615	ENSP00000283141:L615P	ENSP00000283141:L615P	L	+	2	0	SYCP2L	11050708	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.092000	0.15066	-0.479000	0.06813	0.533000	0.62120	CTC	.	.		0.348	SYCP2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039845.3	NM_194299	
KIAA0319	9856	hgsc.bcm.edu	37	6	24596529	24596529	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:24596529A>G	ENST00000378214.3	-	3	897	c.373T>C	c.(373-375)Tcc>Ccc	p.S125P	KIAA0319_ENST00000430948.2_Missense_Mutation_p.S80P|KIAA0319_ENST00000535378.1_Missense_Mutation_p.S116P|KIAA0319_ENST00000543707.1_Missense_Mutation_p.S125P|KIAA0319_ENST00000537886.1_Missense_Mutation_p.S125P	NM_001168375.1|NM_014809.3	NP_001161847.1|NP_055624.2	Q5VV43	K0319_HUMAN	KIAA0319	125					negative regulation of dendrite development (GO:2000171)|neuron migration (GO:0001764)	early endosome (GO:0005769)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(3)|endometrium(6)|kidney(3)|large_intestine(11)|lung(19)|ovary(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)	53						CCCGAGGGGGAGCCCCTGTTC	0.552																																					p.S125P		Atlas-SNP	.											KIAA0319,NS,adenocarcinoma,0,1	KIAA0319	117	.	0			c.T373C						.						63.0	72.0	69.0					6																	24596529		2203	4300	6503	SO:0001583	missense	9856	exon3			AGGGGGAGCCCCT	AB002317	CCDS34348.1, CCDS54969.1, CCDS54970.1, CCDS54971.1, CCDS75409.1	6p22.3	2013-12-13			ENSG00000137261	ENSG00000137261			21580	protein-coding gene	gene with protein product	"""neuronal migration"""	609269				9205841, 15514892	Standard	NM_014809		Approved	NMIG	uc003neh.1	Q5VV43	OTTHUMG00000014358	ENST00000378214.3:c.373T>C	chr6.hg19:g.24596529A>G	ENSP00000367459:p.Ser125Pro	170.0	2.0		139.0	6.0	NM_001168377	A7MD37|B2RTU7|B4DHA7|B4DK75|B7ZML3|F5H123|Q9UJC8|Q9Y4G7	Missense_Mutation	SNP	ENST00000378214.3	hg19	CCDS34348.1	.	.	.	.	.	.	.	.	.	.	A	8.735	0.917681	0.17982	.	.	ENSG00000137261	ENST00000537886;ENST00000535378;ENST00000430948;ENST00000378214;ENST00000543707	T;T;T;T;T	0.07327	3.2;3.2;3.2;3.2;3.2	4.43	-3.03	0.05429	.	0.306847	0.23146	N	0.051405	T	0.01320	0.0043	L	0.27053	0.805	0.09310	N	1	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.09377	0.004;0.004;0.002	T	0.43621	-0.9380	10	0.32370	T	0.25	-0.0397	5.2005	0.15262	0.3908:0.2699:0.3393:0.0	.	125;116;125	F5H123;Q5VV43-2;Q5VV43	.;.;K0319_HUMAN	P	125;116;80;125;125	ENSP00000439700:S125P;ENSP00000442403:S116P;ENSP00000401086:S80P;ENSP00000367459:S125P;ENSP00000437656:S125P	ENSP00000367459:S125P	S	-	1	0	KIAA0319	24704508	0.000000	0.05858	0.000000	0.03702	0.775000	0.43874	-0.048000	0.11944	-0.573000	0.05998	0.421000	0.28195	TCC	.	.		0.552	KIAA0319-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040009.1	NM_014809	
SLC17A2	10246	hgsc.bcm.edu	37	6	25917264	25917264	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:25917264T>C	ENST00000265425.3	-	6	721	c.701A>G	c.(700-702)gAc>gGc	p.D234G	SLC17A2_ENST00000377850.3_Missense_Mutation_p.D234G|SLC17A2_ENST00000360488.3_Missense_Mutation_p.D234G			O00624	NPT3_HUMAN	solute carrier family 17, member 2	234					phosphate ion transmembrane transport (GO:0035435)|phosphate-containing compound metabolic process (GO:0006796)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	sodium:phosphate symporter activity (GO:0005436)			endometrium(3)|kidney(1)|large_intestine(9)|lung(12)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	31						ATGCATGGGGTCATCATAAAT	0.483																																					p.D234G		Atlas-SNP	.											.	SLC17A2	70	.	0			c.A701G						.						142.0	119.0	127.0					6																	25917264		2203	4300	6503	SO:0001583	missense	10246	exon7			ATGGGGTCATCAT	U90544	CCDS4567.1, CCDS69060.1	6p22.2	2013-07-18	2013-07-18		ENSG00000112337	ENSG00000112337		"""Solute carriers"""	10930	protein-coding gene	gene with protein product		611049	"""solute carrier family 17 (sodium phosphate), member 2"""			9149941	Standard	NM_001286123		Approved	NPT3	uc003nfl.3	O00624	OTTHUMG00000014413	ENST00000265425.3:c.701A>G	chr6.hg19:g.25917264T>C	ENSP00000265425:p.Asp234Gly	150.0	0.0		124.0	5.0	NM_005835	A6NK81|A6NLD6|Q5TB84|Q76P85	Missense_Mutation	SNP	ENST00000265425.3	hg19		.	.	.	.	.	.	.	.	.	.	T	18.83	3.708161	0.68615	.	.	ENSG00000112337	ENST00000360488;ENST00000377850;ENST00000265425	T;T;T	0.58797	0.31;0.31;0.31	4.65	4.65	0.58169	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.64402	D	0.000013	T	0.67767	0.2928	M	0.80183	2.485	0.35035	D	0.759147	D;D;D	0.89917	1.0;0.996;0.999	D;D;D	0.77004	0.989;0.959;0.982	T	0.73395	-0.3996	10	0.54805	T	0.06	.	10.6641	0.45719	0.0:0.0:0.0:1.0	.	234;234;234	O00624;A6NK81;O00624-2	NPT3_HUMAN;.;.	G	234	ENSP00000353677:D234G;ENSP00000367081:D234G;ENSP00000265425:D234G	ENSP00000265425:D234G	D	-	2	0	SLC17A2	26025243	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.632000	0.54287	2.067000	0.61834	0.460000	0.39030	GAC	.	.		0.483	SLC17A2-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000040075.1		
HIST1H1C	3006	hgsc.bcm.edu	37	6	26056377	26056377	+	Missense_Mutation	SNP	C	C	T	rs186228942		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:26056377C>T	ENST00000343677.2	-	1	322	c.280G>A	c.(280-282)Gtg>Atg	p.V94M		NM_005319.3	NP_005310.1	P16403	H12_HUMAN	histone cluster 1, H1c	94	H15. {ECO:0000255|PROSITE- ProRule:PRU00837}.				nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)	nuclear euchromatin (GO:0005719)|nucleosome (GO:0000786)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(6)|kidney(1)|large_intestine(1)|lung(8)|ovary(4)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)	34						TTCGTTTGCACCAGAGTGCCC	0.537																																					p.V94M		Atlas-SNP	.											.	HIST1H1C	80	.	0			c.G280A						.						108.0	113.0	111.0					6																	26056377		2203	4300	6503	SO:0001583	missense	3006	exon1			TTTGCACCAGAGT	X57129	CCDS4577.1	6p21.3	2012-10-02	2006-10-11	2003-02-21	ENSG00000187837	ENSG00000187837		"""Histones / Replication-dependent"""	4716	protein-coding gene	gene with protein product		142710	"""H1 histone family, member 2"", ""histone 1, H1c"""	H1F2		2759094, 12408966	Standard	NM_005319		Approved	H1.2, H1s-1, H1c	uc003nfw.3	P16403	OTTHUMG00000016140	ENST00000343677.2:c.280G>A	chr6.hg19:g.26056377C>T	ENSP00000339566:p.Val94Met	318.0	1.0		240.0	103.0	NM_005319	A8K4I2	Missense_Mutation	SNP	ENST00000343677.2	hg19	CCDS4577.1	.	.	.	.	.	.	.	.	.	.	C	17.76	3.468828	0.63625	.	.	ENSG00000187837	ENST00000343677	T	0.09817	2.94	5.63	5.63	0.86233	Histone H1/H5 (3);Winged helix-turn-helix transcription repressor DNA-binding (1);	0.210714	0.39909	N	0.001234	T	0.34308	0.0893	M	0.93328	3.405	0.58432	D	0.999999	D	0.71674	0.998	D	0.77004	0.989	T	0.38308	-0.9667	10	0.87932	D	0	-29.6342	12.3739	0.55269	0.0:0.9231:0.0:0.0768	.	94	P16403	H12_HUMAN	M	94	ENSP00000339566:V94M	ENSP00000339566:V94M	V	-	1	0	HIST1H1C	26164356	1.000000	0.71417	1.000000	0.80357	0.282000	0.26991	2.516000	0.45520	2.814000	0.96858	0.655000	0.94253	GTG	.	C|1.000;G|0.000		0.537	HIST1H1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043372.1	NM_005319	
HIST1H4G	8369	hgsc.bcm.edu	37	6	26246913	26246913	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:26246913A>G	ENST00000244537.4	-	1	346	c.293T>C	c.(292-294)cTg>cCg	p.L98P		NM_003547.2	NP_003538.1	Q99525	H4G_HUMAN	histone cluster 1, H4g	98						nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|endometrium(1)|large_intestine(1)|lung(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	7		all_hematologic(11;0.0945)|Acute lymphoblastic leukemia(11;0.167)				AAAGCCTTACAGGGTTCTTCC	0.562																																					p.L98P		Atlas-SNP	.											.	HIST1H4G	18	.	0			c.T293C						.						53.0	44.0	47.0					6																	26246913		2203	4300	6503	SO:0001583	missense	8369	exon1			CCTTACAGGGTTC	Z80788	CCDS4599.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000124578	ENSG00000275663		"""Histones / Replication-dependent"""	4792	protein-coding gene	gene with protein product		602832	"""H4 histone family, member L"", ""histone 1, H4g"""	H4FL		9119399, 12408966	Standard	NM_003547		Approved	H4/l	uc003nhf.3	Q99525	OTTHUMG00000014444	ENST00000244537.4:c.293T>C	chr6.hg19:g.26246913A>G	ENSP00000244537:p.Leu98Pro	138.0	0.0		115.0	40.0	NM_003547		Missense_Mutation	SNP	ENST00000244537.4	hg19	CCDS4599.1	.	.	.	.	.	.	.	.	.	.	.	9.569	1.120585	0.20877	.	.	ENSG00000124578	ENST00000244537	.	.	.	3.05	3.05	0.35203	Histone-fold (1);	.	.	.	.	T	0.70290	0.3207	.	.	.	0.58432	D	0.999995	D	0.89917	1.0	D	0.70227	0.968	T	0.75133	-0.3425	7	0.87932	D	0	.	11.2158	0.48825	1.0:0.0:0.0:0.0	.	98	Q99525	H4G_HUMAN	P	98	.	ENSP00000244537:L98P	L	-	2	0	HIST1H4G	26354892	1.000000	0.71417	0.853000	0.33588	0.003000	0.03518	8.352000	0.90075	1.376000	0.46267	0.321000	0.21382	CTG	.	.		0.562	HIST1H4G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040107.1	NM_003547	
EHMT2	10919	hgsc.bcm.edu	37	6	31850734	31850734	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:31850734T>C	ENST00000375537.4	-	24	3053	c.3047A>G	c.(3046-3048)gAg>gGg	p.E1016G	EHMT2_ENST00000480912.1_5'UTR|EHMT2_ENST00000395728.3_Missense_Mutation_p.E1073G|EHMT2_ENST00000375528.4_Missense_Mutation_p.E1039G|EHMT2_ENST00000375530.4_Missense_Mutation_p.E982G|EHMT2-AS1_ENST00000434689.1_RNA	NM_006709.3	NP_006700.3	Q96KQ7	EHMT2_HUMAN	euchromatic histone-lysine N-methyltransferase 2	1016	Pre-SET. {ECO:0000255|PROSITE- ProRule:PRU00157}.				DNA methylation (GO:0006306)|DNA methylation on cytosine within a CG sequence (GO:0010424)|fertilization (GO:0009566)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|organ growth (GO:0035265)|peptidyl-lysine dimethylation (GO:0018027)|regulation of DNA replication (GO:0006275)|spermatid development (GO:0007286)|synaptonemal complex assembly (GO:0007130)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|histone methyltransferase activity (H3-K27 specific) (GO:0046976)|histone methyltransferase activity (H3-K9 specific) (GO:0046974)|histone-lysine N-methyltransferase activity (GO:0018024)|p53 binding (GO:0002039)|protein-lysine N-methyltransferase activity (GO:0016279)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|kidney(2)|large_intestine(3)|lung(6)|ovary(2)|prostate(4)|upper_aerodigestive_tract(1)	21						CTGGTTACACTCGAAAATCAG	0.572																																					p.E1016G		Atlas-SNP	.											.	EHMT2	45	.	0			c.A3047G						.						71.0	71.0	71.0					6																	31850734		1511	2709	4220	SO:0001583	missense	10919	exon24			TTACACTCGAAAA	AF134726	CCDS4725.1, CCDS4726.1, CCDS75425.1	6p21.3	2013-01-10	2004-03-22	2005-06-09	ENSG00000204371	ENSG00000204371	2.1.1.43	"""Chromatin-modifying enzymes / K-methyltransferases"", ""Ankyrin repeat domain containing"""	14129	protein-coding gene	gene with protein product		604599	"""chromosome 6 open reading frame 30"", ""HLA-B associated transcript 8"""	C6orf30, BAT8		8457211, 11316813	Standard	XM_005274833		Approved	G9A, Em:AF134726.3, NG36/G9a, KMT1C	uc003nxz.1	Q96KQ7	OTTHUMG00000031180	ENST00000375537.4:c.3047A>G	chr6.hg19:g.31850734T>C	ENSP00000364687:p.Glu1016Gly	128.0	0.0		92.0	4.0	NM_006709	B0UZY2|Q14349|Q5JP83|Q5JQ92|Q5JQA1|Q5JQG3|Q6PK06|Q96MH5|Q96QD0|Q9UQL8|Q9Y331	Missense_Mutation	SNP	ENST00000375537.4	hg19	CCDS4725.1	.	.	.	.	.	.	.	.	.	.	T	22.7	4.324471	0.81580	.	.	ENSG00000204371	ENST00000395728;ENST00000375528;ENST00000375530;ENST00000375537;ENST00000442298	D;D;D;D	0.86694	-2.16;-2.16;-2.16;-2.16	4.24	4.24	0.50183	Pre-SET zinc-binding sub-group (1);Pre-SET domain (2);	0.000000	0.85682	D	0.000000	D	0.95178	0.8437	H	0.97896	4.1	0.58432	D	0.999993	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	0.96364	0.9268	10	0.87932	D	0	.	12.4856	0.55871	0.0:0.0:0.0:1.0	.	1039;982;1016;837	A2ABF8;Q96KQ7-2;Q96KQ7;Q59FM7	.;.;EHMT2_HUMAN;.	G	1073;1039;982;1016;837	ENSP00000379078:E1073G;ENSP00000364678:E1039G;ENSP00000364680:E982G;ENSP00000364687:E1016G	ENSP00000364678:E1039G	E	-	2	0	EHMT2	31958713	1.000000	0.71417	0.998000	0.56505	0.830000	0.47004	7.629000	0.83207	1.787000	0.52448	0.459000	0.35465	GAG	.	.		0.572	EHMT2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076355.5	NM_006709	
C2	717	hgsc.bcm.edu	37	6	31903769	31903769	+	Missense_Mutation	SNP	T	T	C	rs541199729		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:31903769T>C	ENST00000299367.5	+	7	1195	c.919T>C	c.(919-921)Tct>Cct	p.S307P	CFB_ENST00000556679.1_Intron|C2_ENST00000442278.2_Missense_Mutation_p.S175P|CFB_ENST00000456570.1_Intron|C2_ENST00000469372.1_Missense_Mutation_p.S61P|CFB_ENST00000477310.1_Intron|C2_ENST00000452323.2_Intron	NM_000063.4	NP_000054.2	P06681	CO2_HUMAN	complement component 2	307	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|positive regulation of apoptotic cell clearance (GO:2000427)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)			haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(12)|ovary(1)|skin(2)|urinary_tract(2)	27		Ovarian(999;0.00965)		LUAD - Lung adenocarcinoma(999;0.247)		AGTCCTCATGTCTGTCCTGAA	0.502																																					p.S307P		Atlas-SNP	.											.	C2	50	.	0			c.T919C						.						110.0	98.0	102.0					6																	31903769		1511	2709	4220	SO:0001583	missense	717	exon7			CTCATGTCTGTCC		CCDS4728.1, CCDS54991.1, CCDS56416.1, CCDS75427.1, CCDS75428.1	6p21.3	2014-09-17			ENSG00000166278	ENSG00000166278		"""Complement system"""	1248	protein-coding gene	gene with protein product		613927					Standard	NM_001145903		Approved		uc011hbs.1	P06681	OTTHUMG00000031190	ENST00000299367.5:c.919T>C	chr6.hg19:g.31903769T>C	ENSP00000299367:p.Ser307Pro	124.0	0.0		93.0	4.0	NM_000063	B4DPF3|B4DV20|E9PFN7|O19694|Q13904	Missense_Mutation	SNP	ENST00000299367.5	hg19	CCDS4728.1	.	.	.	.	.	.	.	.	.	.	T	14.52	2.561228	0.45590	.	.	ENSG00000166278	ENST00000469372;ENST00000497706;ENST00000432397;ENST00000299367;ENST00000442278	T;T;T;T	0.76968	-1.06;-1.06;-1.06;-1.06	5.73	5.73	0.89815	von Willebrand factor, type A (3);	0.000000	0.38605	N	0.001621	T	0.81559	0.4848	.	.	.	0.80722	D	1	P;B;B;P;D	0.76494	0.895;0.281;0.442;0.863;0.999	B;B;B;P;D	0.72075	0.444;0.128;0.199;0.504;0.976	T	0.82078	-0.0635	9	0.38643	T	0.18	-17.5078	10.1003	0.42499	0.0:0.0:0.1682:0.8318	.	278;61;175;307;94	B4DV48;B4DQI1;E9PFN7;P06681;E9PDZ0	.;.;.;CO2_HUMAN;.	P	61;94;94;307;175	ENSP00000418923:S61P;ENSP00000417482:S94P;ENSP00000299367:S307P;ENSP00000395683:S175P	ENSP00000299367:S307P	S	+	1	0	C2	32011748	0.867000	0.29959	0.996000	0.52242	0.502000	0.33828	0.659000	0.24994	2.188000	0.69820	0.383000	0.25322	TCT	.	.		0.502	C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076379.9		
NOTCH4	4855	hgsc.bcm.edu	37	6	32169107	32169107	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:32169107T>C	ENST00000375023.3	-	22	4064	c.3926A>G	c.(3925-3927)gAc>gGc	p.D1309G		NM_004557.3	NP_004548.3	Q99466	NOTC4_HUMAN	notch 4	1309					cell differentiation (GO:0030154)|cell fate determination (GO:0001709)|embryo development (GO:0009790)|endothelial cell morphogenesis (GO:0001886)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|mammary gland development (GO:0030879)|morphogenesis of a branching structure (GO:0001763)|negative regulation of cell differentiation (GO:0045596)|negative regulation of endothelial cell differentiation (GO:0045602)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|patterning of blood vessels (GO:0001569)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(47)|ovary(5)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(1)	100						CAGCTGCTGGTCTAGGGCTGG	0.637																																					p.D1309G		Atlas-SNP	.											.	NOTCH4	201	.	0			c.A3926G						.						37.0	41.0	39.0					6																	32169107		1508	2709	4217	SO:0001583	missense	4855	exon22			TGCTGGTCTAGGG		CCDS34420.1	6p21.3	2013-01-10	2010-06-24		ENSG00000204301	ENSG00000204301		"""Ankyrin repeat domain containing"""	7884	protein-coding gene	gene with protein product		164951	"""Notch (Drosophila) homolog 4"", ""Notch homolog 4 (Drosophila)"""	INT3		7835890	Standard	NM_004557		Approved		uc003obb.3	Q99466	OTTHUMG00000031044	ENST00000375023.3:c.3926A>G	chr6.hg19:g.32169107T>C	ENSP00000364163:p.Asp1309Gly	129.0	0.0		93.0	4.0	NM_004557	B0V183|B0V1X5|O00306|Q5SSY7|Q99458|Q99940|Q9H3S8|Q9UII9|Q9UIJ0	Missense_Mutation	SNP	ENST00000375023.3	hg19	CCDS34420.1	.	.	.	.	.	.	.	.	.	.	T	10.62	1.402555	0.25291	.	.	ENSG00000204301	ENST00000375023	T	0.81163	-1.46	4.37	4.37	0.52481	.	0.364566	0.19536	N	0.111902	T	0.57080	0.2029	L	0.27053	0.805	0.80722	D	1	B	0.14012	0.009	B	0.20184	0.028	T	0.58853	-0.7563	10	0.40728	T	0.16	.	11.615	0.51083	0.0:0.0:0.0:1.0	.	1309	Q99466	NOTC4_HUMAN	G	1309	ENSP00000364163:D1309G	ENSP00000364163:D1309G	D	-	2	0	NOTCH4	32277085	0.998000	0.40836	0.999000	0.59377	0.651000	0.38670	3.197000	0.51028	1.862000	0.54008	0.374000	0.22700	GAC	.	.		0.637	NOTCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076045.2		
RING1	6015	hgsc.bcm.edu	37	6	33180112	33180112	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:33180112A>G	ENST00000374656.4	+	7	1365	c.1157A>G	c.(1156-1158)gAg>gGg	p.E386G	RING1_ENST00000478431.1_3'UTR	NM_002931.3	NP_002922.2	Q06587	RING1_HUMAN	ring finger protein 1	386	Necessary for interaction with CBX2. {ECO:0000250}.				anterior/posterior pattern specification (GO:0009952)|camera-type eye morphogenesis (GO:0048593)|histone H2A monoubiquitination (GO:0035518)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(5)|large_intestine(1)|lung(3)|ovary(2)|prostate(2)|skin(4)	17						CTGGTGAATGAGAAATTCTGG	0.557																																					p.E386G		Atlas-SNP	.											.	RING1	40	.	0			c.A1157G						.						28.0	24.0	26.0					6																	33180112		1507	2706	4213	SO:0001583	missense	6015	exon7			TGAATGAGAAATT		CCDS34424.1	6p21.3	2013-01-09			ENSG00000204227	ENSG00000204227		"""RING-type (C3HC4) zinc fingers"""	10018	protein-coding gene	gene with protein product		602045				1906426	Standard	NM_002931		Approved	RNF1	uc003odk.3	Q06587	OTTHUMG00000031278	ENST00000374656.4:c.1157A>G	chr6.hg19:g.33180112A>G	ENSP00000363787:p.Glu386Gly	191.0	0.0		154.0	7.0	NM_002931	A8JZZ0|Q5JP96|Q5SQW2|Q86V19	Missense_Mutation	SNP	ENST00000374656.4	hg19	CCDS34424.1	.	.	.	.	.	.	.	.	.	.	A	13.12	2.142262	0.37825	.	.	ENSG00000204227	ENST00000374656	D	0.88354	-2.37	4.92	4.92	0.64577	.	0.000000	0.85682	D	0.000000	D	0.89532	0.6742	L	0.43152	1.355	0.51767	D	0.99993	D	0.71674	0.998	D	0.70227	0.968	D	0.91220	0.5006	10	0.87932	D	0	-17.1428	12.5707	0.56334	1.0:0.0:0.0:0.0	.	386	Q06587	RING1_HUMAN	G	386	ENSP00000363787:E386G	ENSP00000363787:E386G	E	+	2	0	RING1	33288090	1.000000	0.71417	0.995000	0.50966	0.025000	0.11179	8.207000	0.89746	2.046000	0.60703	0.523000	0.50628	GAG	.	.		0.557	RING1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076609.2		
DNAH8	1769	hgsc.bcm.edu	37	6	38690855	38690855	+	5'Flank	SNP	G	G	A	rs180723141	byFrequency	TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:38690855G>A	ENST00000359357.3	+	0	0				DNAH8_ENST00000449981.2_Silent_p.P90P			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8						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)	p.P90P(1)		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						GGCTTGCACCGCGACCGGTTC	0.527																																					p.P90P		Atlas-SNP	.											DNAH8_ENST00000373278,colon,carcinoma,0,1	DNAH8	1239	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G270A						.						108.0	98.0	101.0					6																	38690855		876	1991	2867	SO:0001631	upstream_gene_variant	1769	exon2			TGCACCGCGACCG	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		chr6.hg19:g.38690855G>A	Exception_encountered	168.0	0.0		118.0	44.0	NM_001206927	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Silent	SNP	ENST00000359357.3	hg19																																																																																				.	G|0.997;C|0.003		0.527	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927	
SRF	6722	hgsc.bcm.edu	37	6	43143627	43143627	+	Missense_Mutation	SNP	G	G	A			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:43143627G>A	ENST00000265354.4	+	3	1322	c.964G>A	c.(964-966)Gtg>Atg	p.V322M	SRF_ENST00000457278.2_Missense_Mutation_p.V118M	NM_003131.2	NP_003122.1	P11831	SRF_HUMAN	serum response factor (c-fos serum response element-binding transcription factor)	322					angiogenesis involved in wound healing (GO:0060055)|associative learning (GO:0008306)|cardiac myofibril assembly (GO:0055003)|cardiac vascular smooth muscle cell differentiation (GO:0060947)|cell migration involved in sprouting angiogenesis (GO:0002042)|cell-matrix adhesion (GO:0007160)|cellular response to glucose stimulus (GO:0071333)|cellular senescence (GO:0090398)|contractile actin filament bundle assembly (GO:0030038)|developmental growth (GO:0048589)|dorsal aorta morphogenesis (GO:0035912)|epithelial cell-cell adhesion (GO:0090136)|epithelial structure maintenance (GO:0010669)|erythrocyte development (GO:0048821)|eyelid development in camera-type eye (GO:0061029)|heart development (GO:0007507)|heart looping (GO:0001947)|heart trabecula formation (GO:0060347)|hematopoietic stem cell differentiation (GO:0060218)|hippocampus development (GO:0021766)|long term synaptic depression (GO:0060292)|long-term memory (GO:0007616)|megakaryocyte development (GO:0035855)|mesoderm formation (GO:0001707)|morphogenesis of an epithelial sheet (GO:0002011)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of beta-amyloid clearance (GO:1900222)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|neuron development (GO:0048666)|neuron migration (GO:0001764)|neuron projection development (GO:0031175)|patterning of blood vessels (GO:0001569)|platelet activation (GO:0030168)|platelet formation (GO:0030220)|positive regulation of cell differentiation (GO:0045597)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of transcription by glucose (GO:0046016)|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 initiation from RNA polymerase II promoter (GO:0060261)|positive regulation of transcription via serum response element binding (GO:0010735)|positive thymic T cell selection (GO:0045059)|primitive streak formation (GO:0090009)|regulation of cell adhesion (GO:0030155)|regulation of smooth muscle cell differentiation (GO:0051150)|regulation of water loss via skin (GO:0033561)|response to cytokine (GO:0034097)|response to hormone (GO:0009725)|response to hypoxia (GO:0001666)|response to toxic substance (GO:0009636)|sarcomere organization (GO:0045214)|skin morphogenesis (GO:0043589)|stress fiber assembly (GO:0043149)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)|tight junction assembly (GO:0070830)|transcription from RNA polymerase II promoter (GO:0006366)|trophectodermal cell differentiation (GO:0001829)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|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)|serum response element binding (GO:0010736)|transcription factor binding (GO:0008134)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)	12			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.011)|OV - Ovarian serous cystadenocarcinoma(102;0.0423)			CAATGGGACTGTGCTGAAGAG	0.612																																					p.V322M		Atlas-SNP	.											.	SRF	24	.	0			c.G964A						.						114.0	101.0	106.0					6																	43143627		2203	4300	6503	SO:0001583	missense	6722	exon3			GGGACTGTGCTGA	J03161	CCDS4889.1	6p	2008-02-05			ENSG00000112658	ENSG00000112658			11291	protein-coding gene	gene with protein product		600589				3203386	Standard	NM_003131		Approved	MCM1	uc003oui.3	P11831	OTTHUMG00000014722	ENST00000265354.4:c.964G>A	chr6.hg19:g.43143627G>A	ENSP00000265354:p.Val322Met	146.0	0.0		100.0	4.0	NM_003131	Q5T648	Missense_Mutation	SNP	ENST00000265354.4	hg19	CCDS4889.1	.	.	.	.	.	.	.	.	.	.	G	22.6	4.316191	0.81469	.	.	ENSG00000112658	ENST00000265354;ENST00000457278	D	0.84800	-1.9	4.82	4.82	0.62117	.	0.000000	0.85682	D	0.000000	D	0.84611	0.5510	L	0.47716	1.5	0.80722	D	1	D	0.59357	0.985	P	0.54060	0.741	D	0.86513	0.1811	10	0.62326	D	0.03	-4.0164	17.8792	0.88835	0.0:0.0:1.0:0.0	.	322	P11831	SRF_HUMAN	M	322;118	ENSP00000265354:V322M	ENSP00000265354:V322M	V	+	1	0	SRF	43251605	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	6.244000	0.72391	2.203000	0.70933	0.462000	0.41574	GTG	.	.		0.612	SRF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040581.1	NM_003131	
EYS	346007	hgsc.bcm.edu	37	6	65016918	65016918	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:65016918A>G	ENST00000370621.3	-	30	6662	c.6136T>C	c.(6136-6138)Tgg>Cgg	p.W2046R	EYS_ENST00000503581.1_Missense_Mutation_p.W2046R|EYS_ENST00000370616.2_Missense_Mutation_p.W2046R			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	2046	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				detection of light stimulus involved in visual perception (GO:0050908)|skeletal muscle tissue regeneration (GO:0043403)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	69						AAAGATCTCCAGTTATTTATT	0.338																																					p.W2046R		Atlas-SNP	.											.	EYS	527	.	0			c.T6136C						.						198.0	162.0	173.0					6																	65016918		692	1588	2280	SO:0001583	missense	346007	exon30			ATCTCCAGTTATT		CCDS4967.1, CCDS47445.1, CCDS47446.1	6q12	2014-01-28	2008-10-20	2008-10-20	ENSG00000188107	ENSG00000188107			21555	protein-coding gene	gene with protein product		612424	"""chromosome 6 open reading frame 180"", ""EGF-like-domain, multiple 11"", ""retinitis pigmentosa 25 (autosomal recessive)"", ""EGF-like-domain, multiple 10"", ""chromosome 6 open reading frame 178"", ""chromosome 6 open reading frame 179"""	C6orf180, EGFL11, RP25, EGFL10, C6orf178, C6orf179		18836446, 18976725	Standard	NM_001142800		Approved	dJ1018A4.2, bA166P24.2, SPAM, bA307F22.3, dJ303F19.1, bA74E24.1	uc011dxu.1	Q5T1H1	OTTHUMG00000014971	ENST00000370621.3:c.6136T>C	chr6.hg19:g.65016918A>G	ENSP00000359655:p.Trp2046Arg	80.0	0.0		64.0	5.0	NM_001142800	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Missense_Mutation	SNP	ENST00000370621.3	hg19		.	.	.	.	.	.	.	.	.	.	A	12.57	1.978562	0.34942	.	.	ENSG00000188107	ENST00000503581;ENST00000370621;ENST00000370616	T;T;T	0.66099	-0.19;-0.19;-0.19	5.2	-3.76	0.04359	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);	.	.	.	.	T	0.14184	0.0343	N	0.08118	0	0.09310	N	0.999999	B;B	0.32160	0.358;0.244	B;B	0.30495	0.116;0.054	T	0.15925	-1.0420	9	0.23891	T	0.37	.	6.4241	0.21760	0.2192:0.3184:0.4624:0.0	.	2046;2046	Q5T1H1-1;Q5T1H1	.;EYS_HUMAN	R	2046	ENSP00000424243:W2046R;ENSP00000359655:W2046R;ENSP00000359650:W2046R	ENSP00000359650:W2046R	W	-	1	0	EYS	65074877	0.001000	0.12720	0.001000	0.08648	0.453000	0.32348	-0.257000	0.08745	-0.582000	0.05929	-0.316000	0.08728	TGG	.	.		0.338	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050	
EYS	346007	hgsc.bcm.edu	37	6	66200486	66200486	+	Splice_Site	SNP	C	C	A			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:66200486C>A	ENST00000370621.3	-	5	1389		c.e5+1		EYS_ENST00000370618.3_Splice_Site|EYS_ENST00000342421.5_Splice_Site|EYS_ENST00000503581.1_Splice_Site|EYS_ENST00000370616.2_Splice_Site|EYS_ENST00000393380.2_Splice_Site			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)						detection of light stimulus involved in visual perception (GO:0050908)|skeletal muscle tissue regeneration (GO:0043403)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	69						GCATTTTTTACCTGAAAATTG	0.274																																					.		Atlas-SNP	.											.	EYS	527	.	0			c.862+1G>T						.						58.0	53.0	55.0					6																	66200486		2203	4294	6497	SO:0001630	splice_region_variant	346007	exon6			TTTTTACCTGAAA		CCDS4967.1, CCDS47445.1, CCDS47446.1	6q12	2014-01-28	2008-10-20	2008-10-20	ENSG00000188107	ENSG00000188107			21555	protein-coding gene	gene with protein product		612424	"""chromosome 6 open reading frame 180"", ""EGF-like-domain, multiple 11"", ""retinitis pigmentosa 25 (autosomal recessive)"", ""EGF-like-domain, multiple 10"", ""chromosome 6 open reading frame 178"", ""chromosome 6 open reading frame 179"""	C6orf180, EGFL11, RP25, EGFL10, C6orf178, C6orf179		18836446, 18976725	Standard	NM_001142800		Approved	dJ1018A4.2, bA166P24.2, SPAM, bA307F22.3, dJ303F19.1, bA74E24.1	uc011dxu.1	Q5T1H1	OTTHUMG00000014971	ENST00000370621.3:c.862+1G>T	chr6.hg19:g.66200486C>A		468.0	0.0		372.0	15.0	NM_001142800	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Splice_Site	SNP	ENST00000370621.3	hg19		.	.	.	.	.	.	.	.	.	.	C	7.600	0.672484	0.14776	.	.	ENSG00000188107	ENST00000503581;ENST00000370621;ENST00000370616;ENST00000393380;ENST00000342421;ENST00000370618	.	.	.	4.54	2.52	0.30459	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	6.0309	0.19679	0.2503:0.6524:0.0:0.0973	.	.	.	.	.	-1	.	.	.	-	.	.	EYS	66257207	1.000000	0.71417	0.035000	0.18076	0.300000	0.27592	3.082000	0.50128	0.302000	0.22762	0.655000	0.94253	.	.	.		0.274	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050	Intron
RIMS1	22999	hgsc.bcm.edu	37	6	73102485	73102485	+	Missense_Mutation	SNP	C	C	T			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:73102485C>T	ENST00000521978.1	+	31	4591	c.4591C>T	c.(4591-4593)Cgc>Tgc	p.R1531C	RIMS1_ENST00000523963.1_Missense_Mutation_p.R656C|RIMS1_ENST00000491071.2_Missense_Mutation_p.R1354C|RIMS1_ENST00000520567.1_Missense_Mutation_p.R1181C|RIMS1_ENST00000431478.2_3'UTR|RIMS1_ENST00000348717.5_Missense_Mutation_p.R1314C|RIMS1_ENST00000264839.7_Missense_Mutation_p.R1380C|RIMS1_ENST00000538414.1_Missense_Mutation_p.R337C|RIMS1_ENST00000425662.2_Missense_Mutation_p.R599C|RIMS1_ENST00000517960.1_Missense_Mutation_p.R1314C|RIMS1_ENST00000518273.1_Missense_Mutation_p.R1210C|RIMS1_ENST00000517827.1_Missense_Mutation_p.R665C|RIMS1_ENST00000401910.3_Missense_Mutation_p.R851C|RIMS1_ENST00000414192.2_Missense_Mutation_p.R58C|RIMS1_ENST00000522291.1_Missense_Mutation_p.R1130C	NM_014989.5	NP_055804.2	Q86UR5	RIMS1_HUMAN	regulating synaptic membrane exocytosis 1	1531					calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|glutamate secretion (GO:0014047)|intracellular protein transport (GO:0006886)|membrane fusion (GO:0061025)|neurotransmitter secretion (GO:0007269)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of gene expression (GO:0010628)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|protein complex assembly (GO:0006461)|regulated secretory pathway (GO:0045055)|regulation of catalytic activity (GO:0050790)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of neurotransmitter secretion (GO:0046928)|response to stimulus (GO:0050896)|secretion (GO:0046903)|synaptic transmission (GO:0007268)|synaptic vesicle exocytosis (GO:0016079)|visual perception (GO:0007601)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|Rab GTPase binding (GO:0017137)|small GTPase regulator activity (GO:0005083)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(25)|liver(4)|lung(35)|ovary(9)|pancreas(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	102		all_epithelial(107;0.179)|all_hematologic(105;0.212)				GCTTGTTGGCCGCCAAACCCT	0.388																																					p.R1531C		Atlas-SNP	.											RIMS1,rectum,carcinoma,0,1	RIMS1	278	.	0			c.C4591T						.						86.0	82.0	83.0					6																	73102485		1840	4103	5943	SO:0001583	missense	22999	exon31			GTTGGCCGCCAAA	AB002338	CCDS47449.1, CCDS55029.1, CCDS55030.1, CCDS55031.1, CCDS55032.1, CCDS55033.1	6q12-q13	2008-10-16	2002-06-12	2002-06-14	ENSG00000079841	ENSG00000079841			17282	protein-coding gene	gene with protein product	"""Rab3-interacting molecule"""	606629	"""RAB3 interacting protein 2"""	RAB3IP2, CORD7		9205841, 11438518	Standard	NM_001168407		Approved	RIM, KIAA0340, RIM1	uc003pga.4	Q86UR5	OTTHUMG00000015009	ENST00000521978.1:c.4591C>T	chr6.hg19:g.73102485C>T	ENSP00000428417:p.Arg1531Cys	143.0	0.0		80.0	33.0	NM_014989	A7MBN6|B7Z2M0|B7Z2Q9|B7Z3S3|B7Z6S2|E7EX08|E9PCB7|E9PCZ1|E9PF48|E9PHF5|E9PHR1|O15048|Q5JY21|Q5JY25|Q5SZK1|Q8TDY9|Q8TDZ5|Q9HBA1|Q9HBA2|Q9HBA3|Q9HBA4|Q9HBA5|Q9HBA6	Missense_Mutation	SNP	ENST00000521978.1	hg19	CCDS47449.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.72|18.72	3.683389|3.683389	0.68157|0.68157	.|.	.|.	ENSG00000079841|ENSG00000079841	ENST00000517433|ENST00000491071;ENST00000350827;ENST00000352008;ENST00000348717;ENST00000349908;ENST00000346609;ENST00000264839;ENST00000517960;ENST00000518273;ENST00000520567;ENST00000522291;ENST00000521978;ENST00000401910;ENST00000523963;ENST00000425662;ENST00000453976;ENST00000517827;ENST00000370420;ENST00000538414;ENST00000414192	.|T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	.|0.43294	.|0.95;2.12;2.05;2.13;2.32;2.35;2.35;2.0;2.07;2.34;2.26;1.41;2.26;1.71;1.67;1.96	5.5|5.5	2.56|2.56	0.30785|0.30785	.|.	.|0.000000	.|0.64402	.|D	.|0.000020	T|T	0.58552|0.58552	0.2130|0.2130	M|M	0.84683|0.84683	2.71|2.71	0.80722|0.80722	D|D	1|1	.|D;D;D;D;D;D;D;D;D;D;D;D;D	.|0.89917	.|1.0;1.0;1.0;0.998;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	.|D;D;D;D;D;D;D;D;D;D;D;D;D	.|0.97110	.|0.999;0.996;0.992;0.969;0.996;0.998;0.994;1.0;0.995;0.996;0.979;0.998;0.979	T|T	0.69000|0.69000	-0.5261|-0.5261	5|10	.|0.87932	.|D	.|0	-10.7348|-10.7348	14.3795|14.3795	0.66902|0.66902	0.467:0.533:0.0:0.0|0.467:0.533:0.0:0.0	.|.	.|155;337;665;656;1380;851;1130;434;1210;1314;607;1354;1531	.|B7Z6K9;B7Z7W2;B7Z3S3;E9PHF5;E9PHR1;E9PF48;E7EX08;Q5JY22;E7ERQ1;E7ENC2;Q5JY21;C9JNW6;Q86UR5	.|.;.;.;.;.;.;.;.;.;.;.;.;RIMS1_HUMAN	L|C	876|1354;1380;1354;1314;1210;1130;1380;1314;1210;1181;1130;1531;851;656;599;696;665;579;337;58	.|ENSP00000430101:R1354C;ENSP00000275037:R1314C;ENSP00000264839:R1380C;ENSP00000429959:R1314C;ENSP00000430408:R1210C;ENSP00000430502:R1181C;ENSP00000430932:R1130C;ENSP00000428417:R1531C;ENSP00000385649:R851C;ENSP00000428328:R656C;ENSP00000411235:R599C;ENSP00000389503:R696C;ENSP00000428367:R665C;ENSP00000359448:R579C;ENSP00000439730:R337C;ENSP00000402273:R58C	.|ENSP00000264839:R1380C	P|R	+|+	2|1	0|0	RIMS1|RIMS1	73159206|73159206	0.877000|0.877000	0.30153|0.30153	0.998000|0.998000	0.56505|0.56505	0.984000|0.984000	0.73092|0.73092	1.520000|1.520000	0.35899|0.35899	0.646000|0.646000	0.30693|0.30693	0.591000|0.591000	0.81541|0.81541	CCG|CGC	.	.		0.388	RIMS1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374968.1		
CD109	135228	hgsc.bcm.edu	37	6	74502402	74502402	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:74502402T>C	ENST00000287097.5	+	23	2867	c.2755T>C	c.(2755-2757)Tat>Cat	p.Y919H	CD109_ENST00000437994.2_Missense_Mutation_p.Y919H|CD109_ENST00000474094.1_3'UTR|CD109_ENST00000422508.2_Missense_Mutation_p.Y842H			Q6YHK3	CD109_HUMAN	CD109 molecule	919					negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of wound healing (GO:0061045)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)|transforming growth factor beta binding (GO:0050431)			NS(2)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(18)|liver(2)|lung(26)|ovary(2)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						TCGGATGCCTTATGGCTGTGG	0.358																																					p.Y919H		Atlas-SNP	.											.	CD109	170	.	0			c.T2755C						.						164.0	147.0	153.0					6																	74502402		2203	4300	6503	SO:0001583	missense	135228	exon23			ATGCCTTATGGCT	AF410459	CCDS4982.1, CCDS55038.1, CCDS55039.1	6q14.1	2008-02-05	2006-03-28		ENSG00000156535	ENSG00000156535		"""CD molecules"""	21685	protein-coding gene	gene with protein product		608859	"""CD109 antigen (Gov platelet alloantigens)"""			11861284, 11861285	Standard	XM_005248659		Approved	FLJ38569, DKFZp762L1111, CPAMD7	uc003php.3	Q6YHK3	OTTHUMG00000015040	ENST00000287097.5:c.2755T>C	chr6.hg19:g.74502402T>C	ENSP00000287097:p.Tyr919His	106.0	0.0		99.0	4.0	NM_133493	A5YKK4|B2R948|B3KW25|Q0P6K7|Q5SYA8|Q5XUM7|Q5XUM9|Q6MZI7|Q8N3A7|Q8N915|Q8TDJ2|Q8TDJ3	Missense_Mutation	SNP	ENST00000287097.5	hg19	CCDS4982.1	.	.	.	.	.	.	.	.	.	.	T	16.65	3.182865	0.57800	.	.	ENSG00000156535	ENST00000437994;ENST00000422508;ENST00000287097	T;T;T	0.54675	0.56;0.56;0.56	5.87	3.49	0.39957	Terpenoid cylases/protein prenyltransferase alpha-alpha toroid (1);Alpha-2-macroglobulin, thiol-ester bond-forming (1);Alpha-2-macroglobulin, conserved site (1);	0.280178	0.36034	N	0.002822	T	0.34832	0.0911	L	0.56280	1.765	0.38385	D	0.945239	B;P;P	0.45569	0.313;0.861;0.607	B;B;B	0.42738	0.14;0.396;0.385	T	0.29792	-1.0000	10	0.87932	D	0	.	10.4107	0.44291	0.0:0.1319:0.0:0.8681	.	842;919;919	Q6YHK3-2;Q6YHK3-4;Q6YHK3	.;.;CD109_HUMAN	H	919;842;919	ENSP00000388062:Y919H;ENSP00000404475:Y842H;ENSP00000287097:Y919H	ENSP00000287097:Y919H	Y	+	1	0	CD109	74559123	1.000000	0.71417	0.997000	0.53966	0.997000	0.91878	3.388000	0.52509	0.569000	0.29329	0.533000	0.62120	TAT	.	.		0.358	CD109-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041230.3	NM_133493	
IBTK	25998	hgsc.bcm.edu	37	6	82910419	82910419	+	Missense_Mutation	SNP	C	C	T			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:82910419C>T	ENST00000306270.7	-	20	3346	c.2797G>A	c.(2797-2799)Gca>Aca	p.A933T	IBTK_ENST00000510291.1_Missense_Mutation_p.A933T|IBTK_ENST00000503631.1_Missense_Mutation_p.A732T	NM_015525.2	NP_056340.2	Q9P2D0	IBTK_HUMAN	inhibitor of Bruton agammaglobulinemia tyrosine kinase	933					negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein tyrosine kinase activity (GO:0061099)|release of sequestered calcium ion into cytosol (GO:0051209)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|protein tyrosine kinase inhibitor activity (GO:0030292)			central_nervous_system(2)|endometrium(9)|kidney(3)|large_intestine(10)|lung(19)|ovary(3)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	54		all_cancers(76;3.38e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.0037)		BRCA - Breast invasive adenocarcinoma(397;0.0901)		CTATCCATTGCTGGAATCTGC	0.308																																					p.A933T		Atlas-SNP	.											.	IBTK	128	.	0			c.G2797A						.						75.0	72.0	73.0					6																	82910419		2203	4300	6503	SO:0001583	missense	25998	exon20			CCATTGCTGGAAT	AF235049	CCDS34490.1, CCDS75486.1	6q14.3	2013-01-10	2003-10-06	2003-10-08	ENSG00000005700	ENSG00000005700		"""BTB/POZ domain containing"", ""Ankyrin repeat domain containing"""	17853	protein-coding gene	gene with protein product		606457	"""Bruton agammaglobulinemia tyrosine kinase inhibitor"""	BTKI		11577348	Standard	XM_006715453		Approved	DKFZP564B116, BTBD26	uc003pjl.1	Q9P2D0	OTTHUMG00000015102	ENST00000306270.7:c.2797G>A	chr6.hg19:g.82910419C>T	ENSP00000305721:p.Ala933Thr	157.0	0.0		100.0	4.0	NM_015525	Q2QKU2|Q2QKU3|Q2QKU4|Q5TFD7|Q5TFD9|Q8IUQ9|Q8IUY7|Q8TAI4|Q9HBI8|Q9Y3T8	Missense_Mutation	SNP	ENST00000306270.7	hg19	CCDS34490.1	.	.	.	.	.	.	.	.	.	.	C	16.26	3.072175	0.55646	.	.	ENSG00000005700	ENST00000306270;ENST00000503631;ENST00000510291	T;T;T	0.33216	1.8;1.42;1.8	5.83	5.83	0.93111	.	0.105207	0.64402	D	0.000004	T	0.24928	0.0605	M	0.64997	1.995	0.53005	D	0.999963	B;B;P;P	0.44521	0.13;0.349;0.837;0.54	B;B;P;B	0.46172	0.139;0.159;0.506;0.21	T	0.02398	-1.1165	10	0.15066	T	0.55	-10.9631	15.5776	0.76404	0.0:0.8629:0.1371:0.0	.	732;933;933;933	E9PDR5;E7EPI0;Q9P2D0-2;Q9P2D0	.;.;.;IBTK_HUMAN	T	933;732;933	ENSP00000305721:A933T;ENSP00000422762:A732T;ENSP00000426405:A933T	ENSP00000305721:A933T	A	-	1	0	IBTK	82967138	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.013000	0.64023	2.741000	0.93983	0.655000	0.94253	GCA	.	.		0.308	IBTK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041337.2	NM_015525	
DOPEY1	23033	hgsc.bcm.edu	37	6	83839069	83839069	+	Missense_Mutation	SNP	A	A	G	rs370284003		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:83839069A>G	ENST00000349129.2	+	16	2443	c.2183A>G	c.(2182-2184)gAt>gGt	p.D728G	DOPEY1_ENST00000237163.5_Missense_Mutation_p.D709G|DOPEY1_ENST00000369739.3_Missense_Mutation_p.D719G	NM_015018.3	NP_055833.2	Q5JWR5	DOP1_HUMAN	dopey family member 1	728					protein transport (GO:0015031)					breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(16)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	67		all_cancers(76;2.29e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.00203)		BRCA - Breast invasive adenocarcinoma(397;0.053)		TCACAAGGAGATGTAAAAGAG	0.403																																					p.D728G		Atlas-SNP	.											.	DOPEY1	190	.	0			c.A2183G						.	A	GLY/ASP,GLY/ASP	0,4406		0,0,2203	79.0	77.0	77.0		2183,2156	4.5	1.0	6		77	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	DOPEY1	NM_015018.3,NM_001199942.1	94,94	0,1,6502	GG,GA,AA		0.0116,0.0,0.0077	benign,benign	728/2466,719/2477	83839069	1,13005	2203	4300	6503	SO:0001583	missense	23033	exon16			AAGGAGATGTAAA	AK027030	CCDS4996.1, CCDS64467.1	6q15	2013-03-05	2006-02-02	2006-02-02	ENSG00000083097	ENSG00000083097			21194	protein-coding gene	gene with protein product			"""KIAA1117"""	KIAA1117		16301316, 16303751, 10931277	Standard	NM_015018		Approved	dJ202D23.2	uc011dyy.2	Q5JWR5	OTTHUMG00000016365	ENST00000349129.2:c.2183A>G	chr6.hg19:g.83839069A>G	ENSP00000195654:p.Asp728Gly	168.0	0.0		121.0	5.0	NM_015018	Q86XV1|Q9H5J5|Q9NSL4|Q9UPN5|Q9Y414	Missense_Mutation	SNP	ENST00000349129.2	hg19	CCDS4996.1	.	.	.	.	.	.	.	.	.	.	A	12.99	2.103880	0.37145	0.0	1.16E-4	ENSG00000083097	ENST00000349129;ENST00000237163;ENST00000369739	T;T	0.23950	1.88;1.88	5.68	4.52	0.55395	.	0.247012	0.39083	N	0.001461	T	0.08891	0.0220	L	0.39633	1.23	0.80722	D	1	B;B;B	0.14012	0.009;0.003;0.0	B;B;B	0.10450	0.005;0.003;0.002	T	0.08868	-1.0701	10	0.18710	T	0.47	.	11.7905	0.52068	0.9311:0.0:0.0689:0.0	.	619;719;728	E1P545;B2RWN9;Q5JWR5	.;.;DOP1_HUMAN	G	728;709;709	ENSP00000195654:D728G;ENSP00000237163:D709G	ENSP00000237163:D709G	D	+	2	0	DOPEY1	83895788	1.000000	0.71417	1.000000	0.80357	0.909000	0.53808	3.138000	0.50570	0.972000	0.38314	0.528000	0.53228	GAT	.	.		0.403	DOPEY1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043785.2	NM_015018	
CEP162	22832	hgsc.bcm.edu	37	6	84930848	84930848	+	Silent	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:84930848T>C	ENST00000403245.3	-	3	213	c.99A>G	c.(97-99)agA>agG	p.R33R	KIAA1009_ENST00000257766.4_5'UTR	NM_014895.2	NP_055710.2														breast(2)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(17)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	43		all_cancers(76;1.5e-06)|Acute lymphoblastic leukemia(125;2.69e-07)|all_hematologic(105;0.000151)|all_epithelial(107;0.00258)		BRCA - Breast invasive adenocarcinoma(397;0.089)		TTTTAGATTGTCTAGCTGTTT	0.294																																					p.R33R		Atlas-SNP	.											.	KIAA1009	119	.	0			c.A99G						.						189.0	176.0	180.0					6																	84930848		1814	4074	5888	SO:0001819	synonymous_variant	22832	exon3			AGATTGTCTAGCT																												ENST00000403245.3:c.99A>G	chr6.hg19:g.84930848T>C		178.0	0.0		115.0	5.0	NM_014895		Silent	SNP	ENST00000403245.3	hg19	CCDS34494.2																																																																																			.	.		0.294	KIAA1009-004	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317315.1		
SNX14	57231	hgsc.bcm.edu	37	6	86259455	86259455	+	Silent	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:86259455T>C	ENST00000314673.3	-	8	953	c.777A>G	c.(775-777)aaA>aaG	p.K259K	SNX14_ENST00000369627.2_Silent_p.K259K|SNX14_ENST00000513865.1_Silent_p.K259K|SNX14_ENST00000508980.1_5'UTR|SNX14_ENST00000505648.1_Silent_p.K207K|SNX14_ENST00000346348.3_Silent_p.K215K	NM_153816.3	NP_722523.1	Q9Y5W7	SNX14_HUMAN	sorting nexin 14	259	PXA. {ECO:0000255|PROSITE- ProRule:PRU00147, ECO:0000255|PROSITE- ProRule:PRU00553}.				protein transport (GO:0015031)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	integral component of membrane (GO:0016021)	phosphatidylinositol binding (GO:0035091)			NS(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(11)|skin(1)	22		all_cancers(76;4.83e-07)|Acute lymphoblastic leukemia(125;3.3e-08)|Prostate(29;2.55e-07)|all_hematologic(105;3.66e-05)|all_epithelial(107;0.000695)|Lung NSC(302;0.197)|all_lung(197;0.24)		BRCA - Breast invasive adenocarcinoma(108;0.0423)		AGTCTGTTGCTTTAGGAGGCA	0.338																																					p.K259K		Atlas-SNP	.											.	SNX14	58	.	0			c.A777G						.						67.0	69.0	69.0					6																	86259455		2203	4299	6502	SO:0001819	synonymous_variant	57231	exon8			TGTTGCTTTAGGA	AF121863	CCDS5003.1, CCDS5004.1, CCDS75490.1	6q15	2008-10-22			ENSG00000135317	ENSG00000135317		"""Sorting nexins"""	14977	protein-coding gene	gene with protein product						11485546, 11736640	Standard	XM_005248738		Approved	RGS-PX2	uc003pkr.3	Q9Y5W7	OTTHUMG00000015140	ENST00000314673.3:c.777A>G	chr6.hg19:g.86259455T>C		94.0	0.0		73.0	4.0	NM_153816	B4DI55|Q4VBR3|Q5TCF9|Q5TCG0|Q6NUI7|Q6PI37|Q9BSD1	Silent	SNP	ENST00000314673.3	hg19	CCDS5004.1																																																																																			.	.		0.338	SNX14-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041393.2	NM_153816	
ZNF292	23036	hgsc.bcm.edu	37	6	87970226	87970226	+	Silent	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:87970226A>G	ENST00000369577.3	+	8	6922	c.6879A>G	c.(6877-6879)agA>agG	p.R2293R	ZNF292_ENST00000339907.4_Silent_p.R2288R	NM_015021.1	NP_055836.1	O60281	ZN292_HUMAN	zinc finger protein 292	2293						nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(27)|lung(21)|ovary(4)|prostate(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	89		all_cancers(76;3.82e-09)|Prostate(29;1.34e-10)|Acute lymphoblastic leukemia(125;2.17e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;5.31e-05)		BRCA - Breast invasive adenocarcinoma(108;0.0199)		TTCGTCCAAGAAGATTAACAC	0.428																																					p.R2293R		Atlas-SNP	.											.	ZNF292	479	.	0			c.A6879G						.						53.0	52.0	52.0					6																	87970226		1855	4097	5952	SO:0001819	synonymous_variant	23036	exon8			TCCAAGAAGATTA	AB011102	CCDS47457.1	6q15	2008-10-23			ENSG00000188994	ENSG00000188994		"""Zinc fingers, C2H2-type"""	18410	protein-coding gene	gene with protein product						9628581	Standard	NM_015021		Approved	KIAA0530, ZFP292, bA393I2.3, Zn-15, Zn-16	uc003plm.4	O60281	OTTHUMG00000015164	ENST00000369577.3:c.6879A>G	chr6.hg19:g.87970226A>G		99.0	0.0		85.0	4.0	NM_015021	Q5W0B2|Q7Z3L7|Q9H8G3|Q9H8J4	Silent	SNP	ENST00000369577.3	hg19	CCDS47457.1																																																																																			.	.		0.428	ZNF292-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000376192.2	NM_015021	
FBXL4	26235	hgsc.bcm.edu	37	6	99328458	99328458	+	Missense_Mutation	SNP	G	G	T			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:99328458G>T	ENST00000369244.2	-	8	1788	c.1360C>A	c.(1360-1362)Cag>Aag	p.Q454K	FBXL4_ENST00000229971.1_Missense_Mutation_p.Q454K	NM_001278716.1	NP_001265645.1	Q9UKA2	FBXL4_HUMAN	F-box and leucine-rich repeat protein 4	454					ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrial intermembrane space (GO:0005758)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)				central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(4)|prostate(3)|skin(2)	18		all_cancers(76;1.56e-06)|Acute lymphoblastic leukemia(125;4.93e-10)|all_hematologic(75;3.55e-07)|all_epithelial(107;0.00893)|Colorectal(196;0.069)|Lung NSC(302;0.197)		BRCA - Breast invasive adenocarcinoma(108;0.0413)		CTGAGGTGCTGAAGCTCTGAA	0.393																																					p.Q454K		Atlas-SNP	.											.	FBXL4	54	.	0			c.C1360A						.						109.0	92.0	98.0					6																	99328458		2203	4300	6503	SO:0001583	missense	26235	exon7			GGTGCTGAAGCTC	AF176699	CCDS5041.1	6q16.1-q16.3	2011-06-09			ENSG00000112234	ENSG00000112234		"""F-boxes / Leucine-rich repeats"""	13601	protein-coding gene	gene with protein product		605654				10531035	Standard	NM_012160		Approved	FBL4, FBL5	uc003ppf.1	Q9UKA2	OTTHUMG00000015259	ENST00000369244.2:c.1360C>A	chr6.hg19:g.99328458G>T	ENSP00000358247:p.Gln454Lys	78.0	0.0		76.0	29.0	NM_012160	B2R7Q5|E1P530|O95919|Q5BJH0|Q9UJU0	Missense_Mutation	SNP	ENST00000369244.2	hg19	CCDS5041.1	.	.	.	.	.	.	.	.	.	.	G	8.948	0.967438	0.18659	.	.	ENSG00000112234	ENST00000369244;ENST00000229971	T;T	0.17213	2.29;2.29	5.58	5.58	0.84498	.	0.104710	0.64402	D	0.000003	T	0.05181	0.0138	L	0.28192	0.835	0.45607	D	0.998547	B	0.06786	0.001	B	0.08055	0.003	T	0.27571	-1.0070	10	0.16896	T	0.51	.	12.8495	0.57850	0.0744:0.0:0.9256:0.0	.	454	Q9UKA2	FBXL4_HUMAN	K	454	ENSP00000358247:Q454K;ENSP00000229971:Q454K	ENSP00000229971:Q454K	Q	-	1	0	FBXL4	99435179	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.673000	0.61604	2.650000	0.89964	0.591000	0.81541	CAG	.	.		0.393	FBXL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041587.2		
AIM1	202	hgsc.bcm.edu	37	6	106967099	106967099	+	Silent	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:106967099T>C	ENST00000369066.3	+	2	1279	c.792T>C	c.(790-792)gtT>gtC	p.V264V		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)		GCCAGCCAGTTCACAAAGGCA	0.448																																					p.V264V		Atlas-SNP	.											.	AIM1	161	.	0			c.T792C						.						58.0	56.0	57.0					6																	106967099		2203	4300	6503	SO:0001819	synonymous_variant	202	exon2			GCCAGTTCACAAA	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.792T>C	chr6.hg19:g.106967099T>C		62.0	0.0		57.0	4.0	NM_001624	Q6P2P0|Q9BTM3	Silent	SNP	ENST00000369066.3	hg19	CCDS34506.1																																																																																			.	.		0.448	AIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041669.1		
TUBE1	51175	hgsc.bcm.edu	37	6	112397152	112397152	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:112397152A>G	ENST00000368662.5	-	8	878	c.800T>C	c.(799-801)cTc>cCc	p.L267P	TUBE1_ENST00000604814.1_5'UTR	NM_016262.4	NP_057346.1	Q9UJT0	TBE_HUMAN	tubulin, epsilon 1	267					centrosome cycle (GO:0007098)|protein polymerization (GO:0051258)	microtubule (GO:0005874)|pericentriolar material (GO:0000242)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			cervix(1)|endometrium(2)|large_intestine(5)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	12		all_cancers(87;0.0101)|all_hematologic(75;0.000258)|Colorectal(196;0.0466)|all_epithelial(87;0.1)		all cancers(137;0.0217)|OV - Ovarian serous cystadenocarcinoma(136;0.0613)|Epithelial(106;0.0636)|GBM - Glioblastoma multiforme(226;0.0972)|BRCA - Breast invasive adenocarcinoma(108;0.246)	Vinblastine(DB00570)	CGTTAGGTTGAGGAGCAAATT	0.348																																					p.L267P		Atlas-SNP	.											.	TUBE1	49	.	0			c.T800C						.						111.0	117.0	115.0					6																	112397152		2203	4300	6503	SO:0001583	missense	51175	exon8			AGGTTGAGGAGCA	AF201334	CCDS5100.1	6q21	2005-11-03			ENSG00000074935	ENSG00000074935		"""Tubulins"""	20775	protein-coding gene	gene with protein product		607345				10620804	Standard	NM_016262		Approved	dJ142L7.2, FLJ22589, TUBE	uc003pvq.3	Q9UJT0	OTTHUMG00000015382	ENST00000368662.5:c.800T>C	chr6.hg19:g.112397152A>G	ENSP00000357651:p.Leu267Pro	163.0	0.0		122.0	5.0	NM_016262	Q5H8W8|Q8NEG3	Missense_Mutation	SNP	ENST00000368662.5	hg19	CCDS5100.1	.	.	.	.	.	.	.	.	.	.	A	21.8	4.198864	0.79015	.	.	ENSG00000074935	ENST00000368662	T	0.68903	-0.36	5.7	5.7	0.88788	Tubulin/FtsZ, GTPase domain (3);	0.000000	0.85682	D	0.000000	T	0.74520	0.3727	L	0.56396	1.775	0.80722	D	1	D	0.89917	1.0	D	0.77557	0.99	T	0.77859	-0.2431	10	0.66056	D	0.02	.	15.9692	0.79998	1.0:0.0:0.0:0.0	.	267	Q9UJT0	TBE_HUMAN	P	267	ENSP00000357651:L267P	ENSP00000357651:L267P	L	-	2	0	TUBE1	112503845	1.000000	0.71417	0.996000	0.52242	0.987000	0.75469	8.968000	0.93407	2.162000	0.67917	0.528000	0.53228	CTC	.	.		0.348	TUBE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041867.1	NM_016262	
HINT3	135114	hgsc.bcm.edu	37	6	126288056	126288056	+	Silent	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:126288056A>G	ENST00000229633.5	+	2	422	c.225A>G	c.(223-225)aaA>aaG	p.K75K		NM_138571.4	NP_612638.3	Q9NQE9	HINT3_HUMAN	histidine triad nucleotide binding protein 3	75	HIT. {ECO:0000255|PROSITE- ProRule:PRU00464}.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)	hydrolase activity (GO:0016787)|nucleotide binding (GO:0000166)			endometrium(1)|large_intestine(1)|lung(1)|stomach(1)	4				UCEC - Uterine corpus endometrioid carcinoma (4;0.153)|GBM - Glioblastoma multiforme(226;0.0321)		TTTGCTTCAAAGATATCAAAC	0.333																																					p.K75K		Atlas-SNP	.											.	HINT3	14	.	0			c.A225G						.						106.0	100.0	102.0					6																	126288056		2203	4300	6503	SO:0001819	synonymous_variant	135114	exon2			CTTCAAAGATATC	AK057688	CCDS5133.1	6q22.33	2007-12-04			ENSG00000111911	ENSG00000111911			18468	protein-coding gene	gene with protein product		609998				11805111	Standard	NM_138571		Approved	FLJ33126	uc003qal.4	Q9NQE9	OTTHUMG00000015514	ENST00000229633.5:c.225A>G	chr6.hg19:g.126288056A>G		97.0	0.0		70.0	4.0	NM_138571	B3KQ91|Q8N0Y9	Silent	SNP	ENST00000229633.5	hg19	CCDS5133.1																																																																																			.	.		0.333	HINT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042090.1	NM_138571	
LAMA2	3908	hgsc.bcm.edu	37	6	129636958	129636958	+	Nonsense_Mutation	SNP	G	G	T			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:129636958G>T	ENST00000421865.2	+	26	3836	c.3787G>T	c.(3787-3789)Gaa>Taa	p.E1263*		NM_000426.3|NM_001079823.1	NP_000417|NP_001073291.1	P24043	LAMA2_HUMAN	laminin, alpha 2	1263	Laminin IV type A 2. {ECO:0000255|PROSITE-ProRule:PRU00458}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|myelination in peripheral nervous system (GO:0022011)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|sarcolemma (GO:0042383)	structural molecule activity (GO:0005198)			NS(2)|biliary_tract(2)|breast(10)|central_nervous_system(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(35)|lung(84)|ovary(10)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(2)	194				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)		CGAGGCTCGGGAAGAAACAGG	0.418																																					p.E1263X		Atlas-SNP	.											LAMA2,right_upper_lobe,carcinoma,0,1	LAMA2	481	.	0			c.G3787T						.						109.0	110.0	109.0					6																	129636958		2203	4300	6503	SO:0001587	stop_gained	3908	exon26			GCTCGGGAAGAAA	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.3787G>T	chr6.hg19:g.129636958G>T	ENSP00000400365:p.Glu1263*	70.0	0.0		69.0	30.0	NM_000426	Q14736|Q5VUM2|Q93022	Nonsense_Mutation	SNP	ENST00000421865.2	hg19	CCDS5138.1	.	.	.	.	.	.	.	.	.	.	G	44	10.630437	0.99440	.	.	ENSG00000196569	ENST00000358023;ENST00000354729;ENST00000421865	.	.	.	5.55	5.55	0.83447	.	0.178129	0.49305	D	0.000142	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.22109	T	0.4	.	19.8741	0.96863	0.0:0.0:1.0:0.0	.	.	.	.	X	1263	.	ENSP00000346769:E1263X	E	+	1	0	LAMA2	129678651	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	9.416000	0.97383	2.761000	0.94854	0.655000	0.94253	GAA	.	.		0.418	LAMA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042180.1		
ENPP3	5169	hgsc.bcm.edu	37	6	132061522	132061522	+	Splice_Site	SNP	T	T	A			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:132061522T>A	ENST00000414305.1	+	25	2785		c.e25+2		ENPP3_ENST00000358229.5_Splice_Site|ENPP3_ENST00000357639.3_Splice_Site			O14638	ENPP3_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase 3						immune response (GO:0006955)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleoside triphosphate catabolic process (GO:0009143)|phosphate-containing compound metabolic process (GO:0006796)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)	metal ion binding (GO:0046872)|NADH pyrophosphatase activity (GO:0035529)|nucleic acid binding (GO:0003676)|nucleoside-triphosphate diphosphatase activity (GO:0047429)|nucleotide diphosphatase activity (GO:0004551)|phosphodiesterase I activity (GO:0004528)|polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(1)|breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(5)|lung(24)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	53	Breast(56;0.0753)			GBM - Glioblastoma multiforme(226;0.0252)|OV - Ovarian serous cystadenocarcinoma(155;0.0511)		AGCTGTCCTGTGAGTATGCTT	0.478																																					.		Atlas-SNP	.											.	ENPP3	117	.	0			c.2457+2T>A						.						97.0	88.0	91.0					6																	132061522		2203	4300	6503	SO:0001630	splice_region_variant	5169	exon24			GTCCTGTGAGTAT	AF005632	CCDS5148.1	6q22	2010-06-23			ENSG00000154269	ENSG00000154269	3.1.4.1, 3.6.1.9	"""CD molecules"""	3358	protein-coding gene	gene with protein product		602182		PDNP3		9344668	Standard	NM_005021		Approved	PD-IBETA, gp130RB13-6, B10, CD203c	uc003qcv.3	O14638	OTTHUMG00000016292	ENST00000414305.1:c.2457+2T>A	chr6.hg19:g.132061522T>A		145.0	0.0		83.0	4.0	NM_005021	Q5JTL3	Splice_Site	SNP	ENST00000414305.1	hg19	CCDS5148.1	.	.	.	.	.	.	.	.	.	.	T	25.9	4.687161	0.88639	.	.	ENSG00000154269	ENST00000414305;ENST00000357639	.	.	.	5.72	5.72	0.89469	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.2988	0.82793	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	ENPP3	132103215	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.337000	0.72958	2.311000	0.77944	0.533000	0.62120	.	.	.		0.478	ENPP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043627.2		Intron
MYB	4602	hgsc.bcm.edu	37	6	135518299	135518299	+	Intron	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:135518299T>C	ENST00000367814.4	+	9	1389				MYB_ENST00000527615.1_Intron|MYB_ENST00000531845.1_Intron|MYB_ENST00000533624.1_Intron|MYB_ENST00000528774.1_Silent_p.P465P|MYB_ENST00000525369.1_Intron|MYB-AS1_ENST00000455534.1_RNA|MYB_ENST00000442647.2_Intron|MYB_ENST00000341911.5_Silent_p.P468P|MYB_ENST00000534044.1_Intron|MYB_ENST00000534121.1_Silent_p.P452P|MYB_ENST00000316528.8_Intron	NM_001161659.1|NM_005375.2	NP_001155131.1|NP_005366.2	P10242	MYB_HUMAN	v-myb avian myeloblastosis viral oncogene homolog						B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|chromatin remodeling (GO:0006338)|embryonic digestive tract development (GO:0048566)|G1/S transition of mitotic cell cycle (GO:0000082)|homeostasis of number of cells (GO:0048872)|in utero embryonic development (GO:0001701)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of histone H3-K9 methylation (GO:0051574)|positive regulation of T-helper cell differentiation (GO:0045624)|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)|thymus development (GO:0048538)	nuclear matrix (GO:0016363)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(4)|endometrium(1)|kidney(2)|large_intestine(3)|lung(13)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	28	all_epithelial(2;0.109)|Breast(56;0.158)|Colorectal(23;0.221)	Lung NSC(302;3.08e-05)|Ovarian(999;0.208)		OV - Ovarian serous cystadenocarcinoma(155;0.0079)|GBM - Glioblastoma multiforme(68;0.0117)		AGGTCTTACCTCCTGCAAGGC	0.517			T	NFIB	adenoid cystic carcinoma																																p.P468P		Atlas-SNP	.		Dom	yes		6	6q22-23	4602	v-myb myeloblastosis viral oncogene homolog		E	.	MYB	137	.	0			c.T1404C						.						126.0	111.0	116.0					6																	135518299		1568	3582	5150	SO:0001627	intron_variant	4602	exon10			CTTACCTCCTGCA		CCDS5174.1, CCDS47481.1, CCDS47482.1, CCDS55058.1, CCDS55059.1, CCDS55060.1, CCDS55061.1, CCDS55062.1	6q22-q23	2013-07-09	2013-07-09		ENSG00000118513	ENSG00000118513			7545	protein-coding gene	gene with protein product		189990				17599807	Standard	NM_001130172		Approved	c-myb	uc003qfh.3	P10242	OTTHUMG00000015629	ENST00000367814.4:c.1203+1159T>C	chr6.hg19:g.135518299T>C		170.0	0.0		99.0	6.0	NM_001130173	E9PI07|E9PLZ5|E9PNA4|E9PNL6|E9PRS2|P78391|P78392|P78525|P78526|Q14023|Q14024|Q708E4|Q708E7|Q9UE83	Silent	SNP	ENST00000367814.4	hg19	CCDS5174.1																																																																																			.	.		0.517	MYB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042347.4		
TNFAIP3	7128	hgsc.bcm.edu	37	6	138200242	138200242	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:138200242A>G	ENST00000237289.4	+	7	1726	c.1660A>G	c.(1660-1662)Agc>Ggc	p.S554G		NM_001270507.1|NM_001270508.1|NM_006290.3	NP_001257436.1|NP_001257437.1|NP_006281.1	P21580	TNAP3_HUMAN	tumor necrosis factor, alpha-induced protein 3	554	Interaction with TNIP1. {ECO:0000250}.				apoptotic process (GO:0006915)|B-1 B cell homeostasis (GO:0001922)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to lipopolysaccharide (GO:0071222)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of B cell activation (GO:0050869)|negative regulation of bone resorption (GO:0045779)|negative regulation of CD40 signaling pathway (GO:2000349)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|negative regulation of innate immune response (GO:0045824)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of osteoclast proliferation (GO:0090291)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of smooth muscle cell proliferation (GO:0048662)|negative regulation of toll-like receptor 2 signaling pathway (GO:0034136)|negative regulation of toll-like receptor 3 signaling pathway (GO:0034140)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)|negative regulation of tumor necrosis factor production (GO:0032720)|negative regulation of type I interferon production (GO:0032480)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of protein catabolic process (GO:0045732)|protein deubiquitination (GO:0016579)|protein K11-linked deubiquitination (GO:0035871)|protein K48-linked deubiquitination (GO:0071108)|protein K48-linked ubiquitination (GO:0070936)|protein K63-linked deubiquitination (GO:0070536)|protein oligomerization (GO:0051259)|regulation of defense response to virus by host (GO:0050691)|regulation of germinal center formation (GO:0002634)|regulation of vascular wound healing (GO:0061043)|response to molecule of bacterial origin (GO:0002237)|tolerance induction to lipopolysaccharide (GO:0072573)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|protease binding (GO:0002020)|protein self-association (GO:0043621)|ubiquitin binding (GO:0043130)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-protein transferase activity (GO:0004842)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)	p.0?(25)		breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(196)|kidney(1)|large_intestine(4)|lung(13)|ovary(4)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	225	Breast(32;0.135)|Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000849)|OV - Ovarian serous cystadenocarcinoma(155;0.00468)		CCTCAGCACCAGCCTCCCTCC	0.597			"""D, N, F"""		"""marginal zone B-cell lymphomas, Hodgkin's lymphoma, primary mediastinal B cell lymphoma"""																																p.S554G	GBM(130;153 1739 22295 28918 47987)	Atlas-SNP	.		Rec	yes		6	6q23	7128	"""tumor necrosis factor, alpha-induced protein 3"""		L	.	TNFAIP3	340	.	25	Whole gene deletion(25)	haematopoietic_and_lymphoid_tissue(25)	c.A1660G						.						81.0	87.0	85.0					6																	138200242		2203	4300	6503	SO:0001583	missense	7128	exon7			AGCACCAGCCTCC	M59465	CCDS5187.1	6q23-q25	2013-01-21			ENSG00000118503	ENSG00000118503		"""OTU domain containing"""	11896	protein-coding gene	gene with protein product		191163				2118515	Standard	NM_006290		Approved	A20, OTUD7C	uc031spw.1	P21580	OTTHUMG00000015664	ENST00000237289.4:c.1660A>G	chr6.hg19:g.138200242A>G	ENSP00000237289:p.Ser554Gly	112.0	0.0		81.0	5.0	NM_001270507	B2R767|E1P588|Q2HIX9|Q5VXQ7|Q9NSR6	Missense_Mutation	SNP	ENST00000237289.4	hg19	CCDS5187.1	.	.	.	.	.	.	.	.	.	.	A	3.758	-0.050162	0.07407	.	.	ENSG00000118503	ENST00000237289;ENST00000535574;ENST00000544646	T	0.22945	1.93	5.73	-0.857	0.10693	.	0.615493	0.17661	N	0.166309	T	0.05960	0.0155	L	0.27053	0.805	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.35748	-0.9776	10	0.41790	T	0.15	-2.6623	10.9605	0.47383	0.5957:0.0:0.4043:0.0	.	554	P21580	TNAP3_HUMAN	G	554	ENSP00000237289:S554G	ENSP00000237289:S554G	S	+	1	0	TNFAIP3	138241935	0.118000	0.22208	0.000000	0.03702	0.008000	0.06430	0.670000	0.25157	-0.362000	0.08113	-0.441000	0.05720	AGC	.	.		0.597	TNFAIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042414.1		
KIAA1244	57221	hgsc.bcm.edu	37	6	138584101	138584101	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:138584101A>G	ENST00000251691.4	+	12	1647	c.1481A>G	c.(1480-1482)gAg>gGg	p.E494G		NM_020340.4	NP_065073.3			KIAA1244											NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(11)|lung(17)|ovary(2)|skin(2)	44	Breast(32;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00102)|GBM - Glioblastoma multiforme(68;0.00259)		ACGCCGTGGGAGTCAGGGAAC	0.592																																					p.E494G		Atlas-SNP	.											.	KIAA1244	236	.	0			c.A1481G						.						51.0	39.0	44.0					6																	138584101		2203	4299	6502	SO:0001583	missense	57221	exon12			CGTGGGAGTCAGG	AB033070	CCDS5189.2	6q23.3	2012-04-17			ENSG00000112379	ENSG00000112379		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	21213	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 33"""		"""chromosome 6 open reading frame 92"""	C6orf92			Standard	NM_020340		Approved	dJ171N11.1, BIG3, PPP1R33	uc003qhu.3	Q5TH69	OTTHUMG00000015670	ENST00000251691.4:c.1481A>G	chr6.hg19:g.138584101A>G	ENSP00000251691:p.Glu494Gly	127.0	0.0		63.0	4.0	NM_020340		Missense_Mutation	SNP	ENST00000251691.4	hg19	CCDS5189.2	.	.	.	.	.	.	.	.	.	.	A	14.44	2.537338	0.45176	.	.	ENSG00000112379	ENST00000251691	T	0.21734	1.99	5.52	4.36	0.52297	.	0.693905	0.13313	N	0.397288	T	0.07458	0.0188	L	0.27053	0.805	0.41433	D	0.98787	B	0.12013	0.005	B	0.11329	0.006	T	0.06023	-1.0850	10	0.72032	D	0.01	-30.105	11.088	0.48099	0.9276:0.0:0.0724:0.0	.	494	Q5TH69	BIG3_HUMAN	G	494	ENSP00000251691:E494G	ENSP00000251691:E494G	E	+	2	0	KIAA1244	138625794	1.000000	0.71417	0.992000	0.48379	0.826000	0.46750	5.935000	0.70145	0.927000	0.37143	0.533000	0.62120	GAG	.	.		0.592	KIAA1244-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042425.4	NM_020340	
ECT2L	345930	hgsc.bcm.edu	37	6	139159510	139159510	+	Silent	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:139159510A>G	ENST00000423192.1	+	4	362	c.201A>G	c.(199-201)tcA>tcG	p.S67S	ECT2L_ENST00000367682.2_Silent_p.S67S|ECT2L_ENST00000541398.1_5'UTR			Q008S8	ECT2L_HUMAN	epithelial cell transforming 2 like	67							Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(7)|lung(12)|skin(1)|upper_aerodigestive_tract(1)	30						ACTGGTTTTCAGAAAGGATGC	0.348			"""N, Splice, Mis"""		ETP ALL																																p.S67S		Atlas-SNP	.		Rec	yes		6	6q24.1	345930	epithelial cell transforming sequence 2 oncogene-like		L	.	ECT2L	75	.	0			c.A201G						.						101.0	95.0	97.0					6																	139159510		1827	4085	5912	SO:0001819	synonymous_variant	345930	exon4			GTTTTCAGAAAGG		CCDS43508.1	6q24.1	2014-03-11	2014-03-11		ENSG00000203734	ENSG00000203734		"""Rho guanine nucleotide exchange factors"", ""F-boxes /  ""other"""""	21118	protein-coding gene	gene with protein product	"""lung specific F-box and DH domain containing protein"", ""F-box protein 49"""		"""chromosome 6 open reading frame 91"", ""epithelial cell transforming sequence 2 oncogene-like"""	C6orf91			Standard	NM_001077706		Approved	ARHGEF32, FBXO49, LFDH	uc021zfx.1	Q008S8	OTTHUMG00000015679	ENST00000423192.1:c.201A>G	chr6.hg19:g.139159510A>G		213.0	0.0		154.0	7.0	NM_001195037	B2RUV6|Q5JWK2|Q5JWK3|Q5JWK4	Silent	SNP	ENST00000423192.1	hg19	CCDS43508.1																																																																																			.	.		0.348	ECT2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042441.3	NM_001077706	
SHPRH	257218	hgsc.bcm.edu	37	6	146248366	146248366	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:146248366A>G	ENST00000367505.2	-	15	3424	c.3160T>C	c.(3160-3162)Tcg>Ccg	p.S1054P	SHPRH_ENST00000367503.3_Missense_Mutation_p.S1063P|SHPRH_ENST00000275233.7_Missense_Mutation_p.S1054P|SHPRH_ENST00000438092.2_Missense_Mutation_p.S1063P			Q149N8	SHPRH_HUMAN	SNF2 histone linker PHD RING helicase, E3 ubiquitin protein ligase	1054					DNA repair (GO:0006281)|nucleosome assembly (GO:0006334)|protein polyubiquitination (GO:0000209)	nucleosome (GO:0000786)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(33)|ovary(3)|pancreas(2)|prostate(7)|skin(1)|urinary_tract(1)	79		Ovarian(120;0.0365)		OV - Ovarian serous cystadenocarcinoma(155;1.47e-07)|GBM - Glioblastoma multiforme(68;0.0124)		TGTTCCTCCGAGGAGCGCAAC	0.338																																					p.S1063P		Atlas-SNP	.											.	SHPRH	169	.	0			c.T3187C						.						137.0	119.0	124.0					6																	146248366		1851	4096	5947	SO:0001583	missense	257218	exon15			CCTCCGAGGAGCG	AB095943	CCDS43513.1, CCDS47496.1, CCDS43513.2	6q24.2	2012-02-23	2012-02-23		ENSG00000146414	ENSG00000146414		"""RING-type (C3HC4) zinc fingers"""	19336	protein-coding gene	gene with protein product		608048	"""SNF2 histone linker PHD RING helicase"""			12837266	Standard	NM_001042683		Approved	FLJ90837, KIAA2023, bA545I5.2	uc003qlf.3	Q149N8	OTTHUMG00000015750	ENST00000367505.2:c.3160T>C	chr6.hg19:g.146248366A>G	ENSP00000356475:p.Ser1054Pro	153.0	0.0		118.0	10.0	NM_173082	Q149N9|Q5VV79|Q68DS5|Q7Z5J5|Q8IVE8|Q8IWQ9|Q8N1S8|Q8NBR7	Missense_Mutation	SNP	ENST00000367505.2	hg19	CCDS43513.2	.	.	.	.	.	.	.	.	.	.	A	24.4	4.522569	0.85600	.	.	ENSG00000146414	ENST00000367505;ENST00000367503;ENST00000438092;ENST00000275233	T;T;T;T	0.74842	-0.86;-0.88;-0.87;-0.86	5.55	5.55	0.83447	.	0.000000	0.64402	D	0.000001	T	0.81264	0.4786	M	0.64997	1.995	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.87578	0.996;0.998	T	0.82307	-0.0522	10	0.51188	T	0.08	-19.8107	15.9985	0.80270	1.0:0.0:0.0:0.0	.	1054;1063	Q149N8;Q149N8-4	SHPRH_HUMAN;.	P	1054;1063;1063;1054	ENSP00000356475:S1054P;ENSP00000356473:S1063P;ENSP00000412797:S1063P;ENSP00000275233:S1054P	ENSP00000275233:S1054P	S	-	1	0	SHPRH	146290059	1.000000	0.71417	0.992000	0.48379	0.928000	0.56348	8.933000	0.92911	2.233000	0.73108	0.455000	0.32223	TCG	.	.		0.338	SHPRH-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042571.2	NM_173082	
ADGB	79747	hgsc.bcm.edu	37	6	146987973	146987973	+	Silent	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:146987973A>G	ENST00000397944.3	+	7	850	c.774A>G	c.(772-774)agA>agG	p.R258R	ADGB_ENST00000367493.3_5'UTR	NM_024694.3	NP_078970.3	Q8N7X0	ADGB_HUMAN	androglobin	258	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.			Missing (in Ref. 1; AL832192). {ECO:0000305}.	oxygen transport (GO:0015671)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)			breast(1)|endometrium(2)|kidney(2)	5						CAGACAGGAGAGAGCTGGGGG	0.353																																					p.R258R		Atlas-SNP	.											.	ADGB	93	.	0			c.A774G						.						156.0	141.0	146.0					6																	146987973		692	1590	2282	SO:0001819	synonymous_variant	79747	exon7			CAGGAGAGAGCTG	AK026774		6q24.2	2012-02-03	2012-02-03	2012-02-03	ENSG00000118492	ENSG00000118492			21212	protein-coding gene	gene with protein product		614630	"""chromosome 6 open reading frame 103"""	C6orf103		22115833	Standard	NM_024694		Approved	FLJ23121, dJ408K24.1	uc010khx.3	Q8N7X0	OTTHUMG00000015758	ENST00000397944.3:c.774A>G	chr6.hg19:g.146987973A>G		135.0	0.0		92.0	7.0	NM_024694	Q5T402|Q5T904|Q5T905	Silent	SNP	ENST00000397944.3	hg19																																																																																				.	.		0.353	ADGB-009	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376350.2	NM_024694	
TIAM2	26230	hgsc.bcm.edu	37	6	155565153	155565153	+	Silent	SNP	C	C	T			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:155565153C>T	ENST00000461783.3	+	19	4630	c.3357C>T	c.(3355-3357)agC>agT	p.S1119S	TIAM2_ENST00000528391.2_Silent_p.S455S|TIAM2_ENST00000360366.4_Silent_p.S1143S|TIAM2_ENST00000275246.7_Silent_p.S44S|TIAM2_ENST00000318981.5_Silent_p.S1119S|TIAM2_ENST00000529824.2_Silent_p.S1119S|TIAM2_ENST00000367174.2_Silent_p.S495S|TIAM2_ENST00000456877.2_Silent_p.S431S|TIAM2_ENST00000456144.1_Silent_p.S1119S			Q8IVF5	TIAM2_HUMAN	T-cell lymphoma invasion and metastasis 2	1119	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|cellular lipid metabolic process (GO:0044255)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	cell projection (GO:0042995)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)|receptor signaling protein activity (GO:0005057)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(20)|lung(21)|ovary(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(4)	65		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;8.1e-13)|BRCA - Breast invasive adenocarcinoma(81;0.0053)		AGGATTTGAGCTGCCTCTTTG	0.433																																					p.S1119S		Atlas-SNP	.											.	TIAM2	161	.	0			c.C3357T						.						156.0	151.0	153.0					6																	155565153		2203	4300	6503	SO:0001819	synonymous_variant	26230	exon16			TTTGAGCTGCCTC		CCDS34558.1, CCDS34559.1	6q25	2013-01-10			ENSG00000146426	ENSG00000146426		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	11806	protein-coding gene	gene with protein product		604709				10512681	Standard	NM_012454		Approved	STEF	uc003qqe.3	Q8IVF5	OTTHUMG00000015880	ENST00000461783.3:c.3357C>T	chr6.hg19:g.155565153C>T		149.0	0.0		101.0	6.0	NM_012454	B2RP56|C9JZV2|Q6NXN9|Q6ZUP9|Q9UFG6|Q9UKV9|Q9UKW0	Silent	SNP	ENST00000461783.3	hg19	CCDS34558.1																																																																																			.	.		0.433	TIAM2-005	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000387980.2	NM_012454	
CLDN20	49861	hgsc.bcm.edu	37	6	155596902	155596902	+	Missense_Mutation	SNP	G	G	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:155596902G>C	ENST00000367165.3	+	2	429	c.49G>C	c.(49-51)Ggg>Cgg	p.G17R	TFB1M_ENST00000367166.4_Intron	NM_001001346.3	NP_001001346.1	P56880	CLD20_HUMAN	claudin 20	17					calcium-independent cell-cell adhesion (GO:0016338)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|tight junction assembly (GO:0070830)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)	p.G17R(1)		endometrium(1)|lung(2)	3				OV - Ovarian serous cystadenocarcinoma(155;7.82e-13)|BRCA - Breast invasive adenocarcinoma(81;0.0114)		GGCCTTATCTGGGGTCTCTGG	0.493																																					p.G17R		Atlas-SNP	.											CLDN20,NS,carcinoma,0,1	CLDN20	10	.	1	Substitution - Missense(1)	endometrium(1)	c.G49C						.						99.0	103.0	102.0					6																	155596902		2203	4300	6503	SO:0001583	missense	49861	exon2			TTATCTGGGGTCT	BC020838	CCDS5249.1	6q25	2008-08-01			ENSG00000171217	ENSG00000171217		"""Claudins"""	2042	protein-coding gene	gene with protein product						16836752	Standard	NM_001001346		Approved		uc003qql.2	P56880	OTTHUMG00000015882	ENST00000367165.3:c.49G>C	chr6.hg19:g.155596902G>C	ENSP00000356133:p.Gly17Arg	285.0	0.0		216.0	0.0	NM_001001346		Missense_Mutation	SNP	ENST00000367165.3	hg19	CCDS5249.1	.	.	.	.	.	.	.	.	.	.	G	29.4	5.001899	0.93227	.	.	ENSG00000171217	ENST00000367165	D	0.89681	-2.55	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	D	0.96476	0.8850	H	0.96547	3.84	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97406	0.9999	10	0.87932	D	0	.	19.451	0.94867	0.0:0.0:1.0:0.0	.	17	P56880	CLD20_HUMAN	R	17	ENSP00000356133:G17R	ENSP00000356133:G17R	G	+	1	0	CLDN20	155638594	1.000000	0.71417	0.942000	0.38095	0.906000	0.53458	9.624000	0.98398	2.593000	0.87608	0.655000	0.94253	GGG	.	.		0.493	CLDN20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042818.1	NM_001001346	
TFB1M	51106	hgsc.bcm.edu	37	6	155619614	155619614	+	Missense_Mutation	SNP	C	C	T			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:155619614C>T	ENST00000367166.4	-	3	446	c.391G>A	c.(391-393)Gat>Aat	p.D131N		NM_016020.3	NP_057104.2	Q8WVM0	TFB1M_HUMAN	transcription factor B1, mitochondrial	131					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	mitochondrial nucleoid (GO:0042645)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|rRNA (adenine-N6,N6-)-dimethyltransferase activity (GO:0000179)			lung(11)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;1.48e-12)|BRCA - Breast invasive adenocarcinoma(81;0.0131)		CACTCACCATCTTCCCAGGGT	0.318																																					p.D131N		Atlas-SNP	.											.	TFB1M	30	.	0			c.G391A						.						69.0	67.0	68.0					6																	155619614		2203	4300	6503	SO:0001583	missense	51106	exon3			CACCATCTTCCCA	AF151833	CCDS5248.1	6q25.1-q25.3	2011-01-28			ENSG00000029639	ENSG00000029639			17037	protein-coding gene	gene with protein product	"""dimethyladenosine transferase 1, mitochondrial"""	607033				10810093, 11809803	Standard	NM_016020		Approved	mtTFB, CGI-75	uc003qqj.4	Q8WVM0	OTTHUMG00000015881	ENST00000367166.4:c.391G>A	chr6.hg19:g.155619614C>T	ENSP00000356134:p.Asp131Asn	56.0	0.0		63.0	4.0	NM_016020	Q05DR0|Q9Y384	Missense_Mutation	SNP	ENST00000367166.4	hg19	CCDS5248.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.082067	0.76528	.	.	ENSG00000029639	ENST00000367166	T	0.36157	1.27	5.65	5.65	0.86999	Ribosomal RNA adenine methylase transferase, N-terminal (1);	0.094410	0.64402	D	0.000001	T	0.36580	0.0972	M	0.65975	2.015	0.58432	D	0.999998	P	0.37548	0.599	P	0.44673	0.457	T	0.06162	-1.0842	10	0.23302	T	0.38	.	20.0781	0.97751	0.0:1.0:0.0:0.0	.	131	Q8WVM0	TFB1M_HUMAN	N	131	ENSP00000356134:D131N	ENSP00000356134:D131N	D	-	1	0	TFB1M	155661306	1.000000	0.71417	1.000000	0.80357	0.803000	0.45373	5.415000	0.66411	2.817000	0.96982	0.563000	0.77884	GAT	.	.		0.318	TFB1M-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042809.1		
ARID1B	57492	hgsc.bcm.edu	37	6	157511264	157511264	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:157511264A>G	ENST00000350026.5	+	14	3744	c.3743A>G	c.(3742-3744)cAg>cGg	p.Q1248R	ARID1B_ENST00000275248.4_Missense_Mutation_p.Q1243R|ARID1B_ENST00000346085.5_Missense_Mutation_p.Q1261R|ARID1B_ENST00000367148.1_Missense_Mutation_p.Q1301R	NM_017519.2	NP_059989.2	Q8NFD5	ARI1B_HUMAN	AT rich interactive domain 1B (SWI1-like)	1248					chromatin-mediated maintenance of transcription (GO:0048096)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)			NS(2)|breast(5)|central_nervous_system(4)|endometrium(12)|kidney(4)|large_intestine(11)|lung(30)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|urinary_tract(3)	81		Breast(66;0.000162)|Ovarian(120;0.0265)		OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05)		GCCCCCTACCAGCAGGGCATG	0.547																																					p.Q1261R		Atlas-SNP	.											.	ARID1B	320	.	0			c.A3782G						.						111.0	110.0	110.0					6																	157511264		2203	4296	6499	SO:0001583	missense	57492	exon15			CCTACCAGCAGGG	AF521671	CCDS5251.1, CCDS5251.2, CCDS55072.1	6q25.3	2014-09-17			ENSG00000049618	ENSG00000049618		"""-"""	18040	protein-coding gene	gene with protein product		614556					Standard	NM_017519		Approved	KIAA1235, ELD/OSA1, p250R, BAF250b, DAN15, 6A3-5	uc003qqo.3	Q8NFD5	OTTHUMG00000015890	ENST00000350026.5:c.3743A>G	chr6.hg19:g.157511264A>G	ENSP00000055163:p.Gln1248Arg	123.0	0.0		92.0	4.0	NM_020732	Q5JRD1|Q5VYC4|Q8IZY8|Q8TEV0|Q8TF02|Q99491|Q9ULI5	Missense_Mutation	SNP	ENST00000350026.5	hg19	CCDS5251.2	.	.	.	.	.	.	.	.	.	.	A	17.80	3.477210	0.63849	.	.	ENSG00000049618	ENST00000346085;ENST00000350026;ENST00000367148;ENST00000275248;ENST00000414678	T;T;T;T;T	0.02472	4.5;4.45;4.58;4.6;4.28	5.95	4.77	0.60923	.	0.000000	0.85682	D	0.000000	T	0.03011	0.0089	L	0.54323	1.7	0.58432	D	0.999994	P;P;P	0.50272	0.89;0.933;0.933	B;P;P	0.49829	0.419;0.623;0.623	T	0.51052	-0.8754	10	0.48119	T	0.1	.	12.363	0.55213	0.8735:0.0:0.0:0.1265	.	1248;1261;1243	Q8NFD5;Q8NFD5-2;G3XAA0	ARI1B_HUMAN;.;.	R	1261;1248;1301;1243;770	ENSP00000344546:Q1261R;ENSP00000055163:Q1248R;ENSP00000356116:Q1301R;ENSP00000275248:Q1243R;ENSP00000412835:Q770R	ENSP00000275248:Q1243R	Q	+	2	0	ARID1B	157552956	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.962000	0.93254	1.037000	0.40024	0.533000	0.62120	CAG	.	.		0.547	ARID1B-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000372723.1	NM_020732	
PNLDC1	154197	hgsc.bcm.edu	37	6	160230045	160230045	+	Splice_Site	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:160230045A>G	ENST00000610273.1	+	9	777		c.e9-1		PNLDC1_ENST00000392167.3_Splice_Site	NM_001271862.1|NM_173516.1	NP_001258791.1|NP_775787.1	Q8NA58	PNDC1_HUMAN	poly(A)-specific ribonuclease (PARN)-like domain containing 1							integral component of membrane (GO:0016021)|nucleus (GO:0005634)	nucleic acid binding (GO:0003676)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(2)|large_intestine(11)|lung(9)|ovary(1)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	31		Breast(66;0.00519)|Ovarian(120;0.123)		OV - Ovarian serous cystadenocarcinoma(65;1.55e-18)|BRCA - Breast invasive adenocarcinoma(81;5.87e-06)		CCTGCTTTTCAGGTGGTAGTG	0.433																																					.		Atlas-SNP	.											.	PNLDC1	66	.	0			c.607-2A>G						.						123.0	128.0	127.0					6																	160230045		2203	4300	6503	SO:0001630	splice_region_variant	154197	exon9			CTTTTCAGGTGGT	AK097559	CCDS5271.1, CCDS5271.2, CCDS64561.1	6q25.3	2008-02-05			ENSG00000146453	ENSG00000146453			21185	protein-coding gene	gene with protein product							Standard	NM_001271862		Approved	FLJ40240, dJ195P10.2	uc003qsy.2	Q8NA58	OTTHUMG00000015941	ENST00000610273.1:c.607-1A>G	chr6.hg19:g.160230045A>G		172.0	0.0		115.0	5.0	NM_173516	Q5TAP7|Q8N7X5	Splice_Site	SNP	ENST00000610273.1	hg19	CCDS5271.1	.	.	.	.	.	.	.	.	.	.	A	10.58	1.388903	0.25118	.	.	ENSG00000146453	ENST00000275275;ENST00000392167	.	.	.	5.46	-3.5	0.04710	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.4397	0.32808	0.3707:0.5298:0.0995:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	PNLDC1	160150035	1.000000	0.71417	0.415000	0.26534	0.397000	0.30659	5.586000	0.67503	-0.422000	0.07405	0.533000	0.62120	.	.	.		0.433	PNLDC1-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_173516	Intron
PDCD2	5134	hgsc.bcm.edu	37	6	170892201	170892201	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:170892201T>C	ENST00000541970.1	-	3	680	c.602A>G	c.(601-603)gAg>gGg	p.E201G	PDCD2_ENST00000453163.2_Missense_Mutation_p.E201G|PDCD2_ENST00000443345.2_Missense_Mutation_p.E168G|PDCD2_ENST00000542896.1_Missense_Mutation_p.E201G|PDCD2_ENST00000537445.1_Missense_Mutation_p.E168G|PDCD2_ENST00000392090.2_Missense_Mutation_p.E168G	NM_001199462.1|NM_002598.3	NP_001186391.1|NP_002589.2	Q16342	PDCD2_HUMAN	programmed cell death 2	201					apoptotic process (GO:0006915)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|large_intestine(1)|lung(5)	9		Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;6.91e-23)|BRCA - Breast invasive adenocarcinoma(81;4.82e-06)|GBM - Glioblastoma multiforme(31;0.142)		AGGCATAATCTCATCTTCTGT	0.358																																					p.E201G	Colon(60;1476 1726 39478)	Atlas-SNP	.											.	PDCD2	13	.	0			c.A602G						.						126.0	124.0	125.0					6																	170892201		2203	4300	6503	SO:0001583	missense	5134	exon3			ATAATCTCATCTT	AJ420535	CCDS5316.1, CCDS47521.1, CCDS56460.1, CCDS56461.1, CCDS56462.1, CCDS75557.1	6q27	2008-02-05			ENSG00000071994	ENSG00000071994		"""Zinc fingers, MYND-type"""	8762	protein-coding gene	gene with protein product		600866				7606924	Standard	NM_002598		Approved	ZMYND7, RP8	uc003qxw.3	Q16342	OTTHUMG00000016083	ENST00000541970.1:c.602A>G	chr6.hg19:g.170892201T>C	ENSP00000439467:p.Glu201Gly	145.0	0.0		109.0	5.0	NM_002598	E9PCU7|F5GYS7|Q58HM9|Q58HN0|Q9UH12	Missense_Mutation	SNP	ENST00000541970.1	hg19	CCDS5316.1	.	.	.	.	.	.	.	.	.	.	.	11.52	1.664237	0.29604	.	.	ENSG00000071994	ENST00000541970;ENST00000392090;ENST00000542896;ENST00000453163;ENST00000537445;ENST00000443345	.	.	.	4.12	2.91	0.33838	Programmed cell death protein 2, C-terminal (1);	1.107890	0.06556	N	0.745960	T	0.32793	0.0841	M	0.67700	2.07	0.31291	N	0.689384	B;B;B;B;B;B;B	0.22414	0.006;0.011;0.012;0.012;0.069;0.006;0.006	B;B;B;B;B;B;B	0.23419	0.004;0.009;0.004;0.006;0.046;0.033;0.038	T	0.22452	-1.0216	8	.	.	.	-31.6789	9.5721	0.39433	0.0:0.0865:0.0:0.9135	.	150;168;201;168;201;201;168	Q7Z6S7;F5GYS7;E9PCU7;Q58HM9;F5H4V9;Q16342;Q58HN0	.;.;.;.;.;PDCD2_HUMAN;.	G	201;168;201;201;168;168	.	.	E	-	2	0	PDCD2	170734126	0.045000	0.20229	0.029000	0.17559	0.013000	0.08279	1.263000	0.33004	0.699000	0.31761	0.455000	0.32223	GAG	.	.		0.358	PDCD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043269.2	NM_002598	
SUN1	23353	hgsc.bcm.edu	37	7	881594	881594	+	Missense_Mutation	SNP	A	A	G	rs78842948	byFrequency	TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:881594A>G	ENST00000405266.1	+	3	302	c.278A>G	c.(277-279)cAg>cGg	p.Q93R	SUN1_ENST00000456758.2_Missense_Mutation_p.Q151R|SUN1_ENST00000401592.1_Missense_Mutation_p.Q93R|SUN1_ENST00000403868.1_Missense_Mutation_p.Q93R|SUN1_ENST00000457378.2_Missense_Mutation_p.Q114R|SUN1_ENST00000469755.1_3'UTR|SUN1_ENST00000452783.2_Missense_Mutation_p.Q93R|SUN1_ENST00000425407.2_Missense_Mutation_p.Q43R|SUN1_ENST00000389574.3_Missense_Mutation_p.Q43R			O94901	SUN1_HUMAN	Sad1 and UNC84 domain containing 1	93	LMNA-binding.				cytoskeletal anchoring at nuclear membrane (GO:0090286)|nuclear envelope organization (GO:0006998)|nuclear matrix anchoring at nuclear membrane (GO:0090292)	acrosomal membrane (GO:0002080)|integral component of nuclear inner membrane (GO:0005639)|nuclear envelope (GO:0005635)|SUN-KASH complex (GO:0034993)				NS(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(17)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						ACAACAAAACAGCGCAGAAGC	0.423																																					p.Q114R		Atlas-SNP	.											.	SUN1	157	.	0			c.A341G						.						85.0	82.0	83.0					7																	881594		1952	4150	6102	SO:0001583	missense	23353	exon5			CAAAACAGCGCAG	AF202724	CCDS43533.1, CCDS47525.1, CCDS55078.1, CCDS55079.1, CCDS55080.1	7p22.3	2010-01-27	2010-01-27	2010-01-27	ENSG00000164828	ENSG00000164828			18587	protein-coding gene	gene with protein product	"""Sad1 unc-84 domain protein 1"""	607723	"""unc-84 homolog A (C. elegans)"""	UNC84A		11593002	Standard	NM_001130965		Approved	KIAA0810, FLJ12407	uc021zym.1	O94901	OTTHUMG00000151426	ENST00000405266.1:c.278A>G	chr7.hg19:g.881594A>G	ENSP00000384116:p.Gln93Arg	81.0	0.0		88.0	4.0	NM_001171945	A5PL20|B3KMV7|B4DZF7|B7WNY4|B7WP53|E9PDU4|E9PF23|F8WD13|Q96CZ7|Q9HA14|Q9UH98	Missense_Mutation	SNP	ENST00000405266.1	hg19		.	.	.	.	.	.	.	.	.	.	A	12.40	1.925821	0.34002	.	.	ENSG00000164828	ENST00000456758;ENST00000389574;ENST00000457378;ENST00000452783;ENST00000435699;ENST00000439679;ENST00000457598;ENST00000421580;ENST00000405266;ENST00000401592;ENST00000403868;ENST00000297445;ENST00000425407;ENST00000450881	T;T;T;T;T;T;T;T;T;T;T;T;T	0.47177	0.85;0.85;0.85;0.85;0.85;0.85;0.85;0.85;0.85;0.85;0.85;0.85;0.85	5.68	4.49	0.54785	.	1.930510	0.01867	N	0.036993	T	0.71434	0.3339	M	0.72894	2.215	0.80722	D	1	D;D;D;D;D	0.76494	0.999;0.998;0.992;0.998;0.999	D;D;D;D;D	0.79784	0.977;0.975;0.912;0.993;0.961	T	0.37934	-0.9684	10	0.38643	T	0.18	-22.4615	12.4432	0.55637	0.8595:0.1405:0.0:0.0	.	93;93;114;43;93	E9PDU4;E9PF23;F8WD13;O94901-5;O94901-3	.;.;.;.;.	R	151;43;114;93;93;93;93;93;93;93;93;93;43;68	ENSP00000388743:Q151R;ENSP00000374225:Q43R;ENSP00000395952:Q114R;ENSP00000413439:Q93R;ENSP00000388430:Q93R;ENSP00000413188:Q93R;ENSP00000404965:Q93R;ENSP00000394381:Q93R;ENSP00000384116:Q93R;ENSP00000384015:Q93R;ENSP00000383947:Q93R;ENSP00000392309:Q43R;ENSP00000392595:Q68R	ENSP00000297445:Q93R	Q	+	2	0	SUN1	848120	0.998000	0.40836	0.039000	0.18376	0.049000	0.14656	6.021000	0.70832	0.945000	0.37605	0.533000	0.62120	CAG	.	A|0.983;C|0.017		0.423	SUN1-001	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000322566.1	NM_025154	
HOXA7	3204	hgsc.bcm.edu	37	7	27194547	27194547	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:27194547T>C	ENST00000242159.3	-	2	807	c.674A>G	c.(673-675)gAg>gGg	p.E225G	RP1-170O19.22_ENST00000467897.2_RNA|RP1-170O19.23_ENST00000498652.1_RNA|HOXA-AS3_ENST00000524304.1_RNA|HOXA-AS3_ENST00000518848.1_RNA|HOXA-AS3_ENST00000521197.1_RNA|HOXA-AS3_ENST00000518947.2_RNA|HOXA-AS3_ENST00000521231.1_RNA|HOXA7_ENST00000523796.2_5'UTR	NM_006896.3	NP_008827.2	P31268	HXA7_HUMAN	homeobox A7	225	Asp/Glu-rich (highly acidic).|Poly-Glu.				angiogenesis (GO:0001525)|anterior/posterior pattern specification (GO:0009952)|embryonic skeletal system morphogenesis (GO:0048704)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of keratinocyte differentiation (GO:0045617)|negative regulation of leukocyte migration (GO:0002686)|negative regulation of monocyte differentiation (GO:0045656)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell differentiation (GO:0048863)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			endometrium(3)|large_intestine(1)|lung(10)|prostate(1)|urinary_tract(1)	16						ctcgtcttcctcttcttcatc	0.617																																					p.E225G		Atlas-SNP	.											.	HOXA7	34	.	0			c.A674G						.						49.0	55.0	53.0					7																	27194547		2202	4299	6501	SO:0001583	missense	3204	exon2			TCTTCCTCTTCTT		CCDS5408.1	7p15.2	2011-06-20	2005-12-22		ENSG00000122592	ENSG00000122592		"""Homeoboxes / ANTP class : HOXL subclass"""	5108	protein-coding gene	gene with protein product		142950	"""homeo box A7"""	HOX1A, HOX1		1973146, 1358459	Standard	NM_006896		Approved		uc003sys.3	P31268	OTTHUMG00000023217	ENST00000242159.3:c.674A>G	chr7.hg19:g.27194547T>C	ENSP00000242159:p.Glu225Gly	147.0	0.0		169.0	7.0	NM_006896	A4D191|O43368|O43486|O95655|Q9NSC8|Q9UDM1	Missense_Mutation	SNP	ENST00000242159.3	hg19	CCDS5408.1	.	.	.	.	.	.	.	.	.	.	T	12.79	2.042103	0.35989	.	.	ENSG00000122592	ENST00000242159	D	0.91843	-2.92	4.49	4.49	0.54785	.	0.389458	0.24544	N	0.037601	T	0.82176	0.4980	N	0.08118	0	0.38086	D	0.936825	B	0.17667	0.023	B	0.16289	0.015	T	0.78193	-0.2299	10	0.23891	T	0.37	.	12.3864	0.55335	0.0:0.0:0.0:1.0	.	225	P31268	HXA7_HUMAN	G	225	ENSP00000242159:E225G	ENSP00000242159:E225G	E	-	2	0	HOXA7	27161072	0.999000	0.42202	0.584000	0.28653	0.377000	0.30045	5.326000	0.65875	1.667000	0.50832	0.379000	0.24179	GAG	.	.		0.617	HOXA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358695.1		
ADCYAP1R1	117	hgsc.bcm.edu	37	7	31132336	31132336	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:31132336T>C	ENST00000304166.4	+	13	1322	c.1033T>C	c.(1033-1035)Tcc>Ccc	p.S345P	ADCYAP1R1_ENST00000409489.1_Missense_Mutation_p.S345P|ADCYAP1R1_ENST00000409363.1_Missense_Mutation_p.S324P|ADCYAP1R1_ENST00000396211.2_Missense_Mutation_p.S345P	NM_001118.4|NM_001199635.1|NM_001199636.1	NP_001109.2|NP_001186564.1|NP_001186565.1	P41586	PACR_HUMAN	adenylate cyclase activating polypeptide 1 (pituitary) receptor type I	345					activation of adenylate cyclase activity (GO:0007190)|cell differentiation (GO:0030154)|cell surface receptor signaling pathway (GO:0007166)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|spermatogenesis (GO:0007283)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	receptor activity (GO:0004872)|vasoactive intestinal polypeptide receptor activity (GO:0004999)			endometrium(1)|large_intestine(4)|liver(2)|lung(24)|ovary(1)|skin(2)|stomach(1)	35						AGGCAATGAGTCCAGCATCTA	0.478																																					p.S345P	Ovarian(44;225 1186 2158 11092)	Atlas-SNP	.											.	ADCYAP1R1	78	.	0			c.T1033C						.						103.0	95.0	98.0					7																	31132336		2203	4300	6503	SO:0001583	missense	117	exon13			AATGAGTCCAGCA		CCDS5433.1, CCDS56480.1, CCDS56481.1	7p14.3	2012-09-20			ENSG00000078549	ENSG00000078549		"""GPCR / Class B : VIP and PACAP (ADCYAP1) receptors"""	242	protein-coding gene	gene with protein product	"""PACAP receptor 1"""	102981				7902709	Standard	NM_001199635		Approved	PAC1, PACAPR, PAC1R	uc003tcg.3	P41586	OTTHUMG00000023884	ENST00000304166.4:c.1033T>C	chr7.hg19:g.31132336T>C	ENSP00000306620:p.Ser345Pro	165.0	0.0		180.0	8.0	NM_001118	A8K1Y1|B7ZLA7|B8ZZK3|Q17S10	Missense_Mutation	SNP	ENST00000304166.4	hg19	CCDS5433.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	26.5|26.5	4.744555|4.744555	0.89663|0.89663	.|.	.|.	ENSG00000078549|ENSG00000078549	ENST00000304166;ENST00000381667;ENST00000409363;ENST00000396211;ENST00000409489|ENST00000436116	T;T;T;T|.	0.46819|.	1.14;1.11;0.86;1.13|.	5.72|5.72	5.72|5.72	0.89469|0.89469	GPCR, family 2-like (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.70780|0.70780	0.3263|0.3263	M|M	0.61703|0.61703	1.905|1.905	0.80722|0.80722	D|D	1|1	P;D;D;P;D|.	0.76494|.	0.78;0.983;0.999;0.953;0.983|.	B;P;D;P;P|.	0.81914|.	0.377;0.88;0.995;0.808;0.88|.	T|T	0.69687|0.69687	-0.5078|-0.5078	10|5	0.66056|.	D|.	0.02|.	.|.	14.2607|14.2607	0.66083|0.66083	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	345;345;345;324;345|.	B7ZLA7;Q17S10;E9PFU5;B8ZZK3;P41586|.	.;.;.;.;PACR_HUMAN|.	P|A	345;116;324;345;345|61	ENSP00000306620:S345P;ENSP00000387335:S324P;ENSP00000379514:S345P;ENSP00000386395:S345P|.	ENSP00000306620:S345P|.	S|V	+|+	1|2	0|0	ADCYAP1R1|ADCYAP1R1	31098861|31098861	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	4.673000|4.673000	0.61604|0.61604	2.317000|2.317000	0.78254|0.78254	0.460000|0.460000	0.39030|0.39030	TCC|GTC	.	.		0.478	ADCYAP1R1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000215041.3	NM_001118	
DPY19L1	23333	hgsc.bcm.edu	37	7	35057514	35057514	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:35057514T>C	ENST00000310974.4	-	3	316	c.172A>G	c.(172-174)Atg>Gtg	p.M58V		NM_015283.1	NP_056098.1	Q2PZI1	D19L1_HUMAN	dpy-19-like 1 (C. elegans)	58						integral component of membrane (GO:0016021)|membrane (GO:0016020)	transferase activity, transferring glycosyl groups (GO:0016757)			endometrium(3)|kidney(5)|large_intestine(8)|lung(8)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(4)	31						CGAAAAGCCATCTCCCTTTCC	0.303																																					p.M58V		Atlas-SNP	.											.	DPY19L1	56	.	0			c.A172G						.						80.0	79.0	79.0					7																	35057514		1969	4205	6174	SO:0001583	missense	23333	exon3			AAGCCATCTCCCT	AB020684	CCDS43567.1	7p14.3-p14.2	2006-04-26			ENSG00000173852	ENSG00000173852			22205	protein-coding gene	gene with protein product		613892					Standard	NM_015283		Approved	KIAA0877	uc003tem.4	Q2PZI1	OTTHUMG00000154888	ENST00000310974.4:c.172A>G	chr7.hg19:g.35057514T>C	ENSP00000308695:p.Met58Val	86.0	0.0		103.0	6.0	NM_015283	O94954|Q4G151	Missense_Mutation	SNP	ENST00000310974.4	hg19	CCDS43567.1	.	.	.	.	.	.	.	.	.	.	T	17.75	3.465948	0.63625	.	.	ENSG00000173852	ENST00000310974	T	0.55930	0.49	5.22	5.22	0.72569	.	0.000000	0.85682	U	0.000000	T	0.72898	0.3518	M	0.80183	2.485	0.58432	D	0.999997	P	0.50156	0.932	D	0.67103	0.949	T	0.76732	-0.2851	10	0.66056	D	0.02	-18.7281	14.5697	0.68203	0.0:0.0:0.0:1.0	.	58	Q2PZI1	D19L1_HUMAN	V	58	ENSP00000308695:M58V	ENSP00000308695:M58V	M	-	1	0	DPY19L1	35024039	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.459000	0.80802	2.102000	0.63906	0.477000	0.44152	ATG	.	.		0.303	DPY19L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337506.1		
EPDR1	54749	hgsc.bcm.edu	37	7	37988590	37988590	+	Missense_Mutation	SNP	G	G	T			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:37988590G>T	ENST00000199448.4	+	2	797	c.418G>T	c.(418-420)Ggg>Tgg	p.G140W	EPDR1_ENST00000476620.1_Missense_Mutation_p.G38W|EPDR1_ENST00000559325.1_Missense_Mutation_p.G260W|EPDR1_ENST00000423717.1_Intron|EPDR1_ENST00000425345.1_Missense_Mutation_p.G79W	NM_017549.4	NP_060019.2	Q9UM22	EPDR1_HUMAN	ependymin related 1	140					cell-matrix adhesion (GO:0007160)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	calcium ion binding (GO:0005509)			breast(1)|endometrium(1)|large_intestine(2)|lung(9)|ovary(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	22						GTACTCCATCGGGGGGCCTCA	0.512																																					p.G140W		Atlas-SNP	.											EPDR1,NS,carcinoma,0,1	EPDR1	48	.	0			c.G418T						.						89.0	88.0	88.0					7																	37988590		2203	4300	6503	SO:0001583	missense	54749	exon2			TCCATCGGGGGGC	BC018299	CCDS5454.1, CCDS5454.2, CCDS59051.1, CCDS59052.1	7p14.1	2013-07-31	2013-07-31		ENSG00000086289	ENSG00000086289			17572	protein-coding gene	gene with protein product			"""ependymin related protein 1 (zebrafish)"""			11749721, 11248421	Standard	NM_001242946		Approved	MERP-1, MERP1, UCC1, EPDR	uc003tfp.4	Q9UM22	OTTHUMG00000102187	ENST00000199448.4:c.418G>T	chr7.hg19:g.37988590G>T	ENSP00000199448:p.Gly140Trp	136.0	0.0		182.0	0.0	NM_017549	A8K4C0|C9JYS3|Q06BL0|Q99M77	Missense_Mutation	SNP	ENST00000199448.4	hg19	CCDS5454.2	.	.	.	.	.	.	.	.	.	.	G	27.6	4.842274	0.91197	.	.	ENSG00000086289	ENST00000476620;ENST00000199448;ENST00000425345	.	.	.	5.24	5.24	0.73138	.	0.000000	0.85682	D	0.000000	D	0.82986	0.5156	M	0.81942	2.565	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.85000	0.0899	9	0.87932	D	0	-22.3895	17.7611	0.88465	0.0:0.0:1.0:0.0	.	79;260	C9JYS3;A4D1W8	.;.	W	38;260;79	.	ENSP00000199448:G260W	G	+	1	0	EPDR1	37955115	1.000000	0.71417	0.994000	0.49952	0.971000	0.66376	9.657000	0.98554	2.729000	0.93468	0.655000	0.94253	GGG	.	.		0.512	EPDR1-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220037.3	NM_017549	
PON1	5444	hgsc.bcm.edu	37	7	94935617	94935617	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:94935617A>G	ENST00000222381.3	-	7	991	c.760T>C	c.(760-762)Tgg>Cgg	p.W254R	PON1_ENST00000542556.1_Missense_Mutation_p.W254R	NM_000446.5	NP_000437.3	P27169	PON1_HUMAN	paraoxonase 1	254					aromatic compound catabolic process (GO:0019439)|carboxylic acid catabolic process (GO:0046395)|dephosphorylation (GO:0016311)|organophosphate catabolic process (GO:0046434)|phosphatidylcholine metabolic process (GO:0046470)|positive regulation of binding (GO:0051099)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of transporter activity (GO:0032411)|response to external stimulus (GO:0009605)|response to toxic substance (GO:0009636)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)|intracellular membrane-bounded organelle (GO:0043231)|spherical high-density lipoprotein particle (GO:0034366)	aryldialkylphosphatase activity (GO:0004063)|arylesterase activity (GO:0004064)|calcium ion binding (GO:0005509)|phospholipid binding (GO:0005543)|protein homodimerization activity (GO:0042803)			autonomic_ganglia(1)|endometrium(2)|large_intestine(6)|lung(11)|pancreas(3)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	27	all_cancers(62;1.04e-10)|all_epithelial(64;3.67e-09)|Lung NSC(181;0.239)		STAD - Stomach adenocarcinoma(171;0.0031)		Cefazolin(DB01327)	GTTAAAGTCCAATTAGCATGC	0.323																																					p.W254R	GBM(119;715 1622 17358 22490 33240)	Atlas-SNP	.											.	PON1	55	.	0			c.T760C						.						148.0	146.0	146.0					7																	94935617		2203	4300	6503	SO:0001583	missense	5444	exon7			AAGTCCAATTAGC	AF539592	CCDS5638.1	7q21.3	2014-03-14			ENSG00000005421	ENSG00000005421	3.1.1.2	"""Paraoxonases"""	9204	protein-coding gene	gene with protein product	"""esterase A"", ""arylesterase 1"""	168820		PON		8661009, 15450851	Standard	NM_000446		Approved	ESA	uc003uns.3	P27169	OTTHUMG00000153894	ENST00000222381.3:c.760T>C	chr7.hg19:g.94935617A>G	ENSP00000222381:p.Trp254Arg	109.0	0.0		119.0	5.0	NM_000446	B2RA40|Q16052|Q6B0J6|Q9UCB1	Missense_Mutation	SNP	ENST00000222381.3	hg19	CCDS5638.1	.	.	.	.	.	.	.	.	.	.	A	9.485	1.099095	0.20552	.	.	ENSG00000005421	ENST00000222381;ENST00000542556	T;T	0.39787	1.06;1.06	4.83	3.6	0.41247	Six-bladed beta-propeller, TolB-like (1);	0.272271	0.42053	D	0.000771	T	0.44829	0.1312	M	0.84683	2.71	0.42629	D	0.993372	B;B	0.22211	0.066;0.014	B;B	0.14023	0.01;0.004	T	0.45818	-0.9235	10	0.23891	T	0.37	-8.365	12.2817	0.54767	0.8593:0.1407:0.0:0.0	.	254;254	F5H4W9;P27169	.;PON1_HUMAN	R	254	ENSP00000222381:W254R;ENSP00000444854:W254R	ENSP00000222381:W254R	W	-	1	0	PON1	94773553	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.489000	0.45285	2.156000	0.67533	0.459000	0.35465	TGG	.	.		0.323	PON1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000332865.2	NM_000446	
PON2	5445	hgsc.bcm.edu	37	7	95035443	95035443	+	Silent	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:95035443A>G	ENST00000222572.3	-	8	1140	c.894T>C	c.(892-894)ccT>ccC	p.P298P	PON2_ENST00000433091.2_Silent_p.P286P|PON2_ENST00000483292.1_5'UTR|PON2_ENST00000536183.1_Silent_p.P319P			Q15165	PON2_HUMAN	paraoxonase 2	298					aromatic compound catabolic process (GO:0019439)|response to oxidative stress (GO:0006979)	extracellular region (GO:0005576)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	arylesterase activity (GO:0004064)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(3)|prostate(1)	9	all_cancers(62;9.35e-11)|all_epithelial(64;3.37e-09)		STAD - Stomach adenocarcinoma(171;0.0151)			CTGACGAGGGAGGATTGTTCG	0.378																																					p.P298P	GBM(42;803 823 13649 23368 31463)	Atlas-SNP	.											.	PON2	32	.	0			c.T894C						.						103.0	105.0	104.0					7																	95035443		2203	4300	6503	SO:0001819	synonymous_variant	5445	exon8			CGAGGGAGGATTG	M63012, AF001601	CCDS5640.1, CCDS47644.1	7q21.3	2014-03-14			ENSG00000105854	ENSG00000105854	3.1.1.2	"""Paraoxonases"""	9205	protein-coding gene	gene with protein product	"""paraoxonase nirs"", ""arylesterase 2"""	602447				8661009, 9714608	Standard	XM_005250453		Approved		uc003unv.3	Q15165	OTTHUMG00000153948	ENST00000222572.3:c.894T>C	chr7.hg19:g.95035443A>G		72.0	0.0		56.0	4.0	NM_000305	A4D1H7|B2RCP9|B4DJD5|O15114|O15115|O75856|Q5FBX7|Q86YL0	Silent	SNP	ENST00000222572.3	hg19	CCDS5640.1																																																																																			.	.		0.378	PON2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333142.1	NM_000305	
LMTK2	22853	hgsc.bcm.edu	37	7	97821054	97821054	+	Nonsense_Mutation	SNP	G	G	A			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:97821054G>A	ENST00000297293.5	+	11	1570	c.1277G>A	c.(1276-1278)tGg>tAg	p.W426*		NM_014916.3	NP_055731.2	Q8IWU2	LMTK2_HUMAN	lemur tyrosine kinase 2	426					early endosome to late endosome transport (GO:0045022)|endocytic recycling (GO:0032456)|negative regulation of catalytic activity (GO:0043086)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|receptor recycling (GO:0001881)|transferrin transport (GO:0033572)	early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|myosin VI binding (GO:0070853)|protein phosphatase inhibitor activity (GO:0004864)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(25)|ovary(1)|pancreas(2)|skin(2)|stomach(3)	59	all_cancers(62;3.23e-09)|all_epithelial(64;7.65e-10)|Lung NSC(181;0.00902)|all_lung(186;0.0104)|Esophageal squamous(72;0.0125)					GAACAGCAGTGGAACGCTCTG	0.562																																					p.W426X		Atlas-SNP	.											.	LMTK2	228	.	0			c.G1277A						.						95.0	82.0	87.0					7																	97821054		2203	4300	6503	SO:0001587	stop_gained	22853	exon11			AGCAGTGGAACGC	AB029002	CCDS5654.1	7q22.1	2014-06-12			ENSG00000164715	ENSG00000164715			17880	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 100"""	610989				15005709	Standard	NM_014916		Approved	KIAA1079, KPI2, KPI-2, cprk, LMR2, BREK, AATYK2, PPP1R100	uc003upd.2	Q8IWU2	OTTHUMG00000154256	ENST00000297293.5:c.1277G>A	chr7.hg19:g.97821054G>A	ENSP00000297293:p.Trp426*	220.0	1.0		218.0	110.0	NM_014916	A4D272|Q75MG7|Q9UPS3	Nonsense_Mutation	SNP	ENST00000297293.5	hg19	CCDS5654.1	.	.	.	.	.	.	.	.	.	.	G	40	8.350838	0.98772	.	.	ENSG00000164715	ENST00000297293	.	.	.	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	18.551	0.91065	0.0:0.0:1.0:0.0	.	.	.	.	X	426	.	ENSP00000297293:W426X	W	+	2	0	LMTK2	97658990	1.000000	0.71417	1.000000	0.80357	0.880000	0.50808	9.420000	0.97426	2.710000	0.92621	0.655000	0.94253	TGG	.	.		0.562	LMTK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334560.1	NM_014916	
ZNF394	84124	hgsc.bcm.edu	37	7	99091600	99091600	+	Missense_Mutation	SNP	G	G	T			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:99091600G>T	ENST00000337673.6	-	3	1441	c.1238C>A	c.(1237-1239)cCg>cAg	p.P413Q	ZNF394_ENST00000426306.2_3'UTR|ZNF394_ENST00000394177.3_5'Flank|ZNF789_ENST00000494186.1_Intron|ZNF789_ENST00000493485.1_Intron	NM_032164.2	NP_115540.2	Q53GI3	ZN394_HUMAN	zinc finger protein 394	413					transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|liver(1)|lung(5)|stomach(1)|urinary_tract(1)	16	all_cancers(62;2.54e-08)|all_epithelial(64;2.55e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)					ACAGGTGTACGGCTTCTCGCC	0.498																																					p.P413Q	Ovarian(24;589 697 9939 12704 40742)	Atlas-SNP	.											ZNF394,NS,carcinoma,0,1	ZNF394	48	.	0			c.C1238A						.						101.0	101.0	101.0					7																	99091600		2203	4300	6503	SO:0001583	missense	84124	exon3			GTGTACGGCTTCT	BC025241	CCDS5666.1	7q22.1	2014-01-28			ENSG00000160908	ENSG00000160908		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	18832	protein-coding gene	gene with protein product							Standard	NM_032164		Approved	ZKSCAN14, FLJ12298, ZSCAN46	uc003uqs.3	Q53GI3	OTTHUMG00000154660	ENST00000337673.6:c.1238C>A	chr7.hg19:g.99091600G>T	ENSP00000337363:p.Pro413Gln	285.0	0.0		288.0	0.0	NM_032164	A4D281|Q05DA6|Q6P5X9|Q8TB27|Q9HA37|Q9UD51	Missense_Mutation	SNP	ENST00000337673.6	hg19	CCDS5666.1	.	.	.	.	.	.	.	.	.	.	G	15.49	2.849151	0.51270	.	.	ENSG00000160908	ENST00000337673	T	0.28454	1.61	3.54	3.54	0.40534	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.151199	0.31542	N	0.007463	T	0.51907	0.1702	M	0.69463	2.115	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.57124	-0.7865	10	0.87932	D	0	.	13.4733	0.61292	0.0:0.0:1.0:0.0	.	413	Q53GI3	ZN394_HUMAN	Q	413	ENSP00000337363:P413Q	ENSP00000337363:P413Q	P	-	2	0	ZNF394	98929536	1.000000	0.71417	0.454000	0.27019	0.160000	0.22226	5.811000	0.69187	2.287000	0.76781	0.650000	0.86243	CCG	.	.		0.498	ZNF394-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336498.1	NM_032164	
PAX4	5078	hgsc.bcm.edu	37	7	127252045	127252045	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:127252045T>C	ENST00000341640.2	-	7	906	c.701A>G	c.(700-702)cAg>cGg	p.Q234R	PAX4_ENST00000378740.2_Missense_Mutation_p.Q234R|PAX4_ENST00000463946.1_Missense_Mutation_p.Q232R|PAX4_ENST00000338516.3_Intron	NM_006193.2	NP_006184.2	O43316	PAX4_HUMAN	paired box 4	242					cell differentiation (GO:0030154)|circadian rhythm (GO:0007623)|endocrine pancreas development (GO:0031018)|negative regulation of apoptotic process (GO:0043066)|organ morphogenesis (GO:0009887)|positive regulation of cell differentiation (GO:0045597)|response to cAMP (GO:0051591)|response to drug (GO:0042493)|retina development in camera-type eye (GO:0060041)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|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 negative regulation of transcription (GO:0001206)			cervix(1)|kidney(2)|large_intestine(6)|lung(20)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	35						AGTCAGCCCCTGGGAAGCACC	0.552																																					p.Q234R	Ovarian(113;737 1605 7858 27720 34092)	Atlas-SNP	.											.	PAX4	66	.	0			c.A701G						.						59.0	55.0	56.0					7																	127252045		2203	4300	6503	SO:0001583	missense	5078	exon7			AGCCCCTGGGAAG		CCDS5797.1	7q32.1	2011-06-20	2007-07-12		ENSG00000106331	ENSG00000106331		"""Paired boxes"", ""Homeoboxes / PRD class"""	8618	protein-coding gene	gene with protein product		167413	"""paired box gene 4"""				Standard	NM_006193		Approved	MODY9	uc010lld.1	O43316	OTTHUMG00000157562	ENST00000341640.2:c.701A>G	chr7.hg19:g.127252045T>C	ENSP00000339906:p.Gln234Arg	87.0	0.0		93.0	4.0	NM_006193	O95161|Q6B0H0	Missense_Mutation	SNP	ENST00000341640.2	hg19	CCDS5797.1	.	.	.	.	.	.	.	.	.	.	T	12.62	1.992062	0.35131	.	.	ENSG00000106331	ENST00000341640;ENST00000378740;ENST00000463946	D;D	0.94092	-3.35;-3.2	5.27	4.11	0.48088	.	6.684740	0.00496	N	0.000141	D	0.90400	0.6995	L	0.43152	1.355	0.80722	D	1	B;B;B;B	0.12630	0.006;0.002;0.003;0.006	B;B;B;B	0.15052	0.006;0.002;0.002;0.012	T	0.69094	-0.5236	10	0.13853	T	0.58	.	8.1187	0.30959	0.0:0.0925:0.0:0.9075	.	234;232;242;232	O43316-4;Q1W386;O43316;G3V4Q1	.;.;PAX4_HUMAN;.	R	234;242;232	ENSP00000339906:Q234R;ENSP00000451923:Q232R	ENSP00000339906:Q234R	Q	-	2	0	PAX4	127039281	0.754000	0.28360	0.932000	0.37286	0.567000	0.35839	0.501000	0.22578	0.946000	0.37632	0.533000	0.62120	CAG	.	.		0.552	PAX4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349165.1		
ZNF746	155061	hgsc.bcm.edu	37	7	149172419	149172419	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:149172419T>C	ENST00000340622.3	-	7	1271	c.991A>G	c.(991-993)Agc>Ggc	p.S331G	ZNF746_ENST00000458143.2_Missense_Mutation_p.S332G			Q6NUN9	ZN746_HUMAN	zinc finger protein 746	331					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of neuron death (GO:1901216)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(4)|lung(11)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	34	Melanoma(164;0.165)		OV - Ovarian serous cystadenocarcinoma(82;0.00358)			CTGCCCTGGCTTTCCCAGGCT	0.652																																					p.S332G		Atlas-SNP	.											.	ZNF746	68	.	0			c.A994G						.						36.0	39.0	38.0					7																	149172419		2203	4300	6503	SO:0001583	missense	155061	exon7			CCTGGCTTTCCCA	AK055975	CCDS5897.1, CCDS55180.1	7q36.1	2013-01-08			ENSG00000181220	ENSG00000181220		"""Zinc fingers, C2H2-type"", ""-"""	21948	protein-coding gene	gene with protein product		613914					Standard	NM_152557		Approved	FLJ31413	uc010lpi.2	Q6NUN9	OTTHUMG00000158972	ENST00000340622.3:c.991A>G	chr7.hg19:g.149172419T>C	ENSP00000345140:p.Ser331Gly	59.0	0.0		90.0	4.0	NM_001163474	A8K6Z9|Q6ZRF9	Missense_Mutation	SNP	ENST00000340622.3	hg19	CCDS5897.1	.	.	.	.	.	.	.	.	.	.	T	13.08	2.131117	0.37630	.	.	ENSG00000181220	ENST00000340622;ENST00000458143	T;T	0.09350	3.02;2.99	4.74	3.56	0.40772	.	1.078000	0.07210	N	0.858969	T	0.05364	0.0142	N	0.08118	0	0.09310	N	1	B;B	0.24426	0.103;0.063	B;B	0.21917	0.037;0.016	T	0.45716	-0.9242	10	0.16896	T	0.51	-18.1524	4.0703	0.09879	0.1824:0.0969:0.0:0.7207	.	332;331	Q6NUN9-2;Q6NUN9	.;ZN746_HUMAN	G	331;332	ENSP00000345140:S331G;ENSP00000395007:S332G	ENSP00000345140:S331G	S	-	1	0	ZNF746	148803352	0.002000	0.14202	0.711000	0.30485	0.962000	0.63368	1.391000	0.34475	0.644000	0.30656	0.460000	0.39030	AGC	.	.		0.652	ZNF746-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352730.1	NM_152557	
KRBA1	84626	hgsc.bcm.edu	37	7	149420823	149420824	+	Splice_Site	DNP	AG	AG	TA			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A|G	A|G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:149420823_149420824AG>TA	ENST00000485033.2	+	7	772		c.e7-1		KRBA1_ENST00000319551.8_Splice_Site|KRBA1_ENST00000479560.1_Splice_Site|KRBA1_ENST00000255992.10_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)			CTTTTTCCTTAGTGAAGACCGA	0.559																																					.		Atlas-SNP	.											.	KRBA1	68	.	0			c.773-2A>T|c.773-1G>A						.																																			SO:0001630	splice_region_variant	84626	exon8			TTCCTTAGTGAAG|TCCTTAGTGAAGA	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	Exception_encountered	chr7.hg19:g.149420823_149420824delinsTA		144.0|147.0	0.0		126.0|128.0	9.0|8.0	NM_032534	A7E2F5|E7ENE9|Q8N4X0|Q96JG5	Splice_Site	SNP	ENST00000485033.2	hg19																																																																																				.	.		0.559	KRBA1-004	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000349841.3	NM_032534	Intron
SSPO	23145	hgsc.bcm.edu	37	7	149486904	149486904	+	RNA	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:149486904A>G	ENST00000378016.2	+	0	4678							A2VEC9	SSPO_HUMAN	SCO-spondin						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	peptidase inhibitor activity (GO:0030414)					Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			GGCCAGCGCCAGCCCTGGTGA	0.657																																					p.S1560G		Atlas-SNP	.											.	.	.	.	0			c.A4678G						.						16.0	18.0	18.0					7																	149486904		1919	4115	6034			23145	exon31			AGCGCCAGCCCTG	AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"""subcommissural organ spondin"", ""SCO protein, thrombospondin domain containing"""		"""SCO-spondin homolog (Bos taurus)"""			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		chr7.hg19:g.149486904A>G		104.0	0.0		114.0	5.0	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	hg19																																																																																				.	.		0.657	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
KMT2C	58508	hgsc.bcm.edu	37	7	151859254	151859254	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:151859254T>C	ENST00000262189.6	-	43	11626	c.11408A>G	c.(11407-11409)gAc>gGc	p.D3803G	KMT2C_ENST00000355193.2_Missense_Mutation_p.D3803G	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	3803					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)										CTTTGTACAGTCATCTTCTGA	0.338																																					p.D3803G		Atlas-SNP	.											.	MLL3	1564	.	0			c.A11408G						.						43.0	47.0	45.0					7																	151859254		2202	4300	6502	SO:0001583	missense	58508	exon43			GTACAGTCATCTT	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.11408A>G	chr7.hg19:g.151859254T>C	ENSP00000262189:p.Asp3803Gly	166.0	0.0		147.0	6.0	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	hg19	CCDS5931.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	8.998|8.998	0.979427|0.979427	0.18812|0.18812	.|.	.|.	ENSG00000055609|ENSG00000055609	ENST00000262189;ENST00000355193;ENST00000424877|ENST00000360104	D;D;D|.	0.88586|.	-1.73;-1.69;-2.4|.	5.21|5.21	0.807|0.807	0.18714|0.18714	.|.	0.613334|.	0.13625|.	U|.	0.374139|.	T|.	0.24547|.	0.0595|.	L|L	0.36672|0.36672	1.1|1.1	0.09310|0.09310	N|N	0.999999|0.999999	B;B;B|.	0.20887|.	0.049;0.0;0.0|.	B;B;B|.	0.19148|.	0.024;0.0;0.0|.	T|.	0.23547|.	-1.0185|.	10|.	0.44086|.	T|.	0.13|.	.|.	1.6582|1.6582	0.02786|0.02786	0.13:0.1826:0.1352:0.5521|0.13:0.1826:0.1352:0.5521	.|.	3803;2864;3803|.	Q8NEZ4;Q8NEZ4-2;Q8NEZ4-3|.	MLL3_HUMAN;.;.|.	G|W	3803;3803;389|1308	ENSP00000262189:D3803G;ENSP00000347325:D3803G;ENSP00000410411:D389G|.	ENSP00000262189:D3803G|.	D|X	-|-	2|3	0|0	MLL3|MLL3	151490187|151490187	0.919000|0.919000	0.31177|0.31177	0.000000|0.000000	0.03702|0.03702	0.976000|0.976000	0.68499|0.68499	2.319000|2.319000	0.43788|0.43788	-0.037000|-0.037000	0.13646|0.13646	0.528000|0.528000	0.53228|0.53228	GAC|TGA	.	.		0.338	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3		
DLGAP2	9228	hgsc.bcm.edu	37	8	1497492	1497492	+	Silent	SNP	C	C	T	rs375164454		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:1497492C>T	ENST00000421627.2	+	2	767	c.633C>T	c.(631-633)ccC>ccT	p.P211P		NM_004745.3	NP_004736.2	Q9P1A6	DLGP2_HUMAN	discs, large (Drosophila) homolog-associated protein 2	290					neuron-neuron synaptic transmission (GO:0007270)	cell junction (GO:0030054)|neurofilament (GO:0005883)|postsynaptic membrane (GO:0045211)				breast(1)|endometrium(6)|lung(31)|prostate(3)	41		Ovarian(12;0.0271)|Hepatocellular(245;0.0838)|Colorectal(14;0.0846)		BRCA - Breast invasive adenocarcinoma(11;0.000169)|READ - Rectum adenocarcinoma(644;0.171)		AGCCCCGGCCCGGCATGAGCA	0.706																																					p.P211P		Atlas-SNP	.											.	DLGAP2	292	.	0			c.C633T						.	C		1,4383		0,1,2191	27.0	38.0	34.0		633	-10.8	0.0	8		34	0,8584		0,0,4292	no	coding-synonymous	DLGAP2	NM_004745.3		0,1,6483	TT,TC,CC		0.0,0.0228,0.0077		211/976	1497492	1,12967	2192	4292	6484	SO:0001819	synonymous_variant	9228	exon2			CCGGCCCGGCATG	AB000275	CCDS47760.1, CCDS75689.1	8p23	2007-12-06	2001-11-28		ENSG00000198010	ENSG00000198010			2906	protein-coding gene	gene with protein product		605438	"""discs, large (Drosophila) homolog-associated protein 2"""			9286858, 10854099	Standard	NM_004745		Approved	DAP-2	uc003wpl.4	Q9P1A6	OTTHUMG00000163599	ENST00000421627.2:c.633C>T	chr8.hg19:g.1497492C>T		103.0	0.0		61.0	42.0	NM_004745	A1QCF8|A1QCF9|A5D8Y2|O14488|O14664|Q9P1A7	Silent	SNP	ENST00000421627.2	hg19	CCDS47760.1	.	.	.	.	.	.	.	.	.	.	C	0.053	-1.245796	0.01481	2.28E-4	0.0	ENSG00000198010	ENST00000520901	T	0.39592	1.07	5.42	-10.8	0.00216	.	0.299402	0.37715	N	0.001974	T	0.40473	0.1118	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.69544	-0.5117	7	0.87932	D	0	-3.4284	7.252	0.26154	0.0744:0.2286:0.5326:0.1644	.	.	.	.	L	228	ENSP00000430563:P228L	ENSP00000430563:P228L	P	+	2	0	DLGAP2	1484899	0.181000	0.23161	0.000000	0.03702	0.004000	0.04260	-0.751000	0.04803	-2.976000	0.00284	-2.530000	0.00182	CCG	.	.		0.706	DLGAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374478.1	NM_004745	
ERI1	90459	hgsc.bcm.edu	37	8	8865648	8865648	+	Missense_Mutation	SNP	C	C	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:8865648C>G	ENST00000523898.1	+	3	956	c.277C>G	c.(277-279)Ctt>Gtt	p.L93V	ERI1_ENST00000250263.7_Missense_Mutation_p.L93V|ERI1_ENST00000519292.1_Missense_Mutation_p.L93V			Q8IV48	ERI1_HUMAN	exoribonuclease 1	93	SAP. {ECO:0000255|PROSITE- ProRule:PRU00186}.				gene silencing by RNA (GO:0031047)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|rRNA 3'-end processing (GO:0031125)	cytoplasm (GO:0005737)|histone pre-mRNA 3'end processing complex (GO:0071204)|nucleolus (GO:0005730)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|histone pre-mRNA stem-loop binding (GO:0071207)|metal ion binding (GO:0046872)|ribosome binding (GO:0043022)|rRNA binding (GO:0019843)			NS(1)|endometrium(2)|large_intestine(1)|lung(6)|prostate(1)	11						AGAATTCAAGCTTGAAACTAG	0.294																																					p.L93V		Atlas-SNP	.											.	ERI1	20	.	0			c.C277G						.						35.0	37.0	37.0					8																	8865648		2203	4297	6500	SO:0001583	missense	90459	exon2			TTCAAGCTTGAAA	BC035279	CCDS5972.1	8p23.1	2008-12-16	2008-12-16	2008-12-16	ENSG00000104626	ENSG00000104626		"""Enhanced RNAi three prime mRNA exonucleases"""	23994	protein-coding gene	gene with protein product	"""exoribonuclease 1"", ""enhanced RNAi three prime mRNA exonuclease homolog 1 (C.elegans)"""	608739	"""three prime histone mRNA exonuclease 1"""	THEX1		14536070	Standard	NM_153332		Approved	3'HEXO	uc003wsk.2	Q8IV48	OTTHUMG00000129328	ENST00000523898.1:c.277C>G	chr8.hg19:g.8865648C>G	ENSP00000429615:p.Leu93Val	77.0	0.0		50.0	31.0	NM_153332	A8K4U7|Q9NSX3	Missense_Mutation	SNP	ENST00000523898.1	hg19	CCDS5972.1	.	.	.	.	.	.	.	.	.	.	C	19.46	3.831148	0.71258	.	.	ENSG00000104626	ENST00000523898;ENST00000250263;ENST00000519292	T;T;T	0.53857	0.6;0.6;0.6	4.82	4.82	0.62117	DNA-binding SAP (3);	0.000000	0.85682	D	0.000000	T	0.58821	0.2149	L	0.59436	1.845	0.80722	D	1	P	0.34684	0.463	B	0.42959	0.403	T	0.62483	-0.6845	10	0.54805	T	0.06	-21.7298	17.2738	0.87109	0.0:1.0:0.0:0.0	.	93	Q8IV48	ERI1_HUMAN	V	93	ENSP00000429615:L93V;ENSP00000250263:L93V;ENSP00000430190:L93V	ENSP00000250263:L93V	L	+	1	0	ERI1	8903058	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.304000	0.78882	2.374000	0.81015	0.563000	0.77884	CTT	.	.		0.294	ERI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251471.2	NM_153332	
RP1L1	94137	hgsc.bcm.edu	37	8	10467809	10467809	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:10467809A>G	ENST00000382483.3	-	4	4022	c.3799T>C	c.(3799-3801)Tgc>Cgc	p.C1267R		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	1267					cell projection organization (GO:0030030)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|visual perception (GO:0007601)	axoneme (GO:0005930)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)				breast(5)|central_nervous_system(2)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(16)|lung(82)|ovary(8)|prostate(5)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	148				COAD - Colon adenocarcinoma(149;0.0811)		GCACAAGCGCAGGCTCGGGCG	0.522																																					p.C1267R		Atlas-SNP	.											.	RP1L1	453	.	0			c.T3799C						.						119.0	121.0	120.0					8																	10467809		2047	4193	6240	SO:0001583	missense	94137	exon4			AAGCGCAGGCTCG	AY168346	CCDS43708.1	8p23.1	2011-12-06			ENSG00000183638	ENSG00000183638			15946	protein-coding gene	gene with protein product		608581				12634863	Standard	NM_178857		Approved	DCDC4B	uc003wtc.3	Q8IWN7	OTTHUMG00000163806	ENST00000382483.3:c.3799T>C	chr8.hg19:g.10467809A>G	ENSP00000371923:p.Cys1267Arg	272.0	0.0		116.0	5.0	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Missense_Mutation	SNP	ENST00000382483.3	hg19	CCDS43708.1	.	.	.	.	.	.	.	.	.	.	A	4.797	0.148143	0.09134	.	.	ENSG00000183638	ENST00000382483	T	0.03982	3.74	3.1	-4.57	0.03421	.	1.137500	0.06901	N	0.805886	T	0.01800	0.0057	N	0.08118	0	0.09310	N	1	B	0.16603	0.018	B	0.06405	0.002	T	0.46020	-0.9221	10	0.05620	T	0.96	4.8821	4.0931	0.09978	0.2682:0.1845:0.0:0.5473	.	1267	A6NKC6	.	R	1267	ENSP00000371923:C1267R	ENSP00000371923:C1267R	C	-	1	0	RP1L1	10505219	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-1.287000	0.02785	-0.484000	0.06763	0.260000	0.18958	TGC	.	.		0.522	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1		
SLC7A2	6542	hgsc.bcm.edu	37	8	17417985	17417985	+	Missense_Mutation	SNP	T	T	C	rs536330311		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:17417985T>C	ENST00000494857.1	+	10	1665	c.1447T>C	c.(1447-1449)Tcc>Ccc	p.S483P	SLC7A2_ENST00000470360.1_Missense_Mutation_p.S522P|SLC7A2_ENST00000522656.1_Missense_Mutation_p.S483P|SLC7A2_ENST00000398090.3_Missense_Mutation_p.S522P|SLC7A2_ENST00000004531.10_Missense_Mutation_p.S523P	NM_001008539.3	NP_001008539.3	P52569	CTR2_HUMAN	solute carrier family 7 (cationic amino acid transporter, y+ system), member 2	483					amino acid transport (GO:0006865)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|macrophage activation (GO:0042116)|nitric oxide biosynthetic process (GO:0006809)|nitric oxide production involved in inflammatory response (GO:0002537)|regulation of inflammatory response (GO:0050727)|regulation of macrophage activation (GO:0043030)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	basic amino acid transmembrane transporter activity (GO:0015174)|high-affinity arginine transmembrane transporter activity (GO:0005289)|L-lysine transmembrane transporter activity (GO:0015189)|L-ornithine transmembrane transporter activity (GO:0000064)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(4)|lung(8)|ovary(2)|skin(1)|stomach(1)	25				Colorectal(111;0.0577)|COAD - Colon adenocarcinoma(73;0.216)	L-Lysine(DB00123)|L-Ornithine(DB00129)	CTTCTGCCCCTCCCTTCTGCC	0.537																																					p.S523P		Atlas-SNP	.											.	SLC7A2	157	.	0			c.T1567C						.						151.0	137.0	142.0					8																	17417985		2203	4300	6503	SO:0001583	missense	6542	exon9			TGCCCCTCCCTTC	D29990	CCDS6002.2, CCDS34852.1, CCDS55203.1	8p22	2013-05-22			ENSG00000003989	ENSG00000003989		"""Solute carriers"""	11060	protein-coding gene	gene with protein product		601872		ATRC2		8954799	Standard	NM_001164771		Approved	CAT-2, HCAT2	uc011kye.2	P52569	OTTHUMG00000130819	ENST00000494857.1:c.1447T>C	chr8.hg19:g.17417985T>C	ENSP00000419140:p.Ser483Pro	207.0	0.0		93.0	5.0	NM_001164771	B7ZL54|O15291|O15292|Q14CQ6|Q6NSZ7|Q86TC6	Missense_Mutation	SNP	ENST00000494857.1	hg19	CCDS34852.1	.	.	.	.	.	.	.	.	.	.	t	9.214	1.031615	0.19590	.	.	ENSG00000003989	ENST00000494857;ENST00000522656;ENST00000470360;ENST00000004531;ENST00000398090	D;D;D;D;D	0.88664	-2.25;-2.25;-2.41;-2.27;-2.41	5.27	4.12	0.48240	.	0.103983	0.64402	D	0.000002	T	0.78489	0.4291	N	0.20483	0.58	0.29014	N	0.886682	B;B;B	0.09022	0.002;0.0;0.001	B;B;B	0.08055	0.003;0.003;0.002	T	0.68413	-0.5415	10	0.41790	T	0.15	.	6.4963	0.22144	0.1391:0.0726:0.0:0.7883	.	523;522;483	P52569-3;P52569-2;P52569	.;.;CTR2_HUMAN	P	483;483;522;523;522	ENSP00000419140:S483P;ENSP00000430464:S483P;ENSP00000419873:S522P;ENSP00000004531:S523P;ENSP00000381164:S522P	ENSP00000004531:S523P	S	+	1	0	SLC7A2	17462277	1.000000	0.71417	0.861000	0.33841	0.111000	0.19643	1.921000	0.40035	0.954000	0.37851	-0.257000	0.10917	TCC	.	.		0.537	SLC7A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253367.3	NM_003046	
PCM1	5108	hgsc.bcm.edu	37	8	17829875	17829875	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:17829875A>G	ENST00000519253.1	+	23	3873	c.3622A>G	c.(3622-3624)Agg>Ggg	p.R1208G	PCM1_ENST00000327578.8_5'Flank|PCM1_ENST00000524226.1_Missense_Mutation_p.R1209G|PCM1_ENST00000325083.8_Missense_Mutation_p.R1208G			Q15154	PCM1_HUMAN	pericentriolar material 1	1208					centrosome organization (GO:0051297)|cilium assembly (GO:0042384)|cytoplasmic microtubule organization (GO:0031122)|G2/M transition of mitotic cell cycle (GO:0000086)|interkinetic nuclear migration (GO:0022027)|intraciliary transport involved in cilium morphogenesis (GO:0035735)|microtubule anchoring (GO:0034453)|microtubule anchoring at centrosome (GO:0034454)|mitotic cell cycle (GO:0000278)|negative regulation of neurogenesis (GO:0050768)|neuronal stem cell maintenance (GO:0097150)|positive regulation of intracellular protein transport (GO:0090316)|protein localization to centrosome (GO:0071539)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|pericentriolar material (GO:0000242)|protein complex (GO:0043234)	identical protein binding (GO:0042802)		PCM1/JAK2(30)	breast(4)|endometrium(8)|kidney(5)|large_intestine(16)|lung(11)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	48				Colorectal(111;0.0789)		GGAAAGCAGTAGGACACCATG	0.343			T	"""RET, JAK2"""	"""papillary thyroid, CML, MPD"""																																p.R1208G		Atlas-SNP	.		Dom	yes		8	8p22-p21.3	5108	pericentriolar material 1  (PTC4)		"""E, L"""	.	PCM1	120	.	0			c.A3622G						.						65.0	61.0	62.0					8																	17829875		1852	4086	5938	SO:0001583	missense	5108	exon23			AGCAGTAGGACAC		CCDS47812.1	8p22-p21.3	2008-08-08			ENSG00000078674	ENSG00000078674			8727	protein-coding gene	gene with protein product		600299				8120099, 15659651	Standard	NM_006197		Approved	PTC4	uc003wyi.4	Q15154	OTTHUMG00000163699	ENST00000519253.1:c.3622A>G	chr8.hg19:g.17829875A>G	ENSP00000431099:p.Arg1208Gly	182.0	0.0		95.0	5.0	NM_006197	Q58F13|Q6P1K7|Q8NB85|Q9BWC1|Q9H4A2	Missense_Mutation	SNP	ENST00000519253.1	hg19		.	.	.	.	.	.	.	.	.	.	A	15.59	2.879702	0.51801	.	.	ENSG00000078674	ENST00000325083;ENST00000519253;ENST00000524226	T;T;T	0.55234	0.53;0.53;0.53	5.37	4.15	0.48705	.	0.409562	0.30704	N	0.009046	T	0.47173	0.1431	L	0.44542	1.39	0.80722	D	1	B;B;B;B	0.34329	0.449;0.277;0.449;0.277	B;B;B;B	0.37091	0.241;0.116;0.241;0.116	T	0.53563	-0.8421	10	0.59425	D	0.04	-9.7344	12.9826	0.58572	0.8661:0.1339:0.0:0.0	.	70;1208;1209;1208	B4DJ00;E7ETA6;E7EV56;Q15154	.;.;.;PCM1_HUMAN	G	1208;1208;1209	ENSP00000327077:R1208G;ENSP00000431099:R1208G;ENSP00000430521:R1209G	ENSP00000327077:R1208G	R	+	1	2	PCM1	17874155	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	3.016000	0.49607	2.171000	0.68590	0.402000	0.26972	AGG	.	.		0.343	PCM1-003	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000374800.1	NM_006197	
SH2D4A	63898	hgsc.bcm.edu	37	8	19190562	19190562	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:19190562T>C	ENST00000265807.3	+	3	689	c.278T>C	c.(277-279)cTc>cCc	p.L93P	SH2D4A_ENST00000519207.1_Missense_Mutation_p.L93P|SH2D4A_ENST00000518040.1_Missense_Mutation_p.L48P	NM_001174160.1|NM_022071.3	NP_001167631.1|NP_071354.2	Q9H788	SH24A_HUMAN	SH2 domain containing 4A	93					negative regulation of phosphatase activity (GO:0010923)	cytoplasm (GO:0005737)	phosphatase binding (GO:0019902)			endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|stomach(1)	16				Colorectal(111;0.0732)		TATGATGTGCTCTGTAATGAA	0.473																																					p.L93P		Atlas-SNP	.											.	SH2D4A	49	.	0			c.T278C						.						124.0	121.0	122.0					8																	19190562		2203	4300	6503	SO:0001583	missense	63898	exon3			ATGTGCTCTGTAA	AY190323	CCDS6009.1, CCDS55206.1	8p21	2013-02-14			ENSG00000104611	ENSG00000104611		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""SH2 domain containing"""	26102	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 38"""	614968					Standard	NM_022071		Approved	FLJ20967, SH2A, PPP1R38	uc003wzc.3	Q9H788	OTTHUMG00000097005	ENST00000265807.3:c.278T>C	chr8.hg19:g.19190562T>C	ENSP00000265807:p.Leu93Pro	142.0	0.0		63.0	4.0	NM_022071	B4DDR1|Q5XKC1|Q6NXE9|Q86YM2|Q96C88|Q9H7F7	Missense_Mutation	SNP	ENST00000265807.3	hg19	CCDS6009.1	.	.	.	.	.	.	.	.	.	.	T	10.40	1.339888	0.24339	.	.	ENSG00000104611	ENST00000265807;ENST00000518040;ENST00000519207;ENST00000523736	T;T;T;T	0.15256	2.44;2.44;2.44;2.44	5.58	4.43	0.53597	.	0.242085	0.34802	N	0.003679	T	0.18383	0.0441	L	0.56769	1.78	0.58432	D	0.999999	B;B	0.18461	0.028;0.009	B;B	0.15870	0.014;0.01	T	0.02596	-1.1136	10	0.87932	D	0	.	9.6753	0.40037	0.0:0.0825:0.0:0.9175	.	48;93	B4DDR1;Q9H788	.;SH24A_HUMAN	P	93;48;93;79	ENSP00000265807:L93P;ENSP00000429482:L48P;ENSP00000428684:L93P;ENSP00000428048:L79P	ENSP00000265807:L93P	L	+	2	0	SH2D4A	19234842	1.000000	0.71417	0.994000	0.49952	0.207000	0.24258	4.409000	0.59768	0.954000	0.37851	0.374000	0.22700	CTC	.	.		0.473	SH2D4A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214094.1	NM_022071	
CDCA2	157313	hgsc.bcm.edu	37	8	25325868	25325868	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:25325868A>G	ENST00000330560.3	+	6	1151	c.674A>G	c.(673-675)cAg>cGg	p.Q225R	CDCA2_ENST00000380665.3_Missense_Mutation_p.Q210R	NM_152562.2	NP_689775.2	Q69YH5	CDCA2_HUMAN	cell division cycle associated 2	225					mitotic nuclear division (GO:0007067)|positive regulation of protein dephosphorylation (GO:0035307)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(3)|cervix(1)|endometrium(3)|kidney(7)|large_intestine(7)|lung(10)|ovary(1)|prostate(3)	35		all_cancers(63;0.0378)|Ovarian(32;0.000878)|all_epithelial(46;0.0162)|Breast(100;0.0164)|Prostate(55;0.191)		UCEC - Uterine corpus endometrioid carcinoma (27;0.022)|Epithelial(17;1.37e-11)|Colorectal(74;0.0129)|COAD - Colon adenocarcinoma(73;0.0443)		ATTGGTCTCCAGATATTCAAT	0.403																																					p.Q225R		Atlas-SNP	.											.	CDCA2	78	.	0			c.A674G						.						117.0	120.0	119.0					8																	25325868		2203	4300	6503	SO:0001583	missense	157313	exon6			GTCTCCAGATATT	BG354575	CCDS6049.1	8p21.2	2014-06-12			ENSG00000184661	ENSG00000184661			14623	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 81"""					12188893, 16492807	Standard	NM_152562		Approved	Repo-Man, PPP1R81	uc003xep.1	Q69YH5	OTTHUMG00000099429	ENST00000330560.3:c.674A>G	chr8.hg19:g.25325868A>G	ENSP00000328228:p.Gln225Arg	145.0	0.0		71.0	4.0	NM_152562	Q3SX74|Q4G0W0|Q5RKN0|Q69YI4|Q6P464|Q8N7C1	Missense_Mutation	SNP	ENST00000330560.3	hg19	CCDS6049.1	.	.	.	.	.	.	.	.	.	.	A	10.20	1.285250	0.23478	.	.	ENSG00000184661	ENST00000330560;ENST00000380665	T;T	0.32515	1.45;1.45	5.05	1.32	0.21799	.	1.721060	0.02819	N	0.125391	T	0.18341	0.0440	N	0.22421	0.69	0.09310	N	1	B;B;B	0.26809	0.019;0.16;0.16	B;B;B	0.26770	0.022;0.073;0.073	T	0.12863	-1.0531	10	0.07644	T	0.81	0.848	3.2514	0.06815	0.6428:0.0:0.186:0.1712	.	225;210;225	B7Z5Q5;E9PEI0;Q69YH5	.;.;CDCA2_HUMAN	R	225;210	ENSP00000328228:Q225R;ENSP00000370040:Q210R	ENSP00000328228:Q225R	Q	+	2	0	CDCA2	25381785	0.007000	0.16637	0.005000	0.12908	0.014000	0.08584	0.711000	0.25764	0.083000	0.17047	0.529000	0.55759	CAG	.	.		0.403	CDCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216891.3	NM_152562	
PPP2R2A	5520	hgsc.bcm.edu	37	8	26211994	26211994	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:26211994A>G	ENST00000380737.3	+	4	520	c.191A>G	c.(190-192)cAg>cGg	p.Q64R	PPP2R2A_ENST00000315985.7_Missense_Mutation_p.Q74R	NM_002717.3	NP_002708.1	P63151	2ABA_HUMAN	protein phosphatase 2, regulatory subunit B, alpha	64					G2/M transition of mitotic cell cycle (GO:0000086)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope reassembly (GO:0007084)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|protein dephosphorylation (GO:0006470)|regulation of catalytic activity (GO:0050790)|response to morphine (GO:0043278)|RNA metabolic process (GO:0016070)|signal transduction (GO:0007165)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)|protein serine/threonine phosphatase activity (GO:0004722)			kidney(1)|large_intestine(2)|ovary(1)	4		all_cancers(63;0.086)|Ovarian(32;2.61e-05)|all_epithelial(46;0.0514)|Prostate(55;0.157)		UCEC - Uterine corpus endometrioid carcinoma (27;0.000754)|Epithelial(17;3.02e-15)|all cancers(2;1.52e-13)|OV - Ovarian serous cystadenocarcinoma(2;1.89e-10)|Colorectal(74;0.155)		AACAAAATCCAGTCTCATAGC	0.313																																					p.Q74R		Atlas-SNP	.											.	PPP2R2A	44	.	0			c.A221G						.						74.0	77.0	76.0					8																	26211994		2203	4300	6503	SO:0001583	missense	5520	exon4			AAATCCAGTCTCA	M64929	CCDS34867.1, CCDS55213.1	8p21.2	2013-01-10	2010-04-14		ENSG00000221914	ENSG00000221914	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"", ""WD repeat domain containing"""	9304	protein-coding gene	gene with protein product	"""PP2A subunit B isoform alpha"""	604941	"""protein phosphatase 2 (formerly 2A), regulatory subunit B (PR 52), alpha isoform"", ""protein phosphatase 2 (formerly 2A), regulatory subunit B, alpha isoform"""			1849734	Standard	NM_001177591		Approved	PR52A, PR55A, B55A		P63151	OTTHUMG00000163850	ENST00000380737.3:c.191A>G	chr8.hg19:g.26211994A>G	ENSP00000370113:p.Gln64Arg	162.0	0.0		68.0	4.0	NM_001177591	B2RBU8|B4E1T7|P50409|Q00007	Missense_Mutation	SNP	ENST00000380737.3	hg19	CCDS34867.1	.	.	.	.	.	.	.	.	.	.	A	9.582	1.123757	0.20959	.	.	ENSG00000221914	ENST00000380737;ENST00000315985	T;T	0.29655	1.57;1.56	5.97	4.75	0.60458	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.163914	0.41396	U	0.000887	T	0.08802	0.0218	N	0.00538	-1.39	0.37224	D	0.905387	B;B	0.02656	0.0;0.0	B;B	0.08055	0.001;0.003	T	0.24225	-1.0166	10	0.12103	T	0.63	-5.53	11.8334	0.52309	0.7323:0.2677:0.0:0.0	.	74;64	B4E1T7;P63151	.;2ABA_HUMAN	R	64;74	ENSP00000370113:Q64R;ENSP00000325074:Q74R	ENSP00000325074:Q74R	Q	+	2	0	PPP2R2A	26267911	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.241000	0.51376	2.285000	0.76669	0.528000	0.53228	CAG	.	.		0.313	PPP2R2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375954.2	NM_002717	
MAK16	84549	hgsc.bcm.edu	37	8	33346292	33346292	+	Silent	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:33346292T>C	ENST00000360128.6	+	4	673	c.216T>C	c.(214-216)gcT>gcC	p.A72A	TTI2_ENST00000519356.1_Intron	NM_032509.3	NP_115898.2	Q9BXY0	MAK16_HUMAN	MAK16 homolog (S. cerevisiae)	72						nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(2)|urinary_tract(1)	8						AACGAGCGGCTTTTCCTCGGC	0.418																																					p.A72A		Atlas-SNP	.											.	MAK16	25	.	0			c.T216C						.						84.0	82.0	83.0					8																	33346292		2203	4300	6503	SO:0001819	synonymous_variant	84549	exon4			AGCGGCTTTTCCT	AF251062	CCDS6089.1	8p12	2011-10-13	2008-06-04	2008-06-04	ENSG00000198042	ENSG00000198042		"""RNA binding motif (RRM) containing"""	13703	protein-coding gene	gene with protein product			"""RNA binding motif protein 13"""	RBM13			Standard	NM_032509		Approved	MAK16L	uc003xjj.3	Q9BXY0	OTTHUMG00000163957	ENST00000360128.6:c.216T>C	chr8.hg19:g.33346292T>C		159.0	0.0		75.0	4.0	NM_032509	B2RB44|Q5U5T1|Q86UC4|Q96SY6	Silent	SNP	ENST00000360128.6	hg19	CCDS6089.1																																																																																			.	.		0.418	MAK16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376559.3	NM_032509	
WHSC1L1	54904	hgsc.bcm.edu	37	8	38148152	38148153	+	Missense_Mutation	DNP	TC	TC	AG			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T|C	T|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:38148152_38148153TC>AG	ENST00000317025.8	-	17	3475_3476	c.2958_2959GA>CT	c.(2956-2961)ctGAac>ctCTac	p.N987Y	WHSC1L1_ENST00000527502.1_Missense_Mutation_p.N987Y|WHSC1L1_ENST00000433384.2_Missense_Mutation_p.N938Y	NM_023034.1	NP_075447.1	Q9BZ95	NSD3_HUMAN	Wolf-Hirschhorn syndrome candidate 1-like 1	987	PWWP 2. {ECO:0000255|PROSITE- ProRule:PRU00162}.				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)			CCCTGGATGTTCAGTGGCACAG	0.455			T	NUP98	AML																																p.N987Y|p.L986L		Atlas-SNP	.		Dom	yes		8	8p12	54904	Wolf-Hirschhorn syndrome candidate 1-like 1 (NSD3)		L	.	WHSC1L1	137	.	0			c.A2959T|c.G2958C						.																																			SO:0001583	missense	54904	exon17			GGATGTTCAGTGG|GATGTTCAGTGGC	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.2958_2959delinsAG	chr8.hg19:g.38148152_38148153delinsAG	ENSP00000313983:p.Asn987Tyr	173.0|174.0	0.0		149.0|148.0	53.0|52.0	NM_023034	B7ZL11|D3DSX1|Q1RMD3|Q3B796|Q6ZSA5|Q9BYU8|Q9BYU9|Q9H2M8|Q9H9W9|Q9NXA6	Missense_Mutation|Silent	SNP	ENST00000317025.8	hg19	CCDS43729.1																																																																																			.	.		0.455	WHSC1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381924.3	NM_023034	
PXDNL	137902	hgsc.bcm.edu	37	8	52321457	52321457	+	Silent	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:52321457A>G	ENST00000356297.4	-	17	2827	c.2727T>C	c.(2725-2727)gcT>gcC	p.A909A	PXDNL_ENST00000543296.1_Silent_p.A909A	NM_144651.4	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog (Drosophila)-like	909					hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	endonuclease activity (GO:0004519)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	48		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)				GGTCTCTGAGAGCCTGGGATT	0.587																																					p.A909A		Atlas-SNP	.											.	PXDNL	414	.	0			c.T2727C						.						36.0	41.0	39.0					8																	52321457		1962	4138	6100	SO:0001819	synonymous_variant	137902	exon17			TCTGAGAGCCTGG		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.2727T>C	chr8.hg19:g.52321457A>G		66.0	0.0		92.0	5.0	NM_144651	B5ME43|B6CGZ3|H0YBM9|Q6ZMR2|Q96LH9	Silent	SNP	ENST00000356297.4	hg19	CCDS47855.1	.	.	.	.	.	.	.	.	.	.	A	0.362	-0.938952	0.02340	.	.	ENSG00000147485	ENST00000522933	.	.	.	4.17	-8.15	0.01065	.	.	.	.	.	T	0.16041	0.0386	.	.	.	0.29347	N	0.865632	.	.	.	.	.	.	T	0.29912	-0.9996	4	.	.	.	.	2.0469	0.03562	0.1763:0.4275:0.1848:0.2115	.	.	.	.	P	28	.	.	L	-	2	0	PXDNL	52484010	0.000000	0.05858	0.001000	0.08648	0.008000	0.06430	-0.916000	0.04029	-0.713000	0.04981	-0.250000	0.11733	CTC	.	.		0.587	PXDNL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377905.1	NM_144651	
LYPLA1	10434	hgsc.bcm.edu	37	8	55014376	55014376	+	Missense_Mutation	SNP	C	C	T	rs568447147		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:55014376C>T	ENST00000316963.3	-	1	201	c.8G>A	c.(7-9)gGc>gAc	p.G3D	LYPLA1_ENST00000522007.1_Missense_Mutation_p.G3D|LYPLA1_ENST00000519926.1_5'UTR|LYPLA1_ENST00000343231.6_Missense_Mutation_p.G3D	NM_001279360.1|NM_006330.2	NP_001266289.1|NP_006321.1	O75608	LYPA1_HUMAN	lysophospholipase I	3					fatty acid metabolic process (GO:0006631)|negative regulation of Golgi to plasma membrane protein transport (GO:0042997)|nitric oxide metabolic process (GO:0046209)|protein depalmitoylation (GO:0002084)|regulation of nitric-oxide synthase activity (GO:0050999)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	lysophospholipase activity (GO:0004622)|palmitoyl-(protein) hydrolase activity (GO:0008474)			central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(3)	6		Lung NSC(129;0.109)|all_epithelial(80;0.11)|all_lung(136;0.181)	OV - Ovarian serous cystadenocarcinoma(7;8.48e-07)|Epithelial(17;9.29e-05)|all cancers(17;0.000689)			CATGTTATTGCCGCACATACA	0.736													C|||	1	0.000199681	0.0	0.0	5008	,	,		6889	0.0		0.001	False		,,,				2504	0.0				p.G3D		Atlas-SNP	.											.	LYPLA1	15	.	0			c.G8A						.						13.0	11.0	12.0					8																	55014376		2182	4262	6444	SO:0001583	missense	10434	exon1			TTATTGCCGCACA	AF081281	CCDS6157.1, CCDS64899.1, CCDS75738.1, CCDS75739.1	8q11.23-q12.1	2008-05-15			ENSG00000120992	ENSG00000120992	3.1.1.5		6737	protein-coding gene	gene with protein product		605599				10064899	Standard	NM_006330		Approved	LPL1	uc003xry.3	O75608	OTTHUMG00000164313	ENST00000316963.3:c.8G>A	chr8.hg19:g.55014376C>T	ENSP00000320043:p.Gly3Asp	170.0	0.0		137.0	6.0	NM_006330	O43202|Q9UQF9	Missense_Mutation	SNP	ENST00000316963.3	hg19	CCDS6157.1	.	.	.	.	.	.	.	.	.	.	C	15.44	2.835586	0.50951	.	.	ENSG00000120992	ENST00000316963;ENST00000523751;ENST00000343231;ENST00000518546;ENST00000522007;ENST00000519926;ENST00000517297;ENST00000521898	T;T;T	0.36520	1.55;1.25;1.37	3.72	3.72	0.42706	.	0.175026	0.49305	D	0.000144	T	0.32882	0.0844	L	0.40543	1.245	0.48452	D	0.999654	B	0.18968	0.032	B	0.29440	0.102	T	0.30880	-0.9963	10	0.87932	D	0	0.0601	12.5131	0.56017	0.0:1.0:0.0:0.0	.	3	O75608	LYPA1_HUMAN	D	3	ENSP00000320043:G3D;ENSP00000344477:G3D;ENSP00000428729:G3D	ENSP00000320043:G3D	G	-	2	0	LYPLA1	55176929	1.000000	0.71417	0.995000	0.50966	0.392000	0.30506	5.456000	0.66665	1.905000	0.55150	0.305000	0.20034	GGC	.	.		0.736	LYPLA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378238.1		
TGS1	96764	hgsc.bcm.edu	37	8	56711514	56711514	+	Silent	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:56711514A>G	ENST00000260129.5	+	8	2061	c.1584A>G	c.(1582-1584)gaA>gaG	p.E528E		NM_024831.6	NP_079107.6	Q96RS0	TGS1_HUMAN	trimethylguanosine synthase 1	528					7-methylguanosine cap hypermethylation (GO:0036261)|7-methylguanosine RNA capping (GO:0009452)|cellular lipid metabolic process (GO:0044255)|gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|regulation of transcription, DNA-templated (GO:0006355)|ribonucleoprotein complex biogenesis (GO:0022613)|ribonucleoprotein complex import into nucleus (GO:0071167)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|spliceosomal snRNP assembly (GO:0000387)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|small nuclear ribonucleoprotein complex (GO:0030532)	RNA trimethylguanosine synthase activity (GO:0071164)			breast(3)|central_nervous_system(1)|endometrium(4)|large_intestine(5)|lung(10)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	29		all_lung(136;0.119)|all_epithelial(80;0.125)|Lung NSC(129;0.147)	Epithelial(17;0.00027)|all cancers(17;0.00251)			CAATGGATGAAGAAGCATCAC	0.378																																					p.E528E	Esophageal Squamous(34;275 823 4842 34837 48447)	Atlas-SNP	.											.	TGS1	66	.	0			c.A1584G						.						88.0	76.0	80.0					8																	56711514		2203	4300	6503	SO:0001819	synonymous_variant	96764	exon8			GGATGAAGAAGCA	AY028423	CCDS34894.1	8q11	2010-06-25	2010-06-25	2006-11-27	ENSG00000137574	ENSG00000137574	2.1.1.-		17843	protein-coding gene	gene with protein product		606461	"""nuclear receptor coactivator 6 interacting protein"", ""trimethylguanosine synthase homolog (S. cerevisiae)"""	NCOA6IP		11517327, 11983179, 19307714	Standard	NM_024831		Approved	PIMT	uc003xsj.4	Q96RS0	OTTHUMG00000164294	ENST00000260129.5:c.1584A>G	chr8.hg19:g.56711514A>G		55.0	0.0		76.0	4.0	NM_024831	A6NJQ5|Q5GH23|Q8TDG9|Q96QU3|Q9H5V3	Silent	SNP	ENST00000260129.5	hg19	CCDS34894.1																																																																																			.	.		0.378	TGS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378152.1	NM_024831	
TRPA1	8989	hgsc.bcm.edu	37	8	72951124	72951124	+	Silent	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:72951124A>G	ENST00000262209.4	-	19	2478	c.2271T>C	c.(2269-2271)gaT>gaC	p.D757D	TRPA1_ENST00000519720.1_5'UTR|RP11-383H13.1_ENST00000524152.1_Intron|RP11-383H13.1_ENST00000457356.4_Intron|RP11-383H13.1_ENST00000537896.1_Intron	NM_007332.2	NP_015628.2	O75762	TRPA1_HUMAN	transient receptor potential cation channel, subfamily A, member 1	757					calcium ion transmembrane transport (GO:0070588)|detection of chemical stimulus involved in sensory perception of pain (GO:0050968)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|response to cold (GO:0009409)|response to drug (GO:0042493)|response to hydrogen peroxide (GO:0042542)|response to pain (GO:0048265)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|stereocilium bundle (GO:0032421)	calcium channel activity (GO:0005262)|channel activity (GO:0015267)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(26)|lung(44)|ovary(4)|prostate(6)|stomach(1)	98			Epithelial(68;0.223)		Menthol(DB00825)	TTTCTGAATGATCACTAGTTT	0.308																																					p.D757D		Atlas-SNP	.											.	TRPA1	256	.	0			c.T2271C						.						87.0	83.0	84.0					8																	72951124		2203	4300	6503	SO:0001819	synonymous_variant	8989	exon19			TGAATGATCACTA	Y10601	CCDS34908.1	8q13	2013-01-10	2003-11-20	2003-11-20	ENSG00000104321	ENSG00000104321		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	497	protein-coding gene	gene with protein product		604775	"""ankyrin-like with transmembrane domains 1"""	ANKTM1		16382100	Standard	NM_007332		Approved		uc003xza.3	O75762	OTTHUMG00000164516	ENST00000262209.4:c.2271T>C	chr8.hg19:g.72951124A>G		87.0	0.0		95.0	4.0	NM_007332	A6NIN6	Silent	SNP	ENST00000262209.4	hg19	CCDS34908.1																																																																																			.	.		0.308	TRPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379079.2	NM_007332	
KCNB2	9312	hgsc.bcm.edu	37	8	73480466	73480466	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:73480466A>G	ENST00000523207.1	+	2	1085	c.497A>G	c.(496-498)gAg>gGg	p.E166G		NM_004770.2	NP_004761.2	Q92953	KCNB2_HUMAN	potassium voltage-gated channel, Shab-related subfamily, member 2	166					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of smooth muscle contraction (GO:0006940)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(20)|liver(2)|lung(31)|ovary(2)|pancreas(3)|prostate(2)|skin(8)|upper_aerodigestive_tract(4)|urinary_tract(1)	85	Breast(64;0.137)		Epithelial(68;0.105)		Dalfampridine(DB06637)	GAAGGAGAAGAGTTTGATAAT	0.453																																					p.E166G		Atlas-SNP	.											.	KCNB2	228	.	0			c.A497G						.						125.0	133.0	131.0					8																	73480466		2203	4300	6503	SO:0001583	missense	9312	exon2			GAGAAGAGTTTGA	U69962	CCDS6209.1	8q13.2	2012-07-05			ENSG00000182674	ENSG00000182674		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6232	protein-coding gene	gene with protein product		607738				9612272, 16382104	Standard	NM_004770		Approved	Kv2.2	uc003xzb.3	Q92953	OTTHUMG00000164498	ENST00000523207.1:c.497A>G	chr8.hg19:g.73480466A>G	ENSP00000430846:p.Glu166Gly	118.0	0.0		110.0	5.0	NM_004770	Q7Z7D0|Q9BXD3	Missense_Mutation	SNP	ENST00000523207.1	hg19	CCDS6209.1	.	.	.	.	.	.	.	.	.	.	A	16.85	3.236890	0.58886	.	.	ENSG00000182674	ENST00000523207	D	0.97480	-4.4	6.07	6.07	0.98685	.	0.000000	0.33834	U	0.004516	D	0.95166	0.8433	L	0.43923	1.385	0.51012	D	0.9999	B	0.28801	0.223	B	0.30716	0.119	D	0.93452	0.6803	10	0.45353	T	0.12	.	16.3141	0.82909	1.0:0.0:0.0:0.0	.	166	Q92953	KCNB2_HUMAN	G	166	ENSP00000430846:E166G	ENSP00000430846:E166G	E	+	2	0	KCNB2	73643020	1.000000	0.71417	1.000000	0.80357	0.917000	0.54804	9.339000	0.96797	2.326000	0.78906	0.533000	0.62120	GAG	.	.		0.453	KCNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378998.1	NM_004770	
RAD54B	25788	hgsc.bcm.edu	37	8	95390864	95390864	+	Splice_Site	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:95390864T>C	ENST00000336148.5	-	13	2372		c.e13-2			NM_012415.3	NP_036547.1	Q9Y620	RA54B_HUMAN	RAD54 homolog B (S. cerevisiae)						ATP catabolic process (GO:0006200)|DNA duplex unwinding (GO:0032508)|double-strand break repair via homologous recombination (GO:0000724)|mitotic recombination (GO:0006312)|reciprocal meiotic recombination (GO:0007131)	nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA translocase activity (GO:0015616)|RNA helicase activity (GO:0003724)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(10)|lung(15)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	39	Breast(36;4.5e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00217)			AGACATTGCCTATAGAAAATA	0.348								Direct reversal of damage;Homologous recombination																													.		Atlas-SNP	.											.	RAD54B	88	.	0			c.1696-2A>G						.						73.0	74.0	74.0					8																	95390864		2203	4299	6502	SO:0001630	splice_region_variant	25788	exon12			ATTGCCTATAGAA	AF112481	CCDS6262.1, CCDS56546.1, CCDS75768.1	8q22.1	2014-08-08			ENSG00000197275	ENSG00000197275			17228	protein-coding gene	gene with protein product		604289				10362364, 10851248	Standard	NM_012415		Approved	RDH54	uc003ygk.3	Q9Y620	OTTHUMG00000133658	ENST00000336148.5:c.2248-2A>G	chr8.hg19:g.95390864T>C		101.0	0.0		97.0	28.0	NM_001205263	F6WBS8	Splice_Site	SNP	ENST00000336148.5	hg19	CCDS6262.1	.	.	.	.	.	.	.	.	.	.	T	24.7	4.560588	0.86335	.	.	ENSG00000197275	ENST00000336148;ENST00000546218	.	.	.	5.57	5.57	0.84162	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.7397	0.77882	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	RAD54B	95460040	1.000000	0.71417	0.982000	0.44146	0.982000	0.71751	7.582000	0.82546	2.121000	0.65114	0.533000	0.62120	.	.	.		0.348	RAD54B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257806.3	NM_012415	Intron
COL14A1	7373	hgsc.bcm.edu	37	8	121170404	121170404	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:121170404T>C	ENST00000297848.3	+	3	394	c.124T>C	c.(124-126)Tct>Cct	p.S42P	COL14A1_ENST00000309791.4_Missense_Mutation_p.S42P|COL14A1_ENST00000537875.1_Missense_Mutation_p.S42P|COL14A1_ENST00000247781.3_Missense_Mutation_p.S42P|COL14A1_ENST00000432943.2_3'UTR	NM_021110.1	NP_066933.1			collagen, type XIV, alpha 1											NS(1)|autonomic_ganglia(1)|breast(11)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(9)|large_intestine(31)|lung(42)|ovary(5)|pancreas(1)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	119	Lung NSC(37;6.52e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161)		OV - Ovarian serous cystadenocarcinoma(1;6.47e-38)|STAD - Stomach adenocarcinoma(47;0.00503)			TAATGTAATATCTCATGACAG	0.343																																					p.S42P		Atlas-SNP	.											.	COL14A1	292	.	0			c.T124C						.						69.0	69.0	69.0					8																	121170404		2203	4300	6503	SO:0001583	missense	7373	exon3			GTAATATCTCATG		CCDS34938.1	8q23	2013-02-11	2008-02-04		ENSG00000187955	ENSG00000187955		"""Collagens"", ""Fibronectin type III domain containing"""	2191	protein-coding gene	gene with protein product		120324	"""undulin"""	UND		1716629, 9427527	Standard	NM_021110		Approved		uc003yox.4	Q05707	OTTHUMG00000149877	ENST00000297848.3:c.124T>C	chr8.hg19:g.121170404T>C	ENSP00000297848:p.Ser42Pro	152.0	0.0		121.0	5.0	NM_021110		Missense_Mutation	SNP	ENST00000297848.3	hg19	CCDS34938.1	.	.	.	.	.	.	.	.	.	.	T	19.45	3.829968	0.71258	.	.	ENSG00000187955	ENST00000537875;ENST00000309791;ENST00000297848;ENST00000247781	T;T;T;T	0.59772	3.42;3.42;0.24;0.24	5.38	4.16	0.48862	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.424919	0.25109	N	0.033077	T	0.54287	0.1849	L	0.43152	1.355	0.33108	D	0.540153	D	0.53619	0.961	P	0.51324	0.666	T	0.66905	-0.5805	10	0.72032	D	0.01	.	5.4167	0.16378	0.2514:0.0:0.1447:0.6039	.	42	Q05707	COEA1_HUMAN	P	42	ENSP00000443974:S42P;ENSP00000311809:S42P;ENSP00000297848:S42P;ENSP00000247781:S42P	ENSP00000247781:S42P	S	+	1	0	COL14A1	121239585	0.996000	0.38824	0.959000	0.39883	0.992000	0.81027	1.589000	0.36644	2.035000	0.60131	0.528000	0.53228	TCT	.	.		0.343	COL14A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313657.2	NM_021110	
FER1L6	654463	hgsc.bcm.edu	37	8	125110040	125110040	+	Missense_Mutation	SNP	T	T	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:125110040T>G	ENST00000522917.1	+	37	5005	c.4799T>G	c.(4798-4800)gTg>gGg	p.V1600G	FER1L6_ENST00000399018.1_Missense_Mutation_p.V1600G|FER1L6-AS2_ENST00000520031.1_RNA	NM_001039112.2	NP_001034201.2	Q2WGJ9	FR1L6_HUMAN	fer-1-like family member 6	1600	C2 6. {ECO:0000255|PROSITE- ProRule:PRU00041}.					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)			GAATTGAGAGTGACCATCTGG	0.418																																					p.V1600G		Atlas-SNP	.											.	FER1L6	268	.	0			c.T4799G						.						104.0	98.0	100.0					8																	125110040		1998	4174	6172	SO:0001583	missense	654463	exon37			TGAGAGTGACCAT	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.4799T>G	chr8.hg19:g.125110040T>G	ENSP00000428280:p.Val1600Gly	147.0	0.0		123.0	5.0	NM_001039112		Missense_Mutation	SNP	ENST00000522917.1	hg19	CCDS43767.1	.	.	.	.	.	.	.	.	.	.	T	22.3	4.278294	0.80692	.	.	ENSG00000214814	ENST00000522917;ENST00000399018	D;D	0.97791	-4.54;-4.54	5.5	5.5	0.81552	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.249821	0.33732	U	0.004615	D	0.98635	0.9543	H	0.94423	3.535	0.80722	D	1	P	0.37038	0.579	P	0.47118	0.538	D	0.99872	1.1098	10	0.87932	D	0	-12.879	15.9545	0.79876	0.0:0.0:0.0:1.0	.	1600	Q2WGJ9	FR1L6_HUMAN	G	1600	ENSP00000428280:V1600G;ENSP00000381982:V1600G	ENSP00000381982:V1600G	V	+	2	0	FER1L6	125179221	1.000000	0.71417	0.997000	0.53966	0.937000	0.57800	7.972000	0.88022	2.228000	0.72767	0.529000	0.55759	GTG	.	.		0.418	FER1L6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381400.1	NM_001039112	
ZFAT	57623	hgsc.bcm.edu	37	8	135533127	135533127	+	Splice_Site	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:135533127T>C	ENST00000377838.3	-	13	3407	c.3233A>G	c.(3232-3234)gAg>gGg	p.E1078G	ZFAT_ENST00000520356.1_Splice_Site_p.E1066G|ZFAT_ENST00000523399.1_Splice_Site_p.E1016G|ZFAT_ENST00000517307.1_5'UTR|ZFAT_ENST00000520727.1_Splice_Site_p.E1066G|ZFAT_ENST00000429442.2_Splice_Site_p.E1066G|ZFAT_ENST00000520214.1_Splice_Site_p.E1066G	NM_001174157.1|NM_020863.3	NP_001167628.1|NP_065914.2	Q9P243	ZFAT_HUMAN	zinc finger and AT hook domain containing	1078					hematopoietic progenitor cell differentiation (GO:0002244)|spongiotrophoblast layer development (GO:0060712)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(10)|kidney(9)|large_intestine(8)|lung(16)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	54	all_epithelial(106;8.26e-19)|Lung NSC(106;3.47e-07)|all_lung(105;1.39e-06)|Ovarian(258;0.0102)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0432)			AAAAATTACCTCCCACTTGGG	0.413																																					p.E1078G		Atlas-SNP	.											.	ZFAT	265	.	0			c.A3233G						.						55.0	53.0	53.0					8																	135533127		1831	4080	5911	SO:0001630	splice_region_variant	57623	exon13			ATTACCTCCCACT	BC025423	CCDS43768.1, CCDS47924.1, CCDS43768.2, CCDS55275.1, CCDS55276.1	8q24.23	2008-06-05	2008-01-25	2008-01-25	ENSG00000066827	ENSG00000066827		"""Zinc fingers, C2H2-type"""	19899	protein-coding gene	gene with protein product		610931	"""zinc finger protein 406"""	ZNF406, ZFAT1		10819331, 18329245	Standard	NM_020863		Approved	KIAA1485	uc003yup.3	Q9P243	OTTHUMG00000164321	ENST00000377838.3:c.3234+1A>G	chr8.hg19:g.135533127T>C		130.0	0.0		143.0	7.0	NM_020863	B7ZL15|E9PER3|Q3MIM5|Q6PJ01|Q75PJ6|Q75PJ7|Q75PJ9|Q86X64	Missense_Mutation	SNP	ENST00000377838.3	hg19	CCDS47924.1	.	.	.	.	.	.	.	.	.	.	T	25.6	4.655457	0.88056	.	.	ENSG00000066827	ENST00000520356;ENST00000520727;ENST00000429442;ENST00000377838;ENST00000520214;ENST00000318135;ENST00000523399	T;T;T;T;T;T	0.11277	2.89;2.8;2.81;2.79;2.8;2.81	5.53	5.53	0.82687	.	0.116019	0.56097	D	0.000027	T	0.21227	0.0511	L	0.29908	0.895	0.51233	D	0.999912	D;D;D;D	0.89917	0.999;0.999;0.999;1.0	D;D;D;D	0.83275	0.986;0.994;0.951;0.996	T	0.02813	-1.1107	10	0.30078	T	0.28	-39.7844	14.5267	0.67894	0.0:0.0:0.0:1.0	.	197;1016;1066;1078	B7Z741;E9PER3;E9PBN4;Q9P243	.;.;.;ZFAT_HUMAN	G	1066;1066;1066;1078;1066;965;1016	ENSP00000427879:E1066G;ENSP00000427831:E1066G;ENSP00000394501:E1066G;ENSP00000367069:E1078G;ENSP00000428483:E1066G;ENSP00000429091:E1016G	ENSP00000326997:E965G	E	-	2	0	ZFAT	135602309	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.468000	0.73551	2.113000	0.64589	0.524000	0.50904	GAG	.	.		0.413	ZFAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378272.1	NM_001029939	Missense_Mutation
COL22A1	169044	hgsc.bcm.edu	37	8	139672699	139672699	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:139672699T>C	ENST00000303045.6	-	44	3711	c.3265A>G	c.(3265-3267)Aga>Gga	p.R1089G	COL22A1_ENST00000341807.4_5'UTR|COL22A1_ENST00000435777.1_Missense_Mutation_p.R1069G	NM_152888.1	NP_690848.1	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	1089	Collagen-like 9.|Gly-rich.|Pro-rich.				extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(14)|large_intestine(29)|lung(107)|ovary(13)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(15)|urinary_tract(4)	211	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			GGAGGCCCTCTTTCTCCTGGA	0.458										HNSCC(7;0.00092)																											p.R1089G		Atlas-SNP	.											.	COL22A1	390	.	0			c.A3265G						.						67.0	57.0	61.0					8																	139672699		2203	4300	6503	SO:0001583	missense	169044	exon44			GCCCTCTTTCTCC	AF406780	CCDS6376.1	8q24.3	2013-01-16			ENSG00000169436	ENSG00000169436		"""Collagens"""	22989	protein-coding gene	gene with protein product		610026					Standard	NM_152888		Approved		uc003yvd.3	Q8NFW1	OTTHUMG00000150035	ENST00000303045.6:c.3265A>G	chr8.hg19:g.139672699T>C	ENSP00000303153:p.Arg1089Gly	151.0	0.0		163.0	9.0	NM_152888	B7ZMH0|C9K0G4|Q8IVT9	Missense_Mutation	SNP	ENST00000303045.6	hg19	CCDS6376.1	.	.	.	.	.	.	.	.	.	.	T	14.50	2.555107	0.45487	.	.	ENSG00000169436	ENST00000303045;ENST00000435777;ENST00000545577	D;D	0.96073	-3.64;-3.9	4.83	4.83	0.62350	.	0.000000	0.52532	U	0.000065	D	0.97133	0.9063	M	0.82630	2.6	0.38530	D	0.948947	D;D	0.62365	0.989;0.991	D;D	0.78314	0.985;0.991	D	0.96645	0.9477	10	0.24483	T	0.36	.	10.9608	0.47385	0.0:0.0:0.0:1.0	.	1069;1089	Q8NFW1-2;Q8NFW1	.;COMA1_HUMAN	G	1089;1069;782	ENSP00000303153:R1089G;ENSP00000387655:R1069G	ENSP00000303153:R1089G	R	-	1	2	COL22A1	139741881	1.000000	0.71417	1.000000	0.80357	0.841000	0.47740	1.666000	0.37460	2.162000	0.67917	0.450000	0.29827	AGA	.	.		0.458	COL22A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000315905.2	XM_291257	
ARC	23237	hgsc.bcm.edu	37	8	143694836	143694836	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:143694836T>C	ENST00000356613.2	-	1	1997	c.797A>G	c.(796-798)gAg>gGg	p.E266G	ARC_ENST00000581404.1_5'Flank	NM_015193.4	NP_056008.1	O60936	NOL3_HUMAN	activity-regulated cytoskeleton-associated protein	0					apoptotic process (GO:0006915)|mRNA processing (GO:0006397)|negative regulation of apoptotic process (GO:0043066)|regulation of gene expression (GO:0010468)|response to hypoxia (GO:0001666)|response to injury involved in regulation of muscle adaptation (GO:0014876)|RNA splicing (GO:0008380)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|sarcoplasm (GO:0016528)	identical protein binding (GO:0042802)|RNA binding (GO:0003723)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|lung(3)|upper_aerodigestive_tract(1)	13	all_cancers(97;3.55e-12)|all_epithelial(106;1.03e-08)|Lung NSC(106;0.000353)|all_lung(105;0.00092)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)	Acute lymphoblastic leukemia(644;0.0279)				CTTCTTGAACTCCACCCAGTT	0.622																																					p.E266G		Atlas-SNP	.											.	ARC	34	.	0			c.A797G						.						43.0	45.0	44.0					8																	143694836		2203	4299	6502	SO:0001583	missense	23237	exon1			TTGAACTCCACCC	AF193421	CCDS34950.1	8q24.3	2008-08-01			ENSG00000198576	ENSG00000198576			648	protein-coding gene	gene with protein product		612461				10970730, 17466953	Standard	NM_015193		Approved	KIAA0278, Arg3.1	uc003ywn.2	Q7LC44	OTTHUMG00000134310	ENST00000356613.2:c.797A>G	chr8.hg19:g.143694836T>C	ENSP00000349022:p.Glu266Gly	115.0	0.0		117.0	7.0	NM_015193	B4DFL0|O60937	Missense_Mutation	SNP	ENST00000356613.2	hg19	CCDS34950.1	.	.	.	.	.	.	.	.	.	.	T	19.84	3.901245	0.72754	.	.	ENSG00000198576	ENST00000356613	.	.	.	4.92	4.92	0.64577	.	0.000000	0.47455	U	0.000223	T	0.49795	0.1578	N	0.19112	0.55	0.38121	D	0.937841	D	0.54964	0.969	P	0.53313	0.723	T	0.59043	-0.7528	9	0.59425	D	0.04	-17.5234	13.7151	0.62691	0.0:0.0:0.0:1.0	.	266	Q7LC44	ARC_HUMAN	G	266	.	ENSP00000349022:E266G	E	-	2	0	ARC	143691838	0.958000	0.32768	1.000000	0.80357	0.993000	0.82548	1.921000	0.40035	1.840000	0.53500	0.379000	0.24179	GAG	.	.		0.622	ARC-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259274.2		
ADCK5	203054	hgsc.bcm.edu	37	8	145617320	145617320	+	Silent	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:145617320A>G	ENST00000308860.6	+	11	1169	c.1125A>G	c.(1123-1125)aaA>aaG	p.K375K	CPSF1_ENST00000531727.1_5'Flank|MIR939_ENST00000401314.1_RNA	NM_174922.3	NP_777582.4	Q3MIX3	ADCK5_HUMAN	aarF domain containing kinase 5	375	Protein kinase.					integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	protein serine/threonine kinase activity (GO:0004674)			endometrium(1)|lung(2)|prostate(2)|skin(1)|stomach(2)	8	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;8.96e-41)|Epithelial(56;4.08e-40)|all cancers(56;4.51e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0323)|Colorectal(110;0.055)			CGGACGGGAAAGCGGAGCTGG	0.667																																					p.K375K		Atlas-SNP	.											.	ADCK5	36	.	0			c.A1125G						.						24.0	27.0	26.0					8																	145617320		2189	4296	6485	SO:0001819	synonymous_variant	203054	exon11			CGGGAAAGCGGAG	BC032402	CCDS34965.1, CCDS34965.2	8q24.3	2004-07-06			ENSG00000173137	ENSG00000173137			21738	protein-coding gene	gene with protein product							Standard	NM_174922		Approved	FLJ35454	uc003zch.3	Q3MIX3	OTTHUMG00000165190	ENST00000308860.6:c.1125A>G	chr8.hg19:g.145617320A>G		100.0	0.0		128.0	6.0	NM_174922	B3KS46|Q5U4P1|Q6P2S4|Q8N5V3	Silent	SNP	ENST00000308860.6	hg19	CCDS34965.1																																																																																			.	.		0.667	ADCK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382556.2	NM_174922	
DMRT3	58524	hgsc.bcm.edu	37	9	977116	977116	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:977116T>C	ENST00000190165.2	+	1	153	c.115T>C	c.(115-117)Tcc>Ccc	p.S39P		NM_021240.2	NP_067063.1	Q9NQL9	DMRT3_HUMAN	doublesex and mab-3 related transcription factor 3	39					adult walking behavior (GO:0007628)|male sex differentiation (GO:0046661)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|sex differentiation (GO:0007548)|transcription, DNA-templated (GO:0006351)|transmission of nerve impulse (GO:0019226)|ventral spinal cord interneuron specification (GO:0021521)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(1)|large_intestine(5)|lung(11)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	26		all_lung(10;1.39e-08)|Lung NSC(10;1.42e-08)		Lung(218;0.0196)		TGGCGTCCTGTCCTGGCTCAA	0.682																																					p.S39P		Atlas-SNP	.											.	DMRT3	83	.	0			c.T115C						.						23.0	19.0	21.0					9																	977116		2200	4299	6499	SO:0001583	missense	58524	exon1			GTCCTGTCCTGGC	AJ301581	CCDS6443.1	9p24.3	2008-07-21	2001-12-17	2001-12-07	ENSG00000064218	ENSG00000064218			13909	protein-coding gene	gene with protein product	"""testis-specific protein"""	614754	"""DMRT-like family A3"""	DMRTA3		11543627, 10729223	Standard	NM_021240		Approved		uc003zgw.2	Q9NQL9	OTTHUMG00000019436	ENST00000190165.2:c.115T>C	chr9.hg19:g.977116T>C	ENSP00000190165:p.Ser39Pro	168.0	0.0		94.0	4.0	NM_021240	Q7LA03|Q7LCH8|Q96SC7|Q9NRQ9	Missense_Mutation	SNP	ENST00000190165.2	hg19	CCDS6443.1	.	.	.	.	.	.	.	.	.	.	T	23.6	4.438993	0.83885	.	.	ENSG00000064218	ENST00000190165	T	0.29655	1.56	3.75	3.75	0.43078	DM DNA-binding (6);	0.000000	0.85682	D	0.000000	T	0.63792	0.2541	M	0.93375	3.41	0.80722	D	1	D	0.76494	0.999	D	0.87578	0.998	T	0.74281	-0.3716	10	0.87932	D	0	-27.9163	12.7597	0.57356	0.0:0.0:0.0:1.0	.	39	Q9NQL9	DMRT3_HUMAN	P	39	ENSP00000190165:S39P	ENSP00000190165:S39P	S	+	1	0	DMRT3	967116	1.000000	0.71417	1.000000	0.80357	0.867000	0.49689	4.136000	0.58004	1.465000	0.48006	0.379000	0.24179	TCC	.	.		0.682	DMRT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051490.1	NM_021240	
KIAA0020	9933	hgsc.bcm.edu	37	9	2834151	2834151	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:2834151T>C	ENST00000397885.2	-	4	526	c.320A>G	c.(319-321)aAg>aGg	p.K107R		NM_014878.4	NP_055693.4	Q15397	K0020_HUMAN	KIAA0020	107						endoplasmic reticulum (GO:0005783)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(4)|ovary(1)	21				GBM - Glioblastoma multiforme(50;0.0319)		CCATTTGGGCTTCTTGGCTGC	0.348																																					p.K107R		Atlas-SNP	.											.	KIAA0020	56	.	0			c.A320G						.						68.0	69.0	69.0					9																	2834151		2202	4300	6502	SO:0001583	missense	9933	exon4			TTGGGCTTCTTGG	AL832239	CCDS6448.2	9p24.2	2012-11-29			ENSG00000080608	ENSG00000080608			29676	protein-coding gene	gene with protein product	"""penguin homolog (Drosophila)"", ""minor histocompatibility antigen HA-8"""	609960				7584026, 7584028, 21266351	Standard	NM_014878		Approved	XTP5, PEN, PUF6, hPUF-A, HA-8	uc003zhp.1	Q15397	OTTHUMG00000019450	ENST00000397885.2:c.320A>G	chr9.hg19:g.2834151T>C	ENSP00000380982:p.Lys107Arg	112.0	0.0		96.0	4.0	NM_014878	A8K804|Q547G7|Q5SZY9|Q6IB47|Q96B27|Q96L78|Q96L79|Q96L80	Missense_Mutation	SNP	ENST00000397885.2	hg19	CCDS6448.2	.	.	.	.	.	.	.	.	.	.	T	16.16	3.044148	0.55110	.	.	ENSG00000080608	ENST00000397885	T	0.29655	1.56	5.54	4.41	0.53225	.	0.000000	0.85682	D	0.000000	T	0.50973	0.1647	M	0.74389	2.26	0.58432	D	0.999997	D	0.71674	0.998	D	0.63793	0.918	T	0.51888	-0.8648	10	0.54805	T	0.06	-2.1886	11.3176	0.49401	0.0:0.0711:0.0:0.9289	.	107	Q15397	K0020_HUMAN	R	107	ENSP00000380982:K107R	ENSP00000380982:K107R	K	-	2	0	KIAA0020	2824151	1.000000	0.71417	0.993000	0.49108	0.596000	0.36781	6.420000	0.73349	0.944000	0.37579	-0.250000	0.11733	AAG	.	.		0.348	KIAA0020-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051529.3	NM_014878	
RPS6	6194	hgsc.bcm.edu	37	9	19378464	19378464	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:19378464A>G	ENST00000380394.4	-	4	456	c.398T>C	c.(397-399)cTg>cCg	p.L133P	RP11-513M16.8_ENST00000609982.1_RNA|RPS6_ENST00000498815.1_5'Flank|RPS6_ENST00000315377.4_Missense_Mutation_p.L102P|RPS6_ENST00000380384.1_Missense_Mutation_p.L102P	NM_001010.2	NP_001001.2	P62753	RS6_HUMAN	ribosomal protein S6	133					activation-induced cell death of T cells (GO:0006924)|cellular protein metabolic process (GO:0044267)|erythrocyte development (GO:0048821)|G1/S transition of mitotic cell cycle (GO:0000082)|gastrulation (GO:0007369)|gene expression (GO:0010467)|glucose homeostasis (GO:0042593)|insulin receptor signaling pathway (GO:0008286)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|oogenesis stage (GO:0022605)|placenta development (GO:0001890)|positive regulation of apoptotic process (GO:0043065)|ribosomal small subunit assembly (GO:0000028)|ribosomal small subunit biogenesis (GO:0042274)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|T cell differentiation in thymus (GO:0033077)|T cell proliferation involved in immune response (GO:0002309)|TOR signaling (GO:0031929)|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)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|cytosolic small ribosomal subunit (GO:0022627)|dendrite (GO:0030425)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|polysome (GO:0005844)|ribonucleoprotein complex (GO:0030529)|small ribosomal subunit (GO:0015935)	poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|structural constituent of ribosome (GO:0003735)			endometrium(3)|lung(2)|ovary(1)|urinary_tract(1)	7		Colorectal(97;3.46e-05)|Myeloproliferative disorder(762;0.0255)		Lung(42;0.161)|LUSC - Lung squamous cell carcinoma(42;0.234)		TTTGGGGCCCAGGCGGCGAGG	0.418																																					p.L133P		Atlas-SNP	.											.	RPS6	25	.	0			c.T398C						.						67.0	68.0	68.0					9																	19378464		2203	4300	6503	SO:0001583	missense	6194	exon4			GGGCCCAGGCGGC		CCDS6492.1	9p21	2011-04-05			ENSG00000137154	ENSG00000137154		"""S ribosomal proteins"""	10429	protein-coding gene	gene with protein product	"""40S ribosomal protein S6"", ""phosphoprotein NP33"""	180460				1577483	Standard	NM_001010		Approved	S6	uc003znv.1	P62753	OTTHUMG00000019642	ENST00000380394.4:c.398T>C	chr9.hg19:g.19378464A>G	ENSP00000369757:p.Leu133Pro	139.0	0.0		105.0	5.0	NM_001010	P08227|P10660|Q4VBY7|Q8N6Z7	Missense_Mutation	SNP	ENST00000380394.4	hg19	CCDS6492.1	.	.	.	.	.	.	.	.	.	.	A	17.05	3.289660	0.59976	.	.	ENSG00000137154	ENST00000380394;ENST00000380384;ENST00000315377	T;T;T	0.54675	0.57;0.56;0.56	5.32	5.32	0.75619	.	0.000000	0.64402	D	0.000001	T	0.74824	0.3767	M	0.84948	2.725	0.80722	D	1	D;B	0.89917	1.0;0.366	D;B	0.74348	0.983;0.25	T	0.78725	-0.2092	9	.	.	.	-10.2462	15.5723	0.76349	1.0:0.0:0.0:0.0	.	102;133	A2A3R5;P62753	.;RS6_HUMAN	P	133;102;102	ENSP00000369757:L133P;ENSP00000369745:L102P;ENSP00000369743:L102P	.	L	-	2	0	RPS6	19368464	1.000000	0.71417	1.000000	0.80357	0.459000	0.32528	9.190000	0.94934	2.139000	0.66308	0.533000	0.62120	CTG	.	.		0.418	RPS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051858.1	NM_001010	
TEK	7010	hgsc.bcm.edu	37	9	27169606	27169606	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:27169606T>C	ENST00000380036.4	+	4	1049	c.607T>C	c.(607-609)Ttc>Ctc	p.F203L	TEK_ENST00000406359.4_Missense_Mutation_p.F203L|TEK_ENST00000519097.1_Missense_Mutation_p.F99L	NM_000459.3	NP_000450	Q02763	TIE2_HUMAN	TEK tyrosine kinase, endothelial	203					angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cell-cell signaling (GO:0007267)|cell-matrix adhesion (GO:0007160)|definitive hemopoiesis (GO:0060216)|endochondral ossification (GO:0001958)|endothelial cell proliferation (GO:0001935)|glomerulus vasculature development (GO:0072012)|heart development (GO:0007507)|heart trabecula formation (GO:0060347)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|negative regulation of angiogenesis (GO:0016525)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of inflammatory response (GO:0050728)|organ regeneration (GO:0031100)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|protein autophosphorylation (GO:0046777)|protein oligomerization (GO:0051259)|regulation of endothelial cell apoptotic process (GO:2000351)|regulation of establishment or maintenance of cell polarity (GO:0032878)|regulation of vascular permeability (GO:0043114)|response to cAMP (GO:0051591)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|response to peptide hormone (GO:0043434)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|sprouting angiogenesis (GO:0002040)|substrate adhesion-dependent cell spreading (GO:0034446)|Tie signaling pathway (GO:0048014)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|receptor activity (GO:0004872)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(3)|central_nervous_system(3)|kidney(1)|lung(2)|ovary(3)|skin(3)	15		all_neural(11;7.57e-10)|Myeloproliferative disorder(762;0.0255)		Lung(218;4.08e-05)|LUSC - Lung squamous cell carcinoma(38;0.00027)	Ponatinib(DB08901)|Regorafenib(DB08896)|Vandetanib(DB05294)	CACCTCGGCCTTCACCAGGCT	0.473																																					p.F203L		Atlas-SNP	.											TEK_ENST00000380036,colon,carcinoma,0,4	TEK	250	.	0			c.T607C						.						105.0	97.0	100.0					9																	27169606		2203	4300	6503	SO:0001583	missense	7010	exon4			TCGGCCTTCACCA	L06139	CCDS6519.1, CCDS75825.1	9p21	2013-02-11	2008-07-31		ENSG00000120156	ENSG00000120156		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	11724	protein-coding gene	gene with protein product		600221	"""venous malformations, multiple cutaneous and mucosal"""	VMCM		1312667, 7833915	Standard	XM_005251561		Approved	TIE2, TIE-2, VMCM1, CD202b	uc003zqi.4	Q02763	OTTHUMG00000019712	ENST00000380036.4:c.607T>C	chr9.hg19:g.27169606T>C	ENSP00000369375:p.Phe203Leu	101.0	0.0		82.0	4.0	NM_000459	A8K6W0|B4DH20|B4DHD3|D3DRK5|E7EWI2|Q5TCU2|Q8IV34	Missense_Mutation	SNP	ENST00000380036.4	hg19	CCDS6519.1	.	.	.	.	.	.	.	.	.	.	T	19.77	3.888708	0.72524	.	.	ENSG00000120156	ENST00000519097;ENST00000380036;ENST00000346448;ENST00000406359;ENST00000519080	T;T;T;T	0.71103	-0.51;-0.5;-0.54;3.11	5.48	5.48	0.80851	Immunoglobulin-like fold (1);	0.123114	0.37348	N	0.002137	T	0.61185	0.2327	L	0.35487	1.065	0.40886	D	0.984034	B;P;P;P;P;P	0.48640	0.243;0.821;0.913;0.646;0.646;0.688	B;B;B;B;B;B	0.41036	0.066;0.346;0.234;0.091;0.158;0.157	T	0.62987	-0.6737	10	0.31617	T	0.26	.	15.5207	0.75862	0.0:0.0:0.0:1.0	.	99;236;203;56;203;203	E7EWI2;Q59HG2;B5A953;E5RIV9;B4DHD3;Q02763	.;.;.;.;.;TIE2_HUMAN	L	99;203;203;203;56	ENSP00000430686:F99L;ENSP00000369375:F203L;ENSP00000383977:F203L;ENSP00000428337:F56L	ENSP00000343716:F203L	F	+	1	0	TEK	27159606	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	3.758000	0.55220	2.211000	0.71520	0.459000	0.35465	TTC	.	.		0.473	TEK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051965.3		
NFX1	4799	hgsc.bcm.edu	37	9	33307273	33307273	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:33307273A>G	ENST00000379540.3	+	5	1414	c.1352A>G	c.(1351-1353)cAg>cGg	p.Q451R	NFX1_ENST00000379521.4_Missense_Mutation_p.Q451R|NFX1_ENST00000318524.6_Missense_Mutation_p.Q451R	NM_002504.4	NP_002495.2	Q12986	NFX1_HUMAN	nuclear transcription factor, X-box binding 1	451					inflammatory response (GO:0006954)|negative regulation of MHC class II biosynthetic process (GO:0045347)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(4)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	25			LUSC - Lung squamous cell carcinoma(29;0.00506)	GBM - Glioblastoma multiforme(74;0.224)		CAGCCTGGCCAGGACTGCCCA	0.458																																					p.Q451R		Atlas-SNP	.											.	NFX1	85	.	0			c.A1352G						.						151.0	147.0	148.0					9																	33307273		2203	4300	6503	SO:0001583	missense	4799	exon5			CTGGCCAGGACTG	U19759	CCDS6538.1, CCDS6539.1, CCDS6540.1	9p12	2013-12-13			ENSG00000086102	ENSG00000086102			7803	protein-coding gene	gene with protein product		603255				7964459, 2511169	Standard	NM_002504		Approved	NFX2, MGC20369, Tex42, TEG-42	uc003zsq.3	Q12986	OTTHUMG00000019772	ENST00000379540.3:c.1352A>G	chr9.hg19:g.33307273A>G	ENSP00000368856:p.Gln451Arg	207.0	0.0		128.0	6.0	NM_147134	A8K6H8|Q5VXW6|Q96EL5|Q9BXI1	Missense_Mutation	SNP	ENST00000379540.3	hg19	CCDS6538.1	.	.	.	.	.	.	.	.	.	.	A	10.65	1.408916	0.25378	.	.	ENSG00000086102	ENST00000379540;ENST00000379521;ENST00000536210;ENST00000318524	T;T;T	0.41400	1.0;1.0;1.0	5.47	5.47	0.80525	.	0.208500	0.41194	D	0.000927	T	0.40398	0.1115	L	0.41824	1.3	0.23769	N	0.996897	D;D;P;D;B	0.63880	0.993;0.976;0.88;0.986;0.139	P;B;B;P;B	0.52646	0.705;0.274;0.424;0.561;0.176	T	0.25502	-1.0130	10	0.15499	T	0.54	-4.8251	8.9071	0.35530	0.8338:0.0:0.0:0.1662	.	451;335;451;451;451	F5GXD0;A0JLR2;Q12986;Q12986-2;Q12986-3	.;.;NFX1_HUMAN;.;.	R	451	ENSP00000368856:Q451R;ENSP00000368836:Q451R;ENSP00000317695:Q451R	ENSP00000317695:Q451R	Q	+	2	0	NFX1	33297273	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.683000	0.37638	2.092000	0.63282	0.477000	0.44152	CAG	.	.		0.458	NFX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052069.1		
AQP3	360	hgsc.bcm.edu	37	9	33442208	33442208	+	Splice_Site	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:33442208T>C	ENST00000297991.4	-	6	792	c.712A>G	c.(712-714)Acc>Gcc	p.T238A	AQP3_ENST00000493581.1_5'UTR	NM_004925.4	NP_004916.1	Q92482	AQP3_HUMAN	aquaporin 3 (Gill blood group)	238					excretion (GO:0007588)|odontogenesis (GO:0042476)|positive regulation of immune system process (GO:0002684)|regulation of keratinocyte differentiation (GO:0045616)|renal water absorption (GO:0070295)|response to calcium ion (GO:0051592)|response to retinoic acid (GO:0032526)|response to vitamin D (GO:0033280)|transmembrane transport (GO:0055085)|transport (GO:0006810)|urea transport (GO:0015840)|water transport (GO:0006833)	basolateral plasma membrane (GO:0016323)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	glycerol channel activity (GO:0015254)|transporter activity (GO:0005215)|water channel activity (GO:0015250)			endometrium(2)|large_intestine(3)|lung(2)|ovary(1)	8			LUSC - Lung squamous cell carcinoma(29;0.00788)	GBM - Glioblastoma multiforme(74;0.0899)		TGCTGGCCGGTCCTGGGGGGA	0.642																																					p.T238A		Atlas-SNP	.											.	AQP3	18	.	0			c.A712G						.						21.0	23.0	22.0					9																	33442208		2192	4282	6474	SO:0001630	splice_region_variant	360	exon6			GGCCGGTCCTGGG		CCDS6542.1	9p13	2014-07-18	2006-02-23		ENSG00000165272	ENSG00000165272		"""Ion channels / Aquaporins"", ""Blood group antigens"""	636	protein-coding gene	gene with protein product	"""Gill blood group"""	600170	"""aquaporin 3"", ""aquaporin 3 (GIL blood group)"""			7558005	Standard	NM_004925		Approved	GIL	uc003zsx.3	Q92482	OTTHUMG00000019769	ENST00000297991.4:c.711-1A>G	chr9.hg19:g.33442208T>C		121.0	0.0		105.0	5.0	NM_004925	A8K843|B2RE16|D3DRL3|O00108|Q6FGT2|Q6FGW6	Missense_Mutation	SNP	ENST00000297991.4	hg19	CCDS6542.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	1.905|1.905	-0.452141|-0.452141	0.04540|0.04540	.|.	.|.	ENSG00000165272|ENSG00000165272	ENST00000343952|ENST00000297991	.|T	.|0.10288	.|2.89	5.59|5.59	5.59|5.59	0.84812|0.84812	.|Aquaporin-like (2);	.|0.132399	.|0.50627	.|D	.|0.000101	T|T	0.02418|0.02418	0.0074|0.0074	N|N	0.00566|0.00566	-1.37|-1.37	0.37308|0.37308	D|D	0.909006|0.909006	B|B	0.06786|0.11235	0.001|0.004	B|B	0.01281|0.13407	0.0|0.009	T|T	0.33394|0.33394	-0.9870|-0.9870	8|10	0.46703|0.02654	T|T	0.11|1	-9.2426|-9.2426	7.9441|7.9441	0.29976|0.29976	0.0:0.1963:0.0:0.8037|0.0:0.1963:0.0:0.8037	.|.	165|238	C9JAH5|Q92482	.|AQP3_HUMAN	G|A	165|238	.|ENSP00000297991:T238A	ENSP00000339229:D165G|ENSP00000297991:T238A	D|T	-|-	2|1	0|0	AQP3|AQP3	33432208|33432208	0.443000|0.443000	0.25641|0.25641	1.000000|1.000000	0.80357|0.80357	0.758000|0.758000	0.43043|0.43043	1.577000|1.577000	0.36515|0.36515	2.125000|2.125000	0.65367|0.65367	0.460000|0.460000	0.39030|0.39030	GAC|ACC	.	.		0.642	AQP3-001	KNOWN	mRNA_start_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052055.1	NM_004925	Missense_Mutation
UBAP2	55833	hgsc.bcm.edu	37	9	33971700	33971700	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:33971700T>C	ENST00000379238.1	-	8	745	c.628A>G	c.(628-630)Aca>Gca	p.T210A	UBAP2_ENST00000449054.1_Missense_Mutation_p.T210A|UBAP2_ENST00000379239.4_Intron|UBAP2_ENST00000418786.2_Intron|UBAP2_ENST00000360802.1_Missense_Mutation_p.T210A|UBAP2_ENST00000539807.1_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)		ACTAGCTTTGTCCCACACACA	0.388																																					p.T210A		Atlas-SNP	.											.	UBAP2	82	.	0			c.A628G						.						133.0	131.0	132.0					9																	33971700		2203	4300	6503	SO:0001583	missense	55833	exon8			GCTTTGTCCCACA	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.628A>G	chr9.hg19:g.33971700T>C	ENSP00000368540:p.Thr210Ala	180.0	0.0		132.0	6.0	NM_018449		Missense_Mutation	SNP	ENST00000379238.1	hg19	CCDS6547.1	.	.	.	.	.	.	.	.	.	.	T	12.66	2.005458	0.35415	.	.	ENSG00000137073	ENST00000379238;ENST00000449054;ENST00000360802;ENST00000379260;ENST00000421278	T;T;T	0.11495	2.77;2.77;2.77	5.63	0.293	0.15742	.	0.431234	0.24757	N	0.035851	T	0.04543	0.0124	N	0.25485	0.75	0.80722	D	1	B;P	0.39391	0.374;0.671	B;B	0.33254	0.16;0.145	T	0.50259	-0.8849	10	0.13470	T	0.59	-3.0822	3.4001	0.07320	0.1741:0.3316:0.0:0.4944	.	135;210	F5H4D5;Q5T6F2	.;UBAP2_HUMAN	A	210;210;210;150;86	ENSP00000368540:T210A;ENSP00000416932:T210A;ENSP00000354039:T210A	ENSP00000354039:T210A	T	-	1	0	UBAP2	33961700	0.926000	0.31397	0.963000	0.40424	0.900000	0.52787	0.502000	0.22594	0.019000	0.15079	0.528000	0.53228	ACA	.	.		0.388	UBAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001071.1	NM_018449	
OR13J1	392309	hgsc.bcm.edu	37	9	35870002	35870002	+	Missense_Mutation	SNP	G	G	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:35870002G>C	ENST00000377981.2	-	1	459	c.397C>G	c.(397-399)Cac>Gac	p.H133D		NM_001004487.1	NP_001004487.1	Q8NGT2	O13J1_HUMAN	olfactory receptor, family 13, subfamily J, member 1	133			H -> R (in dbSNP:rs7044405).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.H133Y(1)		central_nervous_system(1)|large_intestine(1)|lung(3)|skin(1)	6	all_epithelial(49;0.169)		LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00494)|STAD - Stomach adenocarcinoma(86;0.194)			ATGAGCACGTGGTACCTGAGT	0.622																																					p.H133D		Atlas-SNP	.											OR13J1,colon,carcinoma,0,1	OR13J1	37	.	1	Substitution - Missense(1)	large_intestine(1)	c.C397G						.																																			SO:0001583	missense	392309	exon1			GCACGTGGTACCT		CCDS35011.1	9p13.3	2013-09-24			ENSG00000168828	ENSG00000168828		"""GPCR / Class A : Olfactory receptors"""	15108	protein-coding gene	gene with protein product							Standard	NM_001004487		Approved		uc011lph.2	Q8NGT2	OTTHUMG00000019879	ENST00000377981.2:c.397C>G	chr9.hg19:g.35870002G>C	ENSP00000367219:p.His133Asp	209.0	0.0		135.0	0.0	NM_001004487	B2RN66|Q6IF20|Q96R40	Missense_Mutation	SNP	ENST00000377981.2	hg19	CCDS35011.1	.	.	.	.	.	.	.	.	.	.	G	12.13	1.846178	0.32606	.	.	ENSG00000168828	ENST00000377981	T	0.01323	5.01	4.62	3.71	0.42584	GPCR, rhodopsin-like superfamily (1);	0.112691	0.40302	N	0.001130	T	0.01558	0.0050	L	0.29908	0.895	0.19775	N	0.999955	B	0.26195	0.144	B	0.19391	0.025	T	0.45614	-0.9249	10	0.62326	D	0.03	.	12.4119	0.55471	0.0:0.0:0.8305:0.1695	.	133	Q8NGT2	O13J1_HUMAN	D	133	ENSP00000367219:H133D	ENSP00000367219:H133D	H	-	1	0	OR13J1	35860002	0.000000	0.05858	0.894000	0.35097	0.540000	0.34992	-0.698000	0.05092	1.527000	0.49086	0.650000	0.86243	CAC	.	.		0.622	OR13J1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052381.1		
PTAR1	375743	hgsc.bcm.edu	37	9	72338481	72338481	+	Silent	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:72338481T>C	ENST00000340434.4	-	6	711	c.708A>G	c.(706-708)ggA>ggG	p.G236G	PTAR1_ENST00000377200.5_Silent_p.G157G	NM_001099666.1	NP_001093136.1	Q7Z6K3	PTAR1_HUMAN	protein prenyltransferase alpha subunit repeat containing 1	236					protein prenylation (GO:0018342)		protein prenyltransferase activity (GO:0008318)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)	5						GGTAGTGAAATCCACTGTGGT	0.398																																					p.G236G		Atlas-SNP	.											.	PTAR1	46	.	0			c.A708G						.						98.0	92.0	94.0					9																	72338481		1853	4110	5963	SO:0001819	synonymous_variant	375743	exon6			GTGAAATCCACTG	BC053622	CCDS47978.1	9q21.13	2008-10-01			ENSG00000188647	ENSG00000188647		"""Prenyltransferase alpha subunit repeat containing"""	30449	protein-coding gene	gene with protein product						12477932	Standard	NM_001099666		Approved		uc004ahj.4	Q7Z6K3	OTTHUMG00000019982	ENST00000340434.4:c.708A>G	chr9.hg19:g.72338481T>C		234.0	0.0		143.0	6.0	NM_001099666	Q5T7V5|Q5T7V6	Silent	SNP	ENST00000340434.4	hg19	CCDS47978.1	.	.	.	.	.	.	.	.	.	.	T	3.965	-0.009517	0.07727	.	.	ENSG00000188647	ENST00000415701	.	.	.	5.69	3.27	0.37495	.	.	.	.	.	T	0.57330	0.2046	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50268	-0.8848	4	.	.	.	-9.3541	7.9037	0.29750	0.1228:0.0668:0.0:0.8104	.	.	.	.	V	3	.	.	I	-	1	0	PTAR1	71528301	1.000000	0.71417	1.000000	0.80357	0.427000	0.31564	2.074000	0.41529	0.466000	0.27193	-0.290000	0.09829	ATT	.	.		0.398	PTAR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052582.4	NM_001099666	
TMEM2	23670	hgsc.bcm.edu	37	9	74347404	74347404	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:74347404T>C	ENST00000377044.4	-	7	1965	c.1426A>G	c.(1426-1428)Ata>Gta	p.I476V	TMEM2_ENST00000377066.5_Missense_Mutation_p.I413V	NM_001135820.1|NM_013390.2	NP_001129292.1|NP_037522.1	Q9UHN6	TMEM2_HUMAN	transmembrane protein 2	476					multicellular organismal development (GO:0007275)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(15)|liver(1)|lung(19)|ovary(2)|prostate(5)|skin(1)|stomach(1)|urinary_tract(2)	56		all_epithelial(88;4.56e-14)|Myeloproliferative disorder(762;0.0255)		GBM - Glioblastoma multiforme(74;7.45e-21)|OV - Ovarian serous cystadenocarcinoma(323;1.02e-16)		ACACCGTCTATGATCTCACCC	0.418																																					p.I476V		Atlas-SNP	.											.	TMEM2	112	.	0			c.A1426G						.						94.0	85.0	88.0					9																	74347404		2203	4300	6503	SO:0001583	missense	23670	exon7			CGTCTATGATCTC		CCDS6638.1, CCDS47979.1	9q21.13	2011-07-19			ENSG00000135048	ENSG00000135048			11869	protein-coding gene	gene with protein product		605835					Standard	NM_013390		Approved		uc011lsa.1	Q9UHN6	OTTHUMG00000020000	ENST00000377044.4:c.1426A>G	chr9.hg19:g.74347404T>C	ENSP00000366243:p.Ile476Val	174.0	0.0		112.0	41.0	NM_013390	A6H8W9|B2RTQ6|Q5T838|Q5T839|Q5T840|Q5T841|Q8NBP6|Q9P2D5	Missense_Mutation	SNP	ENST00000377044.4	hg19	CCDS6638.1	.	.	.	.	.	.	.	.	.	.	T	5.804	0.332631	0.10956	.	.	ENSG00000135048	ENST00000377044;ENST00000377066	D;T	0.92752	-3.1;-0.55	5.54	-6.81	0.01704	Pectin lyase fold/virulence factor (1);	0.763445	0.13367	N	0.393239	T	0.77745	0.4176	N	0.05158	-0.105	0.23162	N	0.998199	B;B	0.02656	0.0;0.0	B;B	0.08055	0.001;0.003	T	0.62455	-0.6851	10	0.27082	T	0.32	.	11.4444	0.50114	0.0:0.5174:0.1002:0.3824	.	476;413	Q9UHN6;Q9UHN6-2	TMEM2_HUMAN;.	V	476;413	ENSP00000366243:I476V;ENSP00000366266:I413V	ENSP00000366243:I476V	I	-	1	0	TMEM2	73537224	0.002000	0.14202	0.704000	0.30370	0.992000	0.81027	-0.542000	0.06091	-1.195000	0.02680	-0.263000	0.10527	ATA	.	.		0.418	TMEM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052618.2	NM_013390	
RORB	6096	hgsc.bcm.edu	37	9	77249628	77249628	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:77249628A>G	ENST00000396204.2	+	3	208	c.208A>G	c.(208-210)Aga>Gga	p.R70G	RORB_ENST00000376896.3_Missense_Mutation_p.R59G			Q92753	RORB_HUMAN	RAR-related orphan receptor B	70					amacrine cell differentiation (GO:0035881)|cellular response to retinoic acid (GO:0071300)|eye photoreceptor cell development (GO:0042462)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of circadian rhythm (GO:0042752)|regulation of transcription, DNA-templated (GO:0006355)|retina development in camera-type eye (GO:0060041)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|rhythmic process (GO:0048511)|transcription initiation from RNA polymerase II promoter (GO:0006367)|visual perception (GO:0007601)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			breast(2)|large_intestine(4)|lung(1)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	12					Melatonin(DB01065)	CAGAACGAACAGAAACCGTTG	0.448																																					p.R59G		Atlas-SNP	.											RORB_ENST00000376896,NS,carcinoma,0,1	RORB	89	.	0			c.A175G						.						82.0	76.0	78.0					9																	77249628		2203	4300	6503	SO:0001583	missense	6096	exon3			ACGAACAGAAACC	Y08639	CCDS6646.1	9q22	2013-01-16			ENSG00000198963	ENSG00000198963		"""Nuclear hormone receptors"""	10259	protein-coding gene	gene with protein product		601972				7926749	Standard	NM_006914		Approved	RZRB, NR1F2, ROR-BETA	uc004ajh.3	Q92753	OTTHUMG00000020026	ENST00000396204.2:c.208A>G	chr9.hg19:g.77249628A>G	ENSP00000379507:p.Arg70Gly	128.0	0.0		95.0	5.0	NM_006914	Q8WX73	Missense_Mutation	SNP	ENST00000396204.2	hg19		.	.	.	.	.	.	.	.	.	.	A	22.0	4.227069	0.79576	.	.	ENSG00000198963	ENST00000376896;ENST00000396204	D;D	0.98987	-5.3;-5.3	5.82	4.65	0.58169	Zinc finger, NHR/GATA-type (1);Zinc finger, nuclear hormone receptor-type (4);	0.000000	0.85682	D	0.000000	D	0.99441	0.9802	H	0.95004	3.61	0.80722	D	1	D;D	0.89917	1.0;0.988	D;D	0.97110	1.0;0.959	D	0.98501	1.0614	10	0.87932	D	0	.	13.0159	0.58757	0.8653:0.1347:0.0:0.0	.	70;59	Q92753;Q58EY0	RORB_HUMAN;.	G	59;70	ENSP00000366093:R59G;ENSP00000379507:R70G	ENSP00000366093:R59G	R	+	1	2	RORB	76439448	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.180000	0.50895	0.992000	0.38840	0.533000	0.62120	AGA	.	.		0.448	RORB-201	KNOWN	basic	protein_coding	protein_coding			
ROR2	4920	hgsc.bcm.edu	37	9	94493324	94493324	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:94493324A>G	ENST00000375708.3	-	7	1249	c.1051T>C	c.(1051-1053)Tcc>Ccc	p.S351P	ROR2_ENST00000550066.1_5'UTR|ROR2_ENST00000375715.1_Missense_Mutation_p.S211P	NM_004560.3	NP_004551.2	Q01974	ROR2_HUMAN	receptor tyrosine kinase-like orphan receptor 2	351	Kringle. {ECO:0000255|PROSITE- ProRule:PRU00121}.				cartilage condensation (GO:0001502)|cell differentiation (GO:0030154)|embryonic genitalia morphogenesis (GO:0030538)|inner ear morphogenesis (GO:0042472)|JNK cascade (GO:0007254)|multicellular organismal development (GO:0007275)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell migration (GO:0030335)|positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)|somitogenesis (GO:0001756)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|Wnt signaling pathway, calcium modulating pathway (GO:0007223)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	clathrin-coated endocytic vesicle membrane (GO:0030669)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|Wnt-protein binding (GO:0017147)			autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(31)|ovary(3)|prostate(6)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	71						TCTGTGCTGGACAGGTGGTGG	0.627																																					p.S351P		Atlas-SNP	.											.	ROR2	167	.	0			c.T1051C						.						58.0	60.0	59.0					9																	94493324		2203	4300	6503	SO:0001583	missense	4920	exon7			TGCTGGACAGGTG	M97639	CCDS6691.1	9q22	2013-01-11			ENSG00000169071	ENSG00000169071		"""Immunoglobulin superfamily / I-set domain containing"""	10257	protein-coding gene	gene with protein product		602337		NTRKR2, BDB, BDB1		1334494, 10700182	Standard	NM_004560		Approved		uc004arj.2	Q01974	OTTHUMG00000020211	ENST00000375708.3:c.1051T>C	chr9.hg19:g.94493324A>G	ENSP00000364860:p.Ser351Pro	176.0	0.0		124.0	5.0	NM_004560	Q59GF5|Q5SPI5|Q9HAY7|Q9HB61	Missense_Mutation	SNP	ENST00000375708.3	hg19	CCDS6691.1	.	.	.	.	.	.	.	.	.	.	A	5.865	0.343745	0.11126	.	.	ENSG00000169071	ENST00000375715;ENST00000375708	T;T	0.62941	-0.01;-0.01	3.81	2.64	0.31445	Kringle (4);Kringle-like fold (1);	0.636870	0.12806	U	0.437586	T	0.47488	0.1448	L	0.31926	0.97	0.41468	D	0.988086	B;B;B	0.16603	0.001;0.018;0.005	B;B;B	0.18871	0.009;0.023;0.014	T	0.24764	-1.0151	10	0.22706	T	0.39	.	8.3068	0.32047	0.4804:0.0:0.0:0.5196	.	351;351;211	A1L4F5;Q01974;B1APY4	.;ROR2_HUMAN;.	P	211;351	ENSP00000364867:S211P;ENSP00000364860:S351P	ENSP00000364860:S351P	S	-	1	0	ROR2	93533145	0.861000	0.29849	0.539000	0.28077	0.660000	0.38997	0.756000	0.26419	0.614000	0.30107	0.459000	0.35465	TCC	.	.		0.627	ROR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053040.1		
C9orf156	51531	hgsc.bcm.edu	37	9	100672289	100672289	+	Missense_Mutation	SNP	C	C	T	rs371444295		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:100672289C>T	ENST00000375119.3	-	4	1095	c.1019G>A	c.(1018-1020)cGg>cAg	p.R340Q	C9orf156_ENST00000478126.1_5'UTR	NM_016481.3	NP_057565.3	Q9BU70	NAP1_HUMAN	chromosome 9 open reading frame 156	340					viral process (GO:0016032)		hydrolase activity (GO:0016787)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(3)|prostate(1)|skin(1)	13		Acute lymphoblastic leukemia(62;0.158)				AGGAGTAAACCGCACTTCTAA	0.532																																					p.R340Q		Atlas-SNP	.											.	C9orf156	35	.	0			c.G1019A						.	C	GLN/ARG	0,4406		0,0,2203	43.0	41.0	42.0		1019	5.0	1.0	9		42	1,8599		0,1,4299	no	missense	C9orf156	NM_016481.3	43	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	340/442	100672289	1,13005	2203	4300	6503	SO:0001583	missense	51531	exon4			GTAAACCGCACTT	AK023069	CCDS6730.1	9q31.1	2011-03-02			ENSG00000136932	ENSG00000136932			30967	protein-coding gene	gene with protein product	"""Nef (lentivirus myristoylated factor) associated protein 1"""						Standard	NM_016481		Approved	HSPC219, NAP1	uc004axv.1	Q9BU70	OTTHUMG00000021007	ENST00000375119.3:c.1019G>A	chr9.hg19:g.100672289C>T	ENSP00000364260:p.Arg340Gln	92.0	0.0		75.0	4.0	NM_016481	Q5T113|Q86SK0|Q9NXJ7|Q9P0Q7	Missense_Mutation	SNP	ENST00000375119.3	hg19	CCDS6730.1	.	.	.	.	.	.	.	.	.	.	C	29.8	5.037893	0.93630	0.0	1.16E-4	ENSG00000136932	ENST00000375119;ENST00000375118	T;T	0.42131	0.98;0.98	5.03	5.03	0.67393	Uncharacterised domain UPF0066, YaeB-like domain (1);	0.000000	0.85682	D	0.000000	T	0.59569	0.2203	L	0.52573	1.65	0.58432	D	0.999993	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.61426	-0.7065	10	0.66056	D	0.02	-19.1885	16.2258	0.82288	0.0:1.0:0.0:0.0	.	194;340	Q5T114;Q9BU70	.;NAP1_HUMAN	Q	340;194	ENSP00000364260:R340Q;ENSP00000364259:R194Q	ENSP00000364259:R194Q	R	-	2	0	C9orf156	99712110	1.000000	0.71417	0.997000	0.53966	0.926000	0.56050	5.451000	0.66632	2.503000	0.84419	0.563000	0.77884	CGG	.	.		0.532	C9orf156-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055401.1	NM_016481	
TBC1D2	55357	hgsc.bcm.edu	37	9	100973055	100973055	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:100973055T>C	ENST00000375064.1	-	8	1594	c.1556A>G	c.(1555-1557)gAg>gGg	p.E519G	TBC1D2_ENST00000493589.2_Intron|TBC1D2_ENST00000375066.5_Missense_Mutation_p.E519G|TBC1D2_ENST00000375063.1_Missense_Mutation_p.E59G|TBC1D2_ENST00000342112.5_Missense_Mutation_p.E301G	NM_001267571.1	NP_001254500.1	Q9BYX2	TBD2A_HUMAN	TBC1 domain family, member 2	519					positive regulation of Rab GTPase activity (GO:0032851)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)	cadherin binding (GO:0045296)|Rab GTPase activator activity (GO:0005097)			breast(1)|endometrium(5)|kidney(2)|large_intestine(7)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	24		Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;2.55e-37)		CCCCAGGGCCTCCTGCAGCCT	0.617																																					p.E519G		Atlas-SNP	.											.	TBC1D2	70	.	0			c.A1556G						.						36.0	28.0	31.0					9																	100973055		2191	4282	6473	SO:0001583	missense	55357	exon8			AGGGCCTCCTGCA	AY026527	CCDS35080.1, CCDS59137.1, CCDS75865.1	9q22.32	2011-11-30			ENSG00000095383	ENSG00000095383			18026	protein-coding gene	gene with protein product	"""prostate antigen recognized and identified by SEREX"""	609871					Standard	NM_018421		Approved	PARIS1, TBC1D2A, Armus	uc011lvb.2	Q9BYX2	OTTHUMG00000020343	ENST00000375064.1:c.1556A>G	chr9.hg19:g.100973055T>C	ENSP00000364205:p.Glu519Gly	294.0	0.0		195.0	8.0	NM_001267571	B3KWD1|B4DQ05|B9A6J7|Q59EU0|Q5TBQ5|Q6IPC7|Q7L1K8|Q8WYT1|Q9H6A2|Q9NSH4	Missense_Mutation	SNP	ENST00000375064.1	hg19		.	.	.	.	.	.	.	.	.	.	T	12.51	1.959198	0.34565	.	.	ENSG00000095383	ENST00000375064;ENST00000375066;ENST00000342112;ENST00000375063	T;T;T;T	0.09630	3.26;2.96;3.39;3.02	5.6	4.42	0.53409	.	0.157654	0.56097	D	0.000030	T	0.15262	0.0368	M	0.62723	1.935	0.38741	D	0.953895	P;P	0.46142	0.799;0.873	B;P	0.47346	0.343;0.544	T	0.03969	-1.0988	10	0.45353	T	0.12	.	6.0753	0.19911	0.0:0.0812:0.319:0.5998	.	519;519	Q9BYX2;Q9BYX2-2	TBD2A_HUMAN;.	G	519;519;301;59	ENSP00000364205:E519G;ENSP00000364207:E519G;ENSP00000341567:E301G;ENSP00000364203:E59G	ENSP00000341567:E301G	E	-	2	0	TBC1D2	100012876	1.000000	0.71417	0.988000	0.46212	0.441000	0.31987	2.750000	0.47500	0.901000	0.36495	0.460000	0.39030	GAG	.	.		0.617	TBC1D2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000053366.1	NM_018421	
AKAP2	11217	hgsc.bcm.edu	37	9	112898992	112898992	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:112898992T>C	ENST00000259318.7	+	2	682	c.475T>C	c.(475-477)Tca>Cca	p.S159P	AKAP2_ENST00000555236.1_Missense_Mutation_p.S390P|PALM2-AKAP2_ENST00000374530.3_Missense_Mutation_p.S390P|AKAP2_ENST00000510514.5_Missense_Mutation_p.S390P|AKAP2_ENST00000374525.1_Missense_Mutation_p.S248P|PALM2-AKAP2_ENST00000302798.7_Missense_Mutation_p.S390P|AKAP2_ENST00000434623.2_Missense_Mutation_p.S248P	NM_001136562.2	NP_001130034.1	Q9Y2D5	AKAP2_HUMAN	A kinase (PRKA) anchor protein 2	159										breast(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(16)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	33						CACAACCAGCTCACGGTGTTC	0.577																																					p.S390P		Atlas-SNP	.											.	PALM2-AKAP2	117	.	0			c.T1168C						.						72.0	66.0	68.0					9																	112898992		2203	4300	6503	SO:0001583	missense	445815	exon8			ACCAGCTCACGGT	AB023137	CCDS43861.1, CCDS48003.1, CCDS56581.1	9q31.3	2009-10-16			ENSG00000241978	ENSG00000241978		"""A-kinase anchor proteins"""	372	protein-coding gene	gene with protein product	"""protein kinase A2"""	604582		PRKA2		10231032	Standard	NM_001136562		Approved	AKAP-KL, KIAA0920, DKFZp564L0716		Q9Y2D5	OTTHUMG00000156811	ENST00000259318.7:c.475T>C	chr9.hg19:g.112898992T>C	ENSP00000259318:p.Ser159Pro	240.0	0.0		159.0	7.0	NM_007203	B1ALX9|B2RTU4|B3KQ00|B4DTZ2|B7ZW07|B9EJB5|Q9UG26	Missense_Mutation	SNP	ENST00000259318.7	hg19	CCDS48003.1	.	.	.	.	.	.	.	.	.	.	T	12.37	1.917242	0.33815	.	.	ENSG00000157654;ENSG00000157654;ENSG00000241978;ENSG00000241978;ENSG00000241978;ENSG00000241978;ENSG00000241978;ENSG00000241978	ENST00000374530;ENST00000302798;ENST00000555236;ENST00000510514;ENST00000434623;ENST00000374525;ENST00000480388;ENST00000259318	T;T;T;T;T;T;T;T	0.43294	0.95;0.95;0.95;0.95;0.95;0.95;0.95;0.95	5.85	5.85	0.93711	.	0.168137	0.42420	D	0.000711	T	0.62660	0.2446	M	0.63843	1.955	0.49130	D	0.999753	D;D;P;D;D;P;P;B	0.89917	0.999;1.0;0.615;1.0;0.999;0.946;0.946;0.355	D;D;B;D;D;P;P;B	0.85130	0.981;0.997;0.142;0.997;0.994;0.507;0.507;0.142	T	0.64922	-0.6293	10	0.66056	D	0.02	-12.0597	15.4167	0.74974	0.0:0.0:0.0:1.0	.	159;248;242;248;249;390;390;208	Q9Y2D5;Q9Y2D5-7;B4E2K2;Q9Y2D5-5;B1ALY1;Q9Y2D5-6;Q9Y2D5-4;C9JVY5	AKAP2_HUMAN;.;.;.;.;.;.;.	P	390;390;390;390;248;248;208;159	ENSP00000363654:S390P;ENSP00000305861:S390P;ENSP00000451476:S390P;ENSP00000421522:S390P;ENSP00000404782:S248P;ENSP00000363649:S248P;ENSP00000419268:S208P;ENSP00000259318:S159P	ENSP00000259318:S159P	S	+	1	0	PALM2-AKAP2;AKAP2	111938813	1.000000	0.71417	0.997000	0.53966	0.021000	0.10359	4.002000	0.57053	2.232000	0.73038	0.533000	0.62120	TCA	.	.		0.577	AKAP2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000346067.3	NM_001004065	
MUSK	4593	hgsc.bcm.edu	37	9	113457797	113457797	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:113457797A>G	ENST00000374448.4	+	4	607	c.473A>G	c.(472-474)gAc>gGc	p.D158G	MUSK_ENST00000189978.5_Missense_Mutation_p.D158G|MUSK_ENST00000416899.2_Missense_Mutation_p.D158G|MUSK_ENST00000374439.1_Missense_Mutation_p.D40G|MUSK_ENST00000374440.3_Missense_Mutation_p.D40G	NM_001166281.1|NM_005592.3	NP_001159753.1|NP_005583.1	O15146	MUSK_HUMAN	muscle, skeletal, receptor tyrosine kinase	158	Ig-like 2.				cell differentiation (GO:0030154)|extracellular matrix organization (GO:0030198)|memory (GO:0007613)|multicellular organismal development (GO:0007275)|neuromuscular junction development (GO:0007528)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of protein geranylgeranylation (GO:2000541)|positive regulation of protein phosphorylation (GO:0001934)|protein autophosphorylation (GO:0046777)|regulation of synaptic growth at neuromuscular junction (GO:0008582)|regulation of transcription, DNA-templated (GO:0006355)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|neuromuscular junction (GO:0031594)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(7)|lung(23)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	49						ATAAAGGGAGACAGCCCTCTC	0.353																																					p.D158G		Atlas-SNP	.											.	MUSK	112	.	0			c.A473G						.						56.0	50.0	52.0					9																	113457797		1820	4063	5883	SO:0001583	missense	4593	exon4			AGGGAGACAGCCC	AF006464	CCDS48005.1, CCDS75874.1	9q31.3-q32	2013-01-29			ENSG00000030304	ENSG00000030304		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	7525	protein-coding gene	gene with protein product		601296				7546737	Standard	NM_005592		Approved		uc022blv.1	O15146	OTTHUMG00000020485	ENST00000374448.4:c.473A>G	chr9.hg19:g.113457797A>G	ENSP00000363571:p.Asp158Gly	115.0	0.0		89.0	4.0	NM_001166281	Q32MJ8|Q32MJ9|Q5VZW7|Q5VZW8	Missense_Mutation	SNP	ENST00000374448.4	hg19	CCDS48005.1	.	.	.	.	.	.	.	.	.	.	A	19.19	3.779688	0.70107	.	.	ENSG00000030304	ENST00000189978;ENST00000374448;ENST00000543335;ENST00000374447;ENST00000545907;ENST00000374440;ENST00000416899;ENST00000374439	T;T;T	0.19250	2.16;2.16;2.16	5.97	5.97	0.96955	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.195954	0.53938	D	0.000057	T	0.20861	0.0502	N	0.03948	-0.315	0.51233	D	0.999911	P;D	0.61697	0.847;0.99	P;P	0.59221	0.794;0.854	T	0.34477	-0.9827	10	0.39692	T	0.17	.	15.6346	0.76941	1.0:0.0:0.0:0.0	.	158;158	O15146;F5H6T2	MUSK_HUMAN;.	G	158;158;158;158;158;40;158;40	ENSP00000363571:D158G;ENSP00000363563:D40G;ENSP00000363562:D40G	ENSP00000189978:D158G	D	+	2	0	MUSK	112497618	1.000000	0.71417	0.921000	0.36526	0.820000	0.46376	8.010000	0.88615	2.285000	0.76669	0.477000	0.44152	GAC	.	.		0.353	MUSK-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding			
TLR4	7099	hgsc.bcm.edu	37	9	120476424	120476424	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:120476424T>C	ENST00000355622.6	+	3	2119	c.2018T>C	c.(2017-2019)aTc>aCc	p.I673T	TLR4_ENST00000472304.1_3'UTR|TLR4_ENST00000394487.4_Missense_Mutation_p.I633T	NM_138554.4|NM_138557.2	NP_612564.1|NP_612567.1	O00206	TLR4_HUMAN	toll-like receptor 4	673	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				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)	GGTGAAAACATCTATGATGCC	0.423																																					p.I673T		Atlas-SNP	.											.	TLR4	220	.	0			c.T2018C						.						127.0	116.0	120.0					9																	120476424		2203	4300	6503	SO:0001583	missense	7099	exon3			AAAACATCTATGA	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.2018T>C	chr9.hg19:g.120476424T>C	ENSP00000363089:p.Ile673Thr	125.0	0.0		93.0	4.0	NM_138554	A8K1Y8|A9XLP9|A9XLQ0|A9XLQ1|B4E194|D1CS52|D1CS53|Q5VZI8|Q5VZI9|Q9UK78|Q9UM57	Missense_Mutation	SNP	ENST00000355622.6	hg19	CCDS6818.1	.	.	.	.	.	.	.	.	.	.	T	0.004	-2.360984	0.00214	.	.	ENSG00000136869	ENST00000394487;ENST00000355622	T;T	0.02345	4.33;4.33	6.03	-3.2	0.05156	Toll/interleukin-1 receptor homology (TIR) domain (3);	0.952331	0.08833	N	0.887012	T	0.01189	0.0039	N	0.01464	-0.85	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.46456	-0.9190	10	0.02654	T	1	.	15.6154	0.76764	0.0:0.4039:0.0:0.5961	.	673	O00206	TLR4_HUMAN	T	633;673	ENSP00000377997:I633T;ENSP00000363089:I673T	ENSP00000363089:I673T	I	+	2	0	TLR4	119516245	0.000000	0.05858	0.002000	0.10522	0.310000	0.27922	-0.787000	0.04618	-0.621000	0.05633	-0.854000	0.03029	ATC	.	.		0.423	TLR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055549.3	NM_138554	
RABGAP1	23637	hgsc.bcm.edu	37	9	125772702	125772702	+	Missense_Mutation	SNP	G	G	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:125772702G>C	ENST00000373647.4	+	11	1578	c.1444G>C	c.(1444-1446)Gaa>Caa	p.E482Q		NM_012197.3	NP_036329.3	Q9Y3P9	RBGP1_HUMAN	RAB GTPase activating protein 1	482					cell cycle (GO:0007049)|positive regulation of GTPase activity (GO:0043547)|regulation of GTP catabolic process (GO:0033124)	centrosome (GO:0005813)|cytosol (GO:0005829)|microtubule associated complex (GO:0005875)	DNA binding (GO:0003677)|GTPase activator activity (GO:0005096)|Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)|tubulin binding (GO:0015631)			breast(3)|endometrium(3)|kidney(5)|large_intestine(8)|lung(11)|ovary(3)|prostate(4)|stomach(3)|upper_aerodigestive_tract(1)	41						AAGTGAATCAGAAAGAGAGAG	0.383																																					p.E482Q		Atlas-SNP	.											.	RABGAP1	164	.	0			c.G1444C						.						108.0	103.0	105.0					9																	125772702		2203	4300	6503	SO:0001583	missense	23637	exon11			GAATCAGAAAGAG	AJ011679	CCDS6848.2	9q34.11	2013-07-09			ENSG00000011454	ENSG00000011454			17155	protein-coding gene	gene with protein product	"""rab6 GTPase activating protein (GAP and centrosome-associated)"", ""TBC1 domain family, member 11"""	615882				10202141	Standard	NM_012197		Approved	GAPCenA, TBC1D11	uc011lzh.2	Q9Y3P9	OTTHUMG00000020633	ENST00000373647.4:c.1444G>C	chr9.hg19:g.125772702G>C	ENSP00000362751:p.Glu482Gln	84.0	0.0		75.0	31.0	NM_012197	B9A6L2|Q05CW2|Q6ZMY1|Q9HA28|Q9P0E2|Q9UG67	Missense_Mutation	SNP	ENST00000373647.4	hg19	CCDS6848.2	.	.	.	.	.	.	.	.	.	.	G	19.71	3.878331	0.72294	.	.	ENSG00000011454	ENST00000373647	T	0.06608	3.28	5.71	5.71	0.89125	.	0.059702	0.64402	D	0.000004	T	0.08268	0.0206	L	0.38953	1.18	0.80722	D	1	B	0.26672	0.156	B	0.21546	0.035	T	0.23226	-1.0194	10	0.42905	T	0.14	-19.9126	19.85	0.96736	0.0:0.0:1.0:0.0	.	482	Q9Y3P9	RBGP1_HUMAN	Q	482	ENSP00000362751:E482Q	ENSP00000362751:E482Q	E	+	1	0	RABGAP1	124812523	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.842000	0.92136	2.697000	0.92050	0.563000	0.77884	GAA	.	.		0.383	RABGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053976.3	NM_012197	
TTC16	158248	hgsc.bcm.edu	37	9	130493103	130493103	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:130493103A>G	ENST00000373289.3	+	14	2121	c.2041A>G	c.(2041-2043)Agc>Ggc	p.S681G	TOR2A_ENST00000472723.1_5'Flank|TTC16_ENST00000489226.1_3'UTR	NM_144965.1	NP_659402.1	Q8NEE8	TTC16_HUMAN	tetratricopeptide repeat domain 16	681										central_nervous_system(2)|endometrium(3)|lung(7)|ovary(3)|pancreas(2)|prostate(4)|skin(1)	22						CCAGAGGCAGAGCCTTAGCAA	0.572																																					p.S681G		Atlas-SNP	.											.	TTC16	55	.	0			c.A2041G						.						83.0	80.0	81.0					9																	130493103		2203	4300	6503	SO:0001583	missense	158248	exon14			AGGCAGAGCCTTA	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.2041A>G	chr9.hg19:g.130493103A>G	ENSP00000362386:p.Ser681Gly	225.0	0.0		171.0	7.0	NM_144965	B4DYG4|B5ME24|Q5JU66|Q96M72	Missense_Mutation	SNP	ENST00000373289.3	hg19	CCDS6875.1	.	.	.	.	.	.	.	.	.	.	A	7.686	0.690133	0.15039	.	.	ENSG00000167094	ENST00000373289	T	0.15952	2.38	3.28	3.28	0.37604	.	1.504790	0.03898	N	0.279859	T	0.10121	0.0248	N	0.04335	-0.225	0.40408	D	0.979728	B;B	0.12630	0.006;0.006	B;B	0.09377	0.004;0.004	T	0.18085	-1.0348	10	0.46703	T	0.11	-1.2238	8.3034	0.32027	1.0:0.0:0.0:0.0	.	668;681	B4DZ42;Q8NEE8	.;TTC16_HUMAN	G	681	ENSP00000362386:S681G	ENSP00000362386:S681G	S	+	1	0	TTC16	129532924	0.087000	0.21565	0.044000	0.18714	0.096000	0.18686	0.942000	0.29017	1.744000	0.51775	0.358000	0.22013	AGC	.	.		0.572	TTC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054224.1	NM_144965	
SH2D3C	10044	hgsc.bcm.edu	37	9	130536685	130536685	+	Silent	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:130536685T>C	ENST00000314830.8	-	2	212	c.99A>G	c.(97-99)agA>agG	p.R33R	SH2D3C_ENST00000471939.1_5'Flank|SH2D3C_ENST00000373277.4_5'Flank	NM_170600.2	NP_733745.1	Q8N5H7	SH2D3_HUMAN	SH2 domain containing 3C	33					JNK cascade (GO:0007254)|positive regulation of signal transduction (GO:0009967)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|membrane (GO:0016020)	guanyl-nucleotide exchange factor activity (GO:0005085)|SH3/SH2 adaptor activity (GO:0005070)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(16)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						CTGAGGATCGTCTCAGAGTGA	0.532																																					p.R33R		Atlas-SNP	.											.	SH2D3C	102	.	0			c.A99G						.						64.0	60.0	61.0					9																	130536685		2203	4300	6503	SO:0001819	synonymous_variant	10044	exon2			GGATCGTCTCAGA	AF124251	CCDS6877.1, CCDS6878.1, CCDS48026.1, CCDS48028.1, CCDS59145.1	9q33.1-q33.3	2013-02-14	2002-01-14		ENSG00000095370	ENSG00000095370		"""SH2 domain containing"""	16884	protein-coding gene	gene with protein product		604722	"""SH2 domain-containing 3C"""			10187783	Standard	NM_170600		Approved	NSP3	uc004bsc.3	Q8N5H7	OTTHUMG00000020717	ENST00000314830.8:c.99A>G	chr9.hg19:g.130536685T>C		132.0	0.0		117.0	5.0	NM_170600	A8K5S8|E9PG48|Q5HYE5|Q5JU31|Q6UY42|Q8N6X3|Q9Y2X5	Silent	SNP	ENST00000314830.8	hg19	CCDS6877.1																																																																																			.	.		0.532	SH2D3C-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054264.1	NM_005489	
NUP188	23511	hgsc.bcm.edu	37	9	131745770	131745770	+	Silent	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:131745770T>C	ENST00000372577.2	+	19	1923	c.1902T>C	c.(1900-1902)cgT>cgC	p.R634R		NM_015354.1	NP_056169.1	Q5SRE5	NU188_HUMAN	nucleoporin 188kDa	634					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)				breast(2)|central_nervous_system(3)|endometrium(6)|kidney(4)|large_intestine(9)|lung(20)|ovary(6)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	60						CTGATCTTCGTCACACAGGTT	0.473																																					p.R634R		Atlas-SNP	.											.	NUP188	140	.	0			c.T1902C						.						122.0	94.0	104.0					9																	131745770		2203	4300	6503	SO:0001819	synonymous_variant	23511	exon19			TCTTCGTCACACA	D79991	CCDS35156.1	9q34.13	2014-01-28	2004-03-19	2004-03-24	ENSG00000095319	ENSG00000095319			17859	protein-coding gene	gene with protein product		615587	"""KIAA0169"""	KIAA0169		11029043	Standard	NM_015354		Approved		uc004bws.2	Q5SRE5	OTTHUMG00000020768	ENST00000372577.2:c.1902T>C	chr9.hg19:g.131745770T>C		167.0	0.0		99.0	4.0	NM_015354	Q14675|Q2TA87|Q7Z3K8|Q8IWF1	Silent	SNP	ENST00000372577.2	hg19	CCDS35156.1																																																																																			.	.		0.473	NUP188-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054529.2		
C9orf50	375759	hgsc.bcm.edu	37	9	132377810	132377810	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:132377810T>C	ENST00000372478.4	-	4	1034	c.833A>G	c.(832-834)gAg>gGg	p.E278G	NTMT1_ENST00000372486.1_Intron	NM_199350.3	NP_955382.3	Q5SZB4	CI050_HUMAN	chromosome 9 open reading frame 50	278										central_nervous_system(1)|endometrium(4)|large_intestine(2)|ovary(1)|skin(1)|urinary_tract(1)	10		Ovarian(14;0.00556)				CTGCAGGGTCTCGTCAGCGAA	0.647																																					p.E278G		Atlas-SNP	.											.	C9orf50	25	.	0			c.A833G						.						71.0	61.0	65.0					9																	132377810		2203	4300	6503	SO:0001583	missense	375759	exon4			AGGGTCTCGTCAG	AK093122	CCDS35159.1	9q34.2	2012-03-15			ENSG00000179058	ENSG00000179058			23677	protein-coding gene	gene with protein product							Standard	NM_199350		Approved	FLJ35803	uc004byc.4	Q5SZB4	OTTHUMG00000020786	ENST00000372478.4:c.833A>G	chr9.hg19:g.132377810T>C	ENSP00000361556:p.Glu278Gly	105.0	0.0		88.0	4.0	NM_199350	Q2M1I2|Q8NA65	Missense_Mutation	SNP	ENST00000372478.4	hg19	CCDS35159.1	.	.	.	.	.	.	.	.	.	.	t	12.96	2.093219	0.36952	.	.	ENSG00000179058	ENST00000372478	T	0.38887	1.11	3.17	3.17	0.36434	.	0.000000	0.38217	N	0.001765	T	0.48786	0.1519	L	0.36672	1.1	0.29947	N	0.820566	D	0.89917	1.0	D	0.87578	0.998	T	0.40232	-0.9574	10	0.45353	T	0.12	-29.485	8.1854	0.31335	0.0:0.0:0.0:1.0	.	278	Q5SZB4	CI050_HUMAN	G	278	ENSP00000361556:E278G	ENSP00000361556:E278G	E	-	2	0	C9orf50	131417631	1.000000	0.71417	0.913000	0.36048	0.665000	0.39181	3.256000	0.51492	1.692000	0.51112	0.357000	0.21978	GAG	.	.		0.647	C9orf50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054593.1	NM_199350	
CEL	1056	hgsc.bcm.edu	37	9	135939849	135939849	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:135939849T>C	ENST00000372080.4	+	2	150	c.134T>C	c.(133-135)cTc>cCc	p.L45P	CEL_ENST00000351304.7_Missense_Mutation_p.L42P	NM_001807.3	NP_001798.2	P19835	CEL_HUMAN	carboxyl ester lipase	42	Heparin-binding.				cholesterol catabolic process (GO:0006707)|fatty acid catabolic process (GO:0009062)|intestinal cholesterol absorption (GO:0030299)|intestinal lipid catabolic process (GO:0044258)|lipid digestion (GO:0044241)|lipid metabolic process (GO:0006629)|pancreatic juice secretion (GO:0030157)|protein esterification (GO:0018350)|small molecule metabolic process (GO:0044281)|triglyceride metabolic process (GO:0006641)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	acylglycerol lipase activity (GO:0047372)|catalytic activity (GO:0003824)|heparin binding (GO:0008201)|hydrolase activity (GO:0016787)|sterol esterase activity (GO:0004771)|triglyceride lipase activity (GO:0004806)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(9)|pancreas(2)|skin(1)	20				OV - Ovarian serous cystadenocarcinoma(145;1.03e-40)|Epithelial(140;3.58e-37)|GBM - Glioblastoma multiforme(294;0.00164)|READ - Rectum adenocarcinoma(205;0.196)		AAGCTCGGCCTCCTGGGTGAC	0.627																																					p.L45P		Atlas-SNP	.											.	CEL	71	.	0			c.T134C						.						93.0	105.0	101.0					9																	135939849		2059	4198	6257	SO:0001583	missense	1056	exon2			TCGGCCTCCTGGG	M54994	CCDS43896.1	9q34.3	2013-03-13	2013-03-13		ENSG00000170835	ENSG00000170835	3.1.1.3, 3.1.1.13		1848	protein-coding gene	gene with protein product	"""bile salt-stimulated lipase"""	114840				1676983	Standard	NM_001807		Approved	BSSL, MODY8	uc010naa.2	P19835	OTTHUMG00000020855	ENST00000372080.4:c.134T>C	chr9.hg19:g.135939849T>C	ENSP00000361151:p.Leu45Pro	212.0	0.0		127.0	7.0	NM_001807	Q16398|Q5T7U7|Q9UCH1|Q9UP41	Missense_Mutation	SNP	ENST00000372080.4	hg19	CCDS43896.1	.	.	.	.	.	.	.	.	.	.	T	17.41	3.381891	0.61845	.	.	ENSG00000170835	ENST00000372080;ENST00000351304;ENST00000303626	T;T	0.66815	-0.23;-0.23	4.97	3.83	0.44106	Carboxylesterase, type B (1);	0.232505	0.43110	D	0.000606	T	0.73361	0.3577	L	0.42686	1.345	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.73814	-0.3864	10	0.87932	D	0	.	9.7227	0.40313	0.0:0.0832:0.0:0.9168	.	42	P19835	CEL_HUMAN	P	45;42;45	ENSP00000361151:L45P;ENSP00000342217:L42P	ENSP00000304021:L45P	L	+	2	0	CEL	134929670	1.000000	0.71417	0.979000	0.43373	0.500000	0.33767	4.346000	0.59367	0.853000	0.35312	0.459000	0.35465	CTC	.	.		0.627	CEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054823.1		
REXO4	57109	hgsc.bcm.edu	37	9	136272192	136272192	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:136272192T>C	ENST00000371942.3	-	8	1353	c.1154A>G	c.(1153-1155)cAg>cGg	p.Q385R	REXO4_ENST00000371935.2_Missense_Mutation_p.Q213R	NM_020385.2	NP_065118.2	Q9GZR2	REXO4_HUMAN	REX4, RNA exonuclease 4 homolog (S. cerevisiae)	385	Exonuclease.				regulation of transcription, DNA-templated (GO:0006355)	nucleolus (GO:0005730)|nucleus (GO:0005634)	exonuclease activity (GO:0004527)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(1)|large_intestine(4)|lung(7)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	15				OV - Ovarian serous cystadenocarcinoma(145;8.58e-08)|Epithelial(140;9.55e-07)|all cancers(34;1.05e-05)		CTGGGCATCCTGAATCTAGAC	0.592											OREG0019587	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Q385R		Atlas-SNP	.											.	REXO4	27	.	0			c.A1154G						.						149.0	115.0	126.0					9																	136272192		2203	4300	6503	SO:0001583	missense	57109	exon8			GCATCCTGAATCT	AF273304	CCDS6969.1, CCDS65179.1	9q34	2008-02-05	2005-08-22	2005-08-22	ENSG00000148300	ENSG00000148300			12820	protein-coding gene	gene with protein product		602930	"""Xenopus prevents mitotic catatrophe 2 homolog"", ""XPMC2 prevents mitotic catastrophe 2 homolog (Xenopus laevis)"""	XPMC2H		9325058	Standard	NM_020385		Approved		uc004cdm.3	Q9GZR2	OTTHUMG00000020870	ENST00000371942.3:c.1154A>G	chr9.hg19:g.136272192T>C	ENSP00000361010:p.Gln385Arg	165.0	0.0	1624	100.0	4.0	NM_020385	B2RAT2|Q5T8S4|Q5T8S5|Q5T8S6|Q9GZW3	Missense_Mutation	SNP	ENST00000371942.3	hg19	CCDS6969.1	.	.	.	.	.	.	.	.	.	.	T	14.08	2.429097	0.43122	.	.	ENSG00000148300	ENST00000371942;ENST00000371935;ENST00000454825	T;T;T	0.22336	1.96;1.96;1.96	5.27	5.27	0.74061	Exonuclease (1);Exonuclease, RNase T/DNA polymerase III (1);Ribonuclease H-like (1);	0.000000	0.85682	D	0.000000	T	0.47340	0.1440	M	0.86573	2.825	0.49389	D	0.999783	B;P	0.46859	0.064;0.885	B;P	0.58130	0.159;0.833	T	0.54642	-0.8263	10	0.87932	D	0	.	12.9216	0.58234	0.0:0.0:0.0:1.0	.	213;385	Q9GZR2-2;Q9GZR2	.;REXO4_HUMAN	R	385;213;213	ENSP00000361010:Q385R;ENSP00000361003:Q213R;ENSP00000394229:Q213R	ENSP00000361003:Q213R	Q	-	2	0	REXO4	135262013	1.000000	0.71417	0.866000	0.34008	0.092000	0.18411	7.238000	0.78173	1.984000	0.57885	0.459000	0.35465	CAG	.	.		0.592	REXO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054899.1		
NSMF	26012	hgsc.bcm.edu	37	9	140350938	140350938	+	Splice_Site	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:140350938T>C	ENST00000371475.3	-	4	860	c.629A>G	c.(628-630)gAc>gGc	p.D210G	NSMF_ENST00000371474.3_Splice_Site_p.D210G|NSMF_ENST00000371468.1_5'Flank|NSMF_ENST00000541195.1_5'Flank|NSMF_ENST00000265663.7_Splice_Site_p.D210G|NSMF_ENST00000371482.1_5'Flank|NSMF_ENST00000339554.3_Splice_Site_p.D9G|NSMF_ENST00000484316.1_5'Flank|NSMF_ENST00000371472.2_Splice_Site_p.D210G|NSMF_ENST00000371473.3_Splice_Site_p.D210G|NSMF_ENST00000392812.4_Splice_Site_p.D210G|NSMF_ENST00000437259.1_Splice_Site_p.D210G	NM_001130969.1	NP_001124441.1	Q6X4W1	NSMF_HUMAN	NMDA receptor synaptonuclear signaling and neuronal migration factor	210	Necessary and sufficient to elicit dendritic processes and synaptic contacts. {ECO:0000250}.				cellular response to amino acid stimulus (GO:0071230)|cellular response to electrical stimulus (GO:0071257)|cellular response to gonadotropin stimulus (GO:0071371)|positive regulation of neuron migration (GO:2001224)|positive regulation of protein dephosphorylation (GO:0035307)|regulation of dendrite morphogenesis (GO:0048814)|regulation of neuron apoptotic process (GO:0043523)|regulation of neuronal synaptic plasticity (GO:0048168)	apical dendrite (GO:0097440)|cell junction (GO:0030054)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|membrane (GO:0016020)|neuron projection (GO:0043005)|nuclear envelope (GO:0005635)|nuclear euchromatin (GO:0005719)|nuclear matrix (GO:0016363)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|perikaryon (GO:0043204)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	calcium-dependent protein binding (GO:0048306)										AGGGATGTCGTCTAAGAGAGA	0.542																																					p.D210G		Atlas-SNP	.											.	NSMF	3	.	0			c.A629G						.						116.0	124.0	122.0					9																	140350938		2203	4300	6503	SO:0001630	splice_region_variant	26012	exon4			ATGTCGTCTAAGA		CCDS7044.1, CCDS48067.1, CCDS48068.1, CCDS48069.1, CCDS55357.1	9q34.3	2013-01-14	2013-01-14	2013-01-14	ENSG00000165802	ENSG00000165802			29843	protein-coding gene	gene with protein product		608137	"""nasal embryonic LHRH factor"""	NELF		11230166, 10898796	Standard	NM_015537		Approved		uc004cna.3	Q6X4W1	OTTHUMG00000020989	ENST00000371475.3:c.629-1A>G	chr9.hg19:g.140350938T>C		127.0	0.0		92.0	5.0	NM_001130970	Q2TB96|Q6X4V7|Q6X4V8|Q6X4V9|Q8N2M2|Q96SY1|Q9NPM4|Q9NPP3|Q9NPS3	Missense_Mutation	SNP	ENST00000371475.3	hg19	CCDS48069.1	.	.	.	.	.	.	.	.	.	.	T	10.28	1.306273	0.23736	.	.	ENSG00000165802	ENST00000339554;ENST00000371475;ENST00000265663;ENST00000437259;ENST00000392812;ENST00000371474;ENST00000371473;ENST00000371472	T;T;T;T;T;T;T;T	0.50277	0.82;0.81;0.78;0.76;0.76;0.75;0.79;0.78	4.55	4.55	0.56014	.	0.217452	0.36665	N	0.002473	T	0.32585	0.0834	N	0.19112	0.55	0.80722	D	1	B;B;B;B;B	0.32781	0.384;0.222;0.384;0.183;0.183	B;B;B;B;B	0.30572	0.117;0.086;0.117;0.058;0.058	T	0.17745	-1.0359	10	0.41790	T	0.15	.	13.0745	0.59079	0.0:0.0:0.0:1.0	.	210;210;210;210;210	Q6X4W1-3;Q2TB96;Q6X4W1-4;Q6X4W1;Q6X4W1-2	.;.;.;NELF_HUMAN;.	G	9;210;210;210;210;210;210;210	ENSP00000342966:D9G;ENSP00000360530:D210G;ENSP00000265663:D210G;ENSP00000412007:D210G;ENSP00000376559:D210G;ENSP00000360529:D210G;ENSP00000360528:D210G;ENSP00000360527:D210G	ENSP00000265663:D210G	D	-	2	0	NELF	139470759	1.000000	0.71417	0.963000	0.40424	0.026000	0.11368	4.678000	0.61641	1.686000	0.51046	0.379000	0.24179	GAC	.	.		0.542	NSMF-204	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015537	Missense_Mutation
EHMT1	79813	hgsc.bcm.edu	37	9	140611475	140611475	+	Silent	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:140611475A>G	ENST00000460843.1	+	3	510	c.483A>G	c.(481-483)aaA>aaG	p.K161K	EHMT1_ENST00000334856.6_Silent_p.K130K|EHMT1_ENST00000371394.2_3'UTR|EHMT1_ENST00000462484.1_Silent_p.K161K	NM_024757.4	NP_079033.4	Q9H9B1	EHMT1_HUMAN	euchromatic histone-lysine N-methyltransferase 1	161					chromatin modification (GO:0016568)|DNA methylation (GO:0006306)|embryo development (GO:0009790)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-lysine dimethylation (GO:0018027)|peptidyl-lysine monomethylation (GO:0018026)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	histone methyltransferase activity (H3-K27 specific) (GO:0046976)|histone methyltransferase activity (H3-K9 specific) (GO:0046974)|histone-lysine N-methyltransferase activity (GO:0018024)|methyltransferase activity (GO:0008168)|p53 binding (GO:0002039)|protein-lysine N-methyltransferase activity (GO:0016279)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(16)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	41	all_cancers(76;0.164)			OV - Ovarian serous cystadenocarcinoma(145;0.000183)|Epithelial(140;0.000728)		GGGCTGGCAAAGGCAGGACTC	0.647																																					p.K161K		Atlas-SNP	.											.	EHMT1	196	.	0			c.A483G						.						40.0	42.0	41.0					9																	140611475		2203	4299	6502	SO:0001819	synonymous_variant	79813	exon3			TGGCAAAGGCAGG	AY083210	CCDS7050.1, CCDS7050.2, CCDS56595.1	9q34.3	2013-09-20			ENSG00000181090	ENSG00000181090	2.1.1.43	"""Chromatin-modifying enzymes / K-methyltransferases"", ""Ankyrin repeat domain containing"""	24650	protein-coding gene	gene with protein product		607001	"""euchromatic histone methyltransferase 1"""			11347906, 12004135	Standard	NM_024757		Approved	Eu-HMTase1, FLJ12879, KIAA1876, bA188C12.1, KMT1D	uc011mfc.2	Q9H9B1	OTTHUMG00000020995	ENST00000460843.1:c.483A>G	chr9.hg19:g.140611475A>G		69.0	0.0		54.0	4.0	NM_001145527	B1AQ58|B1AQ59|Q86X08|Q8TCN7|Q96F53|Q96JF1|Q96KH4	Silent	SNP	ENST00000460843.1	hg19	CCDS7050.2																																																																																			.	.		0.647	EHMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055371.2	NM_024757	
LARP4B	23185	hgsc.bcm.edu	37	10	876909	876909	+	Silent	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:876909T>C	ENST00000316157.3	-	8	799	c.759A>G	c.(757-759)gaA>gaG	p.E253E		NM_015155.1	NP_055970.1	Q92615	LAR4B_HUMAN	La ribonucleoprotein domain family, member 4B	253	RRM.				positive regulation of translation (GO:0045727)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleolus (GO:0005730)|polysomal ribosome (GO:0042788)	poly(A) RNA binding (GO:0044822)	p.E253D(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(13)|lung(13)|ovary(2)|skin(2)|urinary_tract(2)	38						TAAATAGTGCTTCTACTTCCT	0.284																																					p.E253E		Atlas-SNP	.											LARP4B,colon,carcinoma,0,2	LARP4B	110	.	1	Substitution - Missense(1)	lung(1)	c.A759G						.						69.0	77.0	75.0					10																	876909		2201	4298	6499	SO:0001819	synonymous_variant	23185	exon9			TAGTGCTTCTACT	D86971	CCDS31131.1	10p15.3	2011-08-24	2009-06-09	2009-06-09	ENSG00000107929	ENSG00000107929		"""La ribonucleoprotein domain containing"""	28987	protein-coding gene	gene with protein product			"""KIAA0217"", ""La ribonucleoprotein domain family, member 5"""	KIAA0217, LARP5		9039502, 20573744	Standard	NM_015155		Approved		uc031ptb.1	Q92615	OTTHUMG00000017534	ENST00000316157.3:c.759A>G	chr10.hg19:g.876909T>C		93.0	0.0		60.0	3.0	NM_015155	A7MD20|Q5T3R3|Q5T3R4|Q5T3R5|Q68CY4	Silent	SNP	ENST00000316157.3	hg19	CCDS31131.1																																																																																			.	.		0.284	LARP4B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046395.2	NM_015155	
PITRM1	10531	hgsc.bcm.edu	37	10	3199171	3199171	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:3199171A>G	ENST00000224949.4	-	13	1467	c.1433T>C	c.(1432-1434)cTg>cCg	p.L478P	PITRM1-AS1_ENST00000601046.1_RNA|PITRM1-AS1_ENST00000598280.1_RNA|PITRM1_ENST00000380989.2_Missense_Mutation_p.L478P|PITRM1_ENST00000451104.2_Missense_Mutation_p.L446P|PITRM1_ENST00000380994.1_Missense_Mutation_p.L36P			Q5JRX3	PREP_HUMAN	pitrilysin metallopeptidase 1	478					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						ATTTTCCTGCAGGCACTGTCT	0.353																																					p.L478P		Atlas-SNP	.											.	PITRM1	109	.	0			c.T1433C						.						64.0	56.0	59.0					10																	3199171		1817	4077	5894	SO:0001583	missense	10531	exon13			TCCTGCAGGCACT	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.1433T>C	chr10.hg19:g.3199171A>G	ENSP00000224949:p.Leu478Pro	138.0	0.0		93.0	4.0	NM_014889	B3KMJ6|B4E0J8|C9JSL2|E7ES23|O95204|Q2M2G6|Q4VBR1|Q5JRW7|Q7L5Z7|Q9BSI6|Q9BVJ5|Q9UPP8	Missense_Mutation	SNP	ENST00000224949.4	hg19	CCDS59208.1	.	.	.	.	.	.	.	.	.	.	a	20.2	3.944531	0.73672	.	.	ENSG00000107959	ENST00000224949;ENST00000380980;ENST00000380989;ENST00000380994;ENST00000451104	T;T;T;T	0.12774	2.65;2.65;2.65;2.65	5.49	5.49	0.81192	Metalloenzyme, LuxS/M16 peptidase-like, metal-binding (1);	0.000000	0.85682	D	0.000000	T	0.41026	0.1141	M	0.83953	2.67	0.80722	D	1	D;P;D;D;D;D	0.63046	0.984;0.932;0.992;0.987;0.987;0.987	P;P;D;D;D;D	0.68621	0.827;0.702;0.959;0.927;0.927;0.927	T	0.39742	-0.9599	10	0.66056	D	0.02	-26.133	15.8835	0.79222	1.0:0.0:0.0:0.0	.	471;446;478;478;478;471	E9PDX6;E7ES23;Q5JRX3-2;C9JSL2;Q5JRX3;B4DH07	.;.;.;.;PREP_HUMAN;.	P	478;471;478;36;446	ENSP00000224949:L478P;ENSP00000370377:L478P;ENSP00000370382:L36P;ENSP00000401201:L446P	ENSP00000224949:L478P	L	-	2	0	PITRM1	3189171	1.000000	0.71417	0.842000	0.33263	0.765000	0.43378	8.601000	0.90864	2.212000	0.71576	0.460000	0.39030	CTG	.	.		0.353	PITRM1-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000046469.2		
VIM	7431	hgsc.bcm.edu	37	10	17278320	17278320	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:17278320T>C	ENST00000224237.5	+	8	1446	c.1301T>C	c.(1300-1302)gTt>gCt	p.V434A	RP11-124N14.3_ENST00000456355.1_RNA|VIM_ENST00000544301.1_Missense_Mutation_p.V434A			P08670	VIME_HUMAN	vimentin	434	Tail.				apoptotic process (GO:0006915)|astrocyte development (GO:0014002)|Bergmann glial cell differentiation (GO:0060020)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular component movement (GO:0006928)|intermediate filament organization (GO:0045109)|lens fiber cell development (GO:0070307)|muscle filament sliding (GO:0030049)|negative regulation of neuron projection development (GO:0010977)|positive regulation of gene expression (GO:0010628)|viral process (GO:0016032)	cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|neuron projection (GO:0043005)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)	double-stranded RNA binding (GO:0003725)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)|scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of eye lens (GO:0005212)			NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|liver(2)|lung(18)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						CTCCCTCTGGTTGATACCCAC	0.363																																					p.V434A		Atlas-SNP	.											.	VIM	71	.	0			c.T1301C						.						151.0	167.0	161.0					10																	17278320		2203	4300	6503	SO:0001583	missense	7431	exon9			CTCTGGTTGATAC	M14144	CCDS7120.1	10p13	2013-01-16			ENSG00000026025	ENSG00000026025		"""Intermediate filaments type III"""	12692	protein-coding gene	gene with protein product		193060					Standard	NM_003380		Approved		uc001iou.2	P08670	OTTHUMG00000017744	ENST00000224237.5:c.1301T>C	chr10.hg19:g.17278320T>C	ENSP00000224237:p.Val434Ala	103.0	0.0		85.0	4.0	NM_003380	B0YJC2|D3DRU4|Q15867|Q15868|Q15869|Q548L2|Q6LER9|Q8N850|Q96ML2|Q9NTM3	Missense_Mutation	SNP	ENST00000224237.5	hg19	CCDS7120.1	.	.	.	.	.	.	.	.	.	.	T	9.246	1.039461	0.19669	.	.	ENSG00000026025	ENST00000544301;ENST00000224237	D;D	0.96992	-4.2;-4.2	6.01	6.01	0.97437	.	0.000000	0.41938	D	0.000785	D	0.90714	0.7086	N	0.05441	-0.05	0.48288	D	0.999624	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	D	0.86699	0.1928	10	0.25106	T	0.35	.	16.5319	0.84362	0.0:0.0:0.0:1.0	.	434;434	Q53HU8;P08670	.;VIME_HUMAN	A	434	ENSP00000446007:V434A;ENSP00000224237:V434A	ENSP00000224237:V434A	V	+	2	0	VIM	17318326	0.999000	0.42202	0.984000	0.44739	0.724000	0.41520	2.999000	0.49473	2.295000	0.77249	0.523000	0.50628	GTT	.	.		0.363	VIM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047015.1	NM_003380	
CACNB2	783	hgsc.bcm.edu	37	10	18439889	18439889	+	Silent	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:18439889T>C	ENST00000324631.7	+	2	258	c.198T>C	c.(196-198)aaT>aaC	p.N66N	CACNB2_ENST00000377331.2_Silent_p.N38N|CACNB2_ENST00000352115.6_Silent_p.N66N|CACNB2_ENST00000282343.8_Silent_p.N38N|CACNB2_ENST00000377328.1_Silent_p.N66N|CACNB2_ENST00000467034.1_3'UTR	NM_201593.2|NM_201596.2	NP_963887.2|NP_963890.2	Q08289	CACB2_HUMAN	calcium channel, voltage-dependent, beta 2 subunit	66					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|neuromuscular junction development (GO:0007528)|positive regulation of calcium ion transport (GO:0051928)|synaptic transmission (GO:0007268)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|voltage-gated calcium channel complex (GO:0005891)	calcium channel activity (GO:0005262)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(12)|prostate(1)|skin(3)|stomach(2)	31					Amlodipine(DB00381)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	CTACCTCAAATAGTTTTGTTC	0.313																																					p.N66N		Atlas-SNP	.											.	CACNB2	220	.	0			c.T198C						.						131.0	138.0	135.0					10																	18439889		2203	4300	6503	SO:0001819	synonymous_variant	783	exon2			CTCAAATAGTTTT	U95019	CCDS7125.1, CCDS7126.1, CCDS7127.1, CCDS7128.1, CCDS7129.1, CCDS41493.1, CCDS41494.1	10p12	2014-09-17			ENSG00000165995	ENSG00000165995		"""Calcium channel subunits"""	1402	protein-coding gene	gene with protein product		600003		MYSB, CACNLB2		9254841, 8494331	Standard	NM_201596		Approved		uc001ipr.2	Q08289	OTTHUMG00000017764	ENST00000324631.7:c.198T>C	chr10.hg19:g.18439889T>C		169.0	0.0		127.0	48.0	NM_201597	A6PVM5|A6PVM7|A6PVM8|O00304|Q5QJ99|Q5QJA0|Q5VVG9|Q5VVH0|Q5VWV6|Q6TME1|Q6TME2|Q6TME3|Q8WX81|Q96NZ3|Q96NZ4|Q96NZ5|Q9BWU2|Q9HD32|Q9Y340|Q9Y341	Silent	SNP	ENST00000324631.7	hg19	CCDS7125.1																																																																																			.	.		0.313	CACNB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047072.2	NM_000724	
PTF1A	256297	hgsc.bcm.edu	37	10	23482645	23482645	+	Missense_Mutation	SNP	C	C	T			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:23482645C>T	ENST00000376504.3	+	2	1001	c.797C>T	c.(796-798)cCc>cTc	p.P266L		NM_178161.2	NP_835455.1	Q7RTS3	PTF1A_HUMAN	pancreas specific transcription factor, 1a	266					amacrine cell differentiation (GO:0035881)|cerebellum development (GO:0021549)|embryo development (GO:0009790)|endocrine pancreas development (GO:0031018)|exocrine pancreas development (GO:0031017)|neuron fate commitment (GO:0048663)|pancreas development (GO:0031016)|regulation of neural retina development (GO:0061074)|regulation of transcription, DNA-templated (GO:0006355)|retina layer formation (GO:0010842)|retinoic acid receptor signaling pathway (GO:0048384)|tissue development (GO:0009888)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|E-box binding (GO:0070888)|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)			endometrium(1)|large_intestine(1)|lung(3)|pancreas(1)|skin(1)	7						TCCCCCTCCCCCAGCGACCCT	0.502																																					p.P266L		Atlas-SNP	.											.	PTF1A	24	.	0			c.C797T						.						158.0	180.0	172.0					10																	23482645		2203	4300	6503	SO:0001583	missense	256297	exon2			CCTCCCCCAGCGA	BK000272	CCDS7143.1	10p12.31	2013-05-21			ENSG00000168267	ENSG00000168267		"""Basic helix-loop-helix proteins"""	23734	protein-coding gene	gene with protein product		607194				8703005	Standard	NM_178161		Approved	PTF1-p48, bHLHa29	uc001irp.3	Q7RTS3	OTTHUMG00000017815	ENST00000376504.3:c.797C>T	chr10.hg19:g.23482645C>T	ENSP00000365687:p.Pro266Leu	148.0	0.0		100.0	4.0	NM_178161	Q9HC25	Missense_Mutation	SNP	ENST00000376504.3	hg19	CCDS7143.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.090143	0.76756	.	.	ENSG00000168267	ENST00000376504	D	0.95069	-3.6	5.6	5.6	0.85130	.	0.000000	0.85682	D	0.000000	D	0.96688	0.8919	L	0.59436	1.845	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.96683	0.9505	10	0.59425	D	0.04	-8.961	19.2737	0.94021	0.0:1.0:0.0:0.0	.	266	Q7RTS3	PTF1A_HUMAN	L	266	ENSP00000365687:P266L	ENSP00000365687:P266L	P	+	2	0	PTF1A	23522651	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	7.367000	0.79558	2.649000	0.89929	0.555000	0.69702	CCC	.	.		0.502	PTF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047210.1	NM_178161	
ANKRD26	22852	hgsc.bcm.edu	37	10	27322293	27322293	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:27322293T>C	ENST00000376087.4	-	25	3833	c.3668A>G	c.(3667-3669)cAa>cGa	p.Q1223R	ANKRD26_ENST00000376070.3_Missense_Mutation_p.Q780R|ANKRD26_ENST00000436985.2_Missense_Mutation_p.Q1239R	NM_001256053.1|NM_014915.2	NP_001242982.1|NP_055730.2	Q9UPS8	ANR26_HUMAN	ankyrin repeat domain 26	1222					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						TTGTTGAAGTTGTCTCACAAC	0.284																																					p.Q1223R		Atlas-SNP	.											.	ANKRD26	179	.	0			c.A3668G						.						141.0	127.0	131.0					10																	27322293		1840	4094	5934	SO:0001583	missense	22852	exon25			TGAAGTTGTCTCA	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.3668A>G	chr10.hg19:g.27322293T>C	ENSP00000365255:p.Gln1223Arg	110.0	0.0		81.0	4.0	NM_014915	A6NH29|Q2TAZ3|Q6ZR14|Q9H1Q1|Q9NSK9|Q9NTD5|Q9NW69	Missense_Mutation	SNP	ENST00000376087.4	hg19	CCDS41499.1	.	.	.	.	.	.	.	.	.	.	T	18.79	3.698455	0.68386	.	.	ENSG00000107890	ENST00000376070;ENST00000376087;ENST00000436985	T;T;T	0.77489	3.65;-1.1;-1.1	5.41	4.27	0.50696	.	0.000000	0.51477	D	0.000088	T	0.69913	0.3164	L	0.56124	1.755	0.32221	N	0.575286	P;B;P	0.39480	0.582;0.447;0.675	B;B;B	0.34722	0.188;0.092;0.13	T	0.76061	-0.3097	10	0.72032	D	0.01	.	9.5387	0.39237	0.0:0.0841:0.0:0.9159	.	1223;1222;1239	Q9UPS8-3;Q9UPS8;A1L497	.;ANR26_HUMAN;.	R	780;1223;1239	ENSP00000365238:Q780R;ENSP00000365255:Q1223R;ENSP00000405112:Q1239R	ENSP00000365238:Q780R	Q	-	2	0	ANKRD26	27362299	1.000000	0.71417	0.996000	0.52242	0.988000	0.76386	6.695000	0.74593	0.917000	0.36895	0.477000	0.44152	CAA	.	.		0.284	ANKRD26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047296.1		
PTCHD3	374308	hgsc.bcm.edu	37	10	27688005	27688005	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:27688005A>G	ENST00000438700.3	-	4	1639	c.1522T>C	c.(1522-1524)Tct>Cct	p.S508P		NM_001034842.3	NP_001030014.2	Q3KNS1	PTHD3_HUMAN	patched domain containing 3	508	SSD. {ECO:0000255|PROSITE- ProRule:PRU00199}.				spermatid development (GO:0007286)	integral component of membrane (GO:0016021)|sperm midpiece (GO:0097225)	hedgehog receptor activity (GO:0008158)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(17)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	55						GACCTAAAAGAGCTCATAATC	0.393																																					p.S508P		Atlas-SNP	.											.	PTCHD3	140	.	0			c.T1522C						.						98.0	90.0	93.0					10																	27688005		2203	4300	6503	SO:0001583	missense	374308	exon4			TAAAAGAGCTCAT	AK126025	CCDS31173.1	10p12.1	2006-05-26			ENSG00000182077	ENSG00000182077			24776	protein-coding gene	gene with protein product		611791					Standard	NM_001034842		Approved	FLJ44037, PTR	uc001itu.2	Q3KNS1	OTTHUMG00000017860	ENST00000438700.3:c.1522T>C	chr10.hg19:g.27688005A>G	ENSP00000417658:p.Ser508Pro	131.0	0.0		113.0	5.0	NM_001034842	I3L499|Q6ZU28	Missense_Mutation	SNP	ENST00000438700.3	hg19	CCDS31173.1	.	.	.	.	.	.	.	.	.	.	A	0.427	-0.905089	0.02453	.	.	ENSG00000182077	ENST00000438700	D	0.83992	-1.79	4.08	2.93	0.34026	Sterol-sensing domain (1);	0.564710	0.19601	N	0.110392	T	0.68284	0.2984	L	0.31371	0.925	0.26782	N	0.969579	B	0.13145	0.007	B	0.17433	0.018	T	0.51156	-0.8741	10	0.19147	T	0.46	-10.37	4.2472	0.10677	0.634:0.1749:0.1911:0.0	.	508	Q3KNS1	PTHD3_HUMAN	P	508	ENSP00000417658:S508P	ENSP00000417658:S508P	S	-	1	0	PTCHD3	27728011	0.347000	0.24853	0.994000	0.49952	0.142000	0.21351	0.242000	0.18087	0.609000	0.30018	0.397000	0.26171	TCT	.	.		0.393	PTCHD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047325.3	XM_370541	
ZEB1	6935	hgsc.bcm.edu	37	10	31809977	31809977	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:31809977T>C	ENST00000320985.10	+	7	1824	c.1714T>C	c.(1714-1716)Tct>Cct	p.S572P	ZEB1_ENST00000446923.2_Missense_Mutation_p.S556P|ZEB1_ENST00000361642.5_Missense_Mutation_p.S573P|ZEB1_ENST00000559858.1_3'UTR|ZEB1_ENST00000542815.3_Missense_Mutation_p.S505P|ZEB1_ENST00000560721.2_Missense_Mutation_p.S552P			P37275	ZEB1_HUMAN	zinc finger E-box binding homeobox 1	572					cartilage development (GO:0051216)|cell proliferation (GO:0008283)|cellular response to amino acid stimulus (GO:0071230)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cochlea morphogenesis (GO:0090103)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic skeletal system morphogenesis (GO:0048704)|forebrain development (GO:0030900)|immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|pattern specification process (GO:0007389)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of mesenchymal cell proliferation (GO:0010464)|regulation of smooth muscle cell differentiation (GO:0051150)|regulation of T cell differentiation in thymus (GO:0033081)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|response to activity (GO:0014823)|response to nutrient levels (GO:0031667)|semicircular canal morphogenesis (GO:0048752)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|E-box binding (GO:0070888)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(2)|breast(4)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(14)|lung(38)|ovary(3)|skin(6)|upper_aerodigestive_tract(4)	77		Prostate(175;0.0156)				GCCTGAGTCCTCTGTTTCATC	0.448																																					p.S573P	Ovarian(40;423 959 14296 36701 49589)	Atlas-SNP	.											.	ZEB1	173	.	0			c.T1717C						.						76.0	76.0	76.0					10																	31809977		2203	4300	6503	SO:0001583	missense	6935	exon7			GAGTCCTCTGTTT	AK091478	CCDS7169.1, CCDS44370.1, CCDS53505.1, CCDS53506.1, CCDS53507.1	10p11.22	2014-02-14	2007-02-15	2007-02-15	ENSG00000148516	ENSG00000148516		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	11642	protein-coding gene	gene with protein product		189909	"""transcription factor 8 (represses interleukin 2 expression)"", ""posterior polymorphous corneal dystrophy 3"""	TCF8, PPCD3		1427828, 1840704, 15384081, 16252232	Standard	NM_001128128		Approved	BZP, ZEB, AREB6, NIL-2-A, Zfhep, Zfhx1a, FECD6	uc001ivu.4	P37275	OTTHUMG00000017907	ENST00000320985.10:c.1714T>C	chr10.hg19:g.31809977T>C	ENSP00000319248:p.Ser572Pro	107.0	0.0		114.0	5.0	NM_001174096	B4DJV0|B4DUW9|E9PCM7|F5H4I8|Q12924|Q13800|Q2KJ05|Q5T968|Q5VZ84|Q8NB68	Missense_Mutation	SNP	ENST00000320985.10	hg19	CCDS7169.1	.	.	.	.	.	.	.	.	.	.	T	6.365	0.435363	0.12045	.	.	ENSG00000148516	ENST00000542879;ENST00000537225;ENST00000361642;ENST00000546250;ENST00000542815;ENST00000320985;ENST00000437844;ENST00000541037;ENST00000543514;ENST00000446923	T;T;T;T;T	0.12569	2.97;2.67;2.71;2.67;2.72	5.45	1.41	0.22369	.	0.719450	0.13046	N	0.418161	T	0.04318	0.0119	N	0.02011	-0.69	0.31820	N	0.626042	B;B;B;B;B;B;B;B	0.09022	0.002;0.0;0.001;0.0;0.0;0.002;0.0;0.0	B;B;B;B;B;B;B;B	0.15052	0.012;0.001;0.002;0.001;0.0;0.005;0.001;0.001	T	0.29181	-1.0020	10	0.30078	T	0.28	-7.9253	4.0274	0.09693	0.0:0.2953:0.3971:0.3076	.	505;572;556;572;572;552;573;572	F5H4I8;F5H1R1;E9PCM7;B2RBI8;A0JLS9;Q5VZ84;Q2KJ05;P37275	.;.;.;.;.;.;.;ZEB1_HUMAN	P	354;572;573;572;505;572;552;431;463;556	ENSP00000444282:S354P;ENSP00000354487:S573P;ENSP00000444891:S505P;ENSP00000319248:S572P;ENSP00000391612:S556P	ENSP00000319248:S572P	S	+	1	0	ZEB1	31849983	0.999000	0.42202	0.397000	0.26308	0.820000	0.46376	1.027000	0.30115	0.442000	0.26555	0.533000	0.62120	TCT	.	.		0.448	ZEB1-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000419083.2	NM_030751	
CUL2	8453	hgsc.bcm.edu	37	10	35328009	35328009	+	Splice_Site	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:35328009A>G	ENST00000374748.1	-	10	1029	c.716T>C	c.(715-717)gTt>gCt	p.V239A	CUL2_ENST00000537177.1_Splice_Site_p.V258A|CUL2_ENST00000374742.1_Splice_Site_p.V239A|CUL2_ENST00000374746.1_Splice_Site_p.V239A|CUL2_ENST00000374749.3_Splice_Site_p.V239A|CUL2_ENST00000602371.1_Splice_Site_p.V182A|CUL2_ENST00000374751.3_Splice_Site_p.V239A			Q13617	CUL2_HUMAN	cullin 2	239					cell cycle arrest (GO:0007050)|cellular response to hypoxia (GO:0071456)|G1/S transition of mitotic cell cycle (GO:0000082)|intrinsic apoptotic signaling pathway (GO:0097193)|negative regulation of cell proliferation (GO:0008285)|protein ubiquitination (GO:0016567)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	Cul2-RING ubiquitin ligase complex (GO:0031462)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|VCB complex (GO:0030891)	ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(11)|ovary(3)|prostate(2)|skin(1)|urinary_tract(2)	31						TCTACCTAGAACCTATAAAAA	0.313																																					p.V258A		Atlas-SNP	.											.	CUL2	63	.	0			c.T773C						.						61.0	58.0	59.0					10																	35328009		2202	4293	6495	SO:0001630	splice_region_variant	8453	exon9			CCTAGAACCTATA	U83410	CCDS7179.1, CCDS73086.1	10p11.2	2011-05-24			ENSG00000108094	ENSG00000108094			2552	protein-coding gene	gene with protein product		603135				8681378	Standard	NM_003591		Approved		uc021ppa.1	Q13617	OTTHUMG00000017950	ENST00000374748.1:c.715-1T>C	chr10.hg19:g.35328009A>G		82.0	0.0		82.0	4.0	NM_001198778	B3KT95|B7Z6K8|D3DRY6|G3V1S2|O00200|Q5T2B6|Q9UNF9	Missense_Mutation	SNP	ENST00000374748.1	hg19	CCDS7179.1	.	.	.	.	.	.	.	.	.	.	A	15.03	2.711983	0.48517	.	.	ENSG00000108094	ENST00000374751;ENST00000374748;ENST00000374746;ENST00000374749;ENST00000374754;ENST00000374742;ENST00000537177	T;T;T;T;T;T	0.29655	1.56;1.56;1.56;1.56;1.56;1.56	5.44	5.44	0.79542	Cullin, N-terminal (1);Cullin repeat-like-containing domain (1);	0.052061	0.85682	D	0.000000	T	0.22244	0.0536	N	0.16743	0.435	0.80722	D	1	B;B;B	0.25105	0.078;0.118;0.044	B;B;B	0.31547	0.103;0.081;0.132	T	0.07947	-1.0746	10	0.15499	T	0.54	-25.6801	15.7856	0.78300	1.0:0.0:0.0:0.0	.	239;258;239	Q5T2B5;G3V1S2;Q13617	.;.;CUL2_HUMAN	A	239;239;239;239;182;239;258	ENSP00000363883:V239A;ENSP00000363880:V239A;ENSP00000363878:V239A;ENSP00000363881:V239A;ENSP00000363874:V239A;ENSP00000444856:V258A	ENSP00000363874:V239A	V	-	2	0	CUL2	35368015	1.000000	0.71417	1.000000	0.80357	0.545000	0.35147	9.339000	0.96797	2.186000	0.69663	0.455000	0.32223	GTT	.	.		0.313	CUL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047538.1	NM_003591	Missense_Mutation
ANKRD30A	91074	hgsc.bcm.edu	37	10	37508232	37508232	+	Missense_Mutation	SNP	C	C	A			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:37508232C>A	ENST00000602533.1	+	34	3523	c.3424C>A	c.(3424-3426)Cac>Aac	p.H1142N	ANKRD30A_ENST00000361713.1_Missense_Mutation_p.H1142N|ANKRD30A_ENST00000374660.1_Missense_Mutation_p.H1261N			Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A	1198					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(8)|endometrium(14)|kidney(21)|large_intestine(13)|lung(70)|ovary(8)|pancreas(1)|prostate(3)|skin(15)|stomach(1)|urinary_tract(3)	158						AATTGAATCACACCATCCTAG	0.393																																					p.H1142N		Atlas-SNP	.											.	ANKRD30A	448	.	0			c.C3424A						.						68.0	66.0	67.0					10																	37508232		1867	4098	5965	SO:0001583	missense	91074	exon34			GAATCACACCATC	AF269087	CCDS7193.1	10p11.21	2013-01-10			ENSG00000148513	ENSG00000148513		"""Ankyrin repeat domain containing"""	17234	protein-coding gene	gene with protein product	"""breast cancer antigen NY-BR-1"""	610856				11280766	Standard	NM_052997		Approved	NY-BR-1	uc001iza.1	Q9BXX3	OTTHUMG00000017968	ENST00000602533.1:c.3424C>A	chr10.hg19:g.37508232C>A	ENSP00000473551:p.His1142Asn	244.0	0.0		164.0	54.0	NM_052997	Q5W025	Missense_Mutation	SNP	ENST00000602533.1	hg19		.	.	.	.	.	.	.	.	.	.	c	0.428	-0.904682	0.02453	.	.	ENSG00000148513	ENST00000361713;ENST00000374660	T;T	0.13778	2.56;2.56	2.81	0.189	0.15119	.	.	.	.	.	T	0.09862	0.0242	L	0.40543	1.245	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.34625	-0.9821	9	0.66056	D	0.02	.	2.4956	0.04621	0.4258:0.1339:0.0:0.4403	.	1198	Q9BXX3	AN30A_HUMAN	N	1142;1261	ENSP00000354432:H1142N;ENSP00000363792:H1261N	ENSP00000354432:H1142N	H	+	1	0	ANKRD30A	37548238	0.803000	0.28956	0.051000	0.19133	0.001000	0.01503	1.569000	0.36428	-0.172000	0.10779	-1.930000	0.00511	CAC	.	.		0.393	ANKRD30A-001	KNOWN	NMD_exception|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000047588.2	NM_052997	
ZNF25	219749	hgsc.bcm.edu	37	10	38241944	38241944	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:38241944A>G	ENST00000302609.7	-	6	694	c.482T>C	c.(481-483)cTc>cCc	p.L161P	AL117337.1_ENST00000582458.1_RNA|ZNF25_ENST00000374633.1_5'UTR	NM_145011.2	NP_659448.1	P17030	ZNF25_HUMAN	zinc finger protein 25	161					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)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(11)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28		all_neural(218;0.0218)|Breast(68;0.0389)|Ovarian(717;0.0443)|Renal(717;0.157)				ATGTCTTATGAGGTCTTCATT	0.368																																					p.L161P		Atlas-SNP	.											.	ZNF25	66	.	0			c.T482C						.						149.0	154.0	152.0					10																	38241944		2203	4300	6503	SO:0001583	missense	219749	exon6			CTTATGAGGTCTT	AK056452	CCDS7195.1	10p11.2	2013-01-08	2006-05-10		ENSG00000175395	ENSG00000175395		"""Zinc fingers, C2H2-type"", ""-"""	13043	protein-coding gene	gene with protein product		194528	"""zinc finger protein 25 (KOX 19)"""			1639412, 8464732	Standard	NM_145011		Approved	KOX19, FLJ31890, Zfp9	uc001ize.1	P17030	OTTHUMG00000019344	ENST00000302609.7:c.482T>C	chr10.hg19:g.38241944A>G	ENSP00000302222:p.Leu161Pro	119.0	0.0		87.0	4.0	NM_145011	A9Z1X5|Q8IYE3|Q8NDD6|Q96MU2	Missense_Mutation	SNP	ENST00000302609.7	hg19	CCDS7195.1	.	.	.	.	.	.	.	.	.	.	A	14.29	2.491627	0.44249	.	.	ENSG00000175395	ENST00000302609;ENST00000374633	T	0.75260	-0.92	4.84	4.84	0.62591	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.188994	0.26258	N	0.025417	D	0.86364	0.5915	M	0.91406	3.205	0.45172	D	0.998184	D	0.61080	0.989	P	0.59056	0.851	D	0.89201	0.3557	10	0.72032	D	0.01	-13.3187	12.7429	0.57264	1.0:0.0:0.0:0.0	.	161	P17030	ZNF25_HUMAN	P	161;125	ENSP00000302222:L161P	ENSP00000302222:L161P	L	-	2	0	ZNF25	38281950	0.989000	0.36119	0.695000	0.30226	0.391000	0.30476	4.591000	0.61019	2.172000	0.68678	0.524000	0.50904	CTC	.	.		0.368	ZNF25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051214.1	NM_145011, NM_006966	
ZNF37A	7587	hgsc.bcm.edu	37	10	38407552	38407552	+	Silent	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:38407552A>G	ENST00000361085.5	+	7	1818	c.1473A>G	c.(1471-1473)agA>agG	p.R491R	ZNF37A_ENST00000351773.3_Silent_p.R491R	NM_001178101.1|NM_003421.2	NP_001171572.1|NP_003412.1	P17032	ZN37A_HUMAN	zinc finger protein 37A	491					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(13)|prostate(1)	28						CTCATATAAGACAGAAACCCT	0.408																																					p.R491R		Atlas-SNP	.											.	ZNF37A	118	.	0			c.A1473G						.						59.0	60.0	59.0					10																	38407552		2203	4300	6503	SO:0001819	synonymous_variant	7587	exon7			TATAAGACAGAAA	X69115	CCDS31183.1	10p11.2	2013-01-08	2006-05-11		ENSG00000075407	ENSG00000075407		"""Zinc fingers, C2H2-type"", ""-"""	13102	protein-coding gene	gene with protein product			"""zinc finger protein 37a (KOX 21)"""			2014798, 8464732	Standard	NM_001178101		Approved	KOX21, ZNF37	uc001izl.3	P17032	OTTHUMG00000017990	ENST00000361085.5:c.1473A>G	chr10.hg19:g.38407552A>G		129.0	0.0		81.0	4.0	NM_003421	B3KRQ3|D3DRZ3|Q96B88	Silent	SNP	ENST00000361085.5	hg19	CCDS31183.1																																																																																			.	.		0.408	ZNF37A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047624.2	NM_003421	
FRMPD2	143162	hgsc.bcm.edu	37	10	49448531	49448531	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:49448531T>C	ENST00000374201.3	-	6	874	c.572A>G	c.(571-573)gAg>gGg	p.E191G	FRMPD2_ENST00000407470.4_Missense_Mutation_p.E160G|FRMPD2_ENST00000305531.3_Missense_Mutation_p.E167G	NM_001018071.3|NM_001042512.2	NP_001018081|NP_001035977.2	Q68DX3	FRPD2_HUMAN	FERM and PDZ domain containing 2	191	KIND. {ECO:0000255|PROSITE- ProRule:PRU00709}.				tight junction assembly (GO:0070830)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|tight junction (GO:0005923)	1-phosphatidylinositol binding (GO:0005545)			NS(2)|autonomic_ganglia(2)|breast(5)|cervix(1)|endometrium(3)|kidney(7)|large_intestine(15)|lung(24)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	66				Kidney(211;0.201)		AACTCTTTTCTCCACCTGGGG	0.532																																					p.E191G		Atlas-SNP	.											.	FRMPD2	157	.	0			c.A572G						.						63.0	57.0	59.0					10																	49448531		2203	4300	6503	SO:0001583	missense	143162	exon6			CTTTTCTCCACCT	AK123038	CCDS31195.1	10q11	2010-10-13			ENSG00000170324	ENSG00000170324			28572	protein-coding gene	gene with protein product		613323	"""PDZ domain containing 5C"""	PDZD5C, PDZK5C			Standard	NM_001018071		Approved	MGC35285	uc001jdv.3	Q68DX3	OTTHUMG00000018171	ENST00000374201.3:c.572A>G	chr10.hg19:g.49448531T>C	ENSP00000363317:p.Glu191Gly	122.0	0.0		61.0	4.0	NM_001018071	B7WNW0|B7ZML5|Q2VY07|Q6GMQ9|Q6ZN38|Q6ZWI2|Q8N5T9	Missense_Mutation	SNP	ENST00000374201.3	hg19	CCDS31195.1	.	.	.	.	.	.	.	.	.	.	T	12.28	1.890484	0.33348	.	.	ENSG00000170324	ENST00000374201;ENST00000305531;ENST00000407470	T;T;T	0.35236	1.32;1.32;1.32	4.37	3.23	0.37069	KIND (2);	.	.	.	.	T	0.27765	0.0683	L	0.38531	1.155	0.28214	N	0.9268	B;B;B	0.24043	0.096;0.034;0.096	B;B;B	0.25614	0.062;0.02;0.062	T	0.22521	-1.0214	9	0.56958	D	0.05	.	6.7008	0.23225	0.0:0.108:0.0:0.892	.	167;191;160	Q68DX3-2;Q68DX3;F8WCT2	.;FRPD2_HUMAN;.	G	191;167;160	ENSP00000363317:E191G;ENSP00000307079:E167G;ENSP00000384339:E160G	ENSP00000307079:E167G	E	-	2	0	FRMPD2	49118537	0.970000	0.33590	0.989000	0.46669	0.745000	0.42441	1.365000	0.34182	0.834000	0.34852	0.533000	0.62120	GAG	.	.		0.532	FRMPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047923.3	NM_152428	
HERC4	26091	hgsc.bcm.edu	37	10	69785411	69785412	+	Missense_Mutation	DNP	CC	CC	AA			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:69785411_69785412CC>AA	ENST00000395198.3	-	8	1046_1047	c.799_800GG>TT	c.(799-801)GGa>TTa	p.G267L	HERC4_ENST00000395187.2_3'UTR|HERC4_ENST00000412272.2_Missense_Mutation_p.G267L|HERC4_ENST00000373700.4_Missense_Mutation_p.G267L|HERC4_ENST00000277817.6_Missense_Mutation_p.G157L	NM_022079.2	NP_071362.1	Q5GLZ8	HERC4_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase 4	267					cell differentiation (GO:0030154)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	27						CCCTCCAGCTCCAAAAGTAAAC	0.371																																					p.G267V|p.G267X		Atlas-SNP	.											.	HERC4	78	.	0			c.G800T|c.G799T						.																																			SO:0001583	missense	26091	exon8			CCAGCTCCAAAAG|CAGCTCCAAAAGT	AY221963	CCDS7274.1, CCDS41533.1, CCDS60541.1, CCDS60542.1	10q21.3	2013-09-20	2012-02-23		ENSG00000148634	ENSG00000148634			24521	protein-coding gene	gene with protein product		609248	"""hect domain and RLD 4"""			10997877	Standard	NM_022079		Approved	DKFZP564G092, KIAA1593	uc001jng.4	Q5GLZ8	OTTHUMG00000018343	ENST00000395198.3:c.799_800delinsAA	chr10.hg19:g.69785411_69785412delinsAA	ENSP00000378624:p.Gly267Leu	133.0|132.0	0.0		106.0|101.0	47.0|42.0	NM_022079	Q5GC98|Q5GC99|Q5GCA0|Q8IXP9|Q9HCH9	Missense_Mutation|Nonsense_Mutation	SNP	ENST00000395198.3	hg19	CCDS41533.1																																																																																			.	.		0.371	HERC4-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359262.1	NM_015601	
PPA1	5464	hgsc.bcm.edu	37	10	71969401	71969401	+	Silent	SNP	T	T	C	rs150430650		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:71969401T>C	ENST00000373232.3	-	7	651	c.552A>G	c.(550-552)gaA>gaG	p.E184E		NM_021129.3	NP_066952.1	Q15181	IPYR_HUMAN	pyrophosphatase (inorganic) 1	184					diphosphate metabolic process (GO:0071344)|gene expression (GO:0010467)|phosphate-containing compound metabolic process (GO:0006796)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	inorganic diphosphatase activity (GO:0004427)|magnesium ion binding (GO:0000287)			breast(2)|endometrium(1)|large_intestine(2)|lung(3)|skin(2)	10						CCACAGTAGCTTCTAAGTAGC	0.343																																					p.E184E		Atlas-SNP	.											.	PPA1	24	.	0			c.A552G						.						108.0	111.0	110.0					10																	71969401		2203	4300	6503	SO:0001819	synonymous_variant	5464	exon7			AGTAGCTTCTAAG	AF154065	CCDS7299.1	10q11.1-q24	2012-10-02	2005-10-07	2005-10-07	ENSG00000180817	ENSG00000180817	3.6.1.1		9226	protein-coding gene	gene with protein product	"""cytosolic inorganic pyrophosphatase"", ""inorganic pyrophosphatase 1"", ""pyrophosphate phospho-hydrolase"""	179030	"""pyrophosphatase (inorganic)"""	PP		10542310, 975879	Standard	NM_021129		Approved	SID6-8061, Ppase, IOPPP, PP1	uc001jqv.1	Q15181	OTTHUMG00000018399	ENST00000373232.3:c.552A>G	chr10.hg19:g.71969401T>C		337.0	0.0		251.0	18.0	NM_021129	Q2M348|Q5SQT7|Q6P7P4|Q9UQJ5|Q9Y5B1	Silent	SNP	ENST00000373232.3	hg19	CCDS7299.1																																																																																			.	.		0.343	PPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048490.2	NM_021129	
PPA1	5464	hgsc.bcm.edu	37	10	71969413	71969413	+	Silent	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:71969413A>G	ENST00000373232.3	-	7	639	c.540T>C	c.(538-540)ccT>ccC	p.P180P		NM_021129.3	NP_066952.1	Q15181	IPYR_HUMAN	pyrophosphatase (inorganic) 1	180					diphosphate metabolic process (GO:0071344)|gene expression (GO:0010467)|phosphate-containing compound metabolic process (GO:0006796)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	inorganic diphosphatase activity (GO:0004427)|magnesium ion binding (GO:0000287)			breast(2)|endometrium(1)|large_intestine(2)|lung(3)|skin(2)	10						CTAAGTAGCCAGGTTTCAGCC	0.348																																					p.P180P		Atlas-SNP	.											.	PPA1	24	.	0			c.T540C						.						104.0	107.0	106.0					10																	71969413		2203	4300	6503	SO:0001819	synonymous_variant	5464	exon7			GTAGCCAGGTTTC	AF154065	CCDS7299.1	10q11.1-q24	2012-10-02	2005-10-07	2005-10-07	ENSG00000180817	ENSG00000180817	3.6.1.1		9226	protein-coding gene	gene with protein product	"""cytosolic inorganic pyrophosphatase"", ""inorganic pyrophosphatase 1"", ""pyrophosphate phospho-hydrolase"""	179030	"""pyrophosphatase (inorganic)"""	PP		10542310, 975879	Standard	NM_021129		Approved	SID6-8061, Ppase, IOPPP, PP1	uc001jqv.1	Q15181	OTTHUMG00000018399	ENST00000373232.3:c.540T>C	chr10.hg19:g.71969413A>G		318.0	0.0		245.0	18.0	NM_021129	Q2M348|Q5SQT7|Q6P7P4|Q9UQJ5|Q9Y5B1	Silent	SNP	ENST00000373232.3	hg19	CCDS7299.1																																																																																			.	.		0.348	PPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048490.2	NM_021129	
UNC5B	219699	hgsc.bcm.edu	37	10	73059012	73059012	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:73059012T>C	ENST00000335350.6	+	17	3232	c.2816T>C	c.(2815-2817)gTg>gCg	p.V939A	UNC5B_ENST00000373192.4_Missense_Mutation_p.V928A	NM_170744.4	NP_734465.2	Q8IZJ1	UNC5B_HUMAN	unc-5 homolog B (C. elegans)	939	Death.				anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of apoptotic process (GO:0043065)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(17)|ovary(4)|prostate(4)|skin(4)	49						CTGGTGGCTGTGGCCACCGAC	0.662																																					p.V939A		Atlas-SNP	.											.	UNC5B	123	.	0			c.T2816C						.						118.0	116.0	117.0					10																	73059012		2203	4300	6503	SO:0001583	missense	219699	exon17			TGGCTGTGGCCAC	AB096256	CCDS7309.1, CCDS58083.1	10q22.2	2013-01-11	2001-11-28		ENSG00000107731	ENSG00000107731		"""Immunoglobulin superfamily / I-set domain containing"""	12568	protein-coding gene	gene with protein product		607870	"""unc5 (C.elegans homolog) b"""				Standard	NM_170744		Approved	UNC5H2, p53RDL1	uc001jro.3	Q8IZJ1	OTTHUMG00000018422	ENST00000335350.6:c.2816T>C	chr10.hg19:g.73059012T>C	ENSP00000334329:p.Val939Ala	134.0	0.0		100.0	4.0	NM_170744	Q5T3R9|Q5T3S0|Q86SN3|Q8N1Y2|Q9H9F3	Missense_Mutation	SNP	ENST00000335350.6	hg19	CCDS7309.1	.	.	.	.	.	.	.	.	.	.	T	16.55	3.154050	0.57259	.	.	ENSG00000107731	ENST00000335350;ENST00000373192	T;T	0.49432	0.84;0.78	5.62	5.62	0.85841	Death (1);DEATH-like (2);	0.086033	0.85682	D	0.000000	T	0.30230	0.0758	N	0.04018	-0.295	0.47037	D	0.999298	B;B	0.21071	0.041;0.051	B;B	0.26614	0.043;0.071	T	0.12528	-1.0544	10	0.39692	T	0.17	-22.5639	15.8325	0.78764	0.0:0.0:0.0:1.0	.	928;939	Q8IZJ1-2;Q8IZJ1	.;UNC5B_HUMAN	A	939;928	ENSP00000334329:V939A;ENSP00000362288:V928A	ENSP00000334329:V939A	V	+	2	0	UNC5B	72729018	1.000000	0.71417	1.000000	0.80357	0.808000	0.45660	8.040000	0.89188	2.145000	0.66743	0.254000	0.18369	GTG	.	.		0.662	UNC5B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048541.1	NM_170744	
CHST3	9469	hgsc.bcm.edu	37	10	73767478	73767478	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:73767478A>G	ENST00000373115.4	+	3	1126	c.689A>G	c.(688-690)gAg>gGg	p.E230G		NM_004273.4	NP_004264.2	Q7LGC8	CHST3_HUMAN	carbohydrate (chondroitin 6) sulfotransferase 3	230					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)|sulfur compound metabolic process (GO:0006790)|T cell homeostasis (GO:0043029)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	chondroitin 6-sulfotransferase activity (GO:0008459)|proteoglycan sulfotransferase activity (GO:0050698)|sulfotransferase activity (GO:0008146)			endometrium(1)|lung(5)	6						TCCCTGTGCGAGGACCCCGTC	0.652																																					p.E230G		Atlas-SNP	.											.	CHST3	36	.	0			c.A689G						.						17.0	16.0	16.0					10																	73767478		2197	4286	6483	SO:0001583	missense	9469	exon3			TGTGCGAGGACCC	AB017915	CCDS7312.1	10q22.1	2007-03-14			ENSG00000122863	ENSG00000122863		"""Sulfotransferases, membrane-bound"""	1971	protein-coding gene	gene with protein product		603799				9883891, 9714738	Standard	NM_004273		Approved	C6ST, C6ST1	uc001jsn.3	Q7LGC8	OTTHUMG00000018431	ENST00000373115.4:c.689A>G	chr10.hg19:g.73767478A>G	ENSP00000362207:p.Glu230Gly	122.0	0.0		81.0	6.0	NM_004273	O75099|Q52M30	Missense_Mutation	SNP	ENST00000373115.4	hg19	CCDS7312.1	.	.	.	.	.	.	.	.	.	.	A	24.8	4.566975	0.86439	.	.	ENSG00000122863	ENST00000373115	D	0.96491	-4.03	5.68	5.68	0.88126	Sulfotransferase domain (1);	0.000000	0.85682	D	0.000000	D	0.97536	0.9193	M	0.64997	1.995	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.98107	1.0418	10	0.62326	D	0.03	-35.8093	15.1166	0.72407	1.0:0.0:0.0:0.0	.	230	Q7LGC8	CHST3_HUMAN	G	230	ENSP00000362207:E230G	ENSP00000362207:E230G	E	+	2	0	CHST3	73437484	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.166000	0.64965	2.179000	0.69175	0.459000	0.35465	GAG	.	.		0.652	CHST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048563.1	NM_004273	
MYOZ1	58529	hgsc.bcm.edu	37	10	75394369	75394369	+	Silent	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:75394369T>C	ENST00000359322.4	-	4	739	c.375A>G	c.(373-375)ggA>ggG	p.G125G		NM_021245.3	NP_067068.1			myozenin 1											central_nervous_system(1)|large_intestine(5)|lung(2)|ovary(2)|skin(2)	12	Prostate(51;0.0112)					AGCCATACTGTCCGGCAGAGC	0.657																																					p.G125G		Atlas-SNP	.											.	MYOZ1	24	.	0			c.A375G						.						65.0	65.0	65.0					10																	75394369		2203	4300	6503	SO:0001819	synonymous_variant	58529	exon4			ATACTGTCCGGCA	AF240633	CCDS7330.1	10q22.1	2008-07-03	2002-01-10	2002-01-11	ENSG00000177791	ENSG00000177791			13752	protein-coding gene	gene with protein product	"""calsarcin-2"""	605603	"""myozenin"""	MYOZ		11171996, 10984498	Standard	NM_021245		Approved	FATZ, CS-2	uc001jur.4	Q9NP98	OTTHUMG00000018466	ENST00000359322.4:c.375A>G	chr10.hg19:g.75394369T>C		169.0	0.0		120.0	5.0	NM_021245		Silent	SNP	ENST00000359322.4	hg19	CCDS7330.1																																																																																			.	.		0.657	MYOZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048654.1		
HECTD2	143279	hgsc.bcm.edu	37	10	93221940	93221940	+	Splice_Site	SNP	C	C	T			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:93221940C>T	ENST00000298068.5	+	5	693	c.599C>T	c.(598-600)aCt>aTt	p.T200I	HECTD2_ENST00000446394.1_Splice_Site_p.T200I|HECTD2_ENST00000371681.4_Missense_Mutation_p.T200I|HECTD2_ENST00000536715.1_5'UTR	NM_182765.3	NP_877497	Q5U5R9	HECD2_HUMAN	HECT domain containing E3 ubiquitin protein ligase 2	200					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|endometrium(2)|kidney(4)|large_intestine(10)|lung(7)|skin(1)|urinary_tract(1)	27						TTACTTAATACTGTAAGTATT	0.318																																					p.T200I	NSCLC(12;376 469 1699 39910 41417)	Atlas-SNP	.											.	HECTD2	60	.	0			c.C599T						.						170.0	169.0	169.0					10																	93221940		2203	4292	6495	SO:0001630	splice_region_variant	143279	exon5			TTAATACTGTAAG	AK094625	CCDS7414.1, CCDS7415.1, CCDS60591.1	10q23.32	2013-09-20	2012-02-23		ENSG00000165338	ENSG00000165338			26736	protein-coding gene	gene with protein product			"""HECT domain containing 2"""			8619474, 9110174	Standard	NM_001284274		Approved	FLJ37306	uc001khl.2	Q5U5R9	OTTHUMG00000018742	ENST00000298068.5:c.600+1C>T	chr10.hg19:g.93221940C>T		124.0	0.0		95.0	4.0	NM_173497	Q5VZ97|Q5VZ98|Q5VZ99|Q8N1X7|Q8TCP5	Missense_Mutation	SNP	ENST00000298068.5	hg19	CCDS7414.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.065920	0.76187	.	.	ENSG00000165338	ENST00000446394;ENST00000371681;ENST00000298068	T;T;T	0.55052	1.24;0.54;1.25	5.57	5.57	0.84162	.	0.000000	0.85682	D	0.000000	T	0.69369	0.3103	M	0.62723	1.935	0.80722	D	1	B;P;D	0.89917	0.179;0.483;1.0	B;B;D	0.83275	0.057;0.057;0.996	T	0.62053	-0.6935	10	0.15952	T	0.53	.	19.1506	0.93487	0.0:1.0:0.0:0.0	.	200;200;200	E7ERR3;Q5U5R9;Q5VZ98	.;HECD2_HUMAN;.	I	200	ENSP00000401023:T200I;ENSP00000360746:T200I;ENSP00000298068:T200I	ENSP00000298068:T200I	T	+	2	0	HECTD2	93211920	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	6.488000	0.73637	2.637000	0.89404	0.555000	0.69702	ACT	.	.		0.318	HECTD2-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098620.1		Missense_Mutation
ENTPD1	953	hgsc.bcm.edu	37	10	97620281	97620281	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:97620281T>C	ENST00000371205.4	+	8	1413	c.1130T>C	c.(1129-1131)gTc>gCc	p.V377A	ENTPD1_ENST00000371203.5_Missense_Mutation_p.V239A|ENTPD1_ENST00000371207.3_Missense_Mutation_p.V389A|ENTPD1-AS1_ENST00000416301.1_RNA|ENTPD1_ENST00000539125.1_Missense_Mutation_p.V239A|RP11-248J23.7_ENST00000491114.1_5'Flank|RP11-429G19.3_ENST00000433113.1_RNA|ENTPD1_ENST00000453258.2_Missense_Mutation_p.V384A|ENTPD1-AS1_ENST00000451364.1_RNA|ENTPD1_ENST00000543964.1_Missense_Mutation_p.V269A			P49961	ENTP1_HUMAN	ectonucleoside triphosphate diphosphohydrolase 1	377					ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell death (GO:0008219)|G-protein coupled receptor signaling pathway (GO:0007186)|platelet activation (GO:0030168)|purine ribonucleoside diphosphate catabolic process (GO:0009181)	basal lamina (GO:0005605)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|nucleoside-diphosphatase activity (GO:0017110)|nucleoside-triphosphatase activity (GO:0017111)			cervix(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(3)|prostate(1)|skin(1)	16		Colorectal(252;0.0821)		Epithelial(162;1.31e-07)|all cancers(201;5.33e-06)		TCAGAGAAAGTCTCTCAGGAA	0.438																																					p.V389A		Atlas-SNP	.											.	ENTPD1	44	.	0			c.T1166C						.						122.0	111.0	115.0					10																	97620281		2203	4300	6503	SO:0001583	missense	953	exon8			AGAAAGTCTCTCA	S73813	CCDS7444.1, CCDS53556.1, CCDS53557.1, CCDS53558.1, CCDS41554.1	10q24.1	2014-03-03			ENSG00000138185	ENSG00000138185		"""CD molecules"""	3363	protein-coding gene	gene with protein product		601752		CD39		9226376, 24482476	Standard	NM_001098175		Approved	NTPDase-1, ATPDase, SPG64	uc010qoj.2	P49961	OTTHUMG00000018818	ENST00000371205.4:c.1130T>C	chr10.hg19:g.97620281T>C	ENSP00000360248:p.Val377Ala	149.0	0.0		119.0	6.0	NM_001164178	A9Z1X8|B4DWB9|B4E1X1|B7Z599|G3XAF6|Q5T561|Q5T562|Q86VV3|Q9UQQ9|Q9Y3Q9	Missense_Mutation	SNP	ENST00000371205.4	hg19	CCDS7444.1	.	.	.	.	.	.	.	.	.	.	T	9.275	1.046689	0.19748	.	.	ENSG00000138185	ENST00000453258;ENST00000371207;ENST00000543964;ENST00000539125;ENST00000371203;ENST00000371205	T;T;T;T;T;T	0.10960	2.82;2.82;2.82;2.82;2.82;2.82	4.08	-2.59	0.06209	.	4.928260	0.00166	N	0.000012	T	0.08268	0.0206	L	0.41415	1.275	0.09310	N	1	B;B;B;B	0.27192	0.171;0.141;0.108;0.171	B;B;B;B	0.27796	0.083;0.05;0.061;0.083	T	0.25433	-1.0132	10	0.25751	T	0.34	2.8227	0.4026	0.00428	0.2858:0.1259:0.2138:0.3745	.	389;389;384;377	B4DWB9;G3XAF6;P49961-2;P49961	.;.;.;ENTP1_HUMAN	A	384;389;269;239;239;377	ENSP00000390955:V384A;ENSP00000360250:V389A;ENSP00000442968:V269A;ENSP00000440027:V239A;ENSP00000360246:V239A;ENSP00000360248:V377A	ENSP00000360246:V239A	V	+	2	0	ENTPD1	97610271	0.000000	0.05858	0.000000	0.03702	0.165000	0.22458	-0.614000	0.05604	-0.143000	0.11334	0.455000	0.32223	GTC	.	.		0.438	ENTPD1-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049566.1	NM_001776	
ANKRD2	26287	hgsc.bcm.edu	37	10	99337615	99337615	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:99337615A>G	ENST00000307518.5	+	2	494	c.227A>G	c.(226-228)gAg>gGg	p.E76G	ANKRD2_ENST00000298808.5_Missense_Mutation_p.E76G|ANKRD2_ENST00000455090.1_Missense_Mutation_p.E49G|ANKRD2_ENST00000370655.1_Missense_Mutation_p.E49G			Q9GZV1	ANKR2_HUMAN	ankyrin repeat domain 2 (stretch responsive muscle)	76	May mediate interaction with PML, p53/TP53 and YBX1.				muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|skeletal muscle cell differentiation (GO:0035914)	cytosol (GO:0005829)|euchromatin (GO:0000791)|I band (GO:0031674)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	protein kinase B binding (GO:0043422)|structural constituent of muscle (GO:0008307)			breast(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|stomach(1)	7		all_hematologic(284;1.95e-06)|Colorectal(252;0.0163)		Epithelial(162;1.18e-94)|all cancers(201;9.31e-86)|BRCA - Breast invasive adenocarcinoma(275;0.0233)|STAD - Stomach adenocarcinoma(243;0.181)|KIRC - Kidney renal clear cell carcinoma(50;0.206)|Kidney(138;0.241)		CTGGAGGATGAGAAGCACCAC	0.612																																					p.E76G		Atlas-SNP	.											ANKRD2,NS,carcinoma,0,1	ANKRD2	27	.	0			c.A227G						.						52.0	40.0	44.0					10																	99337615		2199	4290	6489	SO:0001583	missense	26287	exon2			AGGATGAGAAGCA	AJ304805	CCDS7466.1, CCDS44468.1	10q23	2013-01-10			ENSG00000165887	ENSG00000165887		"""Ankyrin repeat domain containing"""	495	protein-coding gene	gene with protein product		610734				10873377, 15136035, 15677738	Standard	NM_001129981		Approved	ARPP	uc001knw.3	Q9GZV1	OTTHUMG00000018860	ENST00000307518.5:c.227A>G	chr10.hg19:g.99337615A>G	ENSP00000306163:p.Glu76Gly	77.0	0.0		70.0	3.0	NM_001129981	Q3B778|Q5T456|Q70EZ9|Q8WUD7|Q96MG0|Q9NQC9	Missense_Mutation	SNP	ENST00000307518.5	hg19	CCDS7466.1	.	.	.	.	.	.	.	.	.	.	A	19.93	3.918878	0.73098	.	.	ENSG00000165887	ENST00000307518;ENST00000298808;ENST00000370655;ENST00000455090	T;T;T;T	0.56941	0.7;0.46;0.62;0.43	4.65	4.65	0.58169	.	0.082483	0.50627	D	0.000101	T	0.58409	0.2120	L	0.34521	1.04	0.36324	D	0.858415	B;D	0.71674	0.079;0.998	B;D	0.78314	0.051;0.991	T	0.60367	-0.7277	10	0.21540	T	0.41	-39.2181	12.4609	0.55731	1.0:0.0:0.0:0.0	.	76;76	Q9GZV1-2;Q9GZV1	.;ANKR2_HUMAN	G	76;76;49;49	ENSP00000306163:E76G;ENSP00000298808:E76G;ENSP00000359689:E49G;ENSP00000403114:E49G	ENSP00000298808:E76G	E	+	2	0	ANKRD2	99327605	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	4.984000	0.63838	1.949000	0.56562	0.459000	0.35465	GAG	.	.		0.612	ANKRD2-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
CHUK	1147	hgsc.bcm.edu	37	10	101953091	101953091	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:101953091T>C	ENST00000370397.7	-	19	2158	c.2072A>G	c.(2071-2073)gAt>gGt	p.D691G	RP11-316M21.7_ENST00000443919.1_RNA|CHUK_ENST00000590930.1_5'UTR	NM_001278.3	NP_001269.3	O15111	IKKA_HUMAN	conserved helix-loop-helix ubiquitous kinase	691					anatomical structure morphogenesis (GO:0009653)|cellular response to tumor necrosis factor (GO:0071356)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell proliferation (GO:0033598)|morphogenesis of an epithelial sheet (GO:0002011)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoclast differentiation (GO:0030316)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|protein phosphorylation (GO:0006468)|response to amino acid (GO:0043200)|response to drug (GO:0042493)|response to hydroperoxide (GO:0033194)|response to lipopolysaccharide (GO:0032496)|response to toxic substance (GO:0009636)|response to virus (GO:0009615)|Rho protein signal transduction (GO:0007266)|skeletal muscle contraction (GO:0003009)|striated muscle cell differentiation (GO:0051146)|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)	CD40 receptor complex (GO:0035631)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|IkappaB kinase complex (GO:0008385)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	ATP binding (GO:0005524)|IkappaB kinase activity (GO:0008384)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|scaffold protein binding (GO:0097110)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(9)|lung(8)|ovary(2)|prostate(1)|skin(1)|stomach(1)	27		Colorectal(252;0.117)		Epithelial(162;2.05e-10)|all cancers(201;1.91e-08)	Acetylcysteine(DB06151)|Aminosalicylic Acid(DB00233)|Mesalazine(DB00244)|Sulfasalazine(DB00795)	CAGAGAATGATCATGTTCTGC	0.483																																					p.D691G	Ovarian(159;52 1904 10536 35305 37148)	Atlas-SNP	.											.	CHUK	71	.	0			c.A2072G						.						133.0	114.0	121.0					10																	101953091		2203	4300	6503	SO:0001583	missense	1147	exon19			GAATGATCATGTT	AF009225	CCDS7488.1	10q24-q25	2008-08-01			ENSG00000213341	ENSG00000213341			1974	protein-coding gene	gene with protein product		600664		TCF16		7558004, 16902410	Standard	XR_246062		Approved	IKK1, IKK-alpha, IkBKA, NFKBIKA, IKKA	uc001kqp.3	O15111	OTTHUMG00000018899	ENST00000370397.7:c.2072A>G	chr10.hg19:g.101953091T>C	ENSP00000359424:p.Asp691Gly	130.0	0.0		86.0	4.0	NM_001278	O14666|Q13132|Q5W0I4|Q92467	Missense_Mutation	SNP	ENST00000370397.7	hg19	CCDS7488.1	.	.	.	.	.	.	.	.	.	.	T	11.86	1.763857	0.31228	.	.	ENSG00000213341	ENST00000370397	T	0.71934	-0.61	5.84	3.36	0.38483	.	0.281692	0.40554	N	0.001065	T	0.45155	0.1328	N	0.08118	0	0.22424	N	0.999111	B	0.02656	0.0	B	0.01281	0.0	T	0.22661	-1.0210	10	0.44086	T	0.13	-12.4824	5.6874	0.17811	0.1534:0.0:0.2492:0.5974	.	691	O15111	IKKA_HUMAN	G	691	ENSP00000359424:D691G	ENSP00000359424:D691G	D	-	2	0	CHUK	101943081	0.068000	0.21057	1.000000	0.80357	0.926000	0.56050	0.249000	0.18216	2.230000	0.72887	0.528000	0.53228	GAT	.	.		0.483	CHUK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049836.1	NM_001278	
PDCD11	22984	hgsc.bcm.edu	37	10	105160237	105160237	+	Silent	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:105160237A>G	ENST00000369797.3	+	3	280	c.186A>G	c.(184-186)agA>agG	p.R62R		NM_014976.1	NP_055791.1	Q14690	RRP5_HUMAN	programmed cell death 11	62					mRNA processing (GO:0006397)|rRNA processing (GO:0006364)	cytosol (GO:0005829)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(10)|lung(29)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	64		Colorectal(252;0.0747)|Breast(234;0.128)		Epithelial(162;7.21e-09)|all cancers(201;1.17e-08)|BRCA - Breast invasive adenocarcinoma(275;0.208)		TCGAAAAGAGAGAAAGCAGCA	0.398																																					p.R62R		Atlas-SNP	.											.	PDCD11	160	.	0			c.A186G						.						118.0	129.0	126.0					10																	105160237		2203	4300	6503	SO:0001819	synonymous_variant	22984	exon3			AAAGAGAGAAAGC	D80007	CCDS31276.1	10q24.32	2010-07-06			ENSG00000148843	ENSG00000148843			13408	protein-coding gene	gene with protein product		612333				10229231	Standard	XM_005269647		Approved	KIAA0185, ALG-4, RRP5	uc001kwy.1	Q14690	OTTHUMG00000018988	ENST00000369797.3:c.186A>G	chr10.hg19:g.105160237A>G		88.0	0.0		86.0	4.0	NM_014976	Q2TA92|Q5W093|Q6P2J3|Q86VQ8|Q9H4P1	Silent	SNP	ENST00000369797.3	hg19	CCDS31276.1																																																																																			.	.		0.398	PDCD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050151.1		
GSTO1	9446	hgsc.bcm.edu	37	10	106022766	106022766	+	Silent	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:106022766A>G	ENST00000369713.5	+	4	590	c.396A>G	c.(394-396)agA>agG	p.R132R	GSTO1_ENST00000493946.1_3'UTR|GSTO1_ENST00000369710.4_Intron|GSTO1_ENST00000539281.1_Silent_p.R104R	NM_004832.2	NP_004823.1	P78417	GSTO1_HUMAN	glutathione S-transferase omega 1	132	GST C-terminal.				cellular response to arsenic-containing substance (GO:0071243)|glutathione derivative biosynthetic process (GO:1901687)|L-ascorbic acid metabolic process (GO:0019852)|negative regulation of ryanodine-sensitive calcium-release channel activity (GO:0060315)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|positive regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014810)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|small molecule metabolic process (GO:0044281)|xenobiotic catabolic process (GO:0042178)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	glutathione dehydrogenase (ascorbate) activity (GO:0045174)|glutathione transferase activity (GO:0004364)|methylarsonate reductase activity (GO:0050610)|oxidoreductase activity (GO:0016491)			large_intestine(1)|lung(1)|stomach(1)	3		Colorectal(252;0.102)|Breast(234;0.122)		Epithelial(162;8.07e-10)|all cancers(201;2.72e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0147)	Glutathione(DB00143)|Vitamin E(DB00163)	GCTTTATTAGAAGCCAAAATA	0.363																																					p.R132R		Atlas-SNP	.											.	GSTO1	14	.	0			c.A396G						.						85.0	82.0	83.0					10																	106022766		2203	4300	6503	SO:0001819	synonymous_variant	9446	exon4			TATTAGAAGCCAA	AF212303	CCDS7555.1, CCDS53572.1, CCDS53573.1	10q25.1	2012-06-21			ENSG00000148834	ENSG00000148834	2.5.1.18, 1.8.5.1, 1.20.4.2	"""Glutathione S-transferases / Soluble"""	13312	protein-coding gene	gene with protein product		605482				10783391, 12618591	Standard	NM_004832		Approved	GSTTLp28, P28	uc001kya.3	P78417	OTTHUMG00000019001	ENST00000369713.5:c.396A>G	chr10.hg19:g.106022766A>G		94.0	0.0		80.0	4.0	NM_004832	D3DRA3|F5H7H0|Q5TA03|Q7Z3T2	Silent	SNP	ENST00000369713.5	hg19	CCDS7555.1																																																																																			.	.		0.363	GSTO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050193.1	NM_004832	
GPAM	57678	hgsc.bcm.edu	37	10	113941524	113941524	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:113941524T>C	ENST00000348367.4	-	3	216	c.19A>G	c.(19-21)Acc>Gcc	p.T7A	GPAM_ENST00000369425.1_Missense_Mutation_p.T7A|GPAM_ENST00000480130.1_5'UTR|GPAM_ENST00000423155.1_Missense_Mutation_p.T7A			Q9HCL2	GPAT1_HUMAN	glycerol-3-phosphate acyltransferase, mitochondrial	7					acyl-CoA metabolic process (GO:0006637)|CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|defense response to virus (GO:0051607)|fatty acid homeostasis (GO:0055089)|fatty acid metabolic process (GO:0006631)|glycerophospholipid biosynthetic process (GO:0046474)|interleukin-2 secretion (GO:0070970)|negative regulation of activation-induced cell death of T cells (GO:0070236)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid homeostasis (GO:0055091)|phospholipid metabolic process (GO:0006644)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of multicellular organism growth (GO:0040018)|regulation of cytokine secretion (GO:0050707)|response to glucose (GO:0009749)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|plasma membrane (GO:0005886)	glycerol-3-phosphate O-acyltransferase activity (GO:0004366)			breast(2)|central_nervous_system(2)|endometrium(8)|kidney(2)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31				Epithelial(162;0.0306)|all cancers(201;0.123)		GTACCAAGGGTCAGTGCAGAT	0.363																																					p.T7A	Ovarian(161;1017 2606 18293 52943)	Atlas-SNP	.											.	GPAM	68	.	0			c.A19G						.						180.0	156.0	164.0					10																	113941524		2203	4300	6503	SO:0001583	missense	57678	exon3			CAAGGGTCAGTGC	AL832464	CCDS7570.1	10q25.3	2009-07-15			ENSG00000119927	ENSG00000119927			24865	protein-coding gene	gene with protein product	"""glycerol-3-phosphate acyltransferase 1, mitochondrial"""	602395				10997877, 8369314	Standard	NM_020918		Approved	KIAA1560, MGC26846, GPAT1	uc001kzp.3	Q9HCL2	OTTHUMG00000019055	ENST00000348367.4:c.19A>G	chr10.hg19:g.113941524T>C	ENSP00000265276:p.Thr7Ala	163.0	0.0		136.0	7.0	NM_001244949	Q5VW51|Q86TA3	Missense_Mutation	SNP	ENST00000348367.4	hg19	CCDS7570.1	.	.	.	.	.	.	.	.	.	.	T	14.80	2.642276	0.47153	.	.	ENSG00000119927	ENST00000348367;ENST00000423155;ENST00000369425	T;T;T	0.32988	1.43;1.43;1.43	5.79	3.31	0.37934	.	0.488693	0.23422	N	0.048360	T	0.19805	0.0476	N	0.22421	0.69	0.24770	N	0.992871	B;B	0.13594	0.008;0.008	B;B	0.15484	0.013;0.013	T	0.17501	-1.0367	10	0.62326	D	0.03	-15.2378	8.5001	0.33152	0.4922:0.0:0.0:0.5078	.	7;7	Q5VW52;Q9HCL2	.;GPAT1_HUMAN	A	7	ENSP00000265276:T7A;ENSP00000409242:T7A;ENSP00000358433:T7A	ENSP00000265276:T7A	T	-	1	0	GPAM	113931514	1.000000	0.71417	0.997000	0.53966	0.959000	0.62525	2.320000	0.43797	0.987000	0.38709	0.460000	0.39030	ACC	.	.		0.363	GPAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050377.1	NM_020918	
HABP2	3026	hgsc.bcm.edu	37	10	115343043	115343043	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:115343043A>G	ENST00000351270.3	+	10	1259	c.1163A>G	c.(1162-1164)cAg>cGg	p.Q388R	HABP2_ENST00000541666.1_3'UTR|HABP2_ENST00000542051.1_Missense_Mutation_p.Q362R	NM_004132.3	NP_004123.1	Q14520	HABP2_HUMAN	hyaluronan binding protein 2	388	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cell adhesion (GO:0007155)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	glycosaminoglycan binding (GO:0005539)|serine-type endopeptidase activity (GO:0004252)			breast(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(8)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)	23		Colorectal(252;0.0233)|Breast(234;0.0672)		Epithelial(162;0.00319)|all cancers(201;0.0112)	Hyaluronan(DB08818)	TTTCATGAGCAGAGCTTTAGG	0.438																																					p.Q388R		Atlas-SNP	.											.	HABP2	52	.	0			c.A1163G						.						114.0	114.0	114.0					10																	115343043		2203	4300	6503	SO:0001583	missense	3026	exon10			ATGAGCAGAGCTT		CCDS7577.1, CCDS53579.1	10q25.3	2008-08-01	2001-11-28		ENSG00000148702	ENSG00000148702			4798	protein-coding gene	gene with protein product	"""plasma hyaluronan binding protein"", ""factor VII activating protein"""	603924	"""hyaluronan-binding protein 2"""			8827452, 12437095	Standard	NM_004132		Approved	HABP, PHBP, HGFAL, FSAP	uc001lai.4	Q14520	OTTHUMG00000019073	ENST00000351270.3:c.1163A>G	chr10.hg19:g.115343043A>G	ENSP00000277903:p.Gln388Arg	225.0	0.0		175.0	7.0	NM_004132	A8K467|B7Z8U5|F5H5M6|O00663	Missense_Mutation	SNP	ENST00000351270.3	hg19	CCDS7577.1	.	.	.	.	.	.	.	.	.	.	A	18.15	3.559846	0.65538	.	.	ENSG00000148702	ENST00000542051;ENST00000351270	D;D	0.90261	-2.64;-2.64	6.06	6.06	0.98353	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.000000	0.85682	D	0.000000	D	0.94371	0.8190	M	0.62209	1.925	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.94696	0.7878	10	0.72032	D	0.01	.	15.1865	0.73006	1.0:0.0:0.0:0.0	.	388	Q14520	HABP2_HUMAN	R	362;388	ENSP00000443283:Q362R;ENSP00000277903:Q388R	ENSP00000277903:Q388R	Q	+	2	0	HABP2	115333033	1.000000	0.71417	1.000000	0.80357	0.169000	0.22640	7.424000	0.80242	2.315000	0.78130	0.533000	0.62120	CAG	.	.		0.438	HABP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050428.1	NM_004132	
PLEKHS1	79949	hgsc.bcm.edu	37	10	115529653	115529653	+	Silent	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:115529653A>G	ENST00000369310.3	+	6	1090	c.528A>G	c.(526-528)caA>caG	p.Q176Q	PLEKHS1_ENST00000361048.1_Silent_p.Q182Q|PLEKHS1_ENST00000369312.4_Silent_p.Q94Q|PLEKHS1_ENST00000354462.3_5'Flank|PLEKHS1_ENST00000369309.1_5'Flank	NM_182601.1	NP_872407.1	Q5SXH7	PKHS1_HUMAN	pleckstrin homology domain containing, family S member 1	176																	ATGGTCTCCAAGACAAGGTAA	0.483																																					p.Q182Q		Atlas-SNP	.											.	PLEKHS1	19	.	0			c.A546G						.						107.0	103.0	105.0					10																	115529653		2203	4300	6503	SO:0001819	synonymous_variant	79949	exon7			TCTCCAAGACAAG	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.528A>G	chr10.hg19:g.115529653A>G		92.0	0.0		60.0	4.0	NM_024889	A8KA02|B3KX00|B6EDE1|Q5SXH8|Q5SXI0|Q6ZQR5|Q8NE42|Q9H5D9	Silent	SNP	ENST00000369310.3	hg19	CCDS53580.1																																																																																			.	.		0.483	PLEKHS1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050432.1	NM_024889	
PNLIPRP1	5407	hgsc.bcm.edu	37	10	118365014	118365014	+	Missense_Mutation	SNP	C	C	T			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:118365014C>T	ENST00000528052.1	+	12	1360	c.1289C>T	c.(1288-1290)cCc>cTc	p.P430L	PNLIPRP1_ENST00000358834.4_Missense_Mutation_p.P430L|PNLIPRP1_ENST00000534537.1_Missense_Mutation_p.P430L			P54315	LIPR1_HUMAN	pancreatic lipase-related protein 1	430	PLAT. {ECO:0000255|PROSITE- ProRule:PRU00152}.				lipid metabolic process (GO:0006629)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|triglyceride lipase activity (GO:0004806)			breast(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(1)|lung(23)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	38				all cancers(201;0.0161)		CCAACCCTCCCCAAAGTGGGT	0.428																																					p.P430L		Atlas-SNP	.											.	PNLIPRP1	82	.	0			c.C1289T						.						94.0	98.0	96.0					10																	118365014		2203	4300	6503	SO:0001583	missense	5407	exon12			CCCTCCCCAAAGT	BC025784	CCDS7595.1	10q26.12	2006-07-04			ENSG00000187021	ENSG00000187021			9156	protein-coding gene	gene with protein product		604422				1379598	Standard	NM_006229		Approved	PLRP1	uc001lco.1	P54315	OTTHUMG00000019109	ENST00000528052.1:c.1289C>T	chr10.hg19:g.118365014C>T	ENSP00000433933:p.Pro430Leu	212.0	0.0		132.0	6.0	NM_006229	Q68D83|Q68DR6|Q8TAU2|Q9BS82	Missense_Mutation	SNP	ENST00000528052.1	hg19	CCDS7595.1	.	.	.	.	.	.	.	.	.	.	c	19.30	3.800491	0.70567	.	.	ENSG00000187021	ENST00000358834;ENST00000528052;ENST00000534537	T;T;T	0.68181	-0.31;-0.31;-0.31	5.67	5.67	0.87782	Lipoxygenase, LH2 (4);Lipase/lipooxygenase, PLAT/LH2 (1);	0.000000	0.85682	D	0.000000	D	0.84669	0.5523	M	0.86651	2.83	0.80722	D	1	D	0.76494	0.999	D	0.79108	0.992	D	0.86705	0.1932	10	0.72032	D	0.01	-16.5524	18.5642	0.91112	0.0:1.0:0.0:0.0	.	430	P54315	LIPR1_HUMAN	L	430	ENSP00000351695:P430L;ENSP00000433933:P430L;ENSP00000434159:P430L	ENSP00000351695:P430L	P	+	2	0	PNLIPRP1	118355004	0.997000	0.39634	1.000000	0.80357	0.988000	0.76386	3.369000	0.52365	2.657000	0.90304	0.645000	0.84053	CCC	.	.		0.428	PNLIPRP1-011	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384633.1	NM_006229	
FAM175B	23172	hgsc.bcm.edu	37	10	126519940	126519940	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:126519940A>G	ENST00000298492.5	+	8	731	c.686A>G	c.(685-687)aAg>aGg	p.K229R		NM_032182.3	NP_115558.3	Q15018	F175B_HUMAN	family with sequence similarity 175, member B	229					cellular response to freezing (GO:0071497)	BRISC complex (GO:0070552)|cytoplasm (GO:0005737)	polyubiquitin binding (GO:0031593)			NS(1)	1						GATGTTGAAAAGAGTGAGCGA	0.383																																					p.K229R		Atlas-SNP	.											.	FAM175B	39	.	0			c.A686G						.						98.0	84.0	89.0					10																	126519940		2203	4300	6503	SO:0001583	missense	23172	exon8			TTGAAAAGAGTGA	D63877	CCDS31308.2	10q26.2	2013-01-24	2008-07-02	2008-07-02	ENSG00000165660	ENSG00000165660			28975	protein-coding gene	gene with protein product	"""Abraxas brother"""	611144	"""KIAA0157"""	KIAA0157		8590280	Standard	NM_032182		Approved	Em:AC068896.4, ABRO1	uc001lib.4	Q15018	OTTHUMG00000019218	ENST00000298492.5:c.686A>G	chr10.hg19:g.126519940A>G	ENSP00000298492:p.Lys229Arg	94.0	0.0		85.0	4.0	NM_032182	B4DKR2|Q96H11	Missense_Mutation	SNP	ENST00000298492.5	hg19	CCDS31308.2	.	.	.	.	.	.	.	.	.	.	A	28.5	4.924392	0.92319	.	.	ENSG00000165660	ENST00000298492	T	0.48522	0.81	5.7	5.7	0.88788	.	0.100317	0.64402	D	0.000001	T	0.45677	0.1354	L	0.29908	0.895	0.52099	D	0.999941	P	0.51933	0.949	P	0.48952	0.596	T	0.32322	-0.9911	10	0.32370	T	0.25	-52.1624	15.9745	0.80049	1.0:0.0:0.0:0.0	.	229	Q15018	F175B_HUMAN	R	229	ENSP00000298492:K229R	ENSP00000298492:K229R	K	+	2	0	FAM175B	126509930	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.114000	0.77103	2.168000	0.68352	0.533000	0.62120	AAG	.	.		0.383	FAM175B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050891.2	NM_032182	
PTPRE	5791	hgsc.bcm.edu	37	10	129861413	129861413	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:129861413T>C	ENST00000254667.3	+	10	971	c.692T>C	c.(691-693)gTc>gCc	p.V231A	PTPRE_ENST00000419012.2_Missense_Mutation_p.V231A|PTPRE_ENST00000306042.5_Missense_Mutation_p.V173A|PTPRE_ENST00000430713.2_3'UTR	NM_006504.4	NP_006495.1	P23469	PTPRE_HUMAN	protein tyrosine phosphatase, receptor type, E	231	Tyrosine-protein phosphatase 1. {ECO:0000255|PROSITE-ProRule:PRU00160}.				negative regulation of insulin receptor signaling pathway (GO:0046627)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of mast cell activation (GO:0033003)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	22		all_epithelial(44;1.66e-05)|all_lung(145;0.00456)|Lung NSC(174;0.0066)|all_neural(114;0.0936)|Colorectal(57;0.141)|Breast(234;0.166)|Melanoma(40;0.203)			Alendronate(DB00630)	GCGACCATCGTCATGTTAACA	0.498																																					p.V231A	Colon(52;977 1184 20575 41685)	Atlas-SNP	.											.	PTPRE	132	.	0			c.T692C						.						110.0	99.0	103.0					10																	129861413		2203	4300	6503	SO:0001583	missense	5791	exon10			CCATCGTCATGTT	AF406557	CCDS7657.1, CCDS7658.1	10q26	2011-06-09			ENSG00000132334	ENSG00000132334		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"""	9669	protein-coding gene	gene with protein product		600926				8595895	Standard	NM_130435		Approved	PTPE	uc001lkb.3	P23469	OTTHUMG00000019254	ENST00000254667.3:c.692T>C	chr10.hg19:g.129861413T>C	ENSP00000254667:p.Val231Ala	150.0	0.0		101.0	5.0	NM_006504	Q13345|Q5VWH3|Q5VWH4|Q96KQ6	Missense_Mutation	SNP	ENST00000254667.3	hg19	CCDS7657.1	.	.	.	.	.	.	.	.	.	.	T	23.7	4.450301	0.84101	.	.	ENSG00000132334	ENST00000254667;ENST00000439034;ENST00000419012;ENST00000306042	T;T;T	0.23147	1.92;1.92;1.92	4.44	4.44	0.53790	Protein-tyrosine phosphatase, receptor/non-receptor type (3);	0.000000	0.64402	U	0.000002	T	0.51176	0.1659	M	0.76938	2.355	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.996;1.0;1.0;1.0	T	0.57359	-0.7825	10	0.87932	D	0	.	13.3688	0.60701	0.0:0.0:0.0:1.0	.	209;231;173;231	F5H0X4;Q5VWH4;P23469-2;P23469	.;.;.;PTPRE_HUMAN	A	231;209;231;173	ENSP00000254667:V231A;ENSP00000402337:V231A;ENSP00000303350:V173A	ENSP00000254667:V231A	V	+	2	0	PTPRE	129751403	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	7.577000	0.82486	1.999000	0.58509	0.460000	0.39030	GTC	.	.		0.498	PTPRE-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050990.1		
PKP3	11187	hgsc.bcm.edu	37	11	397014	397014	+	Silent	SNP	G	G	A			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:397014G>A	ENST00000331563.2	+	3	589	c.513G>A	c.(511-513)ggG>ggA	p.G171G		NM_007183.2	NP_009114.1	Q9Y446	PKP3_HUMAN	plakophilin 3	171					desmosome assembly (GO:0002159)|establishment of protein localization to plasma membrane (GO:0090002)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|desmosome (GO:0030057)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)			breast(1)|central_nervous_system(1)|endometrium(3)|lung(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11		all_cancers(49;3.02e-09)|all_epithelial(84;2.09e-06)|Breast(177;0.000162)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;1.56e-27)|Epithelial(43;9.31e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0182)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GTGGGGTTGGGAGCCGGGCCG	0.731																																					p.G171G		Atlas-SNP	.											.	PKP3	36	.	0			c.G513A						.						20.0	23.0	22.0					11																	397014		2190	4283	6473	SO:0001819	synonymous_variant	11187	exon3			GGTTGGGAGCCGG	Z98265	CCDS7695.1	11p15	2013-02-14			ENSG00000184363	ENSG00000184363		"""Armadillo repeat containing"""	9025	protein-coding gene	gene with protein product		605561				10374265	Standard	XM_005252760		Approved		uc001lpc.3	Q9Y446	OTTHUMG00000119068	ENST00000331563.2:c.513G>A	chr11.hg19:g.397014G>A		37.0	0.0		40.0	17.0	NM_007183	F8J390|Q53EX8	Silent	SNP	ENST00000331563.2	hg19	CCDS7695.1																																																																																			.	.		0.731	PKP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239281.1	NM_007183	
ANO9	338440	hgsc.bcm.edu	37	11	418960	418960	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:418960A>G	ENST00000332826.6	-	21	2048	c.1964T>C	c.(1963-1965)cTg>cCg	p.L655P	SIGIRR_ENST00000382520.2_5'Flank|SIGIRR_ENST00000332725.3_5'Flank|SIGIRR_ENST00000397632.3_5'Flank	NM_001012302.2	NP_001012302	A1A5B4	ANO9_HUMAN	anoctamin 9	655					calcium activated galactosylceramide scrambling (GO:0061591)|calcium activated phosphatidylcholine scrambling (GO:0061590)|calcium activated phosphatidylserine scrambling (GO:0061589)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|negative regulation of intracellular calcium activated chloride channel activity (GO:1902939)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)|phospholipid scramblase activity (GO:0017128)			central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(1)|lung(5)|ovary(1)|prostate(4)|skin(4)	21						GAAGACGGACAGGCTGTGGTT	0.612																																					p.L655P		Atlas-SNP	.											.	ANO9	61	.	0			c.T1964C						.						170.0	151.0	157.0					11																	418960		2203	4300	6503	SO:0001583	missense	338440	exon21			ACGGACAGGCTGT	U33271	CCDS31326.1	11p15.5	2014-04-09	2008-08-28	2008-08-28	ENSG00000185101	ENSG00000185101		"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	20679	protein-coding gene	gene with protein product			"""tumor protein p53 inducible protein 5"", ""transmembrane protein 16J"""	TP53I5, TMEM16J		9305847, 24692353	Standard	NM_001012302		Approved	PIG5	uc001lpi.2	A1A5B4	OTTHUMG00000165446	ENST00000332826.6:c.1964T>C	chr11.hg19:g.418960A>G	ENSP00000332788:p.Leu655Pro	177.0	0.0		157.0	7.0	NM_001012302	B3KUC4|B4E134|Q8TEN4	Missense_Mutation	SNP	ENST00000332826.6	hg19	CCDS31326.1	.	.	.	.	.	.	.	.	.	.	a	21.1	4.104828	0.77096	.	.	ENSG00000185101	ENST00000332826	D	0.82803	-1.65	4.44	4.44	0.53790	.	0.000000	0.53938	D	0.000046	D	0.93135	0.7814	H	0.94964	3.605	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.94890	0.8047	10	0.87932	D	0	.	14.0161	0.64525	1.0:0.0:0.0:0.0	.	356;655	A1A5B4-2;A1A5B4	.;ANO9_HUMAN	P	655	ENSP00000332788:L655P	ENSP00000332788:L655P	L	-	2	0	ANO9	408960	1.000000	0.71417	0.980000	0.43619	0.751000	0.42716	6.142000	0.71750	1.796000	0.52611	0.391000	0.25812	CTG	.	.		0.612	ANO9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384116.1	NM_001012302	
PTDSS2	81490	hgsc.bcm.edu	37	11	488548	488548	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:488548T>C	ENST00000308020.5	+	8	931	c.755T>C	c.(754-756)gTc>gCc	p.V252A		NM_030783.1	NP_110410.1	Q9BVG9	PTSS2_HUMAN	phosphatidylserine synthase 2	252					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylserine biosynthetic process (GO:0006659)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	CDP-diacylglycerol-serine O-phosphatidyltransferase activity (GO:0003882)			autonomic_ganglia(1)|breast(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|skin(1)	9		all_cancers(49;1.59e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;2.76e-26)|Epithelial(43;2.56e-25)|OV - Ovarian serous cystadenocarcinoma(40;7.54e-20)|BRCA - Breast invasive adenocarcinoma(625;8.76e-05)|Lung(200;0.0407)|LUSC - Lung squamous cell carcinoma(625;0.0735)	Phosphatidylserine(DB00144)	GACGTGCTCGTCTGCAACGGG	0.622																																					p.V252A		Atlas-SNP	.											.	PTDSS2	27	.	0			c.T755C						.						106.0	89.0	95.0					11																	488548		2203	4300	6503	SO:0001583	missense	81490	exon8			TGCTCGTCTGCAA	BC001210	CCDS7696.1	11p15	2008-05-02			ENSG00000174915	ENSG00000174915			15463	protein-coding gene	gene with protein product		612793				14984733	Standard	NM_030783		Approved	PSS2	uc001lpj.3	Q9BVG9	OTTHUMG00000119087	ENST00000308020.5:c.755T>C	chr11.hg19:g.488548T>C	ENSP00000308258:p.Val252Ala	151.0	0.0		119.0	5.0	NM_030783		Missense_Mutation	SNP	ENST00000308020.5	hg19	CCDS7696.1	.	.	.	.	.	.	.	.	.	.	T	17.50	3.404288	0.62288	.	.	ENSG00000174915	ENST00000308020	.	.	.	4.33	4.33	0.51752	.	0.568705	0.16126	N	0.228405	T	0.61553	0.2356	M	0.64170	1.965	0.53688	D	0.999976	B	0.32918	0.39	B	0.34536	0.185	T	0.66131	-0.6000	9	0.62326	D	0.03	-12.7402	13.9771	0.64279	0.0:0.0:0.0:1.0	.	252	Q9BVG9	PTSS2_HUMAN	A	252	.	ENSP00000308258:V252A	V	+	2	0	PTDSS2	478548	1.000000	0.71417	0.860000	0.33809	0.703000	0.40648	7.668000	0.83897	1.973000	0.57446	0.459000	0.35465	GTC	.	.		0.622	PTDSS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239301.2		
TALDO1	6888	hgsc.bcm.edu	37	11	759019	759019	+	Missense_Mutation	SNP	G	G	T			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:759019G>T	ENST00000319006.3	+	3	444	c.291G>T	c.(289-291)aaG>aaT	p.K97N	TALDO1_ENST00000528097.1_Missense_Mutation_p.K97N			P37837	TALDO_HUMAN	transaldolase 1	97					carbohydrate metabolic process (GO:0005975)|energy reserve metabolic process (GO:0006112)|fructose 6-phosphate metabolic process (GO:0006002)|glyceraldehyde-3-phosphate metabolic process (GO:0019682)|pentose-phosphate shunt (GO:0006098)|pentose-phosphate shunt, non-oxidative branch (GO:0009052)|small molecule metabolic process (GO:0044281)|xylulose biosynthetic process (GO:0005999)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	monosaccharide binding (GO:0048029)|sedoheptulose-7-phosphate:D-glyceraldehyde-3-phosphate glyceronetransferase activity (GO:0004801)			breast(1)|kidney(2)|large_intestine(5)|lung(4)|prostate(2)	14		all_cancers(49;1.13e-08)|all_epithelial(84;2.95e-05)|Breast(177;0.000286)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.159)|all_lung(207;0.198)		all cancers(45;4.66e-26)|Epithelial(43;2.97e-25)|OV - Ovarian serous cystadenocarcinoma(40;1.48e-19)|BRCA - Breast invasive adenocarcinoma(625;4.41e-05)|Lung(200;0.0595)|LUSC - Lung squamous cell carcinoma(625;0.0712)		AAATACTAAAGAAGATTCCGG	0.443																																					p.K97N		Atlas-SNP	.											.	TALDO1	25	.	0			c.G291T						.						134.0	144.0	141.0					11																	759019		2203	4300	6503	SO:0001583	missense	6888	exon3			ACTAAAGAAGATT		CCDS7712.1	11p15.5-p15.4	2009-12-02			ENSG00000177156	ENSG00000177156	2.2.1.2		11559	protein-coding gene	gene with protein product		602063				9339383	Standard	NM_006755		Approved		uc001lqz.3	P37837	OTTHUMG00000133318	ENST00000319006.3:c.291G>T	chr11.hg19:g.759019G>T	ENSP00000321259:p.Lys97Asn	160.0	0.0		121.0	48.0	NM_006755	B2R8M2|O00751|Q8WV32|Q8WZ45	Missense_Mutation	SNP	ENST00000319006.3	hg19	CCDS7712.1	.	.	.	.	.	.	.	.	.	.	G	33	5.207784	0.95033	.	.	ENSG00000177156	ENST00000319006;ENST00000528097	D;D	0.86230	-2.09;-2.09	4.9	4.9	0.64082	Aldolase-type TIM barrel (1);	0.000000	0.85682	D	0.000000	D	0.88706	0.6509	M	0.70275	2.135	0.80722	D	1	P;B	0.35363	0.497;0.339	B;B	0.40982	0.345;0.236	D	0.89509	0.3770	10	0.59425	D	0.04	-16.3143	17.2585	0.87064	0.0:0.0:1.0:0.0	.	97;97	F2Z393;P37837	.;TALDO_HUMAN	N	97	ENSP00000321259:K97N;ENSP00000437098:K97N	ENSP00000321259:K97N	K	+	3	2	TALDO1	749019	1.000000	0.71417	0.999000	0.59377	0.979000	0.70002	6.731000	0.74785	2.437000	0.82529	0.561000	0.74099	AAG	.	.		0.443	TALDO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257116.1	NM_006755	
MMP26	56547	hgsc.bcm.edu	37	11	5010948	5010948	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:5010948T>C	ENST00000380390.1	+	3	386	c.170T>C	c.(169-171)cTc>cCc	p.L57P	MMP26_ENST00000477339.1_3'UTR|MMP26_ENST00000300762.1_Missense_Mutation_p.L57P			Q9NRE1	MMP26_HUMAN	matrix metallopeptidase 26	57					collagen catabolic process (GO:0030574)|proteolysis (GO:0006508)	proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(11)|pancreas(1)|skin(3)|stomach(1)	22		Medulloblastoma(188;0.0025)|Breast(177;0.0204)|all_neural(188;0.0227)		Epithelial(150;1.33e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0287)|LUSC - Lung squamous cell carcinoma(625;0.191)	Marimastat(DB00786)	CAAACACAGCTCCTGCAACAA	0.507																																					p.L57P		Atlas-SNP	.											.	MMP26	49	.	0			c.T170C						.						75.0	60.0	65.0					11																	5010948		2201	4298	6499	SO:0001583	missense	56547	exon2			CACAGCTCCTGCA	AF230354	CCDS7752.1	11p15	2008-07-18	2005-08-08		ENSG00000167346	ENSG00000167346	3.4.24.1		14249	protein-coding gene	gene with protein product	"""matrilysin 2"""	605470	"""matrix metalloproteinase 26"""			10801841, 10824119	Standard	NM_021801		Approved	endometase, MGC126590, MGC126592	uc001lzv.3	Q9NRE1	OTTHUMG00000066442	ENST00000380390.1:c.170T>C	chr11.hg19:g.5010948T>C	ENSP00000369753:p.Leu57Pro	91.0	0.0		60.0	4.0	NM_021801	Q3MJ78|Q9GZS2|Q9NR87	Missense_Mutation	SNP	ENST00000380390.1	hg19	CCDS7752.1	.	.	.	.	.	.	.	.	.	.	T	9.028	0.986513	0.18889	.	.	ENSG00000167346	ENST00000380390;ENST00000300762	T;T	0.38240	1.15;1.15	3.73	2.55	0.30701	Metallopeptidase, catalytic domain (1);	0.630671	0.12428	U	0.469764	T	0.24774	0.0601	L	0.46157	1.445	0.36742	D	0.88227	P	0.46277	0.875	B	0.34652	0.187	T	0.22417	-1.0217	10	0.87932	D	0	-0.3599	4.33	0.11059	0.2016:0.0:0.2086:0.5898	.	57	Q9NRE1	MMP26_HUMAN	P	57	ENSP00000369753:L57P;ENSP00000300762:L57P	ENSP00000300762:L57P	L	+	2	0	MMP26	4967524	0.007000	0.16637	0.008000	0.14137	0.350000	0.29205	-0.116000	0.10724	0.304000	0.22809	0.455000	0.32223	CTC	.	.		0.507	MMP26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142058.3	NM_021801	
PIK3C2A	5286	hgsc.bcm.edu	37	11	17139207	17139207	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:17139207T>C	ENST00000265970.7	-	18	3046	c.3047A>G	c.(3046-3048)gAt>gGt	p.D1016G	PIK3C2A_ENST00000531428.1_Intron|PIK3C2A_ENST00000540361.1_Missense_Mutation_p.D636G|RNU6-593P_ENST00000364716.1_RNA	NM_002645.2	NP_002636.2	O00443	P3C2A_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 alpha	1016	PIK helical. {ECO:0000255|PROSITE- ProRule:PRU00878}.				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						ATGCAGGGCATCTTTGAGAAG	0.398																																					p.D1016G		Atlas-SNP	.											.	PIK3C2A	148	.	0			c.A3047G						.						84.0	78.0	80.0					11																	17139207		2200	4293	6493	SO:0001583	missense	5286	exon18			AGGGCATCTTTGA	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.3047A>G	chr11.hg19:g.17139207T>C	ENSP00000265970:p.Asp1016Gly	149.0	0.0		102.0	5.0	NM_002645	B0LPH2|B4E2G4|Q14CQ9	Missense_Mutation	SNP	ENST00000265970.7	hg19	CCDS7824.1	.	.	.	.	.	.	.	.	.	.	T	22.0	4.227565	0.79576	.	.	ENSG00000011405	ENST00000265970;ENST00000540361	T;T	0.62498	0.02;0.02	5.15	5.15	0.70609	Phosphoinositide 3-kinase, accessory (PIK) domain (3);Armadillo-type fold (1);	0.094057	0.64402	D	0.000001	T	0.77405	0.4125	M	0.72479	2.2	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.77749	-0.2471	10	0.41790	T	0.15	-13.8277	14.9612	0.71158	0.0:0.0:0.0:1.0	.	1016	O00443	P3C2A_HUMAN	G	1016;636	ENSP00000265970:D1016G;ENSP00000438687:D636G	ENSP00000265970:D1016G	D	-	2	0	PIK3C2A	17095783	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	5.601000	0.67606	1.946000	0.56461	0.477000	0.44152	GAT	.	.		0.398	PIK3C2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387553.1	NM_002645	
SERGEF	26297	hgsc.bcm.edu	37	11	18014534	18014534	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:18014534T>C	ENST00000265965.5	-	7	780	c.629A>G	c.(628-630)gAg>gGg	p.E210G	SERGEF_ENST00000532265.1_Missense_Mutation_p.E96G|SERGEF_ENST00000528200.1_Missense_Mutation_p.E210G	NM_012139.2	NP_036271.1	Q9UGK8	SRGEF_HUMAN	secretion regulating guanine nucleotide exchange factor	210					negative regulation of protein secretion (GO:0050709)|positive regulation of Ran GTPase activity (GO:0032853)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|nucleolus (GO:0005730)|nucleus (GO:0005634)	Ran guanyl-nucleotide exchange factor activity (GO:0005087)			autonomic_ganglia(1)|central_nervous_system(1)|large_intestine(5)|lung(5)	12						TTTAGAATTCTCTAGACCTAC	0.448																																					p.E210G		Atlas-SNP	.											.	SERGEF	38	.	0			c.A629G						.						105.0	96.0	99.0					11																	18014534		2200	4293	6493	SO:0001583	missense	26297	exon7			GAATTCTCTAGAC	AJ243950	CCDS7828.1	11p14.3	2006-03-09			ENSG00000129158	ENSG00000129158			17499	protein-coding gene	gene with protein product		606051				10571079, 12459492	Standard	NM_012139		Approved	DelGEF, Gnefr	uc001mnm.3	Q9UGK8	OTTHUMG00000166420	ENST00000265965.5:c.629A>G	chr11.hg19:g.18014534T>C	ENSP00000265965:p.Glu210Gly	160.0	0.0		86.0	4.0	NM_012139	Q9UGK9	Missense_Mutation	SNP	ENST00000265965.5	hg19	CCDS7828.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	18.31|18.31	3.595681|3.595681	0.66219|0.66219	.|.	.|.	ENSG00000129158|ENSG00000129158	ENST00000265965;ENST00000528200;ENST00000525920;ENST00000532265;ENST00000529728;ENST00000530613;ENST00000532389|ENST00000529151	T;T;T;T;T;T;T|.	0.80824|.	-1.42;-1.42;-1.42;-1.42;-1.42;-1.42;-1.42|.	5.19|5.19	4.07|4.07	0.47477|0.47477	Regulator of chromosome condensation/beta-lactamase-inhibitor protein II (2);|.	0.404705|.	0.27797|.	N|.	0.017805|.	T|T	0.66479|0.66479	0.2793|0.2793	M|M	0.77103|0.77103	2.36|2.36	0.34629|0.34629	D|D	0.71943|0.71943	D;B;D;D|.	0.59357|.	0.968;0.005;0.967;0.985|.	P;B;P;P|.	0.53518|.	0.476;0.005;0.676;0.728|.	T|T	0.74575|0.74575	-0.3620|-0.3620	10|5	0.27082|.	T|.	0.32|.	-19.7625|-19.7625	8.7695|8.7695	0.34724|0.34724	0.0:0.0868:0.0:0.9132|0.0:0.0868:0.0:0.9132	.|.	96;96;210;210|.	B4DFC0;E9PMV6;Q9UGK8-2;Q9UGK8|.	.;.;.;SRGEF_HUMAN|.	G|G	210;210;80;96;96;96;96|74	ENSP00000265965:E210G;ENSP00000434188:E210G;ENSP00000436648:E80G;ENSP00000431314:E96G;ENSP00000437297:E96G;ENSP00000436080:E96G;ENSP00000435898:E96G|.	ENSP00000265965:E210G|.	E|R	-|-	2|1	0|2	SERGEF|SERGEF	17971110|17971110	1.000000|1.000000	0.71417|0.71417	0.990000|0.990000	0.47175|0.47175	0.987000|0.987000	0.75469|0.75469	2.201000|2.201000	0.42734|0.42734	1.111000|1.111000	0.41721|0.41721	0.533000|0.533000	0.62120|0.62120	GAG|AGA	.	.		0.448	SERGEF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389538.1	NM_012139	
CCDC73	493860	hgsc.bcm.edu	37	11	32739625	32739625	+	Silent	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:32739625T>C	ENST00000335185.5	-	3	247	c.204A>G	c.(202-204)caA>caG	p.Q68Q	CCDC73_ENST00000531481.1_Silent_p.Q68Q|CCDC73_ENST00000534415.1_5'UTR	NM_001008391.2	NP_001008392.2	Q6ZRK6	CCD73_HUMAN	coiled-coil domain containing 73	68										NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	51	Breast(20;0.112)					taCTCACCTTTTGCCATTTAA	0.398																																					p.E68E		Atlas-SNP	.											.	CCDC73	136	.	0			c.A204G						.						151.0	154.0	153.0					11																	32739625		1863	4107	5970	SO:0001819	synonymous_variant	493860	exon3			CACCTTTTGCCAT	AK128159	CCDS41630.1	11p13	2006-02-11			ENSG00000186714	ENSG00000186714			23261	protein-coding gene	gene with protein product		612328					Standard	NM_001008391		Approved	NY-SAR-79	uc001mtv.4	Q6ZRK6	OTTHUMG00000166279	ENST00000335185.5:c.204A>G	chr11.hg19:g.32739625T>C		63.0	0.0		45.0	5.0	NM_001008391	Q6P5Q7|Q6ZMW0|Q86WE7	Silent	SNP	ENST00000335185.5	hg19	CCDS41630.1																																																																																			.	.		0.398	CCDC73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388874.2	NM_001008391	
UBE2L6	9246	hgsc.bcm.edu	37	11	57327822	57327822	+	Silent	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:57327822A>G	ENST00000287156.4	-	2	306	c.111T>C	c.(109-111)gcT>gcC	p.A37A	UBE2L6_ENST00000340573.4_5'UTR	NM_004223.4	NP_004214.1	O14933	UB2L6_HUMAN	ubiquitin-conjugating enzyme E2L 6	37					cellular protein modification process (GO:0006464)|cytokine-mediated signaling pathway (GO:0019221)|innate immune response (GO:0045087)|ISG15-protein conjugation (GO:0032020)|modification-dependent protein catabolic process (GO:0019941)|negative regulation of type I interferon production (GO:0032480)	cytosol (GO:0005829)	ISG15 ligase activity (GO:0042296)|ubiquitin-protein transferase activity (GO:0004842)			large_intestine(1)|lung(3)|ovary(1)	5						GTAGGAGGAGAGCGTGCCACA	0.567																																					p.A37A		Atlas-SNP	.											.	UBE2L6	20	.	0			c.T111C						.						210.0	172.0	185.0					11																	57327822		2201	4296	6497	SO:0001819	synonymous_variant	9246	exon2			GAGGAGAGCGTGC	AF031141, AK093462, BC032491	CCDS7960.1, CCDS7961.1	11q12.1	2008-02-01			ENSG00000156587	ENSG00000156587		"""Ubiquitin-conjugating enzymes E2"""	12490	protein-coding gene	gene with protein product		603890				9153201	Standard	NM_004223		Approved	UBCH8	uc001nkn.2	O14933	OTTHUMG00000167047	ENST00000287156.4:c.111T>C	chr11.hg19:g.57327822A>G		171.0	0.0		95.0	6.0	NM_004223	A6NDM6|A8MY53|Q8N5D8|Q9UEZ0	Silent	SNP	ENST00000287156.4	hg19	CCDS7960.1																																																																																			.	.		0.567	UBE2L6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392657.1	NM_004223	
SERPING1	710	hgsc.bcm.edu	37	11	57369544	57369544	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:57369544T>C	ENST00000278407.4	+	4	814	c.587T>C	c.(586-588)aTc>aCc	p.I196T	SERPING1_ENST00000378323.4_Missense_Mutation_p.I201T|SERPING1_ENST00000378324.2_Missense_Mutation_p.I144T|SERPING1_ENST00000403558.1_Missense_Mutation_p.I230T|SERPING1_ENST00000340687.6_Missense_Mutation_p.I196T|SERPING1_ENST00000531605.1_3'UTR	NM_000062.2	NP_000053.2	P05155	IC1_HUMAN	serpin peptidase inhibitor, clade G (C1 inhibitor), member 1	196					blood circulation (GO:0008015)|blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|complement activation, classical pathway (GO:0006958)|fibrinolysis (GO:0042730)|innate immune response (GO:0045087)|negative regulation of complement activation, lectin pathway (GO:0001869)|negative regulation of endopeptidase activity (GO:0010951)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule lumen (GO:0031093)	serine-type endopeptidase inhibitor activity (GO:0004867)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(11)|pancreas(2)|prostate(1)|urinary_tract(1)	27						CTGGAGAGCATCCTCTCTTAC	0.547																																					p.I196T		Atlas-SNP	.											.	SERPING1	57	.	0			c.T587C						.						116.0	90.0	99.0					11																	57369544		2201	4296	6497	SO:0001583	missense	710	exon3			AGAGCATCCTCTC	X54486	CCDS7962.1	11q12.1	2014-09-17	2008-07-31		ENSG00000149131	ENSG00000149131		"""Serine (or cysteine) peptidase inhibitors"""	1228	protein-coding gene	gene with protein product	"""plasma protease C1 inhibitor"", ""angioedema, hereditary"""	606860	"""serine (or cysteine) proteinase inhibitor, clade G (C1 inhibitor), member 1, (angioedema, hereditary)"""	C1NH		2026152, 24172014	Standard	NM_000062		Approved	C1IN, C1-INH, HAE1, HAE2	uc001nkp.1	P05155	OTTHUMG00000150304	ENST00000278407.4:c.587T>C	chr11.hg19:g.57369544T>C	ENSP00000278407:p.Ile196Thr	144.0	0.0		137.0	6.0	NM_001032295	A6NMU0|A8KAI9|B2R6L5|B4E1F0|B4E1H2|Q16304|Q547W3|Q59EI5|Q7Z455|Q96FE0|Q9UC49|Q9UCF9	Missense_Mutation	SNP	ENST00000278407.4	hg19	CCDS7962.1	.	.	.	.	.	.	.	.	.	.	T	14.04	2.417116	0.42918	.	.	ENSG00000149131	ENST00000278407;ENST00000340687;ENST00000378323;ENST00000378324;ENST00000403558	D;D;D;D;D	0.84070	-1.8;-1.8;-1.8;-1.8;-1.8	5.76	4.63	0.57726	Serpin domain (3);	0.708670	0.13954	N	0.351283	T	0.78755	0.4333	N	0.04203	-0.255	0.20873	N	0.999832	B;P;B;B	0.36171	0.006;0.541;0.0;0.0	B;P;B;B	0.55161	0.364;0.77;0.017;0.017	T	0.70468	-0.4863	10	0.56958	D	0.05	.	8.6205	0.33857	0.0:0.0868:0.0:0.9132	.	201;230;196;196	B4E1F0;E9PGN7;E9KL26;P05155	.;.;.;IC1_HUMAN	T	196;196;201;144;230	ENSP00000278407:I196T;ENSP00000341861:I196T;ENSP00000367574:I201T;ENSP00000367575:I144T;ENSP00000384420:I230T	ENSP00000278407:I196T	I	+	2	0	SERPING1	57126120	0.963000	0.33076	0.787000	0.31911	0.308000	0.27856	1.717000	0.37991	1.009000	0.39289	0.482000	0.46254	ATC	.	.		0.547	SERPING1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317465.1	NM_000062	
OR5B2	390190	hgsc.bcm.edu	37	11	58190586	58190586	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:58190586T>C	ENST00000302581.2	-	1	200	c.149A>G	c.(148-150)gAc>gGc	p.D50G		NM_001005566.2	NP_001005566.1	Q96R09	OR5B2_HUMAN	olfactory receptor, family 5, subfamily B, member 2	50						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|large_intestine(2)|lung(19)|ovary(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32	Esophageal squamous(5;0.0027)	Breast(21;0.0778)				GAGACAAGAGTCCATCAGGAT	0.507																																					p.D50G		Atlas-SNP	.											.	OR5B2	75	.	0			c.A149G						.						106.0	99.0	102.0					11																	58190586		2201	4295	6496	SO:0001583	missense	390190	exon1			CAAGAGTCCATCA	AB065852	CCDS31550.1	11q12.1	2012-08-09			ENSG00000172365	ENSG00000172365		"""GPCR / Class A : Olfactory receptors"""	8323	protein-coding gene	gene with protein product							Standard	NM_001005566		Approved	OST073	uc010rkg.2	Q96R09	OTTHUMG00000167517	ENST00000302581.2:c.149A>G	chr11.hg19:g.58190586T>C	ENSP00000303076:p.Asp50Gly	201.0	0.0		112.0	6.0	NM_001005566	B2RNJ6|B9EGY7|Q6IEV7|Q8NGF5	Missense_Mutation	SNP	ENST00000302581.2	hg19	CCDS31550.1	.	.	.	.	.	.	.	.	.	.	T	6.378	0.437924	0.12104	.	.	ENSG00000172365	ENST00000302581	T	0.02890	4.12	3.8	2.65	0.31530	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.08223	0.0205	M	0.91561	3.22	0.09310	N	1	B	0.16166	0.016	B	0.23574	0.047	T	0.11275	-1.0594	9	0.66056	D	0.02	-3.1424	8.1655	0.31224	0.0:0.1006:0.0:0.8994	.	50	Q96R09	OR5B2_HUMAN	G	50	ENSP00000303076:D50G	ENSP00000303076:D50G	D	-	2	0	OR5B2	57947162	0.043000	0.20138	0.009000	0.14445	0.011000	0.07611	2.453000	0.44970	0.634000	0.30469	0.524000	0.50904	GAC	.	.		0.507	OR5B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394887.2	NM_001005566	
PATL1	219988	hgsc.bcm.edu	37	11	59419993	59419993	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:59419993T>C	ENST00000300146.9	-	11	1454	c.1370A>G	c.(1369-1371)gAg>gGg	p.E457G		NM_152716.2	NP_689929.2	Q86TB9	PATL1_HUMAN	protein associated with topoisomerase II homolog 1 (yeast)	457	Involved in nuclear spleckles localization.|Region C.				cytoplasmic mRNA processing body assembly (GO:0033962)|deadenylation-dependent decapping of nuclear-transcribed mRNA (GO:0000290)|exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|poly(G) binding (GO:0034046)|poly(U) RNA binding (GO:0008266)|RNA binding (GO:0003723)			central_nervous_system(1)|endometrium(2)|lung(5)|ovary(1)|prostate(2)	11						CTTGGTGCGCTCCTTCTTAGG	0.428																																					p.E457G		Atlas-SNP	.											.	PATL1	92	.	0			c.A1370G						.						130.0	121.0	124.0					11																	59419993		1903	4107	6010	SO:0001583	missense	219988	exon11			GTGCGCTCCTTCT	AK094193	CCDS44613.1	11q12.1	2012-06-07	2007-10-18		ENSG00000166889	ENSG00000166889			26721	protein-coding gene	gene with protein product		614660				17936923	Standard	NM_152716		Approved	FLJ36874, Pat1b	uc001noe.4	Q86TB9	OTTHUMG00000167423	ENST00000300146.9:c.1370A>G	chr11.hg19:g.59419993T>C	ENSP00000300146:p.Glu457Gly	200.0	0.0		113.0	5.0	NM_152716	B3KXT9|Q2TA86|Q6P166|Q8N9M6|Q8NI63	Missense_Mutation	SNP	ENST00000300146.9	hg19	CCDS44613.1	.	.	.	.	.	.	.	.	.	.	T	28.2	4.897304	0.91962	.	.	ENSG00000166889	ENST00000300146;ENST00000428532	T	0.50813	0.73	5.38	5.38	0.77491	.	0.000000	0.85682	D	0.000000	T	0.63988	0.2558	M	0.61703	1.905	0.80722	D	1	D;D	0.76494	0.99;0.999	P;D	0.81914	0.852;0.995	T	0.60372	-0.7276	10	0.22706	T	0.39	-15.8112	15.0564	0.71917	0.0:0.0:0.0:1.0	.	427;457	Q86TB9-4;Q86TB9	.;PATL1_HUMAN	G	457;427	ENSP00000300146:E457G	ENSP00000300146:E457G	E	-	2	0	PATL1	59176569	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.424000	0.80242	2.037000	0.60232	0.482000	0.46254	GAG	.	.		0.428	PATL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394559.1	NM_152716	
TMEM216	51259	hgsc.bcm.edu	37	11	61165731	61165731	+	Intron	SNP	C	C	A	rs11382548	byFrequency	TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:61165731C>A	ENST00000515837.2	+	5	1376				TMEM216_ENST00000334888.5_Splice_Site|TMEM216_ENST00000398979.3_Intron			Q9P0N5	TM216_HUMAN	transmembrane protein 216						cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|TCTN-B9D complex (GO:0036038)				endometrium(1)|large_intestine(2)|lung(1)|prostate(2)	6						TTTCTGCCATCGTATGGACAG	0.473																																					.		Atlas-SNP	.											.	TMEM216	14	.	0			c.432-2C>A						.						85.0	82.0	83.0					11																	61165731		1945	4154	6099	SO:0001627	intron_variant	51259	exon5			TGCCATCGTATGG		CCDS53640.1	11q13.1	2014-09-17			ENSG00000187049	ENSG00000187049			25018	protein-coding gene	gene with protein product		613277	"""cerebello-oculo-renal syndrome 2"", ""Meckel syndrome, type 2"""	CORS2, MKS2		11042152, 20036350, 20512146	Standard	NM_016499		Approved	MGC13379, HSPC244, JBTS2	uc021qkf.1	Q9P0N5		ENST00000515837.2:c.432-11C>A	chr11.hg19:g.61165731C>A		178.0	0.0		107.0	5.0	NM_001173991	A8MZ23|B7Z8N1	Splice_Site	SNP	ENST00000515837.2	hg19	CCDS53640.1	.	.	.	.	.	.	.	.	.	.	C	16.43	3.122110	0.56613	.	.	ENSG00000187049	ENST00000334888	.	.	.	5.75	3.64	0.41730	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	5.196	0.15239	0.0:0.7087:0.0:0.2913	.	.	.	.	.	-1	.	.	.	+	.	.	TMEM216	60922307	0.985000	0.35326	1.000000	0.80357	0.961000	0.63080	1.261000	0.32980	1.403000	0.46800	0.561000	0.74099	.	.	.		0.473	TMEM216-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000398430.1	NM_016499	
CPSF7	79869	hgsc.bcm.edu	37	11	61196700	61196700	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:61196700T>C	ENST00000394888.4	-	2	180	c.8A>G	c.(7-9)gAa>gGa	p.E3G	RP11-286N22.8_ENST00000543044.1_5'Flank|SDHAF2_ENST00000537782.1_5'Flank|SDHAF2_ENST00000301761.2_5'Flank|CPSF7_ENST00000439958.3_Missense_Mutation_p.E3G|SDHAF2_ENST00000542074.1_5'Flank|SDHAF2_ENST00000543265.1_5'Flank|CPSF7_ENST00000541963.1_Missense_Mutation_p.E3G|CPSF7_ENST00000340437.4_Missense_Mutation_p.E46G|SDHAF2_ENST00000534878.1_5'Flank|CPSF7_ENST00000448745.1_Missense_Mutation_p.E3G	NM_001136040.2	NP_001129512.1	Q8N684	CPSF7_HUMAN	cleavage and polyadenylation specific factor 7, 59kDa	3					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA splicing, via spliceosome (GO:0000398)|protein tetramerization (GO:0051262)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	membrane (GO:0016020)|mRNA cleavage factor complex (GO:0005849)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(1)|kidney(2)|large_intestine(5)|lung(5)|skin(2)|upper_aerodigestive_tract(1)	22						GTCCACTCCTTCTGACATGGC	0.473																																					p.E46G		Atlas-SNP	.											.	CPSF7	46	.	0			c.A137G						.						163.0	157.0	159.0					11																	61196700		2202	4299	6501	SO:0001583	missense	79869	exon2			ACTCCTTCTGACA		CCDS8006.2, CCDS44619.1, CCDS44620.1	11q12.2	2013-06-18			ENSG00000149532	ENSG00000149532		"""RNA binding motif (RRM) containing"""	30098	protein-coding gene	gene with protein product	"""pre mRNA cleavage factor I, 59 kDa subunit"", ""cleavage factor Im complex 59 kDa subunit"""					12477932	Standard	NM_024811		Approved	FLJ12529	uc001nrp.3	Q8N684	OTTHUMG00000168198	ENST00000394888.4:c.8A>G	chr11.hg19:g.61196700T>C	ENSP00000378352:p.Glu3Gly	91.0	0.0		87.0	4.0	NM_024811	B3KU04|C9K0Q4|Q7Z3H9|Q9H025|Q9H9V1	Missense_Mutation	SNP	ENST00000394888.4	hg19	CCDS44619.1	.	.	.	.	.	.	.	.	.	.	T	18.47	3.630367	0.67015	.	.	ENSG00000149532	ENST00000340437;ENST00000394888;ENST00000439958;ENST00000448745;ENST00000477890;ENST00000539952;ENST00000544585;ENST00000413232;ENST00000541963;ENST00000450000;ENST00000449811;ENST00000413184	.	.	.	5.12	5.12	0.69794	.	0.305062	0.31624	N	0.007334	T	0.58963	0.2159	L	0.29908	0.895	0.40142	D	0.976848	D;P;D;P	0.58268	0.982;0.86;0.969;0.914	P;B;P;P	0.55055	0.767;0.354;0.634;0.556	T	0.61936	-0.6960	9	0.46703	T	0.11	.	14.7451	0.69485	0.0:0.0:0.0:1.0	.	3;3;46;3	F5H1W4;Q8N684;Q8N684-3;Q8N684-2	.;CPSF7_HUMAN;.;.	G	46;3;3;3;3;3;3;3;3;3;3;3	.	ENSP00000345412:E46G	E	-	2	0	CPSF7	60953276	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.903000	0.63272	2.150000	0.67090	0.460000	0.39030	GAA	.	.		0.473	CPSF7-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347835.2	NM_024811	
OTUB1	55611	hgsc.bcm.edu	37	11	63764415	63764415	+	Splice_Site	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:63764415T>C	ENST00000538426.1	+	5	467		c.e5+2		OTUB1_ENST00000543988.1_Splice_Site|OTUB1_ENST00000541478.1_Intron|OTUB1_ENST00000422031.2_Splice_Site|OTUB1_ENST00000535715.1_Splice_Site|OTUB1_ENST00000543004.1_Splice_Site|OTUB1_ENST00000428192.2_Splice_Site	NM_017670.2	NP_060140.2	Q96FW1	OTUB1_HUMAN	OTU deubiquitinase, ubiquitin aldehyde binding 1						cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|immune system process (GO:0002376)|negative regulation of double-strand break repair (GO:2000780)|negative regulation of histone H2A K63-linked ubiquitination (GO:1901315)|protein K48-linked deubiquitination (GO:0071108)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	NEDD8-specific protease activity (GO:0019784)|omega peptidase activity (GO:0008242)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-specific protease activity (GO:0004843)			breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)	6						CACAACACGGTGAGCCCTGGT	0.597																																					.		Atlas-SNP	.											.	OTUB1	19	.	0			c.423+2T>C						.						82.0	69.0	74.0					11																	63764415		2201	4297	6498	SO:0001630	splice_region_variant	55611	exon5			ACACGGTGAGCCC	AY177200	CCDS8055.1	11q13.1	2014-02-24	2014-02-24			ENSG00000167770		"""OTU domain containing"""	23077	protein-coding gene	gene with protein product		608337	"""OTU domain, ubiquitin aldehyde binding 1"""			12704427, 19383985	Standard	NM_017670		Approved	FLJ20113, FLJ40710	uc001nyf.1	Q96FW1		ENST00000538426.1:c.423+2T>C	chr11.hg19:g.63764415T>C		103.0	0.0		70.0	5.0	NM_017670	Q32Q78|Q96II3|Q9NXQ4|Q9P0B8	Splice_Site	SNP	ENST00000538426.1	hg19	CCDS8055.1	.	.	.	.	.	.	.	.	.	.	T	20.5	4.005261	0.74932	.	.	ENSG00000167770	ENST00000535715;ENST00000428192;ENST00000422031;ENST00000538426;ENST00000543004;ENST00000543988	.	.	.	3.72	3.72	0.42706	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.6845	0.45835	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	OTUB1	63520991	1.000000	0.71417	1.000000	0.80357	0.928000	0.56348	3.989000	0.56958	1.691000	0.51100	0.459000	0.35465	.	.	.		0.597	OTUB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396277.1	NM_017670	Intron
CTSW	1521	hgsc.bcm.edu	37	11	65649694	65649694	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:65649694T>C	ENST00000307886.3	+	4	381	c.335T>C	c.(334-336)gTc>gCc	p.V112A	CTSW_ENST00000528419.1_Missense_Mutation_p.V112A	NM_001335.3	NP_001326	P56202	CATW_HUMAN	cathepsin W	112					immune response (GO:0006955)	membrane (GO:0016020)	cysteine-type peptidase activity (GO:0008234)			central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(5)	9				READ - Rectum adenocarcinoma(159;0.168)		GCTGGAGGGGTCCCCAGCATG	0.582																																					p.V112A		Atlas-SNP	.											.	CTSW	18	.	0			c.T335C						.						67.0	72.0	70.0					11																	65649694		2201	4296	6497	SO:0001583	missense	1521	exon4			GAGGGGTCCCCAG	AF055903	CCDS8117.1	11q13.1	2008-02-01	2006-12-05		ENSG00000172543	ENSG00000172543		"""Cathepsins"""	2546	protein-coding gene	gene with protein product		602364	"""cathepsin W (lymphopain)"""			9108299, 9675123	Standard	NM_001335		Approved		uc001ogc.1	P56202	OTTHUMG00000166663	ENST00000307886.3:c.335T>C	chr11.hg19:g.65649694T>C	ENSP00000311300:p.Val112Ala	194.0	0.0		130.0	6.0	NM_001335	Q86VT4	Missense_Mutation	SNP	ENST00000307886.3	hg19	CCDS8117.1	.	.	.	.	.	.	.	.	.	.	T	0.540	-0.854055	0.02630	.	.	ENSG00000172543	ENST00000307886;ENST00000528419;ENST00000526034	T;T;T	0.28666	1.6;1.6;1.6	4.2	-2.06	0.07298	.	2.672720	0.01187	N	0.007228	T	0.08891	0.0220	N	0.01091	-1.02	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.0	T	0.22941	-1.0202	10	0.07813	T	0.8	.	3.6051	0.08039	0.3113:0.4625:0.0:0.2262	.	112;112	P56202;E9PI30	CATW_HUMAN;.	A	112;112;111	ENSP00000311300:V112A;ENSP00000436568:V112A;ENSP00000434267:V111A	ENSP00000311300:V112A	V	+	2	0	CTSW	65406270	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-2.467000	0.00993	-0.348000	0.08286	0.533000	0.62120	GTC	.	.		0.582	CTSW-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391042.1	NM_001335	
C11orf68	83638	hgsc.bcm.edu	37	11	65684997	65684997	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:65684997A>G	ENST00000530188.1	-	1	834	c.689T>C	c.(688-690)tTc>tCc	p.F230S	DRAP1_ENST00000376991.2_5'Flank|DRAP1_ENST00000312515.2_5'Flank|DRAP1_ENST00000527119.1_5'Flank|DRAP1_ENST00000532933.1_5'Flank|C11orf68_ENST00000438576.2_Missense_Mutation_p.F272S|C11orf68_ENST00000449692.3_Missense_Mutation_p.F271S			Q9H3H3	CK068_HUMAN	chromosome 11 open reading frame 68	230							poly(A) RNA binding (GO:0044822)			large_intestine(1)|lung(3)	4				READ - Rectum adenocarcinoma(159;0.166)		CCCAAGCTGGAAACGGCTCTC	0.602																																					p.F272S		Atlas-SNP	.											.	C11orf68	15	.	0			c.T815C						.						68.0	66.0	67.0					11																	65684997		2201	4296	6497	SO:0001583	missense	83638	exon2			AGCTGGAAACGGC	AF073483	CCDS8122.2, CCDS44652.1	11q13.1	2012-08-09			ENSG00000175573	ENSG00000175573			28801	protein-coding gene	gene with protein product	"""basophilic leukemia-expressed protein"""					16511166	Standard	NM_031450		Approved	P5326, BLES03	uc001ogi.3	Q9H3H3	OTTHUMG00000157153	ENST00000530188.1:c.689T>C	chr11.hg19:g.65684997A>G	ENSP00000433914:p.Phe230Ser	101.0	0.0		91.0	4.0	NM_001135635	J3KQG9|Q9BT13	Missense_Mutation	SNP	ENST00000530188.1	hg19		.	.	.	.	.	.	.	.	.	.	A	20.4	3.985453	0.74589	.	.	ENSG00000175573	ENST00000438576;ENST00000449692;ENST00000530188	T;T;T	0.41400	1.0;1.0;1.0	5.03	3.77	0.43336	Translation Initiation factor eIF- 4e-like  domain (2);	0.119294	0.56097	D	0.000021	T	0.37100	0.0991	N	0.19112	0.55	0.49213	D	0.999766	D;D	0.64830	0.994;0.989	P;P	0.57720	0.826;0.675	T	0.06844	-1.0804	10	0.25106	T	0.35	-11.7888	7.2932	0.26378	0.6722:0.0:0.0:0.3278	.	271;230	Q9H3H3-2;Q9H3H3	.;CK068_HUMAN	S	272;271;230	ENSP00000398350:F272S;ENSP00000409681:F271S;ENSP00000433914:F230S	ENSP00000398350:F272S	F	-	2	0	C11orf68	65441573	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	3.807000	0.55591	2.023000	0.59567	0.459000	0.35465	TTC	.	.		0.602	C11orf68-003	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000391173.1	NM_031450	
SART1	9092	hgsc.bcm.edu	37	11	65744188	65744188	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:65744188A>G	ENST00000312397.5	+	14	1900	c.1808A>G	c.(1807-1809)aAc>aGc	p.N603S		NM_005146.4	NP_005137.1	O43290	SNUT1_HUMAN	squamous cell carcinoma antigen recognized by T cells	603					cell cycle arrest (GO:0007050)|intrinsic apoptotic signaling pathway (GO:0097193)|mRNA splicing, via spliceosome (GO:0000398)|positive regulation of cytotoxic T cell differentiation (GO:0045585)|spliceosomal snRNP assembly (GO:0000387)	Cajal body (GO:0015030)|catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(1)|large_intestine(1)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11						GGGGAGGAGAACATCGGCTGG	0.662																																					p.N603S		Atlas-SNP	.											.	SART1	41	.	0			c.A1808G						.						29.0	27.0	28.0					11																	65744188		2201	4296	6497	SO:0001583	missense	9092	exon14			AGGAGAACATCGG	AB006198	CCDS31611.1	11q13.1	2009-01-06	2006-12-07		ENSG00000175467	ENSG00000175467			10538	protein-coding gene	gene with protein product	"""small nuclear ribonucleoprotein 110kDa (U4/U6.U5)"""	605941	"""squamous cell carcinoma antigen recognised by T cells"""			9449708	Standard	NM_005146		Approved	Ara1, Snu66, SNRNP110	uc001ogl.3	O43290	OTTHUMG00000166771	ENST00000312397.5:c.1808A>G	chr11.hg19:g.65744188A>G	ENSP00000310448:p.Asn603Ser	155.0	0.0		82.0	5.0	NM_005146	A6NDN1|Q53GB5	Missense_Mutation	SNP	ENST00000312397.5	hg19	CCDS31611.1	.	.	.	.	.	.	.	.	.	.	A	14.95	2.687408	0.48097	.	.	ENSG00000175467	ENST00000312397;ENST00000542816	T	0.24538	1.85	4.44	4.44	0.53790	.	0.000000	0.85682	D	0.000000	T	0.30262	0.0759	L	0.36672	1.1	0.47341	D	0.999395	P	0.48503	0.911	P	0.51487	0.671	T	0.05289	-1.0894	10	0.87932	D	0	-26.3971	11.6832	0.51470	1.0:0.0:0.0:0.0	.	603	O43290	SNUT1_HUMAN	S	603;445	ENSP00000310448:N603S	ENSP00000310448:N603S	N	+	2	0	SART1	65500764	1.000000	0.71417	0.999000	0.59377	0.257000	0.26127	4.409000	0.59768	1.869000	0.54173	0.402000	0.26972	AAC	.	.		0.662	SART1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391409.1		
SPTBN2	6712	hgsc.bcm.edu	37	11	66463797	66463797	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:66463797T>C	ENST00000533211.1	-	21	4560	c.4229A>G	c.(4228-4230)gAc>gGc	p.D1410G	SPTBN2_ENST00000529997.1_Missense_Mutation_p.D1410G|SPTBN2_ENST00000309996.2_Missense_Mutation_p.D1410G			O15020	SPTN2_HUMAN	spectrin, beta, non-erythrocytic 2	1410					actin filament capping (GO:0051693)|adult behavior (GO:0030534)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|cell death (GO:0008219)|cerebellar Purkinje cell layer morphogenesis (GO:0021692)|multicellular organism growth (GO:0035264)|synapse assembly (GO:0007416)|vesicle-mediated transport (GO:0016192)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular space (GO:0005615)|neuronal cell body (GO:0043025)|spectrin (GO:0008091)	actin binding (GO:0003779)|phospholipid binding (GO:0005543)|structural constituent of cytoskeleton (GO:0005200)			autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|cervix(1)|endometrium(10)|kidney(5)|large_intestine(15)|liver(1)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	74						CTTGCCGTAGTCATCCGAGTG	0.602																																					p.D1410G		Atlas-SNP	.											.	SPTBN2	188	.	0			c.A4229G						.						55.0	48.0	50.0					11																	66463797		2200	4295	6495	SO:0001583	missense	6712	exon20			CCGTAGTCATCCG	AB008567, AF026487, AF026488, AF079569	CCDS8150.1	11q13.2	2013-01-10			ENSG00000173898	ENSG00000173898		"""Pleckstrin homology (PH) domain containing"""	11276	protein-coding gene	gene with protein product		604985	"""spinocerebellar ataxia 5"""	SCA5		9826670, 16429157	Standard	NM_006946		Approved		uc001ojd.3	O15020	OTTHUMG00000167262	ENST00000533211.1:c.4229A>G	chr11.hg19:g.66463797T>C	ENSP00000432568:p.Asp1410Gly	127.0	0.0		77.0	4.0	NM_006946	O14872|O14873	Missense_Mutation	SNP	ENST00000533211.1	hg19	CCDS8150.1	.	.	.	.	.	.	.	.	.	.	T	25.8	4.679457	0.88542	.	.	ENSG00000173898	ENST00000533211;ENST00000309996;ENST00000529997	T;T;T	0.56611	0.45;0.45;0.45	5.09	5.09	0.68999	.	0.000000	0.85682	D	0.000000	T	0.73938	0.3651	M	0.85630	2.765	0.58432	D	0.999999	D	0.76494	0.999	D	0.70016	0.967	T	0.78919	-0.2014	10	0.72032	D	0.01	.	13.9729	0.64252	0.0:0.0:0.0:1.0	.	1410	O15020	SPTN2_HUMAN	G	1410	ENSP00000432568:D1410G;ENSP00000311489:D1410G;ENSP00000433593:D1410G	ENSP00000311489:D1410G	D	-	2	0	SPTBN2	66220373	1.000000	0.71417	1.000000	0.80357	0.901000	0.52897	7.806000	0.86020	2.138000	0.66242	0.455000	0.32223	GAC	.	.		0.602	SPTBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393892.2	NM_006946	
ALDH3B2	222	hgsc.bcm.edu	37	11	67433122	67433122	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:67433122T>C	ENST00000349015.3	-	7	778	c.340A>G	c.(340-342)Att>Gtt	p.I114V	ALDH3B2_ENST00000531881.1_5'Flank|ALDH3B2_ENST00000530069.1_Missense_Mutation_p.I114V	NM_000695.3	NP_000686	P48448	AL3B2_HUMAN	aldehyde dehydrogenase 3 family, member B2	114					alcohol metabolic process (GO:0006066)|ethanol catabolic process (GO:0006068)|lipid metabolic process (GO:0006629)		3-chloroallyl aldehyde dehydrogenase activity (GO:0004028)|aldehyde dehydrogenase [NAD(P)+] activity (GO:0004030)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(5)|prostate(2)|stomach(1)|urinary_tract(1)	18						GTCATGACAATCTTGCCCACA	0.647																																					p.I114V		Atlas-SNP	.											.	ALDH3B2	46	.	0			c.A340G						.						117.0	126.0	123.0					11																	67433122		2200	4294	6494	SO:0001583	missense	222	exon7			TGACAATCTTGCC	U37519	CCDS31622.1	11q13.2	2014-09-04			ENSG00000132746	ENSG00000132746	1.2.1.5	"""Aldehyde dehydrogenases"""	411	protein-coding gene	gene with protein product	"""aldehyde dehydrogenase 8"", ""acetaldehyde dehydrogenase 8"""	601917		ALDH8		8890755, 9161417	Standard	NM_000695		Approved		uc001oms.3	P48448	OTTHUMG00000167284	ENST00000349015.3:c.340A>G	chr11.hg19:g.67433122T>C	ENSP00000255084:p.Ile114Val	138.0	0.0		121.0	6.0	NM_001031615	Q53Y98|Q8NAL5|Q96IB2	Missense_Mutation	SNP	ENST00000349015.3	hg19	CCDS31622.1	.	.	.	.	.	.	.	.	.	.	T	9.294	1.051396	0.19827	.	.	ENSG00000132746	ENST00000530069;ENST00000349015;ENST00000525827	T;T;T	0.75821	-0.97;-0.97;-0.97	4.16	-1.74	0.08056	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, N-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.463335	0.21531	N	0.073058	T	0.61739	0.2371	L	0.49699	1.58	0.09310	N	1	B	0.09022	0.002	B	0.17433	0.018	T	0.52764	-0.8532	10	0.56958	D	0.05	.	5.4538	0.16580	0.0:0.1568:0.2723:0.5709	.	114	P48448	AL3B2_HUMAN	V	114	ENSP00000431595:I114V;ENSP00000255084:I114V;ENSP00000433718:I114V	ENSP00000255084:I114V	I	-	1	0	ALDH3B2	67189698	0.128000	0.22383	0.055000	0.19348	0.597000	0.36814	0.373000	0.20484	-0.399000	0.07668	0.379000	0.24179	ATT	.	.		0.647	ALDH3B2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394004.1	NM_000695	
PPP6R3	55291	hgsc.bcm.edu	37	11	68382138	68382138	+	3'UTR	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:68382138A>G	ENST00000393800.2	+	0	4429				PPP6R3_ENST00000265637.4_3'UTR|PPP6R3_ENST00000527403.2_3'UTR|PPP6R3_ENST00000265636.5_3'UTR|PPP6R3_ENST00000393799.2_3'UTR|CTD-2007L18.5_ENST00000564469.1_lincRNA|PPP6R3_ENST00000393801.3_3'UTR|PPP6R3_ENST00000529710.1_Missense_Mutation_p.Q790R	NM_001164161.1|NM_001164162.1|NM_001164163.1	NP_001157633.1|NP_001157634.1|NP_001157635.1	Q5H9R7	PP6R3_HUMAN	protein phosphatase 6, regulatory subunit 3						regulation of phosphoprotein phosphatase activity (GO:0043666)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein phosphatase binding (GO:0019903)			breast(2)|endometrium(6)|kidney(3)|large_intestine(10)|liver(2)|lung(9)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37						CAGTGGAGTCAGCAGTAAGCC	0.502																																					p.Q790R		Atlas-SNP	.											.	PPP6R3	159	.	0			c.A2369G						.						168.0	160.0	163.0					11																	68382138		692	1591	2283	SO:0001624	3_prime_UTR_variant	55291	exon23			GGAGTCAGCAGTA	AF264779	CCDS8182.1, CCDS53671.1, CCDS53672.1, CCDS53673.1, CCDS53674.1, CCDS53675.1	11q13	2012-04-17	2010-06-28	2010-06-28	ENSG00000110075	ENSG00000110075		"""Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits"""	1173	protein-coding gene	gene with protein product	"""sporulation-induced transcript 4-associated protein"""	610879	"""chromosome 11 open reading frame 23"", ""SAPS domain family, member 3"""	C11orf23, SAPS3		11401438, 16769727	Standard	NM_018312		Approved	SAPLa, DKFZp781E2374, DKFZp781O2362, DKFZp781E17107, SAP190, SAPL, PP6R3, FLJ11058, FLJ43065, KIAA1558, MGC125711, MGC125712	uc001onv.3	Q5H9R7		ENST00000393800.2:c.*1553A>G	chr11.hg19:g.68382138A>G		132.0	0.0		114.0	5.0	NM_001164164	Q3B7I1|Q3I4Y0|Q3KR35|Q68CR3|Q7L4R8|Q8N3B2|Q96MB2|Q9H2K5|Q9H2K6|Q9HCL4|Q9NUY3	Missense_Mutation	SNP	ENST00000393800.2	hg19	CCDS53672.1	.	.	.	.	.	.	.	.	.	.	A	9.825	1.186958	0.21870	.	.	ENSG00000110075	ENST00000529710	T	0.21734	1.99	4.36	-7.93	0.01156	.	.	.	.	.	T	0.08537	0.0212	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.30475	-0.9977	8	0.29301	T	0.29	.	1.8042	0.03077	0.3886:0.2247:0.2754:0.1113	.	790	Q5H9R7-3	.	R	790	ENSP00000437329:Q790R	ENSP00000437329:Q790R	Q	+	2	0	PPP6R3	68138714	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.006000	0.01459	-1.328000	0.02261	-0.256000	0.11100	CAG	.	.		0.502	PPP6R3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395275.1	NM_018312	
OR2AT4	341152	hgsc.bcm.edu	37	11	74799967	74799967	+	Silent	SNP	G	G	A			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:74799967G>A	ENST00000305159.3	-	1	832	c.792C>T	c.(790-792)taC>taT	p.Y264Y		NM_001005285.1	NP_001005285.1	A6NND4	O2AT4_HUMAN	olfactory receptor, family 2, subfamily AT, member 4	264						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(3)|lung(3)|ovary(1)|upper_aerodigestive_tract(2)	12						TGTAGGCCACGTAGGCTATGG	0.527																																					p.Y264Y		Atlas-SNP	.											OR2AT4,NS,carcinoma,-2,1	OR2AT4	32	.	0			c.C792T						.						93.0	85.0	88.0					11																	74799967		2200	4293	6493	SO:0001819	synonymous_variant	341152	exon1			GGCCACGTAGGCT	BK004820	CCDS31639.1	11q13.4	2012-08-09			ENSG00000171561	ENSG00000171561		"""GPCR / Class A : Olfactory receptors"""	19620	protein-coding gene	gene with protein product							Standard	NM_001005285		Approved		uc010rro.2	A6NND4	OTTHUMG00000165370	ENST00000305159.3:c.792C>T	chr11.hg19:g.74799967G>A		235.0	0.0		146.0	69.0	NM_001005285	B9EGZ8	Silent	SNP	ENST00000305159.3	hg19	CCDS31639.1																																																																																			.	.		0.527	OR2AT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383734.1	NM_001005285	
TENM4	26011	hgsc.bcm.edu	37	11	78433744	78433744	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:78433744A>G	ENST00000278550.7	-	24	4231	c.3769T>C	c.(3769-3771)Tct>Cct	p.S1257P		NM_001098816.2	NP_001092286.2	Q6N022	TEN4_HUMAN	teneurin transmembrane protein 4	1257					cardiac cell fate specification (GO:0060912)|cardiac muscle cell proliferation (GO:0060038)|central nervous system myelin formation (GO:0032289)|gastrulation with mouth forming second (GO:0001702)|neuron development (GO:0048666)|positive regulation of gastrulation (GO:2000543)|positive regulation of myelination (GO:0031643)|positive regulation of oligodendrocyte differentiation (GO:0048714)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)										ACATTTCCAGAGGGGAAGATC	0.512																																					p.S1257P		Atlas-SNP	.											.	.	.	.	0			c.T3769C						.						116.0	116.0	116.0					11																	78433744		1937	4130	6067	SO:0001583	missense	26011	exon24			TTCCAGAGGGGAA	AB037723	CCDS44688.1	11q13	2012-10-02	2012-10-02	2012-10-02		ENSG00000149256			29945	protein-coding gene	gene with protein product		610084	"""odz, odd Oz/ten-m homolog 4 (Drosophila)"""	ODZ4		12000766, 10625539	Standard	NM_001098816		Approved	KIAA1302, Ten-M4	uc001ozl.4	Q6N022		ENST00000278550.7:c.3769T>C	chr11.hg19:g.78433744A>G	ENSP00000278550:p.Ser1257Pro	146.0	0.0		100.0	4.0	NM_001098816	A6ND26|Q7Z3C7|Q96MS6|Q9P2P4|Q9Y4S2	Missense_Mutation	SNP	ENST00000278550.7	hg19	CCDS44688.1	.	.	.	.	.	.	.	.	.	.	A	17.73	3.461786	0.63513	.	.	ENSG00000149256	ENST00000278550	D	0.90676	-2.71	5.64	5.64	0.86602	Six-bladed beta-propeller, TolB-like (1);	0.054825	0.64402	D	0.000001	D	0.90501	0.7024	M	0.79475	2.455	0.50039	D	0.999846	P	0.39391	0.671	B	0.37943	0.261	D	0.90196	0.4253	9	.	.	.	.	16.0238	0.80522	1.0:0.0:0.0:0.0	.	1257	Q6N022	TEN4_HUMAN	P	1257	ENSP00000278550:S1257P	.	S	-	1	0	ODZ4	78111392	1.000000	0.71417	0.997000	0.53966	0.989000	0.77384	6.539000	0.73856	2.367000	0.80283	0.528000	0.53228	TCT	.	.		0.512	TENM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391406.2		
MTNR1B	4544	hgsc.bcm.edu	37	11	92715099	92715099	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:92715099A>G	ENST00000257068.2	+	2	716	c.710A>G	c.(709-711)gAg>gGg	p.E237G		NM_005959.3	NP_005950.1	P49286	MTR1B_HUMAN	melatonin receptor 1B	237					G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|glucose homeostasis (GO:0042593)|regulation of insulin secretion (GO:0050796)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|melatonin receptor activity (GO:0008502)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(19)|ovary(1)|prostate(2)|urinary_tract(1)	33		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)			Agomelatine(DB06594)|Melatonin(DB01065)|Ramelteon(DB00980)	GCCAAGCCAGAGAGCAGGCTG	0.567																																					p.E237G		Atlas-SNP	.											.	MTNR1B	75	.	0			c.A710G						.						86.0	73.0	77.0					11																	92715099		2201	4298	6499	SO:0001583	missense	4544	exon2			AGCCAGAGAGCAG	AB033598	CCDS8290.1	11q21-q22	2012-08-08			ENSG00000134640	ENSG00000134640		"""GPCR / Class A : Melatonin receptors"""	7464	protein-coding gene	gene with protein product		600804					Standard	NM_005959		Approved		uc001pdk.1	P49286	OTTHUMG00000167364	ENST00000257068.2:c.710A>G	chr11.hg19:g.92715099A>G	ENSP00000257068:p.Glu237Gly	156.0	0.0		112.0	5.0	NM_005959		Missense_Mutation	SNP	ENST00000257068.2	hg19	CCDS8290.1	.	.	.	.	.	.	.	.	.	.	A	11.74	1.730245	0.30684	.	.	ENSG00000134640	ENST00000257068	T	0.36878	1.23	4.21	1.63	0.23807	GPCR, rhodopsin-like superfamily (1);	0.264094	0.35495	N	0.003179	T	0.28732	0.0712	L	0.46741	1.465	0.21697	N	0.999583	B	0.12013	0.005	B	0.18561	0.022	T	0.20571	-1.0271	10	0.25106	T	0.35	-3.4918	11.1761	0.48601	0.712:0.288:0.0:0.0	.	237	P49286	MTR1B_HUMAN	G	237	ENSP00000257068:E237G	ENSP00000257068:E237G	E	+	2	0	MTNR1B	92354747	1.000000	0.71417	0.056000	0.19401	0.799000	0.45148	5.305000	0.65750	0.744000	0.32741	0.402000	0.26972	GAG	.	.		0.567	MTNR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394323.1		
DYNC2H1	79659	hgsc.bcm.edu	37	11	103229059	103229059	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:103229059T>C	ENST00000375735.2	+	83	12272	c.12128T>C	c.(12127-12129)gTc>gCc	p.V4043A	DYNC2H1_ENST00000334267.7_Intron|DYNC2H1_ENST00000398093.3_Missense_Mutation_p.V4050A	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	4043					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)		CTTTCTCCTGTCCTCAATCTC	0.388																																					p.V4050A		Atlas-SNP	.											.	DYNC2H1	246	.	0			c.T12149C						.						75.0	66.0	68.0					11																	103229059		1840	4089	5929	SO:0001583	missense	79659	exon84			CTCCTGTCCTCAA	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.12128T>C	chr11.hg19:g.103229059T>C	ENSP00000364887:p.Val4043Ala	139.0	0.0		106.0	5.0	NM_001080463	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Missense_Mutation	SNP	ENST00000375735.2	hg19	CCDS53701.1	.	.	.	.	.	.	.	.	.	.	T	17.28	3.348564	0.61183	.	.	ENSG00000187240	ENST00000375735;ENST00000398093;ENST00000540621;ENST00000533197	T;T;T	0.52526	2.92;2.92;0.66	5.62	5.62	0.85841	Dynein heavy chain (1);	1.002820	0.08030	N	0.993405	T	0.43523	0.1251	L	0.34521	1.04	0.48511	D	0.999666	B;B	0.26445	0.149;0.123	B;B	0.28553	0.091;0.055	T	0.06534	-1.0821	10	0.32370	T	0.25	.	14.8043	0.69942	0.0:0.0:0.0:1.0	.	4043;4050	Q8NCM8;Q8NCM8-2	DYHC2_HUMAN;.	A	4043;4050;289;30	ENSP00000364887:V4043A;ENSP00000381167:V4050A;ENSP00000436736:V30A	ENSP00000364887:V4043A	V	+	2	0	DYNC2H1	102734269	0.989000	0.36119	0.989000	0.46669	0.998000	0.95712	7.305000	0.78891	2.146000	0.66826	0.459000	0.35465	GTC	.	.		0.388	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652	
LAYN	143903	hgsc.bcm.edu	37	11	111425961	111425961	+	Missense_Mutation	SNP	C	C	T			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:111425961C>T	ENST00000375615.3	+	6	813	c.628C>T	c.(628-630)Ctt>Ttt	p.L210F	LAYN_ENST00000528924.1_3'UTR|LAYN_ENST00000436913.2_Missense_Mutation_p.L57F|LAYN_ENST00000525126.1_Missense_Mutation_p.L210F|LAYN_ENST00000375614.2_Missense_Mutation_p.L202F|LAYN_ENST00000533265.1_Missense_Mutation_p.L202F	NM_001258390.1	NP_001245319.1	Q6UX15	LAYN_HUMAN	layilin	210						cell surface (GO:0009986)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|ruffle (GO:0001726)	carbohydrate binding (GO:0030246)|hyaluronic acid binding (GO:0005540)			breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(3)|skin(1)	14		all_cancers(61;9.06e-10)|all_epithelial(67;1.34e-05)|Melanoma(852;1.74e-05)|all_hematologic(158;0.000885)|Acute lymphoblastic leukemia(157;0.000966)|Medulloblastoma(222;0.0523)|all_neural(223;0.0663)|Breast(348;0.086)		Epithelial(105;1.5e-06)|BRCA - Breast invasive adenocarcinoma(274;1.63e-06)|all cancers(92;2.45e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0476)	Hyaluronan(DB08818)	AACACCTGTACTTCCAGAAGA	0.408																																					p.L210F	Ovarian(17;551 586 12136 22082 22900)	Atlas-SNP	.											.	LAYN	35	.	0			c.C628T						.						83.0	78.0	80.0					11																	111425961		2201	4297	6498	SO:0001583	missense	143903	exon6			CCTGTACTTCCAG		CCDS31676.1, CCDS58178.1, CCDS58179.1	11q23.1	2006-02-09			ENSG00000204381	ENSG00000204381			29471	protein-coding gene	gene with protein product						15913605	Standard	NM_001258390		Approved	FLJ30977, FLJ31092	uc001plr.2	Q6UX15	OTTHUMG00000166721	ENST00000375615.3:c.628C>T	chr11.hg19:g.111425961C>T	ENSP00000364765:p.Leu210Phe	185.0	0.0		136.0	6.0	NM_001258390	A6NJB0|B4DJU0|Q8TAY8|Q96NC5|Q96NF3	Missense_Mutation	SNP	ENST00000375615.3	hg19	CCDS58178.1	.	.	.	.	.	.	.	.	.	.	C	11.95	1.791993	0.31685	.	.	ENSG00000204381	ENST00000375614;ENST00000375615;ENST00000525126;ENST00000436913;ENST00000533265;ENST00000541011;ENST00000530962	T;T;T;T	0.06449	3.79;3.39;3.3;3.99	4.99	-3.16	0.05217	.	1.775820	0.02629	N	0.104077	T	0.16854	0.0405	M	0.63428	1.95	0.09310	N	0.999998	D;P;P;P;P	0.76494	0.999;0.802;0.883;0.536;0.928	D;B;B;B;P	0.83275	0.996;0.312;0.391;0.154;0.494	T	0.35599	-0.9782	9	.	.	.	0.1172	0.4986	0.00576	0.2968:0.2051:0.1255:0.3726	.	57;202;210;210;202	B4DJU0;E9PMI0;Q6UX15;E9PQU7;Q6UX15-2	.;.;LAYN_HUMAN;.;.	F	202;210;210;57;202;165;58	ENSP00000364764:L202F;ENSP00000364765:L210F;ENSP00000434328:L210F;ENSP00000434972:L202F	.	L	+	1	0	LAYN	110931171	0.014000	0.17966	0.014000	0.15608	0.210000	0.24377	-0.043000	0.12043	-0.429000	0.07329	-0.165000	0.13383	CTT	.	.		0.408	LAYN-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000391187.1	NM_178834	
CEP164	22897	hgsc.bcm.edu	37	11	117222658	117222658	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:117222658A>G	ENST00000278935.3	+	5	494	c.347A>G	c.(346-348)aAg>aGg	p.K116R		NM_001271933.1|NM_014956.4	NP_001258862.1|NP_055771.4	Q9UPV0	CE164_HUMAN	centrosomal protein 164kDa	116	Interaction with ATRIP.|Lys-rich.				cilium assembly (GO:0042384)|DNA repair (GO:0006281)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary transition fiber (GO:0097539)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|kidney(7)|large_intestine(12)|lung(18)|ovary(3)|prostate(3)	47	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;4e-05)|Epithelial(105;0.0008)		aaaaaaaaaaaggaaaagaaa	0.502																																					p.K116R		Atlas-SNP	.											CEP164,caecum,carcinoma,0,1	CEP164	121	.	0			c.A347G						.						33.0	34.0	34.0					11																	117222658		2201	4296	6497	SO:0001583	missense	22897	exon4			AAAAAAAGGAAAA	AB028975	CCDS31683.1	11q23.3	2014-02-20			ENSG00000110274	ENSG00000110274			29182	protein-coding gene	gene with protein product		614848				10470851, 14654843	Standard	NM_014956		Approved	KIAA1052, NPHP15	uc001prc.3	Q9UPV0	OTTHUMG00000167070	ENST00000278935.3:c.347A>G	chr11.hg19:g.117222658A>G	ENSP00000278935:p.Lys116Arg	57.0	0.0		62.0	3.0	NM_001271933	Q6PKH9|Q7Z2X9|Q9NVS0|Q9UFJ6	Missense_Mutation	SNP	ENST00000278935.3	hg19	CCDS31683.1	.	.	.	.	.	.	.	.	.	.	A	15.14	2.744661	0.49151	.	.	ENSG00000110274	ENST00000533153;ENST00000278935;ENST00000525416;ENST00000545330;ENST00000533570;ENST00000529538	T;T;T;T	0.76060	-0.34;-0.03;-0.29;-0.99	5.95	4.82	0.62117	.	0.243999	0.29172	N	0.012934	T	0.80221	0.4583	M	0.62723	1.935	0.34770	D	0.733632	D;P;B;D	0.56521	0.959;0.482;0.023;0.976	P;B;B;P	0.56960	0.65;0.11;0.01;0.81	D	0.85776	0.1358	10	0.62326	D	0.03	-27.2573	11.2799	0.49188	0.9276:0.0:0.0724:0.0	.	116;70;116;116	E9PI34;B7Z884;Q9UPV0;Q9UPV0-2	.;.;CE164_HUMAN;.	R	70;116;70;70;116;116	ENSP00000436034:K70R;ENSP00000278935:K116R;ENSP00000435759:K70R;ENSP00000431302:K116R	ENSP00000278935:K116R	K	+	2	0	CEP164	116727868	1.000000	0.71417	1.000000	0.80357	0.830000	0.47004	8.713000	0.91408	1.068000	0.40764	0.533000	0.62120	AAG	.	.		0.502	CEP164-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392893.1	NM_014956	
CD3G	917	hgsc.bcm.edu	37	11	118220461	118220461	+	Missense_Mutation	SNP	A	A	G	rs483352927		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:118220461A>G	ENST00000532917.1	+	3	151	c.83A>G	c.(82-84)aAc>aGc	p.N28S	CD3G_ENST00000532903.1_3'UTR|CD3G_ENST00000392883.2_5'UTR	NM_000073.2	NP_000064.1	P09693	CD3G_HUMAN	CD3g molecule, gamma (CD3-TCR complex)	28					cell surface receptor signaling pathway (GO:0007166)|establishment or maintenance of cell polarity (GO:0007163)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|protein complex assembly (GO:0006461)|protein transport (GO:0015031)|regulation of immune response (GO:0050776)|regulation of lymphocyte apoptotic process (GO:0070228)|T cell activation (GO:0042110)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	alpha-beta T cell receptor complex (GO:0042105)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|T cell receptor complex (GO:0042101)	protein heterodimerization activity (GO:0046982)|receptor signaling complex scaffold activity (GO:0030159)|T cell receptor binding (GO:0042608)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|kidney(1)|large_intestine(2)|skin(1)	6	all_hematologic(175;0.046)	Medulloblastoma(222;0.0425)|Breast(348;0.181)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.04e-05)	Muromonab(DB00075)	ATTTCAGGAAACCACTTGGTT	0.403																																					p.N28S		Atlas-SNP	.											.	CD3G	31	.	0			c.A83G						.						77.0	74.0	75.0					11																	118220461		2200	4296	6496	SO:0001583	missense	917	exon3			CAGGAAACCACTT	X60491	CCDS8395.1	11q23	2014-09-17	2006-03-28		ENSG00000160654	ENSG00000160654		"""CD molecules"""	1675	protein-coding gene	gene with protein product		186740	"""CD3g antigen, gamma polypeptide (TiT3 complex)"""				Standard	NM_000073		Approved		uc001psu.2	P09693	OTTHUMG00000166971	ENST00000532917.1:c.83A>G	chr11.hg19:g.118220461A>G	ENSP00000431445:p.Asn28Ser	123.0	0.0		116.0	5.0	NM_000073	Q2HIZ6	Missense_Mutation	SNP	ENST00000532917.1	hg19	CCDS8395.1	.	.	.	.	.	.	.	.	.	.	A	3.587	-0.084497	0.07097	.	.	ENSG00000160654	ENST00000532917	T	0.53857	0.6	5.73	-0.901	0.10540	Immunoglobulin-like fold (1);	2.039550	0.01799	N	0.032805	T	0.36936	0.0985	L	0.40543	1.245	0.22562	N	0.998981	B	0.09022	0.002	B	0.06405	0.002	T	0.03403	-1.1040	10	0.09843	T	0.71	.	1.1051	0.01692	0.4722:0.1384:0.243:0.1464	.	28	P09693	CD3G_HUMAN	S	28	ENSP00000431445:N28S	ENSP00000431445:N28S	N	+	2	0	CD3G	117725671	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.061000	0.11693	-0.127000	0.11661	0.455000	0.32223	AAC	.	.		0.403	CD3G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392135.1	NM_000073	
PHLDB1	23187	hgsc.bcm.edu	37	11	118526376	118526376	+	Silent	SNP	C	C	T			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:118526376C>T	ENST00000361417.2	+	22	4347	c.3936C>T	c.(3934-3936)taC>taT	p.Y1312Y	PHLDB1_ENST00000527898.1_Silent_p.Y363Y|PHLDB1_ENST00000356063.5_Silent_p.Y1265Y|PHLDB1_ENST00000534672.1_3'UTR|PHLDB1_ENST00000524713.1_Silent_p.Y455Y	NM_015157.3	NP_055972.1	Q86UU1	PHLB1_HUMAN	pleckstrin homology-like domain, family B, member 1	1312	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.									breast(3)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(10)|liver(3)|lung(14)|ovary(2)|pancreas(1)|prostate(3)|skin(1)	46	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0523)|all_hematologic(192;0.0735)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;3.4e-05)		AAGTGTACTACGACCACCTGC	0.607																																					p.Y1312Y		Atlas-SNP	.											.	PHLDB1	103	.	0			c.C3936T						.						110.0	93.0	99.0					11																	118526376		2200	4295	6495	SO:0001819	synonymous_variant	23187	exon21			GTACTACGACCAC		CCDS8401.1, CCDS44750.1	11q23.3	2013-01-10			ENSG00000019144	ENSG00000019144		"""Pleckstrin homology (PH) domain containing"""	23697	protein-coding gene	gene with protein product		612834				14532993	Standard	NM_015157		Approved	FLJ00141, LL5a, KIAA0638	uc001pts.3	Q86UU1	OTTHUMG00000166341	ENST00000361417.2:c.3936C>T	chr11.hg19:g.118526376C>T		88.0	0.0		64.0	27.0	NM_001144758	B0YJ63|B0YJ64|O75133|Q4KMF8|Q8TEQ2	Silent	SNP	ENST00000361417.2	hg19	CCDS8401.1																																																																																			.	.		0.607	PHLDB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389279.1	NM_015157	
TRAPPC4	51399	hgsc.bcm.edu	37	11	118889616	118889616	+	Silent	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:118889616T>C	ENST00000533632.1	+	1	475	c.111T>C	c.(109-111)gaT>gaC	p.D37D	TRAPPC4_ENST00000528230.1_Silent_p.D37D|TRAPPC4_ENST00000434101.2_Silent_p.D37D|RPS25_ENST00000528547.1_5'Flank|MIR3656_ENST00000577421.1_RNA|TRAPPC4_ENST00000525303.1_Silent_p.D37D|RPS25_ENST00000527673.1_5'Flank|TRAPPC4_ENST00000533058.1_Silent_p.D37D|TRAPPC4_ENST00000359005.4_Silent_p.D37D	NM_016146.4	NP_057230.1	Q9Y296	TPPC4_HUMAN	trafficking protein particle complex 4	37					dendrite development (GO:0016358)|ER to Golgi vesicle-mediated transport (GO:0006888)|extracellular matrix organization (GO:0030198)	cis-Golgi network (GO:0005801)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi stack (GO:0005795)|synapse (GO:0045202)|synaptic vesicle (GO:0008021)|TRAPP complex (GO:0030008)				NS(1)|endometrium(1)|large_intestine(2)|lung(1)	5	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0523)|all_neural(223;0.224)|all_hematologic(192;0.243)		BRCA - Breast invasive adenocarcinoma(274;7.58e-05)		ATCCGCTGGATCTGCTGCTCA	0.592																																					p.D37D		Atlas-SNP	.											.	TRAPPC4	8	.	0			c.T111C						.						100.0	95.0	97.0					11																	118889616		2200	4295	6495	SO:0001819	synonymous_variant	51399	exon1			GCTGGATCTGCTG	AF078862	CCDS8407.1	11q23.3	2011-10-10				ENSG00000196655		"""Trafficking protein particle complex"""	19943	protein-coding gene	gene with protein product		610971				10810093	Standard	NM_016146		Approved	TRS23, SBDN, PTD009	uc010ryo.2	Q9Y296		ENST00000533632.1:c.111T>C	chr11.hg19:g.118889616T>C		119.0	0.0		74.0	4.0	NM_016146	A8K3A5|B4DME1	Silent	SNP	ENST00000533632.1	hg19	CCDS8407.1																																																																																			.	.		0.592	TRAPPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389332.1	NM_016146	
OR10S1	219873	hgsc.bcm.edu	37	11	123847962	123847962	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:123847962T>C	ENST00000531945.1	-	1	526	c.437A>G	c.(436-438)tAc>tGc	p.Y146C		NM_001004474.1	NP_001004474.1	Q8NGN2	O10S1_HUMAN	olfactory receptor, family 10, subfamily S, member 1	146						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(16)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	36		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0399)		GGCCACTGGGTAGTGCAGGGG	0.547																																					p.Y146C		Atlas-SNP	.											.	OR10S1	78	.	0			c.A437G						.						98.0	86.0	90.0					11																	123847962		2202	4299	6501	SO:0001583	missense	219873	exon1			ACTGGGTAGTGCA	BK004509	CCDS31701.1	11q24.1	2012-08-09			ENSG00000196248	ENSG00000196248		"""GPCR / Class A : Olfactory receptors"""	14807	protein-coding gene	gene with protein product							Standard	NM_001004474		Approved		uc001pzm.1	Q8NGN2	OTTHUMG00000165963	ENST00000531945.1:c.437A>G	chr11.hg19:g.123847962T>C	ENSP00000431914:p.Tyr146Cys	147.0	0.0		90.0	4.0	NM_001004474	B9EH43|Q6IEV3|Q96R78	Missense_Mutation	SNP	ENST00000531945.1	hg19	CCDS31701.1	.	.	.	.	.	.	.	.	.	.	T	20.2	3.956951	0.73902	.	.	ENSG00000196248	ENST00000531945	T	0.33865	1.39	4.74	4.74	0.60224	GPCR, rhodopsin-like superfamily (1);	0.000000	0.38005	U	0.001846	T	0.69133	0.3077	H	0.94542	3.55	0.42479	D	0.992853	D	0.89917	1.0	D	0.72625	0.978	T	0.79652	-0.1714	10	0.87932	D	0	-10.7432	14.1974	0.65679	0.0:0.0:0.0:1.0	.	146	Q8NGN2	O10S1_HUMAN	C	146	ENSP00000431914:Y146C	ENSP00000431914:Y146C	Y	-	2	0	OR10S1	123353172	1.000000	0.71417	1.000000	0.80357	0.883000	0.51084	7.513000	0.81739	2.019000	0.59389	0.467000	0.42956	TAC	.	.		0.547	OR10S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387265.2	NM_001004474	
OR10G9	219870	hgsc.bcm.edu	37	11	123894415	123894415	+	Silent	SNP	G	G	C	rs150463109	byFrequency	TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:123894415G>C	ENST00000375024.1	+	1	696	c.696G>C	c.(694-696)ggG>ggC	p.G232G		NM_001001953.1	NP_001001953.1	Q8NGN4	O10G9_HUMAN	olfactory receptor, family 10, subfamily G, member 9	232						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(33)|prostate(2)|skin(4)|stomach(8)|urinary_tract(1)	61		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0399)		CCTCAGAGGGGAGGCACAGAG	0.542																																					p.G232G		Atlas-SNP	.											.	OR10G9	80	.	0			c.G696C						.						166.0	144.0	152.0					11																	123894415		2201	4299	6500	SO:0001819	synonymous_variant	219870	exon1			AGAGGGGAGGCAC	AB065756	CCDS31703.1	11q24.1	2012-08-09			ENSG00000236981	ENSG00000236981		"""GPCR / Class A : Olfactory receptors"""	15129	protein-coding gene	gene with protein product				OR10G10P			Standard	NM_001001953		Approved		uc010sad.2	Q8NGN4	OTTHUMG00000165967	ENST00000375024.1:c.696G>C	chr11.hg19:g.123894415G>C		441.0	0.0		376.0	173.0	NM_001001953		Silent	SNP	ENST00000375024.1	hg19	CCDS31703.1																																																																																			.	G|0.997;T|0.003		0.542	OR10G9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387269.1	NM_001001953	
PATE3	100169851	hgsc.bcm.edu	37	11	125659284	125659284	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:125659284T>C	ENST00000445202.1	+	2	94	c.53T>C	c.(52-54)gTg>gCg	p.V18A		NM_001129883.3	NP_001123355.3	B3GLJ2	PATE3_HUMAN	prostate and testis expressed 3	18						extracellular region (GO:0005576)											TCTCCAGCAGTGACATCACTT	0.507																																					p.V18A		Atlas-SNP	.											.	PATE3	4	.	0			c.T53C						.						125.0	102.0	109.0					11																	125659284		692	1591	2283	SO:0001583	missense	100169851	exon2			CAGCAGTGACATC	EF426753	CCDS44764.1	11q24.2	2008-12-17			ENSG00000236027	ENSG00000236027		"""PATE family"""	35426	protein-coding gene	gene with protein product						18390568	Standard	NM_001129883		Approved	PATE-DJ, HEL-127	uc009zbs.3	B3GLJ2	OTTHUMG00000165857	ENST00000445202.1:c.53T>C	chr11.hg19:g.125659284T>C	ENSP00000395505:p.Val18Ala	113.0	0.0		100.0	4.0	NM_001129883	B5KFZ3	Missense_Mutation	SNP	ENST00000445202.1	hg19	CCDS44764.1	.	.	.	.	.	.	.	.	.	.	T	7.846	0.722982	0.15439	.	.	ENSG00000236027	ENST00000445202	T	0.21932	1.98	3.98	-2.21	0.06973	.	.	.	.	.	T	0.08403	0.0209	.	.	.	0.09310	N	1	B	0.09022	0.002	B	0.12156	0.007	T	0.38693	-0.9649	8	0.15499	T	0.54	.	1.8352	0.03138	0.1853:0.1417:0.4608:0.2123	.	18	B3GLJ2	PATE3_HUMAN	A	18	ENSP00000395505:V18A	ENSP00000395505:V18A	V	+	2	0	PATE3	125164494	0.001000	0.12720	0.054000	0.19295	0.334000	0.28698	-1.071000	0.03437	-0.359000	0.08150	0.454000	0.30748	GTG	.	.		0.507	PATE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386731.1	NM_001129883	
TEAD4	7004	hgsc.bcm.edu	37	12	3126664	3126664	+	Missense_Mutation	SNP	G	G	A			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:3126664G>A	ENST00000397122.2	+	4	353	c.68G>A	c.(67-69)cGg>cAg	p.R23Q	TEAD4_ENST00000358409.2_Intron|TEAD4_ENST00000359864.2_Missense_Mutation_p.R152Q	NM_201443.2	NP_958851.1	Q15561	TEAD4_HUMAN	TEA domain family member 4	152					gene expression (GO:0010467)|hippo signaling (GO:0035329)|muscle organ development (GO:0007517)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal system development (GO:0001501)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(1)	10	Ovarian(42;0.211)		OV - Ovarian serous cystadenocarcinoma(31;0.000563)|COAD - Colon adenocarcinoma(12;0.0831)			GCCCTcgcccggggccccggc	0.667																																					p.R152Q		Atlas-SNP	.											.	TEAD4	45	.	0			c.G455A						.						30.0	29.0	30.0					12																	3126664		2203	4300	6503	SO:0001583	missense	7004	exon6			TCGCCCGGGGCCC	X94438	CCDS31729.1, CCDS31730.1, CCDS41737.1	12p13.3-p13.2	2008-05-14				ENSG00000197905			11717	protein-coding gene	gene with protein product		601714		TCF13L1		9889009, 8921372	Standard	NM_003213		Approved	TEF-3, TEFR-1, EFTR-2, RTEF-1	uc010sej.2	Q15561		ENST00000397122.2:c.68G>A	chr12.hg19:g.3126664G>A	ENSP00000380311:p.Arg23Gln	304.0	0.0		197.0	78.0	NM_003213	H0Y308|Q6MZR9|Q8NEV5|Q92883|Q96BK2	Missense_Mutation	SNP	ENST00000397122.2	hg19	CCDS41737.1	.	.	.	.	.	.	.	.	.	.	G	14.17	2.455934	0.43634	.	.	ENSG00000197905	ENST00000359864;ENST00000543035;ENST00000397122	T;T;T	0.54479	0.57;1.61;0.58	5.95	3.18	0.36537	.	0.133068	0.49305	N	0.000157	T	0.34542	0.0901	N	0.19112	0.55	0.23101	N	0.998292	.	.	.	.	.	.	T	0.20438	-1.0275	8	0.16420	T	0.52	-17.3336	8.9551	0.35812	0.2792:0.0:0.7208:0.0	.	.	.	.	Q	152;152;23	ENSP00000352926:R152Q;ENSP00000444528:R152Q;ENSP00000380311:R23Q	ENSP00000352926:R152Q	R	+	2	0	TEAD4	2996925	1.000000	0.71417	1.000000	0.80357	0.208000	0.24298	1.921000	0.40035	0.433000	0.26313	-0.793000	0.03317	CGG	.	.		0.667	TEAD4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398477.1	NM_003213	
C12orf5	57103	hgsc.bcm.edu	37	12	4459033	4459033	+	Missense_Mutation	SNP	G	G	A			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:4459033G>A	ENST00000179259.4	+	4	308	c.241G>A	c.(241-243)Gta>Ata	p.V81I	C12orf5_ENST00000537251.1_3'UTR	NM_020375.2	NP_065108.1	Q9NQ88	TIGAR_HUMAN	chromosome 12 open reading frame 5	81					intestinal epithelial cell development (GO:0060576)|negative regulation of macromitophagy (GO:1901525)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|response to gamma radiation (GO:0010332)|response to xenobiotic stimulus (GO:0009410)	intracellular (GO:0005622)	fructose-2,6-bisphosphate 2-phosphatase activity (GO:0004331)			endometrium(1)|large_intestine(1)|lung(5)|skin(3)	10			all cancers(3;1.15e-07)|Colorectal(7;0.00165)|OV - Ovarian serous cystadenocarcinoma(31;0.00596)|COAD - Colon adenocarcinoma(12;0.0229)|GBM - Glioblastoma multiforme(3;0.0266)|STAD - Stomach adenocarcinoma(119;0.206)			AGATATGACGGTAAAGTATGA	0.353																																					p.V81I	Colon(1;100 192 35375 49454 52532)	Atlas-SNP	.											C12orf5,NS,adenoma,0,1	C12orf5	28	.	0			c.G241A						.						97.0	100.0	99.0					12																	4459033		2203	4300	6503	SO:0001583	missense	57103	exon4			ATGACGGTAAAGT	AJ272206	CCDS8525.1	12p13.32	2014-05-29	2009-11-24	2009-11-24	ENSG00000078237	ENSG00000078237	3.1.3.46		1185	protein-coding gene	gene with protein product	"""TP53-induced glycolysis and apoptosis regulator"""	610775				16140933, 16839880, 18945750, 19713938	Standard	NM_020375		Approved	TIGAR	uc001qmp.3	Q9NQ88		ENST00000179259.4:c.241G>A	chr12.hg19:g.4459033G>A	ENSP00000179259:p.Val81Ile	199.0	0.0		159.0	0.0	NM_020375	B2R840	Missense_Mutation	SNP	ENST00000179259.4	hg19	CCDS8525.1	.	.	.	.	.	.	.	.	.	.	G	2.436	-0.329820	0.05314	.	.	ENSG00000078237	ENST00000179259	T	0.71103	-0.54	4.58	4.58	0.56647	Histidine phosphatase superfamily, clade-1 (2);	0.167136	0.51477	D	0.000092	T	0.47284	0.1437	N	0.10645	0.015	0.09310	N	0.999994	B	0.21520	0.057	B	0.23275	0.045	T	0.27020	-1.0086	10	0.30078	T	0.28	-22.6516	8.4664	0.32958	0.1791:0.0:0.8209:0.0	.	81	Q9NQ88	TIGAR_HUMAN	I	81	ENSP00000179259:V81I	ENSP00000179259:V81I	V	+	1	0	C12orf5	4329294	1.000000	0.71417	0.857000	0.33713	0.340000	0.28889	2.645000	0.46621	2.536000	0.85505	0.655000	0.94253	GTA	.	.		0.353	C12orf5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398290.1	NM_020375	
KCNA5	3741	hgsc.bcm.edu	37	12	5154463	5154463	+	Missense_Mutation	SNP	G	G	C	rs76708779	byFrequency	TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:5154463G>C	ENST00000252321.3	+	1	1379	c.1150G>C	c.(1150-1152)Gga>Cga	p.G384R		NM_002234.3	NP_002225.2	P22460	KCNA5_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 5	384	Poly-Gly.				atrial cardiac muscle cell action potential (GO:0086014)|membrane hyperpolarization (GO:0060081)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|negative regulation of potassium ion transport (GO:0043267)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|positive regulation of myoblast proliferation (GO:2000288)|potassium ion export (GO:0071435)|potassium ion homeostasis (GO:0055075)|potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of insulin secretion (GO:0050796)|regulation of membrane potential (GO:0042391)|regulation of potassium ion transport (GO:0043266)|regulation of vasoconstriction (GO:0019229)|response to hypoxia (GO:0001666)|synaptic transmission (GO:0007268)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|intracellular canaliculus (GO:0046691)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|delayed rectifier potassium channel activity (GO:0005251)|outward rectifier potassium channel activity (GO:0015271)|potassium channel inhibitor activity (GO:0019870)|protein kinase binding (GO:0019901)|scaffold protein binding (GO:0097110)|voltage-gated potassium channel activity involved in atrial cardiac muscle cell action potential repolarization (GO:0086089)			NS(1)|breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|liver(1)|lung(21)|ovary(5)|prostate(2)|upper_aerodigestive_tract(2)	52					Dalfampridine(DB06637)	GCCAGGGGGTGGAGGAGGCGG	0.622																																					p.G384R		Atlas-SNP	.											KCNA5,NS,carcinoma,0,1	KCNA5	138	.	0			c.G1150C						.						56.0	52.0	53.0					12																	5154463		2203	4300	6503	SO:0001583	missense	3741	exon1			GGGGGTGGAGGAG	M83254	CCDS8536.1	12p13	2012-07-05				ENSG00000130037		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6224	protein-coding gene	gene with protein product		176267				16382104	Standard	NM_002234		Approved	Kv1.5, HK2, HPCN1	uc001qni.4	P22460		ENST00000252321.3:c.1150G>C	chr12.hg19:g.5154463G>C	ENSP00000252321:p.Gly384Arg	273.0	1.0		222.0	0.0	NM_002234	Q4KKT8|Q4VAJ1|Q4VAJ2|Q9UDA4	Missense_Mutation	SNP	ENST00000252321.3	hg19	CCDS8536.1	.	.	.	.	.	.	.	.	.	.	G	9.013	0.982930	0.18889	.	.	ENSG00000130037	ENST00000252321	D	0.97710	-4.5	4.62	4.62	0.57501	Ion transport (1);	2.171590	0.03002	U	0.148348	D	0.96156	0.8747	N	0.05050	-0.12	0.09310	N	0.999996	D	0.54964	0.969	P	0.59288	0.855	D	0.91348	0.5102	10	0.45353	T	0.12	.	8.6668	0.34125	0.1726:0.0:0.8274:0.0	.	384	P22460	KCNA5_HUMAN	R	384	ENSP00000252321:G384R	ENSP00000252321:G384R	G	+	1	0	KCNA5	5024724	0.030000	0.19436	0.120000	0.21714	0.199000	0.23934	1.527000	0.35975	2.390000	0.81377	0.561000	0.74099	GGA	.	G|0.995;A|0.005		0.622	KCNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398925.2	NM_002234	
DPPA3	359787	hgsc.bcm.edu	37	12	7864219	7864219	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:7864219T>C	ENST00000345088.2	+	1	170	c.53T>C	c.(52-54)cTc>cCc	p.L18P		NM_199286.2	NP_954980.1	Q6W0C5	DPPA3_HUMAN	developmental pluripotency associated 3	18					chromatin modification (GO:0016568)|embryonic cleavage (GO:0040016)|negative regulation of DNA demethylation (GO:1901536)|protection of DNA demethylation of female pronucleus (GO:0044726)|regulation of genetic imprinting (GO:2000653)	cytoplasm (GO:0005737)|female pronucleus (GO:0001939)|nucleus (GO:0005634)	methylated histone binding (GO:0035064)			endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|skin(2)	8				Kidney(36;0.0887)		CCACAAATGCTCACCGAAGAA	0.493																																					p.L18P		Atlas-SNP	.											.	DPPA3	26	.	0			c.T53C						.						66.0	57.0	60.0					12																	7864219		2203	4300	6503	SO:0001583	missense	359787	exon1			AAATGCTCACCGA	AY317075	CCDS8582.1	12p13.31	2012-10-02			ENSG00000187569	ENSG00000187569			19199	protein-coding gene	gene with protein product		608408					Standard	NM_199286		Approved	Stella	uc001qtf.3	Q6W0C5	OTTHUMG00000168434	ENST00000345088.2:c.53T>C	chr12.hg19:g.7864219T>C	ENSP00000339250:p.Leu18Pro	122.0	0.0		107.0	5.0	NM_199286	Q0P5U3|Q6JZS6	Missense_Mutation	SNP	ENST00000345088.2	hg19	CCDS8582.1	.	.	.	.	.	.	.	.	.	.	T	8.395	0.840553	0.16891	.	.	ENSG00000187569	ENST00000345088	T	0.42900	0.96	2.82	0.816	0.18768	.	.	.	.	.	T	0.21801	0.0525	N	0.14661	0.345	0.09310	N	1	B	0.09022	0.002	B	0.08055	0.003	T	0.17623	-1.0363	9	0.36615	T	0.2	1.5698	4.1081	0.10047	0.0:0.5724:0.0:0.4276	.	18	Q6W0C5	DPPA3_HUMAN	P	18	ENSP00000339250:L18P	ENSP00000339250:L18P	L	+	2	0	DPPA3	7755486	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.148000	0.10219	0.201000	0.20466	0.533000	0.62120	CTC	.	.		0.493	DPPA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399718.1	NM_199286	
TAS2R10	50839	hgsc.bcm.edu	37	12	10978230	10978230	+	Silent	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:10978230T>C	ENST00000240619.2	-	1	727	c.639A>G	c.(637-639)ggA>ggG	p.G213G		NM_023921.1	NP_076410.1	Q9NYW0	T2R10_HUMAN	taste receptor, type 2, member 10	213					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)			breast(1)|central_nervous_system(1)|large_intestine(7)|lung(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	17						AGTCTCTCAATCCTGTCACAT	0.363																																					p.G213G		Atlas-SNP	.											.	TAS2R10	44	.	0			c.A639G						.						107.0	105.0	106.0					12																	10978230		2203	4300	6503	SO:0001819	synonymous_variant	50839	exon1			TCTCAATCCTGTC	AF227136	CCDS8634.1	12p13	2012-08-22			ENSG00000121318	ENSG00000121318		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	14918	protein-coding gene	gene with protein product		604791				10761934, 10766242	Standard	NM_023921		Approved	T2R10, TRB2	uc001qyy.1	Q9NYW0	OTTHUMG00000168508	ENST00000240619.2:c.639A>G	chr12.hg19:g.10978230T>C		131.0	0.0		114.0	5.0	NM_023921	Q3MIM9|Q6NTD9	Silent	SNP	ENST00000240619.2	hg19	CCDS8634.1																																																																																			.	.		0.363	TAS2R10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399934.1		
PIK3C2G	5288	hgsc.bcm.edu	37	12	18552597	18552597	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:18552597T>C	ENST00000266497.5	+	14	2046	c.2008T>C	c.(2008-2010)Tct>Cct	p.S670P	PIK3C2G_ENST00000433979.1_Missense_Mutation_p.S670P|PIK3C2G_ENST00000538779.1_Missense_Mutation_p.S711P			O75747	P3C2G_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 gamma	670	PIK helical. {ECO:0000255|PROSITE- ProRule:PRU00878}.				chemotaxis (GO:0006935)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|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 binding (GO:0035091)|phosphatidylinositol phosphate kinase activity (GO:0016307)			breast(5)|central_nervous_system(6)|endometrium(2)|kidney(4)|large_intestine(8)|lung(31)|ovary(2)|prostate(1)|skin(2)|stomach(4)|upper_aerodigestive_tract(1)	66		Hepatocellular(102;0.194)				TTTCAGACTCTCTGAAGAAAA	0.373																																					p.S670P		Atlas-SNP	.											.	PIK3C2G	315	.	0			c.T2008C						.						64.0	65.0	64.0					12																	18552597		1810	4075	5885	SO:0001583	missense	5288	exon15			AGACTCTCTGAAG	AJ000008	CCDS44839.1, CCDS73452.1	12p12	2012-07-13	2012-07-13		ENSG00000139144	ENSG00000139144	2.7.1.154		8973	protein-coding gene	gene with protein product		609001	"""phosphoinositide-3-kinase, class 2, gamma polypeptide"""			9878262	Standard	XM_005253393		Approved		uc001rdt.3	O75747	OTTHUMG00000168841	ENST00000266497.5:c.2008T>C	chr12.hg19:g.18552597T>C	ENSP00000266497:p.Ser670Pro	113.0	0.0		104.0	6.0	NM_004570	A1L3U0	Missense_Mutation	SNP	ENST00000266497.5	hg19	CCDS44839.1	.	.	.	.	.	.	.	.	.	.	T	17.77	3.470345	0.63625	.	.	ENSG00000139144	ENST00000433979;ENST00000266497;ENST00000538779	T;T;T	0.65549	-0.16;-0.16;-0.16	5.03	3.86	0.44501	Phosphoinositide 3-kinase, accessory (PIK) domain (3);Armadillo-type fold (1);	0.084055	0.50627	D	0.000117	T	0.73148	0.3550	L	0.61218	1.895	0.39200	D	0.963122	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.77004	0.989;0.981;0.989	T	0.72991	-0.4123	10	0.39692	T	0.17	-17.1781	10.5523	0.45097	0.1446:0.0:0.0:0.8554	.	710;711;670	B7ZLY6;F5H369;O75747	.;.;P3C2G_HUMAN	P	670;670;711	ENSP00000404845:S670P;ENSP00000266497:S670P;ENSP00000445381:S711P	ENSP00000266497:S670P	S	+	1	0	PIK3C2G	18443864	1.000000	0.71417	0.998000	0.56505	0.981000	0.71138	3.446000	0.52928	0.913000	0.36797	0.477000	0.44152	TCT	.	.		0.373	PIK3C2G-002	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401316.1	NM_004570	
SPX	80763	hgsc.bcm.edu	37	12	21684114	21684114	+	Silent	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:21684114T>C	ENST00000256969.2	+	6	502	c.336T>C	c.(334-336)agT>agC	p.S112S	C12orf39_ENST00000543800.1_3'UTR	NM_030572.2	NP_085049.1	Q9BT56	SPXN_HUMAN		112					long-chain fatty acid import (GO:0044539)|negative regulation of appetite (GO:0032099)|negative regulation of heart rate (GO:0010459)|negative regulation of renal sodium excretion (GO:0035814)|positive regulation of systemic arterial blood pressure (GO:0003084)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of sensory perception of pain (GO:0051930)	cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)	neuropeptide hormone activity (GO:0005184)|type 2 galanin receptor binding (GO:0031765)|type 3 galanin receptor binding (GO:0031766)			endometrium(3)|large_intestine(1)|lung(2)|urinary_tract(1)	7						TGGAAGACAGTCTGCTTAACT	0.294																																					p.S112S		Atlas-SNP	.											.	C12orf39	18	.	0			c.T336C						.						80.0	79.0	79.0					12																	21684114		2202	4299	6501	SO:0001819	synonymous_variant	80763	exon6			AGACAGTCTGCTT																												ENST00000256969.2:c.336T>C	chr12.hg19:g.21684114T>C		236.0	0.0		148.0	6.0	NM_030572	B3KND6	Silent	SNP	ENST00000256969.2	hg19	CCDS31757.1																																																																																			.	.		0.294	C12orf39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402389.1		
CASC1	55259	hgsc.bcm.edu	37	12	25308338	25308338	+	Silent	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:25308338T>C	ENST00000320267.9	-	4	270	c.189A>G	c.(187-189)gaA>gaG	p.E63E	CASC1_ENST00000557684.1_5'UTR|CASC1_ENST00000395987.3_Silent_p.E69E|CASC1_ENST00000354189.5_Silent_p.E127E|CASC1_ENST00000537577.1_5'UTR|CASC1_ENST00000395990.2_Silent_p.E23E|CASC1_ENST00000545133.1_Silent_p.E4E	NM_001082973.1	NP_001076442	Q6TDU7	CASC1_HUMAN	cancer susceptibility candidate 1	63	Glu-rich.									breast(3)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|liver(1)|lung(3)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	31	Acute lymphoblastic leukemia(6;0.00112)|all_hematologic(7;0.00152)|Melanoma(3;0.0301)|Colorectal(261;0.11)		OV - Ovarian serous cystadenocarcinoma(3;7.42e-20)|Epithelial(3;7.58e-16)|all cancers(3;1.07e-13)			CATTTCTCCTTTCTAGATCCT	0.338																																					p.E127E		Atlas-SNP	.											.	CASC1	146	.	0			c.A381G						.						91.0	93.0	93.0					12																	25308338		2203	4297	6500	SO:0001819	synonymous_variant	55259	exon5			TCTCCTTTCTAGA	AK093102	CCDS31759.2, CCDS41762.1, CCDS41763.1, CCDS55810.1, CCDS55811.1	12p12.1	2012-04-17			ENSG00000118307	ENSG00000118307		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	29599	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 54"""					14583591	Standard	NM_018272		Approved	LAS1, FLJ10921, PPP1R54	uc001rgk.3	Q6TDU7	OTTHUMG00000150195	ENST00000320267.9:c.189A>G	chr12.hg19:g.25308338T>C		96.0	0.0		88.0	4.0	NM_001082972	B4DNP2|F5H6T6|Q17RL2|Q4G171|Q5U5K5|Q9NV50	Silent	SNP	ENST00000320267.9	hg19	CCDS41762.1	.	.	.	.	.	.	.	.	.	.	T	10.39	1.337184	0.24253	.	.	ENSG00000118307	ENST00000556006	.	.	.	4.71	0.895	0.19247	.	.	.	.	.	T	0.21962	0.0529	.	.	.	0.22050	N	0.999399	.	.	.	.	.	.	T	0.21895	-1.0232	4	.	.	.	-7.6911	2.6752	0.05079	0.1935:0.2087:0.0:0.5979	.	.	.	.	E	39	.	.	K	-	1	0	CASC1	25199605	0.979000	0.34478	0.847000	0.33407	0.959000	0.62525	0.766000	0.26560	0.418000	0.25898	0.523000	0.50628	AAG	.	.		0.338	CASC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000316761.1	NM_018272	
PPFIBP1	8496	hgsc.bcm.edu	37	12	27800732	27800732	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:27800732A>G	ENST00000318304.8	+	6	711	c.428A>G	c.(427-429)gAg>gGg	p.E143G	PPFIBP1_ENST00000542629.1_Missense_Mutation_p.E143G|PPFIBP1_ENST00000228425.6_Missense_Mutation_p.E143G|PPFIBP1_ENST00000537927.1_5'UTR|PPFIBP1_ENST00000535047.1_Missense_Mutation_p.E143G	NM_001198916.1|NM_177444.2	NP_001185845.1|NP_803193	Q86W92	LIPB1_HUMAN	PTPRF interacting protein, binding protein 1 (liprin beta 1)	143					cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)			PPFIBP1/ALK(3)	central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(13)|prostate(2)|skin(1)	32	Lung SC(9;0.0873)					TGTCTTGAAGAGCACAGAGAG	0.453																																					p.E143G		Atlas-SNP	.											.	PPFIBP1	153	.	0			c.A428G						.						172.0	170.0	170.0					12																	27800732		2203	4300	6503	SO:0001583	missense	8496	exon6			TTGAAGAGCACAG	AF034802	CCDS8713.1, CCDS55812.1, CCDS55813.1, CCDS55814.1	12p12.1	2013-01-10						"""Sterile alpha motif (SAM) domain containing"""	9249	protein-coding gene	gene with protein product		603141				9624153, 11836260	Standard	NM_003622		Approved	L2, hSGT2, hSgt2p, SGT2	uc001ric.2	Q86W92		ENST00000318304.8:c.428A>G	chr12.hg19:g.27800732A>G	ENSP00000314724:p.Glu143Gly	193.0	0.0		131.0	7.0	NM_003622	O75336|Q86X70|Q9NY03|Q9ULJ0	Missense_Mutation	SNP	ENST00000318304.8	hg19	CCDS55812.1	.	.	.	.	.	.	.	.	.	.	A	20.4	3.981728	0.74474	.	.	ENSG00000110841	ENST00000543820;ENST00000545381;ENST00000318304;ENST00000535047;ENST00000542629;ENST00000228425	T;T;T;T;T	0.18016	2.24;2.24;2.24;2.24;2.24	5.26	5.26	0.73747	.	0.000000	0.34338	U	0.004054	T	0.33030	0.0849	L	0.43923	1.385	0.80722	D	1	P;D;D;P	0.89917	0.573;1.0;0.986;0.902	B;D;D;B	0.85130	0.227;0.997;0.939;0.415	T	0.02093	-1.1215	10	0.29301	T	0.29	-28.2831	14.8457	0.70259	1.0:0.0:0.0:0.0	.	143;143;143;143	Q86W92;Q86W92-2;Q86W92-4;Q86W92-5	LIPB1_HUMAN;.;.;.	G	145;143;143;143;143;143	ENSP00000445822:E143G;ENSP00000314724:E143G;ENSP00000444046:E143G;ENSP00000443442:E143G;ENSP00000228425:E143G	ENSP00000228425:E143G	E	+	2	0	PPFIBP1	27691999	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.280000	0.95786	1.975000	0.57531	0.528000	0.53228	GAG	.	.		0.453	PPFIBP1-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402877.1	NM_003622	
TMTC1	83857	hgsc.bcm.edu	37	12	29667503	29667503	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:29667503T>C	ENST00000539277.1	-	16	2400	c.2342A>G	c.(2341-2343)aAa>aGa	p.K781R	TMTC1_ENST00000319685.8_5'UTR|TMTC1_ENST00000551659.1_Missense_Mutation_p.K843R|TMTC1_ENST00000256062.5_Missense_Mutation_p.K673R|TMTC1_ENST00000552618.1_Missense_Mutation_p.K805R	NM_001193451.1	NP_001180380.1	Q8IUR5	TMTC1_HUMAN	transmembrane and tetratricopeptide repeat containing 1	781						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				breast(1)|endometrium(4)|kidney(3)|large_intestine(17)|lung(45)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	75	Lung NSC(12;7.61e-10)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.032)					GTCCTTTGGTTTCAGCTGGAG	0.363																																					p.K781R		Atlas-SNP	.											.	TMTC1	147	.	0			c.A2342G						.						94.0	94.0	94.0					12																	29667503		2203	4300	6503	SO:0001583	missense	83857	exon16			TTTGGTTTCAGCT		CCDS8718.1, CCDS53772.1	12p11.22	2014-06-09	2006-01-06			ENSG00000133687		"""Tetratricopeptide (TTC) repeat domain containing"""	24099	protein-coding gene	gene with protein product		615855				24764305	Standard	NM_001193451		Approved	ARG99, OLF, FLJ31400, FLJ41625	uc021qwi.1	Q8IUR5	OTTHUMG00000169324	ENST00000539277.1:c.2342A>G	chr12.hg19:g.29667503T>C	ENSP00000442046:p.Lys781Arg	117.0	0.0		99.0	4.0	NM_001193451	D0EP37|F5H8B5|Q6PIU4|Q6ZSM5|Q96N52|Q9BXM2	Missense_Mutation	SNP	ENST00000539277.1	hg19	CCDS53772.1	.	.	.	.	.	.	.	.	.	.	T	16.53	3.149075	0.57151	.	.	ENSG00000133687	ENST00000540901;ENST00000256062;ENST00000551659;ENST00000552618;ENST00000539277	T;T;T;T	0.62788	-0.0;-0.0;-0.0;-0.0	5.09	5.09	0.68999	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.149585	0.64402	D	0.000020	T	0.66925	0.2839	L	0.45744	1.44	0.80722	D	1	P;D;P	0.57571	0.872;0.98;0.763	B;P;B	0.56960	0.301;0.81;0.229	T	0.65389	-0.6180	10	0.34782	T	0.22	-19.3133	12.5219	0.56065	0.0:0.0:0.0:1.0	.	781;843;126	Q8IUR5;F8VTQ9;Q8IUR5-4	TMTC1_HUMAN;.;.	R	544;673;843;805;781	ENSP00000256062:K673R;ENSP00000448112:K843R;ENSP00000449043:K805R;ENSP00000442046:K781R	ENSP00000256062:K673R	K	-	2	0	TMTC1	29558770	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.362000	0.66098	2.027000	0.59764	0.533000	0.62120	AAA	.	.		0.363	TMTC1-002	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000403509.1	NM_031920	
IPO8	10526	hgsc.bcm.edu	37	12	30818240	30818240	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:30818240T>C	ENST00000256079.4	-	13	1680	c.1342A>G	c.(1342-1344)Agt>Ggt	p.S448G	IPO8_ENST00000544829.1_Missense_Mutation_p.S243G	NM_006390.3	NP_006381.2	O15397	IPO8_HUMAN	importin 8	448					intracellular protein transport (GO:0006886)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	Ran GTPase binding (GO:0008536)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(16)|liver(1)|lung(22)|prostate(2)|skin(2)|urinary_tract(2)	52	all_lung(12;6.66e-10)|Lung NSC(12;4.84e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0355)|Lung SC(12;0.0905)|Esophageal squamous(101;0.233)					TTGAATAAACTCTTCTATTAG	0.299																																					p.S448G		Atlas-SNP	.											.	IPO8	105	.	0			c.A1342G						.						71.0	76.0	74.0					12																	30818240		2201	4293	6494	SO:0001583	missense	10526	exon13			ATAAACTCTTCTA	U77494	CCDS8719.1, CCDS53773.1	12p11.21	2011-05-23	2003-03-11	2003-03-14	ENSG00000133704	ENSG00000133704		"""Importins"""	9853	protein-coding gene	gene with protein product		605600	"""RAN binding protein 8"""	RANBP8		9214382	Standard	NM_006390		Approved	IMP8	uc001rjd.3	O15397	OTTHUMG00000169172	ENST00000256079.4:c.1342A>G	chr12.hg19:g.30818240T>C	ENSP00000256079:p.Ser448Gly	174.0	0.0		150.0	6.0	NM_006390	B7Z7M3	Missense_Mutation	SNP	ENST00000256079.4	hg19	CCDS8719.1	.	.	.	.	.	.	.	.	.	.	T	14.54	2.564746	0.45694	.	.	ENSG00000133704	ENST00000256079;ENST00000544829	T;T	0.61627	0.09;0.09	5.02	5.02	0.67125	Armadillo-like helical (1);Armadillo-type fold (1);	0.189360	0.56097	D	0.000024	T	0.55862	0.1947	L	0.42245	1.32	0.34625	D	0.719025	B;P	0.36183	0.232;0.542	B;P	0.44921	0.193;0.464	T	0.68262	-0.5455	10	0.48119	T	0.1	-9.8359	10.3089	0.43697	0.147:0.0:0.0:0.853	.	243;448	B7Z7M3;O15397	.;IPO8_HUMAN	G	448;243	ENSP00000256079:S448G;ENSP00000444520:S243G	ENSP00000256079:S448G	S	-	1	0	IPO8	30709507	1.000000	0.71417	1.000000	0.80357	0.809000	0.45718	2.830000	0.48136	2.005000	0.58758	0.528000	0.53228	AGT	.	.		0.299	IPO8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402700.2	NM_006390	
PKP2	5318	hgsc.bcm.edu	37	12	33031092	33031092	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:33031092A>G	ENST00000070846.6	-	3	746	c.722T>C	c.(721-723)cTc>cCc	p.L241P	PKP2_ENST00000340811.4_Missense_Mutation_p.L241P	NM_004572.3	NP_004563.2	Q99959	PKP2_HUMAN	plakophilin 2	241					adherens junction maintenance (GO:0034334)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cardiac muscle cell action potential (GO:0086001)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cell-cell signaling involved in cardiac conduction (GO:0086019)|desmosome assembly (GO:0002159)|gap junction assembly (GO:0016264)|heart development (GO:0007507)|intermediate filament bundle assembly (GO:0045110)|lipid homeostasis (GO:0055088)|maintenance of organ identity (GO:0048496)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|positive regulation of sodium ion transport (GO:0010765)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of tight junction assembly (GO:2000810)|single organismal cell-cell adhesion (GO:0016337)|ventricular cardiac muscle cell action potential (GO:0086005)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	adherens junction (GO:0005912)|cell junction (GO:0030054)|cell-cell junction (GO:0005911)|desmosome (GO:0030057)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intermediate filament binding (GO:0019215)|ion channel binding (GO:0044325)|protein complex scaffold (GO:0032947)|protein kinase C binding (GO:0005080)|sodium channel regulator activity (GO:0017080)	p.L241R(1)		NS(1)|breast(2)|endometrium(1)|kidney(9)|large_intestine(8)|lung(21)|ovary(1)|pancreas(2)|prostate(2)|skin(2)|urinary_tract(1)	50	Lung NSC(5;9.35e-07)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.239)					GGGGTACGTGAGCAGGGCCGG	0.612																																					p.L241P		Atlas-SNP	.											PKP2,caecum,carcinoma,0,1	PKP2	110	.	1	Substitution - Missense(1)	large_intestine(1)	c.T722C						.						72.0	64.0	67.0					12																	33031092		2203	4298	6501	SO:0001583	missense	5318	exon3			TACGTGAGCAGGG	X97675	CCDS8731.1, CCDS31771.1	12p11	2014-09-17				ENSG00000057294		"""Armadillo repeat containing"""	9024	protein-coding gene	gene with protein product		602861				8922383	Standard	NM_001005242		Approved		uc001rlj.4	Q99959	OTTHUMG00000169500	ENST00000070846.6:c.722T>C	chr12.hg19:g.33031092A>G	ENSP00000070846:p.Leu241Pro	249.0	2.0		175.0	7.0	NM_004572	A0AV37|B8QFA1|B8QGS6|B8QGS7|D3DUW9|Q4VC01|Q99960	Missense_Mutation	SNP	ENST00000070846.6	hg19	CCDS8731.1	.	.	.	.	.	.	.	.	.	.	A	9.274	1.046450	0.19748	.	.	ENSG00000057294	ENST00000340811;ENST00000070846;ENST00000537278	T;T	0.80393	-1.37;-1.35	5.29	4.12	0.48240	.	4.458510	0.00550	N	0.000248	T	0.69006	0.3063	N	0.16743	0.435	0.09310	N	0.999999	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.001	T	0.54833	-0.8234	10	0.35671	T	0.21	-6.4718	4.6101	0.12399	0.6874:0.1868:0.1258:0.0	.	241;241;241	Q99959-2;A0AV37;Q99959	.;.;PKP2_HUMAN	P	241	ENSP00000342800:L241P;ENSP00000070846:L241P	ENSP00000070846:L241P	L	-	2	0	PKP2	32922359	0.000000	0.05858	0.058000	0.19502	0.668000	0.39293	0.310000	0.19356	0.827000	0.34685	0.529000	0.55759	CTC	.	.		0.612	PKP2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404449.1	NM_004572	
PRICKLE1	144165	hgsc.bcm.edu	37	12	42858256	42858256	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:42858256A>G	ENST00000455697.1	-	7	1865	c.1580T>C	c.(1579-1581)cTg>cCg	p.L527P	PRICKLE1_ENST00000548696.1_Missense_Mutation_p.L527P|PRICKLE1_ENST00000345127.3_Missense_Mutation_p.L527P|RP11-328C8.4_ENST00000547824.1_RNA|PRICKLE1_ENST00000552240.1_Missense_Mutation_p.L527P|PRICKLE1_ENST00000445766.2_Missense_Mutation_p.L527P	NM_001144882.1|NM_001144883.1	NP_001138354.1|NP_001138355.1	Q96MT3	PRIC1_HUMAN	prickle homolog 1 (Drosophila)	527					negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cardiac muscle cell myoblast differentiation (GO:2000691)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein ubiquitination (GO:0031398)|protein import into nucleus (GO:0006606)	cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(12)|liver(1)|lung(13)|ovary(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	47	all_cancers(12;4.25e-05)|Breast(8;0.176)			GBM - Glioblastoma multiforme(48;0.2)		CTCTGGTTTCAGGTCTGACAG	0.443																																					p.L527P		Atlas-SNP	.											.	PRICKLE1	105	.	0			c.T1580C						.						140.0	137.0	138.0					12																	42858256		2203	4300	6503	SO:0001583	missense	144165	exon7			GGTTTCAGGTCTG	AK056499	CCDS8742.1	12p11-q12	2010-08-13	2006-09-12			ENSG00000139174			17019	protein-coding gene	gene with protein product		608500	"""prickle-like 1 (Drosophila)"""			12525887, 18976727	Standard	NM_153026		Approved	FLJ31937, EPM1B	uc010skv.2	Q96MT3		ENST00000455697.1:c.1580T>C	chr12.hg19:g.42858256A>G	ENSP00000401060:p.Leu527Pro	328.0	0.0		264.0	98.0	NM_001144882	Q14C83|Q71QF8|Q96N00	Missense_Mutation	SNP	ENST00000455697.1	hg19	CCDS8742.1	.	.	.	.	.	.	.	.	.	.	A	17.45	3.391579	0.62066	.	.	ENSG00000139174	ENST00000455697;ENST00000445766;ENST00000548696;ENST00000345127;ENST00000552240	T;T;T;T;T	0.66280	-0.2;-0.2;-0.2;-0.2;-0.2	5.55	5.55	0.83447	.	0.079095	0.56097	D	0.000038	T	0.77301	0.4110	M	0.72894	2.215	0.80722	D	1	D	0.89917	1.0	D	0.66351	0.943	T	0.79999	-0.1566	10	0.72032	D	0.01	-10.8538	15.993	0.80220	1.0:0.0:0.0:0.0	.	527	Q96MT3	PRIC1_HUMAN	P	527	ENSP00000401060:L527P;ENSP00000398947:L527P;ENSP00000448359:L527P;ENSP00000345064:L527P;ENSP00000449819:L527P	ENSP00000345064:L527P	L	-	2	0	PRICKLE1	41144523	1.000000	0.71417	0.995000	0.50966	0.983000	0.72400	8.910000	0.92685	2.236000	0.73375	0.528000	0.53228	CTG	.	.		0.443	PRICKLE1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404069.1		
PUS7L	83448	hgsc.bcm.edu	37	12	44139933	44139933	+	Silent	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:44139933A>G	ENST00000416848.2	-	4	1667	c.1179T>C	c.(1177-1179)gaT>gaC	p.D393D	PUS7L_ENST00000431332.3_Silent_p.D80D|PUS7L_ENST00000344862.5_Silent_p.D393D|PUS7L_ENST00000551923.1_Silent_p.D393D	NM_001098615.1|NM_001271826.1	NP_001092085.1|NP_001258755.1	Q9H0K6	PUS7L_HUMAN	pseudouridylate synthase 7 homolog (S. cerevisiae)-like	393					pseudouridine synthesis (GO:0001522)|tRNA processing (GO:0008033)		pseudouridine synthase activity (GO:0009982)|RNA binding (GO:0003723)			NS(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(15)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32	all_cancers(12;0.00027)	Lung NSC(34;0.114)|all_lung(34;0.24)		GBM - Glioblastoma multiforme(48;0.0402)		TAATGACAATATCAAAGTGAT	0.289																																					p.D393D		Atlas-SNP	.											.	PUS7L	73	.	0			c.T1179C						.						43.0	41.0	42.0					12																	44139933		2202	4296	6498	SO:0001819	synonymous_variant	83448	exon4			GACAATATCAAAG	BX647494	CCDS8743.1, CCDS61104.1	12q12	2006-02-07				ENSG00000129317			25276	protein-coding gene	gene with protein product						11230166	Standard	NM_001098615		Approved	DKFZP434G1415	uc001rnr.5	Q9H0K6	OTTHUMG00000169423	ENST00000416848.2:c.1179T>C	chr12.hg19:g.44139933A>G		111.0	0.0		89.0	4.0	NM_001098614	B3KUJ1|Q05CU0|Q6AHZ3|Q6NUP2	Silent	SNP	ENST00000416848.2	hg19	CCDS8743.1																																																																																			.	.		0.289	PUS7L-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403931.1	NM_031292	
COL2A1	1280	hgsc.bcm.edu	37	12	48387630	48387630	+	Missense_Mutation	SNP	C	C	T			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:48387630C>T	ENST00000380518.3	-	14	1050	c.886G>A	c.(886-888)Gac>Aac	p.D296N	COL2A1_ENST00000337299.6_Missense_Mutation_p.D227N	NM_001844.4|NM_033150.2	NP_001835.3|NP_149162.2	P02458	CO2A1_HUMAN	collagen, type II, alpha 1	296	Triple-helical region.				axon guidance (GO:0007411)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|cellular response to BMP stimulus (GO:0071773)|central nervous system development (GO:0007417)|chondrocyte differentiation (GO:0002062)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|embryonic skeletal joint morphogenesis (GO:0060272)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart morphogenesis (GO:0003007)|inner ear morphogenesis (GO:0042472)|limb bud formation (GO:0060174)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|notochord development (GO:0030903)|otic vesicle development (GO:0071599)|palate development (GO:0060021)|proteoglycan metabolic process (GO:0006029)|regulation of gene expression (GO:0010468)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|tissue homeostasis (GO:0001894)|visual perception (GO:0007601)	basement membrane (GO:0005604)|collagen type II trimer (GO:0005585)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|lung(25)|ovary(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(3)	64		Acute lymphoblastic leukemia(13;0.108)|all_hematologic(14;0.214)			Collagenase(DB00048)	TTAGCACCGTCCAGGCCTGGA	0.532																																					p.D296N		Atlas-SNP	.											.	COL2A1	368	.	0			c.G886A						.						79.0	76.0	77.0					12																	48387630		2203	4300	6503	SO:0001583	missense	1280	exon14			CACCGTCCAGGCC	X16468	CCDS8759.1, CCDS41778.1	12q12-q13.2	2013-11-14	2008-02-04		ENSG00000139219	ENSG00000139219		"""Collagens"""	2200	protein-coding gene	gene with protein product		120140	"""collagen, type II, alpha 1 (primary osteoarthritis, spondyloepiphyseal dysplasia, congenital)"", ""arthroophthalmopathy, progressive (Stickler syndrome)"""	SEDC, AOM		1677770	Standard	NM_033150		Approved	STL1	uc001rqu.3	P02458	OTTHUMG00000149896	ENST00000380518.3:c.886G>A	chr12.hg19:g.48387630C>T	ENSP00000369889:p.Asp296Asn	253.0	0.0		169.0	71.0	NM_001844	A6NGA0|Q12985|Q14009|Q14044|Q14045|Q14046|Q14047|Q14056|Q14058|Q16672|Q1JQ82|Q2V4X7|Q6LBY1|Q6LBY2|Q6LBY3|Q96IT5|Q99227|Q9UE38|Q9UE39|Q9UE40|Q9UE41|Q9UE42|Q9UE43	Missense_Mutation	SNP	ENST00000380518.3	hg19	CCDS41778.1	.	.	.	.	.	.	.	.	.	.	C	15.74	2.921489	0.52653	.	.	ENSG00000139219	ENST00000380518;ENST00000395281;ENST00000337299	D;D	0.92699	-3.09;-3.09	5.12	4.22	0.49857	.	0.000000	0.85682	D	0.000000	D	0.86485	0.5944	N	0.26092	0.79	0.53688	D	0.999973	B;B	0.11235	0.003;0.004	B;B	0.15484	0.005;0.013	T	0.83200	-0.0079	10	0.72032	D	0.01	.	12.5558	0.56252	0.0:0.9185:0.0:0.0815	.	227;296	P02458-1;P02458	.;CO2A1_HUMAN	N	296;227;227	ENSP00000369889:D296N;ENSP00000338213:D227N	ENSP00000338213:D227N	D	-	1	0	COL2A1	46673897	1.000000	0.71417	0.819000	0.32651	0.778000	0.44026	5.679000	0.68160	1.384000	0.46424	0.655000	0.94253	GAC	.	.		0.532	COL2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313810.2	NM_001844	
FAM186B	84070	hgsc.bcm.edu	37	12	49993487	49993487	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:49993487T>C	ENST00000257894.2	-	4	2097	c.1936A>G	c.(1936-1938)Acc>Gcc	p.T646A	FAM186B_ENST00000551047.1_Intron|FAM186B_ENST00000544141.1_Missense_Mutation_p.T556A	NM_032130.2	NP_115506.1	Q8IYM0	F186B_HUMAN	family with sequence similarity 186, member B	646						protein complex (GO:0043234)				breast(1)|endometrium(2)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						GAGGGCCAGGTCAGCCTTCGG	0.532																																					p.T646A		Atlas-SNP	.											.	FAM186B	72	.	0			c.A1936G						.						78.0	71.0	74.0					12																	49993487		2203	4300	6503	SO:0001583	missense	84070	exon4			GCCAGGTCAGCCT	AL136748	CCDS8788.1	12q13.12	2008-09-17	2008-09-17	2008-09-17	ENSG00000135436	ENSG00000135436			25296	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 25"""	C12orf25		11230166	Standard	NM_032130		Approved	DKFZP434J0113	uc001ruo.3	Q8IYM0	OTTHUMG00000167427	ENST00000257894.2:c.1936A>G	chr12.hg19:g.49993487T>C	ENSP00000257894:p.Thr646Ala	119.0	0.0		86.0	4.0	NM_032130	B4DZ15|Q8TCP7|Q9H0L3	Missense_Mutation	SNP	ENST00000257894.2	hg19	CCDS8788.1	.	.	.	.	.	.	.	.	.	.	T	7.969	0.748676	0.15710	.	.	ENSG00000135436	ENST00000544141;ENST00000532262;ENST00000257894	T;T;T	0.12147	2.71;2.71;2.92	4.72	-9.44	0.00603	.	1.359190	0.04820	N	0.436840	T	0.06600	0.0169	L	0.31294	0.92	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.002	T	0.28170	-1.0052	9	.	.	.	-0.6912	0.9145	0.01301	0.4187:0.2184:0.2004:0.1626	.	556;646	B4DZ15;Q8IYM0	.;F186B_HUMAN	A	556;259;646	ENSP00000438569:T556A;ENSP00000436995:T259A;ENSP00000257894:T646A	.	T	-	1	0	FAM186B	48279754	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.023000	0.00641	-2.805000	0.00350	-0.280000	0.10049	ACC	.	.		0.532	FAM186B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394583.2	NM_032130	
FAM186A	121006	hgsc.bcm.edu	37	12	50749223	50749223	+	Silent	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:50749223T>C	ENST00000327337.5	-	4	1391	c.1392A>G	c.(1390-1392)aaA>aaG	p.K464K	FAM186A_ENST00000543111.1_Silent_p.K464K	NM_001145475.1	NP_001138947.1	A6NE01	F186A_HUMAN	family with sequence similarity 186, member A	464				KKA -> TKG (in Ref. 2; AL833333). {ECO:0000305}.													CATATGTGGCTTTTTTGTGGC	0.388																																					p.K464K	NSCLC(138;1796 1887 12511 19463 37884)	Atlas-SNP	.											.	FAM186A	181	.	0			c.A1392G						.						149.0	103.0	117.0					12																	50749223		692	1591	2283	SO:0001819	synonymous_variant	121006	exon4			TGTGGCTTTTTTG		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.1392A>G	chr12.hg19:g.50749223T>C		176.0	0.0		126.0	6.0	NM_001145475		Silent	SNP	ENST00000327337.5	hg19	CCDS44878.1																																																																																			.	.		0.388	FAM186A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396838.1	XM_001718353	
KRT72	140807	hgsc.bcm.edu	37	12	52981443	52981443	+	Missense_Mutation	SNP	G	G	A			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:52981443G>A	ENST00000537672.2	-	7	1292	c.1282C>T	c.(1282-1284)Cgc>Tgc	p.R428C	KRT72_ENST00000354310.4_Missense_Mutation_p.R386C|KRT72_ENST00000293745.2_Missense_Mutation_p.R428C|KRT72_ENST00000398066.3_Missense_Mutation_p.R240C	NM_001146225.1	NP_001139697.1	Q14CN4	K2C72_HUMAN	keratin 72	428	Coil 2.|Rod.		R -> L (in dbSNP:rs11170183). {ECO:0000269|PubMed:14702039}.			extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(14)|ovary(5)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)	36				BRCA - Breast invasive adenocarcinoma(357;0.195)		AGCAGCTTGCGGTAGGTGGCG	0.612																																					p.R428C		Atlas-SNP	.											KRT72,caecum,carcinoma,+1,1	KRT72	70	.	0			c.C1282T						.						107.0	98.0	101.0					12																	52981443		2203	4300	6503	SO:0001583	missense	140807	exon7			GCTTGCGGTAGGT	AY033495	CCDS8833.1, CCDS53795.1	12q13.13	2013-06-25			ENSG00000170486	ENSG00000170486		"""-"", ""Intermediate filaments type II, keratins (basic)"""	28932	protein-coding gene	gene with protein product		608246				12648212, 11703281, 16831889	Standard	NM_080747		Approved	K6IRS2, KRT6IRS2, KRT6, K6irs	uc001saq.2	Q14CN4	OTTHUMG00000169744	ENST00000537672.2:c.1282C>T	chr12.hg19:g.52981443G>A	ENSP00000441160:p.Arg428Cys	267.0	0.0		161.0	0.0	NM_001146225	B4DEI8|H9KV51|Q8NA87|Q8WWY9|Q8WWZ0	Missense_Mutation	SNP	ENST00000537672.2	hg19	CCDS8833.1	.	.	.	.	.	.	.	.	.	.	G	17.89	3.499073	0.64298	.	.	ENSG00000170486	ENST00000537672;ENST00000293745;ENST00000354310;ENST00000398066	D;D;D;D	0.94828	-3.53;-3.53;-3.53;-3.53	4.92	1.52	0.23074	Filament (1);Intermediate filament protein, conserved site (1);	0.000000	0.44483	D	0.000445	D	0.97688	0.9242	H	0.95004	3.61	0.44409	D	0.997323	D	0.76494	0.999	D	0.66716	0.946	D	0.98190	1.0462	10	0.72032	D	0.01	.	15.7025	0.77552	0.0:0.0:0.2567:0.7433	.	428	Q14CN4	K2C72_HUMAN	C	428;428;386;240	ENSP00000441160:R428C;ENSP00000293745:R428C;ENSP00000346269:R386C;ENSP00000446151:R240C	ENSP00000293745:R428C	R	-	1	0	KRT72	51267710	1.000000	0.71417	0.998000	0.56505	0.987000	0.75469	0.987000	0.29603	0.133000	0.18654	-0.284000	0.09977	CGC	.	.		0.612	KRT72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405693.1	NM_080747	
SARNP	84324	hgsc.bcm.edu	37	12	56154345	56154345	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:56154345T>C	ENST00000336133.3	-	10	635	c.581A>G	c.(580-582)gAg>gGg	p.E194G	RP11-762I7.4_ENST00000547009.1_RNA|SARNP_ENST00000444631.2_Missense_Mutation_p.E134G|SARNP_ENST00000552080.1_Missense_Mutation_p.E194G|RP11-762I7.5_ENST00000546837.1_Silent_p.R506R	NM_033082.3	NP_149073.1	P82979	SARNP_HUMAN	SAP domain containing ribonucleoprotein	194					mRNA export from nucleus (GO:0006406)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|transcription, DNA-templated (GO:0006351)	intracellular membrane-bounded organelle (GO:0043231)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|transcription export complex (GO:0000346)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	6						CTCTGTATCCTCTGTGGTTCC	0.398																																					p.E194G		Atlas-SNP	.											.	SARNP	19	.	0			c.A581G						.						140.0	131.0	134.0					12																	56154345		2203	4300	6503	SO:0001583	missense	84324	exon10			GTATCCTCTGTGG	AJ409089	CCDS8892.1	12q13.2	2009-07-09				ENSG00000205323			24432	protein-coding gene	gene with protein product	"""hepatocellular carcinoma 1"", ""cytokine induced protein 29 kDa"""	610049				11356193, 11922608	Standard	NM_033082		Approved	THO1, Hcc-1, CIP29		P82979	OTTHUMG00000170441	ENST00000336133.3:c.581A>G	chr12.hg19:g.56154345T>C	ENSP00000337632:p.Glu194Gly	124.0	0.0		98.0	4.0	NM_033082	A8K393|Q9P066	Missense_Mutation	SNP	ENST00000336133.3	hg19	CCDS8892.1	.	.	.	.	.	.	.	.	.	.	T	27.1	4.801171	0.90538	.	.	ENSG00000205323	ENST00000444631;ENST00000336133;ENST00000552080	.	.	.	5.72	5.72	0.89469	.	0.183998	0.49305	D	0.000146	T	0.45034	0.1322	L	0.49778	1.585	0.51482	D	0.999922	P	0.40970	0.734	B	0.31751	0.135	T	0.52434	-0.8576	9	0.66056	D	0.02	-13.3564	14.2653	0.66113	0.0:0.0:0.0:1.0	.	194	P82979	SARNP_HUMAN	G	134;194;194	.	ENSP00000337632:E194G	E	-	2	0	SARNP	54440612	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.989000	0.56958	2.320000	0.78422	0.528000	0.53228	GAG	.	.		0.398	SARNP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409159.2	NM_033082	
MIP	4284	hgsc.bcm.edu	37	12	56848277	56848277	+	Missense_Mutation	SNP	C	C	A			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:56848277C>A	ENST00000257979.4	-	1	149	c.121G>T	c.(121-123)Gtt>Ttt	p.V41F	MIP_ENST00000555551.1_Intron	NM_012064.3	NP_036196.1	P30301	MIP_HUMAN	major intrinsic protein of lens fiber	41					canalicular bile acid transport (GO:0015722)|lens development in camera-type eye (GO:0002088)|response to stimulus (GO:0050896)|transmembrane transport (GO:0055085)|visual perception (GO:0007601)|water transport (GO:0006833)	gap junction (GO:0005921)|integral component of plasma membrane (GO:0005887)|intracellular canaliculus (GO:0046691)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	calmodulin binding (GO:0005516)|structural constituent of eye lens (GO:0005212)|transporter activity (GO:0005215)|water channel activity (GO:0015250)			kidney(1)|large_intestine(2)|lung(8)|prostate(1)|skin(3)|urinary_tract(1)	16						ACCTGCAGAACATGCAGGGGT	0.572																																					p.V41F		Atlas-SNP	.											.	MIP	39	.	0			c.G121T						.						84.0	80.0	81.0					12																	56848277		2203	4300	6503	SO:0001583	missense	4284	exon1			GCAGAACATGCAG		CCDS8919.1	12q13	2012-10-02				ENSG00000135517		"""Ion channels / Aquaporins"""	7103	protein-coding gene	gene with protein product	aquaporin 0	154050				1840563, 7536742	Standard	NM_012064		Approved	MP26, LIM1, AQP0	uc001slh.3	P30301		ENST00000257979.4:c.121G>T	chr12.hg19:g.56848277C>A	ENSP00000257979:p.Val41Phe	439.0	0.0		334.0	133.0	NM_012064	Q17R41	Missense_Mutation	SNP	ENST00000257979.4	hg19	CCDS8919.1	.	.	.	.	.	.	.	.	.	.	C	18.63	3.665011	0.67700	.	.	ENSG00000135517	ENST00000257979	D	0.85171	-1.95	5.31	3.49	0.39957	Aquaporin-like (2);	0.058543	0.64402	D	0.000002	T	0.79896	0.4525	N	0.16368	0.405	0.58432	D	0.999999	P	0.39376	0.67	P	0.48770	0.589	T	0.78575	-0.2151	10	0.59425	D	0.04	-20.4468	9.2039	0.37278	0.0:0.7625:0.0:0.2375	.	41	P30301	MIP_HUMAN	F	41	ENSP00000257979:V41F	ENSP00000257979:V41F	V	-	1	0	MIP	55134544	0.767000	0.28508	0.978000	0.43139	0.901000	0.52897	0.272000	0.18644	0.749000	0.32854	0.655000	0.94253	GTT	.	.		0.572	MIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409620.1	NM_012064	
TSPAN31	6302	hgsc.bcm.edu	37	12	58140374	58140374	+	Silent	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:58140374A>G	ENST00000257910.3	+	4	589	c.315A>G	c.(313-315)acA>acG	p.T105T	CDK4_ENST00000551888.1_5'Flank|TSPAN31_ENST00000553221.1_3'UTR|TSPAN31_ENST00000547472.1_Silent_p.T22T|TSPAN31_ENST00000547992.1_Intron	NM_005981.3	NP_005972.1	Q12999	TSN31_HUMAN	tetraspanin 31	105					positive regulation of cell proliferation (GO:0008284)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)				endometrium(1)|kidney(1)|lung(5)	7	all_cancers(7;4.96e-69)|Lung NSC(6;5.5e-25)|all_lung(6;3.87e-23)|all_epithelial(6;1.66e-15)|Glioma(12;6.95e-05)|all_neural(12;0.00016)|Melanoma(17;0.122)		GBM - Glioblastoma multiforme(5;4.21e-120)|all cancers(5;3.75e-83)|BRCA - Breast invasive adenocarcinoma(9;0.0294)			TCTTTCAGACAGATGTCATCA	0.433																																					p.T105T		Atlas-SNP	.											.	TSPAN31	20	.	0			c.A315G						.						142.0	126.0	132.0					12																	58140374		2203	4300	6503	SO:0001819	synonymous_variant	6302	exon4			TCAGACAGATGTC		CCDS8952.1	12q13-q14	2013-02-14	2005-08-16	2005-08-16		ENSG00000135452		"""Tetraspanins"""	10539	protein-coding gene	gene with protein product		181035	"""sarcoma amplified sequence"""	SAS			Standard	NM_005981		Approved		uc001spt.3	Q12999		ENST00000257910.3:c.315A>G	chr12.hg19:g.58140374A>G		208.0	0.0		122.0	5.0	NM_005981	O00577|Q53X76	Silent	SNP	ENST00000257910.3	hg19	CCDS8952.1																																																																																			.	.		0.433	TSPAN31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408778.1		
PTPRB	5787	hgsc.bcm.edu	37	12	70928316	70928316	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:70928316T>C	ENST00000261266.5	-	29	5695	c.5666A>G	c.(5665-5667)gAc>gGc	p.D1889G	RP11-588H23.3_ENST00000548687.1_RNA|PTPRB_ENST00000550857.1_Missense_Mutation_p.D1799G|RP11-588H23.3_ENST00000549460.1_RNA|PTPRB_ENST00000550358.1_Missense_Mutation_p.D2019G|RP11-588H23.3_ENST00000551438.1_RNA|PTPRB_ENST00000538708.1_Missense_Mutation_p.D1799G|RP11-588H23.3_ENST00000546836.1_RNA|PTPRB_ENST00000451516.2_Missense_Mutation_p.D1799G|RP11-588H23.3_ENST00000547656.1_RNA|PTPRB_ENST00000334414.6_Missense_Mutation_p.D2107G	NM_002837.4	NP_002828.3	P23467	PTPRB_HUMAN	protein tyrosine phosphatase, receptor type, B	1889	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				angiogenesis (GO:0001525)|dephosphorylation (GO:0016311)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|protein dephosphorylation (GO:0006470)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(4)|central_nervous_system(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(46)|prostate(4)|skin(18)|upper_aerodigestive_tract(1)|urinary_tract(3)	107	Renal(347;0.236)		GBM - Glioblastoma multiforme(2;2.17e-05)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00306)|STAD - Stomach adenocarcinoma(21;0.149)			GTTGATGTAGTCCCTGACAGT	0.547																																					p.D2107G		Atlas-SNP	.											.	PTPRB	676	.	0			c.A6320G						.						44.0	43.0	44.0					12																	70928316		1903	4128	6031	SO:0001583	missense	5787	exon31			ATGTAGTCCCTGA	X54131	CCDS44943.1, CCDS44944.1, CCDS55845.1, CCDS55846.1	12q15-q21	2013-02-11						"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9665	protein-coding gene	gene with protein product		176882		PTPB		2169617	Standard	NM_001109754		Approved		uc001swc.4	P23467	OTTHUMG00000169499	ENST00000261266.5:c.5666A>G	chr12.hg19:g.70928316T>C	ENSP00000261266:p.Asp1889Gly	235.0	0.0		142.0	6.0	NM_001109754	B7ZKS8|B7ZKT0|C9JX87|F5H3G6|Q14D85|Q3MIV7	Missense_Mutation	SNP	ENST00000261266.5	hg19	CCDS44944.1	.	.	.	.	.	.	.	.	.	.	T	17.62	3.434254	0.62955	.	.	ENSG00000127329	ENST00000334414;ENST00000451516;ENST00000550358;ENST00000538708;ENST00000550857;ENST00000261266	D;D;D;D;D;D	0.83506	-1.73;-1.73;-1.73;-1.73;-1.73;-1.73	5.67	5.67	0.87782	Protein-tyrosine phosphatase, receptor/non-receptor type (3);Protein-tyrosine/Dual-specificity phosphatase (1);	0.000000	0.85682	D	0.000000	D	0.87767	0.6260	L	0.39898	1.24	0.80722	D	1	P;P;D;P;B	0.89917	0.697;0.936;1.0;0.888;0.414	P;P;D;P;P	0.91635	0.612;0.897;0.999;0.815;0.457	D	0.89075	0.3472	10	0.87932	D	0	.	15.9212	0.79575	0.0:0.0:0.0:1.0	.	1799;1799;2107;1889;2019	P23467-2;F5H3G6;P23467-3;P23467;F8VU56	.;.;.;PTPRB_HUMAN;.	G	2107;1799;2019;1799;1799;1889	ENSP00000334928:D2107G;ENSP00000393028:D1799G;ENSP00000448058:D2019G;ENSP00000438927:D1799G;ENSP00000447302:D1799G;ENSP00000261266:D1889G	ENSP00000261266:D1889G	D	-	2	0	PTPRB	69214583	1.000000	0.71417	1.000000	0.80357	0.833000	0.47200	6.186000	0.72026	2.155000	0.67459	0.460000	0.39030	GAC	.	.		0.547	PTPRB-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404439.1		
NAP1L1	4673	hgsc.bcm.edu	37	12	76449901	76449901	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:76449901T>C	ENST00000261182.8	-	7	956	c.470A>G	c.(469-471)aAa>aGa	p.K157R	NAP1L1_ENST00000535020.2_Missense_Mutation_p.K157R|NAP1L1_ENST00000542344.1_Missense_Mutation_p.K115R|NAP1L1_ENST00000548044.1_Missense_Mutation_p.K116R|NAP1L1_ENST00000431879.3_Missense_Mutation_p.K89R|NAP1L1_ENST00000552342.1_Missense_Mutation_p.K168R|NAP1L1_ENST00000547773.1_Missense_Mutation_p.K94R|NAP1L1_ENST00000544816.1_5'UTR|NAP1L1_ENST00000393263.3_Missense_Mutation_p.K157R|NAP1L1_ENST00000547993.1_5'UTR|NAP1L1_ENST00000549596.1_Missense_Mutation_p.K157R	NM_004537.4|NM_139207.2	NP_004528.1|NP_631946.1	P55209	NP1L1_HUMAN	nucleosome assembly protein 1-like 1	157					DNA replication (GO:0006260)|nucleosome assembly (GO:0006334)|positive regulation of cell proliferation (GO:0008284)	membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			kidney(1)|large_intestine(1)|lung(3)|ovary(2)|prostate(1)|skin(1)	9		Colorectal(145;0.09)				TTCTTCATCTTTTTTCTCATC	0.323																																					p.K157R		Atlas-SNP	.											NAP1L1,NS,carcinoma,0,1	NAP1L1	33	.	0			c.A470G						.						66.0	62.0	63.0					12																	76449901		2202	4299	6501	SO:0001583	missense	4673	exon7			TCATCTTTTTTCT		CCDS9013.1	12q21.1	2010-03-17			ENSG00000187109	ENSG00000187109			7637	protein-coding gene	gene with protein product		164060				8297347	Standard	NM_004537		Approved	NRP, NAP1, NAP1L, MGC8688, MGC23410	uc001sxx.2	P55209		ENST00000261182.8:c.470A>G	chr12.hg19:g.76449901T>C	ENSP00000261182:p.Lys157Arg	565.0	2.0		428.0	0.0	NM_004537	B3KNT8	Missense_Mutation	SNP	ENST00000261182.8	hg19	CCDS9013.1	.	.	.	.	.	.	.	.	.	.	T	18.36	3.606596	0.66445	.	.	ENSG00000187109	ENST00000261182;ENST00000552056;ENST00000393263;ENST00000431879;ENST00000547773;ENST00000542344;ENST00000535020;ENST00000549596;ENST00000552342;ENST00000548044;ENST00000550934;ENST00000551992;ENST00000548273;ENST00000551600;ENST00000547704	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.26067	1.76;1.76;1.76;1.76;1.76;1.76;1.76;1.76;1.76;1.76;1.76;1.76;1.76;1.76;1.76	6.05	4.91	0.64330	.	0.041854	0.85682	D	0.000000	T	0.35008	0.0917	M	0.66939	2.045	0.54753	D	0.999985	P;P;P;P;B;B;B	0.41188	0.696;0.741;0.523;0.578;0.221;0.066;0.061	B;P;B;P;B;B;B	0.48334	0.438;0.574;0.358;0.574;0.091;0.033;0.063	T	0.07177	-1.0786	10	0.18710	T	0.47	.	11.8846	0.52594	0.0:0.0684:0.0:0.9316	.	157;115;168;157;89;94;157	F5H4R6;B7Z9C2;F8W0J6;B3KNT8;B3KV44;F8W543;P55209	.;.;.;.;.;.;NP1L1_HUMAN	R	157;151;157;89;94;115;157;157;168;116;130;157;116;163;164	ENSP00000261182:K157R;ENSP00000450236:K151R;ENSP00000376947:K157R;ENSP00000409795:K89R;ENSP00000448167:K94R;ENSP00000444759:K115R;ENSP00000445008:K157R;ENSP00000447793:K157R;ENSP00000447196:K168R;ENSP00000449649:K116R;ENSP00000448133:K130R;ENSP00000448764:K157R;ENSP00000446787:K116R;ENSP00000448836:K163R;ENSP00000446756:K164R	ENSP00000261182:K157R	K	-	2	0	NAP1L1	74736168	1.000000	0.71417	0.988000	0.46212	0.944000	0.59088	8.036000	0.88901	1.107000	0.41642	-0.263000	0.10527	AAA	.	.		0.323	NAP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405850.3	NM_139207	
PPFIA2	8499	hgsc.bcm.edu	37	12	81851632	81851632	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:81851632A>G	ENST00000549396.1	-	5	477	c.317T>C	c.(316-318)cTg>cCg	p.L106P	PPFIA2_ENST00000552948.1_Missense_Mutation_p.L106P|PPFIA2_ENST00000443686.3_Missense_Mutation_p.L32P|PPFIA2_ENST00000550584.2_Missense_Mutation_p.L106P|PPFIA2_ENST00000545296.2_5'UTR|PPFIA2_ENST00000549325.1_Missense_Mutation_p.L88P|PPFIA2_ENST00000407050.4_Missense_Mutation_p.L32P|PPFIA2_ENST00000550359.2_5'UTR|RP11-315E17.1_ENST00000550272.1_RNA|PPFIA2_ENST00000548586.1_Missense_Mutation_p.L106P|PPFIA2_ENST00000333447.7_Missense_Mutation_p.L88P	NM_001220476.1|NM_001282536.1|NM_003625.3	NP_001207405.1|NP_001269465.1|NP_003616.2	O75334	LIPA2_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 2	106					cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|presynaptic active zone (GO:0048786)				NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(37)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(5)	85						TTCTTTTGTCAGTGCAGCAAA	0.284																																					p.L106P		Atlas-SNP	.											.	PPFIA2	207	.	0			c.T317C						.						88.0	74.0	78.0					12																	81851632		1785	4055	5840	SO:0001583	missense	8499	exon4			TTTGTCAGTGCAG	AF034799	CCDS55850.1, CCDS55851.1, CCDS55852.1, CCDS55853.1, CCDS55854.1, CCDS55855.1, CCDS55856.1, CCDS55857.1, CCDS59236.1, CCDS73503.1	12q21.31	2013-01-10						"""Sterile alpha motif (SAM) domain containing"""	9246	protein-coding gene	gene with protein product	"""Liprin-alpha2"""	603143				9624153	Standard	NM_003625		Approved		uc031qis.1	O75334		ENST00000549396.1:c.317T>C	chr12.hg19:g.81851632A>G	ENSP00000450337:p.Leu106Pro	118.0	0.0		95.0	4.0	NM_001220476	B3KVT5|B3KXA0|B7Z2A6|B7Z3U9|B7Z663|B7ZKZ5|E7ERB8|E7ETG6|F8VP68|Q2M3G8	Missense_Mutation	SNP	ENST00000549396.1	hg19	CCDS55857.1	.	.	.	.	.	.	.	.	.	.	A	23.0	4.362692	0.82353	.	.	ENSG00000139220	ENST00000549396;ENST00000549325;ENST00000407050;ENST00000541501;ENST00000333447;ENST00000548586;ENST00000443686;ENST00000552948;ENST00000551442;ENST00000547623	T;T;T;T;T;T;T;T;T	0.53640	1.12;1.12;1.12;1.12;1.12;1.12;1.12;1.12;0.61	5.66	5.66	0.87406	.	0.000000	0.64402	D	0.000003	T	0.64011	0.2560	L	0.52759	1.655	0.80722	D	1	D;D	0.69078	0.997;0.995	D;D	0.80764	0.994;0.986	T	0.66744	-0.5846	10	0.87932	D	0	-9.0674	15.8839	0.79226	1.0:0.0:0.0:0.0	.	6;106	B7Z4H8;O75334	.;LIPA2_HUMAN	P	106;88;32;117;88;106;32;106;88;106	ENSP00000450337:L106P;ENSP00000450298:L88P;ENSP00000385093:L32P;ENSP00000327416:L88P;ENSP00000449338:L106P;ENSP00000388373:L32P;ENSP00000447868:L106P;ENSP00000449469:L88P;ENSP00000447918:L106P	ENSP00000327416:L88P	L	-	2	0	PPFIA2	80375763	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.828000	0.92047	2.158000	0.67659	0.533000	0.62120	CTG	.	.		0.284	PPFIA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408030.1		
GALNT4	8693	hgsc.bcm.edu	37	12	89917665	89917665	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:89917665T>C	ENST00000529983.2	-	1	918	c.662A>G	c.(661-663)gAc>gGc	p.D221G	POC1B_ENST00000549035.1_Intron|POC1B_ENST00000313546.3_Intron|POC1B_ENST00000541909.1_Intron|POC1B-GALNT4_ENST00000547474.1_Intron|POC1B_ENST00000393179.4_Intron|POC1B_ENST00000549504.1_Intron|GALNT4_ENST00000413530.1_Intron|RP11-734K2.4_ENST00000605233.1_RNA|POC1B-GALNT4_ENST00000548729.1_Missense_Mutation_p.D218G	NM_003774.4	NP_003765.2	Q8N4A0	GALT4_HUMAN	polypeptide N-acetylgalactosaminyltransferase 4	221	Catalytic subdomain A.				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						AGTGAGGACGTCCCCAGTGGC	0.507											OREG0022018	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D221G		Atlas-SNP	.											.	GALNT4	38	.	0			c.A662G						.						81.0	82.0	82.0					12																	89917665		1946	4139	6085	SO:0001583	missense	8693	exon1			AGGACGTCCCCAG	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.662A>G	chr12.hg19:g.89917665T>C	ENSP00000436604:p.Asp221Gly	136.0	0.0	1271	85.0	4.0	NM_003774	B2R775|B4DMX6|O00208	Missense_Mutation	SNP	ENST00000529983.2	hg19	CCDS53817.1	.	.	.	.	.	.	.	.	.	.	T	19.79	3.893521	0.72639	.	.	ENSG00000259075;ENSG00000257594	ENST00000548729;ENST00000529983	T;T	0.66815	-0.23;-0.23	5.88	5.88	0.94601	Glycosyl transferase, family 2 (1);	.	.	.	.	T	0.76343	0.3974	M	0.79805	2.47	0.36632	D	0.876357	P;P	0.38473	0.58;0.633	B;P	0.46208	0.373;0.507	T	0.83223	-0.0067	9	0.87932	D	0	.	15.4562	0.75314	0.0:0.0:0.0:1.0	.	218;221	F8VUJ3;Q8N4A0	.;GALT4_HUMAN	G	218;221	ENSP00000447852:D218G;ENSP00000436604:D221G	ENSP00000436604:D221G	D	-	2	0	GALNT4;RP11-1109F11.4	88441796	1.000000	0.71417	0.990000	0.47175	0.997000	0.91878	6.167000	0.71902	2.246000	0.74042	0.533000	0.62120	GAC	.	.		0.507	GALNT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388973.2	NM_003774	
PLXNC1	10154	hgsc.bcm.edu	37	12	94692568	94692568	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:94692568A>G	ENST00000258526.4	+	27	4484	c.4235A>G	c.(4234-4236)aAc>aGc	p.N1412S	PLXNC1_ENST00000547057.1_Missense_Mutation_p.N459S|PLXNC1_ENST00000545312.1_Missense_Mutation_p.N151S	NM_005761.2	NP_005752.1	O60486	PLXC1_HUMAN	plexin C1	1412					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|receptor binding (GO:0005102)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(12)|lung(30)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	64						TGGAAAACAAACAGGTGGGAA	0.343																																					p.N1412S		Atlas-SNP	.											.	PLXNC1	135	.	0			c.A4235G						.						56.0	59.0	58.0					12																	94692568		2203	4300	6503	SO:0001583	missense	10154	exon27			AAACAAACAGGTG	AF030339	CCDS9049.1	12q23	2009-04-17				ENSG00000136040		"""CD molecules"", ""Plexins"""	9106	protein-coding gene	gene with protein product		604259					Standard	NR_037687		Approved	VESPR, CD232	uc001tdc.3	O60486	OTTHUMG00000170235	ENST00000258526.4:c.4235A>G	chr12.hg19:g.94692568A>G	ENSP00000258526:p.Asn1412Ser	56.0	0.0		63.0	4.0	NM_005761	Q59H25	Missense_Mutation	SNP	ENST00000258526.4	hg19	CCDS9049.1	.	.	.	.	.	.	.	.	.	.	A	23.8	4.456106	0.84209	.	.	ENSG00000136040	ENST00000258526;ENST00000547057;ENST00000545312	T;T;T	0.22336	1.96;1.96;1.96	5.95	5.95	0.96441	Plexin, cytoplasmic RasGAP domain (1);Rho GTPase activation protein (1);	0.000000	0.85682	D	0.000000	T	0.48768	0.1518	M	0.75150	2.29	0.80722	D	1	D;D	0.89917	0.997;1.0	D;D	0.87578	0.994;0.998	T	0.50634	-0.8805	10	0.87932	D	0	.	16.4237	0.83790	1.0:0.0:0.0:0.0	.	459;1412	B4DHQ7;O60486	.;PLXC1_HUMAN	S	1412;459;151	ENSP00000258526:N1412S;ENSP00000446720:N459S;ENSP00000439225:N151S	ENSP00000258526:N1412S	N	+	2	0	PLXNC1	93216699	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.339000	0.96797	2.279000	0.76181	0.533000	0.62120	AAC	.	.		0.343	PLXNC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408126.2		
GAS2L3	283431	hgsc.bcm.edu	37	12	101018209	101018209	+	Silent	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:101018209A>G	ENST00000539410.1	+	9	2012	c.1626A>G	c.(1624-1626)ggA>ggG	p.G542G	GAS2L3_ENST00000547754.1_Silent_p.G542G|GAS2L3_ENST00000537247.1_Silent_p.G438G|GAS2L3_ENST00000266754.5_Silent_p.G542G			Q86XJ1	GA2L3_HUMAN	growth arrest-specific 2 like 3	542					actin cytoskeleton organization (GO:0030036)|cell cycle arrest (GO:0007050)|microtubule cytoskeleton organization (GO:0000226)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)	actin binding (GO:0003779)|microtubule binding (GO:0008017)			endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(15)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	35						CATCCGATGGAGCCCCACAAG	0.458																																					p.G542G		Atlas-SNP	.											.	GAS2L3	76	.	0			c.A1626G						.						48.0	47.0	48.0					12																	101018209		2203	4300	6503	SO:0001819	synonymous_variant	283431	exon10			CGATGGAGCCCCA	AK095594	CCDS9079.1	12q23.1	2014-09-11			ENSG00000139354	ENSG00000139354			27475	protein-coding gene	gene with protein product							Standard	NM_174942		Approved		uc001thu.3	Q86XJ1	OTTHUMG00000170439	ENST00000539410.1:c.1626A>G	chr12.hg19:g.101018209A>G		85.0	0.0		62.0	4.0	NM_174942	B2RCN2	Silent	SNP	ENST00000539410.1	hg19	CCDS9079.1																																																																																			.	.		0.458	GAS2L3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409143.1	NM_174942	
GNPTAB	79158	hgsc.bcm.edu	37	12	102158140	102158140	+	Missense_Mutation	SNP	A	A	G	rs281864996		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:102158140A>G	ENST00000299314.7	-	13	2817	c.2555T>C	c.(2554-2556)aTc>aCc	p.I852T	RNU6-101P_ENST00000410323.1_RNA	NM_024312.4	NP_077288.2	Q3T906	GNPTA_HUMAN	N-acetylglucosamine-1-phosphate transferase, alpha and beta subunits	852					carbohydrate phosphorylation (GO:0046835)|cell differentiation (GO:0030154)|lysosome organization (GO:0007040)|protein secretion (GO:0009306)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|UDP-N-acetylglucosamine-lysosomal-enzyme N-acetylglucosaminephosphotransferase activity (GO:0003976)			NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(8)|lung(8)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	37						TTTCCCTGTGATTTTCTTTTC	0.403																																					p.I852T		Atlas-SNP	.											.	GNPTAB	120	.	0			c.T2555C						.						258.0	255.0	256.0					12																	102158140		2203	4300	6503	SO:0001583	missense	79158	exon13			CCTGTGATTTTCT	AY687932	CCDS9088.1	12q23.3	2013-01-10				ENSG00000111670		"""EF-hand domain containing"""	29670	protein-coding gene	gene with protein product		607840		GNPTA		10574462, 16116615	Standard	NM_024312		Approved	KIAA1208, MGC4170	uc001tit.3	Q3T906	OTTHUMG00000170444	ENST00000299314.7:c.2555T>C	chr12.hg19:g.102158140A>G	ENSP00000299314:p.Ile852Thr	141.0	0.0		124.0	5.0	NM_024312	A2RRQ9|Q3ZQK2|Q6IPW5|Q86TQ2|Q96N13|Q9ULL2	Missense_Mutation	SNP	ENST00000299314.7	hg19	CCDS9088.1	.	.	.	.	.	.	.	.	.	.	A	6.778	0.512407	0.12944	.	.	ENSG00000111670	ENST00000299314	D	0.95980	-3.87	4.66	-6.51	0.01878	.	1.082130	0.07043	N	0.830477	D	0.86834	0.6028	N	0.22421	0.69	0.09310	N	1	B	0.15473	0.013	B	0.11329	0.006	T	0.78198	-0.2297	10	0.02654	T	1	-1.1474	8.6838	0.34225	0.3297:0.3919:0.2784:0.0	.	852	Q3T906	GNPTA_HUMAN	T	852	ENSP00000299314:I852T	ENSP00000299314:I852T	I	-	2	0	GNPTAB	100682271	0.000000	0.05858	0.000000	0.03702	0.382000	0.30200	-0.563000	0.05943	-0.804000	0.04410	0.533000	0.62120	ATC	.	.		0.403	GNPTAB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409182.1		
CCDC53	51019	hgsc.bcm.edu	37	12	102455700	102455700	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:102455700T>C	ENST00000240079.6	-	1	202	c.41A>G	c.(40-42)gAc>gGc	p.D14G	RP11-554E23.4_ENST00000552707.1_RNA|CCDC53_ENST00000539515.1_Intron|CCDC53_ENST00000545679.1_Missense_Mutation_p.D14G	NM_016053.2	NP_057137.1	Q9Y3C0	CCD53_HUMAN	coiled-coil domain containing 53	14						actin cytoskeleton (GO:0015629)|intracellular membrane-bounded organelle (GO:0043231)|WASH complex (GO:0071203)				endometrium(1)|kidney(1)|large_intestine(1)|lung(1)	4						CTTGGTCAGGTCTATGCCTGA	0.632																																					p.D14G		Atlas-SNP	.											.	CCDC53	14	.	0			c.A41G						.						27.0	31.0	30.0					12																	102455700		1925	4125	6050	SO:0001583	missense	51019	exon1			GTCAGGTCTATGC	AF151874	CCDS44959.1, CCDS73512.1	12q23.3	2014-05-09			ENSG00000120860	ENSG00000120860			24256	protein-coding gene	gene with protein product						10810093, 20498093	Standard	XM_005268939		Approved	CGI-116	uc010svw.2	Q9Y3C0	OTTHUMG00000168187	ENST00000240079.6:c.41A>G	chr12.hg19:g.102455700T>C	ENSP00000240079:p.Asp14Gly	84.0	0.0		74.0	4.0	NM_016053	B2RC74|Q53FF0|Q6IAI4|Q96QK0	Missense_Mutation	SNP	ENST00000240079.6	hg19	CCDS44959.1	.	.	.	.	.	.	.	.	.	.	T	22.9	4.344310	0.82022	.	.	ENSG00000120860	ENST00000240079;ENST00000545679	.	.	.	5.42	5.42	0.78866	.	0.000000	0.85682	D	0.000000	T	0.71728	0.3374	M	0.81497	2.545	0.80722	D	1	B;B	0.29232	0.238;0.153	B;B	0.33846	0.171;0.083	T	0.74231	-0.3732	9	0.72032	D	0.01	.	15.6229	0.76820	0.0:0.0:0.0:1.0	.	14;14	F5GZ97;Q9Y3C0	.;CCD53_HUMAN	G	14	.	ENSP00000240079:D14G	D	-	2	0	CCDC53	100979830	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.734000	0.74801	2.279000	0.76181	0.402000	0.26972	GAC	.	.		0.632	CCDC53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398685.1	NM_016053	
TCTN1	79600	hgsc.bcm.edu	37	12	111078953	111078953	+	Splice_Site	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:111078953A>G	ENST00000551590.1	+	9	1259	c.1103A>G	c.(1102-1104)cAg>cGg	p.Q368R	TCTN1_ENST00000397655.3_Splice_Site_p.Q354R|TCTN1_ENST00000377654.3_Splice_Site_p.Q190R|TCTN1_ENST00000397659.4_Splice_Site_p.Q368R|HVCN1_ENST00000548312.1_Intron			Q2MV58	TECT1_HUMAN	tectonic family member 1	368					central nervous system interneuron axonogenesis (GO:0021956)|cilium morphogenesis (GO:0060271)|dorsal/ventral neural tube patterning (GO:0021904)|in utero embryonic development (GO:0001701)|neural tube formation (GO:0001841)|regulation of smoothened signaling pathway (GO:0008589)|somatic motor neuron differentiation (GO:0021523)|telencephalon development (GO:0021537)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|membrane (GO:0016020)|TCTN-B9D complex (GO:0036038)				NS(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(9)|urinary_tract(1)	15						CATTTTCTTCAGGTAAGGTTG	0.373																																					p.Q368R		Atlas-SNP	.											.	TCTN1	37	.	0			c.A1103G						.						132.0	121.0	125.0					12																	111078953		1870	4093	5963	SO:0001630	splice_region_variant	79600	exon9			TTCTTCAGGTAAG	AK055891	CCDS41833.1, CCDS41834.1, CCDS41835.1	12q24.11	2011-09-07			ENSG00000204852	ENSG00000204852		"""Tectonic proteins"""	26113	protein-coding gene	gene with protein product		609863				16357211	Standard	NM_001082537		Approved	FLJ21127, TECT1, JBTS13	uc001trn.4	Q2MV58	OTTHUMG00000150051	ENST00000551590.1:c.1104+1A>G	chr12.hg19:g.111078953A>G		140.0	0.0		82.0	4.0	NM_001082537	A8MX11|Q49A60|Q6P5X1|Q6UXW2|Q8NAE9|Q96N72|Q9H798	Missense_Mutation	SNP	ENST00000551590.1	hg19	CCDS41835.1	.	.	.	.	.	.	.	.	.	.	A	21.2	4.110449	0.77210	.	.	ENSG00000204852	ENST00000397650;ENST00000551590;ENST00000397655;ENST00000377654;ENST00000397657;ENST00000397659;ENST00000397652	D;D;D;D	0.82803	-1.65;-1.65;-1.65;-1.65	5.87	4.73	0.59995	Domain of unknown function DUF1619 (1);	0.108690	0.64402	N	0.000004	D	0.91047	0.7183	M	0.85710	2.77	0.47476	D	0.999434	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.998;0.998;0.998;0.993;0.999	D	0.91301	0.5067	10	0.62326	D	0.03	-13.764	11.8497	0.52405	0.9317:0.0:0.0683:0.0	.	368;354;368;308;312	Q2MV58;Q2MV58-3;Q2MV58-2;C9J1H5;C9J1H4	TECT1_HUMAN;.;.;.;.	R	308;368;354;190;190;368;312	ENSP00000448735:Q368R;ENSP00000380775:Q354R;ENSP00000366882:Q190R;ENSP00000380779:Q368R	ENSP00000366882:Q190R	Q	+	2	0	TCTN1	109563336	1.000000	0.71417	0.995000	0.50966	0.835000	0.47333	5.088000	0.64486	1.049000	0.40321	0.533000	0.62120	CAG	.	.		0.373	TCTN1-001	KNOWN	non_canonical_TEC|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000316016.2	NM_024549	Missense_Mutation
MAPKAPK5	8550	hgsc.bcm.edu	37	12	112330837	112330837	+	Missense_Mutation	SNP	A	A	T			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:112330837A>T	ENST00000551404.2	+	14	1502	c.1394A>T	c.(1393-1395)gAg>gTg	p.E465V	MAPKAPK5_ENST00000550735.2_Missense_Mutation_p.E463V			Q8IW41	MAPK5_HUMAN	mitogen-activated protein kinase-activated protein kinase 5	465					activation of MAPK activity (GO:0000187)|MAPK cascade (GO:0000165)|negative regulation of TOR signaling (GO:0032007)|protein autophosphorylation (GO:0046777)|Ras protein signal transduction (GO:0007265)|regulation of translation (GO:0006417)|signal transduction (GO:0007165)|stress-induced premature senescence (GO:0090400)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|MAP kinase kinase activity (GO:0004708)|p53 binding (GO:0002039)|protein serine/threonine kinase activity (GO:0004674)			endometrium(1)|lung(11)|ovary(1)	13						GTGATAGAAGAGCAAACCACG	0.338																																					p.E465V		Atlas-SNP	.											.	MAPKAPK5	56	.	0			c.A1394T						.						79.0	79.0	79.0					12																	112330837		1888	4122	6010	SO:0001583	missense	8550	exon14			TAGAAGAGCAAAC	AF032437	CCDS44975.1, CCDS44976.1	12q24.13	2012-05-30			ENSG00000089022	ENSG00000089022			6889	protein-coding gene	gene with protein product		606723				9628874	Standard	NM_003668		Approved	PRAK	uc001tta.4	Q8IW41	OTTHUMG00000169605	ENST00000551404.2:c.1394A>T	chr12.hg19:g.112330837A>T	ENSP00000449381:p.Glu465Val	143.0	0.0		95.0	40.0	NM_139078	B3KVA5|O60491|Q86X46|Q9BVX9|Q9UG86	Missense_Mutation	SNP	ENST00000551404.2	hg19	CCDS44975.1	.	.	.	.	.	.	.	.	.	.	A	22.2	4.262163	0.80358	.	.	ENSG00000089022	ENST00000550735;ENST00000202788;ENST00000428907;ENST00000551404;ENST00000547067	T;T	0.57595	0.4;0.39	5.74	5.74	0.90152	.	0.000000	0.85682	D	0.000000	T	0.59676	0.2211	N	0.19112	0.55	0.80722	D	1	D;D;D	0.61080	0.981;0.981;0.989	D;D;D	0.72625	0.95;0.95;0.978	T	0.65512	-0.6150	10	0.87932	D	0	.	16.0382	0.80645	1.0:0.0:0.0:0.0	.	459;465;463	C9J458;Q8IW41;Q8IW41-2	.;MAPK5_HUMAN;.	V	463;465;463;465;126	ENSP00000449667:E463V;ENSP00000449381:E465V	ENSP00000202788:E465V	E	+	2	0	MAPKAPK5	110815220	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.613000	0.90913	2.194000	0.70268	0.533000	0.62120	GAG	.	.		0.338	MAPKAPK5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000405019.2	NM_139078	
HECTD4	283450	hgsc.bcm.edu	37	12	112685271	112685271	+	Silent	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:112685271T>C	ENST00000430131.2	-	27	4211	c.3066A>G	c.(3064-3066)tcA>tcG	p.S1022S	HECTD4_ENST00000550722.1_Silent_p.S1298S|HECTD4_ENST00000377560.5_Silent_p.S1272S			Q9Y4D8	HECD4_HUMAN	HECT domain containing E3 ubiquitin protein ligase 4	1022					glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)										CTAACCTCAGTGATAGGACCA	0.303																																					p.S1310S		Atlas-SNP	.											.	.	.	.	0			c.A3930G						.						57.0	54.0	55.0					12																	112685271		1840	4069	5909	SO:0001819	synonymous_variant	283450	exon28			CCTCAGTGATAGG	AK091473		12q24.13	2013-07-17	2012-08-14	2012-08-14	ENSG00000173064	ENSG00000173064			26611	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 51"""	C12orf51		21270382	Standard	NM_001109662		Approved	FLJ34154, KIAA0614	uc021reb.1	Q9Y4D8	OTTHUMG00000150719	ENST00000430131.2:c.3066A>G	chr12.hg19:g.112685271T>C		188.0	0.0		121.0	5.0	NM_001109662	L8B0P6|Q3MJD5|Q6P0A0|Q7L530|Q8NB70|Q8WU73|Q96NT9|Q9NZS4|Q9UFT6	Silent	SNP	ENST00000430131.2	hg19																																																																																				.	.		0.303	HECTD4-202	KNOWN	basic	protein_coding	protein_coding		NM_173813	
MED13L	23389	hgsc.bcm.edu	37	12	116428868	116428868	+	Silent	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:116428868A>G	ENST00000281928.3	-	17	4097	c.3891T>C	c.(3889-3891)gcT>gcC	p.A1297A		NM_015335.4	NP_056150.1	Q71F56	MD13L_HUMAN	mediator complex subunit 13-like	1297						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			NS(2)|breast(1)|endometrium(9)|kidney(3)|large_intestine(18)|lung(34)|ovary(4)|prostate(4)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	85	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0407)		TTCTCACCAGAGCTTCGTCCA	0.468																																					p.A1297A		Atlas-SNP	.											.	MED13L	193	.	0			c.T3891C						.						101.0	96.0	98.0					12																	116428868		2203	4300	6503	SO:0001819	synonymous_variant	23389	exon17			CACCAGAGCTTCG	AB028948	CCDS9177.1	12q24.22	2010-07-29	2007-07-30	2007-07-30	ENSG00000123066	ENSG00000123066			22962	protein-coding gene	gene with protein product		608771	"""thyroid hormone receptor associated protein 2"""	THRAP2			Standard	NM_015335		Approved	KIAA1025, TRAP240L	uc001tvw.3	Q71F56	OTTHUMG00000169404	ENST00000281928.3:c.3891T>C	chr12.hg19:g.116428868A>G		106.0	0.0		94.0	4.0	NM_015335	A1L469|Q68DN4|Q9H8C0|Q9NSY9|Q9UFD8|Q9UPX5	Silent	SNP	ENST00000281928.3	hg19	CCDS9177.1																																																																																			.	.		0.468	MED13L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403879.3		
RFC5	5985	hgsc.bcm.edu	37	12	118464801	118464801	+	Missense_Mutation	SNP	A	A	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:118464801A>C	ENST00000454402.2	+	8	889	c.771A>C	c.(769-771)caA>caC	p.Q257H	RFC5_ENST00000392542.2_Missense_Mutation_p.Q236H|RFC5_ENST00000229043.3_Missense_Mutation_p.Q172H|RFC5_ENST00000543153.1_3'UTR	NM_001206801.1|NM_007370.5	NP_001193730.1|NP_031396.1	P40937	RFC5_HUMAN	replication factor C (activator 1) 5, 36.5kDa	257					DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA strand elongation involved in DNA replication (GO:0006271)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	DNA replication factor C complex (GO:0005663)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)			NS(1)|breast(1)|endometrium(1)|large_intestine(3)|lung(3)	9	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					TGTTGAATCAAGATTTCACCA	0.547																																					p.Q257H		Atlas-SNP	.											.	RFC5	35	.	0			c.A771C						.						141.0	139.0	140.0					12																	118464801		2203	4300	6503	SO:0001583	missense	5985	exon8			GAATCAAGATTTC		CCDS9185.1, CCDS41843.2	12q24.3	2010-04-21	2002-08-29		ENSG00000111445	ENSG00000111445		"""ATPases / AAA-type"""	9973	protein-coding gene	gene with protein product		600407	"""replication factor C (activator 1) 5 (36.5kD)"""			7774928	Standard	NM_007370		Approved	RFC36	uc001twq.3	P40937	OTTHUMG00000156438	ENST00000454402.2:c.771A>C	chr12.hg19:g.118464801A>C	ENSP00000408295:p.Gln257His	123.0	0.0		72.0	30.0	NM_007370	A8MZ62|B3KSX8	Missense_Mutation	SNP	ENST00000454402.2	hg19	CCDS9185.1	.	.	.	.	.	.	.	.	.	.	A	14.60	2.582831	0.46006	.	.	ENSG00000111445	ENST00000229043;ENST00000454402;ENST00000392542	T;T;T	0.43688	0.94;0.94;0.94	5.75	-2.69	0.06022	Replication factor C (1);DNA polymerase III, clamp loader complex, gamma/delta/delta subunit, C-terminal (1);	0.387817	0.30483	N	0.009530	T	0.20780	0.0500	N	0.14661	0.345	0.33998	D	0.649963	B;B;B	0.06786	0.0;0.001;0.001	B;B;B	0.12837	0.005;0.008;0.008	T	0.03249	-1.1056	10	0.52906	T	0.07	-8.3921	7.9384	0.29944	0.3877:0.1176:0.4947:0.0	.	236;271;257	A8MZ62;Q59GW7;P40937	.;.;RFC5_HUMAN	H	172;257;236	ENSP00000229043:Q172H;ENSP00000408295:Q257H;ENSP00000376325:Q236H	ENSP00000229043:Q172H	Q	+	3	2	RFC5	116949184	0.971000	0.33674	0.938000	0.37757	0.930000	0.56654	0.192000	0.17096	-0.374000	0.07967	-0.316000	0.08728	CAA	.	.		0.547	RFC5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344196.2	NM_007370	
RFC5	5985	hgsc.bcm.edu	37	12	118464813	118464813	+	Silent	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:118464813A>G	ENST00000454402.2	+	8	901	c.783A>G	c.(781-783)acA>acG	p.T261T	RFC5_ENST00000392542.2_Silent_p.T240T|RFC5_ENST00000229043.3_Silent_p.T176T|RFC5_ENST00000543153.1_3'UTR	NM_001206801.1|NM_007370.5	NP_001193730.1|NP_031396.1	P40937	RFC5_HUMAN	replication factor C (activator 1) 5, 36.5kDa	261					DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA strand elongation involved in DNA replication (GO:0006271)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	DNA replication factor C complex (GO:0005663)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)			NS(1)|breast(1)|endometrium(1)|large_intestine(3)|lung(3)	9	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					ATTTCACCACAGCCTACAGAA	0.552																																					p.T261T		Atlas-SNP	.											.	RFC5	35	.	0			c.A783G						.						135.0	135.0	135.0					12																	118464813		2203	4300	6503	SO:0001819	synonymous_variant	5985	exon8			CACCACAGCCTAC		CCDS9185.1, CCDS41843.2	12q24.3	2010-04-21	2002-08-29		ENSG00000111445	ENSG00000111445		"""ATPases / AAA-type"""	9973	protein-coding gene	gene with protein product		600407	"""replication factor C (activator 1) 5 (36.5kD)"""			7774928	Standard	NM_007370		Approved	RFC36	uc001twq.3	P40937	OTTHUMG00000156438	ENST00000454402.2:c.783A>G	chr12.hg19:g.118464813A>G		116.0	0.0		68.0	26.0	NM_007370	A8MZ62|B3KSX8	Silent	SNP	ENST00000454402.2	hg19	CCDS9185.1																																																																																			.	.		0.552	RFC5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344196.2	NM_007370	
GCN1L1	10985	hgsc.bcm.edu	37	12	120582745	120582745	+	Missense_Mutation	SNP	G	G	T			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:120582745G>T	ENST00000300648.6	-	40	5149	c.5137C>A	c.(5137-5139)Cgc>Agc	p.R1713S		NM_006836.1	NP_006827	Q92616	GCN1L_HUMAN	GCN1 general control of amino-acid synthesis 1-like 1 (yeast)	1713					regulation of translation (GO:0006417)|translation (GO:0006412)	cytoplasm (GO:0005737)|membrane (GO:0016020)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)			NS(2)|breast(2)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(13)|liver(1)|lung(36)|ovary(4)|prostate(7)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	94	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					GCGCCTGAGCGATCCACAGAG	0.602																																					p.R1713S		Atlas-SNP	.											.	GCN1L1	207	.	0			c.C5137A						.						73.0	78.0	76.0					12																	120582745		2129	4250	6379	SO:0001583	missense	10985	exon40			CTGAGCGATCCAC	U77700	CCDS41847.1	12q24.2	2008-07-03	2001-11-28						4199	protein-coding gene	gene with protein product		605614	"""GCN1 (general control of amino-acid synthesis 1, yeast)-like 1"""			9234705	Standard	NM_006836		Approved	KIAA0219, GCN1, GCN1L	uc001txo.3	Q92616	OTTHUMG00000169338	ENST00000300648.6:c.5137C>A	chr12.hg19:g.120582745G>T	ENSP00000300648:p.Arg1713Ser	129.0	0.0		87.0	34.0	NM_006836	A8KAY1|O95001|O95651|Q6P2S3|Q86X65|Q8N5I5|Q8WU80|Q99736|Q9UE60	Missense_Mutation	SNP	ENST00000300648.6	hg19	CCDS41847.1	.	.	.	.	.	.	.	.	.	.	G	29.4	5.004690	0.93287	.	.	ENSG00000089154	ENST00000300648	T	0.67523	-0.27	5.5	5.5	0.81552	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.87253	0.6131	M	0.93375	3.41	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.89906	0.4048	10	0.87932	D	0	-16.5971	19.7578	0.96301	0.0:0.0:1.0:0.0	.	1713	Q92616	GCN1L_HUMAN	S	1713	ENSP00000300648:R1713S	ENSP00000300648:R1713S	R	-	1	0	GCN1L1	119067128	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	9.554000	0.98121	2.748000	0.94277	0.655000	0.94253	CGC	.	.		0.602	GCN1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403592.1		
SIRT4	23409	hgsc.bcm.edu	37	12	120750552	120750552	+	Splice_Site	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:120750552A>G	ENST00000202967.4	+	3	850	c.791A>G	c.(790-792)cAg>cGg	p.Q264R	RNU6-1088P_ENST00000516850.1_RNA|SIRT4_ENST00000537892.1_3'UTR	NM_012240.2	NP_036372.1			sirtuin 4											haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(3)	9	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					TCATCCTTGCAGGTATCTGAC	0.498																																					p.Q264R		Atlas-SNP	.											.	SIRT4	29	.	0			c.A791G						.						59.0	56.0	57.0					12																	120750552		2203	4300	6503	SO:0001630	splice_region_variant	23409	exon3			CCTTGCAGGTATC	AF083109	CCDS9194.1	12q24.31	2010-06-25	2010-06-25		ENSG00000089163	ENSG00000089163			14932	protein-coding gene	gene with protein product		604482	"""sirtuin (silent mating type information regulation 2, S. cerevisiae, homolog) 4"", ""sirtuin (silent mating type information regulation 2 homolog) 4 (S. cerevisiae)"""			10381378	Standard	NM_012240		Approved	SIR2L4	uc001tyc.3	Q9Y6E7	OTTHUMG00000169028	ENST00000202967.4:c.792+1A>G	chr12.hg19:g.120750552A>G		131.0	0.0		123.0	6.0	NM_012240		Missense_Mutation	SNP	ENST00000202967.4	hg19	CCDS9194.1	.	.	.	.	.	.	.	.	.	.	A	20.3	3.972673	0.74246	.	.	ENSG00000089163	ENST00000202967	T	0.17691	2.26	4.59	4.59	0.56863	.	0.000000	0.85682	D	0.000000	T	0.36963	0.0986	M	0.83384	2.64	0.80722	D	1	P	0.51240	0.943	P	0.55965	0.788	T	0.26430	-1.0103	10	0.21014	T	0.42	-24.562	14.7214	0.69308	1.0:0.0:0.0:0.0	.	264	Q9Y6E7	SIRT4_HUMAN	R	264	ENSP00000202967:Q264R	ENSP00000202967:Q264R	Q	+	2	0	SIRT4	119234935	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	8.964000	0.93389	2.014000	0.59158	0.529000	0.55759	CAG	.	.		0.498	SIRT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402003.1	NM_012240	Missense_Mutation
SACS	26278	hgsc.bcm.edu	37	13	23929049	23929049	+	Missense_Mutation	SNP	C	C	A			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr13:23929049C>A	ENST00000382292.3	-	7	1975	c.1702G>T	c.(1702-1704)Gac>Tac	p.D568Y	SACS_ENST00000382298.3_Missense_Mutation_p.D568Y|SACS_ENST00000476776.1_5'Flank|SACS_ENST00000402364.1_5'UTR			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	568					cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		CTGACCCAGTCACAGCTAATT	0.473																																					p.D568Y		Atlas-SNP	.											.	SACS	871	.	0			c.G1702T						.						102.0	97.0	98.0					13																	23929049		2203	4300	6503	SO:0001583	missense	26278	exon8			CCCAGTCACAGCT	AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"""Heat shock proteins / DNAJ (HSP40)"""	10519	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 138"""	604490	"""spastic ataxia of Charlevoix-Saguenay (sacsin)"""			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.1702G>T	chr13.hg19:g.23929049C>A	ENSP00000371729:p.Asp568Tyr	180.0	0.0		142.0	48.0	NM_014363	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Missense_Mutation	SNP	ENST00000382292.3	hg19	CCDS9300.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	3.352|3.352	-0.132318|-0.132318	0.06753|0.06753	.|.	.|.	ENSG00000151835|ENSG00000151835	ENST00000382292;ENST00000382298;ENST00000423156|ENST00000455470	T;T;T|.	0.17054|.	2.3;2.3;2.3|.	5.74|5.74	3.05|3.05	0.35203|0.35203	.|.	0.784986|.	0.13011|.	N|.	0.420898|.	T|.	0.23289|.	0.0563|.	N|N	0.19112|0.19112	0.55|0.55	0.09310|0.09310	N|N	1|1	B;B;B|.	0.31290|.	0.318;0.098;0.0|.	B;B;B|.	0.32624|.	0.149;0.123;0.004|.	T|.	0.22068|.	-1.0227|.	10|.	0.48119|.	T|.	0.1|.	.|.	6.9614|6.9614	0.24599|0.24599	0.0788:0.5348:0.2873:0.0991|0.0788:0.5348:0.2873:0.0991	.|.	467;355;568|.	B2REB1;E9PAL4;Q9NZJ4|.	.;.;SACS_HUMAN|.	Y|L	568;568;192|467	ENSP00000371729:D568Y;ENSP00000371735:D568Y;ENSP00000390925:D192Y|.	ENSP00000371729:D568Y|.	D|X	-|-	1|2	0|2	SACS|SACS	22827049|22827049	0.483000|0.483000	0.25956|0.25956	0.000000|0.000000	0.03702|0.03702	0.017000|0.017000	0.09413|0.09413	2.444000|2.444000	0.44890|0.44890	0.426000|0.426000	0.26116|0.26116	0.561000|0.561000	0.74099|0.74099	GAC|TGA	.	.		0.473	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363	
MTUS2	23281	hgsc.bcm.edu	37	13	29600946	29600946	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr13:29600946A>G	ENST00000431530.3	+	1	2199	c.2141A>G	c.(2140-2142)cAg>cGg	p.Q714R		NM_001033602.2	NP_001028774.2	Q5JR59	MTUS2_HUMAN	microtubule associated tumor suppressor candidate 2	704	Mediates interaction with MAPRE1.					cytoplasm (GO:0005737)|microtubule (GO:0005874)	microtubule binding (GO:0008017)|protein homodimerization activity (GO:0042803)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(3)|prostate(1)|skin(1)	20						CCAGACCTGCAGAAGCCAAGG	0.517																																					p.Q714R		Atlas-SNP	.											MTUS2_ENST00000431530,right_upper_lobe,carcinoma,0,1	MTUS2	279	.	0			c.A2141G						.						59.0	61.0	61.0					13																	29600946		1899	4110	6009	SO:0001583	missense	23281	exon1			ACCTGCAGAAGCC	AB018317	CCDS41874.1, CCDS45022.1	13q12.3	2013-01-17	2009-10-20	2009-10-20	ENSG00000132938	ENSG00000132938			20595	protein-coding gene	gene with protein product	"""+TIP of 150 kDa"", ""cardiac zipper protein"""		"""KIAA0774"""	KIAA0774		19543227	Standard	NM_001033602		Approved	TIP150, CAZIP, ICIS	uc001usl.4	Q5JR59	OTTHUMG00000016657	ENST00000431530.3:c.2141A>G	chr13.hg19:g.29600946A>G	ENSP00000392057:p.Gln714Arg	26.0	0.0		34.0	2.0	NM_001033602	A7E292|B4DF81|O94872|Q08E97|Q5JQR3|Q8N5E2	Missense_Mutation	SNP	ENST00000431530.3	hg19	CCDS45022.1	.	.	.	.	.	.	.	.	.	.	a	23.4	4.410080	0.83340	.	.	ENSG00000132938	ENST00000431530	T	0.36699	1.24	6.17	6.17	0.99709	.	0.000000	0.56097	D	0.000034	T	0.59293	0.2183	M	0.68952	2.095	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.57969	-0.7719	9	.	.	.	.	16.0034	0.80327	1.0:0.0:0.0:0.0	.	704	Q5JR59	MTUS2_HUMAN	R	714	ENSP00000392057:Q714R	.	Q	+	2	0	MTUS2	28498946	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.857000	0.55972	2.371000	0.80710	0.533000	0.62120	CAG	.	.		0.517	MTUS2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044336.3	XM_166270	
B3GALTL	145173	hgsc.bcm.edu	37	13	31821164	31821164	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr13:31821164T>C	ENST00000343307.4	+	5	424	c.275T>C	c.(274-276)cTc>cCc	p.L92P		NM_194318.3	NP_919299.3	Q6Y288	B3GLT_HUMAN	beta 1,3-galactosyltransferase-like	92					fucose metabolic process (GO:0006004)|protein glycosylation (GO:0006486)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	transferase activity, transferring glycosyl groups (GO:0016757)			breast(1)|cervix(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19		Lung SC(185;0.0257)		all cancers(112;0.00436)|Epithelial(112;0.0285)|OV - Ovarian serous cystadenocarcinoma(117;0.0512)|GBM - Glioblastoma multiforme(144;0.184)		TCTCAGGAGCTCCCCAGTGTC	0.363																																					p.L92P		Atlas-SNP	.											.	B3GALTL	48	.	0			c.T275C						.						132.0	113.0	119.0					13																	31821164		2203	4300	6503	SO:0001583	missense	145173	exon5			AGGAGCTCCCCAG	AB101481	CCDS9341.1	13q12.3	2014-03-24			ENSG00000187676	ENSG00000187676		"""Beta 3-glycosyltransferases"""	20207	protein-coding gene	gene with protein product		610308				12943678, 16899492, 17032646	Standard	NM_194318		Approved	B3GTL, B3Glc-T	uc010aaz.3	Q6Y288	OTTHUMG00000016688	ENST00000343307.4:c.275T>C	chr13.hg19:g.31821164T>C	ENSP00000343002:p.Leu92Pro	194.0	0.0		150.0	6.0	NM_194318	A8K5F8|Q5W0H2|Q6NUI3	Missense_Mutation	SNP	ENST00000343307.4	hg19	CCDS9341.1	.	.	.	.	.	.	.	.	.	.	T	2.161	-0.392174	0.04932	.	.	ENSG00000187676	ENST00000343307	T	0.72942	-0.7	5.61	-2.01	0.07410	.	0.459579	0.23293	N	0.049772	T	0.47985	0.1475	L	0.27053	0.805	0.25348	N	0.988896	B	0.11235	0.004	B	0.08055	0.003	T	0.20240	-1.0281	10	0.41790	T	0.15	-0.0451	3.9961	0.09559	0.1231:0.0693:0.3836:0.424	.	92	Q6Y288	B3GLT_HUMAN	P	92	ENSP00000343002:L92P	ENSP00000343002:L92P	L	+	2	0	B3GALTL	30719164	0.001000	0.12720	0.037000	0.18230	0.141000	0.21300	0.309000	0.19332	-0.541000	0.06257	0.377000	0.23210	CTC	.	.		0.363	B3GALTL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044396.3	NM_194318	
FRY	10129	hgsc.bcm.edu	37	13	32776158	32776158	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr13:32776158T>C	ENST00000380250.3	+	30	4323	c.3827T>C	c.(3826-3828)aTc>aCc	p.I1276T		NM_023037.2	NP_075463.2	Q5TBA9	FRY_HUMAN	furry homolog (Drosophila)	1276						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				NS(3)|breast(4)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(31)|lung(50)|ovary(5)|pancreas(1)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	132		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)		ATTTATGAAATCTCCATGCAG	0.378																																					p.I1276T		Atlas-SNP	.											.	FRY	312	.	0			c.T3827C						.						136.0	121.0	126.0					13																	32776158		1893	4115	6008	SO:0001583	missense	10129	exon30			ATGAAATCTCCAT	AL049784	CCDS41875.1	13q13.1	2008-02-05	2005-11-24	2005-11-24	ENSG00000073910	ENSG00000073910			20367	protein-coding gene	gene with protein product		614818	"""chromosome 13 open reading frame 14"""	C13orf14		14702039, 8812419	Standard	NM_023037		Approved	bA37E23.1, 13CDNA73, CG003	uc001utx.3	Q5TBA9	OTTHUMG00000016696	ENST00000380250.3:c.3827T>C	chr13.hg19:g.32776158T>C	ENSP00000369600:p.Ile1276Thr	142.0	0.0		112.0	5.0	NM_023037	Q9Y3N6	Missense_Mutation	SNP	ENST00000380250.3	hg19	CCDS41875.1	.	.	.	.	.	.	.	.	.	.	T	12.99	2.103089	0.37145	.	.	ENSG00000073910	ENST00000380250;ENST00000380257	T	0.62941	-0.01	5.77	5.77	0.91146	.	0.051843	0.85682	D	0.000000	T	0.57902	0.2085	N	0.25144	0.715	0.80722	D	1	B	0.23490	0.086	B	0.40410	0.328	T	0.54016	-0.8356	10	0.22109	T	0.4	.	16.0977	0.81139	0.0:0.0:0.0:1.0	.	1276	Q5TBA9	FRY_HUMAN	T	1276;115	ENSP00000369600:I1276T	ENSP00000369600:I1276T	I	+	2	0	FRY	31674158	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.954000	0.87848	2.216000	0.71823	0.528000	0.53228	ATC	.	.		0.378	FRY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044405.1	NM_023037	
BRCA2	675	hgsc.bcm.edu	37	13	32911166	32911166	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr13:32911166T>C	ENST00000380152.3	+	11	2907	c.2674T>C	c.(2674-2676)Ttc>Ctc	p.F892L	BRCA2_ENST00000544455.1_Missense_Mutation_p.F892L			P51587	BRCA2_HUMAN	breast cancer 2, early onset	892	Interaction with NPM1.				brain development (GO:0007420)|cell aging (GO:0007569)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|female gonad development (GO:0008585)|hemopoiesis (GO:0030097)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|inner cell mass cell proliferation (GO:0001833)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|male meiosis I (GO:0007141)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|nucleotide-excision repair (GO:0006289)|oocyte maturation (GO:0001556)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokinesis (GO:0032465)|replication fork protection (GO:0048478)|response to gamma radiation (GO:0010332)|response to UV-C (GO:0010225)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283)	BRCA2-MAGE-D1 complex (GO:0033593)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|secretory granule (GO:0030141)	gamma-tubulin binding (GO:0043015)|H3 histone acetyltransferase activity (GO:0010484)|H4 histone acetyltransferase activity (GO:0010485)|protease binding (GO:0002020)|single-stranded DNA binding (GO:0003697)			NS(3)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(32)|liver(1)|lung(41)|oesophagus(5)|ovary(22)|pancreas(4)|prostate(3)|salivary_gland(1)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	183		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		TAATTTTGTCTTCCAAGTAGC	0.318			"""D, Mis, N, F, S"""		"""breast, ovarian, pancreatic"""	"""breast, ovarian, pancreatic, leukemia  (FANCB, FANCD1)"""		Homologous recombination	Pancreatic Cancer, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Prostate Cancer;Hereditary Breast-Ovarian Cancer, BRCA2 type;Fanconi Anemia type D1, bi-allelic BRCA2 mutations;Fanconi Anemia	TCGA Ovarian(8;0.087)																											p.F892L	Esophageal Squamous(138;838 1285 7957 30353 30468 36915 49332)	Atlas-SNP	.	yes	Rec	yes	Hereditary breast/ovarian cancer	13	13q12	675	familial breast/ovarian cancer gene 2		"""L, E"""	.	BRCA2	812	.	0			c.T2674C						.						53.0	57.0	55.0					13																	32911166		2203	4297	6500	SO:0001583	missense	675	exon11	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;HPC; ;FANCD1;Pancytopenia Dysmelia, FA (several complementation groups)	TTTGTCTTCCAAG	U43746	CCDS9344.1	13q12-q13	2014-09-17	2003-10-14		ENSG00000139618	ENSG00000139618		"""Fanconi anemia, complementation groups"""	1101	protein-coding gene	gene with protein product	"""BRCA1/BRCA2-containing complex, subunit 2"""	600185	"""Fanconi anemia, complementation group D1"""	FANCD1, FACD, FANCD		8091231, 7581463, 15057823	Standard	NM_000059		Approved	FAD, FAD1, BRCC2	uc001uub.1	P51587	OTTHUMG00000017411	ENST00000380152.3:c.2674T>C	chr13.hg19:g.32911166T>C	ENSP00000369497:p.Phe892Leu	160.0	0.0		148.0	6.0	NM_000059	O00183|O15008|Q13879|Q5TBJ7	Missense_Mutation	SNP	ENST00000380152.3	hg19	CCDS9344.1	.	.	.	.	.	.	.	.	.	.	T	15.01	2.705580	0.48412	.	.	ENSG00000139618	ENST00000380152;ENST00000544455	T;T	0.59638	0.25;0.25	5.77	3.32	0.38043	.	0.610727	0.16404	N	0.215917	T	0.38241	0.1033	L	0.31578	0.945	0.09310	N	1	B	0.18461	0.028	B	0.13407	0.009	T	0.21930	-1.0231	10	0.15066	T	0.55	.	5.2141	0.15332	0.1567:0.0841:0.0:0.7592	.	892	P51587	BRCA2_HUMAN	L	892	ENSP00000369497:F892L;ENSP00000439902:F892L	ENSP00000369497:F892L	F	+	1	0	BRCA2	31809166	0.001000	0.12720	0.003000	0.11579	0.568000	0.35870	0.720000	0.25896	0.442000	0.26555	0.482000	0.46254	TTC	.	.		0.318	BRCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046000.2	NM_000059	
PDS5B	23047	hgsc.bcm.edu	37	13	33332689	33332689	+	Silent	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr13:33332689T>C	ENST00000315596.10	+	28	3393	c.3207T>C	c.(3205-3207)tgT>tgC	p.C1069C		NM_015032.3	NP_055847.1	Q9NTI5	PDS5B_HUMAN	PDS5, regulator of cohesion maintenance, homolog B (S. cerevisiae)	1069					cell proliferation (GO:0008283)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid cohesion (GO:0007064)|negative regulation of cell proliferation (GO:0008285)|regulation of cell proliferation (GO:0042127)	chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)			NS(2)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(14)|lung(14)|ovary(5)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)	62		Lung SC(185;0.0367)		all cancers(112;5.55e-06)|Epithelial(112;2.7e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00303)|BRCA - Breast invasive adenocarcinoma(63;0.0204)		ACACTGTGTGTGATGTTGCCA	0.368																																					p.C1069C		Atlas-SNP	.											.	PDS5B	141	.	0			c.T3207C						.						121.0	114.0	116.0					13																	33332689		1841	4091	5932	SO:0001819	synonymous_variant	23047	exon28			TGTGTGTGATGTT	AB023196	CCDS41878.1	13q12.3	2008-02-05	2007-07-18	2007-07-18	ENSG00000083642	ENSG00000083642			20418	protein-coding gene	gene with protein product		605333	"""androgen-induced proliferation inhibitor"""	APRIN		8812419, 10215036	Standard	NM_015032		Approved	AS3, KIAA0979, FLJ23236, CG008	uc010abf.3	Q9NTI5	OTTHUMG00000016704	ENST00000315596.10:c.3207T>C	chr13.hg19:g.33332689T>C		106.0	0.0		79.0	5.0	NM_015032	Q5R3S3|Q5W0K8|Q6NSC3|Q8IXT6|Q9H5N8|Q9Y2I5|Q9Y451	Silent	SNP	ENST00000315596.10	hg19	CCDS41878.1																																																																																			.	.		0.368	PDS5B-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044428.3	NM_015032	
COG6	57511	hgsc.bcm.edu	37	13	40251685	40251685	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr13:40251685T>C	ENST00000455146.3	+	5	559	c.509T>C	c.(508-510)cTc>cCc	p.L170P	COG6_ENST00000416691.1_Missense_Mutation_p.L170P	NM_020751.2	NP_065802.1	Q9Y2V7	COG6_HUMAN	component of oligomeric golgi complex 6	170					glycosylation (GO:0070085)|intra-Golgi vesicle-mediated transport (GO:0006891)|protein transport (GO:0015031)	Golgi transport complex (GO:0017119)|membrane (GO:0016020)				NS(1)|kidney(2)|large_intestine(5)|lung(4)|skin(1)	13		Lung NSC(96;0.000124)|Breast(139;0.0199)|Prostate(109;0.0233)|Lung SC(185;0.0367)		all cancers(112;6.03e-09)|Epithelial(112;7e-07)|OV - Ovarian serous cystadenocarcinoma(117;0.00015)|BRCA - Breast invasive adenocarcinoma(63;0.00438)|GBM - Glioblastoma multiforme(144;0.0168)		ATGAGTCTTCTCCGAGGTACA	0.358																																					p.L170P		Atlas-SNP	.											.	COG6	49	.	0			c.T509C						.						84.0	79.0	81.0					13																	40251685		2203	4300	6503	SO:0001583	missense	57511	exon5			GTCTTCTCCGAGG	AK026638	CCDS9370.1, CCDS45042.1	13q13.2	2011-08-01			ENSG00000133103	ENSG00000133103		"""Components of oligomeric golgi complex"""	18621	protein-coding gene	gene with protein product		606977				11980916	Standard	NM_020751		Approved	COD2, KIAA1134	uc001uxh.2	Q9Y2V7	OTTHUMG00000016768	ENST00000455146.3:c.509T>C	chr13.hg19:g.40251685T>C	ENSP00000397441:p.Leu170Pro	112.0	0.0		91.0	4.0	NM_001145079	Q5T0U1|Q6AI19|Q86V49|Q9ULT5	Missense_Mutation	SNP	ENST00000455146.3	hg19	CCDS9370.1	.	.	.	.	.	.	.	.	.	.	T	21.1	4.103478	0.76983	.	.	ENSG00000133103	ENST00000416691;ENST00000255468;ENST00000422759;ENST00000455146	T;T;T	0.77489	-1.1;-1.1;-1.1	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	D	0.89989	0.6875	M	0.89785	3.06	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.997;0.999	D	0.92007	0.5615	10	0.87932	D	0	-0.936	15.0173	0.71597	0.0:0.0:0.0:1.0	.	191;170	Q5T0U2;Q9Y2V7	.;COG6_HUMAN	P	170;201;170;170	ENSP00000403733:L170P;ENSP00000412877:L170P;ENSP00000397441:L170P	ENSP00000255468:L201P	L	+	2	0	COG6	39149685	1.000000	0.71417	1.000000	0.80357	0.850000	0.48378	6.973000	0.76116	2.131000	0.65755	0.477000	0.44152	CTC	.	.		0.358	COG6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044622.3		
EPSTI1	94240	hgsc.bcm.edu	37	13	43543237	43543237	+	Silent	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr13:43543237T>C	ENST00000398762.3	-	3	323	c.324A>G	c.(322-324)agA>agG	p.R108R	EPSTI1_ENST00000313624.7_Silent_p.R108R|EPSTI1_ENST00000313640.7_Silent_p.R108R|EPSTI1_ENST00000476830.2_5'UTR			Q96J88	ESIP1_HUMAN	epithelial stromal interaction 1 (breast)	108										endometrium(2)|kidney(1)|large_intestine(1)|lung(11)|ovary(1)|skin(1)	17		Lung NSC(96;3.6e-06)|Breast(139;0.00869)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)		GBM - Glioblastoma multiforme(144;0.000528)|BRCA - Breast invasive adenocarcinoma(63;0.0858)		TACCTAGCCGTCTGGGCACCA	0.557																																					p.R108R		Atlas-SNP	.											.	EPSTI1	47	.	0			c.A324G						.						94.0	74.0	81.0					13																	43543237		2203	4300	6503	SO:0001819	synonymous_variant	94240	exon3			TAGCCGTCTGGGC	AF396928	CCDS9387.1, CCDS31964.1	13q13.3	2011-06-27			ENSG00000133106	ENSG00000133106			16465	protein-coding gene	gene with protein product	"""epithelial stromal interaction protein 1"""	607441				11991720	Standard	NM_033255		Approved	BRESI1, MGC29634	uc001uyw.2	Q96J88	OTTHUMG00000016814	ENST00000398762.3:c.324A>G	chr13.hg19:g.43543237T>C		141.0	0.0		112.0	6.0	NM_001002264	Q8IVC7|Q8NDQ7	Silent	SNP	ENST00000398762.3	hg19	CCDS9387.1																																																																																			.	.		0.557	EPSTI1-010	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000400321.1	NM_001002264	
RNASEH2B	79621	hgsc.bcm.edu	37	13	51523618	51523618	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr13:51523618T>C	ENST00000336617.3	+	9	1117	c.718T>C	c.(718-720)Tca>Cca	p.S240P	RNASEH2B_ENST00000495244.2_3'UTR|RNASEH2B_ENST00000422660.1_Missense_Mutation_p.S240P	NM_024570.3	NP_078846.2	Q5TBB1	RNH2B_HUMAN	ribonuclease H2, subunit B	240					in utero embryonic development (GO:0001701)|negative regulation of gene expression (GO:0010629)|positive regulation of fibroblast proliferation (GO:0048146)|regulation of DNA damage checkpoint (GO:2000001)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|ribonucleotide metabolic process (GO:0009259)|RNA catabolic process (GO:0006401)	nucleus (GO:0005634)|ribonuclease H2 complex (GO:0032299)	RNA-DNA hybrid ribonuclease activity (GO:0004523)			endometrium(2)|liver(1)|lung(1)|upper_aerodigestive_tract(1)	5		Acute lymphoblastic leukemia(7;1.03e-07)|Breast(56;0.00122)|Lung NSC(96;0.00143)|Prostate(109;0.0047)|Hepatocellular(98;0.152)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;9e-08)		ACCTTCAGCCTCATTGCCAAA	0.368																																					p.S240P		Atlas-SNP	.											.	RNASEH2B	26	.	0			c.T718C						.						106.0	102.0	104.0					13																	51523618		2203	4300	6503	SO:0001583	missense	79621	exon9			TCAGCCTCATTGC	AK021774	CCDS9425.1, CCDS45047.1	13q14.3	2014-09-17	2006-08-17	2006-08-17	ENSG00000136104	ENSG00000136104			25671	protein-coding gene	gene with protein product		610326	"""deleted in lymphocytic leukemia 8"", ""Aicardi-Goutieres syndrome 2"""	DLEU8, AGS2		16845400	Standard	NM_001142279		Approved	FLJ11712	uc001vfa.4	Q5TBB1	OTTHUMG00000016937	ENST00000336617.3:c.718T>C	chr13.hg19:g.51523618T>C	ENSP00000337623:p.Ser240Pro	172.0	0.0		173.0	7.0	NM_024570	G3XAJ1|Q05DR2|Q6PK48|Q9HAF7	Missense_Mutation	SNP	ENST00000336617.3	hg19	CCDS9425.1	.	.	.	.	.	.	.	.	.	.	T	8.785	0.929084	0.18131	.	.	ENSG00000136104	ENST00000336617;ENST00000539292;ENST00000422660	D;D	0.96334	-3.94;-3.98	5.96	-4.27	0.03744	.	0.385674	0.31847	N	0.006980	D	0.84224	0.5425	N	0.01438	-0.865	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.12156	0.003;0.007	T	0.76621	-0.2892	10	0.32370	T	0.25	1.846	10.1642	0.42871	0.0:0.6098:0.1214:0.2687	.	240;240	G3XAJ1;Q5TBB1	.;RNH2B_HUMAN	P	240	ENSP00000337623:S240P;ENSP00000389877:S240P	ENSP00000337623:S240P	S	+	1	0	RNASEH2B	50421619	0.000000	0.05858	0.005000	0.12908	0.897000	0.52465	-0.060000	0.11712	-0.500000	0.06614	0.533000	0.62120	TCA	.	.		0.368	RNASEH2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045006.3	NM_024570	
UCHL3	7347	hgsc.bcm.edu	37	13	76143594	76143594	+	Splice_Site	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr13:76143594A>G	ENST00000377595.3	+	6	456		c.e6-1		RP11-29G8.3_ENST00000563635.1_RNA|UCHL3_ENST00000606347.1_3'UTR	NM_001270952.1|NM_006002.4	NP_001257881.1|NP_005993.1	P15374	UCHL3_HUMAN	ubiquitin carboxyl-terminal esterase L3 (ubiquitin thiolesterase)						protein catabolic process (GO:0030163)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	peptidase activity (GO:0008233)|ubiquitin binding (GO:0043130)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			kidney(1)|large_intestine(2)|lung(3)|skin(1)	7				GBM - Glioblastoma multiforme(99;0.0125)		TTCTTATTACAGGCCATCCGA	0.308																																					.		Atlas-SNP	.											.	UCHL3	9	.	0			c.319-2A>G						.						84.0	86.0	85.0					13																	76143594		2203	4300	6503	SO:0001630	splice_region_variant	7347	exon6			TATTACAGGCCAT	M30496	CCDS9453.1, CCDS73586.1	13q21.33	2008-02-05			ENSG00000118939	ENSG00000118939	3.2.1.15		12515	protein-coding gene	gene with protein product		603090				2530630	Standard	NM_001270952		Approved		uc001vjq.4	P15374	OTTHUMG00000017090	ENST00000377595.3:c.427-1A>G	chr13.hg19:g.76143594A>G		95.0	0.0		78.0	4.0	NM_001270952	B2R970|Q5TBK8|Q6IBE9	Splice_Site	SNP	ENST00000377595.3	hg19	CCDS9453.1	.	.	.	.	.	.	.	.	.	.	A	19.04	3.749064	0.69533	.	.	ENSG00000118939	ENST00000377595;ENST00000377589;ENST00000419068	.	.	.	5.03	5.03	0.67393	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.7714	0.69681	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	UCHL3	75041595	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.130000	0.89598	1.872000	0.54250	0.533000	0.62120	.	.	.		0.308	UCHL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045292.2	NM_006002	Intron
SCEL	8796	hgsc.bcm.edu	37	13	78216918	78216918	+	Silent	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr13:78216918T>C	ENST00000349847.3	+	32	2109	c.2025T>C	c.(2023-2025)tgT>tgC	p.C675C	SCEL_ENST00000377246.3_Silent_p.C655C|SCEL_ENST00000535157.1_Silent_p.C633C	NM_144777.2	NP_659001.2	O95171	SCEL_HUMAN	sciellin	675	LIM zinc-binding. {ECO:0000255|PROSITE- ProRule:PRU00125}.				embryo development (GO:0009790)|epidermis development (GO:0008544)|keratinocyte differentiation (GO:0030216)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(18)|ovary(5)|prostate(1)|stomach(1)|urinary_tract(1)	40		Acute lymphoblastic leukemia(28;0.0282)|Breast(118;0.037)		GBM - Glioblastoma multiforme(99;0.0233)		CAATACACTGTGAACCTTGCT	0.313																																					p.C675C		Atlas-SNP	.											.	SCEL	85	.	0			c.T2025C						.						106.0	106.0	106.0					13																	78216918		2203	4298	6501	SO:0001819	synonymous_variant	8796	exon32			ACACTGTGAACCT	AF045941	CCDS9458.1, CCDS9459.1, CCDS53877.1	13q22	2008-07-18			ENSG00000136155	ENSG00000136155			10573	protein-coding gene	gene with protein product		604112				9813070	Standard	NM_003843		Approved	FLJ21667, MGC22531	uc001vki.3	O95171	OTTHUMG00000017107	ENST00000349847.3:c.2025T>C	chr13.hg19:g.78216918T>C		171.0	0.0		118.0	5.0	NM_144777	B7Z797|F5H651|Q53H61|Q5W0S8|Q5W0S9|Q86X00	Silent	SNP	ENST00000349847.3	hg19	CCDS9459.1																																																																																			.	.		0.313	SCEL-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045339.2	NM_144777	
DCT	1638	hgsc.bcm.edu	37	13	95121142	95121142	+	Silent	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr13:95121142T>C	ENST00000377028.5	-	2	866	c.453A>G	c.(451-453)agA>agG	p.R151R	DCT_ENST00000446125.1_Silent_p.R151R|DCT_ENST00000490854.1_5'Flank	NM_001922.3	NP_001913.2	P40126	TYRP2_HUMAN	dopachrome tautomerase	151					cell development (GO:0048468)|developmental pigmentation (GO:0048066)|epidermis development (GO:0008544)|melanin biosynthetic process from tyrosine (GO:0006583)|positive regulation of neuroblast proliferation (GO:0002052)|ventricular zone neuroblast division (GO:0021847)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|melanosome (GO:0042470)	copper ion binding (GO:0005507)|dopachrome isomerase activity (GO:0004167)|oxidoreductase activity (GO:0016491)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(14)|liver(1)|lung(16)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	50	all_neural(89;0.0684)|Medulloblastoma(90;0.163)	all_cancers(2;3.71e-42)|all_epithelial(2;3.76e-31)|all_lung(2;5.16e-14)|Lung NSC(4;1.33e-13)|Breast(118;0.0013)|Hepatocellular(115;0.00886)|Renal(2;0.00988)		COAD - Colon adenocarcinoma(199;7.07e-05)|GBM - Glioblastoma multiforme(99;0.000472)		CGGGGTGTACTCTCTTCTTCG	0.532																																					p.R151R		Atlas-SNP	.											.	DCT	186	.	0			c.A453G						.						233.0	229.0	230.0					13																	95121142		2203	4300	6503	SO:0001819	synonymous_variant	1638	exon2			GTGTACTCTCTTC	D17547	CCDS9470.1, CCDS45060.1	13q32	2012-09-28	2012-09-28		ENSG00000080166	ENSG00000080166	5.3.3.12		2709	protein-coding gene	gene with protein product	"""dopachrome delta-isomerase"""	191275	"""tyrosine-related protein 2"""	TYRP2		8306979	Standard	NM_001922		Approved		uc010afh.3	P40126	OTTHUMG00000017206	ENST00000377028.5:c.453A>G	chr13.hg19:g.95121142T>C		180.0	0.0		131.0	6.0	NM_001129889	Q09GT4	Silent	SNP	ENST00000377028.5	hg19	CCDS9470.1																																																																																			.	.		0.532	DCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045461.3		
STK24	8428	hgsc.bcm.edu	37	13	99109511	99109511	+	Silent	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr13:99109511T>C	ENST00000376547.3	-	10	1351	c.1206A>G	c.(1204-1206)gaA>gaG	p.E402E	STK24_ENST00000539966.1_Silent_p.E371E|STK24_ENST00000397517.2_Silent_p.E390E	NM_003576.3	NP_003567.2	Q9Y6E0	STK24_HUMAN	serine/threonine kinase 24	402					apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|execution phase of apoptosis (GO:0097194)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|negative regulation of cell migration (GO:0030336)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of axon regeneration (GO:0048679)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(7)|ovary(1)|skin(1)	17	all_neural(89;0.0982)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.233)			CTCGCAGCTCTTCAATGGACC	0.587																																					p.E402E		Atlas-SNP	.											.	STK24	40	.	0			c.A1206G						.						59.0	54.0	56.0					13																	99109511		2203	4300	6503	SO:0001819	synonymous_variant	8428	exon10			CAGCTCTTCAATG	AF024636	CCDS9488.1, CCDS32001.1, CCDS66573.1	13q31.2-q32.3	2010-06-25	2010-06-25		ENSG00000102572	ENSG00000102572			11403	protein-coding gene	gene with protein product	"""STE20-like kinase 3"", ""sterile 20-like kinase 3"""	604984	"""serine/threonine kinase 24 (Ste20, yeast homolog)"""			9353338, 10644707	Standard	NM_003576		Approved	MST-3, MST3, MST3B, STK3, STE20	uc001vnn.1	Q9Y6E0	OTTHUMG00000017250	ENST00000376547.3:c.1206A>G	chr13.hg19:g.99109511T>C		87.0	0.0		65.0	4.0	NM_003576	O14840|Q5JV92	Silent	SNP	ENST00000376547.3	hg19	CCDS9488.1	.	.	.	.	.	.	.	.	.	.	T	6.789	0.514626	0.12944	.	.	ENSG00000102572	ENST00000444574	.	.	.	5.26	-8.27	0.01017	.	.	.	.	.	T	0.49847	0.1581	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.57254	-0.7843	4	.	.	.	.	9.798	0.40746	0.2148:0.5515:0.0:0.2337	.	.	.	.	G	308	.	.	R	-	1	2	STK24	97907512	0.000000	0.05858	0.802000	0.32245	0.536000	0.34869	-1.618000	0.02049	-1.416000	0.02019	0.533000	0.62120	AGA	.	.		0.587	STK24-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045549.2	NM_003576	
LIG4	3981	hgsc.bcm.edu	37	13	108862228	108862228	+	Missense_Mutation	SNP	G	G	T			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr13:108862228G>T	ENST00000356922.4	-	2	1661	c.1389C>A	c.(1387-1389)gaC>gaA	p.D463E	LIG4_ENST00000442234.1_Missense_Mutation_p.D463E|LIG4_ENST00000405925.1_Missense_Mutation_p.D463E	NM_002312.3|NM_206937.1	NP_002303.2|NP_996820.1	P49917	DNLI4_HUMAN	ligase IV, DNA, ATP-dependent	463					cell cycle (GO:0007049)|cell division (GO:0051301)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|chromosome organization (GO:0051276)|DNA biosynthetic process (GO:0071897)|DNA ligation (GO:0006266)|DNA ligation involved in DNA recombination (GO:0051102)|DNA ligation involved in DNA repair (GO:0051103)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via nonhomologous end joining (GO:0006303)|establishment of integrated proviral latency (GO:0075713)|in utero embryonic development (GO:0001701)|isotype switching (GO:0045190)|lagging strand elongation (GO:0006273)|negative regulation of neuron apoptotic process (GO:0043524)|neuron apoptotic process (GO:0051402)|nucleotide-excision repair, DNA gap filling (GO:0006297)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of neurogenesis (GO:0050769)|pro-B cell differentiation (GO:0002328)|response to gamma radiation (GO:0010332)|response to X-ray (GO:0010165)|single strand break repair (GO:0000012)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|T cell receptor V(D)J recombination (GO:0033153)|V(D)J recombination (GO:0033151)|viral process (GO:0016032)	condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|DNA ligase IV complex (GO:0032807)|DNA-dependent protein kinase-DNA ligase 4 complex (GO:0005958)|focal adhesion (GO:0005925)|nonhomologous end joining complex (GO:0070419)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA ligase (ATP) activity (GO:0003910)|DNA ligase activity (GO:0003909)|ligase activity (GO:0016874)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(9)|lung(22)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	42	all_lung(23;0.000238)|all_neural(89;0.00256)|Lung NSC(43;0.0056)|Medulloblastoma(90;0.00596)|Lung SC(71;0.104)					CAATTAAAATGTCCAATTCAT	0.433								Non-homologous end-joining																													p.D463E		Atlas-SNP	.											.	LIG4	91	.	0			c.C1389A						.						225.0	230.0	228.0					13																	108862228		2203	4300	6503	SO:0001583	missense	3981	exon3			TAAAATGTCCAAT	X83441	CCDS9508.1	13q33-q34	2014-09-17			ENSG00000174405	ENSG00000174405	6.5.1.1		6601	protein-coding gene	gene with protein product	"""polydeoxyribonucleotide synthase [ATP] 4"", ""polynucleotide ligase"", ""sealase"", ""DNA repair enzyme"", ""DNA joinase"""	601837				7760816	Standard	NM_001098268		Approved		uc001vqo.3	P49917	OTTHUMG00000017328	ENST00000356922.4:c.1389C>A	chr13.hg19:g.108862228G>T	ENSP00000349393:p.Asp463Glu	136.0	0.0		92.0	4.0	NM_206937	Q8IY66|Q8TEU5	Missense_Mutation	SNP	ENST00000356922.4	hg19	CCDS9508.1	.	.	.	.	.	.	.	.	.	.	G	15.81	2.944046	0.53079	.	.	ENSG00000174405	ENST00000405925;ENST00000442234;ENST00000356922	T;T;T	0.71817	-0.6;-0.6;-0.6	5.06	3.3	0.37823	Nucleic acid-binding, OB-fold-like (1);DNA ligase, ATP-dependent, central (1);Nucleic acid-binding, OB-fold (1);	0.000000	0.85682	D	0.000000	T	0.81607	0.4858	M	0.75085	2.285	0.58432	D	0.999998	D	0.89917	1.0	D	0.97110	1.0	T	0.82812	-0.0272	10	0.66056	D	0.02	.	10.9529	0.47341	0.2205:0.0:0.7795:0.0	.	463	P49917	DNLI4_HUMAN	E	463	ENSP00000385955:D463E;ENSP00000402030:D463E;ENSP00000349393:D463E	ENSP00000349393:D463E	D	-	3	2	LIG4	107660229	1.000000	0.71417	0.996000	0.52242	0.982000	0.71751	2.785000	0.47782	1.260000	0.44134	0.551000	0.68910	GAC	.	.		0.433	LIG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045738.4	NM_002312	
CHD8	57680	hgsc.bcm.edu	37	14	21865984	21865984	+	Silent	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr14:21865984T>C	ENST00000557364.1	-	27	5312	c.5049A>G	c.(5047-5049)gaA>gaG	p.E1683E	CHD8_ENST00000555962.1_5'UTR|SNORD8_ENST00000363915.1_RNA|CHD8_ENST00000430710.3_Silent_p.E1404E|CHD8_ENST00000399982.2_Silent_p.E1683E			Q9HCK8	CHD8_HUMAN	chromodomain helicase DNA binding protein 8	1683					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)		ATGCTTACCCTTCTACTATGT	0.398																																					p.E1683E		Atlas-SNP	.											.	CHD8	339	.	0			c.A5049G						.						84.0	78.0	80.0					14																	21865984		1890	4123	6013	SO:0001819	synonymous_variant	57680	exon26			TTACCCTTCTACT	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.5049A>G	chr14.hg19:g.21865984T>C		153.0	0.0		95.0	4.0	NM_001170629	Q4G0D8|Q68DQ0|Q6DKH9|Q6P440|Q6ZNL7|Q8N3Z9|Q8NCY4|Q8TBR9|Q96F26	Silent	SNP	ENST00000557364.1	hg19	CCDS53885.1																																																																																			.	.		0.398	CHD8-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410436.1	NM_020920	
MRPL52	122704	hgsc.bcm.edu	37	14	23302670	23302670	+	Silent	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr14:23302670A>G	ENST00000355151.5	+	4	231	c.201A>G	c.(199-201)aaA>aaG	p.K67K	MRPL52_ENST00000556840.1_Silent_p.K8K|MRPL52_ENST00000555345.1_Silent_p.K8K|MRPL52_ENST00000397496.3_Silent_p.K66K|MRPL52_ENST00000432849.3_Silent_p.K66K|MRPL52_ENST00000311892.6_Intron|MRPL52_ENST00000397505.2_Intron|MRPL52_ENST00000557221.1_Intron|MRPL52_ENST00000461594.1_3'UTR|MRPL52_ENST00000553711.1_Silent_p.K8K|MRPL52_ENST00000555536.1_Silent_p.K8K	NM_178336.2|NM_180982.2|NM_181306.2	NP_848026.1|NP_851313.1|NP_851823.1	Q86TS9	RM52_HUMAN	mitochondrial ribosomal protein L52	67					translation (GO:0006412)	mitochondrial large ribosomal subunit (GO:0005762)	structural constituent of ribosome (GO:0003735)					all_cancers(95;9.47e-05)			GBM - Glioblastoma multiforme(265;0.00551)		TTCGAAGAAAAGCTGAAAGGG	0.478																																					p.K67K		Atlas-SNP	.											.	MRPL52	7	.	0			c.A201G						.						108.0	90.0	96.0					14																	23302670		2203	4300	6503	SO:0001819	synonymous_variant	122704	exon4			AAGAAAAGCTGAA	AK000450	CCDS9575.1, CCDS9576.1, CCDS41917.1, CCDS41918.1	14q11.2	2012-09-13			ENSG00000172590	ENSG00000172590		"""Mitochondrial ribosomal proteins / large subunits"""	16655	protein-coding gene	gene with protein product		611856				11551941, 11943462	Standard	NM_178336		Approved		uc001wgw.4	Q86TS9	OTTHUMG00000028703	ENST00000355151.5:c.201A>G	chr14.hg19:g.23302670A>G		134.0	0.0		83.0	4.0	NM_178336	A6NMQ8|A8MXK5|A8MYI6|G3XCN9|Q6NVH8	Silent	SNP	ENST00000355151.5	hg19	CCDS41917.1																																																																																			.	.		0.478	MRPL52-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000071657.4	NM_180982	
FOXA1	3169	hgsc.bcm.edu	37	14	38061910	38061910	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr14:38061910A>G	ENST00000250448.2	-	2	140	c.79T>C	c.(79-81)Tcc>Ccc	p.S27P	FOXA1_ENST00000540786.1_5'UTR|FOXA1_ENST00000545425.2_5'UTR	NM_004496.3	NP_004487.2	P55317	FOXA1_HUMAN	forkhead box A1	27					anatomical structure formation involved in morphogenesis (GO:0048646)|chromatin remodeling (GO:0006338)|dorsal/ventral neural tube patterning (GO:0021904)|epithelial cell maturation involved in prostate gland development (GO:0060743)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|epithelial-mesenchymal signaling involved in prostate gland development (GO:0060738)|glucose homeostasis (GO:0042593)|hormone metabolic process (GO:0042445)|lung epithelial cell differentiation (GO:0060487)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron fate specification (GO:0048665)|positive regulation of cell-cell adhesion mediated by cadherin (GO:2000049)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prostate gland epithelium morphogenesis (GO:0060740)|prostate gland stromal morphogenesis (GO:0060741)|response to estradiol (GO:0032355)|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development (GO:0060528)	microvillus (GO:0005902)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|endometrium(1)|large_intestine(2)|lung(3)|prostate(12)	19	Breast(36;0.0954)|Esophageal squamous(585;0.164)|Hepatocellular(127;0.213)		Lung(238;5.41e-07)|LUAD - Lung adenocarcinoma(48;2.48e-05)|Epithelial(34;0.0454)|LUSC - Lung squamous cell carcinoma(13;0.0917)|all cancers(34;0.0925)|BRCA - Breast invasive adenocarcinoma(188;0.239)	GBM - Glioblastoma multiforme(112;0.0222)		GGGACGGAGGAGTAGGCCTGG	0.617																																					p.S27P		Atlas-SNP	.											.	FOXA1	56	.	0			c.T79C						.						123.0	107.0	112.0					14																	38061910		2203	4300	6503	SO:0001583	missense	3169	exon2			CGGAGGAGTAGGC	U39840	CCDS9665.1	14q12-q13	2008-04-10		2002-09-20	ENSG00000129514	ENSG00000129514		"""Forkhead boxes"""	5021	protein-coding gene	gene with protein product		602294	"""hepatocyte nuclear factor 3, alpha"""	HNF3A		9119385, 8652662	Standard	NM_004496		Approved		uc001wuf.4	P55317	OTTHUMG00000140253	ENST00000250448.2:c.79T>C	chr14.hg19:g.38061910A>G	ENSP00000250448:p.Ser27Pro	98.0	0.0		75.0	5.0	NM_004496	B2R9H6|B7ZAP5|Q9H2A0	Missense_Mutation	SNP	ENST00000250448.2	hg19	CCDS9665.1	.	.	.	.	.	.	.	.	.	.	A	15.23	2.771320	0.49680	.	.	ENSG00000129514	ENST00000250448	T	0.27890	1.64	4.15	2.99	0.34606	Fork-head N-terminal (1);	0.892392	0.09670	N	0.771264	T	0.33323	0.0859	M	0.64404	1.975	0.80722	D	1	B	0.10296	0.003	B	0.17722	0.019	T	0.09997	-1.0649	10	0.59425	D	0.04	.	9.747	0.40453	0.8453:0.0:0.0:0.1547	.	27	P55317	FOXA1_HUMAN	P	27	ENSP00000250448:S27P	ENSP00000250448:S27P	S	-	1	0	FOXA1	37131661	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	3.417000	0.52714	0.626000	0.30322	0.454000	0.30748	TCC	.	.		0.617	FOXA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276735.1		
ATL1	51062	hgsc.bcm.edu	37	14	51094799	51094799	+	Silent	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr14:51094799A>G	ENST00000358385.6	+	12	1411	c.1170A>G	c.(1168-1170)aaA>aaG	p.K390K	ATL1_ENST00000357032.3_Silent_p.K390K|ATL1_ENST00000441560.2_Silent_p.K390K|ATL1_ENST00000354525.4_Silent_p.K390K	NM_015915.4	NP_056999.2	Q8WXF7	ATLA1_HUMAN	atlastin GTPase 1	390					axonogenesis (GO:0007409)|cell death (GO:0008219)|endoplasmic reticulum organization (GO:0007029)|GTP catabolic process (GO:0006184)|protein homooligomerization (GO:0051260)	cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|Golgi cis cisterna (GO:0000137)|integral component of membrane (GO:0016021)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)			central_nervous_system(1)|cervix(2)|large_intestine(4)|liver(1)|lung(6)|ovary(1)|skin(3)	18						TGCAGACCAAACACCTGCAAC	0.453																																					p.K390K		Atlas-SNP	.											.	ATL1	46	.	0			c.A1170G						.						67.0	69.0	68.0					14																	51094799		2203	4300	6503	SO:0001819	synonymous_variant	51062	exon12			GACCAAACACCTG	AF131801	CCDS9700.1, CCDS32077.1	14q21.3	2014-09-17	2008-09-17	2008-09-17	ENSG00000198513	ENSG00000198513			11231	protein-coding gene	gene with protein product	"""atlastin"""	606439	"""spastic paraplegia 3A (autosomal dominant)"""	SPG3, SPG3A		8252041, 7825576	Standard	NM_015915		Approved	FSP1, AD-FSP	uc001wyd.4	Q8WXF7	OTTHUMG00000140297	ENST00000358385.6:c.1170A>G	chr14.hg19:g.51094799A>G		107.0	0.0		92.0	4.0	NM_015915	A6NND5|A8K2C0|G5E9T1|O95890|Q69YH7|Q96FK0	Silent	SNP	ENST00000358385.6	hg19	CCDS9700.1																																																																																			.	.		0.453	ATL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276884.2		
DLGAP5	9787	hgsc.bcm.edu	37	14	55647496	55647496	+	Splice_Site	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr14:55647496A>G	ENST00000247191.2	-	6	797	c.581T>C	c.(580-582)gTt>gCt	p.V194A	DLGAP5_ENST00000395425.2_Splice_Site_p.V194A	NM_014750.4	NP_055565.3	Q15398	DLGP5_HUMAN	discs, large (Drosophila) homolog-associated protein 5	194					cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|dephosphorylation (GO:0016311)|mitotic chromosome movement towards spindle pole (GO:0007079)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)	cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)|spindle pole centrosome (GO:0031616)	phosphoprotein phosphatase activity (GO:0004721)			biliary_tract(1)|breast(2)|cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	44						AGGCTGCACAACTGTGGGAAA	0.453																																					p.V194A		Atlas-SNP	.											.	DLGAP5	84	.	0			c.T581C						.						132.0	121.0	124.0					14																	55647496		2203	4300	6503	SO:0001630	splice_region_variant	9787	exon6			TGCACAACTGTGG	D13633	CCDS9723.1, CCDS53897.1	14q22.3	2008-05-30	2008-05-30	2008-05-30	ENSG00000126787	ENSG00000126787			16864	protein-coding gene	gene with protein product			"""discs, large homolog 7 (Drosophila)"""	DLG7		7584026, 7584028	Standard	NM_014750		Approved	KIAA0008, DLG1, HURP	uc001xbs.3	Q15398	OTTHUMG00000140310	ENST00000247191.2:c.581-1T>C	chr14.hg19:g.55647496A>G		172.0	0.0		124.0	49.0	NM_014750	A8MTM6|B4DRM8|Q86T11|Q8NG58	Missense_Mutation	SNP	ENST00000247191.2	hg19	CCDS9723.1	.	.	.	.	.	.	.	.	.	.	A	2.792	-0.251016	0.05867	.	.	ENSG00000126787	ENST00000395425;ENST00000247191;ENST00000557645	T;T;T	0.19806	2.12;2.12;2.12	5.03	1.91	0.25777	.	1.660750	0.03176	N	0.171367	T	0.12092	0.0294	N	0.17082	0.46	0.23966	N	0.996324	B;B	0.19200	0.007;0.034	B;B	0.15052	0.006;0.012	T	0.24261	-1.0165	10	0.07325	T	0.83	.	5.2921	0.15733	0.6005:0.0:0.3994:0.0	.	194;194	A8MTM6;Q15398	.;DLGP5_HUMAN	A	194	ENSP00000378815:V194A;ENSP00000247191:V194A;ENSP00000451747:V194A	ENSP00000247191:V194A	V	-	2	0	DLGAP5	54717249	0.004000	0.15560	0.083000	0.20561	0.004000	0.04260	-0.405000	0.07196	0.139000	0.18822	0.533000	0.62120	GTT	.	.		0.453	DLGAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276908.2	NM_014750	Missense_Mutation
PCNXL4	64430	hgsc.bcm.edu	37	14	60581571	60581571	+	Silent	SNP	A	A	G	rs369124921		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr14:60581571A>G	ENST00000406854.1	+	3	1397	c.843A>G	c.(841-843)ggA>ggG	p.G281G	PCNXL4_ENST00000406949.1_Silent_p.G47G|PCNXL4_ENST00000404681.2_Silent_p.G281G|PCNXL4_ENST00000317623.4_Silent_p.G47G			Q63HM2	PCX4_HUMAN	pecanex-like 4 (Drosophila)	281						integral component of membrane (GO:0016021)											TCGGCCTTGGAGGCTCATCTA	0.368																																					p.G47G		Atlas-SNP	.											.	.	.	.	0			c.A141G						.	A		1,3657		0,1,1828	142.0	136.0	138.0		141	2.7	1.0	14		138	0,8148		0,0,4074	no	coding-synonymous	C14orf135	NM_022495.5		0,1,5902	GG,GA,AA		0.0,0.0273,0.0085		47/939	60581571	1,11805	1829	4074	5903	SO:0001819	synonymous_variant	64430	exon2			CCTTGGAGGCTCA	AK022861		14q23.1	2012-07-18	2012-07-18	2012-07-18	ENSG00000126773	ENSG00000126773			20349	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 135"""	C14orf135			Standard	NM_022495		Approved		uc001xer.4	Q63HM2	OTTHUMG00000150361	ENST00000406854.1:c.843A>G	chr14.hg19:g.60581571A>G		112.0	0.0		95.0	5.0	NM_022495	A8MXM2|Q9BQG8|Q9H9F2	Silent	SNP	ENST00000406854.1	hg19																																																																																				.	.		0.368	PCNXL4-005	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000317847.1	NM_022495	
NUMB	8650	hgsc.bcm.edu	37	14	73822379	73822379	+	Silent	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr14:73822379T>C	ENST00000355058.3	-	4	359	c.81A>G	c.(79-81)acA>acG	p.T27T	NUMB_ENST00000555238.1_Silent_p.T27T|NUMB_ENST00000544991.3_Silent_p.T27T|NUMB_ENST00000557597.1_Silent_p.T27T|NUMB_ENST00000554546.1_Silent_p.T27T|NUMB_ENST00000359560.3_Silent_p.T27T|NUMB_ENST00000555738.2_Silent_p.T27T|NUMB_ENST00000559312.1_Silent_p.T27T|NUMB_ENST00000560335.1_Silent_p.T27T|NUMB_ENST00000535282.1_Silent_p.T27T|NUMB_ENST00000454166.4_Silent_p.T27T|NUMB_ENST00000356296.4_Silent_p.T27T|NUMB_ENST00000555394.1_Silent_p.T27T|NUMB_ENST00000554521.2_Silent_p.T27T			P49757	NUMB_HUMAN	numb homolog (Drosophila)	27					adherens junction organization (GO:0034332)|axon guidance (GO:0007411)|lateral ventricle development (GO:0021670)|lung epithelial cell differentiation (GO:0060487)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of protein localization to plasma membrane (GO:1903077)|neuroblast division in subventricular zone (GO:0021849)|Notch signaling pathway (GO:0007219)|positive regulation of cell migration (GO:0030335)|positive regulation of neurogenesis (GO:0050769)|positive regulation of polarized epithelial cell differentiation (GO:0030862)	apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|clathrin-coated vesicle (GO:0030136)|early endosome (GO:0005769)|extrinsic component of plasma membrane (GO:0019897)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(3)|prostate(1)|skin(3)|urinary_tract(1)	28				BRCA - Breast invasive adenocarcinoma(234;0.00471)|OV - Ovarian serous cystadenocarcinoma(108;0.161)		CTTCTTCATCTGTCTGCCACT	0.413																																					p.T27T		Atlas-SNP	.											.	NUMB	56	.	0			c.A81G						.						112.0	106.0	108.0					14																	73822379		2203	4300	6503	SO:0001819	synonymous_variant	8650	exon4			TTCATCTGTCTGC	L40393	CCDS9814.1, CCDS32115.1, CCDS32116.1, CCDS55927.1	14q24.3	2011-11-25	2001-11-28			ENSG00000133961			8060	protein-coding gene	gene with protein product		603728	"""numb (Drosophila) homolog"", ""chromosome 14 open reading frame 41"""	C14orf41			Standard	NM_003744		Approved		uc001xny.1	P49757		ENST00000355058.3:c.81A>G	chr14.hg19:g.73822379T>C		128.0	0.0		99.0	4.0	NM_003744	B1P2N5|B1P2N6|B1P2N7|B1P2N8|B1P2N9|B4E2B1|Q6NUQ7|Q86SY1|Q8WW73|Q9UBG1|Q9UEQ4|Q9UKE8|Q9UKE9|Q9UKF0|Q9UQJ4	Silent	SNP	ENST00000355058.3	hg19	CCDS32116.1																																																																																			.	.		0.413	NUMB-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000414416.1		
ACOT4	122970	hgsc.bcm.edu	37	14	74058947	74058947	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr14:74058947A>G	ENST00000326303.4	+	1	538	c.284A>G	c.(283-285)aAg>aGg	p.K95R		NM_152331.3	NP_689544.3	Q8N9L9	ACOT4_HUMAN	acyl-CoA thioesterase 4	95					acyl-CoA metabolic process (GO:0006637)|dicarboxylic acid catabolic process (GO:0043649)|dicarboxylic acid metabolic process (GO:0043648)|long-chain fatty acid metabolic process (GO:0001676)|saturated monocarboxylic acid metabolic process (GO:0032788)|short-chain fatty acid metabolic process (GO:0046459)|succinyl-CoA metabolic process (GO:0006104)|unsaturated monocarboxylic acid metabolic process (GO:0032789)|very long-chain fatty acid metabolic process (GO:0000038)	peroxisome (GO:0005777)	acyl-CoA hydrolase activity (GO:0047617)|carboxylic ester hydrolase activity (GO:0052689)|palmitoyl-CoA hydrolase activity (GO:0016290)|receptor binding (GO:0005102)|succinyl-CoA hydrolase activity (GO:0004778)			endometrium(1)|large_intestine(3)|lung(4)	8				BRCA - Breast invasive adenocarcinoma(234;0.00331)		CGCTTCCTGAAGCGGGACGTA	0.682																																					p.K95R		Atlas-SNP	.											.	ACOT4	25	.	0			c.A284G						.						26.0	27.0	27.0					14																	74058947		2155	4145	6300	SO:0001583	missense	122970	exon1			TCCTGAAGCGGGA	BC031799	CCDS9817.1	14q24.1	2011-02-16			ENSG00000177465	ENSG00000177465		"""Acyl CoA thioesterases"""	19748	protein-coding gene	gene with protein product		614314				16103133, 16940157	Standard	NM_152331		Approved	FLJ31235, PTE-Ib, PTE2B	uc001xoo.3	Q8N9L9	OTTHUMG00000169485	ENST00000326303.4:c.284A>G	chr14.hg19:g.74058947A>G	ENSP00000323071:p.Lys95Arg	143.0	0.0		85.0	4.0	NM_152331	Q17RF4|Q5BKT6|Q86TX0|Q86TX1|Q96N88	Missense_Mutation	SNP	ENST00000326303.4	hg19	CCDS9817.1	.	.	.	.	.	.	.	.	.	.	A	17.83	3.486010	0.63962	.	.	ENSG00000177465	ENST00000326303	T	0.42513	0.97	4.93	4.93	0.64822	Acyl-CoA thioester hydrolase/bile acid-CoA amino acid N-acetyltransferase (1);	0.182827	0.48286	D	0.000196	T	0.67515	0.2901	M	0.88450	2.955	0.37348	D	0.910666	D	0.67145	0.996	D	0.72625	0.978	T	0.76913	-0.2783	10	0.56958	D	0.05	-7.8835	12.0859	0.53698	0.8568:0.1432:0.0:0.0	.	95	Q8N9L9	ACOT4_HUMAN	R	95	ENSP00000323071:K95R	ENSP00000323071:K95R	K	+	2	0	ACOT4	73128700	1.000000	0.71417	0.998000	0.56505	0.510000	0.34073	4.494000	0.60347	1.974000	0.57490	0.379000	0.24179	AAG	.	.		0.682	ACOT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404298.2	NM_152331	
DNAL1	83544	hgsc.bcm.edu	37	14	74156191	74156191	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr14:74156191A>G	ENST00000553645.2	+	7	546	c.505A>G	c.(505-507)Aga>Gga	p.R169G	DNAL1_ENST00000554871.1_Missense_Mutation_p.R130G|DNAL1_ENST00000554339.1_Missense_Mutation_p.R82G|DNAL1_ENST00000311089.3_Missense_Mutation_p.R56G|DNAL1_ENST00000540526.1_Missense_Mutation_p.R130G	NM_031427.3	NP_113615.2	Q4LDG9	DNAL1_HUMAN	dynein, axonemal, light chain 1	169	LRRCT.									kidney(1)|lung(2)	3				BRCA - Breast invasive adenocarcinoma(234;0.00384)|KIRC - Kidney renal clear cell carcinoma(182;0.095)		AGCAACCAAGAGAGTGCCCAA	0.448																																					p.R169G		Atlas-SNP	.											.	DNAL1	16	.	0			c.A505G						.						88.0	88.0	88.0					14																	74156191		1916	4123	6039	SO:0001583	missense	83544	exon7			ACCAAGAGAGTGC	BC005343	CCDS45134.1, CCDS55928.1	14q24.3	2012-05-03	2006-09-04	2006-09-04	ENSG00000119661	ENSG00000119661			23247	protein-coding gene	gene with protein product		610062	"""chromosome 14 open reading frame 168"""	C14orf168		15845866	Standard	NM_031427		Approved	MGC12435, 1700010H15RiK, CILD16	uc001xoq.4	Q4LDG9		ENST00000553645.2:c.505A>G	chr14.hg19:g.74156191A>G	ENSP00000452037:p.Arg169Gly	235.0	0.0		142.0	6.0	NM_031427	B2RD38|Q5JPB7|Q9BS43	Missense_Mutation	SNP	ENST00000553645.2	hg19	CCDS45134.1	.	.	.	.	.	.	.	.	.	.	A	24.8	4.573670	0.86542	.	.	ENSG00000119661	ENST00000554113;ENST00000555631;ENST00000553645;ENST00000311089;ENST00000554339;ENST00000554871;ENST00000540526	T;T;T;T;T;T	0.79033	-1.23;1.81;1.81;1.81;1.81;1.81	5.68	4.58	0.56647	.	0.000000	0.85682	D	0.000000	T	0.82235	0.4993	M	0.86343	2.81	0.80722	D	1	P	0.42123	0.771	P	0.45829	0.494	D	0.84042	0.0365	10	0.49607	T	0.09	-21.5477	10.8526	0.46780	0.6015:0.3985:0.0:0.0	.	169	Q4LDG9	DNAL1_HUMAN	G	56;56;169;56;82;130;130	ENSP00000452368:R56G;ENSP00000452037:R169G;ENSP00000310360:R56G;ENSP00000450744:R82G;ENSP00000451834:R130G;ENSP00000439695:R130G	ENSP00000310360:R169G	R	+	1	2	DNAL1	73225944	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.491000	0.66887	2.155000	0.67459	0.460000	0.39030	AGA	.	.		0.448	DNAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414565.2	NM_031427	
COQ6	51004	hgsc.bcm.edu	37	14	74422603	74422603	+	Silent	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr14:74422603T>C	ENST00000334571.2	+	4	493	c.453T>C	c.(451-453)gcT>gcC	p.A151A	COQ6_ENST00000554920.1_Silent_p.A151A|COQ6_ENST00000238709.4_Silent_p.A76A|COQ6_ENST00000394026.4_Silent_p.A126A|COQ6_ENST00000555552.1_3'UTR	NM_182476.2	NP_872282.1	Q9Y2Z9	COQ6_HUMAN	coenzyme Q6 monooxygenase	151					small molecule metabolic process (GO:0044281)|ubiquinone biosynthetic process (GO:0006744)	cell projection (GO:0042995)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)	flavin adenine dinucleotide binding (GO:0050660)|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)			breast(1)|endometrium(6)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	16				BRCA - Breast invasive adenocarcinoma(234;0.00337)		TCATGCATGCTCTCACTAAGC	0.478																																					p.A151A		Atlas-SNP	.											.	COQ6	27	.	0			c.T453C						.						169.0	158.0	161.0					14																	74422603		2203	4300	6503	SO:0001819	synonymous_variant	51004	exon4			GCATGCTCTCACT	AF132944	CCDS9823.1, CCDS9824.1, CCDS9824.2	14q24.1	2013-05-01	2013-05-01		ENSG00000119723	ENSG00000119723			20233	protein-coding gene	gene with protein product		614647	"""coenzyme Q6 homolog (yeast)"", ""coenzyme Q6 homolog, monooxygenase (yeast)"", ""coenzyme Q6 homolog, monooxygenase (S. cerevisiae)"""			21540551	Standard	NM_182476		Approved	CGI-10	uc001xph.3	Q9Y2Z9	OTTHUMG00000171260	ENST00000334571.2:c.453T>C	chr14.hg19:g.74422603T>C		166.0	0.0		118.0	5.0	NM_182476	B7Z3K8|Q53GG6|Q86U30|Q96CA1|Q96CK2	Silent	SNP	ENST00000334571.2	hg19	CCDS9823.1																																																																																			.	.		0.478	COQ6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412616.1		
AHSA1	10598	hgsc.bcm.edu	37	14	77935521	77935521	+	Silent	SNP	C	C	A			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr14:77935521C>A	ENST00000216479.3	+	9	1106	c.946C>A	c.(946-948)Cga>Aga	p.R316R	AHSA1_ENST00000555457.1_3'UTR|SNORA46_ENST00000391069.1_RNA	NM_012111.2	NP_036243.1	O95433	AHSA1_HUMAN	AHA1, activator of heat shock 90kDa protein ATPase homolog 1 (yeast)	316					positive regulation of ATPase activity (GO:0032781)|response to stress (GO:0006950)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)	ATPase activator activity (GO:0001671)|chaperone binding (GO:0051087)			endometrium(1)|kidney(3)|large_intestine(1)|prostate(1)|skin(1)|stomach(1)	8			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0281)		AGAGCGGACGCGACAGGGCTG	0.572																																					p.R316R		Atlas-SNP	.											AHSA1,NS,carcinoma,0,1	AHSA1	24	.	0			c.C946A						.						170.0	159.0	162.0					14																	77935521		2203	4300	6503	SO:0001819	synonymous_variant	10598	exon9			CGGACGCGACAGG	AJ243310	CCDS9863.1	14q	2008-02-05	2003-04-04	2003-04-11		ENSG00000100591			1189	protein-coding gene	gene with protein product		608466	"""chromosome 14 open reading frame 3"""	C14orf3			Standard	NM_012111		Approved	p38	uc001xtw.3	O95433		ENST00000216479.3:c.946C>A	chr14.hg19:g.77935521C>A		292.0	0.0		159.0	0.0	NM_012111	B2R9L2|B4DUR9|Q96IL6|Q9P060	Silent	SNP	ENST00000216479.3	hg19	CCDS9863.1	.	.	.	.	.	.	.	.	.	.	C	6.398	0.441552	0.12164	.	.	ENSG00000100591	ENST00000555729	.	.	.	5.46	2.44	0.29823	.	.	.	.	.	T	0.33059	0.0850	.	.	.	0.09310	N	0.999992	.	.	.	.	.	.	T	0.19679	-1.0298	4	.	.	.	-4.2088	7.4374	0.27164	0.5001:0.4161:0.0:0.0837	.	.	.	.	E	110	.	.	A	+	2	0	AHSA1	77005274	0.801000	0.28930	0.972000	0.41901	0.782000	0.44232	1.616000	0.36933	0.865000	0.35603	-0.229000	0.12294	GCG	.	.		0.572	AHSA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414017.1	NM_012111	
TDP1	55775	hgsc.bcm.edu	37	14	90499504	90499504	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr14:90499504A>G	ENST00000335725.4	+	16	1949	c.1699A>G	c.(1699-1701)Atg>Gtg	p.M567V	TDP1_ENST00000393452.3_Missense_Mutation_p.N582S|TDP1_ENST00000357382.3_Missense_Mutation_p.M328V|TDP1_ENST00000393454.2_Missense_Mutation_p.M567V|TDP1_ENST00000555880.1_Intron	NM_018319.3	NP_060789.2	Q9NUW8	TYDP1_HUMAN	tyrosyl-DNA phosphodiesterase 1	567					cell death (GO:0008219)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|single strand break repair (GO:0000012)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	3'-tyrosyl-DNA phosphodiesterase activity (GO:0017005)|double-stranded DNA binding (GO:0003690)|exonuclease activity (GO:0004527)|single-stranded DNA binding (GO:0003697)			NS(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|ovary(3)|prostate(1)|urinary_tract(1)	25		all_cancers(154;0.185)		COAD - Colon adenocarcinoma(157;0.23)		CCAGGAGCCAATGGCCACCTT	0.463								Repair of DNA-protein crosslinks																													p.M567V		Atlas-SNP	.											.	TDP1	47	.	0			c.A1699G						.						60.0	57.0	58.0					14																	90499504		2203	4300	6503	SO:0001583	missense	55775	exon16			GAGCCAATGGCCA	AF182002	CCDS9888.1	14q32.11	2008-08-11				ENSG00000042088			18884	protein-coding gene	gene with protein product		607198				11839309, 12244316	Standard	XM_005267847		Approved	FLJ11090, SCAN1	uc001xxz.3	Q9NUW8		ENST00000335725.4:c.1699A>G	chr14.hg19:g.90499504A>G	ENSP00000337353:p.Met567Val	163.0	0.0		94.0	5.0	NM_018319	Q2HXX4|Q86TV8|Q96BK7|Q9NZM7|Q9NZM8	Missense_Mutation	SNP	ENST00000335725.4	hg19	CCDS9888.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	0.010|0.010	-1.793611|-1.793611	0.00623|0.00623	.|.	.|.	ENSG00000042088|ENSG00000042088	ENST00000393454;ENST00000335725;ENST00000357382|ENST00000393452;ENST00000556063	T;T;T|T	0.39787|0.29917	1.06;1.06;1.06|1.55	5.68|5.68	-4.14|-4.14	0.03892|0.03892	.|.	1.929260|.	0.01799|.	N|.	0.032794|.	T|T	0.08935|0.08935	0.0221|0.0221	N|N	0.00677|0.00677	-1.265|-1.265	0.09310|0.09310	N|N	1|1	B;B;B|B	0.02656|0.02656	0.0;0.0;0.0|0.0	B;B;B|B	0.01281|0.01281	0.0;0.0;0.0|0.0	T|T	0.35400|0.35400	-0.9790|-0.9790	10|9	0.18710|0.54805	T|T	0.47|0.06	-34.4799|-34.4799	9.2837|9.2837	0.37744|0.37744	0.205:0.1235:0.6715:0.0|0.205:0.1235:0.6715:0.0	.|.	567;328;567|582	B2RDI0;Q86TV8;Q9NUW8|E7EPD8	.;.;TYDP1_HUMAN|.	V|S	567;567;328|582;207	ENSP00000377099:M567V;ENSP00000337353:M567V;ENSP00000349952:M328V|ENSP00000377098:N582S	ENSP00000337353:M567V|ENSP00000377098:N582S	M|N	+|+	1|2	0|0	TDP1|TDP1	89569257|89569257	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.122000|0.122000	0.20287|0.20287	-0.699000|-0.699000	0.05087|0.05087	-1.222000|-1.222000	0.02587|0.02587	0.477000|0.477000	0.44152|0.44152	ATG|AAT	.	.		0.463	TDP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411239.1	NM_018319	
SERPINA3	12	hgsc.bcm.edu	37	14	95081176	95081176	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr14:95081176T>C	ENST00000467132.1	+	2	1546	c.398T>C	c.(397-399)cTg>cCg	p.L133P	RP11-986E7.7_ENST00000553947.1_3'UTR|SERPINA3_ENST00000393080.4_Missense_Mutation_p.L133P|SERPINA3_ENST00000482740.1_5'Flank|SERPINA3_ENST00000393078.3_Missense_Mutation_p.L133P			P01011	AACT_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 3	133					acute-phase response (GO:0006953)|inflammatory response (GO:0006954)|maintenance of gastrointestinal epithelium (GO:0030277)|negative regulation of endopeptidase activity (GO:0010951)|regulation of lipid metabolic process (GO:0019216)|regulation of proteolysis (GO:0030162)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleus (GO:0005634)	DNA binding (GO:0003677)|serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(6)|lung(17)|ovary(2)|pancreas(1)|skin(3)|stomach(1)	40		all_cancers(154;0.0525)|all_epithelial(191;0.179)		COAD - Colon adenocarcinoma(157;0.212)|Epithelial(152;0.228)		AGCGATGAGCTGCAGCTGAGT	0.537																																					p.L133P		Atlas-SNP	.											.	SERPINA3	78	.	0			c.T398C						.						64.0	59.0	61.0					14																	95081176		2203	4300	6503	SO:0001583	missense	12	exon2			ATGAGCTGCAGCT	K01500	CCDS32150.1	14q32.1	2014-06-03	2005-08-18		ENSG00000196136	ENSG00000196136		"""Serine (or cysteine) peptidase inhibitors"""	16	protein-coding gene	gene with protein product		107280	"""alpha-1-antichymotrypsin"", ""serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 3"""	AACT		3260956, 24172014	Standard	NM_001085		Approved	ACT, alpha-1-antichymotrypsin	uc001ydp.3	P01011	OTTHUMG00000029851	ENST00000467132.1:c.398T>C	chr14.hg19:g.95081176T>C	ENSP00000450540:p.Leu133Pro	159.0	0.0		96.0	4.0	NM_001085	B3KVQ7|Q13703|Q2TU87|Q2TU88|Q59GP9|Q6LBY8|Q6LDT7|Q6NSC9|Q8N177|Q96DW8|Q9UC47|Q9UNU9	Missense_Mutation	SNP	ENST00000467132.1	hg19	CCDS32150.1	.	.	.	.	.	.	.	.	.	.	T	12.51	1.960668	0.34565	.	.	ENSG00000196136	ENST00000553947;ENST00000393078;ENST00000393080;ENST00000555820;ENST00000467132	D;D;D;D	0.88354	-2.37;-2.37;-2.37;-2.37	5.13	3.97	0.46021	Serpin domain (3);	0.704300	0.12614	N	0.453649	D	0.91536	0.7327	L	0.58510	1.815	0.36505	D	0.86921	P;P	0.49862	0.929;0.683	P;B	0.58210	0.835;0.244	D	0.90756	0.4661	10	0.66056	D	0.02	.	10.8196	0.46597	0.1418:0.0:0.0:0.8582	.	133;158	P01011;G3V5I3	AACT_HUMAN;.	P	158;133;133;133;133	ENSP00000452367:L158P;ENSP00000376793:L133P;ENSP00000376795:L133P;ENSP00000450540:L133P	ENSP00000376793:L133P	L	+	2	0	SERPINA3	94150929	0.017000	0.18338	0.090000	0.20809	0.008000	0.06430	2.137000	0.42130	0.868000	0.35678	0.459000	0.35465	CTG	.	.		0.537	SERPINA3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268080.3	NM_001085	
AK7	122481	hgsc.bcm.edu	37	14	96944888	96944888	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr14:96944888T>C	ENST00000267584.4	+	15	1686	c.1642T>C	c.(1642-1644)Tac>Cac	p.Y548H		NM_152327.3	NP_689540.2	Q96M32	KAD7_HUMAN	adenylate kinase 7	548	Adenylate kinase.				axoneme assembly (GO:0035082)|brain development (GO:0007420)|epithelial cilium movement (GO:0003351)|inflammatory response to antigenic stimulus (GO:0002437)|nucleoside diphosphate phosphorylation (GO:0006165)|nucleoside triphosphate biosynthetic process (GO:0009142)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	adenylate kinase activity (GO:0004017)|ATP binding (GO:0005524)|cytidylate kinase activity (GO:0004127)|nucleoside diphosphate kinase activity (GO:0004550)			breast(2)|cervix(2)|endometrium(3)|large_intestine(8)|lung(11)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	31		all_cancers(154;0.0482)|all_epithelial(191;0.128)|Melanoma(154;0.155)		Epithelial(152;0.134)|COAD - Colon adenocarcinoma(157;0.228)		GGGGACCCACTACAGCCAAGA	0.502																																					p.Y548H		Atlas-SNP	.											.	AK7	69	.	0			c.T1642C						.						105.0	96.0	99.0					14																	96944888		2203	4300	6503	SO:0001583	missense	122481	exon15			ACCCACTACAGCC	AK057426	CCDS9945.1	14q32.31	2012-08-15			ENSG00000140057	ENSG00000140057		"""Adenylate kinases"""	20091	protein-coding gene	gene with protein product		615364					Standard	NM_152327		Approved	FLJ32864	uc001yfn.3	Q96M32	OTTHUMG00000171421	ENST00000267584.4:c.1642T>C	chr14.hg19:g.96944888T>C	ENSP00000267584:p.Tyr548His	227.0	0.0		148.0	6.0	NM_152327	Q8IYP6	Missense_Mutation	SNP	ENST00000267584.4	hg19	CCDS9945.1	.	.	.	.	.	.	.	.	.	.	T	17.18	3.324697	0.60634	.	.	ENSG00000140057	ENST00000267584	D	0.94687	-3.49	5.05	5.05	0.67936	.	0.112267	0.64402	D	0.000006	D	0.96962	0.9008	M	0.83384	2.64	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.96289	0.9212	10	0.25751	T	0.34	-21.7565	14.7748	0.69724	0.0:0.0:0.0:1.0	.	548	Q96M32	KAD7_HUMAN	H	548	ENSP00000267584:Y548H	ENSP00000267584:Y548H	Y	+	1	0	AK7	96014641	1.000000	0.71417	1.000000	0.80357	0.337000	0.28794	7.714000	0.84703	1.896000	0.54893	0.402000	0.26972	TAC	.	.		0.502	AK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413340.1		
EML1	2009	hgsc.bcm.edu	37	14	100375708	100375708	+	Silent	SNP	G	G	T			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr14:100375708G>T	ENST00000262233.6	+	11	1270	c.1131G>T	c.(1129-1131)gcG>gcT	p.A377A	EML1_ENST00000334192.4_Silent_p.A396A|EML1_ENST00000327921.9_Silent_p.A365A	NM_004434.2	NP_004425.2	O00423	EMAL1_HUMAN	echinoderm microtubule associated protein like 1	377	Tandem atypical propeller in EMLs.		A -> V (in dbSNP:rs34198557).		brain development (GO:0007420)|hematopoietic progenitor cell differentiation (GO:0002244)|microtubule cytoskeleton organization (GO:0000226)|mitotic spindle organization (GO:0007052)|neuroblast proliferation (GO:0007405)	cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	calcium ion binding (GO:0005509)|microtubule binding (GO:0008017)|tubulin binding (GO:0015631)	p.A396A(1)		breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	42		Melanoma(154;0.0879)|all_epithelial(191;0.216)				TGTTTGCTGCGGATTTCCACC	0.428																																					p.A396A		Atlas-SNP	.											EML1,colon,carcinoma,+1,1	EML1	97	.	1	Substitution - coding silent(1)	upper_aerodigestive_tract(1)	c.G1188T						.						177.0	174.0	175.0					14																	100375708		2203	4300	6503	SO:0001819	synonymous_variant	2009	exon12			TGCTGCGGATTTC	AK023861	CCDS32154.1, CCDS32155.1	14q32	2013-01-10		2002-02-15		ENSG00000066629		"""WD repeat domain containing"""	3330	protein-coding gene	gene with protein product		602033		EMAPL		9226380, 10521658	Standard	XM_005267397		Approved	EMAP, HuEMAP, ELP79	uc001ygr.3	O00423		ENST00000262233.6:c.1131G>T	chr14.hg19:g.100375708G>T		335.0	0.0		214.0	0.0	NM_001008707	Q86U15|Q8N536|Q8N5C4|Q8WWL6	Silent	SNP	ENST00000262233.6	hg19	CCDS32155.1	.	.	.	.	.	.	.	.	.	.	G	10.27	1.302596	0.23736	.	.	ENSG00000066629	ENST00000554386	.	.	.	5.18	-0.833	0.10782	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-11.5461	2.25	0.04041	0.2513:0.4057:0.1964:0.1466	.	.	.	.	X	70	.	.	G	+	1	0	EML1	99445461	0.462000	0.25791	0.763000	0.31416	0.916000	0.54674	-0.278000	0.08490	-0.044000	0.13491	-0.136000	0.14681	GGA	.	.		0.428	EML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413943.1	NM_001008707	
EML1	2009	hgsc.bcm.edu	37	14	100376661	100376661	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr14:100376661T>C	ENST00000262233.6	+	12	1461	c.1322T>C	c.(1321-1323)aTc>aCc	p.I441T	EML1_ENST00000334192.4_Missense_Mutation_p.I460T|EML1_ENST00000327921.9_Missense_Mutation_p.I429T	NM_004434.2	NP_004425.2	O00423	EMAL1_HUMAN	echinoderm microtubule associated protein like 1	441	Tandem atypical propeller in EMLs.				brain development (GO:0007420)|hematopoietic progenitor cell differentiation (GO:0002244)|microtubule cytoskeleton organization (GO:0000226)|mitotic spindle organization (GO:0007052)|neuroblast proliferation (GO:0007405)	cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	calcium ion binding (GO:0005509)|microtubule binding (GO:0008017)|tubulin binding (GO:0015631)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	42		Melanoma(154;0.0879)|all_epithelial(191;0.216)				AGTGGCAACATCTTAGTATGG	0.358																																					p.I460T		Atlas-SNP	.											.	EML1	97	.	0			c.T1379C						.						93.0	90.0	91.0					14																	100376661		2203	4300	6503	SO:0001583	missense	2009	exon13			GCAACATCTTAGT	AK023861	CCDS32154.1, CCDS32155.1	14q32	2013-01-10		2002-02-15		ENSG00000066629		"""WD repeat domain containing"""	3330	protein-coding gene	gene with protein product		602033		EMAPL		9226380, 10521658	Standard	XM_005267397		Approved	EMAP, HuEMAP, ELP79	uc001ygr.3	O00423		ENST00000262233.6:c.1322T>C	chr14.hg19:g.100376661T>C	ENSP00000262233:p.Ile441Thr	121.0	0.0		74.0	4.0	NM_001008707	Q86U15|Q8N536|Q8N5C4|Q8WWL6	Missense_Mutation	SNP	ENST00000262233.6	hg19	CCDS32155.1	.	.	.	.	.	.	.	.	.	.	T	24.6	4.554824	0.86231	.	.	ENSG00000066629	ENST00000327921;ENST00000262233;ENST00000334192;ENST00000542138	T;T;T	0.52754	0.65;0.65;0.65	5.24	5.24	0.73138	WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (1);WD40-repeat-containing domain (1);	0.047715	0.85682	D	0.000000	T	0.70762	0.3261	M	0.89601	3.045	0.80722	D	1	P;P;D;P	0.55800	0.852;0.922;0.973;0.77	P;P;P;B	0.58660	0.635;0.824;0.843;0.432	T	0.78630	-0.2129	10	0.87932	D	0	-29.9624	15.149	0.72681	0.0:0.0:0.0:1.0	.	429;441;460;460	F8W717;O00423;O00423-3;B3KXA3	.;EMAL1_HUMAN;.;.	T	429;441;460;460	ENSP00000327384:I429T;ENSP00000262233:I441T;ENSP00000334314:I460T	ENSP00000262233:I441T	I	+	2	0	EML1	99446414	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.868000	0.87116	1.979000	0.57680	0.533000	0.62120	ATC	.	.		0.358	EML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413943.1	NM_001008707	
DYNC1H1	1778	hgsc.bcm.edu	37	14	102514166	102514166	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr14:102514166T>C	ENST00000360184.4	+	73	13183	c.13019T>C	c.(13018-13020)aTc>aCc	p.I4340T	RP11-1017G21.4_ENST00000553701.1_RNA|RP11-1017G21.4_ENST00000557242.1_RNA	NM_001376.4	NP_001367.2	Q14204	DYHC1_HUMAN	dynein, cytoplasmic 1, heavy chain 1	4340					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						GTGGACATGATCAGTAAAATG	0.567																																					p.I4340T		Atlas-SNP	.											.	DYNC1H1	395	.	0			c.T13019C						.						124.0	95.0	105.0					14																	102514166		2203	4300	6503	SO:0001583	missense	1778	exon73			ACATGATCAGTAA	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.13019T>C	chr14.hg19:g.102514166T>C	ENSP00000348965:p.Ile4340Thr	89.0	0.0		66.0	4.0	NM_001376	B0I1R0|Q6DKQ7|Q8WU28|Q92814|Q9Y4G5	Missense_Mutation	SNP	ENST00000360184.4	hg19	CCDS9966.1	.	.	.	.	.	.	.	.	.	.	T	16.44	3.124716	0.56613	.	.	ENSG00000197102	ENST00000360184	T	0.10288	2.89	5.37	5.37	0.77165	Dynein heavy chain (1);	0.097569	0.64402	D	0.000001	T	0.18215	0.0437	M	0.78049	2.395	0.58432	D	0.999999	B	0.14438	0.01	B	0.14023	0.01	T	0.01512	-1.1336	10	0.54805	T	0.06	.	15.3709	0.74564	0.0:0.0:0.0:1.0	.	4340	Q14204	DYHC1_HUMAN	T	4340	ENSP00000348965:I4340T	ENSP00000348965:I4340T	I	+	2	0	DYNC1H1	101583919	1.000000	0.71417	1.000000	0.80357	0.923000	0.55619	7.968000	0.87980	2.031000	0.59945	0.533000	0.62120	ATC	.	.		0.567	DYNC1H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414574.1	NM_001376	
AHNAK2	113146	hgsc.bcm.edu	37	14	105407396	105407396	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr14:105407396T>C	ENST00000333244.5	-	7	14511	c.14392A>G	c.(14392-14394)Act>Gct	p.T4798A	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	4798						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)			CTGGGAACAGTCACCTGGTAT	0.502																																					p.T4798A		Atlas-SNP	.											.	AHNAK2	719	.	0			c.A14392G						.						84.0	87.0	86.0					14																	105407396		1943	4139	6082	SO:0001583	missense	113146	exon7			GAACAGTCACCTG	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.14392A>G	chr14.hg19:g.105407396T>C	ENSP00000353114:p.Thr4798Ala	171.0	0.0		112.0	5.0	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	hg19	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	T	3.473	-0.107529	0.06924	.	.	ENSG00000185567	ENST00000333244	T	0.04917	3.53	3.95	-0.848	0.10727	.	.	.	.	.	T	0.03695	0.0105	L	0.29908	0.895	0.09310	N	1	B	0.25312	0.123	B	0.22152	0.038	T	0.48019	-0.9071	9	0.09843	T	0.71	.	4.5371	0.12038	0.0:0.1387:0.358:0.5032	.	4798	Q8IVF2	AHNK2_HUMAN	A	4798	ENSP00000353114:T4798A	ENSP00000353114:T4798A	T	-	1	0	AHNAK2	104478441	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	-1.085000	0.03390	-0.394000	0.07727	0.383000	0.25322	ACT	.	.		0.502	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
MKRN3	7681	hgsc.bcm.edu	37	15	23811295	23811295	+	Silent	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:23811295T>C	ENST00000314520.3	+	1	842	c.366T>C	c.(364-366)tcT>tcC	p.S122S	MKRN3_ENST00000564592.1_Intron|RP11-73C9.1_ENST00000563044.1_RNA|MKRN3_ENST00000568252.1_Intron	NM_005664.3	NP_005655.1	Q13064	MKRN3_HUMAN	makorin ring finger protein 3	122					protein ubiquitination (GO:0016567)	ribonucleoprotein complex (GO:0030529)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(33)|ovary(2)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	61		all_cancers(20;8.44e-25)|all_epithelial(15;3.69e-22)|Lung NSC(15;2.96e-18)|all_lung(15;2.8e-17)|Breast(32;0.000353)|Colorectal(260;0.14)		all cancers(64;3.02e-06)|Epithelial(43;1.94e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0012)		ACGACCTTTCTGGTCGGAAGA	0.602																																					p.S122S		Atlas-SNP	.											.	MKRN3	155	.	0			c.T366C						.						55.0	57.0	56.0					15																	23811295		2203	4300	6503	SO:0001819	synonymous_variant	7681	exon1			CCTTTCTGGTCGG	U19107	CCDS10013.1	15q11-q13	2013-01-09	2008-08-13		ENSG00000179455	ENSG00000179455		"""RING-type (C3HC4) zinc fingers"""	7114	protein-coding gene	gene with protein product	"""zinc finger protein 127"""	603856		ZNF127, D15S9		10196367	Standard	NM_005664		Approved	RNF63, ZFP127, MGC88288	uc001ywh.4	Q13064	OTTHUMG00000129160	ENST00000314520.3:c.366T>C	chr15.hg19:g.23811295T>C		151.0	0.0		100.0	4.0	NM_005664		Silent	SNP	ENST00000314520.3	hg19	CCDS10013.1																																																																																			.	.		0.602	MKRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251225.1	NM_005664	
APBA2	321	hgsc.bcm.edu	37	15	29393815	29393815	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:29393815A>G	ENST00000558402.1	+	11	1951	c.1352A>G	c.(1351-1353)gAc>gGc	p.D451G	APBA2_ENST00000561069.1_Missense_Mutation_p.D451G|APBA2_ENST00000411764.1_Missense_Mutation_p.D439G|APBA2_ENST00000558330.1_Missense_Mutation_p.D439G|APBA2_ENST00000558259.1_Missense_Mutation_p.D451G			Q99767	APBA2_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 2	451	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				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)		ACCATGATGGACCACGCCTTG	0.572																																					p.D451G		Atlas-SNP	.											.	APBA2	132	.	0			c.A1352G						.						97.0	67.0	77.0					15																	29393815		2203	4300	6503	SO:0001583	missense	321	exon9			TGATGGACCACGC	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.1352A>G	chr15.hg19:g.29393815A>G	ENSP00000453293:p.Asp451Gly	182.0	0.0		130.0	6.0	NM_005503	E9PGI4|O60571|Q5XKC0	Missense_Mutation	SNP	ENST00000558402.1	hg19	CCDS10022.1	.	.	.	.	.	.	.	.	.	.	A	23.6	4.437972	0.83885	.	.	ENSG00000034053	ENST00000411764;ENST00000219865;ENST00000382938	T	0.56776	0.44	4.27	4.27	0.50696	Phosphotyrosine interaction domain (3);Pleckstrin homology-type (1);	0.054268	0.64402	D	0.000001	T	0.73048	0.3537	M	0.83483	2.645	0.80722	D	1	D;D;D;D	0.89917	0.998;0.998;1.0;0.973	D;D;D;D	0.97110	0.978;0.988;1.0;0.95	T	0.78097	-0.2337	10	0.87932	D	0	.	13.0159	0.58757	1.0:0.0:0.0:0.0	.	439;143;439;451	Q5XKC0;Q6ZVB1;E9PGI4;Q99767	.;.;.;APBA2_HUMAN	G	439;451;143	ENSP00000409312:D439G	ENSP00000219865:D451G	D	+	2	0	APBA2	27181107	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	8.853000	0.92222	1.916000	0.55485	0.533000	0.62120	GAC	.	.		0.572	APBA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251362.3	NM_005503	
LTK	4058	hgsc.bcm.edu	37	15	41805238	41805238	+	Silent	SNP	G	G	T			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:41805238G>T	ENST00000263800.6	-	2	220	c.124C>A	c.(124-126)Cgg>Agg	p.R42R	LTK_ENST00000453182.2_Silent_p.R42R|LTK_ENST00000355166.5_Silent_p.R42R|LTK_ENST00000561619.1_Intron	NM_002344.5	NP_002335.2	P29376	LTK_HUMAN	leukocyte receptor tyrosine kinase	42			R -> Q (in dbSNP:rs2305030). {ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:7685902}.		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)		TTCGGGTCCCGGGGGCTGGGA	0.632										TSP Lung(18;0.14)																											p.R42R		Atlas-SNP	.											.	LTK	117	.	0			c.C124A						.						19.0	24.0	22.0					15																	41805238		2197	4292	6489	SO:0001819	synonymous_variant	4058	exon2			GGTCCCGGGGGCT	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.124C>A	chr15.hg19:g.41805238G>T		64.0	0.0		70.0	4.0	NM_001135685	A6NNJ8|B4DL89|E9PFX4	Silent	SNP	ENST00000263800.6	hg19	CCDS10077.1																																																																																			.	.		0.632	LTK-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252690.2		
MGA	23269	hgsc.bcm.edu	37	15	41988795	41988795	+	Silent	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:41988795T>C	ENST00000570161.1	+	2	1587	c.1587T>C	c.(1585-1587)ggT>ggC	p.G529G	MGA_ENST00000219905.7_Silent_p.G529G|MGA_ENST00000389936.4_Silent_p.G529G|MGA_ENST00000545763.1_Silent_p.G529G|MGA_ENST00000566586.1_Silent_p.G529G			O43451	MGA_HUMAN	MGA, MAX dimerization protein	0	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)			NS(1)|breast(4)|central_nervous_system(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(33)|ovary(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)	Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	CAGAAAATGGTCTTAGAAAAC	0.378																																					p.G529G		Atlas-SNP	.											.	MGA	264	.	0			c.T1587C						.						73.0	65.0	67.0					15																	41988795		1843	4090	5933	SO:0001819	synonymous_variant	23269	exon3			AAATGGTCTTAGA	AB011090	CCDS55959.1, CCDS55960.1	15q15	2012-11-15	2012-11-15		ENSG00000174197	ENSG00000174197		"""MAX dimerization proteins"", ""T-boxes"""	14010	protein-coding gene	gene with protein product			"""MAX gene associated"""				Standard	NM_001080541		Approved	KIAA0518, MAD5, MXD5, FLJ12634	uc010ucy.2	Q8IWI9		ENST00000570161.1:c.1587T>C	chr15.hg19:g.41988795T>C		131.0	0.0		84.0	4.0	NM_001080541	Q0VAX6|Q75ME7|Q86UM5	Silent	SNP	ENST00000570161.1	hg19	CCDS55959.1																																																																																			.	.		0.378	MGA-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420229.1	NM_001164273.1	
MGA	23269	hgsc.bcm.edu	37	15	42035016	42035016	+	Missense_Mutation	SNP	G	G	A			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:42035016G>A	ENST00000570161.1	+	14	4858	c.4858G>A	c.(4858-4860)Gac>Aac	p.D1620N	MGA_ENST00000219905.7_Missense_Mutation_p.D1620N|MGA_ENST00000389936.4_Missense_Mutation_p.D1620N|MGA_ENST00000545763.1_Intron|MGA_ENST00000566586.1_Intron			O43451	MGA_HUMAN	MGA, MAX dimerization protein	0	Glucoamylase.				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)			NS(1)|breast(4)|central_nervous_system(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(33)|ovary(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)	Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	TGCTATTTCTGACGTGGAAAC	0.453																																					p.D1620N		Atlas-SNP	.											.	MGA	264	.	0			c.G4858A						.						88.0	84.0	85.0					15																	42035016		1891	4122	6013	SO:0001583	missense	23269	exon15			ATTTCTGACGTGG	AB011090	CCDS55959.1, CCDS55960.1	15q15	2012-11-15	2012-11-15		ENSG00000174197	ENSG00000174197		"""MAX dimerization proteins"", ""T-boxes"""	14010	protein-coding gene	gene with protein product			"""MAX gene associated"""				Standard	NM_001080541		Approved	KIAA0518, MAD5, MXD5, FLJ12634	uc010ucy.2	Q8IWI9		ENST00000570161.1:c.4858G>A	chr15.hg19:g.42035016G>A	ENSP00000457035:p.Asp1620Asn	70.0	0.0		48.0	20.0	NM_001164273	Q0VAX6|Q75ME7|Q86UM5	Missense_Mutation	SNP	ENST00000570161.1	hg19	CCDS55959.1	.	.	.	.	.	.	.	.	.	.	G	13.82	2.352171	0.41700	.	.	ENSG00000174197	ENST00000219905;ENST00000389936	D;D	0.84800	-1.9;-1.81	4.96	3.97	0.46021	.	1.710450	0.03356	N	0.196836	T	0.71693	0.3370	N	0.14661	0.345	0.80722	D	1	B;B	0.33694	0.421;0.421	B;B	0.27500	0.08;0.058	T	0.67833	-0.5568	10	0.25106	T	0.35	.	4.8545	0.13552	0.187:0.271:0.542:0.0	.	236;1620	B4DVS1;E7ENI0	.;.	N	1620	ENSP00000219905:D1620N;ENSP00000374586:D1620N	ENSP00000219905:D1620N	D	+	1	0	MGA	39822308	0.998000	0.40836	1.000000	0.80357	0.995000	0.86356	2.443000	0.44881	2.577000	0.86979	0.563000	0.77884	GAC	.	.		0.453	MGA-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420229.1	NM_001164273.1	
MGA	23269	hgsc.bcm.edu	37	15	42035364	42035364	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:42035364A>G	ENST00000570161.1	+	14	5206	c.5206A>G	c.(5206-5208)Aga>Gga	p.R1736G	MGA_ENST00000219905.7_Missense_Mutation_p.R1736G|MGA_ENST00000389936.4_Missense_Mutation_p.R1736G|MGA_ENST00000545763.1_Intron|MGA_ENST00000566586.1_Intron			O43451	MGA_HUMAN	MGA, MAX dimerization protein	0	Glucoamylase.				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)			NS(1)|breast(4)|central_nervous_system(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(33)|ovary(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)	Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	AGTGAGCCAGAGACCAGGTAA	0.418																																					p.R1736G		Atlas-SNP	.											.	MGA	264	.	0			c.A5206G						.						58.0	56.0	56.0					15																	42035364		1917	4146	6063	SO:0001583	missense	23269	exon15			AGCCAGAGACCAG	AB011090	CCDS55959.1, CCDS55960.1	15q15	2012-11-15	2012-11-15		ENSG00000174197	ENSG00000174197		"""MAX dimerization proteins"", ""T-boxes"""	14010	protein-coding gene	gene with protein product			"""MAX gene associated"""				Standard	NM_001080541		Approved	KIAA0518, MAD5, MXD5, FLJ12634	uc010ucy.2	Q8IWI9		ENST00000570161.1:c.5206A>G	chr15.hg19:g.42035364A>G	ENSP00000457035:p.Arg1736Gly	176.0	0.0		149.0	6.0	NM_001164273	Q0VAX6|Q75ME7|Q86UM5	Missense_Mutation	SNP	ENST00000570161.1	hg19	CCDS55959.1	.	.	.	.	.	.	.	.	.	.	A	17.47	3.398223	0.62177	.	.	ENSG00000174197	ENST00000219905;ENST00000389936	D;D	0.87179	-2.0;-2.22	4.9	4.9	0.64082	.	0.416111	0.20973	N	0.082347	D	0.83580	0.5285	N	0.19112	0.55	0.80722	D	1	P;P	0.52842	0.948;0.956	P;P	0.49528	0.614;0.468	D	0.86210	0.1624	10	0.72032	D	0.01	.	14.6863	0.69052	1.0:0.0:0.0:0.0	.	352;1736	B4DVS1;E7ENI0	.;.	G	1736	ENSP00000219905:R1736G;ENSP00000374586:R1736G	ENSP00000219905:R1736G	R	+	1	2	MGA	39822656	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.921000	0.70028	2.056000	0.61249	0.460000	0.39030	AGA	.	.		0.418	MGA-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420229.1	NM_001164273.1	
SPTBN5	51332	hgsc.bcm.edu	37	15	42145939	42145939	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:42145939T>C	ENST00000320955.6	-	58	10048	c.9821A>G	c.(9820-9822)gAg>gGg	p.E3274G	RNA5SP393_ENST00000363423.1_RNA	NM_016642.2	NP_057726.4	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	3274					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)		TCGGCAGGCCTCCGTCTGTAG	0.672																																					p.E3239G		Atlas-SNP	.											.	SPTBN5	171	.	0			c.A9716G						.						25.0	30.0	28.0					15																	42145939		2013	4150	6163	SO:0001583	missense	51332	exon58			CAGGCCTCCGTCT	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.9821A>G	chr15.hg19:g.42145939T>C	ENSP00000317790:p.Glu3274Gly	92.0	0.0		64.0	5.0	NM_016642		Missense_Mutation	SNP	ENST00000320955.6	hg19		.	.	.	.	.	.	.	.	.	.	.	18.32	3.597766	0.66332	.	.	ENSG00000137877	ENST00000320955	T	0.51325	0.71	4.74	4.74	0.60224	.	0.086227	0.44285	D	0.000465	T	0.70937	0.3281	M	0.87547	2.89	0.37850	D	0.929361	D	0.89917	1.0	D	0.75484	0.986	T	0.78595	-0.2143	10	0.54805	T	0.06	.	13.1133	0.59285	0.0:0.0:0.0:1.0	.	3274	Q9NRC6	SPTN5_HUMAN	G	3274	ENSP00000317790:E3274G	ENSP00000317790:E3274G	E	-	2	0	SPTBN5	39933231	0.998000	0.40836	0.208000	0.23602	0.027000	0.11550	3.165000	0.50778	1.900000	0.55004	0.260000	0.18958	GAG	.	.		0.672	SPTBN5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000420237.1	NM_016642	
TUBGCP4	27229	hgsc.bcm.edu	37	15	43668306	43668306	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:43668306A>G	ENST00000260383.7	+	2	343	c.89A>G	c.(88-90)gAc>gGc	p.D30G	TUBGCP4_ENST00000570081.1_3'UTR|TUBGCP4_ENST00000399460.3_5'Flank|TUBGCP4_ENST00000564079.1_Missense_Mutation_p.D30G			Q9UGJ1	GCP4_HUMAN	tubulin, gamma complex associated protein 4	30					G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)|protein complex assembly (GO:0006461)	centrosome (GO:0005813)|cytosol (GO:0005829)|gamma-tubulin ring complex (GO:0008274)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|spindle pole (GO:0000922)	structural constituent of cytoskeleton (GO:0005200)			breast(1)|cervix(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(3)|ovary(4)|prostate(2)|upper_aerodigestive_tract(2)	21		all_cancers(109;1.27e-10)|all_epithelial(112;4.82e-09)|Lung NSC(122;1.72e-06)|all_lung(180;1.59e-05)|Melanoma(134;0.0728)		GBM - Glioblastoma multiforme(94;3.53e-07)		GTATCGCAGGACTTCCCTTTC	0.517											OREG0023088	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D30G		Atlas-SNP	.											.	TUBGCP4	48	.	0			c.A89G						.						148.0	156.0	153.0					15																	43668306		2026	4179	6205	SO:0001583	missense	27229	exon2			CGCAGGACTTCCC	AJ249677	CCDS42030.1, CCDS66745.1	15q15.3	2014-08-12			ENSG00000137822	ENSG00000137822			16691	protein-coding gene	gene with protein product		609610				10562286	Standard	NM_001286414		Approved	76P, FLJ14797	uc001zrn.3	Q9UGJ1	OTTHUMG00000176647	ENST00000260383.7:c.89A>G	chr15.hg19:g.43668306A>G	ENSP00000260383:p.Asp30Gly	142.0	0.0	918	97.0	4.0	NM_014444	B3KNK6|Q969X3|Q9NVF0	Missense_Mutation	SNP	ENST00000260383.7	hg19		.	.	.	.	.	.	.	.	.	.	A	17.57	3.421859	0.62622	.	.	ENSG00000137822	ENST00000260383	T	0.07688	3.17	5.64	5.64	0.86602	.	0.087261	0.85682	D	0.000000	T	0.11024	0.0269	L	0.59436	1.845	0.80722	D	1	B;B	0.14805	0.011;0.008	B;B	0.16289	0.015;0.009	T	0.11108	-1.0601	10	0.17832	T	0.49	-20.0	15.3291	0.74193	1.0:0.0:0.0:0.0	.	30;30	Q9UGJ1;Q9UGJ1-2	GCP4_HUMAN;.	G	30	ENSP00000260383:D30G	ENSP00000260383:D30G	D	+	2	0	TUBGCP4	41455598	1.000000	0.71417	1.000000	0.80357	0.886000	0.51366	8.237000	0.89807	2.265000	0.75225	0.482000	0.46254	GAC	.	.		0.517	TUBGCP4-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000432970.1	NM_014444	
MYO5A	4644	hgsc.bcm.edu	37	15	52720687	52720687	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:52720687T>C	ENST00000399231.3	-	3	461	c.218A>G	c.(217-219)gAc>gGc	p.D73G	MYO5A_ENST00000399233.2_Missense_Mutation_p.D73G|MYO5A_ENST00000358212.6_Missense_Mutation_p.D73G|MYO5A_ENST00000553916.1_Missense_Mutation_p.D73G|MYO5A_ENST00000356338.6_Missense_Mutation_p.D73G	NM_000259.3	NP_000250	Q9Y4I1	MYO5A_HUMAN	myosin VA (heavy chain 12, myoxin)	73	Myosin motor.				actin filament-based movement (GO:0030048)|anagen (GO:0042640)|cellular protein metabolic process (GO:0044267)|cellular response to insulin stimulus (GO:0032869)|endoplasmic reticulum localization (GO:0051643)|exocytosis (GO:0006887)|insulin secretion (GO:0030073)|locomotion involved in locomotory behavior (GO:0031987)|long-chain fatty acid biosynthetic process (GO:0042759)|melanin biosynthetic process (GO:0042438)|melanocyte differentiation (GO:0030318)|melanosome transport (GO:0032402)|membrane organization (GO:0061024)|myelination (GO:0042552)|odontogenesis (GO:0042476)|post-Golgi vesicle-mediated transport (GO:0006892)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)|regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031585)|secretory granule localization (GO:0032252)|synapse organization (GO:0050808)|synaptic transmission (GO:0007268)|transport (GO:0006810)|vesicle transport along actin filament (GO:0030050)|vesicle-mediated transport (GO:0016192)|visual perception (GO:0007601)	actomyosin (GO:0042641)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium tip (GO:0032433)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|insulin-responsive compartment (GO:0032593)|intermediate filament (GO:0005882)|melanosome (GO:0042470)|membrane (GO:0016020)|microtubule plus-end (GO:0035371)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|photoreceptor outer segment (GO:0001750)|ruffle (GO:0001726)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|microfilament motor activity (GO:0000146)|poly(A) RNA binding (GO:0044822)|Rab GTPase binding (GO:0017137)	p.D73V(1)		breast(4)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(7)|large_intestine(12)|lung(19)|ovary(3)|skin(3)|stomach(1)	57				all cancers(107;0.0085)|Colorectal(133;0.077)|READ - Rectum adenocarcinoma(133;0.196)		GGCTGTGAGGTCATTTTCACC	0.423																																					p.D73G		Atlas-SNP	.											MYO5A,right_upper_lobe,carcinoma,0,2	MYO5A	145	.	1	Substitution - Missense(1)	lung(1)	c.A218G						.						177.0	165.0	169.0					15																	52720687		1988	4170	6158	SO:0001583	missense	4644	exon3			GTGAGGTCATTTT		CCDS42037.1, CCDS45262.1	15q21	2014-09-17	2006-09-29		ENSG00000197535	ENSG00000197535		"""Myosins / Myosin superfamily : Class V"""	7602	protein-coding gene	gene with protein product	"""myosin, heavy polypeptide kinase"", ""myosin heavy chain 12"", ""myoxin"", ""myosin V"""	160777	"""myosin VA (heavy polypeptide 12, myoxin)"""	MYH12		8188282, 8022818	Standard	NM_000259		Approved	MYO5, GS1, MYR12	uc002aby.2	Q9Y4I1	OTTHUMG00000137383	ENST00000399231.3:c.218A>G	chr15.hg19:g.52720687T>C	ENSP00000382177:p.Asp73Gly	401.0	2.0		248.0	10.0	NM_000259	A8MZC5|O60653|Q07902|Q16249|Q9UE30|Q9UE31	Missense_Mutation	SNP	ENST00000399231.3	hg19	CCDS42037.1	.	.	.	.	.	.	.	.	.	.	T	27.4	4.828635	0.90955	.	.	ENSG00000197535	ENST00000399231;ENST00000399233;ENST00000356338;ENST00000358212;ENST00000553916	D;D;D;D;D	0.98493	-4.96;-4.96;-4.96;-4.96;-4.96	5.76	5.76	0.90799	Myosin head, motor domain (2);	0.000000	0.85682	D	0.000000	D	0.99450	0.9805	H	0.98738	4.315	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	D	0.98117	1.0423	10	0.72032	D	0.01	.	16.0637	0.80856	0.0:0.0:0.0:1.0	.	73;73	Q9Y4I1;Q9Y4I1-2	MYO5A_HUMAN;.	G	73	ENSP00000382177:D73G;ENSP00000382179:D73G;ENSP00000348693:D73G;ENSP00000350945:D73G;ENSP00000451109:D73G	ENSP00000348693:D73G	D	-	2	0	MYO5A	50507979	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	8.040000	0.89188	2.197000	0.70478	0.533000	0.62120	GAC	.	.		0.423	MYO5A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268102.1	NM_000259	
TCF12	6938	hgsc.bcm.edu	37	15	57484418	57484418	+	Silent	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:57484418A>G	ENST00000267811.5	+	7	757	c.453A>G	c.(451-453)aaA>aaG	p.K151K	TCF12_ENST00000452095.2_Silent_p.K147K|TCF12_ENST00000557843.1_Silent_p.K151K|TCF12_ENST00000333725.5_Silent_p.K151K|TCF12_ENST00000438423.2_Silent_p.K151K	NM_003205.3|NM_207038.1	NP_003196.1|NP_996921.1	Q99081	HTF4_HUMAN	transcription factor 12	151					immune response (GO:0006955)|muscle organ development (GO:0007517)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	bHLH transcription factor binding (GO:0043425)|E-box binding (GO:0070888)|enhancer binding (GO:0035326)|sequence-specific DNA binding transcription factor activity (GO:0003700)|SMAD binding (GO:0046332)|transcription factor binding (GO:0008134)		TCF12/NR4A3(2)	breast(2)|central_nervous_system(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(1)|lung(13)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	36		Colorectal(260;0.0907)		all cancers(107;0.000313)|GBM - Glioblastoma multiforme(80;0.00878)|STAD - Stomach adenocarcinoma(283;0.239)		CTTCAGGAAAACCTGGGACAG	0.468			T	TEC	extraskeletal myxoid chondrosarcoma																																p.K151K		Atlas-SNP	.		Dom	yes		15	15q21	6938	"""transcription factor 12 (HTF4, helix-loop-helix transcription factors 4)"""		M	.	TCF12	242	.	0			c.A453G						.						94.0	95.0	95.0					15																	57484418		2192	4292	6484	SO:0001819	synonymous_variant	6938	exon7			AGGAAAACCTGGG	BC050556	CCDS10159.1, CCDS10160.1, CCDS42042.1	15q21	2013-05-21	2008-07-31		ENSG00000140262	ENSG00000140262		"""Basic helix-loop-helix proteins"""	11623	protein-coding gene	gene with protein product	"""helix-loop-helix transcription factor 4"""	600480				1886779	Standard	NM_003205		Approved	HEB, HTF4, HsT17266, bHLHb20	uc002aeb.3	Q99081	OTTHUMG00000132047	ENST00000267811.5:c.453A>G	chr15.hg19:g.57484418A>G		160.0	0.0		96.0	5.0	NM_207036	Q7Z3D9|Q86TC1|Q86VM2	Silent	SNP	ENST00000267811.5	hg19	CCDS10159.1																																																																																			.	.		0.468	TCF12-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255069.3	NM_003205	
ADAM10	102	hgsc.bcm.edu	37	15	58957384	58957384	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:58957384T>C	ENST00000260408.3	-	5	940	c.497A>G	c.(496-498)aAa>aGa	p.K166R	ADAM10_ENST00000402627.1_Intron|ADAM10_ENST00000396140.2_Intron|ADAM10_ENST00000561288.1_Intron|ADAM10_ENST00000558733.1_5'UTR	NM_001110.2	NP_001101.1	O14672	ADA10_HUMAN	ADAM metallopeptidase domain 10	166					cell death (GO:0008219)|cell-cell signaling (GO:0007267)|collagen catabolic process (GO:0030574)|constitutive protein ectodomain proteolysis (GO:0051089)|epidermal growth factor receptor signaling pathway (GO:0007173)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|in utero embryonic development (GO:0001701)|integrin-mediated signaling pathway (GO:0007229)|membrane protein ectodomain proteolysis (GO:0006509)|monocyte activation (GO:0042117)|negative regulation of cell adhesion (GO:0007162)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|PMA-inducible membrane protein ectodomain proteolysis (GO:0051088)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of T cell chemotaxis (GO:0010820)|protein phosphorylation (GO:0006468)|response to tumor necrosis factor (GO:0034612)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|Golgi-associated vesicle (GO:0005798)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|tetraspanin-enriched microdomain (GO:0097197)	endopeptidase activity (GO:0004175)|integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|receptor binding (GO:0005102)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|kidney(5)|large_intestine(3)|lung(11)|ovary(1)|prostate(2)|skin(3)	27				GBM - Glioblastoma multiforme(80;0.202)		AGGACCGTATTTATGGGGATA	0.348																																					p.K166R		Atlas-SNP	.											.	ADAM10	59	.	0			c.A497G						.						117.0	115.0	115.0					15																	58957384		2192	4292	6484	SO:0001583	missense	102	exon5			CCGTATTTATGGG	AF009615	CCDS10167.1	15q2	2006-09-25	2005-08-18		ENSG00000137845	ENSG00000137845		"""ADAM metallopeptidase domain containing"", ""CD molecules"""	188	protein-coding gene	gene with protein product		602192	"""a disintegrin and metalloproteinase domain 10"""			9344679, 9441766	Standard	XM_005254117		Approved	kuz, MADM, HsT18717, CD156c	uc002afd.1	O14672	OTTHUMG00000132633	ENST00000260408.3:c.497A>G	chr15.hg19:g.58957384T>C	ENSP00000260408:p.Lys166Arg	134.0	0.0		97.0	4.0	NM_001110	B4DU28|Q10742|Q92650	Missense_Mutation	SNP	ENST00000260408.3	hg19	CCDS10167.1	.	.	.	.	.	.	.	.	.	.	T	27.8	4.864689	0.91511	.	.	ENSG00000137845	ENST00000260408;ENST00000439637	T;T	0.80824	1.84;-1.42	5.4	5.4	0.78164	.	0.000000	0.85682	D	0.000000	T	0.75503	0.3858	M	0.64997	1.995	0.80722	D	1	B;B	0.26445	0.149;0.149	B;B	0.24394	0.032;0.053	T	0.70346	-0.4897	10	0.09590	T	0.72	-33.2421	13.9508	0.64116	0.0:0.0:0.0:1.0	.	166;166	A0AV88;O14672	.;ADA10_HUMAN	R	166;113	ENSP00000260408:K166R;ENSP00000391930:K113R	ENSP00000260408:K166R	K	-	2	0	ADAM10	56744676	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.061000	0.64319	2.174000	0.68829	0.528000	0.53228	AAA	.	.		0.348	ADAM10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255880.2	NM_001110	
SLTM	79811	hgsc.bcm.edu	37	15	59204795	59204795	+	Silent	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:59204795T>C	ENST00000380516.2	-	5	615	c.528A>G	c.(526-528)caA>caG	p.Q176Q	SLTM_ENST00000557950.1_5'UTR|SLTM_ENST00000536328.1_5'UTR	NM_001013843.1|NM_024755.2	NP_001013865.1|NP_079031.2	Q9NWH9	SLTM_HUMAN	SAFB-like, transcription modulator	176	Glu-rich.				apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						cttcaccttcttgagcttcaa	0.358																																					p.Q176Q		Atlas-SNP	.											.	SLTM	90	.	0			c.A528G						.						97.0	87.0	90.0					15																	59204795		2192	4292	6484	SO:0001819	synonymous_variant	79811	exon5			ACCTTCTTGAGCT	BC046119	CCDS10168.2	15q21.3	2013-02-12			ENSG00000137776	ENSG00000137776		"""RNA binding motif (RRM) containing"""	20709	protein-coding gene	gene with protein product							Standard	XR_243128		Approved	Met, FLJ13213	uc002afp.3	Q9NWH9	OTTHUMG00000074033	ENST00000380516.2:c.528A>G	chr15.hg19:g.59204795T>C		113.0	0.0		97.0	4.0	NM_001013843	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Silent	SNP	ENST00000380516.2	hg19	CCDS10168.2																																																																																			.	.		0.358	SLTM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157124.1	NM_024755	
SPG21	51324	hgsc.bcm.edu	37	15	65273320	65273320	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:65273320T>C	ENST00000204566.2	-	3	402	c.107A>G	c.(106-108)gAc>gGc	p.D36G	SPG21_ENST00000416889.2_Missense_Mutation_p.D36G|SPG21_ENST00000559199.1_5'UTR|SPG21_ENST00000560564.1_5'UTR|SPG21_ENST00000433215.2_Missense_Mutation_p.D36G	NM_016630.3	NP_057714.1	Q9NZD8	SPG21_HUMAN	spastic paraplegia 21 (autosomal recessive, Mast syndrome)	36					antigen receptor-mediated signaling pathway (GO:0050851)|cell death (GO:0008219)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|membrane (GO:0016020)|nucleus (GO:0005634)|trans-Golgi network transport vesicle (GO:0030140)	CD4 receptor binding (GO:0042609)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(4)|urinary_tract(1)	10						GGGGCCCGCGTCATAGAGCGA	0.443																																					p.D36G		Atlas-SNP	.											.	SPG21	29	.	0			c.A107G						.						83.0	78.0	80.0					15																	65273320		2202	4299	6501	SO:0001583	missense	51324	exon3			CCCGCGTCATAGA	AF208861	CCDS10198.1, CCDS45279.1	15q21-q22	2008-02-05	2007-04-23		ENSG00000090487	ENSG00000090487			20373	protein-coding gene	gene with protein product	"""maspardin"""	608181				11113139, 14564668	Standard	XM_006720564		Approved	ACP33, GL010, BM-019, MAST	uc002aoe.3	Q9NZD8	OTTHUMG00000133098	ENST00000204566.2:c.107A>G	chr15.hg19:g.65273320T>C	ENSP00000204566:p.Asp36Gly	118.0	0.0		97.0	6.0	NM_001127889	B4DW44|Q6ZMB6	Missense_Mutation	SNP	ENST00000204566.2	hg19	CCDS10198.1	.	.	.	.	.	.	.	.	.	.	T	23.7	4.450266	0.84101	.	.	ENSG00000090487	ENST00000204566;ENST00000416889;ENST00000433215	T;T	0.32023	1.47;1.47	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	T	0.58409	0.2120	M	0.80616	2.505	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.995	T	0.62599	-0.6820	10	0.56958	D	0.05	-16.817	15.1312	0.72527	0.0:0.0:0.0:1.0	.	36;36	Q9NZD8-2;Q9NZD8	.;SPG21_HUMAN	G	36	ENSP00000204566:D36G;ENSP00000404111:D36G	ENSP00000204566:D36G	D	-	2	0	SPG21	63060373	1.000000	0.71417	0.867000	0.34043	0.640000	0.38277	7.959000	0.87885	2.167000	0.68274	0.528000	0.53228	GAC	.	.		0.443	SPG21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256758.3	NM_016630	
CLPX	10845	hgsc.bcm.edu	37	15	65449246	65449246	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:65449246T>C	ENST00000300107.3	-	9	1270	c.1082A>G	c.(1081-1083)gAt>gGt	p.D361G		NM_006660.3	NP_006651.2	O76031	CLPX_HUMAN	caseinolytic mitochondrial matrix peptidase chaperone subunit	361					ATP catabolic process (GO:0006200)|positive regulation of peptidase activity (GO:0010952)|protein folding (GO:0006457)|proteolysis involved in cellular protein catabolic process (GO:0051603)	endopeptidase Clp complex (GO:0009368)|mitochondrial endopeptidase Clp complex (GO:0009841)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|metal ion binding (GO:0046872)|peptidase activator activity (GO:0016504)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(4)|prostate(1)|skin(2)	16						GCCAATCTTATCTACTTCATC	0.368																																					p.D361G		Atlas-SNP	.											.	CLPX	49	.	0			c.A1082G						.						137.0	120.0	126.0					15																	65449246		2202	4299	6501	SO:0001583	missense	10845	exon9			ATCTTATCTACTT	AJ006267	CCDS10202.1	15q22.31	2013-09-12	2013-09-12		ENSG00000166855	ENSG00000166855		"""ATPases / AAA-type"""	2088	protein-coding gene	gene with protein product		615611	"""ClpX (caseinolytic protease X, E. coli) homolog"", ""ClpX caseinolytic protease X homolog (E. coli)"", ""ClpX caseinolytic peptidase X homolog (E. coli)"""			22841477	Standard	NM_006660		Approved		uc002aom.3	O76031	OTTHUMG00000133139	ENST00000300107.3:c.1082A>G	chr15.hg19:g.65449246T>C	ENSP00000300107:p.Asp361Gly	153.0	0.0		90.0	5.0	NM_006660	A1L428|A8K8F1|B9EGI8|Q9H4D9	Missense_Mutation	SNP	ENST00000300107.3	hg19	CCDS10202.1	.	.	.	.	.	.	.	.	.	.	T	29.8	5.033794	0.93575	.	.	ENSG00000166855	ENST00000300107;ENST00000546194	T	0.59502	0.26	5.94	5.94	0.96194	ATPase, AAA-2 (1);ATPase, AAA+ type, core (1);	0.000000	0.85682	D	0.000000	D	0.87051	0.6081	H	0.99391	4.545	0.80722	D	1	D;D	0.89917	0.994;1.0	P;D	0.91635	0.9;0.999	D	0.92711	0.6183	10	0.87932	D	0	.	16.3908	0.83537	0.0:0.0:0.0:1.0	.	361;361	Q9H072;O76031	.;CLPX_HUMAN	G	361	ENSP00000300107:D361G	ENSP00000300107:D361G	D	-	2	0	CLPX	63236299	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.040000	0.89188	2.269000	0.75478	0.455000	0.32223	GAT	.	.		0.368	CLPX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256828.2	NM_006660	
DENND4A	10260	hgsc.bcm.edu	37	15	65993392	65993392	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:65993392A>G	ENST00000431932.2	-	19	2906	c.2698T>C	c.(2698-2700)Tca>Cca	p.S900P	DENND4A_ENST00000443035.3_Missense_Mutation_p.S900P	NM_005848.3	NP_005839.3	Q7Z401	MYCPP_HUMAN	DENN/MADD domain containing 4A	900					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						CCCTTACCTGAGAGAGTTGTT	0.284																																					p.S900P		Atlas-SNP	.											.	DENND4A	217	.	0			c.T2698C						.						164.0	153.0	156.0					15																	65993392		1834	4086	5920	SO:0001583	missense	10260	exon19			TACCTGAGAGAGT	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.2698T>C	chr15.hg19:g.65993392A>G	ENSP00000396830:p.Ser900Pro	141.0	0.0		133.0	7.0	NM_001144823	E7EPL3|Q14655|Q86T77|Q8IVX2|Q8NB93	Missense_Mutation	SNP	ENST00000431932.2	hg19	CCDS45285.1	.	.	.	.	.	.	.	.	.	.	A	14.69	2.610352	0.46527	.	.	ENSG00000174485	ENST00000443035;ENST00000431932	T;T	0.05996	3.41;3.36	5.98	5.98	0.97165	.	0.480266	0.14514	U	0.314903	T	0.07007	0.0178	L	0.38953	1.18	0.45005	D	0.998021	B;P	0.49961	0.009;0.93	B;B	0.41571	0.004;0.36	T	0.41034	-0.9531	10	0.35671	T	0.21	.	11.0498	0.47880	0.9227:0.0:0.0773:0.0	.	900;900	E7EPL3;Q7Z401	.;MYCPP_HUMAN	P	900	ENSP00000391167:S900P;ENSP00000396830:S900P	ENSP00000396830:S900P	S	-	1	0	DENND4A	63780446	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.880000	0.75578	2.289000	0.77006	0.482000	0.46254	TCA	.	.		0.284	DENND4A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419611.1	NM_005848	
ZWILCH	55055	hgsc.bcm.edu	37	15	66806411	66806411	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:66806411T>C	ENST00000307897.5	+	3	571	c.191T>C	c.(190-192)gTg>gCg	p.V64A	ZWILCH_ENST00000446801.2_5'UTR|RPL4_ENST00000564517.1_Intron|ZWILCH_ENST00000535141.2_5'UTR|RPL4_ENST00000568588.1_Intron|ZWILCH_ENST00000565627.1_Intron|ZWILCH_ENST00000565960.1_3'UTR	NM_017975.3	NP_060445.3	Q9H900	ZWILC_HUMAN	zwilch kinetochore protein	64					mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)	cytosol (GO:0005829)|kinetochore (GO:0000776)				breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|liver(1)|lung(6)|ovary(1)	18						GTATTCATAGTGGAAAAAGTG	0.343																																					p.V64A		Atlas-SNP	.											.	ZWILCH	46	.	0			c.T191C						.						58.0	58.0	58.0					15																	66806411		2201	4299	6500	SO:0001583	missense	55055	exon3			TCATAGTGGAAAA	AK023175	CCDS10219.1, CCDS73746.1	15q22.31	2013-01-17	2012-12-13		ENSG00000174442	ENSG00000174442			25468	protein-coding gene	gene with protein product		609984	"""Zwilch, kinetochore associated, homolog (Drosophila)"""			12686595	Standard	NM_017975		Approved	FLJ10036, KNTC1AP	uc002aqb.3	Q9H900	OTTHUMG00000133194	ENST00000307897.5:c.191T>C	chr15.hg19:g.66806411T>C	ENSP00000311429:p.Val64Ala	109.0	0.0		72.0	4.0	NM_017975	B3KVB8|Q6N049|Q8N404|Q96SY7|Q9NWG7	Missense_Mutation	SNP	ENST00000307897.5	hg19	CCDS10219.1	.	.	.	.	.	.	.	.	.	.	T	10.69	1.420712	0.25639	.	.	ENSG00000174442	ENST00000307897	T	0.49720	0.77	6.16	2.66	0.31614	.	0.773508	0.12966	N	0.424599	T	0.42040	0.1185	L	0.54323	1.7	0.30310	N	0.788609	B	0.28128	0.201	B	0.28385	0.089	T	0.40308	-0.9570	10	0.48119	T	0.1	-0.8818	8.4821	0.33049	0.0:0.2232:0.0:0.7768	.	64	Q9H900	ZWILC_HUMAN	A	64	ENSP00000311429:V64A	ENSP00000311429:V64A	V	+	2	0	ZWILCH	64593465	0.867000	0.29959	0.202000	0.23494	0.800000	0.45204	1.082000	0.30803	0.218000	0.20820	-0.263000	0.10527	GTG	.	.		0.343	ZWILCH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256904.4	NM_017975	
UACA	55075	hgsc.bcm.edu	37	15	71055745	71055745	+	Start_Codon_SNP	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:71055745A>G	ENST00000322954.6	-	1	187	c.2T>C	c.(1-3)aTg>aCg	p.M1T	UACA_ENST00000539319.1_Start_Codon_SNP_p.M1T	NM_018003.2	NP_060473.2	Q9BZF9	UACA_HUMAN	uveal autoantigen with coiled-coil domains and ankyrin repeats	1					intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|negative regulation of inflammatory response (GO:0050728)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of protein import into nucleus (GO:0042307)|response to UV (GO:0009411)	apoptosome (GO:0043293)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)				breast(2)|endometrium(7)|kidney(4)|large_intestine(13)|lung(17)|ovary(2)|pancreas(1)|prostate(2)|skin(2)	50						GAGGCTCTTCATGGCTAACTC	0.731																																					p.M1T		Atlas-SNP	.											.	UACA	235	.	0			c.T2C						.						7.0	10.0	9.0					15																	71055745		1776	3395	5171	SO:0001582	initiator_codon_variant	55075	exon1			CTCTTCATGGCTA	AF322916	CCDS10235.1, CCDS32280.1	15q22-q24	2013-01-10			ENSG00000137831	ENSG00000137831		"""Ankyrin repeat domain containing"""	15947	protein-coding gene	gene with protein product		612516				11162650, 10997877	Standard	NM_001008224		Approved	FLJ10128, KIAA1561	uc002asr.3	Q9BZF9	OTTHUMG00000133363	ENST00000322954.6:c.2T>C	chr15.hg19:g.71055745A>G	ENSP00000314556:p.Met1Thr	129.0	0.0		90.0	4.0	NM_018003	G3XAG2|Q14DD3|Q8N3B8|Q96NH6|Q9HCL1|Q9NWC6	Missense_Mutation	SNP	ENST00000322954.6	hg19	CCDS10235.1	.	.	.	.	.	.	.	.	.	.	A	21.0	4.088531	0.76756	.	.	ENSG00000137831	ENST00000322954;ENST00000539319	T;T	0.36520	1.25;1.8	4.67	4.67	0.58626	.	0.000000	0.48767	D	0.000163	T	0.54631	0.1870	.	.	.	0.80722	D	1	D;D	0.54601	0.96;0.967	P;P	0.61397	0.888;0.879	T	0.59506	-0.7442	9	0.87932	D	0	-8.7751	10.523	0.44931	1.0:0.0:0.0:0.0	.	1;1	F5H2B9;Q9BZF9	.;UACA_HUMAN	T	1	ENSP00000314556:M1T;ENSP00000438667:M1T	ENSP00000314556:M1T	M	-	2	0	UACA	68842799	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	3.892000	0.56235	1.744000	0.51775	0.397000	0.26171	ATG	.	.		0.731	UACA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257199.2		Missense_Mutation
MYO9A	4649	hgsc.bcm.edu	37	15	72244126	72244126	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:72244126T>C	ENST00000356056.5	-	15	2766	c.2294A>G	c.(2293-2295)gAg>gGg	p.E765G	MYO9A_ENST00000444904.1_Missense_Mutation_p.E746G|MYO9A_ENST00000564571.1_Missense_Mutation_p.E765G|MYO9A_ENST00000424560.1_Missense_Mutation_p.E765G|MYO9A_ENST00000566885.1_Missense_Mutation_p.E360G|MYO9A_ENST00000563542.1_5'UTR	NM_006901.3	NP_008832.2	B2RTY4	MYO9A_HUMAN	myosin IXA	765	Myosin motor.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|visual perception (GO:0007601)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)|motor activity (GO:0003774)			NS(4)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(29)|lung(27)|ovary(1)|pancreas(1)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						ACTGTACTTCTCTTCCTTGCA	0.423																																					p.E765G		Atlas-SNP	.											.	MYO9A	203	.	0			c.A2294G						.						211.0	195.0	200.0					15																	72244126		2199	4297	6496	SO:0001583	missense	4649	exon15			TACTTCTCTTCCT	AF117888	CCDS10239.1	15q22-q23	2011-09-27			ENSG00000066933	ENSG00000066933		"""Myosins / Myosin superfamily : Class IX"""	7608	protein-coding gene	gene with protein product		604875				10409426	Standard	NM_006901		Approved	FLJ11061, FLJ13244, MGC71859	uc002atl.5	B2RTY4	OTTHUMG00000133440	ENST00000356056.5:c.2294A>G	chr15.hg19:g.72244126T>C	ENSP00000348349:p.Glu765Gly	215.0	0.0		146.0	6.0	NM_006901	B0I1T5|C9IYB3|C9JA86|Q14787|Q3YLD7|Q3YLD8|Q6P986|Q9H8T5|Q9NTG2|Q9NUY2|Q9UEP3|Q9UNJ2	Missense_Mutation	SNP	ENST00000356056.5	hg19	CCDS10239.1	.	.	.	.	.	.	.	.	.	.	T	27.6	4.850458	0.91277	.	.	ENSG00000066933	ENST00000356056;ENST00000424560;ENST00000444904;ENST00000261864	D;D;D	0.86366	-2.11;-2.1;-2.11	5.35	5.35	0.76521	Myosin head, motor domain (1);	.	.	.	.	D	0.85635	0.5742	N	0.14661	0.345	0.80722	D	1	D;B;P	0.67145	0.996;0.129;0.933	P;B;P	0.59424	0.857;0.138;0.739	D	0.85851	0.1404	9	0.33940	T	0.23	.	15.6409	0.77001	0.0:0.0:0.0:1.0	.	746;746;765	B2RTY4-2;B7WP69;B2RTY4	.;.;MYO9A_HUMAN	G	765;765;746;746	ENSP00000348349:E765G;ENSP00000399162:E765G;ENSP00000398250:E746G	ENSP00000261864:E746G	E	-	2	0	MYO9A	70031180	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.921000	0.87530	2.151000	0.67156	0.460000	0.39030	GAG	.	.		0.423	MYO9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257308.1	NM_006901	
STOML1	9399	hgsc.bcm.edu	37	15	74281130	74281130	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:74281130T>C	ENST00000316900.5	-	4	528	c.404A>G	c.(403-405)gAc>gGc	p.D135G	STOML1_ENST00000541638.1_Missense_Mutation_p.D93G|STOML1_ENST00000316911.6_Missense_Mutation_p.D85G|STOML1_ENST00000561656.1_Missense_Mutation_p.D48G|STOML1_ENST00000359750.4_Missense_Mutation_p.D135G|STOML1_ENST00000564777.1_Missense_Mutation_p.D85G	NM_001256672.1|NM_001256675.1|NM_001256677.1|NM_004809.4	NP_001243601.1|NP_001243604.1|NP_001243606.1|NP_004800.2	Q9UBI4	STML1_HUMAN	stomatin (EPB72)-like 1	135						integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)	8						CACAGCCCCGTCCTTAGAGGC	0.627																																					p.D135G		Atlas-SNP	.											.	STOML1	22	.	0			c.A404G						.						73.0	70.0	71.0					15																	74281130		2198	4297	6495	SO:0001583	missense	9399	exon4			GCCCCGTCCTTAG	Y16522	CCDS10254.1, CCDS58381.1, CCDS58382.1, CCDS58383.1, CCDS58384.1, CCDS58385.1	15q24-q25	2008-07-18			ENSG00000067221	ENSG00000067221			14560	protein-coding gene	gene with protein product	"""stomatin-like 1"", ""stomatin (EBP72)-like 1"""	608326				9931417	Standard	NM_004809		Approved	hUNC-24, SLP-1, STORP, FLJ36370	uc002awe.4	Q9UBI4	OTTHUMG00000137608	ENST00000316900.5:c.404A>G	chr15.hg19:g.74281130T>C	ENSP00000319323:p.Asp135Gly	111.0	0.0		91.0	6.0	NM_001256672	B3KQN0|B4DUU5|B4DXM9|E7ESC0|H3BRP3|O95675|Q4PNR4|Q6FGL8|Q8WYI7|Q9UMB9|Q9UMC0|Q9Y6H9	Missense_Mutation	SNP	ENST00000316900.5	hg19	CCDS10254.1	.	.	.	.	.	.	.	.	.	.	T	17.88	3.498238	0.64186	.	.	ENSG00000067221	ENST00000316900;ENST00000316911;ENST00000541638;ENST00000359750	D;D;D;D	0.97791	-4.54;-4.54;-4.54;-4.54	4.34	4.34	0.51931	.	0.046263	0.85682	D	0.000000	D	0.98836	0.9607	H	0.94542	3.55	0.80722	D	1	D;D;D;D;D;D	0.69078	0.982;0.997;0.977;0.997;0.964;0.982	P;D;P;D;P;P	0.64321	0.779;0.924;0.78;0.924;0.779;0.762	D	0.99399	1.0927	10	0.72032	D	0.01	-17.3175	12.5167	0.56036	0.0:0.0:0.0:1.0	.	93;135;85;135;135;135	B4DUU5;E7ESC0;Q9UBI4-2;Q4PNR4;Q53HB6;Q9UBI4	.;.;.;.;.;STML1_HUMAN	G	135;85;93;135	ENSP00000319323:D135G;ENSP00000319384:D85G;ENSP00000442478:D93G;ENSP00000352788:D135G	ENSP00000319323:D135G	D	-	2	0	STOML1	72068183	1.000000	0.71417	0.998000	0.56505	0.457000	0.32468	6.904000	0.75708	1.827000	0.53221	0.533000	0.62120	GAC	.	.		0.627	STOML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269022.1	NM_004809	
NRG4	145957	hgsc.bcm.edu	37	15	76301620	76301620	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:76301620A>G	ENST00000394907.3	-	3	206	c.25T>C	c.(25-27)Tgt>Cgt	p.C9R	NRG4_ENST00000305435.10_Missense_Mutation_p.C9R|NRG4_ENST00000535975.1_Missense_Mutation_p.C9R	NM_138573.3	NP_612640.1	Q8WWG1	NRG4_HUMAN	neuregulin 4	9	EGF-like. {ECO:0000255|PROSITE- ProRule:PRU00076}.				epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				large_intestine(1)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	5						CTGGGACCACAGGGCTCTTCG	0.398																																					p.C9R		Atlas-SNP	.											.	NRG4	9	.	0			c.T25C						.						79.0	80.0	80.0					15																	76301620		2197	4294	6491	SO:0001583	missense	145957	exon3			GACCACAGGGCTC	BC017568	CCDS10288.1	15q23	2005-10-30			ENSG00000169752	ENSG00000169752			29862	protein-coding gene	gene with protein product		610894				12477932	Standard	NM_138573		Approved	HRG4	uc002bbo.3	Q8WWG1	OTTHUMG00000142917	ENST00000394907.3:c.25T>C	chr15.hg19:g.76301620A>G	ENSP00000378367:p.Cys9Arg	73.0	0.0		49.0	4.0	NM_138573	A6NIE8	Missense_Mutation	SNP	ENST00000394907.3	hg19	CCDS10288.1	.	.	.	.	.	.	.	.	.	.	A	18.68	3.676083	0.67928	.	.	ENSG00000169752	ENST00000394907;ENST00000535975;ENST00000305435	T;T	0.53640	0.61;0.61	5.37	5.37	0.77165	Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.799345	0.09908	U	0.740151	T	0.77745	0.4176	M	0.93854	3.465	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	T	0.77427	-0.2592	10	0.87932	D	0	-10.6545	13.3384	0.60530	1.0:0.0:0.0:0.0	.	9	Q8WWG1	NRG4_HUMAN	R	9	ENSP00000378367:C9R;ENSP00000441129:C9R	ENSP00000303071:C9R	C	-	1	0	NRG4	74088675	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.094000	0.64523	2.019000	0.59389	0.528000	0.53228	TGT	.	.		0.398	NRG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286632.1	NM_138573	
HOMER2	9455	hgsc.bcm.edu	37	15	83523520	83523520	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:83523520A>G	ENST00000304231.8	-	6	752	c.560T>C	c.(559-561)cTg>cCg	p.L187P	HOMER2_ENST00000426485.1_Intron|HOMER2_ENST00000450735.2_Missense_Mutation_p.L176P|HOMER2_ENST00000399166.2_Intron	NM_199330.2	NP_955362.1	Q9NSB8	HOME2_HUMAN	homer homolog 2 (Drosophila)	187					behavioral response to cocaine (GO:0048148)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|chemical homeostasis within a tissue (GO:0048875)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	apical part of cell (GO:0045177)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)				cervix(1)|endometrium(2)|lung(6)	9						AAGGGTCTGCAGCTCGATCTC	0.652																																					p.L187P		Atlas-SNP	.											.	HOMER2	63	.	0			c.T560C						.						58.0	63.0	61.0					15																	83523520		2161	4257	6418	SO:0001583	missense	9455	exon6			GTCTGCAGCTCGA	AF093264	CCDS45334.1, CCDS45336.1	15q24.3	2008-02-05				ENSG00000103942			17513	protein-coding gene	gene with protein product		604799				9808459, 9808458	Standard	NM_199330		Approved	CPD, Cupidin, Vesl-2, HOMER-2B, HOMER-2, HOMER-2A	uc002bjg.3	Q9NSB8		ENST00000304231.8:c.560T>C	chr15.hg19:g.83523520A>G	ENSP00000305632:p.Leu187Pro	142.0	0.0		91.0	4.0	NM_199330	O95269|O95349|Q9NSB6|Q9NSB7|Q9UNT7	Missense_Mutation	SNP	ENST00000304231.8	hg19	CCDS45334.1	.	.	.	.	.	.	.	.	.	.	A	26.4	4.738742	0.89573	.	.	ENSG00000103942	ENST00000304231;ENST00000450735	T;D	0.83591	1.53;-1.74	5.47	5.47	0.80525	.	0.000000	0.64402	D	0.000001	D	0.91603	0.7347	M	0.86028	2.79	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.92651	0.6133	10	0.62326	D	0.03	.	14.7216	0.69311	1.0:0.0:0.0:0.0	.	176;187	Q9NSB8-2;Q9NSB8	.;HOME2_HUMAN	P	187;176	ENSP00000305632:L187P;ENSP00000407634:L176P	ENSP00000305632:L187P	L	-	2	0	HOMER2	81320574	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	8.833000	0.92089	2.088000	0.63022	0.533000	0.62120	CTG	.	.		0.652	HOMER2-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418689.1		
AKAP13	11214	hgsc.bcm.edu	37	15	86122651	86122651	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:86122651T>C	ENST00000394518.2	+	7	1447	c.1352T>C	c.(1351-1353)gTc>gCc	p.V451A	RP11-815J21.2_ENST00000561409.1_RNA|AKAP13_ENST00000361243.2_Missense_Mutation_p.V451A	NM_001270546.1|NM_007200.4	NP_001257475.1|NP_009131.2	Q12802	AKP13_HUMAN	A kinase (PRKA) anchor protein 13	451					apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nuclear export (GO:0051168)|positive regulation of apoptotic process (GO:0043065)|protein phosphorylation (GO:0006468)|regulation of cardiac muscle hypertrophy (GO:0010611)|regulation of glucocorticoid mediated signaling pathway (GO:1900169)|regulation of protein kinase activity (GO:0045859)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	cAMP-dependent protein kinase activity (GO:0004691)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|central_nervous_system(4)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(13)|liver(1)|lung(43)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	98						AGAGACTTGGTCATGGAGCCA	0.498																																					p.V451A	Melanoma(94;603 1453 3280 32295 32951)	Atlas-SNP	.											.	AKAP13	394	.	0			c.T1352C						.						63.0	67.0	66.0					15																	86122651		2202	4299	6501	SO:0001583	missense	11214	exon7			ACTTGGTCATGGA	M90360	CCDS32319.1, CCDS32320.1, CCDS73778.1	15q24-q25	2013-01-10	2002-06-13			ENSG00000170776		"""A-kinase anchor proteins"", ""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	371	protein-coding gene	gene with protein product		604686	"""lymphoid blast crisis oncogene"""	LBC		9627117, 1860836	Standard	NM_007200		Approved	Ht31, BRX, AKAP-Lbc, c-lbc, PROTO-LB, HA-3, ARHGEF13	uc002blu.2	Q12802		ENST00000394518.2:c.1352T>C	chr15.hg19:g.86122651T>C	ENSP00000378026:p.Val451Ala	248.0	0.0		214.0	9.0	NM_007200	Q14572|Q59FP6|Q86W90|Q8WXQ6|Q96JP6|Q96P79|Q9Y5T0|Q9Y5T6	Missense_Mutation	SNP	ENST00000394518.2	hg19	CCDS32319.1	.	.	.	.	.	.	.	.	.	.	T	11.43	1.636992	0.29157	.	.	ENSG00000170776	ENST00000361243;ENST00000394518;ENST00000394516;ENST00000458540	T;T	0.12774	2.69;2.65	4.55	-4.25	0.03766	.	.	.	.	.	T	0.05777	0.0151	N	0.24115	0.695	0.09310	N	1	B;B	0.09022	0.001;0.002	B;B	0.06405	0.001;0.002	T	0.44329	-0.9335	9	0.02654	T	1	.	5.5114	0.16882	0.0:0.374:0.2986:0.3274	.	451;451	Q12802;Q12802-2	AKP13_HUMAN;.	A	451;451;450;450	ENSP00000354718:V451A;ENSP00000378026:V451A	ENSP00000354718:V451A	V	+	2	0	AKAP13	83923655	0.000000	0.05858	0.000000	0.03702	0.073000	0.16967	-0.902000	0.04088	-0.908000	0.03857	0.460000	0.39030	GTC	.	.		0.498	AKAP13-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417318.1	NM_007200	
TICRR	90381	hgsc.bcm.edu	37	15	90138760	90138760	+	Silent	SNP	A	A	G	rs545887163		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:90138760A>G	ENST00000268138.7	+	7	1923	c.1818A>G	c.(1816-1818)aaA>aaG	p.K606K	TICRR_ENST00000560985.1_Silent_p.K605K			Q7Z2Z1	TICRR_HUMAN	TOPBP1-interacting checkpoint and replication regulator	606					cell cycle checkpoint (GO:0000075)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|formation of translation preinitiation complex (GO:0001731)|mitotic DNA replication checkpoint (GO:0033314)|regulation of DNA-dependent DNA replication initiation (GO:0030174)|response to ionizing radiation (GO:0010212)	nucleus (GO:0005634)	chromatin binding (GO:0003682)										CTGGGGAGAAAGGAATCCAAA	0.438													A|||	1	0.000199681	0.0	0.0	5008	,	,		17318	0.001		0.0	False		,,,				2504	0.0				p.K606K		Atlas-SNP	.											.	.	.	.	0			c.A1818G						.						101.0	97.0	98.0					15																	90138760		1871	4106	5977	SO:0001819	synonymous_variant	90381	exon7			GGAGAAAGGAATC	AK123612	CCDS10352.2	15q26.1	2012-07-11	2012-07-11	2012-07-11	ENSG00000140534	ENSG00000140534			28704	protein-coding gene	gene with protein product	"""TOPBP1-interacting replication-stimulating protein"", ""SLD3 homolog (S. cerevisiae)"""	613298	"""chromosome 15 open reading frame 42"""	C15orf42		20116089, 20080954	Standard	NM_152259		Approved	MGC45866, FLJ41618, Treslin, SLD3	uc002boe.3	Q7Z2Z1	OTTHUMG00000149648	ENST00000268138.7:c.1818A>G	chr15.hg19:g.90138760A>G		181.0	0.0		126.0	6.0	NM_152259	B2RE07|B3KVV9|D3IUT4|Q8N4X8|Q8NCH6|Q9BU55	Silent	SNP	ENST00000268138.7	hg19	CCDS10352.2																																																																																			.	.		0.438	TICRR-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000312856.1	NM_152259	
IGF1R	3480	hgsc.bcm.edu	37	15	99440006	99440006	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:99440006A>G	ENST00000268035.6	+	4	1585	c.974A>G	c.(973-975)gAa>gGa	p.E325G	IGF1R_ENST00000560432.1_3'UTR|IGF1R_ENST00000558762.1_Missense_Mutation_p.E325G	NM_000875.3	NP_000866.1	P08069	IGF1R_HUMAN	insulin-like growth factor 1 receptor	325					axonogenesis (GO:0007409)|brain development (GO:0007420)|epidermis development (GO:0008544)|establishment of cell polarity (GO:0030010)|exocrine pancreas development (GO:0031017)|immune response (GO:0006955)|inactivation of MAPKK activity (GO:0051389)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|male sex determination (GO:0030238)|mammary gland development (GO:0030879)|negative regulation of apoptotic process (GO:0043066)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|peptidyl-tyrosine autophosphorylation (GO:0038083)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokinesis (GO:0032467)|positive regulation of DNA replication (GO:0045740)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mitosis (GO:0045840)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of steroid hormone biosynthetic process (GO:0090031)|prostate gland epithelium morphogenesis (GO:0060740)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein tetramerization (GO:0051262)|regulation of JNK cascade (GO:0046328)|response to vitamin E (GO:0033197)|signal transduction (GO:0007165)	caveola (GO:0005901)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor binding (GO:0005520)|insulin-like growth factor I binding (GO:0031994)|insulin-like growth factor-activated receptor activity (GO:0005010)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)			NS(2)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(13)|lung(20)|ovary(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63	all_cancers(4;4.17e-14)|all_epithelial(3;4.34e-15)|Lung NSC(78;0.00175)|all_lung(78;0.00351)|Melanoma(26;0.00505)|Medulloblastoma(229;0.163)		Epithelial(2;1.94e-12)|all cancers(5;6.83e-11)|BRCA - Breast invasive adenocarcinoma(2;2.88e-09)|OV - Ovarian serous cystadenocarcinoma(32;0.00261)		"""""""Insulin(DB00071)|Insulin Glargine(DB00047)|Insulin Lispro(DB00046)|Insulin Regular(DB00030)|Mecasermin(DB01277)"""	ATCCCTTGTGAAGGTCCTTGC	0.398																																					p.E325G		Atlas-SNP	.											.	IGF1R	147	.	0			c.A974G						.						93.0	84.0	87.0					15																	99440006		2197	4297	6494	SO:0001583	missense	3480	exon4			CTTGTGAAGGTCC	M69229	CCDS10378.1, CCDS73785.1	15q26.3	2013-02-11			ENSG00000140443	ENSG00000140443		"""CD molecules"", ""Fibronectin type III domain containing"""	5465	protein-coding gene	gene with protein product		147370				1316909	Standard	XM_006720486		Approved	JTK13, CD221, IGFIR, MGC18216, IGFR	uc002bul.3	P08069	OTTHUMG00000149851	ENST00000268035.6:c.974A>G	chr15.hg19:g.99440006A>G	ENSP00000268035:p.Glu325Gly	94.0	0.0		89.0	4.0	NM_000875	B1B5Y2|Q14CV2|Q9UCC0	Missense_Mutation	SNP	ENST00000268035.6	hg19	CCDS10378.1	.	.	.	.	.	.	.	.	.	.	A	20.6	4.017997	0.75275	.	.	ENSG00000140443	ENST00000268035	D	0.97404	-4.37	5.79	5.79	0.91817	Growth factor, receptor (1);Furin-like cysteine-rich domain (1);	0.000000	0.64402	D	0.000016	D	0.95465	0.8527	L	0.53729	1.69	0.58432	D	0.999999	P;P	0.45986	0.87;0.499	B;B	0.40741	0.339;0.217	D	0.95081	0.8213	10	0.41790	T	0.15	.	16.1354	0.81481	1.0:0.0:0.0:0.0	.	325;325	C9J5X1;P08069	.;IGF1R_HUMAN	G	325	ENSP00000268035:E325G	ENSP00000268035:E325G	E	+	2	0	IGF1R	97257529	1.000000	0.71417	0.998000	0.56505	0.991000	0.79684	7.497000	0.81536	2.207000	0.71202	0.533000	0.62120	GAA	.	.		0.398	IGF1R-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313537.2	NM_000875	
AXIN1	8312	hgsc.bcm.edu	37	16	341208	341208	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:341208A>G	ENST00000262320.3	-	9	2647	c.2276T>C	c.(2275-2277)aTg>aCg	p.M759T	AXIN1_ENST00000354866.3_Intron	NM_003502.3	NP_003493.1	O15169	AXIN1_HUMAN	axin 1	759	Interaction with PPP2CA.				activation of JUN kinase activity (GO:0007257)|activation of protein kinase activity (GO:0032147)|apoptotic process (GO:0006915)|axial mesoderm formation (GO:0048320)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in neural plate anterior/posterior pattern formation (GO:0060823)|cell death (GO:0008219)|cellular protein complex assembly (GO:0043623)|cellular response to organic cyclic compound (GO:0071407)|cytoplasmic microtubule organization (GO:0031122)|determination of left/right symmetry (GO:0007368)|dorsal/ventral axis specification (GO:0009950)|embryonic eye morphogenesis (GO:0048048)|embryonic skeletal joint morphogenesis (GO:0060272)|forebrain anterior/posterior pattern specification (GO:0021797)|genetic imprinting (GO:0071514)|in utero embryonic development (GO:0001701)|muscle cell development (GO:0055001)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of protein metabolic process (GO:0051248)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|negative regulation of Wnt signaling pathway (GO:0030178)|nucleocytoplasmic transport (GO:0006913)|olfactory placode formation (GO:0030910)|optic placode formation (GO:0001743)|positive regulation of GTPase activity (GO:0043547)|positive regulation of JNK cascade (GO:0046330)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|post-anal tail morphogenesis (GO:0036342)|protein catabolic process (GO:0030163)|protein homooligomerization (GO:0051260)|protein polyubiquitination (GO:0000209)|regulation of catenin import into nucleus (GO:0035412)|sensory perception of sound (GO:0007605)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|Wnt signaling pathway involved in somitogenesis (GO:0090244)|Wnt-activated signaling pathway involved in forebrain neuron fate commitment (GO:0021881)	beta-catenin destruction complex (GO:0030877)|cell cortex (GO:0005938)|cell periphery (GO:0071944)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic microtubule (GO:0005881)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lateral plasma membrane (GO:0016328)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|protein complex scaffold (GO:0032947)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|ubiquitin protein ligase binding (GO:0031625)			biliary_tract(27)|breast(4)|central_nervous_system(6)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(20)|liver(81)|lung(5)|ovary(2)|prostate(3)|salivary_gland(7)|skin(5)|stomach(4)|thyroid(41)|upper_aerodigestive_tract(4)|urinary_tract(2)	221		all_cancers(16;2.75e-07)|all_epithelial(16;1.6e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00774)|all_lung(18;0.0187)				GGAGAGCTCCATGTCCGACAC	0.677																																					p.M759T		Atlas-SNP	.											.	AXIN1	290	.	0			c.T2276C						.						58.0	41.0	47.0					16																	341208		2183	4285	6468	SO:0001583	missense	8312	exon9			AGCTCCATGTCCG	AF009674	CCDS10405.1, CCDS10406.1	16p13.3	2012-04-17			ENSG00000103126	ENSG00000103126		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	903	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 49"""	603816				9230313	Standard	NM_003502		Approved	PPP1R49	uc002cgp.2	O15169	OTTHUMG00000064930	ENST00000262320.3:c.2276T>C	chr16.hg19:g.341208A>G	ENSP00000262320:p.Met759Thr	121.0	0.0		95.0	4.0	NM_003502	Q4TT26|Q4TT27|Q86YA7|Q8WVW6|Q96S28	Missense_Mutation	SNP	ENST00000262320.3	hg19	CCDS10405.1	.	.	.	.	.	.	.	.	.	.	A	1.208	-0.630629	0.03584	.	.	ENSG00000103126	ENST00000262320	T	0.59224	0.28	3.57	2.46	0.29980	.	0.590702	0.15688	N	0.249550	T	0.37919	0.1021	N	0.25647	0.755	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.07908	-1.0748	10	0.12430	T	0.62	-0.7091	7.74	0.28835	0.8929:0.0:0.1071:0.0	.	759	O15169	AXIN1_HUMAN	T	759	ENSP00000262320:M759T	ENSP00000262320:M759T	M	-	2	0	AXIN1	281209	0.996000	0.38824	0.990000	0.47175	0.992000	0.81027	1.118000	0.31246	0.458000	0.26988	0.402000	0.26972	ATG	.	.		0.677	AXIN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139441.3		
CACNA1H	8912	hgsc.bcm.edu	37	16	1245064	1245064	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:1245064A>G	ENST00000348261.5	+	3	640	c.392A>G	c.(391-393)gAg>gGg	p.E131G	CACNA1H_ENST00000358590.4_Missense_Mutation_p.E131G|CACNA1H_ENST00000565831.1_Missense_Mutation_p.E131G	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit	131					aldosterone biosynthetic process (GO:0032342)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|myoblast fusion (GO:0007520)|positive regulation of acrosome reaction (GO:2000344)|regulation of heart contraction (GO:0008016)|regulation of membrane potential (GO:0042391)|transport (GO:0006810)	caveola (GO:0005901)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|metal ion binding (GO:0046872)|scaffold protein binding (GO:0097110)			breast(4)|endometrium(5)|kidney(2)|lung(23)	34		Hepatocellular(780;0.00369)			Amiodarone(DB01118)|Bepridil(DB01244)|Cinnarizine(DB00568)|Felodipine(DB01023)|Flunarizine(DB04841)|Isradipine(DB00270)|Nifedipine(DB01115)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Zonisamide(DB00909)	TGCGGCTCCGAGCGCTGCAAC	0.647											OREG0023543	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E131G		Atlas-SNP	.											.	CACNA1H	317	.	0			c.A392G						.						77.0	83.0	81.0					16																	1245064		2073	4192	6265	SO:0001583	missense	8912	exon3			GCTCCGAGCGCTG	AL031703	CCDS45375.1, CCDS45376.1	16p13.3	2012-03-07	2007-02-16					"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1395	protein-coding gene	gene with protein product		607904				9670923, 16382099	Standard	NM_021098		Approved	Cav3.2	uc002cks.3	O95180		ENST00000348261.5:c.392A>G	chr16.hg19:g.1245064A>G	ENSP00000334198:p.Glu131Gly	130.0	0.0	594	94.0	4.0	NM_021098	B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Missense_Mutation	SNP	ENST00000348261.5	hg19	CCDS45375.1	.	.	.	.	.	.	.	.	.	.	A	16.77	3.214953	0.58452	.	.	ENSG00000196557	ENST00000348261;ENST00000358590	D;D	0.97279	-4.32;-4.32	4.48	4.48	0.54585	.	0.793515	0.11701	N	0.537916	D	0.97779	0.9271	L	0.54323	1.7	0.35120	D	0.766995	D;D	0.89917	1.0;0.97	D;P	0.85130	0.997;0.683	D	0.98220	1.0477	10	0.62326	D	0.03	.	13.2699	0.60155	1.0:0.0:0.0:0.0	.	131;131	O95180-2;O95180	.;CAC1H_HUMAN	G	131	ENSP00000334198:E131G;ENSP00000351401:E131G	ENSP00000334198:E131G	E	+	2	0	CACNA1H	1185065	1.000000	0.71417	0.996000	0.52242	0.081000	0.17604	4.657000	0.61490	1.797000	0.52628	0.392000	0.25879	GAG	.	.		0.647	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	NM_001005407	
CACNA1H	8912	hgsc.bcm.edu	37	16	1252154	1252154	+	Silent	SNP	C	C	T			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:1252154C>T	ENST00000348261.5	+	9	1952	c.1704C>T	c.(1702-1704)gaC>gaT	p.D568D	CACNA1H_ENST00000358590.4_Silent_p.D568D|CACNA1H_ENST00000565831.1_Silent_p.D568D	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit	568					aldosterone biosynthetic process (GO:0032342)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|myoblast fusion (GO:0007520)|positive regulation of acrosome reaction (GO:2000344)|regulation of heart contraction (GO:0008016)|regulation of membrane potential (GO:0042391)|transport (GO:0006810)	caveola (GO:0005901)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|metal ion binding (GO:0046872)|scaffold protein binding (GO:0097110)			breast(4)|endometrium(5)|kidney(2)|lung(23)	34		Hepatocellular(780;0.00369)			Amiodarone(DB01118)|Bepridil(DB01244)|Cinnarizine(DB00568)|Felodipine(DB01023)|Flunarizine(DB04841)|Isradipine(DB00270)|Nifedipine(DB01115)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Zonisamide(DB00909)	GACCCCCCGACGCAGAGTCTG	0.751																																					p.D568D		Atlas-SNP	.											CACNA1H_ENST00000358590,colon,carcinoma,0,2	CACNA1H	317	.	0			c.C1704T						.						2.0	3.0	3.0					16																	1252154		1441	3415	4856	SO:0001819	synonymous_variant	8912	exon9			CCCCGACGCAGAG	AL031703	CCDS45375.1, CCDS45376.1	16p13.3	2012-03-07	2007-02-16					"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1395	protein-coding gene	gene with protein product		607904				9670923, 16382099	Standard	NM_021098		Approved	Cav3.2	uc002cks.3	O95180		ENST00000348261.5:c.1704C>T	chr16.hg19:g.1252154C>T		72.0	1.0		47.0	3.0	NM_021098	B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Silent	SNP	ENST00000348261.5	hg19	CCDS45375.1																																																																																			.	.		0.751	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	NM_001005407	
ZNF200	7752	hgsc.bcm.edu	37	16	3273915	3273915	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:3273915A>G	ENST00000431561.3	-	5	1777	c.1165T>C	c.(1165-1167)Tgt>Cgt	p.C389R	ZNF200_ENST00000414144.2_Missense_Mutation_p.C389R|ZNF200_ENST00000396868.3_Missense_Mutation_p.C388R|ZNF200_ENST00000575948.1_Missense_Mutation_p.C388R|ZNF200_ENST00000396870.4_Missense_Mutation_p.C388R|ZNF200_ENST00000396871.4_Missense_Mutation_p.C388R|AJ003147.9_ENST00000576468.1_RNA	NM_001145447.1|NM_003454.3	NP_001138919.1|NP_003445.2	P98182	ZN200_HUMAN	zinc finger protein 200	389					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(2)|kidney(2)|large_intestine(4)|lung(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	17						CGGGTCTTACAGGCTGAGTGG	0.483																																					p.C389R		Atlas-SNP	.											.	ZNF200	36	.	0			c.T1165C						.						195.0	207.0	203.0					16																	3273915		2197	4300	6497	SO:0001583	missense	7752	exon5			TCTTACAGGCTGA	AF060866	CCDS10497.1, CCDS42112.1, CCDS45395.1	16p13.3	2013-01-08			ENSG00000010539	ENSG00000010539		"""Zinc fingers, C2H2-type"""	12993	protein-coding gene	gene with protein product		603231				9288094, 9787081	Standard	NM_003454		Approved		uc002cuk.2	P98182	OTTHUMG00000129317	ENST00000431561.3:c.1165T>C	chr16.hg19:g.3273915A>G	ENSP00000395723:p.Cys389Arg	141.0	0.0		108.0	5.0	NM_003454	D3DUB7|D3DUB8|O15361|Q5XKM5|Q7Z5V1	Missense_Mutation	SNP	ENST00000431561.3	hg19	CCDS10497.1	.	.	.	.	.	.	.	.	.	.	A	3.233	-0.157040	0.06544	.	.	ENSG00000010539	ENST00000396870;ENST00000396868;ENST00000396871;ENST00000414144;ENST00000431561	T;T;T	0.05786	3.4;3.39;3.44	5.42	3.06	0.35304	Zinc finger, C2H2 (1);	0.536582	0.15812	N	0.243428	T	0.02455	0.0075	N	0.04746	-0.17	0.09310	N	1	P;P;P	0.37636	0.468;0.468;0.603	B;B;B	0.31812	0.064;0.064;0.136	T	0.40496	-0.9560	10	0.33940	T	0.23	-26.442	3.4599	0.07529	0.6953:0.0:0.1061:0.1986	.	388;389;388	D3DUB7;P98182;P98182-2	.;ZN200_HUMAN;.	R	389;388;388;388;389	ENSP00000380077:C388R;ENSP00000380080:C388R;ENSP00000395723:C389R	ENSP00000380077:C388R	C	-	1	0	ZNF200	3213916	0.003000	0.15002	0.284000	0.24805	0.894000	0.52154	1.828000	0.39111	1.019000	0.39547	0.455000	0.32223	TGT	.	.		0.483	ZNF200-005	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000437545.1		
CORO7	79585	hgsc.bcm.edu	37	16	4410485	4410485	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:4410485A>G	ENST00000251166.4	-	20	2127	c.1982T>C	c.(1981-1983)gTg>gCg	p.V661A	CORO7-PAM16_ENST00000572467.1_Missense_Mutation_p.V661A|CORO7_ENST00000539968.1_Missense_Mutation_p.V441A|CORO7_ENST00000537233.2_Missense_Mutation_p.V643A|CORO7-PAM16_ENST00000572274.1_5'Flank|CORO7_ENST00000423908.2_3'UTR|CORO7_ENST00000574025.1_Missense_Mutation_p.V576A	NM_024535.4	NP_078811.3	P57737	CORO7_HUMAN	coronin 7	661					actin filament polymerization (GO:0030041)|Golgi to endosome transport (GO:0006895)|protein transport (GO:0015031)	cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|trans-Golgi network (GO:0005802)	actin binding (GO:0003779)			breast(3)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(8)|prostate(2)|skin(2)|urinary_tract(2)	23						GTAGACCCGCACACGCCCATC	0.652																																					p.V661A		Atlas-SNP	.											.	CORO7	73	.	0			c.T1982C						.						36.0	40.0	38.0					16																	4410485		2193	4297	6490	SO:0001583	missense	79585	exon20			ACCCGCACACGCC	AK097238	CCDS10513.1, CCDS55982.1, CCDS58417.1	16p13.3	2013-01-10			ENSG00000262246	ENSG00000262246		"""Coronins"", ""WD repeat domain containing"""	26161	protein-coding gene	gene with protein product		611668				15327992	Standard	NM_024535		Approved	FLJ22021		P57737	OTTHUMG00000129465	ENST00000251166.4:c.1982T>C	chr16.hg19:g.4410485A>G	ENSP00000251166:p.Val661Ala	155.0	0.0		131.0	7.0	NM_024535	B4DFD6|B4DL18|I3L416|Q17RK4	Missense_Mutation	SNP	ENST00000251166.4	hg19	CCDS10513.1	.	.	.	.	.	.	.	.	.	.	A	22.0	4.230187	0.79688	.	.	ENSG00000103426	ENST00000251166;ENST00000537233;ENST00000539968	T;T	0.66460	-0.21;-0.21	5.18	5.18	0.71444	WD40/YVTN repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.599767	0.16100	N	0.229640	T	0.66992	0.2846	L	0.58583	1.82	0.80722	D	1	B;B;B;P;P	0.40578	0.234;0.201;0.406;0.722;0.67	B;B;B;B;B	0.41440	0.297;0.13;0.32;0.205;0.357	T	0.69510	-0.5126	10	0.54805	T	0.06	-4.6904	14.6767	0.68986	1.0:0.0:0.0:0.0	.	576;643;441;661;642	P57737-2;B4DFD6;B3KUH7;P57737;B4DKU9	.;.;.;CORO7_HUMAN;.	A	661;576;441	ENSP00000251166:V661A;ENSP00000446221:V441A	ENSP00000251166:V661A	V	-	2	0	CORO7	4350486	0.922000	0.31269	0.894000	0.35097	0.654000	0.38779	8.317000	0.89987	1.952000	0.56665	0.379000	0.24179	GTG	.	.		0.652	CORO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251628.2	NM_024535	
TMEM186	25880	hgsc.bcm.edu	37	16	8890335	8890335	+	Missense_Mutation	SNP	C	C	T			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:8890335C>T	ENST00000333050.6	-	2	149	c.116G>A	c.(115-117)aGc>aAc	p.S39N	TMEM186_ENST00000564869.1_Intron|PMM2_ENST00000569958.1_5'Flank|PMM2_ENST00000566983.1_Intron|PMM2_ENST00000268261.4_5'Flank|PMM2_ENST00000537352.1_5'Flank|PMM2_ENST00000539622.1_5'Flank	NM_015421.3	NP_056236.2	Q96B77	TM186_HUMAN	transmembrane protein 186	39						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				NS(1)|endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	9						GGGTGAACTGCTGCCCACCCA	0.537																																					p.S39N		Atlas-SNP	.											.	TMEM186	21	.	0			c.G116A						.						116.0	121.0	120.0					16																	8890335		2197	4300	6497	SO:0001583	missense	25880	exon2			GAACTGCTGCCCA	BC015912	CCDS10535.1	16p13.2	2008-02-05	2007-02-08	2007-02-08	ENSG00000184857	ENSG00000184857			24530	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 51"""	C16orf51		11230166	Standard	NM_015421		Approved	DKFZP564K2062	uc002cze.3	Q96B77	OTTHUMG00000129696	ENST00000333050.6:c.116G>A	chr16.hg19:g.8890335C>T	ENSP00000331640:p.Ser39Asn	204.0	0.0		139.0	6.0	NM_015421	B2RAY0|Q9Y4T4	Missense_Mutation	SNP	ENST00000333050.6	hg19	CCDS10535.1	.	.	.	.	.	.	.	.	.	.	C	12.58	1.980444	0.34942	.	.	ENSG00000184857	ENST00000333050	.	.	.	5.31	2.28	0.28536	.	0.394396	0.21823	N	0.068584	T	0.41050	0.1142	M	0.63428	1.95	0.09310	N	0.999997	B	0.14012	0.009	B	0.16289	0.015	T	0.36866	-0.9730	9	0.51188	T	0.08	-12.7793	6.6541	0.22979	0.0:0.6926:0.1563:0.1511	.	39	Q96B77	TM186_HUMAN	N	39	.	ENSP00000331640:S39N	S	-	2	0	TMEM186	8797836	0.041000	0.20044	0.025000	0.17156	0.008000	0.06430	0.638000	0.24674	0.324000	0.23333	0.655000	0.94253	AGC	.	.		0.537	TMEM186-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251903.1	NM_015421	
ATF7IP2	80063	hgsc.bcm.edu	37	16	10525288	10525288	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:10525288T>C	ENST00000396560.2	+	3	1038	c.811T>C	c.(811-813)Tca>Cca	p.S271P	ATF7IP2_ENST00000543967.1_Intron|ATF7IP2_ENST00000396559.1_Missense_Mutation_p.S271P|ATF7IP2_ENST00000324570.5_Missense_Mutation_p.S271P|ATF7IP2_ENST00000356427.2_Missense_Mutation_p.S271P	NM_024997.3	NP_079273.2	Q5U623	MCAF2_HUMAN	activating transcription factor 7 interacting protein 2	271					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				large_intestine(3)	3						AACATGGCAGTCATCACTTGA	0.318																																					p.S271P		Atlas-SNP	.											.	ATF7IP2	40	.	0			c.T811C						.						51.0	52.0	51.0					16																	10525288		2191	4296	6487	SO:0001583	missense	80063	exon3			TGGCAGTCATCAC	AK022730	CCDS10540.1, CCDS58422.1	16p13.2	2008-02-05			ENSG00000166669	ENSG00000166669			20397	protein-coding gene	gene with protein product		613645					Standard	NM_001256160		Approved	FLJ12668	uc002czu.3	Q5U623	OTTHUMG00000129749	ENST00000396560.2:c.811T>C	chr16.hg19:g.10525288T>C	ENSP00000379808:p.Ser271Pro	235.0	0.0		156.0	7.0	NM_024997	B2RNR2|Q53EZ7|Q658U2|Q6IS97|Q8N9X8|Q9H9L6	Missense_Mutation	SNP	ENST00000396560.2	hg19	CCDS10540.1	.	.	.	.	.	.	.	.	.	.	T	5.177	0.218143	0.09810	.	.	ENSG00000166669	ENST00000396559;ENST00000396560;ENST00000535850;ENST00000356427;ENST00000324570	T;T;T;T;T	0.45668	0.89;0.89;0.89;0.89;0.89	5.61	3.35	0.38373	.	0.427317	0.17377	N	0.176434	T	0.31199	0.0789	L	0.40543	1.245	0.09310	N	1	B;B	0.21606	0.058;0.033	B;B	0.21546	0.035;0.035	T	0.23619	-1.0183	10	0.45353	T	0.12	-0.6523	5.7072	0.17915	0.0:0.087:0.1709:0.7421	.	271;271	Q5U623-2;Q5U623	.;MCAF2_HUMAN	P	271	ENSP00000379807:S271P;ENSP00000379808:S271P;ENSP00000440791:S271P;ENSP00000348799:S271P;ENSP00000322811:S271P	ENSP00000322811:S271P	S	+	1	0	ATF7IP2	10432789	0.000000	0.05858	0.000000	0.03702	0.028000	0.11728	0.113000	0.15499	0.409000	0.25649	0.459000	0.35465	TCA	.	.		0.318	ATF7IP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251961.1	NM_024997	
MKL2	57496	hgsc.bcm.edu	37	16	14352004	14352004	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:14352004T>C	ENST00000341243.5	+	14	2717	c.2717T>C	c.(2716-2718)cTc>cCc	p.L906P	MKL2_ENST00000318282.5_Missense_Mutation_p.L867P|MKL2_ENST00000574045.1_Missense_Mutation_p.L867P|MKL2_ENST00000571589.1_Missense_Mutation_p.L917P			Q9ULH7	MKL2_HUMAN	MKL/myocardin-like 2	906					blood vessel morphogenesis (GO:0048514)|cardiac muscle tissue development (GO:0048738)|embryonic organ development (GO:0048568)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|liver development (GO:0001889)|muscle organ development (GO:0007517)|positive regulation of striated muscle tissue development (GO:0045844)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|smooth muscle cell differentiation (GO:0051145)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			breast(3)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(6)|liver(2)|lung(7)|ovary(4)|pancreas(1)|prostate(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						TTTGATATCCTCATTAAGAGT	0.393																																					p.L867P		Atlas-SNP	.											.	MKL2	103	.	0			c.T2600C						.						102.0	86.0	92.0					16																	14352004		2197	4300	6497	SO:0001583	missense	57496	exon16			ATATCCTCATTAA	AB033069	CCDS32391.1	16p13.12	2012-11-29			ENSG00000186260	ENSG00000186260			29819	protein-coding gene	gene with protein product		609463				10574462	Standard	NM_014048		Approved	MRTF-B, FLJ31823	uc002dcg.3	Q9ULH7	OTTHUMG00000177379	ENST00000341243.5:c.2717T>C	chr16.hg19:g.14352004T>C	ENSP00000345841:p.Leu906Pro	151.0	0.0		124.0	5.0	NM_014048	A6ND53|B4DGT8|Q68CT1|Q6UB16|Q86WW2|Q8N226	Missense_Mutation	SNP	ENST00000341243.5	hg19		.	.	.	.	.	.	.	.	.	.	T	22.5	4.295194	0.81025	.	.	ENSG00000186260	ENST00000318282;ENST00000341243	.	.	.	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	T	0.79975	0.4539	M	0.81497	2.545	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.83039	-0.0158	9	0.87932	D	0	-21.2488	14.7871	0.69810	0.0:0.0:0.0:1.0	.	917;867	B4DGT8;Q9ULH7-4	.;.	P	867;906	.	ENSP00000339086:L867P	L	+	2	0	MKL2	14259505	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.577000	0.82486	2.098000	0.63641	0.460000	0.39030	CTC	.	.		0.393	MKL2-202	KNOWN	basic	protein_coding	protein_coding		NM_014048	
ABCC1	4363	hgsc.bcm.edu	37	16	16235094	16235094	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:16235094A>G	ENST00000399410.3	+	31	4727	c.4552A>G	c.(4552-4554)Aga>Gga	p.R1518G	ABCC1_ENST00000345148.5_Missense_Mutation_p.R1453G|ABCC1_ENST00000351154.5_Missense_Mutation_p.R1459G|ABCC1_ENST00000349029.5_Missense_Mutation_p.R1403G|ABCC1_ENST00000399408.2_Missense_Mutation_p.R1528G|ABCC1_ENST00000346370.5_Missense_Mutation_p.R1462G	NM_004996.3	NP_004987.2	P33527	MRP1_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 1	1518	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				arachidonic acid metabolic process (GO:0019369)|ATP catabolic process (GO:0006200)|cobalamin metabolic process (GO:0009235)|leukotriene metabolic process (GO:0006691)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			breast(3)|endometrium(9)|kidney(3)|large_intestine(12)|lung(20)|ovary(5)|prostate(1)|skin(3)	56					Abiraterone(DB05812)|Aminohippurate(DB00345)|Amprenavir(DB00701)|Atazanavir(DB01072)|Atorvastatin(DB01076)|Colchicine(DB01394)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Diclofenac(DB00586)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Epirubicin(DB00445)|Erythromycin(DB00199)|Etoposide(DB00773)|Fluorescein(DB00693)|Glutathione(DB00143)|Glyburide(DB01016)|Ibuprofen(DB01050)|Idarubicin(DB01177)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Methotrexate(DB00563)|Mifepristone(DB00834)|Mitoxantrone(DB01204)|Ofloxacin(DB01165)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Probenecid(DB01032)|Progesterone(DB00396)|Rifampicin(DB01045)|Ritonavir(DB00503)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Saxagliptin(DB06335)|Sulfinpyrazone(DB01138)|Vandetanib(DB05294)|Vemurafenib(DB08881)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)|Zoledronate(DB00399)	CCTGCAGCAGAGAGGTCTTTT	0.592																																					p.R1518G		Atlas-SNP	.											.	ABCC1	156	.	0			c.A4552G						.						118.0	122.0	121.0					16																	16235094		1921	4115	6036	SO:0001583	missense	4363	exon31			CAGCAGAGAGGTC	L05628	CCDS42122.1	16p13.1	2012-03-14			ENSG00000103222	ENSG00000103222		"""ATP binding cassette transporters / subfamily C"""	51	protein-coding gene	gene with protein product		158343	"""multidrug resistance associated protein 1"""	MRP, MRP1		8098549, 1360704	Standard	NM_004996		Approved	GS-X	uc010bvi.3	P33527	OTTHUMG00000048267	ENST00000399410.3:c.4552A>G	chr16.hg19:g.16235094A>G	ENSP00000382342:p.Arg1518Gly	106.0	0.0		117.0	5.0	NM_004996	A3RJX2|C9JPJ4|O14819|O43333|P78419|Q59GI9|Q9UQ97|Q9UQ99|Q9UQA0	Missense_Mutation	SNP	ENST00000399410.3	hg19	CCDS42122.1	.	.	.	.	.	.	.	.	.	.	A	15.86	2.957170	0.53293	.	.	ENSG00000103222	ENST00000399410;ENST00000399408;ENST00000346370;ENST00000351154;ENST00000345148;ENST00000349029;ENST00000536381	T;T;T;T;T;T	0.68181	-0.31;-0.31;-0.31;-0.31;0.1;-0.31	5.26	4.16	0.48862	ABC transporter-like (1);	0.395203	0.29783	N	0.011204	T	0.42877	0.1222	N	0.01771	-0.73	0.27345	N	0.9564	B;P;B;P;B;B	0.44521	0.011;0.837;0.246;0.554;0.159;0.246	B;P;B;B;B;B	0.44673	0.016;0.457;0.197;0.155;0.097;0.197	T	0.36163	-0.9759	10	0.36615	T	0.2	-5.7442	10.6785	0.45799	0.6928:0.3072:0.0:0.0	.	1403;1453;1462;1459;1518;1528	P33527-5;P33527-4;P33527-3;P33527-2;P33527;P33527-9	.;.;.;.;MRP1_HUMAN;.	G	1518;1528;1462;1459;1453;1403;1202	ENSP00000382342:R1518G;ENSP00000382340:R1528G;ENSP00000263019:R1462G;ENSP00000263017:R1459G;ENSP00000263014:R1453G;ENSP00000263016:R1403G	ENSP00000263014:R1453G	R	+	1	2	ABCC1	16142595	0.995000	0.38212	0.853000	0.33588	0.698000	0.40448	3.563000	0.53784	0.815000	0.34398	0.533000	0.62120	AGA	.	.		0.592	ABCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109701.1	NM_004996	
TBC1D10B	26000	hgsc.bcm.edu	37	16	30369601	30369601	+	Silent	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:30369601A>G	ENST00000409939.3	-	9	2171	c.2091T>C	c.(2089-2091)acT>acC	p.T697T	CD2BP2_ENST00000305596.3_5'Flank|RP11-347C12.10_ENST00000563252.1_lincRNA	NM_015527.3	NP_056342.3	Q4KMP7	TB10B_HUMAN	TBC1 domain family, member 10B	697					positive regulation of Rab GTPase activity (GO:0032851)|regulation of Rab GTPase activity (GO:0032313)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	Rab GTPase activator activity (GO:0005097)			endometrium(2)|kidney(1)|lung(2)|urinary_tract(1)	6			Colorectal(24;0.193)			GTCCCTCAGCAGTGACCACAG	0.692																																					p.T697T		Atlas-SNP	.											.	TBC1D10B	32	.	0			c.T2091C						.						29.0	24.0	26.0					16																	30369601		2192	4291	6483	SO:0001819	synonymous_variant	26000	exon9			CTCAGCAGTGACC	BC063112	CCDS10676.2	16p11.2	2013-07-09			ENSG00000169221	ENSG00000169221			24510	protein-coding gene	gene with protein product		613620				20404108	Standard	NM_015527		Approved	DKFZP434P1750, Rab27A-GAPbeta, FLJ13130, EPI64B	uc002dxt.3	Q4KMP7	OTTHUMG00000132396	ENST00000409939.3:c.2091T>C	chr16.hg19:g.30369601A>G		131.0	0.0		73.0	6.0	NM_015527	B9A6L0|Q6IN54|Q6P530|Q71RG7|Q86VC5|Q9H8Z2|Q9NUN6|Q9UFP2	Silent	SNP	ENST00000409939.3	hg19	CCDS10676.2																																																																																			.	.		0.692	TBC1D10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255527.3	NM_015527	
ITGAL	3683	hgsc.bcm.edu	37	16	30521788	30521788	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:30521788A>G	ENST00000356798.6	+	22	2795	c.2615A>G	c.(2614-2616)cAc>cGc	p.H872R	ITGAL_ENST00000358164.5_Missense_Mutation_p.H788R|ITGAL_ENST00000433423.2_Intron	NM_002209.2	NP_002200.2	P20701	ITAL_HUMAN	integrin, alpha L (antigen CD11A (p180), lymphocyte function-associated antigen 1; alpha polypeptide)	872					activated T cell proliferation (GO:0050798)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|cellular component movement (GO:0006928)|extracellular matrix organization (GO:0030198)|heterophilic cell-cell adhesion (GO:0007157)|inflammatory response (GO:0006954)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of T cell proliferation (GO:0042102)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)|T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell (GO:0002291)	cell surface (GO:0009986)|cell-cell junction (GO:0005911)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|integrin alphaL-beta2 complex (GO:0034687)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|ICAM-3 receptor activity (GO:0030369)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(10)|kidney(4)|large_intestine(12)|lung(32)|ovary(3)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	76					Antithymocyte globulin(DB00098)|Efalizumab(DB00095)|Lovastatin(DB00227)	AAAGCAGGCCACTCGGTGAGT	0.577																																					p.H872R	NSCLC(110;1462 1641 3311 33990 49495)	Atlas-SNP	.											.	ITGAL	149	.	0			c.A2615G						.						83.0	75.0	78.0					16																	30521788		2197	4300	6497	SO:0001583	missense	3683	exon22			CAGGCCACTCGGT		CCDS32433.1, CCDS45461.1	16p13.1-p11	2010-03-23				ENSG00000005844		"""CD molecules"", ""Integrins"""	6148	protein-coding gene	gene with protein product		153370		CD11A		3284962	Standard	NM_002209		Approved	LFA-1	uc002dyi.4	P20701		ENST00000356798.6:c.2615A>G	chr16.hg19:g.30521788A>G	ENSP00000349252:p.His872Arg	176.0	0.0		123.0	6.0	NM_002209	O43746|Q45H73|Q96HB1|Q9UBC8	Missense_Mutation	SNP	ENST00000356798.6	hg19	CCDS32433.1	.	.	.	.	.	.	.	.	.	.	a	11.65	1.701628	0.30142	.	.	ENSG00000005844	ENST00000356798;ENST00000358164	T;T	0.43688	0.94;0.94	4.36	-2.08	0.07254	Integrin alpha-2 (1);	1.623940	0.03218	N	0.177136	T	0.15998	0.0385	N	0.02011	-0.69	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.0	T	0.13282	-1.0515	10	0.45353	T	0.12	.	1.122	0.01727	0.215:0.329:0.2888:0.1672	.	788;872	Q96HB1;P20701	.;ITAL_HUMAN	R	872;788	ENSP00000349252:H872R;ENSP00000350886:H788R	ENSP00000349252:H872R	H	+	2	0	ITGAL	30429289	0.000000	0.05858	0.003000	0.11579	0.406000	0.30931	-0.176000	0.09811	-0.082000	0.12640	0.158000	0.16466	CAC	.	.		0.577	ITGAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434508.2		
ITGAL	3683	hgsc.bcm.edu	37	16	30529197	30529197	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:30529197A>G	ENST00000356798.6	+	28	3293	c.3113A>G	c.(3112-3114)gAg>gGg	p.E1038G	ITGAL_ENST00000358164.5_Missense_Mutation_p.E954G|ITGAL_ENST00000433423.2_Missense_Mutation_p.E272G	NM_002209.2	NP_002200.2	P20701	ITAL_HUMAN	integrin, alpha L (antigen CD11A (p180), lymphocyte function-associated antigen 1; alpha polypeptide)	1038					activated T cell proliferation (GO:0050798)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|cellular component movement (GO:0006928)|extracellular matrix organization (GO:0030198)|heterophilic cell-cell adhesion (GO:0007157)|inflammatory response (GO:0006954)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of T cell proliferation (GO:0042102)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)|T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell (GO:0002291)	cell surface (GO:0009986)|cell-cell junction (GO:0005911)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|integrin alphaL-beta2 complex (GO:0034687)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|ICAM-3 receptor activity (GO:0030369)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(10)|kidney(4)|large_intestine(12)|lung(32)|ovary(3)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	76					Antithymocyte globulin(DB00098)|Efalizumab(DB00095)|Lovastatin(DB00227)	GGGACTCTGGAGCTGGTGGGA	0.622																																					p.E1038G	NSCLC(110;1462 1641 3311 33990 49495)	Atlas-SNP	.											.	ITGAL	149	.	0			c.A3113G						.						80.0	74.0	76.0					16																	30529197		2197	4300	6497	SO:0001583	missense	3683	exon28			CTCTGGAGCTGGT		CCDS32433.1, CCDS45461.1	16p13.1-p11	2010-03-23				ENSG00000005844		"""CD molecules"", ""Integrins"""	6148	protein-coding gene	gene with protein product		153370		CD11A		3284962	Standard	NM_002209		Approved	LFA-1	uc002dyi.4	P20701		ENST00000356798.6:c.3113A>G	chr16.hg19:g.30529197A>G	ENSP00000349252:p.Glu1038Gly	95.0	0.0		81.0	4.0	NM_002209	O43746|Q45H73|Q96HB1|Q9UBC8	Missense_Mutation	SNP	ENST00000356798.6	hg19	CCDS32433.1	.	.	.	.	.	.	.	.	.	.	A	24.7	4.560669	0.86335	.	.	ENSG00000005844	ENST00000356798;ENST00000358164;ENST00000433423	T;T;T	0.58940	0.3;0.65;1.79	4.99	4.99	0.66335	.	0.000000	0.52532	D	0.000075	T	0.72732	0.3497	M	0.72479	2.2	0.31854	N	0.621817	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.997;0.998;0.998	T	0.78270	-0.2269	10	0.72032	D	0.01	.	10.9958	0.47575	1.0:0.0:0.0:0.0	.	272;954;1038	B4E021;Q96HB1;P20701	.;.;ITAL_HUMAN	G	1038;954;272	ENSP00000349252:E1038G;ENSP00000350886:E954G;ENSP00000409377:E272G	ENSP00000349252:E1038G	E	+	2	0	ITGAL	30436698	1.000000	0.71417	0.724000	0.30704	0.840000	0.47671	2.348000	0.44045	2.078000	0.62432	0.460000	0.39030	GAG	.	.		0.622	ITGAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434508.2		
ITGAX	3687	hgsc.bcm.edu	37	16	31382664	31382664	+	Silent	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:31382664T>C	ENST00000268296.4	+	16	1972	c.1851T>C	c.(1849-1851)ccT>ccC	p.P617P	ITGAX_ENST00000562522.1_Silent_p.P617P	NM_000887.3	NP_000878.2	P20702	ITAX_HUMAN	integrin, alpha X (complement component 3 receptor 4 subunit)	617					blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|organ morphogenesis (GO:0009887)	cell surface (GO:0009986)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(42)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	77						GGACCAGACCTGTGCTCTGGG	0.647																																					p.P617P		Atlas-SNP	.											.	ITGAX	198	.	0			c.T1851C						.						47.0	40.0	42.0					16																	31382664		2197	4300	6497	SO:0001819	synonymous_variant	3687	exon16			CAGACCTGTGCTC	BC038237	CCDS10711.1, CCDS67014.1	16p11.2	2010-03-23	2006-02-10		ENSG00000140678	ENSG00000140678		"""CD molecules"", ""Complement system"", ""Integrins"""	6152	protein-coding gene	gene with protein product		151510	"""integrin, alpha X (antigen CD11C (p150), alpha polypeptide)"""	CD11C		3284962, 2303426	Standard	NM_001286375		Approved	CD11c	uc002ebu.1	P20702	OTTHUMG00000132465	ENST00000268296.4:c.1851T>C	chr16.hg19:g.31382664T>C		110.0	0.0		94.0	4.0	NM_000887	Q8IVA6	Silent	SNP	ENST00000268296.4	hg19	CCDS10711.1																																																																																			.	.		0.647	ITGAX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255628.2	NM_000887	
ITGAD	3681	hgsc.bcm.edu	37	16	31405596	31405596	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:31405596A>G	ENST00000389202.2	+	2	120	c.71A>G	c.(70-72)gAg>gGg	p.E24G		NM_005353.2	NP_005344.2	Q13349	ITAD_HUMAN	integrin, alpha D	24					activated T cell proliferation (GO:0050798)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|immune response (GO:0006955)|integrin-mediated signaling pathway (GO:0007229)	cell surface (GO:0009986)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|liver(2)|lung(43)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	71						GATGTGGAGGAGCCTACGATC	0.577																																					p.E24G		Atlas-SNP	.											.	ITGAD	154	.	0			c.A71G						.						95.0	82.0	86.0					16																	31405596		2197	4300	6497	SO:0001583	missense	3681	exon2			TGGAGGAGCCTAC	U40274	CCDS32438.1	16p13.1-p11	2010-03-23				ENSG00000156886		"""CD molecules"", ""Integrins"""	6146	protein-coding gene	gene with protein product		602453				8666289, 9598326	Standard	NM_005353		Approved	CD11d, ADB2	uc002ebv.1	Q13349		ENST00000389202.2:c.71A>G	chr16.hg19:g.31405596A>G	ENSP00000373854:p.Glu24Gly	170.0	0.0		114.0	5.0	NM_005353	Q15575|Q15576	Missense_Mutation	SNP	ENST00000389202.2	hg19	CCDS32438.1	.	.	.	.	.	.	.	.	.	.	A	11.36	1.616205	0.28801	.	.	ENSG00000156886	ENST00000444228;ENST00000389202	T	0.71698	-0.59	4.54	3.41	0.39046	.	.	.	.	.	T	0.53690	0.1812	L	0.28274	0.84	0.09310	N	1	B;B;B	0.20164	0.01;0.042;0.042	B;B;B	0.14023	0.005;0.01;0.01	T	0.35549	-0.9784	9	0.20519	T	0.43	.	8.0133	0.30365	0.7928:0.2072:0.0:0.0	.	24;40;24	B7Z6V7;Q59H14;Q13349	.;.;ITAD_HUMAN	G	40;24	ENSP00000373854:E24G	ENSP00000373854:E24G	E	+	2	0	ITGAD	31313097	0.008000	0.16893	0.215000	0.23724	0.882000	0.50991	2.169000	0.42434	0.551000	0.29008	0.459000	0.35465	GAG	.	.		0.577	ITGAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432836.1	NM_005353	
VPS35	55737	hgsc.bcm.edu	37	16	46696258	46696258	+	Missense_Mutation	SNP	A	A	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:46696258A>C	ENST00000299138.7	-	15	2022	c.1964T>G	c.(1963-1965)cTt>cGt	p.L655R	RP11-93O14.2_ENST00000569353.1_RNA	NM_018206.4	NP_060676.2	Q96QK1	VPS35_HUMAN	vacuolar protein sorting 35 homolog (S. cerevisiae)	655					cell death (GO:0008219)|protein transport (GO:0015031)|retrograde transport, endosome to Golgi (GO:0042147)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|retromer complex (GO:0030904)				breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(11)|pancreas(1)|prostate(1)|urinary_tract(1)	23		all_cancers(37;7.65e-05)|all_epithelial(9;0.000154)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116)				GGATGCAGCAAGGGCACACTG	0.493																																					p.L655R		Atlas-SNP	.											.	VPS35	49	.	0			c.T1964G						.						99.0	87.0	91.0					16																	46696258		2203	4300	6503	SO:0001583	missense	55737	exon15			GCAGCAAGGGCAC	AF175265	CCDS10721.1	16q12	2012-06-27	2006-12-19		ENSG00000069329	ENSG00000069329		"""Parkinson disease"""	13487	protein-coding gene	gene with protein product		601501	"""vacuolar protein sorting 35 (yeast homolog)"", ""vacuolar protein sorting 35 (yeast)"""			11112353, 21763482	Standard	NM_018206		Approved	FLJ10752, MEM3, PARK17	uc002eef.4	Q96QK1	OTTHUMG00000132542	ENST00000299138.7:c.1964T>G	chr16.hg19:g.46696258A>C	ENSP00000299138:p.Leu655Arg	211.0	0.0		141.0	52.0	NM_018206	Q561W2|Q9H016|Q9H096|Q9H4P3|Q9H8J0|Q9NRS7|Q9NVG2|Q9NX80|Q9NZK2	Missense_Mutation	SNP	ENST00000299138.7	hg19	CCDS10721.1	.	.	.	.	.	.	.	.	.	.	.	23.7	4.444215	0.83993	.	.	ENSG00000069329	ENST00000299138;ENST00000541330	T	0.64260	-0.09	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	T	0.78528	0.4297	M	0.86502	2.82	0.80722	D	1	D;D	0.76494	0.999;0.981	D;P	0.70227	0.968;0.557	T	0.78125	-0.2326	10	0.07482	T	0.82	-16.6205	15.624	0.76833	1.0:0.0:0.0:0.0	.	655;520	Q96QK1;F5GYF5	VPS35_HUMAN;.	R	655;520	ENSP00000299138:L655R	ENSP00000299138:L655R	L	-	2	0	VPS35	45253759	1.000000	0.71417	0.993000	0.49108	0.994000	0.84299	9.339000	0.96797	2.090000	0.63153	0.459000	0.35465	CTT	.	.		0.493	VPS35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255742.3		
MYLK3	91807	hgsc.bcm.edu	37	16	46781803	46781803	+	Silent	SNP	C	C	T			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:46781803C>T	ENST00000394809.4	-	1	418	c.303G>A	c.(301-303)caG>caA	p.Q101Q	MYLK3_ENST00000536476.1_Intron	NM_182493.2	NP_872299.2	Q32MK0	MYLK3_HUMAN	myosin light chain kinase 3	101					cardiac myofibril assembly (GO:0055003)|cellular response to interleukin-1 (GO:0071347)|positive regulation of sarcomere organization (GO:0060298)|protein phosphorylation (GO:0006468)|regulation of vascular permeability involved in acute inflammatory response (GO:0002528)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|myosin light chain kinase activity (GO:0004687)			central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(7)|lung(11)|ovary(3)|prostate(3)|skin(5)|stomach(3)	37		all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116)				CCGCATCCTGCTGCATGGCCC	0.697																																					p.Q101Q		Atlas-SNP	.											.	MYLK3	82	.	0			c.G303A						.						34.0	31.0	32.0					16																	46781803		2203	4299	6502	SO:0001819	synonymous_variant	91807	exon1			ATCCTGCTGCATG	AJ247087	CCDS10723.2	16q11.2	2008-10-23			ENSG00000140795	ENSG00000140795			29826	protein-coding gene	gene with protein product	"""MLC kinase"""	612147				17885681	Standard	NM_182493		Approved	caMLCK, MLCK	uc002eei.4	Q32MK0	OTTHUMG00000132543	ENST00000394809.4:c.303G>A	chr16.hg19:g.46781803C>T		150.0	0.0		122.0	5.0	NM_182493	B5BUL9|B7Z5U8|Q32MK1|Q96DV1	Silent	SNP	ENST00000394809.4	hg19	CCDS10723.2																																																																																			.	.		0.697	MYLK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255743.2	NM_182493	
AARS	16	hgsc.bcm.edu	37	16	70302272	70302272	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:70302272T>C	ENST00000261772.8	-	8	1116	c.973A>G	c.(973-975)Aga>Gga	p.R325G		NM_001605.2	NP_001596.2			alanyl-tRNA synthetase											breast(3)|cervix(2)|endometrium(5)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)|prostate(1)	27		Ovarian(137;0.0365)		BRCA - Breast invasive adenocarcinoma(221;0.161)		AGAATCCGTCTCAACACATAT	0.512																																					p.R325G		Atlas-SNP	.											.	AARS	62	.	0			c.A973G						.						83.0	74.0	77.0					16																	70302272		2198	4300	6498	SO:0001583	missense	16	exon8			TCCGTCTCAACAC	D32050	CCDS32474.1	16q22.1	2014-09-17			ENSG00000090861	ENSG00000090861	6.1.1.7	"""Aminoacyl tRNA synthetases / Class II"""	20	protein-coding gene	gene with protein product	"""alanine tRNA ligase 1, cytoplasmic"""	601065				8595897	Standard	NM_001605		Approved		uc002eyn.1	P49588	OTTHUMG00000177042	ENST00000261772.8:c.973A>G	chr16.hg19:g.70302272T>C	ENSP00000261772:p.Arg325Gly	100.0	0.0		69.0	5.0	NM_001605		Missense_Mutation	SNP	ENST00000261772.8	hg19	CCDS32474.1	.	.	.	.	.	.	.	.	.	.	T	19.00	3.742391	0.69418	.	.	ENSG00000090861	ENST00000261772	D	0.87887	-2.31	5.66	1.9	0.25705	Alanyl-tRNA synthetase, class IIc, anti-codon-binding domain (1);Alanyl-tRNA synthetase, class IIc, core domain (1);Alanyl-tRNA synthetase, class IIc, N-terminal (1);	0.044018	0.85682	D	0.000000	D	0.96175	0.8753	H	0.99573	4.635	0.58432	D	0.999999	D;D	0.89917	0.975;1.0	D;D	0.97110	0.949;1.0	D	0.95711	0.8758	10	0.87932	D	0	-6.9159	13.0037	0.58692	0.0:0.0:0.5199:0.4801	.	333;325	E7ETK8;P49588	.;SYAC_HUMAN	G	325	ENSP00000261772:R325G	ENSP00000261772:R325G	R	-	1	2	AARS	68859773	1.000000	0.71417	0.610000	0.28997	0.979000	0.70002	1.724000	0.38064	0.043000	0.15746	0.529000	0.55759	AGA	.	.		0.512	AARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435021.2	NM_001605	
ZFHX3	463	hgsc.bcm.edu	37	16	72829729	72829729	+	Silent	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:72829729T>C	ENST00000268489.5	-	9	7524	c.6852A>G	c.(6850-6852)cgA>cgG	p.R2284R	ZFHX3_ENST00000397992.5_Silent_p.R1370R	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	2284					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)				CCACTATCACTCGGGTTGGAA	0.473																																					p.R2284R		Atlas-SNP	.											.	ZFHX3	404	.	0			c.A6852G						.						159.0	159.0	159.0					16																	72829729		2198	4300	6498	SO:0001819	synonymous_variant	463	exon9			TATCACTCGGGTT	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.6852A>G	chr16.hg19:g.72829729T>C		183.0	0.0		121.0	5.0	NM_006885	D3DWS8|O15101|Q13719	Silent	SNP	ENST00000268489.5	hg19	CCDS10908.1																																																																																			.	.		0.473	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885	
CFDP1	10428	hgsc.bcm.edu	37	16	75339067	75339067	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:75339067T>C	ENST00000283882.3	-	6	796	c.664A>G	c.(664-666)Agt>Ggt	p.S222G		NM_006324.2	NP_006315.1	Q9UEE9	CFDP1_HUMAN	craniofacial development protein 1	222	BCNT-C. {ECO:0000255|PROSITE- ProRule:PRU00610}.				cell adhesion (GO:0007155)|multicellular organismal development (GO:0007275)|negative regulation of fibroblast apoptotic process (GO:2000270)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)					endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)	5						CTCATGCCACTTGATCTTTTT	0.408																																					p.S222G		Atlas-SNP	.											.	CFDP1	17	.	0			c.A664G						.						85.0	87.0	86.0					16																	75339067		2198	4300	6498	SO:0001583	missense	10428	exon6			TGCCACTTGATCT	AB009285	CCDS10916.1	16q22.2-q22.3	2011-08-12			ENSG00000153774	ENSG00000153774			1873	protein-coding gene	gene with protein product	"""Bucentaur"", ""centromere protein 29"""	608108				9602175, 9006920, 11992732	Standard	NM_006324		Approved	BCNT, p97, CP27, SWC5, Yeti, CENP-29	uc002fdy.3	Q9UEE9	OTTHUMG00000137615	ENST00000283882.3:c.664A>G	chr16.hg19:g.75339067T>C	ENSP00000283882:p.Ser222Gly	107.0	0.0		96.0	4.0	NM_006324	O00393|O00404|Q9UEF0|Q9UEF1|Q9UEF8	Missense_Mutation	SNP	ENST00000283882.3	hg19	CCDS10916.1	.	.	.	.	.	.	.	.	.	.	T	8.252	0.809285	0.16537	.	.	ENSG00000153774	ENST00000283882	T	0.45276	0.9	5.45	5.45	0.79879	.	0.249302	0.40469	N	0.001087	T	0.20981	0.0505	N	0.05574	-0.02	0.43965	D	0.996643	B;B	0.12013	0.005;0.005	B;B	0.14023	0.01;0.01	T	0.13019	-1.0525	10	0.16896	T	0.51	-4.2101	8.9547	0.35809	0.0:0.0833:0.0:0.9167	.	222;222	B2R9W9;Q9UEE9	.;CFDP1_HUMAN	G	222	ENSP00000283882:S222G	ENSP00000283882:S222G	S	-	1	0	CFDP1	73896568	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.906000	0.48735	2.060000	0.61445	0.528000	0.53228	AGT	.	.		0.408	CFDP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269031.2	NM_006324	
PKD1L2	114780	hgsc.bcm.edu	37	16	81241219	81241219	+	RNA	SNP	C	C	T			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:81241219C>T	ENST00000525539.1	-	0	781				PKD1L2_ENST00000337114.4_RNA	NM_052892.3	NP_443124.3	Q7Z442	PK1L2_HUMAN	polycystic kidney disease 1-like 2						ion transport (GO:0006811)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)	p.S261I(2)		breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						GAAACTCTCACTGGACACCAT	0.448																																					p.S261N		Atlas-SNP	.											PKD1L2_ENST00000525539,NS,carcinoma,0,2	PKD1L2	361	.	2	Substitution - Missense(2)	kidney(2)	c.G782A						.						118.0	118.0	118.0					16																	81241219		1982	4163	6145			114780	exon5			CTCTCACTGGACA	AY164483	CCDS61998.1, CCDS61999.1	16q23.2	2014-09-11			ENSG00000166473	ENSG00000166473			21715	protein-coding gene	gene with protein product		607894				12782129	Standard	NM_052892		Approved	KIAA1879	uc002fgf.1	Q7Z442	OTTHUMG00000166126		chr16.hg19:g.81241219C>T		81.0	0.0		47.0	4.0	NM_001076780	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Missense_Mutation	SNP	ENST00000525539.1	hg19		.	.	.	.	.	.	.	.	.	.	C	0.014	-1.572444	0.00887	.	.	ENSG00000166473	ENST00000337114	T	0.01258	5.09	5.47	0.0931	0.14475	.	0.645577	0.16079	N	0.230614	T	0.00936	0.0031	.	.	.	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.48375	-0.9041	9	0.21014	T	0.42	0.3378	5.6149	0.17426	0.0:0.1572:0.262:0.5809	.	261;261	Q7Z442-3;Q7Z442	.;PK1L2_HUMAN	N	261	ENSP00000337397:S261N	ENSP00000337397:S261N	S	-	2	0	PKD1L2	79798720	0.057000	0.20700	0.000000	0.03702	0.003000	0.03518	1.679000	0.37597	-0.265000	0.09352	-0.253000	0.11424	AGT	.	.		0.448	PKD1L2-001	KNOWN	non_canonical_polymorphism|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000387972.2		
PKD1L2	114780	hgsc.bcm.edu	37	16	81242150	81242150	+	RNA	SNP	T	T	C	rs55980345|rs532218091|rs548490632|rs386792900	byFrequency	TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:81242150T>C	ENST00000525539.1	-	0	705				PKD1L2_ENST00000337114.4_RNA	NM_052892.3	NP_443124.3	Q7Z442	PK1L2_HUMAN	polycystic kidney disease 1-like 2						ion transport (GO:0006811)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)	p.N236fs*26(6)		breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						GGACACAGGTTTCCAAAGTAG	0.557																																					p.N236D		Atlas-SNP	.											.,52	PKD1L2	361	.	6	Deletion - Frameshift(6)	breast(4)|lung(2)	c.A706G						.						77.0	61.0	66.0					16																	81242150		2025	3850	5875			114780	exon4			ACAGGTTTCCAAA	AY164483	CCDS61998.1, CCDS61999.1	16q23.2	2014-09-11			ENSG00000166473	ENSG00000166473			21715	protein-coding gene	gene with protein product		607894				12782129	Standard	NM_052892		Approved	KIAA1879	uc002fgf.1	Q7Z442	OTTHUMG00000166126		chr16.hg19:g.81242150T>C		4.0	1.0		4.0	3.0	NM_001076780	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Missense_Mutation	SNP	ENST00000525539.1	hg19		.	.	.	.	.	.	.	.	.	.	T	1.316	-0.600871	0.03744	.	.	ENSG00000166473	ENST00000337114	T	0.10668	2.85	4.29	2.17	0.27698	D-galactoside/L-rhamnose binding SUEL lectin domain (2);	0.205291	0.40469	N	0.001088	T	0.03739	0.0106	.	.	.	0.21184	N	0.999765	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.46048	-0.9219	9	0.02654	T	1	-7.787	7.6885	0.28554	0.0:0.7269:0.0:0.2731	.	236;236	Q7Z442-3;Q7Z442	.;PK1L2_HUMAN	D	236	ENSP00000337397:N236D	ENSP00000337397:N236D	N	-	1	0	PKD1L2	79799651	1.000000	0.71417	1.000000	0.80357	0.842000	0.47809	1.014000	0.29950	0.269000	0.21961	-0.624000	0.04008	AAC	.	.		0.557	PKD1L2-001	KNOWN	non_canonical_polymorphism|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000387972.2		
ADAD2	161931	hgsc.bcm.edu	37	16	84230305	84230305	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:84230305T>C	ENST00000315906.5	+	9	1631	c.1579T>C	c.(1579-1581)Ttt>Ctt	p.F527L	RP11-486L19.2_ENST00000561900.1_RNA|ADAD2_ENST00000268624.3_Missense_Mutation_p.F609L|RP11-486L19.2_ENST00000536986.1_RNA|RP11-486L19.2_ENST00000569834.1_RNA|RP11-486L19.2_ENST00000565643.1_RNA	NM_001145400.1	NP_001138872.1	Q8NCV1	ADAD2_HUMAN	adenosine deaminase domain containing 2	527	A to I editase. {ECO:0000255|PROSITE- ProRule:PRU00240}.				RNA processing (GO:0006396)		adenosine deaminase activity (GO:0004000)|RNA binding (GO:0003723)			NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(2)|skin(1)	13						TCTCCGGGCCTTTCACCAGGC	0.642																																					p.F609L		Atlas-SNP	.											.	ADAD2	46	.	0			c.T1825C						.						71.0	75.0	74.0					16																	84230305		2200	4300	6500	SO:0001583	missense	161931	exon10			CGGGCCTTTCACC	AF447586	CCDS10944.1, CCDS45536.1	16q24.1	2007-05-31			ENSG00000140955	ENSG00000140955			30714	protein-coding gene	gene with protein product							Standard	NM_139174		Approved	TENRL, FLJ00337	uc002fhr.2	Q8NCV1	OTTHUMG00000137637	ENST00000315906.5:c.1579T>C	chr16.hg19:g.84230305T>C	ENSP00000325153:p.Phe527Leu	92.0	0.0		100.0	4.0	NM_139174	B2RCL6|Q8NA94	Missense_Mutation	SNP	ENST00000315906.5	hg19	CCDS45536.1	.	.	.	.	.	.	.	.	.	.	T	15.96	2.985827	0.53934	.	.	ENSG00000140955	ENST00000315906;ENST00000268624	D;D	0.94931	-3.56;-3.56	5.27	4.18	0.49190	Adenosine deaminase/editase (2);	0.065249	0.64402	N	0.000010	D	0.96583	0.8885	M	0.85462	2.755	0.39372	D	0.966105	D;D	0.76494	0.998;0.999	D;D	0.72338	0.977;0.973	D	0.96633	0.9468	10	0.87932	D	0	-34.6595	7.0084	0.24849	0.0:0.1003:0.0:0.8997	.	527;609	Q8NCV1;Q8NCV1-2	ADAD2_HUMAN;.	L	527;609	ENSP00000325153:F527L;ENSP00000268624:F609L	ENSP00000268624:F609L	F	+	1	0	ADAD2	82787806	1.000000	0.71417	1.000000	0.80357	0.033000	0.12548	2.896000	0.48656	1.975000	0.57531	0.477000	0.44152	TTT	.	.		0.642	ADAD2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433385.1	NM_139174	
ZNF469	84627	hgsc.bcm.edu	37	16	88497588	88497588	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:88497588A>G	ENST00000437464.1	+	2	3626	c.3626A>G	c.(3625-3627)gAc>gGc	p.D1209G	ZNF469_ENST00000565624.1_Missense_Mutation_p.D1237G	NM_001127464.1	NP_001120936.1	Q96JG9	ZN469_HUMAN	zinc finger protein 469	1209					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|endometrium(6)|kidney(3)|large_intestine(1)|skin(6)	20						TCAGCCCCGGACAGCACAGAA	0.637																																					p.D1209G		Atlas-SNP	.											.	ZNF469	121	.	0			c.A3626G						.						31.0	44.0	40.0					16																	88497588		692	1591	2283	SO:0001583	missense	84627	exon2			CCCCGGACAGCAC	AB058761	CCDS45544.1	16q24	2010-08-04				ENSG00000225614		"""Zinc fingers, C2H2-type"""	23216	protein-coding gene	gene with protein product		612078				11347906	Standard	NM_001127464		Approved	KIAA1858	uc002fku.2	Q96JG9		ENST00000437464.1:c.3626A>G	chr16.hg19:g.88497588A>G	ENSP00000402343:p.Asp1209Gly	156.0	0.0		93.0	4.0	NM_001127464		Missense_Mutation	SNP	ENST00000437464.1	hg19	CCDS45544.1	.	.	.	.	.	.	.	.	.	.	A	8.053	0.766360	0.15983	.	.	ENSG00000225614	ENST00000437464	T	0.08546	3.08	3.99	0.801	0.18679	.	.	.	.	.	T	0.04998	0.0134	N	0.19112	0.55	0.09310	N	1	B	0.18310	0.027	B	0.12837	0.008	T	0.38779	-0.9645	9	0.72032	D	0.01	.	3.0279	0.06097	0.4019:0.2426:0.3555:0.0	.	1209	Q96JG9	ZN469_HUMAN	G	1209	ENSP00000402343:D1209G	ENSP00000402343:D1209G	D	+	2	0	ZNF469	87025089	0.000000	0.05858	0.001000	0.08648	0.007000	0.05969	-0.057000	0.11768	0.535000	0.28714	0.402000	0.26972	GAC	.	.		0.637	ZNF469-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NG_012236	
RABEP1	9135	hgsc.bcm.edu	37	17	5250197	5250197	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:5250197A>G	ENST00000546142.2	+	6	948	c.761A>G	c.(760-762)aAa>aGa	p.K254R	RABEP1_ENST00000262477.6_Missense_Mutation_p.K254R|RABEP1_ENST00000408982.2_Missense_Mutation_p.K254R|RABEP1_ENST00000537505.1_Missense_Mutation_p.K211R|RABEP1_ENST00000341923.6_Missense_Mutation_p.K254R			Q15276	RABE1_HUMAN	rabaptin, RAB GTPase binding effector protein 1	254					apoptotic process (GO:0006915)|endocytosis (GO:0006897)|membrane fusion (GO:0061025)|protein transport (GO:0015031)	early endosome (GO:0005769)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)	GTPase activator activity (GO:0005096)|protein homodimerization activity (GO:0042803)			NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)	8						GATGCTGAGAAACTGCGGAAA	0.328																																					p.K254R		Atlas-SNP	.											.	RABEP1	59	.	0			c.A761G						.						75.0	71.0	72.0					17																	5250197		1832	4085	5917	SO:0001583	missense	9135	exon6			CTGAGAAACTGCG	AF098638	CCDS42243.1, CCDS45592.1	17p13.2	2008-02-05				ENSG00000029725			17677	protein-coding gene	gene with protein product		603616				8521472	Standard	NM_001291582		Approved	neurocrescin, RAB5EP, RABPT5, rabaptin-5	uc002gbm.4	Q15276		ENST00000546142.2:c.761A>G	chr17.hg19:g.5250197A>G	ENSP00000437701:p.Lys254Arg	71.0	0.0		53.0	4.0	NM_004703	B2RAG7|O95369|Q8IVX3	Missense_Mutation	SNP	ENST00000546142.2	hg19	CCDS45592.1	.	.	.	.	.	.	.	.	.	.	A	25.5	4.639999	0.87760	.	.	ENSG00000029725	ENST00000262477;ENST00000408982;ENST00000539669;ENST00000546142;ENST00000341923;ENST00000537505	T;T;T;T;T	0.47869	0.83;0.84;0.83;0.84;0.83	5.26	5.26	0.73747	.	0.098208	0.64402	D	0.000001	T	0.50599	0.1625	N	0.14661	0.345	0.53688	D	0.99997	D;D;D;D;D	0.71674	0.993;0.988;0.997;0.996;0.998	P;P;D;P;D	0.78314	0.84;0.696;0.98;0.883;0.991	T	0.51301	-0.8723	10	0.31617	T	0.26	-25.6589	14.7166	0.69275	1.0:0.0:0.0:0.0	.	211;211;254;254;254	F5H355;B4DMM4;Q05BX6;Q15276;Q15276-2	.;.;.;RABE1_HUMAN;.	R	254;254;254;254;254;211	ENSP00000262477:K254R;ENSP00000386150:K254R;ENSP00000437701:K254R;ENSP00000339569:K254R;ENSP00000445408:K211R	ENSP00000262477:K254R	K	+	2	0	RABEP1	5190921	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.857000	0.92250	2.141000	0.66446	0.451000	0.29950	AAA	.	.		0.328	RABEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439349.1	NM_004703	
NUP88	4927	hgsc.bcm.edu	37	17	5291154	5291154	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:5291154A>G	ENST00000573584.1	-	12	2223	c.1714T>C	c.(1714-1716)Ttc>Ctc	p.F572L	NUP88_ENST00000573169.1_5'Flank	NM_002532.4	NP_002523.2	Q99567	NUP88_HUMAN	nucleoporin 88kDa	572					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	transporter activity (GO:0005215)			endometrium(4)|kidney(4)|large_intestine(4)|lung(3)	15						TGCTCTCTGAACACCTGGGTG	0.478																																					p.F572L		Atlas-SNP	.											.	NUP88	47	.	0			c.T1714C						.						87.0	87.0	87.0					17																	5291154		2203	4300	6503	SO:0001583	missense	4927	exon12			CTCTGAACACCTG	Y08612	CCDS11070.1	17p13	2004-02-18	2002-08-29		ENSG00000108559	ENSG00000108559			8067	protein-coding gene	gene with protein product		602552	"""nucleoporin 88kD"""			9049309	Standard	NM_002532		Approved	MGC8530	uc002gbo.2	Q99567	OTTHUMG00000099453	ENST00000573584.1:c.1714T>C	chr17.hg19:g.5291154A>G	ENSP00000458954:p.Phe572Leu	158.0	0.0		89.0	4.0	NM_002532	D3DTM2|Q9BWE5	Missense_Mutation	SNP	ENST00000573584.1	hg19	CCDS11070.1	.	.	.	.	.	.	.	.	.	.	A	16.15	3.042942	0.55003	.	.	ENSG00000108559	ENST00000225696;ENST00000543132	.	.	.	4.76	4.76	0.60689	.	0.000000	0.85682	D	0.000000	T	0.41673	0.1169	L	0.33792	1.035	0.58432	D	0.999995	B;P	0.46859	0.042;0.885	B;P	0.45538	0.047;0.484	T	0.37197	-0.9716	9	0.02654	T	1	-17.8569	13.9189	0.63919	1.0:0.0:0.0:0.0	.	457;572	B4DP20;Q99567	.;NUP88_HUMAN	L	572;457	.	ENSP00000225696:F572L	F	-	1	0	NUP88	5231878	1.000000	0.71417	0.999000	0.59377	0.983000	0.72400	8.167000	0.89668	2.137000	0.66172	0.454000	0.30748	TTC	.	.		0.478	NUP88-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216918.3	NM_002532	
TP53	7157	hgsc.bcm.edu	37	17	7578503	7578503	+	Missense_Mutation	SNP	C	C	T	rs587782620		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:7578503C>T	ENST00000269305.4	-	5	616	c.427G>A	c.(427-429)Gtg>Atg	p.V143M	TP53_ENST00000574684.1_5'Flank|TP53_ENST00000413465.2_Missense_Mutation_p.V143M|TP53_ENST00000420246.2_Missense_Mutation_p.V143M|TP53_ENST00000359597.4_Missense_Mutation_p.V143M|TP53_ENST00000455263.2_Missense_Mutation_p.V143M|TP53_ENST00000445888.2_Missense_Mutation_p.V143M	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	143	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; strong DNA binding ability at 32.5 degrees Celsius; strong reduction of transcriptional activity at 37.5 degrees Celsius; severely represses interaction with ZNF385A).|V -> E (in sporadic cancers; somatic mutation).|V -> G (in sporadic cancers; somatic mutation).|V -> L (in sporadic cancers; somatic mutation).|V -> M (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.V143M(19)|p.0?(8)|p.V143L(4)|p.V143fs*27(2)|p.V11M(1)|p.L137_W146del10(1)|p.V143fs*29(1)|p.P142_Q144delPVQ(1)|p.K139fs*4(1)|p.A138_V143delAKTCPV(1)|p.V50M(1)|p.V143_S149del(1)|p.C141fs*5(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)	CACAGCTGCACAGGGCAGGTC	0.587		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.V143M	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,0,5	TP53	33396	.	42	Substitution - Missense(25)|Whole gene deletion(8)|Deletion - In frame(4)|Deletion - Frameshift(4)|Insertion - Frameshift(1)	haematopoietic_and_lymphoid_tissue(8)|breast(6)|bone(4)|upper_aerodigestive_tract(3)|central_nervous_system(3)|urinary_tract(3)|lung(3)|ovary(3)|salivary_gland(2)|large_intestine(2)|oesophagus(2)|cervix(1)|stomach(1)|prostate(1)	c.G427A						.						56.0	56.0	56.0					17																	7578503		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;	GCTGCACAGGGCA	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.427G>A	chr17.hg19:g.7578503C>T	ENSP00000269305:p.Val143Met	167.0	0.0		124.0	52.0	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	.	.	.	.	.	.	.	.	.	.	C	13.43	2.235817	0.39498	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315;ENST00000508793	D;D;D;D;D;D;D;D;D	0.99837	-7.06;-7.06;-7.06;-7.06;-7.06;-7.06;-7.06;-7.06;-7.06	5.48	4.51	0.55191	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.343688	0.28219	N	0.016151	D	0.99684	0.9881	M	0.76328	2.33	0.43018	D	0.994566	D;D;D;D;D;D;D	0.89917	1.0;1.0;0.999;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.87578	0.995;0.994;0.985;0.994;0.998;0.998;0.995	D	0.98175	1.0454	10	0.87932	D	0	-32.0412	7.6505	0.28346	0.1615:0.7548:0.0:0.0837	.	104;143;143;50;143;143;143	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	M	143;143;143;143;143;143;132;50;11;50;11;143	ENSP00000410739:V143M;ENSP00000352610:V143M;ENSP00000269305:V143M;ENSP00000398846:V143M;ENSP00000391127:V143M;ENSP00000391478:V143M;ENSP00000425104:V11M;ENSP00000423862:V50M;ENSP00000424104:V143M	ENSP00000269305:V143M	V	-	1	0	TP53	7519228	0.854000	0.29725	0.596000	0.28811	0.011000	0.07611	1.561000	0.36342	1.448000	0.47680	0.655000	0.94253	GTG	.	.		0.587	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	
CHD3	1107	hgsc.bcm.edu	37	17	7793914	7793914	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:7793914A>G	ENST00000330494.7	+	3	389	c.239A>G	c.(238-240)gAg>gGg	p.E80G	CHD3_ENST00000570758.1_3'UTR|CHD3_ENST00000380358.4_Missense_Mutation_p.E139G|CHD3_ENST00000358181.4_Missense_Mutation_p.E80G	NM_001005273.2	NP_001005273.1	Q12873	CHD3_HUMAN	chromodomain helicase DNA binding protein 3	80					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)				TTTGGTTCTGAGCGAGATGAG	0.453																																					p.E139G		Atlas-SNP	.											.	CHD3	169	.	0			c.A416G						.						40.0	43.0	42.0					17																	7793914		2203	4300	6503	SO:0001583	missense	1107	exon3			GTTCTGAGCGAGA	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.239A>G	chr17.hg19:g.7793914A>G	ENSP00000332628:p.Glu80Gly	136.0	0.0		113.0	5.0	NM_001005271	D3DTQ9|E9PG89|Q9Y4I0	Missense_Mutation	SNP	ENST00000330494.7	hg19	CCDS32554.1	.	.	.	.	.	.	.	.	.	.	A	14.10	2.435216	0.43224	.	.	ENSG00000170004	ENST00000380358;ENST00000358181;ENST00000330494	T;D;D	0.90563	1.47;-2.68;-2.69	4.61	4.61	0.57282	.	0.000000	0.40302	N	0.001136	D	0.85204	0.5643	L	0.43152	1.355	0.54753	D	0.999983	B;P;P	0.34522	0.447;0.455;0.455	B;B;B	0.30646	0.118;0.055;0.081	T	0.82645	-0.0355	10	0.20046	T	0.44	-22.9644	14.006	0.64463	1.0:0.0:0.0:0.0	.	80;80;139	Q12873-2;Q12873;E9PG89	.;CHD3_HUMAN;.	G	139;80;80	ENSP00000369716:E139G;ENSP00000350907:E80G;ENSP00000332628:E80G	ENSP00000332628:E80G	E	+	2	0	CHD3	7734639	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	5.159000	0.64923	1.691000	0.51100	0.383000	0.25322	GAG	.	.		0.453	CHD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318050.1	NM_001005273	
WDR16	146845	hgsc.bcm.edu	37	17	9489226	9489226	+	Silent	SNP	C	C	T			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:9489226C>T	ENST00000576499.1	+	2	221	c.207C>T	c.(205-207)tgC>tgT	p.C69C	WDR16_ENST00000352665.5_Silent_p.C69C|WDR16_ENST00000299764.5_Silent_p.C79C|WDR16_ENST00000396219.3_Intron					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						ACGTCTCCTGCTTGGCCATCT	0.453																																					p.C69C		Atlas-SNP	.											.	WDR16	67	.	0			c.C207T						.						186.0	165.0	172.0					17																	9489226		2203	4300	6503	SO:0001819	synonymous_variant	146845	exon2			CTCCTGCTTGGCC	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	ENST00000576499.1:c.207C>T	chr17.hg19:g.9489226C>T		139.0	0.0		93.0	4.0	NM_145054		Silent	SNP	ENST00000576499.1	hg19																																																																																				.	.		0.453	WDR16-009	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000439850.2	NM_145054	
USP43	124739	hgsc.bcm.edu	37	17	9586141	9586141	+	Splice_Site	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:9586141T>C	ENST00000285199.7	+	7	1203	c.1107T>C	c.(1105-1107)gcT>gcC	p.A369A	USP43_ENST00000570475.1_Splice_Site_p.A369A|USP43_ENST00000570827.2_3'UTR	NM_001267576.1|NM_153210.4	NP_001254505.1|NP_694942.3	Q70EL4	UBP43_HUMAN	ubiquitin specific peptidase 43	369	USP.				ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	26						CCCTTCTAGCTCATCCACTGG	0.532																																					p.A369A		Atlas-SNP	.											.	USP43	65	.	0			c.T1107C						.						70.0	72.0	72.0					17																	9586141		1959	4145	6104	SO:0001630	splice_region_variant	124739	exon7			TCTAGCTCATCCA	AK055188	CCDS45610.1, CCDS58516.1	17p12	2005-08-08	2005-08-08			ENSG00000154914		"""Ubiquitin-specific peptidases"""	20072	protein-coding gene	gene with protein product			"""ubiquitin specific protease 43"""			12838346	Standard	NM_153210		Approved	FLJ30626	uc010cod.4	Q70EL4		ENST00000285199.7:c.1106-1T>C	chr17.hg19:g.9586141T>C		122.0	0.0		114.0	5.0	NM_001267576	A6NDT9|B7ZLT9|B7ZVX5|Q8N2C5|Q96DQ6	Silent	SNP	ENST00000285199.7	hg19	CCDS45610.1																																																																																			.	.		0.532	USP43-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439855.3	NM_153210	Silent
USP43	124739	hgsc.bcm.edu	37	17	9604952	9604952	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:9604952A>G	ENST00000285199.7	+	12	2042	c.1946A>G	c.(1945-1947)gAc>gGc	p.D649G	USP43_ENST00000570475.1_Missense_Mutation_p.D649G|USP43_ENST00000570827.2_3'UTR	NM_001267576.1|NM_153210.4	NP_001254505.1|NP_694942.3	Q70EL4	UBP43_HUMAN	ubiquitin specific peptidase 43	649	USP.				ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	26						TACCCGCTGGACTTCCTGTAC	0.617																																					p.D649G		Atlas-SNP	.											.	USP43	65	.	0			c.A1946G						.						26.0	27.0	26.0					17																	9604952		2098	4225	6323	SO:0001583	missense	124739	exon12			CGCTGGACTTCCT	AK055188	CCDS45610.1, CCDS58516.1	17p12	2005-08-08	2005-08-08			ENSG00000154914		"""Ubiquitin-specific peptidases"""	20072	protein-coding gene	gene with protein product			"""ubiquitin specific protease 43"""			12838346	Standard	NM_153210		Approved	FLJ30626	uc010cod.4	Q70EL4		ENST00000285199.7:c.1946A>G	chr17.hg19:g.9604952A>G	ENSP00000285199:p.Asp649Gly	100.0	0.0		89.0	5.0	NM_001267576	A6NDT9|B7ZLT9|B7ZVX5|Q8N2C5|Q96DQ6	Missense_Mutation	SNP	ENST00000285199.7	hg19	CCDS45610.1	.	.	.	.	.	.	.	.	.	.	A	18.15	3.559789	0.65538	.	.	ENSG00000154914	ENST00000285199	T	0.02916	4.11	4.71	4.71	0.59529	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	2.618330	0.03151	U	0.167957	T	0.13372	0.0324	L	0.45470	1.425	0.80722	D	1	D;D;P;D	0.76494	0.999;0.98;0.745;0.999	D;P;P;D	0.76071	0.981;0.791;0.657;0.987	T	0.00118	-1.2033	10	0.49607	T	0.09	-29.4872	12.4203	0.55516	1.0:0.0:0.0:0.0	.	649;338;649;161	B7ZVX5;Q70EL4-3;Q70EL4;Q70EL4-2	.;.;UBP43_HUMAN;.	G	649	ENSP00000285199:D649G	ENSP00000285199:D649G	D	+	2	0	USP43	9545677	1.000000	0.71417	0.998000	0.56505	0.543000	0.35085	8.714000	0.91412	1.874000	0.54306	0.460000	0.39030	GAC	.	.		0.617	USP43-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439855.3	NM_153210	
SPECC1	92521	hgsc.bcm.edu	37	17	20109062	20109062	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:20109062A>G	ENST00000261503.5	+	4	1751	c.1700A>G	c.(1699-1701)gAg>gGg	p.E567G	SPECC1_ENST00000472876.1_Intron|SPECC1_ENST00000395522.2_Missense_Mutation_p.E486G|SPECC1_ENST00000395525.3_Missense_Mutation_p.E486G|SPECC1_ENST00000395527.4_Missense_Mutation_p.E567G|SPECC1_ENST00000536879.1_Intron|SPECC1_ENST00000395530.2_Missense_Mutation_p.E486G|AC004702.2_ENST00000580225.1_lincRNA|SPECC1_ENST00000395529.3_Missense_Mutation_p.E567G|SPECC1_ENST00000584527.1_5'Flank	NM_001033553.2	NP_001028725.1	Q5M775	CYTSB_HUMAN	sperm antigen with calponin homology and coiled-coil domains 1	567					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)		AAAGCCACAGAGGCCAGTGCT	0.473																																					p.E567G		Atlas-SNP	.											.	SPECC1	100	.	0			c.A1700G						.						69.0	71.0	70.0					17																	20109062		2203	4300	6503	SO:0001583	missense	92521	exon4			CCACAGAGGCCAG	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.1700A>G	chr17.hg19:g.20109062A>G	ENSP00000261503:p.Glu567Gly	153.0	0.0		85.0	4.0	NM_001033553	B4DHH0|B7WNS8|Q5IBP1|Q5IBP2|Q5IBP3|Q5IBP4|Q5M772|Q5M773|Q5M774|Q86XT8|Q8N4U4|Q8WU84|Q9HCQ3	Missense_Mutation	SNP	ENST00000261503.5	hg19	CCDS32590.1	.	.	.	.	.	.	.	.	.	.	A	6.165	0.398668	0.11696	.	.	ENSG00000128487	ENST00000395530;ENST00000261503;ENST00000395529;ENST00000395522;ENST00000395527;ENST00000395525	T;T;T;T	0.75050	-0.9;2.12;2.17;2.16	5.37	-1.03	0.10102	.	0.254962	0.45126	N	0.000384	T	0.60612	0.2282	L	0.53780	1.695	0.80722	D	1	B;B;B;B;B	0.22080	0.024;0.018;0.018;0.018;0.064	B;B;B;B;B	0.23716	0.03;0.014;0.023;0.023;0.048	T	0.48043	-0.9069	10	0.66056	D	0.02	-6.7994	0.7713	0.01024	0.4611:0.1322:0.1513:0.2554	.	567;486;486;567;567	A8MV89;Q5M775-4;Q5M775-3;Q5M775-2;Q5M775	.;.;.;.;CYTSB_HUMAN	G	567;567;567;486;486;486	ENSP00000261503:E567G;ENSP00000378900:E567G;ENSP00000378893:E486G;ENSP00000378896:E486G	ENSP00000261503:E567G	E	+	2	0	SPECC1	20049654	1.000000	0.71417	0.000000	0.03702	0.006000	0.05464	2.892000	0.48625	-0.423000	0.07394	0.533000	0.62120	GAG	.	.		0.473	SPECC1-018	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441206.1	NM_152904	
KSR1	8844	hgsc.bcm.edu	37	17	25930890	25930890	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:25930890T>C	ENST00000319524.6	+	13	1607	c.1607T>C	c.(1606-1608)cTc>cCc	p.L536P	KSR1_ENST00000581975.1_3'UTR|KSR1_ENST00000268763.6_Missense_Mutation_p.L399P|KSR1_ENST00000509603.2_Missense_Mutation_p.L514P|KSR1_ENST00000398988.3_Missense_Mutation_p.L399P			Q8IVT5	KSR1_HUMAN	kinase suppressor of ras 1	536					Ras protein signal transduction (GO:0007265)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|large_intestine(5)|lung(12)|prostate(2)|urinary_tract(1)	28	Lung NSC(42;0.00836)		BRCA - Breast invasive adenocarcinoma(3;0.00122)	UCEC - Uterine corpus endometrioid carcinoma (53;0.168)		GCAGCCCCGCTCCCTGAAGCT	0.537											OREG0024261	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L399P	Esophageal Squamous(88;1120 1336 6324 10502 16832)	Atlas-SNP	.											.	KSR1	151	.	0			c.T1196C						.						65.0	75.0	72.0					17																	25930890		1989	4163	6152	SO:0001583	missense	8844	exon13			CCCCGCTCCCTGA	U43586	CCDS58532.1	17q11.2	2012-05-23	2005-12-14	2005-12-14	ENSG00000141068	ENSG00000141068			6465	protein-coding gene	gene with protein product		601132	"""kinase suppressor of ras"""	KSR		8521512	Standard	XM_006722151		Approved	RSU2	uc031qzj.1	Q8IVT5	OTTHUMG00000132051	ENST00000319524.6:c.1607T>C	chr17.hg19:g.25930890T>C	ENSP00000323178:p.Leu536Pro	153.0	0.0	782	104.0	5.0	NM_014238	F8WEA9|H7BYU0|Q13476	Missense_Mutation	SNP	ENST00000319524.6	hg19		.	.	.	.	.	.	.	.	.	.	T	11.01	1.513503	0.27123	.	.	ENSG00000141068	ENST00000319524;ENST00000509603;ENST00000268763;ENST00000398982	T;T;T	0.80033	-1.33;-1.33;-1.32	5.76	-5.87	0.02297	.	1.468070	0.03281	N	0.186136	T	0.59252	0.2180	N	0.11560	0.145	0.20307	N	0.999917	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.46005	-0.9222	10	0.35671	T	0.21	.	4.3566	0.11181	0.1192:0.5168:0.1213:0.2428	.	534;514	Q8IVT5;F5H0K8	KSR1_HUMAN;.	P	536;514;399;399	ENSP00000323178:L536P;ENSP00000438795:L514P;ENSP00000268763:L399P	ENSP00000268763:L399P	L	+	2	0	KSR1	22955017	0.000000	0.05858	0.000000	0.03702	0.102000	0.19082	-0.631000	0.05496	-0.939000	0.03709	0.533000	0.62120	CTC	.	.		0.537	KSR1-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_014238	
NOS2	4843	hgsc.bcm.edu	37	17	26092677	26092677	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:26092677T>C	ENST00000313735.6	-	20	2545	c.2312A>G	c.(2311-2313)gAg>gGg	p.E771G		NM_000625.4	NP_000616.3	P35228	NOS2_HUMAN	nitric oxide synthase 2, inducible	771	FAD-binding FR-type. {ECO:0000255|PROSITE-ProRule:PRU00716}.				arginine catabolic process (GO:0006527)|blood coagulation (GO:0007596)|cellular response to interferon-gamma (GO:0071346)|cellular response to lipopolysaccharide (GO:0071222)|circadian rhythm (GO:0007623)|defense response to bacterium (GO:0042742)|defense response to Gram-negative bacterium (GO:0050829)|inflammatory response (GO:0006954)|innate immune response in mucosa (GO:0002227)|interaction with host (GO:0051701)|negative regulation of blood pressure (GO:0045776)|negative regulation of gene expression (GO:0010629)|negative regulation of protein catabolic process (GO:0042177)|nitric oxide biosynthetic process (GO:0006809)|nitric oxide mediated signal transduction (GO:0007263)|peptidyl-cysteine S-nitrosylation (GO:0018119)|phagosome maturation (GO:0090382)|positive regulation of guanylate cyclase activity (GO:0031284)|positive regulation of killing of cells of other organism (GO:0051712)|positive regulation of leukocyte mediated cytotoxicity (GO:0001912)|positive regulation of vasodilation (GO:0045909)|regulation of cell proliferation (GO:0042127)|regulation of cellular respiration (GO:0043457)|regulation of insulin secretion (GO:0050796)|response to bacterium (GO:0009617)|response to hypoxia (GO:0001666)|superoxide metabolic process (GO:0006801)	cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|peroxisome (GO:0005777)	arginine binding (GO:0034618)|flavin adenine dinucleotide binding (GO:0050660)|FMN binding (GO:0010181)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|NADP binding (GO:0050661)|NADPH-hemoprotein reductase activity (GO:0003958)|nitric-oxide synthase activity (GO:0004517)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|tetrahydrobiopterin binding (GO:0034617)			autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(28)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	56					Dexamethasone(DB01234)|Doxorubicin(DB00997)|L-Arginine(DB00125)|L-Citrulline(DB00155)|Miconazole(DB01110)|Triflusal(DB08814)	CCCAAGGTGCTCCCCCGGCAG	0.632																																					p.E771G		Atlas-SNP	.											.	NOS2	113	.	0			c.A2312G						.						32.0	36.0	34.0					17																	26092677		2203	4300	6503	SO:0001583	missense	4843	exon20			AGGTGCTCCCCCG	U20141	CCDS11223.1	17q11.2	2014-06-12	2008-09-16	2008-09-16	ENSG00000007171	ENSG00000007171	1.14.13.39		7873	protein-coding gene	gene with protein product		163730	"""nitric oxide synthase 2A (inducible, hepatocytes)"""	NOS2A		7682706	Standard	NM_000625		Approved	iNOS, NOS, HEP-NOS	uc002gzu.3	P35228	OTTHUMG00000132445	ENST00000313735.6:c.2312A>G	chr17.hg19:g.26092677T>C	ENSP00000327251:p.Glu771Gly	186.0	0.0		158.0	7.0	NM_000625	A1L3U5|B7ZLY2|O60757|O94994|Q16263|Q16692|Q4TTS5|Q9UD42	Missense_Mutation	SNP	ENST00000313735.6	hg19	CCDS11223.1	.	.	.	.	.	.	.	.	.	.	T	23.4	4.410709	0.83340	.	.	ENSG00000007171	ENST00000313735;ENST00000379105	T	0.33654	1.4	5.19	5.19	0.71726	Riboflavin synthase-like beta-barrel (1);FAD-binding, type 1 (1);NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain-3 (1);Ferredoxin reductase-type FAD-binding domain (1);Flavoprotein pyridine nucleotide cytochrome reductase (1);	0.192304	0.43416	D	0.000561	T	0.59891	0.2227	M	0.84326	2.69	0.58432	D	0.999999	P	0.49862	0.929	P	0.59546	0.859	T	0.66622	-0.5877	10	0.87932	D	0	.	14.2942	0.66300	0.0:0.0:0.0:1.0	.	771	P35228	NOS2_HUMAN	G	771;732	ENSP00000327251:E771G	ENSP00000327251:E771G	E	-	2	0	NOS2	23116804	1.000000	0.71417	0.981000	0.43875	0.514000	0.34195	5.742000	0.68646	1.979000	0.57680	0.374000	0.22700	GAG	.	.		0.632	NOS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255597.1	NM_000625	
SUZ12	23512	hgsc.bcm.edu	37	17	30315475	30315475	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:30315475A>G	ENST00000322652.5	+	10	1389	c.1160A>G	c.(1159-1161)cAg>cGg	p.Q387R	SUZ12_ENST00000580398.1_Missense_Mutation_p.Q364R	NM_015355.2	NP_056170.2	Q15022	SUZ12_HUMAN	SUZ12 polycomb repressive complex 2 subunit	387					histone ubiquitination (GO:0016574)|negative regulation of cell differentiation (GO:0045596)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell proliferation (GO:0008284)|transcription, DNA-templated (GO:0006351)	ESC/E(Z) complex (GO:0035098)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|sex chromatin (GO:0001739)	chromatin binding (GO:0003682)|histone methyltransferase activity (GO:0042054)|metal ion binding (GO:0046872)|methylated histone binding (GO:0035064)|RNA binding (GO:0003723)|sequence-specific DNA binding (GO:0043565)		SSH2/SUZ12(2)|JAZF1/SUZ12(133)	breast(3)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(4)|lung(5)|skin(1)	21		Myeloproliferative disorder(56;0.0255)|all_hematologic(16;0.041)|Ovarian(249;0.182)|Breast(31;0.231)				AGTCTCCATCAGGAAAACAAG	0.398			T	JAZF1	endometrial stromal tumours																																p.Q387R		Atlas-SNP	.		Dom	yes		17	17q11.2	23512	suppressor of zeste 12 homolog (Drosophila)		M	.	SUZ12	61	.	0			c.A1160G						.						75.0	75.0	75.0					17																	30315475		2203	4300	6503	SO:0001583	missense	23512	exon10			TCCATCAGGAAAA	D63881	CCDS11270.1	17q21	2013-06-05	2013-06-05		ENSG00000178691	ENSG00000178691		"""Zinc fingers, C2H2-type"""	17101	protein-coding gene	gene with protein product		606245	"""suppressor of zeste 12 homolog (Drosophila)"""			8590280, 11371647, 18784248	Standard	NM_015355		Approved	JJAZ1, KIAA0160, CHET9	uc002hgs.2	Q15022	OTTHUMG00000132813	ENST00000322652.5:c.1160A>G	chr17.hg19:g.30315475A>G	ENSP00000316578:p.Gln387Arg	217.0	0.0		183.0	9.0	NM_015355	Q96BD9	Missense_Mutation	SNP	ENST00000322652.5	hg19	CCDS11270.1	.	.	.	.	.	.	.	.	.	.	a	13.26	2.183387	0.38511	.	.	ENSG00000178691	ENST00000322652	T	0.44881	0.91	5.53	4.44	0.53790	.	0.155378	0.64402	D	0.000014	T	0.31888	0.0811	L	0.36672	1.1	0.46396	D	0.999025	B;B	0.23650	0.012;0.089	B;B	0.19391	0.004;0.025	T	0.05468	-1.0883	10	0.23302	T	0.38	-11.5643	11.953	0.52966	0.8698:0.0:0.0:0.1302	.	387;387	A8K1U9;Q15022	.;SUZ12_HUMAN	R	387	ENSP00000316578:Q387R	ENSP00000316578:Q387R	Q	+	2	0	SUZ12	27339588	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.095000	0.76952	0.900000	0.36469	0.528000	0.53228	CAG	.	.		0.398	SUZ12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256260.2	NM_015355	
SLFN5	162394	hgsc.bcm.edu	37	17	33586258	33586258	+	Silent	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:33586258T>C	ENST00000299977.4	+	2	697	c.549T>C	c.(547-549)taT>taC	p.Y183Y	SLFN5_ENST00000542451.1_Silent_p.Y183Y|SLFN5_ENST00000592325.1_Silent_p.Y183Y	NM_144975.3	NP_659412.3	Q08AF3	SLFN5_HUMAN	schlafen family member 5	183				Y -> H (in Ref. 1; AAI25202). {ECO:0000305}.	cell differentiation (GO:0030154)	nucleus (GO:0005634)	ATP binding (GO:0005524)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(8)|liver(2)|lung(6)|ovary(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(2)	34		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0191)		GGCTTCAGTATCTGGAAAAAC	0.418																																					p.Y183Y		Atlas-SNP	.											.	SLFN5	92	.	0			c.T549C						.						135.0	130.0	132.0					17																	33586258		2203	4300	6503	SO:0001819	synonymous_variant	162394	exon2			TCAGTATCTGGAA	BX647942	CCDS32619.1	17q12	2006-04-05				ENSG00000166750			28286	protein-coding gene	gene with protein product		614952				9846487	Standard	NM_144975		Approved	MGC19764	uc002hjf.4	Q08AF3		ENST00000299977.4:c.549T>C	chr17.hg19:g.33586258T>C		197.0	0.0		161.0	9.0	NM_144975	Q08AF2|Q8WU54|Q96A82	Silent	SNP	ENST00000299977.4	hg19	CCDS32619.1																																																																																			.	.		0.418	SLFN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448649.2	NM_144975	
SRCIN1	80725	hgsc.bcm.edu	37	17	36689629	36689629	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:36689629T>C	ENST00000264659.7	-	19	3679	c.3455A>G	c.(3454-3456)gAg>gGg	p.E1152G	SRCIN1_ENST00000578925.1_Missense_Mutation_p.E1186G	NM_025248.2	NP_079524.2	Q9C0H9	SRCN1_HUMAN	SRC kinase signaling inhibitor 1	1024					exocytosis (GO:0006887)|negative regulation of protein tyrosine kinase activity (GO:0061099)|positive regulation of protein tyrosine kinase activity (GO:0061098)|regulation of cell migration (GO:0030334)|regulation of dendritic spine morphogenesis (GO:0061001)|substrate adhesion-dependent cell spreading (GO:0034446)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	protein kinase binding (GO:0019901)			endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|prostate(1)	19						GCTCGAGGTCTCATTCGACCC	0.542																																					p.E1152G		Atlas-SNP	.											.	SRCIN1	66	.	0			c.A3455G						.						60.0	62.0	61.0					17																	36689629		1864	4094	5958	SO:0001583	missense	80725	exon19			GAGGTCTCATTCG		CCDS45660.1	17q12	2009-12-14			ENSG00000017373	ENSG00000277363			29506	protein-coding gene	gene with protein product	"""p130Cas-associated protein"", ""SNAP-25-interacting protein"""	610786				11214970	Standard	NM_025248		Approved	SNIP, p140Cap, KIAA1684	uc002hqd.3	Q9C0H9		ENST00000264659.7:c.3455A>G	chr17.hg19:g.36689629T>C	ENSP00000264659:p.Glu1152Gly	157.0	0.0		93.0	4.0	NM_025248	Q75T46|Q8N4W8	Missense_Mutation	SNP	ENST00000264659.7	hg19	CCDS45660.1	.	.	.	.	.	.	.	.	.	.	T	27.0	4.793798	0.90453	.	.	ENSG00000017373	ENST00000264659	T	0.50001	0.76	5.27	5.27	0.74061	.	0.196420	0.34906	N	0.003584	T	0.57695	0.2071	L	0.36672	1.1	0.39645	D	0.970379	D	0.76494	0.999	D	0.75484	0.986	T	0.57087	-0.7871	10	0.33940	T	0.23	-33.2504	14.4655	0.67480	0.0:0.0:0.0:1.0	.	1152	Q9C0H9-5	.	G	1152	ENSP00000264659:E1152G	ENSP00000264659:E1152G	E	-	2	0	SRCIN1	33943155	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.007000	0.63984	2.109000	0.64355	0.460000	0.39030	GAG	.	.		0.542	SRCIN1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000441878.4	NM_025248	
SRCIN1	80725	hgsc.bcm.edu	37	17	36704821	36704821	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:36704821T>C	ENST00000264659.7	-	17	3466	c.3242A>G	c.(3241-3243)gAc>gGc	p.D1081G	SRCIN1_ENST00000578925.1_Missense_Mutation_p.D1115G|SRCIN1_ENST00000398579.4_5'UTR	NM_025248.2	NP_079524.2	Q9C0H9	SRCN1_HUMAN	SRC kinase signaling inhibitor 1	953					exocytosis (GO:0006887)|negative regulation of protein tyrosine kinase activity (GO:0061099)|positive regulation of protein tyrosine kinase activity (GO:0061098)|regulation of cell migration (GO:0030334)|regulation of dendritic spine morphogenesis (GO:0061001)|substrate adhesion-dependent cell spreading (GO:0034446)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	protein kinase binding (GO:0019901)			endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|prostate(1)	19						GCGATCCTCGTCATCCTCGTC	0.672																																					p.D1081G		Atlas-SNP	.											.	SRCIN1	66	.	0			c.A3242G						.						87.0	91.0	89.0					17																	36704821		2102	4200	6302	SO:0001583	missense	80725	exon17			TCCTCGTCATCCT		CCDS45660.1	17q12	2009-12-14			ENSG00000017373	ENSG00000277363			29506	protein-coding gene	gene with protein product	"""p130Cas-associated protein"", ""SNAP-25-interacting protein"""	610786				11214970	Standard	NM_025248		Approved	SNIP, p140Cap, KIAA1684	uc002hqd.3	Q9C0H9		ENST00000264659.7:c.3242A>G	chr17.hg19:g.36704821T>C	ENSP00000264659:p.Asp1081Gly	123.0	0.0		95.0	4.0	NM_025248	Q75T46|Q8N4W8	Missense_Mutation	SNP	ENST00000264659.7	hg19	CCDS45660.1	.	.	.	.	.	.	.	.	.	.	T	17.38	3.375721	0.61735	.	.	ENSG00000017373	ENST00000264659;ENST00000542707;ENST00000398579	T	0.44083	0.93	4.53	4.53	0.55603	.	0.180161	0.46758	D	0.000266	T	0.42131	0.1189	L	0.50333	1.59	0.58432	D	0.999996	P;P;B	0.39480	0.675;0.675;0.449	B;B;B	0.41813	0.367;0.367;0.205	T	0.46331	-0.9199	10	0.72032	D	0.01	-8.7264	12.9793	0.58554	0.0:0.0:0.0:1.0	.	953;953;1081	Q9C0H9-2;Q9C0H9;Q9C0H9-5	.;SRCN1_HUMAN;.	G	1081;862;935	ENSP00000264659:D1081G	ENSP00000264659:D1081G	D	-	2	0	SRCIN1	33958347	1.000000	0.71417	0.606000	0.28943	0.911000	0.54048	7.327000	0.79147	1.904000	0.55121	0.379000	0.24179	GAC	.	.		0.672	SRCIN1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000441878.4	NM_025248	
MLLT6	4302	hgsc.bcm.edu	37	17	36861960	36861960	+	Silent	SNP	C	C	T			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:36861960C>T	ENST00000325718.7	+	1	166	c.75C>T	c.(73-75)tgC>tgT	p.C25C	MLLT6_ENST00000378137.5_Silent_p.C25C|CTB-58E17.3_ENST00000583409.1_RNA|CTB-58E17.1_ENST00000563897.1_lincRNA	NM_005937.3	NP_005928	P55198	AF17_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 6	25					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(3)|lung(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	8	Breast(7;4.43e-21)					TGGTCTACTGCGATGGGCACG	0.736			T	MLL	AL																																p.C25C		Atlas-SNP	.		Dom	yes		17	17q21	4302	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 6 (AF17)"""		L	.	MLLT6	80	.	0			c.C75T						.						53.0	46.0	48.0					17																	36861960		2203	4300	6503	SO:0001819	synonymous_variant	4302	exon1			CTACTGCGATGGG		CCDS11327.1	17q21	2014-04-10	2001-11-28		ENSG00000108292	ENSG00000275023		"""Zinc fingers, PHD-type"""	7138	protein-coding gene	gene with protein product	"""Myeloid/lymphoid or mixed-lineage leukemia, translocated to, 6"", ""trithorax homolog"""	600328	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 6"""			8058765	Standard	NM_005937		Approved	AF17, FLJ23480	uc002hqi.4	P55198	OTTHUMG00000188498	ENST00000325718.7:c.75C>T	chr17.hg19:g.36861960C>T		166.0	0.0		88.0	29.0	NM_005937	Q59F28|Q96IU3|Q9H5F6|Q9UF49	Silent	SNP	ENST00000325718.7	hg19	CCDS11327.1																																																																																			.	.		0.736	MLLT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256799.1	NM_005937	
KRT24	192666	hgsc.bcm.edu	37	17	38856499	38856499	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:38856499T>C	ENST00000264651.2	-	4	1048	c.992A>G	c.(991-993)gAg>gGg	p.E331G		NM_019016.2	NP_061889.2	Q2M2I5	K1C24_HUMAN	keratin 24	331	Coil 2.|Rod.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)	structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(12)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29		Breast(137;0.00526)				CTCCTCAGCCTCTCGGCGGTT	0.552																																					p.E331G	GBM(61;380 1051 14702 23642 31441)	Atlas-SNP	.											.	KRT24	60	.	0			c.A992G						.						147.0	144.0	145.0					17																	38856499		2203	4300	6503	SO:0001583	missense	192666	exon4			TCAGCCTCTCGGC		CCDS11372.1	17q21.2	2013-06-25			ENSG00000167916	ENSG00000167916		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	18527	protein-coding gene	gene with protein product		607742				16831889	Standard	NM_019016		Approved	FLJ20261, MGC138169, MGC138173	uc002hvd.3	Q2M2I5	OTTHUMG00000133372	ENST00000264651.2:c.992A>G	chr17.hg19:g.38856499T>C	ENSP00000264651:p.Glu331Gly	203.0	0.0		144.0	6.0	NM_019016	Q9NXG7	Missense_Mutation	SNP	ENST00000264651.2	hg19	CCDS11372.1	.	.	.	.	.	.	.	.	.	.	T	28.5	4.927192	0.92389	.	.	ENSG00000167916	ENST00000264651	D	0.81739	-1.53	5.86	5.86	0.93980	Prefoldin (1);Filament (1);	.	.	.	.	D	0.91713	0.7380	M	0.92268	3.29	0.58432	D	0.999999	D	0.71674	0.998	D	0.66847	0.947	D	0.93580	0.6912	9	0.87932	D	0	.	16.2605	0.82541	0.0:0.0:0.0:1.0	.	331	Q2M2I5	K1C24_HUMAN	G	331	ENSP00000264651:E331G	ENSP00000264651:E331G	E	-	2	0	KRT24	36110025	1.000000	0.71417	0.853000	0.33588	0.825000	0.46686	6.172000	0.71932	2.237000	0.73441	0.460000	0.39030	GAG	.	.		0.552	KRT24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257217.1	NM_019016	
JUP	3728	hgsc.bcm.edu	37	17	39919572	39919572	+	Splice_Site	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:39919572T>C	ENST00000393931.3	-	8	1278	c.1160A>G	c.(1159-1161)gAg>gGg	p.E387G	JUP_ENST00000310706.5_Splice_Site_p.E387G|JUP_ENST00000540235.1_Intron|JUP_ENST00000393930.1_Splice_Site_p.E387G	NM_002230.2	NP_002221.1	P14923	PLAK_HUMAN	junction plakoglobin	387					adherens junction organization (GO:0034332)|atrioventricular valve morphogenesis (GO:0003181)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cell junction assembly (GO:0034329)|cell migration (GO:0016477)|cell morphogenesis (GO:0000902)|cell-cell junction organization (GO:0045216)|cellular response to indole-3-methanol (GO:0071681)|cytoskeletal anchoring at plasma membrane (GO:0007016)|desmosome assembly (GO:0002159)|detection of mechanical stimulus (GO:0050982)|ectoderm development (GO:0007398)|endothelial cell-cell adhesion (GO:0071603)|establishment of protein localization to plasma membrane (GO:0090002)|gastrulation (GO:0007369)|morphogenesis of embryonic epithelium (GO:0016331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of Wnt signaling pathway involved in heart development (GO:0003308)|nervous system development (GO:0007399)|oocyte development (GO:0048599)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein heterooligomerization (GO:0051291)|regulation of cell proliferation (GO:0042127)|regulation of heart rate by cardiac conduction (GO:0086091)|single organismal cell-cell adhesion (GO:0016337)|skin development (GO:0043588)|ventricular cardiac muscle cell action potential (GO:0086005)	actin cytoskeleton (GO:0015629)|apicolateral plasma membrane (GO:0016327)|basolateral plasma membrane (GO:0016323)|catenin complex (GO:0016342)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|gamma-catenin-TCF7L2 complex (GO:0071665)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|lateral plasma membrane (GO:0016328)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|cadherin binding (GO:0045296)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|structural constituent of cell wall (GO:0005199)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(6)|ovary(3)|upper_aerodigestive_tract(1)	23		Breast(137;0.000162)	BRCA - Breast invasive adenocarcinoma(4;0.233)	BRCA - Breast invasive adenocarcinoma(366;0.15)		CTCCAGGCCCTCCTGGAGGGC	0.587																																					p.E387G	Colon(16;42 520 6044 17852 28530)	Atlas-SNP	.											.	JUP	64	.	0			c.A1160G						.						53.0	49.0	51.0					17																	39919572		2203	4300	6503	SO:0001630	splice_region_variant	3728	exon8			AGGCCCTCCTGGA	AF233882	CCDS11407.1	17q21	2014-09-17	2004-08-09		ENSG00000173801	ENSG00000173801		"""Armadillo repeat containing"""	6207	protein-coding gene	gene with protein product		173325	"""catenin (cadherin-associated protein), gamma 80kDa"""	CTNNG		1889810, 7604000	Standard	NM_021991		Approved	DP3, PDGB, PKGB, DPIII	uc002hxs.2	P14923	OTTHUMG00000133494	ENST00000393931.3:c.1159-1A>G	chr17.hg19:g.39919572T>C		133.0	0.0		85.0	4.0	NM_021991	Q15093|Q15151|Q7L3S5|Q86W21|Q9BWC4|Q9HCX9	Missense_Mutation	SNP	ENST00000393931.3	hg19	CCDS11407.1	.	.	.	.	.	.	.	.	.	.	T	16.11	3.029133	0.54790	.	.	ENSG00000173801	ENST00000393930;ENST00000310706;ENST00000393931	T;T;T	0.66815	-0.23;-0.23;-0.23	4.9	4.9	0.64082	Armadillo-like helical (1);Armadillo-type fold (1);	0.096735	0.64402	D	0.000001	T	0.62684	0.2448	M	0.67397	2.05	0.80722	D	1	P	0.37612	0.602	B	0.31390	0.129	T	0.69716	-0.5070	10	0.87932	D	0	-41.7617	13.8482	0.63481	0.0:0.0:0.0:1.0	.	387	P14923	PLAK_HUMAN	G	387	ENSP00000377507:E387G;ENSP00000311113:E387G;ENSP00000377508:E387G	ENSP00000311113:E387G	E	-	2	0	JUP	37173098	1.000000	0.71417	1.000000	0.80357	0.642000	0.38348	7.760000	0.85248	2.059000	0.61396	0.397000	0.26171	GAG	.	.		0.587	JUP-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257406.1		Missense_Mutation
IFI35	3430	hgsc.bcm.edu	37	17	41164212	41164212	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:41164212A>G	ENST00000415816.2	+	2	261	c.38A>G	c.(37-39)cAg>cGg	p.Q13R	IFI35_ENST00000536969.1_3'UTR|IFI35_ENST00000438323.2_Missense_Mutation_p.Q13R	NM_005533.4	NP_005524.2	P80217	IN35_HUMAN	interferon-induced protein 35	13	Leucine-zipper.				cytokine-mediated signaling pathway (GO:0019221)|type I interferon signaling pathway (GO:0060337)	cytosol (GO:0005829)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(2)|ovary(1)	8		Breast(137;0.00499)		BRCA - Breast invasive adenocarcinoma(366;0.157)		CACGCCCTTCAGGAGGAGCAG	0.587																																					p.Q13R		Atlas-SNP	.											.	IFI35	23	.	0			c.A38G						.						29.0	29.0	29.0					17																	41164212		2191	4285	6476	SO:0001583	missense	3430	exon2			CCCTTCAGGAGGA	BC001356	CCDS11450.1	17q21	2006-04-05			ENSG00000068079	ENSG00000068079			5399	protein-coding gene	gene with protein product		600735					Standard	NM_005533		Approved	IFP35	uc021txx.1	P80217	OTTHUMG00000167720	ENST00000415816.2:c.38A>G	chr17.hg19:g.41164212A>G	ENSP00000394579:p.Gln13Arg	106.0	0.0		94.0	5.0	NM_005533	C9JGX1|Q92984|Q99537|Q9BV98	Missense_Mutation	SNP	ENST00000415816.2	hg19		.	.	.	.	.	.	.	.	.	.	A	6.756	0.508395	0.12883	.	.	ENSG00000068079	ENST00000415816;ENST00000438323	T;T	0.45276	0.9;0.9	4.9	-2.44	0.06502	Interferon induced 35kDa, N-terminal (1);	0.753193	0.12202	N	0.490143	T	0.21427	0.0516	N	0.21448	0.665	0.18873	N	0.999989	B	0.02656	0.0	B	0.08055	0.003	T	0.14282	-1.0478	10	0.29301	T	0.29	.	3.6023	0.08030	0.2968:0.0:0.2224:0.4808	.	13	P80217	IN35_HUMAN	R	13	ENSP00000394579:Q13R;ENSP00000395590:Q13R	ENSP00000394579:Q13R	Q	+	2	0	IFI35	38417738	0.598000	0.26882	0.438000	0.26821	0.034000	0.12701	-0.198000	0.09505	-0.552000	0.06167	-0.301000	0.09380	CAG	.	.		0.587	IFI35-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000395851.1	NM_005533	
TOM1L1	10040	hgsc.bcm.edu	37	17	53027460	53027460	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:53027460A>G	ENST00000575882.1	+	14	1696	c.1343A>G	c.(1342-1344)gAt>gGt	p.D448G	TOM1L1_ENST00000540336.1_Missense_Mutation_p.D336G|TOM1L1_ENST00000536554.1_Missense_Mutation_p.D371G|TOM1L1_ENST00000572158.1_Missense_Mutation_p.D441G|TOM1L1_ENST00000348161.4_Missense_Mutation_p.D371G|COX11_ENST00000573912.1_5'Flank|TOM1L1_ENST00000445275.2_Missense_Mutation_p.D437G	NM_005486.2	NP_005477.2	O75674	TM1L1_HUMAN	target of myb1 (chicken)-like 1	448					activation of protein kinase activity (GO:0032147)|intracellular protein transport (GO:0006886)|negative regulation of mitosis (GO:0045839)|positive regulation of protein autophosphorylation (GO:0031954)|signal transduction (GO:0007165)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|lysosome (GO:0005764)|membrane (GO:0016020)	clathrin binding (GO:0030276)|protein kinase activator activity (GO:0030295)|protein kinase binding (GO:0019901)|ubiquitin binding (GO:0043130)			cervix(1)|endometrium(2)|kidney(3)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|skin(1)	15						ATGGAGTTTGATCCCTTAGCT	0.393																																					p.D448G		Atlas-SNP	.											.	TOM1L1	33	.	0			c.A1343G						.						103.0	98.0	100.0					17																	53027460		2203	4300	6503	SO:0001583	missense	10040	exon14			AGTTTGATCCCTT	AJ010071	CCDS11582.1	17q23.2	2008-01-03	2007-01-12			ENSG00000141198			11983	protein-coding gene	gene with protein product		604701	"""target of myb1 (chicken) homolog-like 1"""			10329004, 15611048, 17977829	Standard	NM_005486		Approved	SRCASM	uc002iud.2	O75674		ENST00000575882.1:c.1343A>G	chr17.hg19:g.53027460A>G	ENSP00000460823:p.Asp448Gly	147.0	0.0		99.0	4.0	NM_005486	Q53G06|Q8N749	Missense_Mutation	SNP	ENST00000575882.1	hg19	CCDS11582.1	.	.	.	.	.	.	.	.	.	.	A	21.5	4.160106	0.78226	.	.	ENSG00000141198	ENST00000445275;ENST00000540336;ENST00000348161;ENST00000536554	T;T;T	0.34275	1.37;1.52;1.52	5.51	5.51	0.81932	.	0.000000	0.64402	D	0.000001	T	0.57110	0.2031	M	0.66939	2.045	0.51767	D	0.999936	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.87578	0.998;0.998;0.998;0.998	T	0.57300	-0.7835	10	0.48119	T	0.1	-25.0899	13.1152	0.59295	1.0:0.0:0.0:0.0	.	336;441;371;448	B4DUW5;B4E1N0;B7Z9E2;O75674	.;.;.;TM1L1_HUMAN	G	448;336;371;371	ENSP00000441242:D336G;ENSP00000343901:D371G;ENSP00000443099:D371G	ENSP00000343901:D371G	D	+	2	0	TOM1L1	50382459	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.280000	0.58959	2.317000	0.78254	0.459000	0.35465	GAT	.	.		0.393	TOM1L1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439029.2	NM_005486	
SCN4A	6329	hgsc.bcm.edu	37	17	62026109	62026109	+	Nonsense_Mutation	SNP	C	C	T			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:62026109C>T	ENST00000435607.1	-	16	3082	c.3006G>A	c.(3004-3006)tgG>tgA	p.W1002*	SCN4A_ENST00000578147.1_Nonsense_Mutation_p.W1002*	NM_000334.4	NP_000325.4	P35499	SCN4A_HUMAN	sodium channel, voltage-gated, type IV, alpha subunit	1002					membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			breast(4)|central_nervous_system(3)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(23)|lung(40)|ovary(3)|pancreas(1)|prostate(6)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	101					Diclofenac(DB00586)|Flecainide(DB01195)|Propofol(DB00818)|Valproic Acid(DB00313)|Zonisamide(DB00909)	AGAGGCAGGGCCAGCGCTGCA	0.642																																					p.W1002X		Atlas-SNP	.											.	SCN4A	205	.	0			c.G3006A						.						32.0	35.0	34.0					17																	62026109		2177	4275	6452	SO:0001587	stop_gained	6329	exon16			GCAGGGCCAGCGC	U24693		17q23.3	2012-02-26	2007-01-23					"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10591	protein-coding gene	gene with protein product		603967		HYKPP		1654742, 1659948, 16382098	Standard	XM_005257566		Approved	Nav1.4, HYPP, SkM1	uc002jds.1	P35499		ENST00000435607.1:c.3006G>A	chr17.hg19:g.62026109C>T	ENSP00000396320:p.Trp1002*	80.0	0.0		90.0	4.0	NM_000334	Q15478|Q16447|Q7Z6B1	Nonsense_Mutation	SNP	ENST00000435607.1	hg19	CCDS45761.1	.	.	.	.	.	.	.	.	.	.	C	38	6.848558	0.97885	.	.	ENSG00000007314	ENST00000435607	.	.	.	4.16	-4.15	0.03881	.	0.621771	0.18186	N	0.148995	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.48119	T	0.1	.	6.7542	0.23503	0.5586:0.2624:0.1791:0.0	.	.	.	.	X	1002	.	ENSP00000396320:W1002X	W	-	3	0	SCN4A	59379841	0.110000	0.22057	0.357000	0.25798	0.788000	0.44548	0.120000	0.15647	-0.871000	0.04042	0.313000	0.20887	TGG	.	.		0.642	SCN4A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_000334	
PSMD12	5718	hgsc.bcm.edu	37	17	65346351	65346351	+	Silent	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:65346351T>C	ENST00000356126.3	-	4	506	c.399A>G	c.(397-399)gaA>gaG	p.E133E	PSMD12_ENST00000357146.4_Silent_p.E113E|PSMD12_ENST00000581618.1_5'Flank	NM_002816.3	NP_002807.1	O00232	PSD12_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 12	133					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)				breast(1)|large_intestine(4)|lung(6)|pancreas(1)|urinary_tract(1)	13	all_cancers(12;2.38e-11)|all_epithelial(3;8.27e-13)					TTACCTTGCCTTCGGTAACCA	0.318																																					p.E133E		Atlas-SNP	.											.	PSMD12	32	.	0			c.A399G						.						76.0	70.0	72.0					17																	65346351		2203	4300	6503	SO:0001819	synonymous_variant	5718	exon4			CTTGCCTTCGGTA	AB003103	CCDS11669.1, CCDS11670.1	17q24.3	2008-05-22			ENSG00000197170	ENSG00000197170		"""Proteasome (prosome, macropain) subunits"""	9557	protein-coding gene	gene with protein product		604450				9426256	Standard	NM_002816		Approved	p55, Rpn5	uc002jfy.3	O00232	OTTHUMG00000140376	ENST00000356126.3:c.399A>G	chr17.hg19:g.65346351T>C		137.0	0.0		154.0	47.0	NM_002816	A6NP15|Q53HA2|Q6P053	Silent	SNP	ENST00000356126.3	hg19	CCDS11669.1																																																																																			.	.		0.318	PSMD12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277103.1	NM_002816, NM_174871	
ARSG	22901	hgsc.bcm.edu	37	17	66391287	66391287	+	Missense_Mutation	SNP	G	G	T			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:66391287G>T	ENST00000448504.2	+	10	1961	c.1165G>T	c.(1165-1167)Gtg>Ttg	p.V389L	ARSG_ENST00000582154.1_3'UTR|ARSG_ENST00000452479.2_Missense_Mutation_p.V225L	NM_014960.4	NP_055775.2	Q96EG1	ARSG_HUMAN	arylsulfatase G	389					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)|sulfur compound metabolic process (GO:0006790)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular space (GO:0005615)|lysosome (GO:0005764)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			NS(2)|endometrium(3)|kidney(1)|large_intestine(8)|lung(8)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	26			BRCA - Breast invasive adenocarcinoma(8;5.34e-07)|LUSC - Lung squamous cell carcinoma(166;0.24)			CTTTGATGGTGTGGACGTCTC	0.572																																					p.V389L		Atlas-SNP	.											.	ARSG	55	.	0			c.G1165T						.						161.0	125.0	137.0					17																	66391287		2203	4300	6503	SO:0001583	missense	22901	exon10			GATGGTGTGGACG	AB023218	CCDS11676.1	17q24.2	2013-07-15	2006-02-15		ENSG00000141337	ENSG00000141337		"""Arylsulfatase family"""	24102	protein-coding gene	gene with protein product		610008				12461688, 16174644	Standard	NM_014960		Approved	KIAA1001	uc002jhc.2	Q96EG1	OTTHUMG00000179810	ENST00000448504.2:c.1165G>T	chr17.hg19:g.66391287G>T	ENSP00000407193:p.Val389Leu	289.0	0.0		281.0	24.0	NM_001267727	Q6UXF2|Q9Y2K4	Missense_Mutation	SNP	ENST00000448504.2	hg19	CCDS11676.1	.	.	.	.	.	.	.	.	.	.	G	7.084	0.570898	0.13623	.	.	ENSG00000141337	ENST00000452479;ENST00000448504	.	.	.	5.25	-0.499	0.12015	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.892392	0.09618	N	0.777970	T	0.14485	0.0350	N	0.05280	-0.08	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.31833	-0.9929	9	0.14656	T	0.56	.	5.2398	0.15465	0.0:0.3568:0.3588:0.2844	.	389	Q96EG1	ARSG_HUMAN	L	389;288	.	ENSP00000407193:V288L	V	+	1	0	ARSG	63902882	0.003000	0.15002	0.033000	0.17914	0.907000	0.53573	-0.117000	0.10708	-0.169000	0.10834	0.555000	0.69702	GTG	.	.		0.572	ARSG-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448369.1	NM_014960	
TRIM65	201292	hgsc.bcm.edu	37	17	73887372	73887372	+	Missense_Mutation	SNP	G	G	A	rs144407004		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:73887372G>A	ENST00000269383.3	-	6	1107	c.1042C>T	c.(1042-1044)Cgc>Tgc	p.R348C		NM_001256124.1|NM_173547.3	NP_001243053.1|NP_775818.2	Q6PJ69	TRI65_HUMAN	tripartite motif containing 65	348	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.					intracellular (GO:0005622)	zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|lung(5)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	12			Epithelial(20;7.53e-06)|all cancers(21;9.11e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00092)|LUSC - Lung squamous cell carcinoma(166;0.154)			TGGTCCTGGCGCGACAGATAG	0.612																																					p.R348C		Atlas-SNP	.											.	TRIM65	23	.	0			c.C1042T						.	G	CYS/ARG	1,4387		0,1,2193	25.0	28.0	27.0		1042	-0.2	0.0	17	dbSNP_134	27	1,8535		0,1,4267	no	missense	TRIM65	NM_173547.2	180	0,2,6460	AA,AG,GG		0.0117,0.0228,0.0155	benign	348/518	73887372	2,12922	2194	4268	6462	SO:0001583	missense	201292	exon6			CCTGGCGCGACAG	BC006138	CCDS11732.1	17q25.1	2013-01-09	2011-01-25		ENSG00000141569	ENSG00000141569		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	27316	protein-coding gene	gene with protein product			"""tripartite motif-containing 65"""			12477932	Standard	NM_173547		Approved		uc002jpx.4	Q6PJ69	OTTHUMG00000132127	ENST00000269383.3:c.1042C>T	chr17.hg19:g.73887372G>A	ENSP00000269383:p.Arg348Cys	131.0	0.0		115.0	35.0	NM_173547	Q4G0F0|Q6DKJ6|Q9BRP6	Missense_Mutation	SNP	ENST00000269383.3	hg19	CCDS11732.1	.	.	.	.	.	.	.	.	.	.	G	2.643	-0.283636	0.05642	2.28E-4	1.17E-4	ENSG00000141569	ENST00000269383	T	0.73789	-0.78	5.2	-0.155	0.13395	Concanavalin A-like lectin/glucanase (1);B30.2/SPRY domain (1);	1.244230	0.05581	N	0.572948	T	0.61578	0.2358	L	0.35723	1.085	0.09310	N	1	B	0.11235	0.004	B	0.06405	0.002	T	0.49995	-0.8879	10	0.54805	T	0.06	.	2.7844	0.05370	0.3849:0.1102:0.3925:0.1124	.	348	Q6PJ69	TRI65_HUMAN	C	348	ENSP00000269383:R348C	ENSP00000269383:R348C	R	-	1	0	TRIM65	71398967	0.000000	0.05858	0.025000	0.17156	0.016000	0.09150	-0.389000	0.07342	0.241000	0.21283	-0.986000	0.02555	CGC	.	G|1.000;A|0.000		0.612	TRIM65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255170.2	NM_173547	
EVPL	2125	hgsc.bcm.edu	37	17	74004439	74004439	+	Missense_Mutation	SNP	T	T	C	rs372600391		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:74004439T>C	ENST00000301607.3	-	22	5100	c.4847A>G	c.(4846-4848)gAg>gGg	p.E1616G	EVPL_ENST00000586740.1_Missense_Mutation_p.E1638G|TEN1-CDK3_ENST00000567351.1_RNA	NM_001988.2	NP_001979.2	Q92817	EVPL_HUMAN	envoplakin	1616	Central fibrous rod domain.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)	cell junction (GO:0030054)|cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(4)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(14)|ovary(2)|pancreas(2)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)	54						CAGCTTCGACTCCTCCTGCAG	0.697																																					p.E1616G		Atlas-SNP	.											.	EVPL	155	.	0			c.A4847G						.						12.0	12.0	12.0					17																	74004439		2195	4275	6470	SO:0001583	missense	2125	exon22			TTCGACTCCTCCT	U53786	CCDS11737.1	17q25	2008-07-18				ENSG00000167880			3503	protein-coding gene	gene with protein product		601590				8938451, 10409435	Standard	NM_001988		Approved	EVPK	uc002jqi.2	Q92817		ENST00000301607.3:c.4847A>G	chr17.hg19:g.74004439T>C	ENSP00000301607:p.Glu1616Gly	88.0	0.0		89.0	4.0	NM_001988	A0AUV5	Missense_Mutation	SNP	ENST00000301607.3	hg19	CCDS11737.1	.	.	.	.	.	.	.	.	.	.	T	13.33	2.203599	0.38905	.	.	ENSG00000167880	ENST00000301607	T	0.69040	-0.37	5.05	3.97	0.46021	.	0.271401	0.36444	N	0.002591	T	0.63105	0.2483	M	0.62723	1.935	0.40318	D	0.978794	B;B	0.25351	0.124;0.061	B;B	0.23275	0.045;0.045	T	0.62937	-0.6748	10	0.72032	D	0.01	-42.4383	12.1255	0.53915	0.0:0.0:0.1437:0.8563	.	1638;1616	B7ZLH8;Q92817	.;EVPL_HUMAN	G	1616	ENSP00000301607:E1616G	ENSP00000301607:E1616G	E	-	2	0	EVPL	71516034	1.000000	0.71417	0.836000	0.33094	0.912000	0.54170	4.769000	0.62300	0.769000	0.33313	-0.375000	0.07067	GAG	.	.		0.697	EVPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449483.1	NM_001988	
SPHK1	8877	hgsc.bcm.edu	37	17	74383417	74383417	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:74383417T>C	ENST00000545180.1	+	8	1714	c.905T>C	c.(904-906)cTc>cCc	p.L302P	SPHK1_ENST00000592299.1_Missense_Mutation_p.L302P|SPHK1_ENST00000323374.4_Missense_Mutation_p.L388P|SPHK1_ENST00000590959.1_Missense_Mutation_p.L316P|SPHK1_ENST00000392496.3_Missense_Mutation_p.L302P			Q9NYA1	SPHK1_HUMAN	sphingosine kinase 1	302				L -> F (in Ref. 2; AAF73423). {ECO:0000305}.	'de novo' posttranslational protein folding (GO:0051084)|blood vessel development (GO:0001568)|brain development (GO:0007420)|calcium-mediated signaling (GO:0019722)|cellular protein metabolic process (GO:0044267)|cellular response to growth factor stimulus (GO:0071363)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to starvation (GO:0009267)|cyclooxygenase pathway (GO:0019371)|female pregnancy (GO:0007565)|inflammatory response (GO:0006954)|intracellular signal transduction (GO:0035556)|lipid phosphorylation (GO:0046834)|negative regulation of apoptotic process (GO:0043066)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of neuron projection development (GO:0010976)|positive regulation of neurotransmitter secretion (GO:0001956)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of smooth muscle contraction (GO:0045987)|protein folding (GO:0006457)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of interleukin-1 beta production (GO:0032651)|regulation of tumor necrosis factor-mediated signaling pathway (GO:0010803)|response to amine (GO:0014075)|response to ATP (GO:0033198)|response to interleukin-1 (GO:0070555)|response to magnesium ion (GO:0032026)|response to progesterone (GO:0032570)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingoid catabolic process (GO:0046521)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingosine metabolic process (GO:0006670)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|D-erythro-sphingosine kinase activity (GO:0017050)|diacylglycerol kinase activity (GO:0004143)|DNA binding (GO:0003677)|magnesium ion binding (GO:0000287)|NAD+ kinase activity (GO:0003951)|protein phosphatase 2A binding (GO:0051721)|sphinganine kinase activity (GO:0008481)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)	11					Fingolimod(DB08868)	CTGCTGCGCCTCTTCCTGGCC	0.597																																					p.L388P	GBM(90;966 1307 27369 33775 44498)	Atlas-SNP	.											.	SPHK1	24	.	0			c.T1163C						.						83.0	68.0	73.0					17																	74383417		2203	4300	6503	SO:0001583	missense	8877	exon6			TGCGCCTCTTCCT	BC030553	CCDS11744.1, CCDS45785.1, CCDS59297.1	17q25.2	2004-02-18				ENSG00000176170			11240	protein-coding gene	gene with protein product		603730				9726979	Standard	NM_182965		Approved	SPHK	uc002jrj.2	Q9NYA1		ENST00000545180.1:c.905T>C	chr17.hg19:g.74383417T>C	ENSP00000440970:p.Leu302Pro	169.0	0.0		169.0	9.0	NM_182965	Q8N632|Q96GK1|Q9HD92|Q9NY70|Q9NYL3	Missense_Mutation	SNP	ENST00000545180.1	hg19	CCDS45785.1	.	.	.	.	.	.	.	.	.	.	T	25.8	4.676522	0.88445	.	.	ENSG00000176170	ENST00000545180;ENST00000323374;ENST00000392496;ENST00000543830	T;T;T	0.17528	2.27;2.27;2.27	5.08	5.08	0.68730	.	0.129908	0.52532	D	0.000065	T	0.40956	0.1138	M	0.79011	2.435	0.80722	D	1	P;D;D	0.60160	0.721;0.985;0.987	B;P;P	0.61940	0.349;0.781;0.896	T	0.41610	-0.9499	10	0.87932	D	0	-7.6684	14.8579	0.70355	0.0:0.0:0.0:1.0	.	388;316;302	Q9NYA1-2;Q96GK1;Q9NYA1	.;.;SPHK1_HUMAN	P	302;388;302;301	ENSP00000440970:L302P;ENSP00000313681:L388P;ENSP00000376285:L302P	ENSP00000313681:L388P	L	+	2	0	SPHK1	71895012	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.515000	0.81761	1.901000	0.55032	0.460000	0.39030	CTC	.	.		0.597	SPHK1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450113.1	NM_182965, NM_021972	
ST6GALNAC2	10610	hgsc.bcm.edu	37	17	74581809	74581809	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:74581809A>G	ENST00000225276.5	-	1	401	c.82T>C	c.(82-84)Ttc>Ctc	p.F28L	ST6GALNAC2_ENST00000586520.1_5'UTR	NM_006456.2	NP_006447.2	Q9UJ37	SIA7B_HUMAN	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 2	28					cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	sialyltransferase activity (GO:0008373)			NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	11						ACCGCCGAGAAGTACAGGGCA	0.751																																					p.F28L		Atlas-SNP	.											.	ST6GALNAC2	29	.	0			c.T82C						.						8.0	10.0	9.0					17																	74581809		2072	4044	6116	SO:0001583	missense	10610	exon1			CCGAGAAGTACAG	U14550	CCDS11747.1	17q25.1	2013-03-01	2003-12-05	2005-02-07	ENSG00000070731	ENSG00000070731	2.4.99.7	"""Sialyltransferases"""	10867	protein-coding gene	gene with protein product		610137	"""sialyltransferase 7 ((alpha-N-acetylneuraminyl-2,3-beta-galactosyl-1,3)-N-acetyl galactosaminide alpha-2,6-sialyltransferase)"", ""sialyltransferase-like 1"""	SIAT7, SIAT7B, SIATL1		11984005	Standard	NM_006456		Approved	ST6GalNAII, STHM	uc002jsg.4	Q9UJ37	OTTHUMG00000180301	ENST00000225276.5:c.82T>C	chr17.hg19:g.74581809A>G	ENSP00000225276:p.Phe28Leu	76.0	0.0		51.0	4.0	NM_006456	Q12971	Missense_Mutation	SNP	ENST00000225276.5	hg19	CCDS11747.1	.	.	.	.	.	.	.	.	.	.	a	7.295	0.611809	0.14066	.	.	ENSG00000070731	ENST00000225276	T	0.28454	1.61	3.27	1.03	0.20045	.	1.130430	0.06718	U	0.774375	T	0.17152	0.0412	N	0.22421	0.69	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.30937	-0.9961	10	0.11182	T	0.66	-2.9009	4.2764	0.10811	0.6821:0.0:0.3179:0.0	.	28	Q9UJ37	SIA7B_HUMAN	L	28	ENSP00000225276:F28L	ENSP00000225276:F28L	F	-	1	0	ST6GALNAC2	72093404	0.050000	0.20438	0.031000	0.17742	0.115000	0.19883	0.090000	0.15025	0.432000	0.26286	0.255000	0.18592	TTC	.	.		0.751	ST6GALNAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450650.1	NM_006456	
ENGASE	64772	hgsc.bcm.edu	37	17	77075671	77075671	+	Missense_Mutation	SNP	C	C	T			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:77075671C>T	ENST00000579016.1	+	4	517	c.517C>T	c.(517-519)Cca>Tca	p.P173S	ENGASE_ENST00000539857.2_Intron	NM_001042573.2	NP_001036038.1	Q8NFI3	ENASE_HUMAN	endo-beta-N-acetylglucosaminidase	173						cytoplasm (GO:0005737)	mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity (GO:0033925)			breast(2)|endometrium(4)|large_intestine(1)|lung(15)|prostate(2)|skin(1)	25						CACCATTCCCCCAGTGGGCTG	0.587																																					p.P173S		Atlas-SNP	.											.	ENGASE	55	.	0			c.C517T						.						97.0	123.0	115.0					17																	77075671		2111	4218	6329	SO:0001583	missense	64772	exon4			ATTCCCCCAGTGG	AF512564	CCDS42394.1	17q25.3	2009-03-03			ENSG00000167280	ENSG00000167280	3.2.1.96		24622	protein-coding gene	gene with protein product	"""Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase"", ""Di-N-acetylchitobiosyl beta-N-acetylglucosaminidase"""	611898				12114544, 18586680	Standard	NM_001042573		Approved	FLJ21865	uc002jwv.4	Q8NFI3	OTTHUMG00000167714	ENST00000579016.1:c.517C>T	chr17.hg19:g.77075671C>T	ENSP00000462333:p.Pro173Ser	152.0	0.0		151.0	9.0	NM_001042573	Q659F0|Q8TB86|Q9H6U4	Missense_Mutation	SNP	ENST00000579016.1	hg19	CCDS42394.1	.	.	.	.	.	.	.	.	.	.	C	19.31	3.802634	0.70682	.	.	ENSG00000167280	ENST00000311595;ENST00000545583	.	.	.	5.22	5.22	0.72569	Glycoside hydrolase, family 85 (1);	0.049431	0.85682	D	0.000000	T	0.75012	0.3792	M	0.72118	2.19	0.80722	D	1	D;P	0.55800	0.973;0.939	P;P	0.57152	0.758;0.814	T	0.78076	-0.2345	9	0.72032	D	0.01	-18.8426	17.3151	0.87221	0.0:1.0:0.0:0.0	.	173;173	Q8NFI3;Q8NFI3-3	ENASE_HUMAN;.	S	173	.	ENSP00000308158:P173S	P	+	1	0	ENGASE	74587266	1.000000	0.71417	0.995000	0.50966	0.271000	0.26615	5.412000	0.66392	2.587000	0.87381	0.655000	0.94253	CCA	.	.		0.587	ENGASE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395807.1	NM_022759	
LAMA1	284217	hgsc.bcm.edu	37	18	7017287	7017287	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr18:7017287T>C	ENST00000389658.3	-	20	2891	c.2798A>G	c.(2797-2799)gAc>gGc	p.D933G		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	933	Laminin EGF-like 9. {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)				CAAGCACTGGTCACACTGCTG	0.498																																					p.D933G		Atlas-SNP	.											.	LAMA1	458	.	0			c.A2798G						.						170.0	123.0	139.0					18																	7017287		2203	4300	6503	SO:0001583	missense	284217	exon20			CACTGGTCACACT	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.2798A>G	chr18.hg19:g.7017287T>C	ENSP00000374309:p.Asp933Gly	183.0	0.0		92.0	5.0	NM_005559		Missense_Mutation	SNP	ENST00000389658.3	hg19	CCDS32787.1	.	.	.	.	.	.	.	.	.	.	T	23.1	4.372282	0.82573	.	.	ENSG00000101680	ENST00000389658	T	0.65916	-0.18	5.44	5.44	0.79542	EGF-like, laminin (4);	0.122628	0.52532	D	0.000078	T	0.79822	0.4512	M	0.82132	2.575	0.58432	D	0.999999	D	0.89917	1.0	D	0.77557	0.99	T	0.82028	-0.0660	10	0.54805	T	0.06	.	15.486	0.75569	0.0:0.0:0.0:1.0	.	933	P25391	LAMA1_HUMAN	G	933	ENSP00000374309:D933G	ENSP00000374309:D933G	D	-	2	0	LAMA1	7007287	1.000000	0.71417	1.000000	0.80357	0.776000	0.43924	7.658000	0.83755	2.068000	0.61886	0.519000	0.50382	GAC	.	.		0.498	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559	
ANKRD12	23253	hgsc.bcm.edu	37	18	9257082	9257082	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr18:9257082A>G	ENST00000262126.4	+	9	4057	c.3817A>G	c.(3817-3819)Att>Gtt	p.I1273V	ANKRD12_ENST00000383440.2_Missense_Mutation_p.I1250V|ANKRD12_ENST00000400020.3_Missense_Mutation_p.I1250V|RP11-888D10.4_ENST00000609701.1_RNA	NM_015208.4	NP_056023.3	Q6UB98	ANR12_HUMAN	ankyrin repeat domain 12	1273						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						GCCGGAGCGGATTAAACCACC	0.433																																					p.I1273V		Atlas-SNP	.											.	ANKRD12	167	.	0			c.A3817G						.						77.0	75.0	75.0					18																	9257082		2203	4300	6503	SO:0001583	missense	23253	exon9			GAGCGGATTAAAC	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.3817A>G	chr18.hg19:g.9257082A>G	ENSP00000262126:p.Ile1273Val	309.0	1.0		235.0	86.0	NM_015208	O94951|Q658K1|Q6QMF7|Q9H231|Q9H784	Missense_Mutation	SNP	ENST00000262126.4	hg19	CCDS11843.1	.	.	.	.	.	.	.	.	.	.	A	3.217	-0.160324	0.06502	.	.	ENSG00000101745	ENST00000383440;ENST00000262126	T;T	0.63913	-0.07;-0.07	5.89	3.49	0.39957	.	0.298503	0.36338	N	0.002644	T	0.39784	0.1091	N	0.16478	0.41	0.22675	N	0.998865	B;B	0.11235	0.004;0.003	B;B	0.10450	0.005;0.002	T	0.18053	-1.0349	10	0.21540	T	0.41	-30.3326	6.0617	0.19842	0.7172:0.1433:0.1395:0.0	.	1250;1273	Q6UB98-2;Q6UB98	.;ANR12_HUMAN	V	1250;1273	ENSP00000372932:I1250V;ENSP00000262126:I1273V	ENSP00000262126:I1273V	I	+	1	0	ANKRD12	9247082	0.384000	0.25164	0.983000	0.44433	0.746000	0.42486	0.790000	0.26900	0.478000	0.27488	0.533000	0.62120	ATT	.	.		0.433	ANKRD12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254478.2	NM_015208	
CABYR	26256	hgsc.bcm.edu	37	18	21723346	21723346	+	Silent	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr18:21723346A>G	ENST00000399496.3	+	3	333	c.168A>G	c.(166-168)aaA>aaG	p.K56K	CABYR_ENST00000399481.2_Intron|CABYR_ENST00000399499.1_Silent_p.K56K|CABYR_ENST00000581397.1_Silent_p.K56K|CABYR_ENST00000327201.6_Intron|CABYR_ENST00000415309.2_Silent_p.K56K	NM_012189.2|NM_153769.1	NP_036321.2|NP_722453.1	O75952	CABYR_HUMAN	calcium binding tyrosine-(Y)-phosphorylation regulated	56					epithelial cilium movement (GO:0003351)|sperm capacitation (GO:0048240)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|motile cilium (GO:0031514)|nucleus (GO:0005634)|sperm fibrous sheath (GO:0035686)	calcium ion binding (GO:0005509)|enzyme binding (GO:0019899)|protein heterodimerization activity (GO:0046982)|SH3 domain binding (GO:0017124)	p.K56K(2)		breast(1)|endometrium(2)|large_intestine(4)|lung(4)	11	all_cancers(21;9.13e-05)|all_epithelial(16;5.49e-07)|Lung NSC(20;0.00171)|all_lung(20;0.0055)|Colorectal(14;0.0305)|Ovarian(20;0.17)					TGGATATAAAAGATCTGGTTA	0.274																																					p.K56K		Atlas-SNP	.											CABYR,NS,carcinoma,0,1	CABYR	51	.	2	Substitution - coding silent(2)	lung(2)	c.A168G						.						39.0	42.0	41.0					18																	21723346		2191	4288	6479	SO:0001819	synonymous_variant	26256	exon3			TATAAAAGATCTG	AF088868	CCDS11881.1, CCDS11882.1, CCDS11883.1, CCDS42420.1, CCDS45840.1	18q11.2	2009-08-06	2007-11-22		ENSG00000154040	ENSG00000154040			15569	protein-coding gene	gene with protein product	"""fibrousheathin 2"", ""cancer/testis antigen 88"""	612135				11820818, 17317841, 16139264	Standard	NM_012189		Approved	FSP-2, CBP86, CT88	uc002kux.3	O75952	OTTHUMG00000037365	ENST00000399496.3:c.168A>G	chr18.hg19:g.21723346A>G		57.0	0.0		72.0	4.0	NM_153769	B2R857|Q8WXW5|Q9HAY3|Q9HAY4|Q9HAY5|Q9HCY9	Silent	SNP	ENST00000399496.3	hg19	CCDS42420.1																																																																																			.	.		0.274	CABYR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000090926.2	NM_153770	
TCEB3B	51224	hgsc.bcm.edu	37	18	44560926	44560926	+	Nonsense_Mutation	SNP	A	A	T	rs373872961		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr18:44560926A>T	ENST00000332567.4	-	1	1062	c.710T>A	c.(709-711)tTg>tAg	p.L237*	KATNAL2_ENST00000245121.5_Intron|KATNAL2_ENST00000356157.7_Intron|KATNAL2_ENST00000592005.1_Intron	NM_016427.2	NP_057511.2	Q8IYF1	ELOA2_HUMAN	transcription elongation factor B polypeptide 3B (elongin A2)	237					regulation of DNA-templated transcription, elongation (GO:0032784)|transcription from RNA polymerase II promoter (GO:0006366)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|lung(24)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58						CTGGGCACACAAGGGGCGTTT	0.602																																					p.L237X		Atlas-SNP	.											.	TCEB3B	141	.	0			c.T710A						.						40.0	42.0	41.0					18																	44560926		2203	4300	6503	SO:0001587	stop_gained	51224	exon1			GCACACAAGGGGC	BC036022	CCDS11932.1	18q21.1	2009-08-04			ENSG00000206181	ENSG00000206181			30771	protein-coding gene	gene with protein product	"""transcription elongation factor (SIII) elongin A2"", ""elongin A2"""	609522				7660129, 8244996	Standard	NM_016427		Approved	HsT832, TCEB3L	uc002lcr.1	Q8IYF1	OTTHUMG00000132649	ENST00000332567.4:c.710T>A	chr18.hg19:g.44560926A>T	ENSP00000331302:p.Leu237*	255.0	1.0		224.0	100.0	NM_016427	Q9P2V9	Nonsense_Mutation	SNP	ENST00000332567.4	hg19	CCDS11932.1	.	.	.	.	.	.	.	.	.	.	A	22.8	4.334294	0.81801	.	.	ENSG00000206181	ENST00000332567	.	.	.	1.37	0.185	0.15096	.	2.229110	0.03378	U	0.200007	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	3.1294	0.06418	0.7396:0.0:0.2604:0.0	.	.	.	.	X	237	.	ENSP00000331302:L237X	L	-	2	0	TCEB3B	42814924	0.001000	0.12720	0.000000	0.03702	0.002000	0.02628	1.249000	0.32839	0.044000	0.15775	0.379000	0.24179	TTG	.	.		0.602	TCEB3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255900.1	NM_016427	
ONECUT2	9480	hgsc.bcm.edu	37	18	55102980	55102980	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr18:55102980T>C	ENST00000491143.2	+	1	64	c.32T>C	c.(31-33)cTc>cCc	p.L11P	AC090340.1_ENST00000581316.1_RNA	NM_004852.2	NP_004843.2	O95948	ONEC2_HUMAN	one cut homeobox 2	11					cell fate commitment (GO:0045165)|cilium assembly (GO:0042384)|endocrine pancreas development (GO:0031018)|epithelial cell development (GO:0002064)|liver development (GO:0001889)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|organ morphogenesis (GO:0009887)|peripheral nervous system neuron development (GO:0048935)|positive regulation of cell migration (GO:0030335)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell-matrix adhesion (GO:0001952)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|lung(4)|ovary(2)|skin(1)	15		Colorectal(73;0.234)		READ - Rectum adenocarcinoma(59;0.227)|Colorectal(16;0.245)		TATCGATGCCTCACCAAAGAC	0.726																																					p.L11P		Atlas-SNP	.											.	ONECUT2	42	.	0			c.T32C						.						13.0	14.0	14.0					18																	55102980		1718	3861	5579	SO:0001583	missense	9480	exon1			GATGCCTCACCAA	Y18198	CCDS42440.1	18q21.31	2012-03-09	2007-07-16		ENSG00000119547	ENSG00000119547		"""Homeoboxes / CUT class"""	8139	protein-coding gene	gene with protein product		604894	"""one cut domain, family member 2"""			9915796	Standard	NM_004852		Approved	OC-2	uc002lgo.3	O95948	OTTHUMG00000159776	ENST00000491143.2:c.32T>C	chr18.hg19:g.55102980T>C	ENSP00000419185:p.Leu11Pro	197.0	0.0		100.0	4.0	NM_004852		Missense_Mutation	SNP	ENST00000491143.2	hg19	CCDS42440.1	.	.	.	.	.	.	.	.	.	.	t	13.84	2.358105	0.41801	.	.	ENSG00000119547	ENST00000262095	.	.	.	1.93	1.93	0.25924	.	.	.	.	.	T	0.45115	0.1326	N	0.08118	0	0.58432	D	0.999996	D	0.63046	0.992	P	0.60789	0.879	T	0.48305	-0.9047	8	0.87932	D	0	.	8.3564	0.32333	0.0:0.0:0.0:1.0	.	11	O95948	ONEC2_HUMAN	P	11	.	ENSP00000262095:L11P	L	+	2	0	ONECUT2	53253978	1.000000	0.71417	1.000000	0.80357	0.918000	0.54935	1.094000	0.30951	0.753000	0.32945	0.242000	0.17961	CTC	.	.		0.726	ONECUT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357264.3		
CDH20	28316	hgsc.bcm.edu	37	18	59221661	59221661	+	Silent	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr18:59221661T>C	ENST00000262717.4	+	12	2537	c.2139T>C	c.(2137-2139)ccT>ccC	p.P713P	CDH20_ENST00000536675.2_Silent_p.P713P|CDH20_ENST00000538374.1_Silent_p.P713P			Q9HBT6	CAD20_HUMAN	cadherin 20, type 2	713					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)				GCTACGTGCCTCAGACGTGCG	0.682																																					p.P713P		Atlas-SNP	.											.	CDH20	117	.	0			c.T2139C						.						42.0	38.0	39.0					18																	59221661		2203	4300	6503	SO:0001819	synonymous_variant	28316	exon11			CGTGCCTCAGACG	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.2139T>C	chr18.hg19:g.59221661T>C		119.0	0.0		84.0	4.0	NM_031891	Q495S3	Silent	SNP	ENST00000262717.4	hg19	CCDS11977.1																																																																																			.	.		0.682	CDH20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256141.2	NM_031891	
TMX3	54495	hgsc.bcm.edu	37	18	66348255	66348255	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr18:66348255A>G	ENST00000299608.2	-	14	1314	c.998T>C	c.(997-999)gTc>gCc	p.V333A		NM_019022.3	NP_061895.3	Q96JJ7	TMX3_HUMAN	thioredoxin-related transmembrane protein 3	333					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						AATAAACTGGACCATGTCTTC	0.363																																					p.V333A		Atlas-SNP	.											.	TMX3	44	.	0			c.T998C						.						145.0	140.0	142.0					18																	66348255		2203	4300	6503	SO:0001583	missense	54495	exon14			AACTGGACCATGT	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.998T>C	chr18.hg19:g.66348255A>G	ENSP00000299608:p.Val333Ala	140.0	0.0		99.0	4.0	NM_019022	B3KV75|Q52LT7|Q8N5J0|Q9NWJ9	Missense_Mutation	SNP	ENST00000299608.2	hg19	CCDS32840.1	.	.	.	.	.	.	.	.	.	.	A	16.75	3.209804	0.58343	.	.	ENSG00000166479	ENST00000299608;ENST00000544714	T	0.29917	1.55	5.81	4.65	0.58169	.	0.412804	0.27214	N	0.020382	T	0.23133	0.0559	L	0.44542	1.39	0.80722	D	1	P	0.39576	0.679	B	0.37387	0.248	T	0.02581	-1.1138	10	0.09338	T	0.73	.	11.1721	0.48577	0.9278:0.0:0.0722:0.0	.	333	Q96JJ7	TMX3_HUMAN	A	333	ENSP00000299608:V333A	ENSP00000299608:V333A	V	-	2	0	TMX3	64499235	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	6.594000	0.74104	1.022000	0.39626	0.533000	0.62120	GTC	.	.		0.363	TMX3-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420155.1	NM_019022	
FBXO15	201456	hgsc.bcm.edu	37	18	71749166	71749166	+	Missense_Mutation	SNP	A	A	T			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr18:71749166A>T	ENST00000419743.2	-	9	1338	c.1259T>A	c.(1258-1260)aTa>aAa	p.I420K	FBXO15_ENST00000580806.1_5'UTR|FBXO15_ENST00000269500.5_Missense_Mutation_p.I344K	NM_001142958.1	NP_001136430.1	Q8NCQ5	FBX15_HUMAN	F-box protein 15	420						SCF ubiquitin ligase complex (GO:0019005)				autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(2)	27		Esophageal squamous(42;0.103)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.143)		TTTTACCTTTATACAGCCATC	0.279																																					p.I420K		Atlas-SNP	.											.	FBXO15	97	.	0			c.T1259A						.						71.0	67.0	68.0					18																	71749166		2202	4298	6500	SO:0001583	missense	201456	exon9			ACCTTTATACAGC	AK094215	CCDS45884.1	18q22.3	2006-03-09	2004-06-15		ENSG00000141665	ENSG00000141665		"""F-boxes /  ""other"""""	13617	protein-coding gene	gene with protein product		609093	"""F-box only protein 15"""			12665572	Standard	NM_152676		Approved	MGC39671, FBX15	uc002llf.2	Q8NCQ5	OTTHUMG00000132842	ENST00000419743.2:c.1259T>A	chr18.hg19:g.71749166A>T	ENSP00000393154:p.Ile420Lys	125.0	0.0		106.0	5.0	NM_001142958	B3KST3	Missense_Mutation	SNP	ENST00000419743.2	hg19	CCDS45884.1	.	.	.	.	.	.	.	.	.	.	A	16.41	3.115189	0.56505	.	.	ENSG00000141665	ENST00000269500;ENST00000419743	T;T	0.46063	0.88;0.88	4.78	4.78	0.61160	.	0.313569	0.34603	N	0.003821	T	0.45155	0.1328	M	0.67953	2.075	0.58432	D	0.999998	P;P	0.50272	0.933;0.933	B;B	0.42386	0.386;0.231	T	0.55042	-0.8202	10	0.87932	D	0	-8.4474	14.6301	0.68650	1.0:0.0:0.0:0.0	.	420;344	B3KST3;Q8NCQ5	.;FBX15_HUMAN	K	344;420	ENSP00000269500:I344K;ENSP00000393154:I420K	ENSP00000269500:I344K	I	-	2	0	FBXO15	69900146	0.710000	0.27896	0.988000	0.46212	0.890000	0.51754	6.256000	0.72473	1.907000	0.55213	0.533000	0.62120	ATA	.	.		0.279	FBXO15-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000444223.1	NM_152676	
ANKRD24	170961	hgsc.bcm.edu	37	19	4216608	4216608	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:4216608T>C	ENST00000600132.1	+	18	1727	c.1451T>C	c.(1450-1452)aTc>aCc	p.I484T	ANKRD24_ENST00000262970.5_Missense_Mutation_p.I574T|ANKRD24_ENST00000318934.4_Missense_Mutation_p.I484T	NM_133475.1	NP_597732.1	Q8TF21	ANR24_HUMAN	ankyrin repeat domain 24	484										endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(9)|prostate(1)|skin(1)	21				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0233)|STAD - Stomach adenocarcinoma(1328;0.181)		GCAGAGGTCATCCCTCTTGCC	0.602																																					p.I484T		Atlas-SNP	.											.	ANKRD24	180	.	0			c.T1451C						.						31.0	32.0	32.0					19																	4216608		2036	4182	6218	SO:0001583	missense	170961	exon18			AGGTCATCCCTCT	AB075861	CCDS45925.1	19p13.3	2013-01-10				ENSG00000089847		"""Ankyrin repeat domain containing"""	29424	protein-coding gene	gene with protein product						11853319	Standard	NM_133475		Approved	KIAA1981	uc010dtt.1	Q8TF21		ENST00000600132.1:c.1451T>C	chr19.hg19:g.4216608T>C	ENSP00000471252:p.Ile484Thr	143.0	0.0		114.0	5.0	NM_133475	O75268|O95781	Missense_Mutation	SNP	ENST00000600132.1	hg19	CCDS45925.1	.	.	.	.	.	.	.	.	.	.	t	14.32	2.500512	0.44455	.	.	ENSG00000089847	ENST00000318934;ENST00000262970	T;T	0.37584	1.25;1.19	4.6	4.6	0.57074	.	0.667324	0.11739	N	0.534234	T	0.26085	0.0636	N	0.19112	0.55	0.30152	N	0.802933	B;P	0.40731	0.421;0.728	B;B	0.39339	0.118;0.297	T	0.07028	-1.0794	10	0.33141	T	0.24	-13.4777	11.6628	0.51356	0.0:0.0:0.0:1.0	.	484;574	Q8TF21;Q8TF21-2	ANR24_HUMAN;.	T	484;574	ENSP00000321731:I484T;ENSP00000262970:I574T	ENSP00000262970:I574T	I	+	2	0	ANKRD24	4167608	1.000000	0.71417	0.991000	0.47740	0.403000	0.30841	3.567000	0.53813	1.854000	0.53819	0.260000	0.18958	ATC	.	.		0.602	ANKRD24-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000458188.1	XM_114000	
PLIN3	10226	hgsc.bcm.edu	37	19	4839252	4839252	+	Silent	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:4839252T>C	ENST00000221957.4	-	8	1433	c.1257A>G	c.(1255-1257)ggA>ggG	p.G419G	PLIN3_ENST00000585479.1_Silent_p.G418G|PLIN3_ENST00000592528.1_Silent_p.G407G|CTC-518P12.6_ENST00000591657.1_RNA	NM_001164189.1|NM_001164194.1|NM_005817.4	NP_001157661.1|NP_001157666.1|NP_005808.3	O60664	PLIN3_HUMAN	perilipin 3	419					vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|lipid particle (GO:0005811)|membrane (GO:0016020)				cervix(1)|endometrium(2)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)	9					Galsulfase(DB01279)|Idursulfase(DB01271)	GGGCAAAGGGTCCCACGAGCC	0.622																																					p.G419G		Atlas-SNP	.											.	PLIN3	36	.	0			c.A1257G						.						66.0	72.0	69.0					19																	4839252		2203	4300	6503	SO:0001819	synonymous_variant	10226	exon8			AAAGGGTCCCACG	AF051314	CCDS12137.1, CCDS59337.1, CCDS59338.1	19p13.3	2009-08-12	2009-08-12	2009-08-12		ENSG00000105355		"""Perilipins"""	16893	protein-coding gene	gene with protein product	"""cargo selection protein (mannose 6 phosphate receptor binding protein)"", ""placental protein 17"", ""MPR-BINDING PROTEIN, 47-KD"""	602702	"""mannose-6-phosphate receptor binding protein 1"""	M6PRBP1		9590177, 6856484, 19638644	Standard	NM_005817		Approved	TIP47, PP17	uc002mbj.2	O60664		ENST00000221957.4:c.1257A>G	chr19.hg19:g.4839252T>C		206.0	0.0		115.0	7.0	NM_005817	A8K4Y9|K7EQF4|Q53G77|Q9BS03|Q9UBD7|Q9UP92	Silent	SNP	ENST00000221957.4	hg19	CCDS12137.1																																																																																			.	.		0.622	PLIN3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000450436.1	NM_005817	
SLC25A23	79085	hgsc.bcm.edu	37	19	6454721	6454721	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:6454721T>C	ENST00000301454.4	-	5	597	c.491A>G	c.(490-492)gAc>gGc	p.D164G	SLC25A23_ENST00000334510.5_Missense_Mutation_p.D164G|SLC25A23_ENST00000414491.2_5'Flank	NM_024103.2	NP_077008.2	Q9BV35	SCMC3_HUMAN	solute carrier family 25 (mitochondrial carrier; phosphate carrier), member 23	164					adenine nucleotide transport (GO:0051503)|cellular response to calcium ion (GO:0071277)|regulation of cellular respiration (GO:0043457)|regulation of oxidative phosphorylation (GO:0002082)|regulation of sequestering of calcium ion (GO:0051282)|transmembrane transport (GO:0055085)|urea homeostasis (GO:0097274)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	calcium ion binding (GO:0005509)			endometrium(3)|kidney(1)|large_intestine(6)|lung(3)|ovary(2)|pancreas(1)|skin(1)	17						CTCGCCAATGTCCAGGACCTA	0.567																																					p.D164G		Atlas-SNP	.											.	SLC25A23	43	.	0			c.A491G						.						49.0	44.0	46.0					19																	6454721		2203	4300	6503	SO:0001583	missense	79085	exon5			CCAATGTCCAGGA	AJ619962	CCDS32882.1	19p13.1	2014-02-06			ENSG00000125648	ENSG00000125648		"""Solute carriers"", ""EF-hand domain containing"""	19375	protein-coding gene	gene with protein product		608746				15123600	Standard	NM_024103		Approved	FLJ30339, MGC2615, APC2	uc002mex.1	Q9BV35	OTTHUMG00000180852	ENST00000301454.4:c.491A>G	chr19.hg19:g.6454721T>C	ENSP00000301454:p.Asp164Gly	109.0	0.0		80.0	4.0	NM_024103	B4DGB6|Q4LBC2|Q705K3|Q86Y43|Q8N2N4|Q96NQ4	Missense_Mutation	SNP	ENST00000301454.4	hg19	CCDS32882.1	.	.	.	.	.	.	.	.	.	.	T	19.87	3.908212	0.72868	.	.	ENSG00000125648	ENST00000264088;ENST00000301454;ENST00000334510	T;T;T	0.81330	-1.48;-1.34;-1.21	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	D	0.90988	0.7166	M	0.88906	2.99	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	D	0.92586	0.6079	10	0.87932	D	0	-44.7766	15.1042	0.72306	0.0:0.0:0.0:1.0	.	164	Q9BV35	SCMC3_HUMAN	G	211;164;164	ENSP00000264088:D211G;ENSP00000301454:D164G;ENSP00000334537:D164G	ENSP00000264088:D211G	D	-	2	0	SLC25A23	6405721	1.000000	0.71417	1.000000	0.80357	0.458000	0.32498	7.671000	0.83941	2.217000	0.71921	0.533000	0.62120	GAC	.	.		0.567	SLC25A23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453325.1	NM_024103	
SLC25A23	79085	hgsc.bcm.edu	37	19	6456486	6456486	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:6456486A>G	ENST00000301454.4	-	4	534	c.428T>C	c.(427-429)cTg>cCg	p.L143P	SLC25A23_ENST00000334510.5_Missense_Mutation_p.L143P|SLC25A23_ENST00000414491.2_5'Flank	NM_024103.2	NP_077008.2	Q9BV35	SCMC3_HUMAN	solute carrier family 25 (mitochondrial carrier; phosphate carrier), member 23	143	EF-hand 3. {ECO:0000255|PROSITE- ProRule:PRU00448}.				adenine nucleotide transport (GO:0051503)|cellular response to calcium ion (GO:0071277)|regulation of cellular respiration (GO:0043457)|regulation of oxidative phosphorylation (GO:0002082)|regulation of sequestering of calcium ion (GO:0051282)|transmembrane transport (GO:0055085)|urea homeostasis (GO:0097274)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	calcium ion binding (GO:0005509)			endometrium(3)|kidney(1)|large_intestine(6)|lung(3)|ovary(2)|pancreas(1)|skin(1)	17						CGAATGCAACAGGAAGTGGTC	0.577																																					p.L143P		Atlas-SNP	.											.	SLC25A23	43	.	0			c.T428C						.						168.0	126.0	140.0					19																	6456486		2203	4300	6503	SO:0001583	missense	79085	exon4			TGCAACAGGAAGT	AJ619962	CCDS32882.1	19p13.1	2014-02-06			ENSG00000125648	ENSG00000125648		"""Solute carriers"", ""EF-hand domain containing"""	19375	protein-coding gene	gene with protein product		608746				15123600	Standard	NM_024103		Approved	FLJ30339, MGC2615, APC2	uc002mex.1	Q9BV35	OTTHUMG00000180852	ENST00000301454.4:c.428T>C	chr19.hg19:g.6456486A>G	ENSP00000301454:p.Leu143Pro	136.0	0.0		122.0	5.0	NM_024103	B4DGB6|Q4LBC2|Q705K3|Q86Y43|Q8N2N4|Q96NQ4	Missense_Mutation	SNP	ENST00000301454.4	hg19	CCDS32882.1	.	.	.	.	.	.	.	.	.	.	A	22.9	4.349068	0.82132	.	.	ENSG00000125648	ENST00000264088;ENST00000301454;ENST00000334510	T;T;T	0.41400	1.0;1.0;1.0	4.86	4.86	0.63082	EF-hand-like domain (1);	0.000000	0.64402	D	0.000002	T	0.65698	0.2716	M	0.84082	2.675	0.80722	D	1	D	0.89917	1.0	D	0.70935	0.971	T	0.71938	-0.4441	10	0.87932	D	0	-14.342	13.4103	0.60938	1.0:0.0:0.0:0.0	.	143	Q9BV35	SCMC3_HUMAN	P	143	ENSP00000264088:L143P;ENSP00000301454:L143P;ENSP00000334537:L143P	ENSP00000264088:L143P	L	-	2	0	SLC25A23	6407486	1.000000	0.71417	0.995000	0.50966	0.988000	0.76386	8.812000	0.91959	1.824000	0.53156	0.402000	0.26972	CTG	.	.		0.577	SLC25A23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453325.1	NM_024103	
HNRNPM	4670	hgsc.bcm.edu	37	19	8533662	8533662	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:8533662A>G	ENST00000325495.4	+	9	880	c.839A>G	c.(838-840)gAg>gGg	p.E280G	HNRNPM_ENST00000348943.3_Missense_Mutation_p.E241G	NM_005968.4	NP_005959.2	P52272	HNRPM_HUMAN	heterogeneous nuclear ribonucleoprotein M	280	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				alternative mRNA splicing, via spliceosome (GO:0000380)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|paraspeckles (GO:0042382)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein domain specific binding (GO:0019904)|RNA binding (GO:0003723)			endometrium(5)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)	25						TTTCAGGATGAGAGGGCCTTA	0.458																																					p.E280G		Atlas-SNP	.											.	HNRNPM	61	.	0			c.A839G						.						79.0	69.0	72.0					19																	8533662		2203	4300	6503	SO:0001583	missense	4670	exon9			AGGATGAGAGGGC	L03532	CCDS12203.1, CCDS12204.1	19p13.2	2013-06-12		2008-04-18	ENSG00000099783	ENSG00000099783		"""RNA binding motif (RRM) containing"""	5046	protein-coding gene	gene with protein product	"""CEA receptor"""	160994		NAGR1, HNRPM		8441656, 7558047	Standard	NM_005968		Approved	HTGR1, HNRNPM4, HNRPM4, CEAR	uc010dwe.3	P52272	OTTHUMG00000182383	ENST00000325495.4:c.839A>G	chr19.hg19:g.8533662A>G	ENSP00000325376:p.Glu280Gly	49.0	0.0		48.0	4.0	NM_005968	Q15584|Q8WZ44|Q96H56|Q9BWL9|Q9Y492	Missense_Mutation	SNP	ENST00000325495.4	hg19	CCDS12203.1	.	.	.	.	.	.	.	.	.	.	A	21.3	4.121480	0.77436	.	.	ENSG00000099783	ENST00000325495;ENST00000348943;ENST00000544159	T;T	0.36157	1.27;2.71	5.61	5.61	0.85477	RNA recognition motif domain (1);	0.095738	0.64402	D	0.000001	T	0.42877	0.1222	L	0.42245	1.32	0.80722	D	1	B;B;P;B;B	0.48911	0.139;0.047;0.917;0.32;0.067	B;B;P;B;B	0.50405	0.171;0.046;0.64;0.086;0.119	T	0.37663	-0.9696	10	0.72032	D	0.01	.	14.676	0.68981	1.0:0.0:0.0:0.0	.	120;280;241;241;180	Q7KYM9;P52272;P52272-2;B4DEG4;Q59ES8	.;HNRPM_HUMAN;.;.;.	G	280;241;180	ENSP00000325376:E280G;ENSP00000325732:E241G	ENSP00000325376:E280G	E	+	2	0	HNRNPM	8439662	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	8.429000	0.90280	2.144000	0.66660	0.529000	0.55759	GAG	.	.		0.458	HNRNPM-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460894.1		
PRAM1	84106	hgsc.bcm.edu	37	19	8564429	8564429	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:8564429A>G	ENST00000423345.4	-	2	783	c.263T>C	c.(262-264)gTc>gCc	p.V88A	PRAM1_ENST00000255612.3_Missense_Mutation_p.V88A			Q96QH2	PRAM_HUMAN	PML-RARA regulated adaptor molecule 1	136	8 X 12 AA repeats of K-P-P-[PQ]-P-[EQ]- [VAF]-T-D-L-P-K.|Pro-rich.				integrin-mediated signaling pathway (GO:0007229)|regulation of neutrophil degranulation (GO:0043313)		lipid binding (GO:0008289)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(5)|prostate(1)|skin(1)	19						GAGGTCAGTGACCTCAGGCGG	0.667																																					p.V88A		Atlas-SNP	.											.	PRAM1	53	.	0			c.T263C						.						14.0	17.0	16.0					19																	8564429		1151	2895	4046	SO:0001583	missense	84106	exon2			TCAGTGACCTCAG	BC028012	CCDS45954.1, CCDS45954.2	19p13.2	2009-01-21				ENSG00000133246			30091	protein-coding gene	gene with protein product		606466				11301322, 15572693	Standard	NM_032152		Approved	PML-RAR	uc002mkd.3	Q96QH2		ENST00000423345.4:c.263T>C	chr19.hg19:g.8564429A>G	ENSP00000408342:p.Val88Ala	67.0	0.0		57.0	6.0	NM_032152	Q8N6W7	Missense_Mutation	SNP	ENST00000423345.4	hg19	CCDS45954.2	.	.	.	.	.	.	.	.	.	.	A	0.892	-0.725077	0.03158	.	.	ENSG00000133246	ENST00000255612;ENST00000423345	T;T	0.16196	2.36;2.36	3.38	2.36	0.29203	.	0.680970	0.12143	N	0.495622	T	0.08891	0.0220	N	0.14661	0.345	0.09310	N	1	B;B	0.12013	0.005;0.004	B;B	0.12156	0.005;0.007	T	0.39663	-0.9603	10	0.18276	T	0.48	.	6.9376	0.24474	0.8825:0.0:0.1175:0.0	.	88;136	Q96QH2-2;Q96QH2	.;PRAM_HUMAN	A	88	ENSP00000255612:V88A;ENSP00000408342:V88A	ENSP00000255612:V88A	V	-	2	0	PRAM1	8470429	0.000000	0.05858	0.002000	0.10522	0.006000	0.05464	0.198000	0.17217	0.673000	0.31224	0.478000	0.44815	GTC	.	.		0.667	PRAM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397040.3	NM_032152	
MBD3L1	85509	hgsc.bcm.edu	37	19	8953814	8953814	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:8953814A>G	ENST00000595891.1	+	3	691	c.460A>G	c.(460-462)Atc>Gtc	p.I154V	MBD3L1_ENST00000305625.2_Missense_Mutation_p.I154V			Q8WWY6	MB3L1_HUMAN	methyl-CpG binding domain protein 3-like 1	154					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|cervix(1)|large_intestine(5)|liver(1)|lung(2)|skin(2)	12						TGAGGAAGATATCAGGAAACA	0.498																																					p.I154V		Atlas-SNP	.											.	MBD3L1	24	.	0			c.A460G						.						42.0	38.0	39.0					19																	8953814		2203	4300	6503	SO:0001583	missense	85509	exon1			GAAGATATCAGGA	AY038022	CCDS12209.1	19p13.2	2011-01-31	2003-03-19	2003-03-21	ENSG00000170948	ENSG00000170948			15774	protein-coding gene	gene with protein product		607963	"""methyl-CpG binding domain protein 3-like"""	MBD3L		12504854	Standard	NM_145208		Approved		uc002mko.2	Q8WWY6		ENST00000595891.1:c.460A>G	chr19.hg19:g.8953814A>G	ENSP00000471575:p.Ile154Val	132.0	0.0		93.0	4.0	NM_145208	B5BUM6|Q2M291	Missense_Mutation	SNP	ENST00000595891.1	hg19	CCDS12209.1	.	.	.	.	.	.	.	.	.	.	A	13.89	2.371245	0.42003	.	.	ENSG00000170948	ENST00000305625	T	0.62232	0.04	3.92	2.9	0.33743	.	0.139066	0.29369	N	0.012359	T	0.61451	0.2348	M	0.83384	2.64	0.47994	D	0.999562	P	0.42735	0.788	B	0.41202	0.35	T	0.61686	-0.7012	10	0.49607	T	0.09	-5.6283	6.1829	0.20482	0.8854:0.0:0.1146:0.0	.	154	Q8WWY6	MB3L1_HUMAN	V	154	ENSP00000304198:I154V	ENSP00000304198:I154V	I	+	1	0	MBD3L1	8814814	1.000000	0.71417	0.950000	0.38849	0.533000	0.34776	3.640000	0.54350	0.840000	0.34995	0.533000	0.62120	ATC	.	.		0.498	MBD3L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459973.1	NM_145208	
MUC16	94025	hgsc.bcm.edu	37	19	9024995	9024995	+	Silent	SNP	G	G	T	rs375977247		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:9024995G>T	ENST00000397910.4	-	16	37070	c.36867C>A	c.(36865-36867)ccC>ccA	p.P12289P		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	12291	SEA 2. {ECO:0000255|PROSITE- ProRule:PRU00188}.				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)		p.P12289P(1)		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						CATCTTTCTCGGGCCTGGGGA	0.542																																					p.P12289P		Atlas-SNP	.											MUC16_ENST00000397910,NS,carcinoma,0,1	MUC16	4315	.	1	Substitution - coding silent(1)	lung(1)	c.C36867A						.						56.0	53.0	54.0					19																	9024995		1856	4101	5957	SO:0001819	synonymous_variant	94025	exon16			TTTCTCGGGCCTG	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.36867C>A	chr19.hg19:g.9024995G>T		173.0	2.0		138.0	0.0	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	hg19	CCDS54212.1																																																																																			.	.		0.542	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
ZNF439	90594	hgsc.bcm.edu	37	19	11977010	11977010	+	Silent	SNP	G	G	A			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:11977010G>A	ENST00000304030.2	+	1	239	c.39G>A	c.(37-39)gaG>gaA	p.E13E	ZNF439_ENST00000592534.1_Intron|ZNF439_ENST00000455282.1_Intron	NM_152262.2	NP_689475.1	Q8NDP4	ZN439_HUMAN	zinc finger protein 439	13					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(7)|pancreas(1)|skin(2)	27						ACACATGTGAGATGTTTCAGG	0.493																																					p.E13E		Atlas-SNP	.											.	ZNF439	67	.	0			c.G39A						.						133.0	132.0	132.0					19																	11977010		2203	4300	6503	SO:0001819	synonymous_variant	90594	exon1			ATGTGAGATGTTT	AL833935	CCDS12268.1	19p13.13	2013-01-08			ENSG00000171291	ENSG00000171291		"""Zinc fingers, C2H2-type"", ""-"""	20873	protein-coding gene	gene with protein product							Standard	NM_152262		Approved	DKFZp571K0837	uc002mss.3	Q8NDP4	OTTHUMG00000156527	ENST00000304030.2:c.39G>A	chr19.hg19:g.11977010G>A		133.0	0.0		87.0	5.0	NM_152262	Q8IYZ7|Q96SU1	Silent	SNP	ENST00000304030.2	hg19	CCDS12268.1																																																																																			.	.		0.493	ZNF439-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344513.1		
BRD4	23476	hgsc.bcm.edu	37	19	15349696	15349696	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:15349696T>C	ENST00000263377.2	-	19	4099	c.3878A>G	c.(3877-3879)cAa>cGa	p.Q1293R	AC004257.3_ENST00000602793.1_lincRNA	NM_058243.2	NP_490597.1	O60885	BRD4_HUMAN	bromodomain containing 4	1293	C-terminal (CTD) region.|Poly-Gln.				cellular response to DNA damage stimulus (GO:0006974)|chromatin remodeling (GO:0006338)|chromosome segregation (GO:0007059)|histone H3-K14 acetylation (GO:0044154)|histone H4-K12 acetylation (GO:0043983)|inner cell mass cell proliferation (GO:0001833)|negative regulation of DNA damage checkpoint (GO:2000002)|positive regulation of DNA binding (GO:0043388)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of inflammatory response (GO:0050727)|regulation of phosphorylation of RNA polymerase II C-terminal domain (GO:1901407)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromosome (GO:0005694)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|positive transcription elongation factor complex b (GO:0008024)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(7)|ovary(2)|urinary_tract(1)	21			OV - Ovarian serous cystadenocarcinoma(3;3.02e-24)|Epithelial(3;4.71e-20)|all cancers(3;2.26e-18)			ctgctgctgttgctcctggcg	0.711			T	C15orf55	lethal midline carcinoma of young people																																p.Q1293R		Atlas-SNP	.		Dom	yes		19	19p13.1	23476	bromodomain containing 4		E	.	BRD4	172	.	0			c.A3878G						.						8.0	9.0	9.0					19																	15349696		2154	4226	6380	SO:0001583	missense	23476	exon19			TGCTGTTGCTCCT	Y12059	CCDS12328.1, CCDS46004.1	19p13.12	2013-09-20	2002-01-14		ENSG00000141867	ENSG00000141867			13575	protein-coding gene	gene with protein product	"""chromosome-associated protein"""	608749	"""bromodomain-containing 4"""			10938129	Standard	NM_058243		Approved	HUNKI, MCAP, CAP, HUNK1	uc002nar.3	O60885	OTTHUMG00000183252	ENST00000263377.2:c.3878A>G	chr19.hg19:g.15349696T>C	ENSP00000263377:p.Gln1293Arg	107.0	0.0		77.0	5.0	NM_058243	O60433|Q4G0X8|Q86YS8|Q96PD3	Missense_Mutation	SNP	ENST00000263377.2	hg19	CCDS12328.1	.	.	.	.	.	.	.	.	.	.	t	13.20	2.166187	0.38217	.	.	ENSG00000141867	ENST00000263377	T	0.16897	2.31	5.1	4.0	0.46444	.	0.662303	0.12533	N	0.460603	T	0.11537	0.0281	N	0.14661	0.345	0.80722	D	1	B	0.27498	0.18	B	0.26969	0.075	T	0.12218	-1.0556	10	0.87932	D	0	.	10.9916	0.47553	0.0:0.0:0.156:0.844	.	1293	O60885	BRD4_HUMAN	R	1293	ENSP00000263377:Q1293R	ENSP00000263377:Q1293R	Q	-	2	0	BRD4	15210696	1.000000	0.71417	0.931000	0.37212	0.871000	0.50021	3.762000	0.55250	2.033000	0.60031	0.524000	0.50904	CAA	.	.		0.711	BRD4-001	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465800.3	NM_058243	
OR10H2	26538	hgsc.bcm.edu	37	19	15838973	15838973	+	Silent	SNP	G	G	A			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:15838973G>A	ENST00000305899.3	+	1	140	c.120G>A	c.(118-120)ctG>ctA	p.L40L		NM_013939.2	NP_039227.1	O60403	O10H2_HUMAN	olfactory receptor, family 10, subfamily H, member 2	40			L -> Q (in dbSNP:rs4569397).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L40L(1)		breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|skin(3)|stomach(1)	27	all_hematologic(1;0.0517)|Acute lymphoblastic leukemia(2;0.074)					TCACGCTGCTGGGCAACCTGC	0.582																																					p.L40L		Atlas-SNP	.											OR10H2,NS,carcinoma,0,1	OR10H2	59	.	1	Substitution - coding silent(1)	lung(1)	c.G120A						.						227.0	188.0	201.0					19																	15838973		2203	4298	6501	SO:0001819	synonymous_variant	26538	exon1			GCTGCTGGGCAAC	AC004597	CCDS12333.1	19p13.1	2012-08-09				ENSG00000171942		"""GPCR / Class A : Olfactory receptors"""	8173	protein-coding gene	gene with protein product							Standard	NM_013939		Approved		uc002nbm.2	O60403		ENST00000305899.3:c.120G>A	chr19.hg19:g.15838973G>A		391.0	1.0		307.0	0.0	NM_013939	Q6IFQ1|Q96R58	Silent	SNP	ENST00000305899.3	hg19	CCDS12333.1																																																																																			.	.		0.582	OR10H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460917.1		
NWD1	284434	hgsc.bcm.edu	37	19	16860649	16860649	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:16860649T>C	ENST00000552788.1	+	4	1196	c.1196T>C	c.(1195-1197)cTg>cCg	p.L399P	NWD1_ENST00000523826.1_Missense_Mutation_p.L193P|NWD1_ENST00000549814.1_Missense_Mutation_p.L399P|NWD1_ENST00000339803.6_Missense_Mutation_p.L264P|NWD1_ENST00000379808.3_Missense_Mutation_p.L399P|NWD1_ENST00000524140.2_Missense_Mutation_p.L399P			Q149M9	NWD1_HUMAN	NACHT and WD repeat domain containing 1	399	NACHT.						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						GCCTATGGGCTGCCCTTGCCC	0.602																																					p.L399P		Atlas-SNP	.											.	NWD1	303	.	0			c.T1196C						.						41.0	43.0	42.0					19																	16860649		2203	4300	6503	SO:0001583	missense	284434	exon6			ATGGGCTGCCCTT	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.1196T>C	chr19.hg19:g.16860649T>C	ENSP00000447224:p.Leu399Pro	100.0	0.0		69.0	4.0	NM_001007525	C9J021|Q68CT3	Missense_Mutation	SNP	ENST00000552788.1	hg19		.	.	.	.	.	.	.	.	.	.	t	18.69	3.677099	0.68042	.	.	ENSG00000188039	ENST00000420818;ENST00000524140;ENST00000549814;ENST00000379808;ENST00000523826;ENST00000552788;ENST00000339803	T;T;T;T;T;T	0.77489	-1.1;-1.1;-1.1;-1.1;-1.1;-1.1	4.53	4.53	0.55603	.	0.000000	0.64402	D	0.000006	D	0.86661	0.5986	M	0.79475	2.455	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.996;0.999;1.0	D	0.86910	0.2060	10	0.46703	T	0.11	-17.5849	12.067	0.53594	0.0:0.0:0.0:1.0	.	399;399;264	Q149M9;Q149M9-3;C9J2Y8	NWD1_HUMAN;.;.	P	264;399;399;399;193;399;264	ENSP00000428579:L399P;ENSP00000447548:L399P;ENSP00000369136:L399P;ENSP00000428955:L193P;ENSP00000447224:L399P;ENSP00000340159:L264P	ENSP00000340159:L264P	L	+	2	0	NWD1	16721649	1.000000	0.71417	0.998000	0.56505	0.890000	0.51754	6.076000	0.71267	1.808000	0.52836	0.520000	0.50463	CTG	.	.		0.602	NWD1-005	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000403569.1	NM_001007525	
JAK3	3718	hgsc.bcm.edu	37	19	17948866	17948866	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:17948866T>C	ENST00000527670.1	-	11	1605	c.1576A>G	c.(1576-1578)Aac>Gac	p.N526D	JAK3_ENST00000534444.1_Missense_Mutation_p.N526D|JAK3_ENST00000458235.1_Missense_Mutation_p.N526D|JAK3_ENST00000526008.1_5'Flank			P52333	JAK3_HUMAN	Janus kinase 3	526	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				B cell differentiation (GO:0030183)|enzyme linked receptor protein signaling pathway (GO:0007167)|innate immune response (GO:0045087)|interleukin-4-mediated signaling pathway (GO:0035771)|intracellular signal transduction (GO:0035556)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|negative regulation of dendritic cell cytokine production (GO:0002731)|negative regulation of FasL biosynthetic process (GO:0045221)|negative regulation of interleukin-10 production (GO:0032693)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of T cell activation (GO:0050868)|negative regulation of T-helper 1 cell differentiation (GO:0045626)|negative regulation of thymocyte apoptotic process (GO:0070244)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of dendritic cell apoptotic process (GO:2000670)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of T cell apoptotic process (GO:0070232)|response to interleukin-15 (GO:0070672)|response to interleukin-2 (GO:0070669)|response to interleukin-4 (GO:0070670)|response to interleukin-9 (GO:0071104)|STAT protein import into nucleus (GO:0007262)|T cell homeostasis (GO:0043029)|tyrosine phosphorylation of STAT protein (GO:0007260)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)			breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(85)|kidney(4)|large_intestine(11)|lung(22)|ovary(3)|prostate(5)|skin(1)|stomach(2)|upper_aerodigestive_tract(5)	147					Tofacitinib(DB08895)	TGGCCCAGGTTCTCATGCTGA	0.587		2	Mis		"""acute megakaryocytic leukemia, ETP ALL"""																																p.N526D		Atlas-SNP	.		Dom	yes		19	19p13.1	3718	Janus kinase 3		L	JAK3_ENST00000458235,bladder,carcinoma,0,2	JAK3	341	.	0			c.A1576G						.						88.0	84.0	85.0					19																	17948866		2203	4300	6503	SO:0001583	missense	3718	exon12			CCAGGTTCTCATG	U31601	CCDS12366.1	19p13-p12	2014-09-17	2009-04-23		ENSG00000105639	ENSG00000105639	2.7.10.1		6193	protein-coding gene	gene with protein product	"""tyrosine-protein kinase JAK3"", ""leukocyte Janus kinase"""	600173				8921370, 9226382	Standard	NM_000215		Approved	L-JAK, JAKL, LJAK, JAK3_HUMAN, JAK-3	uc002nhn.4	P52333	OTTHUMG00000165648	ENST00000527670.1:c.1576A>G	chr19.hg19:g.17948866T>C	ENSP00000432511:p.Asn526Asp	159.0	0.0		115.0	5.0	NM_000215	Q13259|Q13260|Q13611|Q8N1E8|Q99699|Q9Y6S2	Missense_Mutation	SNP	ENST00000527670.1	hg19	CCDS12366.1	.	.	.	.	.	.	.	.	.	.	T	21.8	4.205384	0.79127	.	.	ENSG00000105639	ENST00000458235;ENST00000428406;ENST00000527670;ENST00000534444	T;T;T	0.24538	1.85;1.85;1.85	4.93	4.93	0.64822	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.105140	0.64402	D	0.000005	T	0.27967	0.0689	L	0.43152	1.355	0.37246	D	0.906344	P;P	0.50528	0.936;0.889	P;P	0.50192	0.57;0.634	T	0.10520	-1.0626	10	0.11794	T	0.64	-40.616	12.5164	0.56034	0.0:0.0:0.0:1.0	.	526;526	P52333-2;P52333	.;JAK3_HUMAN	D	526	ENSP00000391676:N526D;ENSP00000432511:N526D;ENSP00000436421:N526D	ENSP00000413248:N526D	N	-	1	0	JAK3	17809866	1.000000	0.71417	1.000000	0.80357	0.814000	0.46013	7.299000	0.78831	1.852000	0.53769	0.260000	0.18958	AAC	.	.		0.587	JAK3-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385549.1	NM_000215	
PDE4C	5143	hgsc.bcm.edu	37	19	18331057	18331057	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:18331057A>G	ENST00000355502.3	-	11	1652	c.781T>C	c.(781-783)Tac>Cac	p.Y261H	PDE4C_ENST00000598111.2_Missense_Mutation_p.Y31H|PDE4C_ENST00000594617.3_Missense_Mutation_p.Y261H|PDE4C_ENST00000447275.3_Missense_Mutation_p.Y155H|PDE4C_ENST00000539010.1_Missense_Mutation_p.Y30H|PDE4C_ENST00000597297.1_Missense_Mutation_p.Y31H|PDE4C_ENST00000262805.12_Missense_Mutation_p.Y229H|AC068499.10_ENST00000594805.3_RNA|PDE4C_ENST00000594465.3_Missense_Mutation_p.Y261H			Q08493	PDE4C_HUMAN	phosphodiesterase 4C, cAMP-specific	261					cAMP catabolic process (GO:0006198)|signal transduction (GO:0007165)	cytosol (GO:0005829)|extracellular space (GO:0005615)|primary cilium (GO:0072372)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(2)|lung(9)|ovary(2)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	33					Caffeine(DB00201)|Dyphylline(DB00651)|Ibudilast(DB05266)|Iloprost(DB01088)|Ketotifen(DB00920)|Roflumilast(DB01656)	CGGGAGATGTACTCGGACACC	0.537																																					p.Y261H		Atlas-SNP	.											.	PDE4C	80	.	0			c.T781C						.						116.0	123.0	121.0					19																	18331057		2203	4300	6503	SO:0001583	missense	5143	exon8			AGATGTACTCGGA		CCDS12373.1, CCDS42523.1, CCDS46016.1	19p13.11	2010-06-24	2010-06-24			ENSG00000105650	3.1.4.17	"""Phosphodiesterases"""	8782	protein-coding gene	gene with protein product	"""phosphodiesterase E1 dunce homolog (Drosophila)"""	600128	"""phosphodiesterase 4C, cAMP-specific (dunce (Drosophila)-homolog phosphodiesterase E1)"""	DPDE1			Standard	NM_001098818		Approved		uc002nik.4	Q08493		ENST00000355502.3:c.781T>C	chr19.hg19:g.18331057A>G	ENSP00000347689:p.Tyr261His	156.0	0.0		129.0	7.0	NM_000923	B3KTC4|Q9UN44|Q9UN45|Q9UN46|Q9UPJ6	Missense_Mutation	SNP	ENST00000355502.3	hg19	CCDS12373.1	.	.	.	.	.	.	.	.	.	.	A	21.8	4.208577	0.79240	.	.	ENSG00000105650	ENST00000536045;ENST00000355502;ENST00000536507;ENST00000262805;ENST00000447275;ENST00000545961;ENST00000336173;ENST00000539010;ENST00000543547	T;T;T;T	0.75938	-0.98;-0.94;-0.86;-0.41	4.83	4.83	0.62350	.	0.371406	0.28635	N	0.014647	D	0.87257	0.6132	M	0.89715	3.055	0.35605	D	0.808203	D;D;D;D	0.76494	0.999;0.991;0.969;0.985	D;D;P;P	0.69142	0.962;0.917;0.781;0.845	D	0.92425	0.5949	10	0.87932	D	0	.	12.3551	0.55171	1.0:0.0:0.0:0.0	.	261;229;67;31	Q08493;Q08493-3;O43850;O76104	PDE4C_HUMAN;.;.;.	H	340;261;249;229;155;67;30;30;370	ENSP00000347689:Y261H;ENSP00000262805:Y229H;ENSP00000402091:Y155H;ENSP00000439470:Y30H	ENSP00000262805:Y229H	Y	-	1	0	PDE4C	18192057	1.000000	0.71417	0.982000	0.44146	0.772000	0.43724	8.815000	0.91973	1.823000	0.53134	0.398000	0.26397	TAC	.	.		0.537	PDE4C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466295.1		
COPE	11316	hgsc.bcm.edu	37	19	19021789	19021789	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:19021789T>C	ENST00000262812.4	-	3	329	c.281A>G	c.(280-282)gAg>gGg	p.E94G	COPE_ENST00000349893.4_Missense_Mutation_p.E94G|COPE_ENST00000351079.4_Missense_Mutation_p.E94G|COPE_ENST00000600932.1_Missense_Mutation_p.E94G|COPE_ENST00000598969.1_5'UTR|AC002985.3_ENST00000596918.1_3'UTR	NM_007263.3	NP_009194.2	O14579	COPE_HUMAN	coatomer protein complex, subunit epsilon	94					COPI coating of Golgi vesicle (GO:0048205)|intra-Golgi vesicle-mediated transport (GO:0006891)|membrane organization (GO:0061024)|protein transport (GO:0015031)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	COPI vesicle coat (GO:0030126)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(2)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|skin(1)	11						CCTCCGACTCTCGTGGGCGAG	0.632																																					p.E94G		Atlas-SNP	.											.	COPE	26	.	0			c.A281G						.						93.0	80.0	84.0					19																	19021789		2203	4300	6503	SO:0001583	missense	11316	exon3			CGACTCTCGTGGG	AJ131182	CCDS12387.1, CCDS12388.1, CCDS12389.1	19p13.11	2008-02-05				ENSG00000105669			2234	protein-coding gene	gene with protein product		606942				10469566	Standard	NM_007263		Approved	epsilon-COP	uc002nkk.3	O14579		ENST00000262812.4:c.281A>G	chr19.hg19:g.19021789T>C	ENSP00000262812:p.Glu94Gly	157.0	0.0		123.0	6.0	NM_007263	A6NE29|A6NKA3|O76097|Q6IBB8|Q9UGP6	Missense_Mutation	SNP	ENST00000262812.4	hg19	CCDS12387.1	.	.	.	.	.	.	.	.	.	.	T	11.29	1.594281	0.28445	.	.	ENSG00000105669	ENST00000262812;ENST00000351079;ENST00000349893;ENST00000538245	T;T;T	0.44083	0.93;0.93;0.93	4.8	4.8	0.61643	.	0.184840	0.48767	D	0.000178	T	0.35828	0.0945	L	0.41236	1.265	0.80722	D	1	B;B;B;B	0.22851	0.0;0.076;0.0;0.0	B;B;B;B	0.29440	0.005;0.102;0.005;0.002	T	0.12889	-1.0530	10	0.23891	T	0.37	-28.9307	13.1643	0.59562	0.0:0.0:0.0:1.0	.	94;94;94;94	Q53HJ6;A6NE29;A6NKA3;O14579	.;.;.;COPE_HUMAN	G	94;94;94;93	ENSP00000262812:E94G;ENSP00000345674:E94G;ENSP00000343134:E94G	ENSP00000262812:E94G	E	-	2	0	COPE	18882789	1.000000	0.71417	0.624000	0.29186	0.200000	0.23975	7.306000	0.78905	1.797000	0.52628	0.421000	0.28195	GAG	.	.		0.632	COPE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464801.1	NM_007263	
MAU2	23383	hgsc.bcm.edu	37	19	19455688	19455688	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:19455688T>C	ENST00000392313.6	+	11	1287	c.1108T>C	c.(1108-1110)Tcc>Ccc	p.S370P	MAU2_ENST00000262815.8_Missense_Mutation_p.S370P	NM_015329.3	NP_056144.3	Q9Y6X3	SCC4_HUMAN	MAU2 sister chromatid cohesion factor	370					maintenance of mitotic sister chromatid cohesion (GO:0034088)|mitotic cell cycle (GO:0000278)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMC loading complex (GO:0032116)	protein N-terminus binding (GO:0047485)			NS(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	18						GTGCCAGCAGTCCCCCCGGCT	0.577																																					p.S370P		Atlas-SNP	.											.	MAU2	38	.	0			c.T1108C						.						31.0	33.0	32.0					19																	19455688		2001	4172	6173	SO:0001583	missense	23383	exon11			CAGCAGTCCCCCC	AB020699	CCDS32969.2	19p13.11	2013-08-28	2013-08-28	2013-08-28	ENSG00000129933	ENSG00000129933			29140	protein-coding gene	gene with protein product	"""sister chromatid cohesion 4"""	614560	"""KIAA0892"", ""MAU2 chromatid cohesion factor homolog (C. elegans)"""	KIAA0892		10048485	Standard	NM_015329		Approved	MGC75361, mau-2, MAU2L, SCC4	uc002nmk.4	Q9Y6X3	OTTHUMG00000150188	ENST00000392313.6:c.1108T>C	chr19.hg19:g.19455688T>C	ENSP00000376127:p.Ser370Pro	126.0	0.0		104.0	6.0	NM_015329	Q66PT1|Q6P3S7|Q6ZTT2|Q9UFX8	Missense_Mutation	SNP	ENST00000392313.6	hg19	CCDS32969.2	.	.	.	.	.	.	.	.	.	.	T	18.28	3.589970	0.66105	.	.	ENSG00000129933	ENST00000392313;ENST00000262815	.	.	.	5.38	5.38	0.77491	Tetratricopeptide-like helical (1);	0.000000	0.85682	U	0.000000	T	0.42517	0.1206	N	0.17082	0.46	0.80722	D	1	B	0.14012	0.009	B	0.12837	0.008	T	0.27262	-1.0079	9	0.35671	T	0.21	.	14.2523	0.66028	0.0:0.0:0.0:1.0	.	370	Q9Y6X3	SCC4_HUMAN	P	370	.	ENSP00000262815:S370P	S	+	1	0	MAU2	19316688	1.000000	0.71417	0.996000	0.52242	0.989000	0.77384	7.725000	0.84808	2.054000	0.61138	0.454000	0.30748	TCC	.	.		0.577	MAU2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000316748.6	NM_015329	
ZNF429	353088	hgsc.bcm.edu	37	19	21719985	21719985	+	Missense_Mutation	SNP	C	C	A			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:21719985C>A	ENST00000358491.4	+	4	1338	c.1130C>A	c.(1129-1131)gCt>gAt	p.A377D	ZNF429_ENST00000597078.1_Intron	NM_001001415.2	NP_001001415.2	Q86V71	ZN429_HUMAN	zinc finger protein 429	377					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(2)|large_intestine(13)|lung(10)|ovary(2)|pancreas(1)|prostate(1)|soft_tissue(1)|upper_aerodigestive_tract(2)	34						TGTGGCAAAGCTTTTAACCAG	0.373																																					p.A377D		Atlas-SNP	.											.	ZNF429	338	.	0			c.C1130A						.						41.0	47.0	45.0					19																	21719985		2099	4257	6356	SO:0001583	missense	353088	exon4			GCAAAGCTTTTAA	AY269786	CCDS42537.1	19p12	2014-02-14			ENSG00000197013	ENSG00000197013		"""Zinc fingers, C2H2-type"", ""-"""	20817	protein-coding gene	gene with protein product							Standard	NM_001001415		Approved		uc002nqd.1	Q86V71	OTTHUMG00000182848	ENST00000358491.4:c.1130C>A	chr19.hg19:g.21719985C>A	ENSP00000351280:p.Ala377Asp	33.0	0.0		28.0	9.0	NM_001001415	A6NLV7|Q9BZE6	Missense_Mutation	SNP	ENST00000358491.4	hg19	CCDS42537.1	.	.	.	.	.	.	.	.	.	.	.	7.998	0.754724	0.15778	.	.	ENSG00000197013	ENST00000358491	T	0.14266	2.52	0.876	0.876	0.19138	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.12433	0.0302	L	0.48877	1.53	0.09310	N	1	B	0.22541	0.071	B	0.23574	0.047	T	0.28839	-1.0031	9	0.87932	D	0	.	6.2723	0.20961	0.0:0.4389:0.5611:0.0	.	377	Q86V71	ZN429_HUMAN	D	377	ENSP00000351280:A377D	ENSP00000351280:A377D	A	+	2	0	ZNF429	21511825	0.000000	0.05858	0.467000	0.27180	0.469000	0.32828	0.344000	0.19962	0.293000	0.22520	0.298000	0.19748	GCT	.	.		0.373	ZNF429-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463981.1	NM_001001415	
ZNF208	7757	hgsc.bcm.edu	37	19	22155940	22155940	+	Silent	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:22155940A>G	ENST00000397126.4	-	4	2044	c.1896T>C	c.(1894-1896)gcT>gcC	p.A632A	ZNF208_ENST00000601773.1_Intron|ZNF208_ENST00000599916.1_Intron	NM_007153.3	NP_009084.2	O43345	ZN208_HUMAN	zinc finger protein 208	632					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(18)|liver(1)|lung(71)|ovary(6)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	113		all_lung(12;0.0961)|Lung NSC(12;0.103)				GCTTCTCTCCAGCATGAATTG	0.398																																					p.A632A		Atlas-SNP	.											.	ZNF208	817	.	0			c.T1896C						.						78.0	86.0	83.0					19																	22155940		2120	4248	6368	SO:0001819	synonymous_variant	7757	exon4			CTCTCCAGCATGA	BC038199	CCDS54240.1	19p12	2013-01-08				ENSG00000160321		"""Zinc fingers, C2H2-type"", ""-"""	12999	protein-coding gene	gene with protein product	"""zinc finger protein 95"""	603977				9724325	Standard	NM_007153		Approved	PMIDP, ZNF95	uc021urr.1	O43345		ENST00000397126.4:c.1896T>C	chr19.hg19:g.22155940A>G		69.0	0.0		83.0	30.0	NM_007153		Silent	SNP	ENST00000397126.4	hg19	CCDS54240.1																																																																																			.	.		0.398	ZNF208-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464302.1	NM_007153	
ZNF676	163223	hgsc.bcm.edu	37	19	22363757	22363757	+	Silent	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:22363757T>C	ENST00000397121.2	-	3	1079	c.762A>G	c.(760-762)aaA>aaG	p.K254K		NM_001001411.2	NP_001001411.2	Q8N7Q3	ZN676_HUMAN	zinc finger protein 676	254					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.K254K(1)		NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(49)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	67		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.114)				ATTCTTCACATTTGTAGGGTT	0.383																																					p.K254K		Atlas-SNP	.											ZNF676,NS,carcinoma,0,1	ZNF676	146	.	1	Substitution - coding silent(1)	lung(1)	c.A762G						.						80.0	87.0	85.0					19																	22363757		2162	4277	6439	SO:0001819	synonymous_variant	163223	exon3			TTCACATTTGTAG	AK097798	CCDS42539.1	19p12	2013-01-08				ENSG00000196109		"""Zinc fingers, C2H2-type"""	20429	protein-coding gene	gene with protein product							Standard	NM_001001411		Approved		uc002nqs.1	Q8N7Q3		ENST00000397121.2:c.762A>G	chr19.hg19:g.22363757T>C		68.0	0.0		50.0	2.0	NM_001001411	A8MVX5	Silent	SNP	ENST00000397121.2	hg19	CCDS42539.1																																																																																			.	.		0.383	ZNF676-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464392.1	NM_001001411	
ZNF99	7652	hgsc.bcm.edu	37	19	22941279	22941279	+	Missense_Mutation	SNP	C	C	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:22941279C>G	ENST00000596209.1	-	4	1522	c.1432G>C	c.(1432-1434)Gag>Cag	p.E478Q	ZNF99_ENST00000397104.3_Missense_Mutation_p.E387Q	NM_001080409.2	NP_001073878.2	A8MXY4	ZNF99_HUMAN	zinc finger protein 99	478					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.E387Q(1)		NS(1)|breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(20)|lung(55)|ovary(2)|prostate(10)|skin(5)|stomach(9)|upper_aerodigestive_tract(2)|urinary_tract(3)	124		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.102)				TAGGGTTTCTCTCCAGTATGA	0.353																																					p.E478Q		Atlas-SNP	.											ZNF99,NS,carcinoma,0,1	ZNF99	273	.	1	Substitution - Missense(1)	prostate(1)	c.G1432C						.																																			SO:0001583	missense	7652	exon4			GTTTCTCTCCAGT	BC021822	CCDS59369.1	19p12	2013-01-08	2006-01-17		ENSG00000213973	ENSG00000213973		"""Zinc fingers, C2H2-type"", ""-"""	13175	protein-coding gene	gene with protein product		603981	"""zinc finger protein 99 (F8281)"", ""chromosome 19 open reading frame 9"""	C19orf9			Standard	NM_001080409		Approved	MGC24986	uc021urt.1	A8MXY4		ENST00000596209.1:c.1432G>C	chr19.hg19:g.22941279C>G	ENSP00000472969:p.Glu478Gln	32.0	1.0		19.0	3.0	NM_001080409	M0R335	Missense_Mutation	SNP	ENST00000596209.1	hg19	CCDS59369.1	.	.	.	.	.	.	.	.	.	.	N	15.37	2.812264	0.50527	.	.	ENSG00000213973	ENST00000397104	T	0.25912	1.77	1.28	1.28	0.21552	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.38188	0.1031	L	0.55834	1.745	0.37534	D	0.918031	D	0.65815	0.995	P	0.61328	0.887	T	0.41980	-0.9478	9	0.72032	D	0.01	.	9.4929	0.38971	0.0:1.0:0.0:0.0	.	387	A8MXY4	ZNF99_HUMAN	Q	387	ENSP00000380293:E387Q	ENSP00000380293:E387Q	E	-	1	0	ZNF99	22733119	0.013000	0.17824	0.386000	0.26170	0.619000	0.37552	0.270000	0.18607	0.675000	0.31264	0.395000	0.25975	GAG	.	.		0.353	ZNF99-001	NOVEL	not_best_in_genome_evidence|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000464591.1	XM_065124	
ZNF536	9745	hgsc.bcm.edu	37	19	30935925	30935925	+	Missense_Mutation	SNP	C	C	A			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:30935925C>A	ENST00000355537.3	+	2	1603	c.1456C>A	c.(1456-1458)Cac>Aac	p.H486N		NM_014717.1	NP_055532.1	O15090	ZN536_HUMAN	zinc finger protein 536	486					negative regulation of neuron differentiation (GO:0045665)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|retinoic acid-responsive element binding (GO:0044323)			NS(3)|breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|lung(119)|ovary(7)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	182	Esophageal squamous(110;0.0834)					GGGGGACAAGCACTCCCTCCT	0.652																																					p.H486N		Atlas-SNP	.											.	ZNF536	424	.	0			c.C1456A						.						35.0	39.0	37.0					19																	30935925		2203	4299	6502	SO:0001583	missense	9745	exon2			GACAAGCACTCCC		CCDS32984.1	19q13.11	2013-01-08				ENSG00000198597		"""Zinc fingers, C2H2-type"""	29025	protein-coding gene	gene with protein product						9205841	Standard	XM_005259445		Approved	KIAA0390	uc002nsu.1	O15090		ENST00000355537.3:c.1456C>A	chr19.hg19:g.30935925C>A	ENSP00000347730:p.His486Asn	75.0	0.0		59.0	19.0	NM_014717	A2RU18	Missense_Mutation	SNP	ENST00000355537.3	hg19	CCDS32984.1	.	.	.	.	.	.	.	.	.	.	C	10.58	1.390145	0.25118	.	.	ENSG00000198597	ENST00000355537	T	0.07908	3.15	5.53	5.53	0.82687	.	0.048823	0.85682	D	0.000000	T	0.11580	0.0282	L	0.40543	1.245	0.51482	D	0.999923	D;D	0.53151	0.958;0.958	P;P	0.45276	0.475;0.475	T	0.13710	-1.0499	10	0.24483	T	0.36	-36.3673	19.4573	0.94900	0.0:1.0:0.0:0.0	.	486;486	A7E228;O15090	.;ZN536_HUMAN	N	486	ENSP00000347730:H486N	ENSP00000347730:H486N	H	+	1	0	ZNF536	35627765	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.788000	0.85771	2.582000	0.87167	0.655000	0.94253	CAC	.	.		0.652	ZNF536-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459667.2	NM_014717	
ZNF507	22847	hgsc.bcm.edu	37	19	32873700	32873700	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:32873700A>G	ENST00000311921.4	+	6	2765	c.2573A>G	c.(2572-2574)gAa>gGa	p.E858G	ZNF507_ENST00000355898.5_Missense_Mutation_p.E858G|ZNF507_ENST00000544431.1_Missense_Mutation_p.E862G	NM_001136156.1|NM_014910.4	NP_001129628.1|NP_055725.2	Q8TCN5	ZN507_HUMAN	zinc finger protein 507	858					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(10)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	31	Esophageal squamous(110;0.162)					GGAAGTTCAGAAAATGCAGTG	0.438																																					p.E858G		Atlas-SNP	.											.	ZNF507	92	.	0			c.A2573G						.						55.0	52.0	53.0					19																	32873700		2203	4300	6503	SO:0001583	missense	22847	exon7			GTTCAGAAAATGC	AB029007	CCDS32985.1	19q13.12	2008-02-05				ENSG00000168813		"""Zinc fingers, C2H2-type"""	23783	protein-coding gene	gene with protein product							Standard	NM_014910		Approved	KIAA1084	uc002ntd.3	Q8TCN5		ENST00000311921.4:c.2573A>G	chr19.hg19:g.32873700A>G	ENSP00000312277:p.Glu858Gly	128.0	0.0		81.0	6.0	NM_001136156	A8K911|Q2TBF1|Q6MZU0|Q9UPR8	Missense_Mutation	SNP	ENST00000311921.4	hg19	CCDS32985.1	.	.	.	.	.	.	.	.	.	.	A	13.63	2.294810	0.40594	.	.	ENSG00000168813	ENST00000355898;ENST00000311921;ENST00000544431	T;T;T	0.07688	3.49;3.49;3.17	5.87	5.87	0.94306	.	0.330421	0.37012	N	0.002298	T	0.13030	0.0316	M	0.66939	2.045	0.39673	D	0.970786	B	0.15141	0.012	B	0.09377	0.004	T	0.01767	-1.1278	10	0.48119	T	0.1	.	14.8516	0.70300	1.0:0.0:0.0:0.0	.	858	Q8TCN5	ZN507_HUMAN	G	858;858;862	ENSP00000348162:E858G;ENSP00000312277:E858G;ENSP00000441549:E862G	ENSP00000312277:E858G	E	+	2	0	ZNF507	37565540	1.000000	0.71417	0.746000	0.31095	0.038000	0.13279	4.769000	0.62300	2.248000	0.74166	0.533000	0.62120	GAA	.	.		0.438	ZNF507-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450301.3	NM_014910	
FAM187B	148109	hgsc.bcm.edu	37	19	35715757	35715757	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:35715757T>C	ENST00000324675.3	-	2	1129	c.1081A>G	c.(1081-1083)Aga>Gga	p.R361G		NM_152481.1	NP_689694.1	Q17R55	F187B_HUMAN	family with sequence similarity 187, member B	361						integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|large_intestine(2)|lung(3)|ovary(2)	9						TGTGTGCTTCTCCTGCCCGGG	0.652																																					p.R361G		Atlas-SNP	.											.	FAM187B	28	.	0			c.A1081G						.						25.0	27.0	26.0					19																	35715757		2202	4294	6496	SO:0001583	missense	148109	exon2			TGCTTCTCCTGCC	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.1081A>G	chr19.hg19:g.35715757T>C	ENSP00000323355:p.Arg361Gly	157.0	0.0		125.0	5.0	NM_152481	Q8N7G6	Missense_Mutation	SNP	ENST00000324675.3	hg19	CCDS12448.1	.	.	.	.	.	.	.	.	.	.	T	12.48	1.949923	0.34377	.	.	ENSG00000177558	ENST00000324675	T	0.27557	1.66	4.38	0.756	0.18421	.	1.038280	0.07644	N	0.930799	T	0.22205	0.0535	L	0.27053	0.805	0.09310	N	1	B	0.26195	0.144	B	0.30782	0.12	T	0.37957	-0.9683	10	0.72032	D	0.01	-8.487	4.8902	0.13722	0.1834:0.0:0.3782:0.4384	.	361	Q17R55	F187B_HUMAN	G	361	ENSP00000323355:R361G	ENSP00000323355:R361G	R	-	1	2	FAM187B	40407597	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.581000	0.05820	0.288000	0.22398	0.460000	0.39030	AGA	.	.		0.652	FAM187B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378854.1	NM_152481	
ZNF829	374899	hgsc.bcm.edu	37	19	37398844	37398844	+	Silent	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:37398844T>C	ENST00000391711.3	-	5	670	c.306A>G	c.(304-306)agA>agG	p.R102R	ZNF829_ENST00000520965.1_Silent_p.R183R|ZNF345_ENST00000432005.2_Intron	NM_001037232.3	NP_001032309.2	Q3KNS6	ZN829_HUMAN	zinc finger protein 829	102	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(2)|kidney(1)|large_intestine(11)|lung(8)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	29	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			AACACAGGCCTCTAGTCAGCT	0.443																																					p.R183R		Atlas-SNP	.											.	ZNF829	70	.	0			c.A549G						.						105.0	105.0	105.0					19																	37398844		2181	4290	6471	SO:0001819	synonymous_variant	374899	exon5			CAGGCCTCTAGTC	BC107131	CCDS42557.1, CCDS59380.1	19q13.12	2013-01-08			ENSG00000185869	ENSG00000185869		"""Zinc fingers, C2H2-type"", ""-"""	34032	protein-coding gene	gene with protein product							Standard	NM_001037232		Approved	DKFZp779O175	uc021utr.1	Q3KNS6	OTTHUMG00000048161	ENST00000391711.3:c.306A>G	chr19.hg19:g.37398844T>C		157.0	0.0		113.0	5.0	NM_001171979	Q3KNS7|Q6ZNN0|Q7Z657	Silent	SNP	ENST00000391711.3	hg19	CCDS42557.1																																																																																			.	.		0.443	ZNF829-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109575.3	NM_001037232	
SERTAD1	29950	hgsc.bcm.edu	37	19	40929172	40929172	+	Silent	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:40929172A>G	ENST00000357949.4	-	2	440	c.282T>C	c.(280-282)ccT>ccC	p.P94P		NM_013376.3	NP_037508.2	Q9UHV2	SRTD1_HUMAN	SERTA domain containing 1	94					positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|transcription, DNA-templated (GO:0006351)					endometrium(2)|lung(1)|prostate(1)|skin(1)	5			Lung(22;6.24e-05)|LUSC - Lung squamous cell carcinoma(20;0.000384)			TGGGGGCTGCAGGTGGGCTAG	0.672																																					p.P94P		Atlas-SNP	.											.	SERTAD1	18	.	0			c.T282C						.						15.0	16.0	16.0					19																	40929172		2199	4297	6496	SO:0001819	synonymous_variant	29950	exon2			GGCTGCAGGTGGG	AF117959	CCDS12557.1	19q13.1-q13.2	2008-02-05				ENSG00000197019			17932	protein-coding gene	gene with protein product	"""CDK4-binding protein p34SEI"", ""transcriptional regulator interacting with the PHD-bromodomain 1"""					6434876, 10580009	Standard	NM_013376		Approved	SEI1, TRIP-Br1	uc002ont.4	Q9UHV2		ENST00000357949.4:c.282T>C	chr19.hg19:g.40929172A>G		182.0	0.0		148.0	6.0	NM_013376	Q9BUE7	Silent	SNP	ENST00000357949.4	hg19	CCDS12557.1																																																																																			.	.		0.672	SERTAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462571.1	NM_013376	
GSK3A	2931	hgsc.bcm.edu	37	19	42736820	42736820	+	Silent	SNP	T	T	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:42736820T>G	ENST00000222330.3	-	9	1240	c.1113A>C	c.(1111-1113)cgA>cgC	p.R371R	GSK3A_ENST00000398249.4_Silent_p.R289R	NM_019884.2	NP_063937.2	P49840	GSK3A_HUMAN	glycogen synthase kinase 3 alpha	371	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cardiac left ventricle morphogenesis (GO:0003214)|cell migration (GO:0016477)|cellular protein metabolic process (GO:0044267)|cellular response to insulin stimulus (GO:0032869)|cellular response to interleukin-3 (GO:0036016)|cellular response to lithium ion (GO:0071285)|cellular response to organic cyclic compound (GO:0071407)|endoplasmic reticulum unfolded protein response (GO:0030968)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glycogen metabolic process (GO:0005977)|hypermethylation of CpG island (GO:0044027)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell growth involved in cardiac muscle cell development (GO:0061052)|negative regulation of glucose import (GO:0046325)|negative regulation of glycogen (starch) synthase activity (GO:2000466)|negative regulation of glycogen biosynthetic process (GO:0045719)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of TOR signaling (GO:0032007)|negative regulation of transferase activity (GO:0051348)|negative regulation of type B pancreatic cell development (GO:2000077)|negative regulation of UDP-glucose catabolic process (GO:0010905)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of adrenergic receptor signaling pathway (GO:0071879)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of glycogen (starch) synthase activity (GO:2000467)|positive regulation of heart contraction (GO:0045823)|positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901030)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein phosphorylation (GO:0006468)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of systemic arterial blood pressure (GO:0003073)|Wnt signaling pathway (GO:0016055)	beta-catenin destruction complex (GO:0030877)|cytosol (GO:0005829)	ATP binding (GO:0005524)|protein kinase A catalytic subunit binding (GO:0034236)|protein serine/threonine kinase activity (GO:0004674)|tau-protein kinase activity (GO:0050321)			endometrium(3)|large_intestine(3)|lung(6)|ovary(3)|prostate(2)|skin(1)|urinary_tract(1)	19		Prostate(69;0.00682)				CTGGCGGCGTTCGAGATTTGA	0.597																																					p.R371R		Atlas-SNP	.											.	GSK3A	45	.	0			c.A1113C						.						50.0	51.0	51.0					19																	42736820		2203	4300	6503	SO:0001819	synonymous_variant	2931	exon9			CGGCGTTCGAGAT		CCDS12599.1	19q13	2008-02-15			ENSG00000105723	ENSG00000105723			4616	protein-coding gene	gene with protein product		606784				9809441	Standard	NM_019884		Approved		uc002otb.1	P49840	OTTHUMG00000150722	ENST00000222330.3:c.1113A>C	chr19.hg19:g.42736820T>G		126.0	0.0		128.0	59.0	NM_019884	O14959	Silent	SNP	ENST00000222330.3	hg19	CCDS12599.1																																																																																			.	.		0.597	GSK3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319782.1		
ZNF221	7638	hgsc.bcm.edu	37	19	44471324	44471324	+	Missense_Mutation	SNP	G	G	A			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:44471324G>A	ENST00000251269.5	+	6	1998	c.1670G>A	c.(1669-1671)gGg>gAg	p.G557E	ZNF221_ENST00000587682.1_Missense_Mutation_p.G557E|ZNF221_ENST00000592350.1_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	115.0	0.0		87.0	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		
EXOC3L2	90332	hgsc.bcm.edu	37	19	45731493	45731493	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:45731493A>G	ENST00000252482.3	-	2	149	c.122T>C	c.(121-123)cTg>cCg	p.L41P	EXOC3L2_ENST00000413988.1_Missense_Mutation_p.L41P			Q2M3D2	EX3L2_HUMAN	exocyst complex component 3-like 2	41					exocytosis (GO:0006887)	exocyst (GO:0000145)				endometrium(1)|large_intestine(5)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	12		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00883)		GTCCTCCTGCAGCACACGGAG	0.632																																					p.L41P		Atlas-SNP	.											.	EXOC3L2	30	.	0			c.T122C						.						73.0	77.0	76.0					19																	45731493		2203	4300	6503	SO:0001583	missense	90332	exon3			TCCTGCAGCACAC	AK093466	CCDS12657.1	19q13.32	2011-07-07			ENSG00000130201	ENSG00000130201			30162	protein-coding gene	gene with protein product						21566143	Standard	NM_138568		Approved	FLJ36147, XTP7	uc002pay.1	Q2M3D2	OTTHUMG00000155018	ENST00000252482.3:c.122T>C	chr19.hg19:g.45731493A>G	ENSP00000252482:p.Leu41Pro	129.0	0.0		110.0	5.0	NM_138568	Q8N9W2|Q96GV2	Missense_Mutation	SNP	ENST00000252482.3	hg19	CCDS12657.1	.	.	.	.	.	.	.	.	.	.	A	14.41	2.526296	0.44969	.	.	ENSG00000130201	ENST00000252482;ENST00000413988	T;T	0.09073	3.02;3.02	4.89	4.89	0.63831	.	0.000000	0.50627	D	0.000102	T	0.26085	0.0636	M	0.72894	2.215	0.53688	D	0.99997	D	0.89917	1.0	D	0.97110	1.0	T	0.00912	-1.1517	10	0.87932	D	0	.	10.8643	0.46844	1.0:0.0:0.0:0.0	.	41	Q2M3D2	EX3L2_HUMAN	P	41	ENSP00000252482:L41P;ENSP00000400713:L41P	ENSP00000252482:L41P	L	-	2	0	EXOC3L2	50423333	0.966000	0.33281	0.666000	0.29783	0.136000	0.21042	4.999000	0.63934	1.836000	0.53414	0.254000	0.18369	CTG	.	.		0.632	EXOC3L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338073.1	NM_138568	
DHX34	9704	hgsc.bcm.edu	37	19	47880440	47880440	+	Missense_Mutation	SNP	T	T	A			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:47880440T>A	ENST00000328771.4	+	13	3032	c.2683T>A	c.(2683-2685)Tgc>Agc	p.C895S		NM_014681.5	NP_055496.2	Q14147	DHX34_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 34	895					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)		CCTGGTGAACTGCGTCCGCAT	0.637																																					p.C895S		Atlas-SNP	.											.	DHX34	98	.	0			c.T2683A						.						72.0	60.0	64.0					19																	47880440		2203	4300	6503	SO:0001583	missense	9704	exon13			GTGAACTGCGTCC	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.2683T>A	chr19.hg19:g.47880440T>A	ENSP00000331907:p.Cys895Ser	134.0	0.0		76.0	30.0	NM_014681	B4DMY8	Missense_Mutation	SNP	ENST00000328771.4	hg19	CCDS12700.1	.	.	.	.	.	.	.	.	.	.	T	16.64	3.179885	0.57800	.	.	ENSG00000134815	ENST00000328771	T	0.02579	4.24	3.43	3.43	0.39272	Domain of unknown function DUF1605 (1);	0.229124	0.29767	N	0.011260	T	0.03783	0.0107	L	0.58669	1.825	0.51482	D	0.999926	P	0.36086	0.536	B	0.31686	0.134	T	0.50056	-0.8872	10	0.40728	T	0.16	-23.6463	11.2761	0.49168	0.0:0.0:0.0:1.0	.	895	Q14147	DHX34_HUMAN	S	895	ENSP00000331907:C895S	ENSP00000331907:C895S	C	+	1	0	DHX34	52572238	1.000000	0.71417	0.999000	0.59377	0.986000	0.74619	5.151000	0.64875	1.561000	0.49584	0.459000	0.35465	TGC	.	.		0.637	DHX34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314313.3	NM_014681	
KPTN	11133	hgsc.bcm.edu	37	19	47983122	47983122	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:47983122T>C	ENST00000338134.3	-	8	892	c.785A>G	c.(784-786)aAg>aGg	p.K262R	KPTN_ENST00000595484.1_5'Flank|KPTN_ENST00000536339.1_Missense_Mutation_p.K22R	NM_007059.2	NP_008990.2	Q9Y664	KPTN_HUMAN	kaptin (actin binding protein)	262					actin filament organization (GO:0007015)|cellular component movement (GO:0006928)|sensory perception of sound (GO:0007605)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)	actin binding (GO:0003779)			breast(1)|lung(3)|ovary(2)|pancreas(2)	8		all_cancers(25;1.55e-10)|all_epithelial(76;3.4e-08)|all_lung(116;1.73e-07)|Lung NSC(112;3.95e-07)|Ovarian(192;0.0139)|all_neural(266;0.026)|Breast(70;0.0503)		OV - Ovarian serous cystadenocarcinoma(262;0.000428)|all cancers(93;0.000631)|Epithelial(262;0.0153)|GBM - Glioblastoma multiforme(486;0.0694)		GAGCTCACCCTTGGCGGCCGA	0.602																																					p.K262R		Atlas-SNP	.											.	KPTN	34	.	0			c.A785G						.						36.0	41.0	39.0					19																	47983122		1985	4150	6135	SO:0001583	missense	11133	exon8			TCACCCTTGGCGG	AF105369	CCDS42583.1	19q13.32	2014-08-13	2001-11-28		ENSG00000118162	ENSG00000118162			6404	protein-coding gene	gene with protein product		615620	"""kaptin (actin-binding protein)"""			10099934	Standard	XM_005258467		Approved	2E4	uc002pgy.3	Q9Y664	OTTHUMG00000183443	ENST00000338134.3:c.785A>G	chr19.hg19:g.47983122T>C	ENSP00000337850:p.Lys262Arg	100.0	0.0		88.0	4.0	NM_007059	B3KN86|B4DQ76|Q96GT1	Missense_Mutation	SNP	ENST00000338134.3	hg19	CCDS42583.1	.	.	.	.	.	.	.	.	.	.	T	12.81	2.048138	0.36181	.	.	ENSG00000118162	ENST00000338134;ENST00000536339	.	.	.	3.31	0.887	0.19200	.	0.703686	0.13491	N	0.383969	T	0.15696	0.0378	N	0.08118	0	0.09310	N	1	B	0.12630	0.006	B	0.15870	0.014	T	0.28996	-1.0026	9	0.16896	T	0.51	-11.0182	7.0573	0.25106	0.0:0.0:0.4742:0.5258	.	262	Q9Y664	KPTN_HUMAN	R	262;22	.	ENSP00000337850:K262R	K	-	2	0	KPTN	52674934	0.003000	0.15002	0.747000	0.31113	0.846000	0.48090	1.123000	0.31308	0.451000	0.26802	0.255000	0.18592	AAG	.	.		0.602	KPTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466672.2		
EHD2	30846	hgsc.bcm.edu	37	19	48229399	48229399	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:48229399T>C	ENST00000263277.3	+	4	1084	c.833T>C	c.(832-834)cTc>cCc	p.L278P	EHD2_ENST00000538399.1_Missense_Mutation_p.L142P|CTD-2571L23.8_ENST00000599924.1_lincRNA	NM_014601.3	NP_055416.2	Q9NZN4	EHD2_HUMAN	EH-domain containing 2	278	Dynamin-type G.				blood coagulation (GO:0007596)|cortical actin cytoskeleton organization (GO:0030866)|endocytic recycling (GO:0032456)|endocytosis (GO:0006897)|positive regulation of endocytic recycling (GO:2001137)|positive regulation of myoblast fusion (GO:1901741)|protein localization to plasma membrane (GO:0072659)	caveola (GO:0005901)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|nucleic acid binding (GO:0003676)			endometrium(3)|large_intestine(7)|lung(2)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	19		all_cancers(25;6.74e-07)|all_lung(116;2.02e-05)|Lung NSC(112;3.77e-05)|all_epithelial(76;4.89e-05)|all_neural(266;0.0332)|Ovarian(192;0.086)		OV - Ovarian serous cystadenocarcinoma(262;0.000336)|all cancers(93;0.000415)|Epithelial(262;0.0132)|GBM - Glioblastoma multiforme(486;0.0537)		GAGCAGGACCTCTTCCGCGAC	0.687																																					p.L278P		Atlas-SNP	.											.	EHD2	59	.	0			c.T833C						.						18.0	18.0	18.0					19																	48229399		2201	4296	6497	SO:0001583	missense	30846	exon4			AGGACCTCTTCCG	AF181263	CCDS12704.1	19q13.3	2014-08-12			ENSG00000024422	ENSG00000024422		"""EF-hand domain containing"""	3243	protein-coding gene	gene with protein product		605890		PAST2		10673336	Standard	NM_014601		Approved		uc002phj.4	Q9NZN4	OTTHUMG00000183266	ENST00000263277.3:c.833T>C	chr19.hg19:g.48229399T>C	ENSP00000263277:p.Leu278Pro	65.0	0.0		48.0	4.0	NM_014601	B2RDH9|B4DNU6|Q96CB6	Missense_Mutation	SNP	ENST00000263277.3	hg19	CCDS12704.1	.	.	.	.	.	.	.	.	.	.	T	19.76	3.887744	0.72410	.	.	ENSG00000024422	ENST00000263277;ENST00000539439;ENST00000540364;ENST00000538399	D;D	0.96587	-4.06;-4.06	3.66	3.66	0.41972	.	0.186089	0.34879	N	0.003613	D	0.98049	0.9357	M	0.89840	3.065	0.80722	D	1	D	0.89917	1.0	D	0.76575	0.988	D	0.98385	1.0560	10	0.87932	D	0	-23.6188	10.6051	0.45390	0.0:0.0:0.0:1.0	.	278	Q9NZN4	EHD2_HUMAN	P	278;278;268;142	ENSP00000263277:L278P;ENSP00000439036:L142P	ENSP00000263277:L278P	L	+	2	0	EHD2	52921211	0.999000	0.42202	0.998000	0.56505	0.992000	0.81027	7.828000	0.86729	1.463000	0.47967	0.374000	0.22700	CTC	.	.		0.687	EHD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465851.1		
PLEKHA4	57664	hgsc.bcm.edu	37	19	49342505	49342505	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:49342505A>G	ENST00000263265.6	-	18	2476	c.1921T>C	c.(1921-1923)Tcg>Ccg	p.S641P	PLEKHA4_ENST00000355496.5_Intron|HSD17B14_ENST00000599157.1_5'Flank|HSD17B14_ENST00000263278.4_5'Flank	NM_020904.2	NP_065955.2	Q9H4M7	PKHA4_HUMAN	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 4	641						cytoplasm (GO:0005737)|membrane (GO:0016020)	1-phosphatidylinositol binding (GO:0005545)			NS(1)|breast(5)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|prostate(3)|skin(2)|urinary_tract(2)	30		all_lung(116;4.89e-05)|Lung NSC(112;8.3e-05)|all_epithelial(76;0.000108)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.00027)|all cancers(93;0.00084)|GBM - Glioblastoma multiforme(486;0.0244)|Epithelial(262;0.0364)		TGGGCTCCCGAGTGTCCTACG	0.512																																					p.S641P		Atlas-SNP	.											.	PLEKHA4	70	.	0			c.T1921C						.						56.0	51.0	53.0					19																	49342505		2203	4300	6503	SO:0001583	missense	57664	exon18			CTCCCGAGTGTCC	AY007233	CCDS12737.1, CCDS54291.1	19q13.33	2013-01-10	2002-01-14			ENSG00000105559		"""Pleckstrin homology (PH) domain containing"""	14339	protein-coding gene	gene with protein product		607769	"""pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 4"""			11001876	Standard	NM_020904		Approved	PEPP1	uc002pkx.3	Q9H4M7		ENST00000263265.6:c.1921T>C	chr19.hg19:g.49342505A>G	ENSP00000263265:p.Ser641Pro	176.0	0.0		116.0	5.0	NM_020904	Q8N4M8|Q8N658	Missense_Mutation	SNP	ENST00000263265.6	hg19	CCDS12737.1	.	.	.	.	.	.	.	.	.	.	a	9.464	1.093886	0.20471	.	.	ENSG00000105559	ENST00000263265	T	0.25250	1.81	2.96	-1.13	0.09775	.	3.198660	0.01273	N	0.009506	T	0.17704	0.0425	N	0.24115	0.695	0.27321	N	0.957047	B	0.22604	0.072	B	0.22601	0.04	T	0.29731	-1.0002	10	0.72032	D	0.01	.	3.3348	0.07097	0.34:0.1992:0.0:0.4608	.	641	Q9H4M7	PKHA4_HUMAN	P	641	ENSP00000263265:S641P	ENSP00000263265:S641P	S	-	1	0	PLEKHA4	54034317	0.795000	0.28851	0.565000	0.28409	0.687000	0.40016	0.083000	0.14871	-0.037000	0.13646	0.364000	0.22116	TCG	.	.		0.512	PLEKHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466216.1		
DHDH	27294	hgsc.bcm.edu	37	19	49442857	49442857	+	Missense_Mutation	SNP	C	C	G	rs543413361		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:49442857C>G	ENST00000221403.2	+	4	558	c.518C>G	c.(517-519)gCc>gGc	p.A173G	DHDH_ENST00000522614.1_Missense_Mutation_p.A173G|DHDH_ENST00000523250.1_Intron	NM_014475.3	NP_055290.1	Q9UQ10	DHDH_HUMAN	dihydrodiol dehydrogenase (dimeric)	173					carbohydrate metabolic process (GO:0005975)|D-xylose catabolic process (GO:0042843)		D-xylose 1-dehydrogenase (NADP+) activity (GO:0047837)|electron carrier activity (GO:0009055)|NAD(P)+ transhydrogenase activity (GO:0008746)|trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity (GO:0047115)			central_nervous_system(1)|large_intestine(3)|lung(3)|ovary(1)|soft_tissue(1)	9		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000158)|all cancers(93;0.000258)|Epithelial(262;0.0173)|GBM - Glioblastoma multiforme(486;0.0179)		GCTGGGGGGGCCCTGCTGGAC	0.602													C|||	1	0.000199681	0.0008	0.0	5008	,	,		17572	0.0		0.0	False		,,,				2504	0.0				p.A173G		Atlas-SNP	.											DHDH,colon,carcinoma,0,1	DHDH	35	.	0			c.C518G						.						53.0	56.0	55.0					19																	49442857		2203	4300	6503	SO:0001583	missense	27294	exon4			GGGGGGCCCTGCT	AB021933	CCDS12741.1	19q13.3	2008-02-05			ENSG00000104808	ENSG00000104808	1.3.1.20		17887	protein-coding gene	gene with protein product		606377				10477285	Standard	NM_014475		Approved	HUM2DD	uc002ple.1	Q9UQ10	OTTHUMG00000165029	ENST00000221403.2:c.518C>G	chr19.hg19:g.49442857C>G	ENSP00000221403:p.Ala173Gly	105.0	1.0		80.0	5.0	NM_014475		Missense_Mutation	SNP	ENST00000221403.2	hg19	CCDS12741.1	.	.	.	.	.	.	.	.	.	.	C	1.710	-0.499278	0.04291	.	.	ENSG00000104808	ENST00000221403;ENST00000522614	T;T	0.38560	1.13;1.13	5.12	0.225	0.15325	.	0.219759	0.45606	N	0.000342	T	0.35653	0.0939	L	0.45228	1.405	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.36138	-0.9760	10	0.42905	T	0.14	-7.1401	17.2381	0.87005	0.0:0.6748:0.3252:0.0	rs58913518	173	Q9UQ10	DHDH_HUMAN	G	173	ENSP00000221403:A173G;ENSP00000428672:A173G	ENSP00000221403:A173G	A	+	2	0	DHDH	54134669	0.094000	0.21725	0.003000	0.11579	0.006000	0.05464	0.971000	0.29396	0.096000	0.17463	-0.270000	0.10280	GCC	.	.		0.602	DHDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381477.1	NM_014475	
EMC10	284361	hgsc.bcm.edu	37	19	50983931	50983931	+	Missense_Mutation	SNP	G	G	T			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:50983931G>T	ENST00000334976.6	+	5	542	c.496G>T	c.(496-498)Ggg>Tgg	p.G166W	EMC10_ENST00000598585.1_Missense_Mutation_p.G166W|EMC10_ENST00000376918.3_Missense_Mutation_p.G166W|CTD-2545M3.2_ENST00000598194.1_RNA	NM_206538.2	NP_996261.1	Q5UCC4	EMC10_HUMAN	ER membrane protein complex subunit 10	166						ER membrane protein complex (GO:0072546)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)											GACGCACCCCGGGGGCTGCCG	0.697																																					p.G166W		Atlas-SNP	.											.	.	.	.	0			c.G496T						.						24.0	25.0	24.0					19																	50983931		2192	4294	6486	SO:0001583	missense	284361	exon5			CACCCCGGGGGCT	BC062607	CCDS12796.1, CCDS42594.1	19q13.33	2012-05-30	2012-05-30	2012-05-30	ENSG00000161671	ENSG00000161671			27609	protein-coding gene	gene with protein product	"""hematopoietic signal peptide-containing secreted 1"", ""hematopoietic signal peptide-containing membrane domain-containing 1"""	614545	"""chromosome 19 open reading frame 63"""	C19orf63		12975309, 22119785	Standard	NM_175063		Approved	INM02, HSS1, HSM1	uc002psl.3	Q5UCC4		ENST00000334976.6:c.496G>T	chr19.hg19:g.50983931G>T	ENSP00000334037:p.Gly166Trp	93.0	0.0		73.0	5.0	NM_175063	Q5UCC6|Q69YT5|Q6UWP3|Q86YL4|Q8N541	Missense_Mutation	SNP	ENST00000334976.6	hg19	CCDS12796.1	.	.	.	.	.	.	.	.	.	.	G	17.72	3.459701	0.63401	.	.	ENSG00000161671	ENST00000334976;ENST00000376918;ENST00000376920	.	.	.	4.26	4.26	0.50523	.	0.000000	0.85682	D	0.000000	T	0.79311	0.4424	M	0.78637	2.42	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;0.999	T	0.82959	-0.0198	9	0.87932	D	0	-3.8968	16.2935	0.82761	0.0:0.0:1.0:0.0	.	166;166;166	Q5UCC4;Q5UCC4-2;Q5UCC4-3	INM02_HUMAN;.;.	W	166	.	ENSP00000334037:G166W	G	+	1	0	C19orf63	55675743	1.000000	0.71417	0.969000	0.41365	0.089000	0.18198	8.578000	0.90777	2.299000	0.77371	0.491000	0.48974	GGG	.	.		0.697	EMC10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464760.2	NM_175063	
ZNF615	284370	hgsc.bcm.edu	37	19	52497175	52497175	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:52497175T>C	ENST00000602063.1	-	6	1503	c.1154A>G	c.(1153-1155)aAc>aGc	p.N385S	ZNF615_ENST00000391795.3_Missense_Mutation_p.N390S|ZNF615_ENST00000594083.1_Missense_Mutation_p.N396S|ZNF615_ENST00000376716.5_Missense_Mutation_p.N385S|ZNF615_ENST00000598071.1_Missense_Mutation_p.N396S			Q8N8J6	ZN615_HUMAN	zinc finger protein 615	385					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(5)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(2)	42		all_neural(266;0.117)		GBM - Glioblastoma multiforme(134;0.00142)|OV - Ovarian serous cystadenocarcinoma(262;0.019)		GATAAGACTGTTCTTCAAGGT	0.398																																					p.N396S		Atlas-SNP	.											.	ZNF615	111	.	0			c.A1187G						.						96.0	91.0	93.0					19																	52497175		2203	4300	6503	SO:0001583	missense	284370	exon7			AGACTGTTCTTCA	AK096691	CCDS12846.1, CCDS59418.1	19q13.41	2013-01-08						"""Zinc fingers, C2H2-type"", ""-"""	24740	protein-coding gene	gene with protein product						12477932	Standard	NM_001199324		Approved	FLJ33710	uc002pyf.2	Q8N8J6		ENST00000602063.1:c.1154A>G	chr19.hg19:g.52497175T>C	ENSP00000473089:p.Asn385Ser	132.0	0.0		113.0	7.0	NM_001199324	B7ZKW9|Q2M2Y6|Q5CZB0|Q6ZMT7|Q6ZRB3	Missense_Mutation	SNP	ENST00000602063.1	hg19	CCDS12846.1	.	.	.	.	.	.	.	.	.	.	T	0.006	-2.083355	0.00371	.	.	ENSG00000197619	ENST00000376716;ENST00000354939;ENST00000391795;ENST00000391793	T;T	0.48522	0.81;0.81	3.26	0.971	0.19698	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.12603	0.0306	N	0.01405	-0.89	0.09310	N	1	B;B;B;B	0.14012	0.005;0.009;0.009;0.005	B;B;B;B	0.09377	0.002;0.004;0.004;0.002	T	0.31308	-0.9948	9	0.02654	T	1	.	1.0254	0.01526	0.2216:0.1139:0.1672:0.4972	.	390;392;396;385	B4DH87;Q8N8J6-3;Q8N8J6-2;Q8N8J6	.;.;.;ZN615_HUMAN	S	385;395;390;395	ENSP00000365906:N385S;ENSP00000375672:N390S	ENSP00000347019:N395S	N	-	2	0	ZNF615	57188987	0.000000	0.05858	0.082000	0.20525	0.797000	0.45037	-0.942000	0.03921	0.341000	0.23771	0.528000	0.53228	AAC	.	.		0.398	ZNF615-009	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462391.1	NM_198480	
ZNF480	147657	hgsc.bcm.edu	37	19	52803707	52803707	+	Silent	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:52803707A>G	ENST00000595962.1	+	2	108	c.42A>G	c.(40-42)aaA>aaG	p.K14K	CTD-2525I3.5_ENST00000594865.1_RNA|ZNF480_ENST00000335090.6_5'UTR|ZNF480_ENST00000334564.7_Silent_p.K14K|CTD-2525I3.6_ENST00000594379.1_RNA|ZNF480_ENST00000490272.1_Silent_p.K14K	NM_144684.2	NP_653285.2	Q8WV37	ZN480_HUMAN	zinc finger protein 480	14					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			endometrium(2)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	12				GBM - Glioblastoma multiforme(134;0.00212)|OV - Ovarian serous cystadenocarcinoma(262;0.00369)		GGAAGAGGAAAGCAAAGGAGT	0.443																																					p.K14K		Atlas-SNP	.											.	ZNF480	123	.	0			c.A42G						.						177.0	141.0	153.0					19																	52803707		2203	4300	6503	SO:0001819	synonymous_variant	147657	exon2			GAGGAAAGCAAAG	AY512662	CCDS12850.2, CCDS74437.1	19q13.41	2013-01-08			ENSG00000198464	ENSG00000198464		"""Zinc fingers, C2H2-type"", ""-"""	23305	protein-coding gene	gene with protein product		613910				15219843	Standard	XM_005258525		Approved	MGC32104	uc010ydl.2	Q8WV37	OTTHUMG00000157507	ENST00000595962.1:c.42A>G	chr19.hg19:g.52803707A>G		114.0	0.0		80.0	4.0	NM_144684	Q5JPG9|Q6P0Q4|Q8N1M5	Silent	SNP	ENST00000595962.1	hg19	CCDS12850.2																																																																																			.	.		0.443	ZNF480-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349001.3	NM_144684	
ZNF528	84436	hgsc.bcm.edu	37	19	52918902	52918902	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:52918902A>G	ENST00000360465.3	+	7	1223	c.797A>G	c.(796-798)gAg>gGg	p.E266G	ZNF528_ENST00000391788.2_3'UTR	NM_032423.2	NP_115799.2	Q3MIS6	ZN528_HUMAN	zinc finger protein 528	266					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(6)|ovary(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	39				GBM - Glioblastoma multiforme(134;0.00249)|OV - Ovarian serous cystadenocarcinoma(262;0.00817)		CATACTGGAGAGAAGCCTTAC	0.388																																					p.E266G		Atlas-SNP	.											.	ZNF528	95	.	0			c.A797G						.						80.0	85.0	83.0					19																	52918902		2203	4300	6503	SO:0001583	missense	84436	exon7			CTGGAGAGAAGCC	AB058730	CCDS33091.1	19q13	2013-01-08			ENSG00000167555	ENSG00000167555		"""Zinc fingers, C2H2-type"", ""-"""	29384	protein-coding gene	gene with protein product		615580				11347906	Standard	NM_032423		Approved	KIAA1827	uc002pzh.3	Q3MIS6	OTTHUMG00000156494	ENST00000360465.3:c.797A>G	chr19.hg19:g.52918902A>G	ENSP00000353652:p.Glu266Gly	112.0	0.0		91.0	6.0	NM_032423	B3KPN4|Q86T88|Q96JK0	Missense_Mutation	SNP	ENST00000360465.3	hg19	CCDS33091.1	.	.	.	.	.	.	.	.	.	.	A	13.95	2.391392	0.42410	.	.	ENSG00000167555	ENST00000360465	T	0.27557	1.66	1.69	0.527	0.17084	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.42381	0.1200	L	0.56199	1.76	0.23227	N	0.998081	D	0.76494	0.999	D	0.72075	0.976	T	0.23226	-1.0194	9	0.87932	D	0	.	3.1613	0.06521	0.5227:0.2412:0.0:0.2361	.	266	Q3MIS6	ZN528_HUMAN	G	266	ENSP00000353652:E266G	ENSP00000353652:E266G	E	+	2	0	ZNF528	57610714	0.998000	0.40836	0.126000	0.21872	0.084000	0.17831	2.076000	0.41548	-0.079000	0.12707	0.260000	0.18958	GAG	.	.		0.388	ZNF528-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344336.1	NM_032423	
ZNF160	90338	hgsc.bcm.edu	37	19	53578336	53578336	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:53578336T>C	ENST00000429604.1	-	5	531	c.116A>G	c.(115-117)gAg>gGg	p.E39G	ZNF160_ENST00000599056.1_Missense_Mutation_p.E39G|ZNF160_ENST00000418871.1_Missense_Mutation_p.E39G|ZNF160_ENST00000599729.1_5'Flank|ZNF160_ENST00000601421.1_Missense_Mutation_p.E3G|ZNF160_ENST00000355147.5_Missense_Mutation_p.E39G	NM_001102603.1|NM_198893.2	NP_001096073.1|NP_942596.1	Q9HCG1	ZN160_HUMAN	zinc finger protein 160	39	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				hemopoiesis (GO:0030097)|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)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(8)|lung(10)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	35				GBM - Glioblastoma multiforme(134;0.02)		CCAGTAGTTCTCCAACATCAC	0.468																																					p.E39G		Atlas-SNP	.											.	ZNF160	75	.	0			c.A116G						.						149.0	131.0	137.0					19																	53578336		2203	4300	6503	SO:0001583	missense	90338	exon5			TAGTTCTCCAACA	X78928	CCDS12859.1	19q13.42	2013-01-08				ENSG00000170949		"""Zinc fingers, C2H2-type"", ""-"""	12948	protein-coding gene	gene with protein product		600398				7774943, 7865130	Standard	NM_198893		Approved	HZF5, F11, KR18, HKr18, FLJ00032, KIAA1611	uc002qar.4	Q9HCG1		ENST00000429604.1:c.116A>G	chr19.hg19:g.53578336T>C	ENSP00000406201:p.Glu39Gly	129.0	0.0		91.0	4.0	NM_001102603	Q14589|Q504Q8|Q96JC5|Q9BVY9|Q9H7N6	Missense_Mutation	SNP	ENST00000429604.1	hg19	CCDS12859.1	.	.	.	.	.	.	.	.	.	.	T	16.89	3.248370	0.59103	.	.	ENSG00000170949	ENST00000429604;ENST00000418871;ENST00000355147	T;T;T	0.04406	3.63;3.63;3.63	2.46	2.46	0.29980	Krueppel-associated box (4);	.	.	.	.	T	0.31638	0.0803	H	0.97962	4.115	0.26898	N	0.967164	D;D	0.89917	1.0;0.999	D;D	0.97110	1.0;0.995	T	0.18209	-1.0344	9	0.87932	D	0	.	8.0455	0.30547	0.0:0.0:0.0:1.0	.	39;39	Q9BVY9;Q9HCG1	.;ZN160_HUMAN	G	39	ENSP00000406201:E39G;ENSP00000409597:E39G;ENSP00000347273:E39G	ENSP00000347273:E39G	E	-	2	0	ZNF160	58270148	0.979000	0.34478	0.999000	0.59377	0.842000	0.47809	2.557000	0.45871	1.116000	0.41820	0.379000	0.24179	GAG	.	.		0.468	ZNF160-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463994.2	NM_033288	
TBC1D20	128637	hgsc.bcm.edu	37	20	421020	421020	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr20:421020T>C	ENST00000354200.4	-	6	787	c.640A>G	c.(640-642)Acc>Gcc	p.T214A	TBC1D20_ENST00000461188.1_5'UTR	NM_144628.2	NP_653229.1	Q96BZ9	TBC20_HUMAN	TBC1 domain family, member 20	214	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				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)				GCAAAGATGGTCCCTACCTCA	0.562																																					p.T214A		Atlas-SNP	.											.	TBC1D20	34	.	0			c.A640G						.						101.0	86.0	91.0					20																	421020		2203	4300	6503	SO:0001583	missense	128637	exon6			AGATGGTCCCTAC	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.640A>G	chr20.hg19:g.421020T>C	ENSP00000346139:p.Thr214Ala	154.0	0.0		82.0	5.0	NM_144628	A8K6I3|B9A6M1|Q5JWQ7|Q6ZSY8|Q96NE1|Q9BYM7|Q9H140	Missense_Mutation	SNP	ENST00000354200.4	hg19	CCDS13002.1	.	.	.	.	.	.	.	.	.	.	T	23.0	4.358342	0.82243	.	.	ENSG00000125875	ENST00000354200;ENST00000246077	T	0.22539	1.95	5.82	4.66	0.58398	Rab-GAP/TBC domain (4);	0.000000	0.85682	D	0.000000	T	0.42108	0.1188	M	0.71036	2.16	0.80722	D	1	D	0.63880	0.993	D	0.67382	0.951	T	0.24764	-1.0151	10	0.48119	T	0.1	-27.7933	12.0041	0.53248	0.0:0.0:0.1443:0.8557	.	214	Q96BZ9	TBC20_HUMAN	A	214;239	ENSP00000346139:T214A	ENSP00000246077:T239A	T	-	1	0	TBC1D20	369020	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.918000	0.69996	2.225000	0.72522	0.460000	0.39030	ACC	.	.		0.562	TBC1D20-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251397.2	NM_144628	
CHGB	1114	hgsc.bcm.edu	37	20	5903325	5903325	+	Missense_Mutation	SNP	G	G	A			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr20:5903325G>A	ENST00000378961.4	+	4	739	c.535G>A	c.(535-537)Ggg>Agg	p.G179R		NM_001819.2	NP_001810.2	P05060	SCG1_HUMAN	chromogranin B (secretogranin 1)	179						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						AGGGGAGCGAGGGGAAGATAG	0.473																																					p.G179R		Atlas-SNP	.											.	CHGB	112	.	0			c.G535A						.						90.0	92.0	91.0					20																	5903325		2203	4300	6503	SO:0001583	missense	1114	exon4			GAGCGAGGGGAAG		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.535G>A	chr20.hg19:g.5903325G>A	ENSP00000368244:p.Gly179Arg	126.0	0.0		99.0	4.0	NM_001819	A8K021|Q59EU9|Q6IBS6|Q9BQV6|Q9UC25|Q9UJA6	Missense_Mutation	SNP	ENST00000378961.4	hg19	CCDS13092.1	.	.	.	.	.	.	.	.	.	.	G	13.94	2.386011	0.42308	.	.	ENSG00000089199	ENST00000378961;ENST00000455042	T;T	0.01665	4.7;4.7	5.57	-0.627	0.11541	.	0.771709	0.11798	N	0.528494	T	0.01800	0.0057	L	0.43923	1.385	0.09310	N	1	B	0.12630	0.006	B	0.17433	0.018	T	0.43814	-0.9368	10	0.36615	T	0.2	-3.5937	5.0458	0.14483	0.593:0.177:0.23:0.0	.	179	P05060	SCG1_HUMAN	R	179;159	ENSP00000368244:G179R;ENSP00000416643:G159R	ENSP00000368244:G179R	G	+	1	0	CHGB	5851325	0.024000	0.19004	0.000000	0.03702	0.004000	0.04260	1.754000	0.38369	0.015000	0.14971	-0.251000	0.11542	GGG	.	.		0.473	CHGB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077897.2	NM_001819	
CRNKL1	51340	hgsc.bcm.edu	37	20	20018161	20018161	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr20:20018161T>C	ENST00000377340.2	-	14	2216	c.2185A>G	c.(2185-2187)Act>Gct	p.T729A	CRNKL1_ENST00000377327.4_Missense_Mutation_p.T717A|CRNKL1_ENST00000521379.1_5'UTR|CRNKL1_ENST00000536226.1_Missense_Mutation_p.T568A	NM_001278628.1|NM_016652.4	NP_001265557.1|NP_057736.4	Q9BZJ0	CRNL1_HUMAN	crooked neck pre-mRNA splicing factor 1	729					mRNA splicing, via spliceosome (GO:0000398)|spliceosomal complex assembly (GO:0000245)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(2)|cervix(2)|endometrium(7)|large_intestine(11)|lung(12)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(6)	45						CTGCATTTAGTCAAACTTCCT	0.353																																					p.T729A		Atlas-SNP	.											.	CRNKL1	101	.	0			c.A2185G						.						125.0	123.0	124.0					20																	20018161		2203	4300	6503	SO:0001583	missense	51340	exon14			ATTTAGTCAAACT	AF255443	CCDS33446.1, CCDS63238.1, CCDS63239.1	20p11.2	2013-10-03	2013-10-03		ENSG00000101343	ENSG00000101343			15762	protein-coding gene	gene with protein product	"""SYF3 pre-mRNA-splicing factor"""	610952	"""crooked neck (Drosophila Crn homolog)-like 1"", ""Crn, crooked neck-like 1 (Drosophila)"", ""crooked neck pre-mRNA splicing factor-like 1 (Drosophila)"""				Standard	NM_016652		Approved	CRN, CLF, SYF3, Clf1	uc002wrs.3	Q9BZJ0	OTTHUMG00000032000	ENST00000377340.2:c.2185A>G	chr20.hg19:g.20018161T>C	ENSP00000366557:p.Thr729Ala	185.0	0.0		149.0	7.0	NM_016652	A8K9T4|Q5JY64|Q8WYI5|Q9BZI9|Q9BZJ1|Q9BZJ2|Q9GZW7|Q9H8F8|Q9NQH5|Q9NYD8	Missense_Mutation	SNP	ENST00000377340.2	hg19	CCDS33446.1	.	.	.	.	.	.	.	.	.	.	T	2.462	-0.323813	0.05350	.	.	ENSG00000101343	ENST00000377327;ENST00000377340;ENST00000536226	T;T;T	0.41065	1.52;1.52;1.01	5.02	0.433	0.16534	.	0.712402	0.14703	N	0.303457	T	0.09862	0.0242	N	0.01003	-1.06	0.09310	N	0.999991	B	0.02656	0.0	B	0.04013	0.001	T	0.25710	-1.0124	10	0.07813	T	0.8	-2.1383	0.7921	0.01059	0.2464:0.332:0.1213:0.3003	.	729	Q9BZJ0	CRNL1_HUMAN	A	717;729;568	ENSP00000366544:T717A;ENSP00000366557:T729A;ENSP00000440733:T568A	ENSP00000366544:T717A	T	-	1	0	CRNKL1	19966161	0.150000	0.22732	1.000000	0.80357	0.989000	0.77384	-0.394000	0.07296	0.245000	0.21373	-0.354000	0.07668	ACT	.	.		0.353	CRNKL1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000127787.1		
PYGB	5834	hgsc.bcm.edu	37	20	25273090	25273090	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr20:25273090A>G	ENST00000216962.4	+	17	2128	c.2018A>G	c.(2017-2019)gAg>gGg	p.E673G		NM_002862.3	NP_002853.2	P11216	PYGB_HUMAN	phosphorylase, glycogen; brain	673					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	glycogen phosphorylase activity (GO:0008184)|pyridoxal phosphate binding (GO:0030170)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	31						GCAGGCACCGAGGCCTCAGGC	0.652																																					p.E673G		Atlas-SNP	.											.	PYGB	84	.	0			c.A2018G						.						93.0	86.0	88.0					20																	25273090		2203	4300	6503	SO:0001583	missense	5834	exon17			GCACCGAGGCCTC		CCDS13171.1	20p11.21	2013-03-01			ENSG00000100994	ENSG00000100994	2.4.1.1	"""Glycogen phosphorylases"""	9723	protein-coding gene	gene with protein product	"""glycogen phosphorylase, brain form"""	138550					Standard	NM_002862		Approved		uc002wup.3	P11216	OTTHUMG00000032117	ENST00000216962.4:c.2018A>G	chr20.hg19:g.25273090A>G	ENSP00000216962:p.Glu673Gly	147.0	0.0		79.0	4.0	NM_002862	Q96AK1|Q9NPX8	Missense_Mutation	SNP	ENST00000216962.4	hg19	CCDS13171.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	26.1|26.1	4.704543|4.704543	0.88924|0.88924	.|.	.|.	ENSG00000100994|ENSG00000100994	ENST00000216962|ENST00000428458	D|.	0.99458|.	-5.93|.	4.28|4.28	4.28|4.28	0.50868|0.50868	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.88930|0.88930	0.6571|0.6571	H|H	0.99117|0.99117	4.435|4.435	0.80722|0.80722	D|D	1|1	D|.	0.67145|.	0.996|.	D|.	0.76071|.	0.987|.	D|D	0.93026|0.93026	0.6444|0.6444	10|5	0.87932|.	D|.	0|.	-46.7873|-46.7873	13.5385|13.5385	0.61659|0.61659	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	673|.	P11216|.	PYGB_HUMAN|.	G|G	673|92	ENSP00000216962:E673G|.	ENSP00000216962:E673G|.	E|R	+|+	2|1	0|2	PYGB|PYGB	25221090|25221090	1.000000|1.000000	0.71417|0.71417	0.994000|0.994000	0.49952|0.49952	0.965000|0.965000	0.64279|0.64279	8.975000|8.975000	0.93437|0.93437	1.933000|1.933000	0.56026|0.56026	0.379000|0.379000	0.24179|0.24179	GAG|AGG	.	.		0.652	PYGB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078415.2	NM_002862	
SRC	6714	hgsc.bcm.edu	37	20	36022608	36022608	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr20:36022608T>C	ENST00000373578.2	+	7	830	c.481T>C	c.(481-483)Tca>Cca	p.S161P	SRC_ENST00000358208.4_Missense_Mutation_p.S161P|SRC_ENST00000373567.2_Missense_Mutation_p.S161P|SRC_ENST00000360723.4_Missense_Mutation_p.S167P|SRC_ENST00000373558.2_Missense_Mutation_p.S167P|SRC_ENST00000445403.1_Missense_Mutation_p.S161P	NM_198291.1	NP_938033.1	P12931	SRC_HUMAN	SRC proto-oncogene, non-receptor tyrosine kinase	161	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				axon guidance (GO:0007411)|blood coagulation (GO:0007596)|bone resorption (GO:0045453)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cellular response to progesterone stimulus (GO:0071393)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain development (GO:0030900)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|membrane organization (GO:0061024)|negative regulation of anoikis (GO:2000811)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of mitochondrial depolarization (GO:0051902)|negative regulation of protein homooligomerization (GO:0032463)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oogenesis (GO:0048477)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet activation (GO:0030168)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of integrin activation (GO:0033625)|positive regulation of podosome assembly (GO:0071803)|positive regulation of protein kinase B signaling (GO:0051897)|progesterone receptor signaling pathway (GO:0050847)|protein autophosphorylation (GO:0046777)|Ras protein signal transduction (GO:0007265)|regulation of bone resorption (GO:0045124)|regulation of caveolin-mediated endocytosis (GO:2001286)|regulation of cell-cell adhesion (GO:0022407)|regulation of early endosome to late endosome transport (GO:2000641)|regulation of epithelial cell migration (GO:0010632)|regulation of intracellular estrogen receptor signaling pathway (GO:0033146)|regulation of protein binding (GO:0043393)|regulation of vascular permeability (GO:0043114)|response to interleukin-1 (GO:0070555)|signal complex assembly (GO:0007172)|signal transduction (GO:0007165)|stress fiber assembly (GO:0043149)|T cell costimulation (GO:0031295)|transforming growth factor beta receptor signaling pathway (GO:0007179)|uterus development (GO:0060065)|viral process (GO:0016032)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|lysosome (GO:0005764)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|ephrin receptor binding (GO:0046875)|growth factor receptor binding (GO:0070851)|heme binding (GO:0020037)|integrin binding (GO:0005178)|ion channel binding (GO:0044325)|kinase activity (GO:0016301)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|phosphoprotein binding (GO:0051219)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|receptor binding (GO:0005102)|SH2 domain binding (GO:0042169)|SH3/SH2 adaptor activity (GO:0005070)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(16)|lung(4)|ovary(1)|prostate(1)|urinary_tract(1)	30		Myeloproliferative disorder(115;0.00878)			Bosutinib(DB06616)|Dasatinib(DB01254)|Ponatinib(DB08901)	CAGACGGGAGTCAGAGCGGTT	0.582																																					p.S161P		Atlas-SNP	.											.	SRC	52	.	0			c.T481C						.						105.0	102.0	103.0					20																	36022608		2203	4300	6503	SO:0001583	missense	6714	exon7			CGGGAGTCAGAGC	AF077754	CCDS13294.1	20q12-q13	2014-06-25	2014-06-25		ENSG00000197122	ENSG00000197122		"""SH2 domain containing"""	11283	protein-coding gene	gene with protein product		190090	"""v-src avian sarcoma (Schmidt-Ruppin A-2) viral oncogene homolog"""	SRC1		2582238	Standard	NM_005417		Approved	ASV, c-src	uc002xgy.3	P12931	OTTHUMG00000032417	ENST00000373578.2:c.481T>C	chr20.hg19:g.36022608T>C	ENSP00000362680:p.Ser161Pro	70.0	0.0		49.0	4.0	NM_005417	E1P5V4|Q76P87|Q86VB9|Q9H5A8	Missense_Mutation	SNP	ENST00000373578.2	hg19	CCDS13294.1	.	.	.	.	.	.	.	.	.	.	T	19.95	3.922004	0.73213	.	.	ENSG00000197122	ENST00000445403;ENST00000373578;ENST00000360723;ENST00000358208;ENST00000373567;ENST00000373558	T;T;T;T;T;T	0.27402	1.67;1.67;1.67;1.67;1.67;1.67	4.88	3.76	0.43208	SH2 motif (5);	0.126165	0.56097	D	0.000035	T	0.49795	0.1578	M	0.88704	2.975	0.80722	D	1	D	0.54601	0.967	P	0.53185	0.72	T	0.56232	-0.8013	10	0.87932	D	0	.	9.1069	0.36703	0.0:0.0:0.3627:0.6373	.	161	P12931	SRC_HUMAN	P	161;161;167;161;161;167	ENSP00000408503:S161P;ENSP00000362680:S161P;ENSP00000353950:S167P;ENSP00000350941:S161P;ENSP00000362668:S161P;ENSP00000362659:S167P	ENSP00000350941:S161P	S	+	1	0	SRC	35456022	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	3.174000	0.50847	0.865000	0.35603	0.459000	0.35465	TCA	.	.		0.582	SRC-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268142.1	NM_005417	
VSTM2L	128434	hgsc.bcm.edu	37	20	36560082	36560082	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr20:36560082A>G	ENST00000373461.4	+	2	414	c.167A>G	c.(166-168)gAg>gGg	p.E56G	VSTM2L_ENST00000373459.4_Intron|VSTM2L_ENST00000373458.3_Missense_Mutation_p.E56G	NM_080607.2	NP_542174.1	Q96N03	VTM2L_HUMAN	V-set and transmembrane domain containing 2 like	56	Ig-like.									central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|lung(4)|ovary(1)|skin(1)	8		Myeloproliferative disorder(115;0.00878)				CGGACGGGCGAGGACGTGGAG	0.637																																					p.E56G		Atlas-SNP	.											.	VSTM2L	20	.	0			c.A167G						.						151.0	137.0	142.0					20																	36560082		2203	4300	6503	SO:0001583	missense	128434	exon2			CGGGCGAGGACGT	AL109964	CCDS13299.1	20q11.23	2013-01-11	2007-08-10	2007-08-10	ENSG00000132821	ENSG00000132821		"""Immunoglobulin superfamily / V-set domain containing"""	16096	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 102"""	C20orf102			Standard	NM_080607		Approved	dJ1118M15.2	uc002xhk.4	Q96N03	OTTHUMG00000032430	ENST00000373461.4:c.167A>G	chr20.hg19:g.36560082A>G	ENSP00000362560:p.Glu56Gly	95.0	0.0		71.0	4.0	NM_080607	E1P5V7|Q5JWZ4|Q5JWZ5|Q8ND45|Q9BR37	Missense_Mutation	SNP	ENST00000373461.4	hg19	CCDS13299.1	.	.	.	.	.	.	.	.	.	.	A	27.9	4.871050	0.91587	.	.	ENSG00000132821	ENST00000373458;ENST00000373461;ENST00000448944	T;T;T	0.29655	1.56;1.56;1.56	4.66	4.66	0.58398	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.107942	0.64402	D	0.000008	T	0.40094	0.1103	L	0.46614	1.455	0.58432	D	0.999999	D	0.56287	0.975	P	0.54372	0.75	T	0.17289	-1.0374	10	0.44086	T	0.13	-23.935	13.5528	0.61743	1.0:0.0:0.0:0.0	.	56	Q96N03	VTM2L_HUMAN	G	56	ENSP00000362557:E56G;ENSP00000362560:E56G;ENSP00000406537:E56G	ENSP00000362557:E56G	E	+	2	0	VSTM2L	35993496	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	9.127000	0.94417	1.859000	0.53934	0.397000	0.26171	GAG	.	.		0.637	VSTM2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079133.1		
PABPC1L	80336	hgsc.bcm.edu	37	20	43541304	43541304	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr20:43541304A>G	ENST00000217073.2	+	2	197	c.197A>G	c.(196-198)gAg>gGg	p.E66G	PABPC1L_ENST00000255136.3_Missense_Mutation_p.E66G|PABPC1L_ENST00000217074.4_Missense_Mutation_p.E66G|PABPC1L_ENST00000537323.1_Missense_Mutation_p.E66G			Q4VXU2	PAP1L_HUMAN	poly(A) binding protein, cytoplasmic 1-like	66	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA polyadenylation (GO:0006378)|oocyte maturation (GO:0001556)	extracellular vesicular exosome (GO:0070062)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			breast(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)	20						TGTCCAGCGGAGCGGGCACTG	0.517																																					p.E66G		Atlas-SNP	.											.	PABPC1L	59	.	0			c.A197G						.						58.0	54.0	56.0					20																	43541304		1568	3582	5150	SO:0001583	missense	80336	exon2			CAGCGGAGCGGGC	AK026760	CCDS42878.1	20q12-q13.1	2013-02-12	2007-11-21	2007-11-21	ENSG00000101104	ENSG00000101104		"""RNA binding motif (RRM) containing"""	15797	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 119"""	C20orf119		11549316	Standard	NM_001124756		Approved	dJ1069P2.3, PABPC1L1, ePAB	uc010ggv.1	Q4VXU2	OTTHUMG00000032553	ENST00000217073.2:c.197A>G	chr20.hg19:g.43541304A>G	ENSP00000217073:p.Glu66Gly	132.0	0.0		122.0	5.0	NM_001124756	Q4VY17	Missense_Mutation	SNP	ENST00000217073.2	hg19	CCDS42878.1	.	.	.	.	.	.	.	.	.	.	A	26.6	4.748989	0.89753	.	.	ENSG00000101104	ENST00000217074;ENST00000255136;ENST00000537323;ENST00000217073	T;T;T;T	0.19250	2.16;2.16;2.16;2.16	5.79	5.79	0.91817	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.098515	0.64402	D	0.000001	T	0.37156	0.0993	L	0.35644	1.08	0.80722	D	1	D	0.76494	0.999	D	0.69307	0.963	T	0.11717	-1.0576	10	0.87932	D	0	.	16.1175	0.81319	1.0:0.0:0.0:0.0	.	66	Q4VXU2	PAP1L_HUMAN	G	66	ENSP00000217074:E66G;ENSP00000255136:E66G;ENSP00000445661:E66G;ENSP00000217073:E66G	ENSP00000217073:E66G	E	+	2	0	PABPC1L	42974718	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.253000	0.95501	2.211000	0.71520	0.460000	0.39030	GAG	.	.		0.517	PABPC1L-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127816.2		
SNX21	90203	hgsc.bcm.edu	37	20	44463730	44463730	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr20:44463730T>C	ENST00000491381.1	+	3	490	c.422T>C	c.(421-423)gTc>gCc	p.V141A	SNX21_ENST00000462307.1_Missense_Mutation_p.V141A|SNX21_ENST00000372541.1_Missense_Mutation_p.V132A|SNX21_ENST00000342644.5_Missense_Mutation_p.V141A|SNX21_ENST00000372542.1_Missense_Mutation_p.V132A|TNNC2_ENST00000372557.1_5'Flank|SNX21_ENST00000344780.4_3'UTR			Q969T3	SNX21_HUMAN	sorting nexin family member 21	141	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				protein transport (GO:0015031)	cytoplasmic vesicle (GO:0031410)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)			breast(1)|endometrium(2)|large_intestine(1)|lung(2)|pancreas(1)	7		Myeloproliferative disorder(115;0.0122)				GCTAACGTTGTCAAGGACCCG	0.587																																					p.V141A		Atlas-SNP	.											.	SNX21	23	.	0			c.T422C						.						51.0	48.0	49.0					20																	44463730		2203	4300	6503	SO:0001583	missense	90203	exon3			ACGTTGTCAAGGA	AK095851	CCDS13376.1, CCDS13377.1, CCDS42883.1	20q13.12	2013-01-10	2006-07-24	2006-07-24	ENSG00000124104	ENSG00000124104		"""Sorting nexins"", ""Tetratricopeptide (TTC) repeat domain containing"""	16154	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 161"""	C20orf161		12461558, 12459172	Standard	NM_152897		Approved	dJ337O18.4, SNX-L	uc002xpv.1	Q969T3	OTTHUMG00000032624	ENST00000491381.1:c.422T>C	chr20.hg19:g.44463730T>C	ENSP00000418593:p.Val141Ala	137.0	0.0		105.0	7.0	NM_033421	Q5JZH5|Q5JZH6|Q5JZH7|Q8WUR6|Q9BR16	Missense_Mutation	SNP	ENST00000491381.1	hg19	CCDS13377.1	.	.	.	.	.	.	.	.	.	.	T	25.0	4.594696	0.86953	.	.	ENSG00000124104	ENST00000462307;ENST00000491381;ENST00000342644;ENST00000372542;ENST00000372541;ENST00000372545	T;T;T	0.31769	1.48;1.48;1.48	5.25	5.25	0.73442	Phox homologous domain (4);	0.131248	0.50627	D	0.000107	T	0.44664	0.1304	L	0.40543	1.245	0.38052	D	0.935818	P;D;D;P;D;D	0.60160	0.873;0.977;0.977;0.925;0.982;0.987	B;P;P;P;D;P	0.70227	0.291;0.766;0.766;0.513;0.968;0.856	T	0.43376	-0.9395	10	0.45353	T	0.12	-20.9992	13.0413	0.58901	0.0:0.0:0.0:1.0	.	132;132;141;141;141;141	Q5JZH4;Q5JZH3;Q969T3;Q5JZH7;Q05DJ0;Q5JZH5	.;.;SNX21_HUMAN;.;.;.	A	141;141;141;132;132;132	ENSP00000418593:V141A;ENSP00000344586:V141A;ENSP00000361620:V132A	ENSP00000344586:V141A	V	+	2	0	SNX21	43897137	1.000000	0.71417	0.998000	0.56505	0.995000	0.86356	6.269000	0.72558	2.200000	0.70718	0.460000	0.39030	GTC	.	.		0.587	SNX21-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079534.1	NM_033421	
ACOT8	10005	hgsc.bcm.edu	37	20	44477311	44477311	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr20:44477311T>C	ENST00000217455.4	-	3	356	c.266A>G	c.(265-267)gAc>gGc	p.D89G		NM_005469.3	NP_005460.2	O14734	ACOT8_HUMAN	acyl-CoA thioesterase 8	89					acyl-CoA metabolic process (GO:0006637)|alpha-linolenic acid metabolic process (GO:0036109)|bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cellular lipid metabolic process (GO:0044255)|dicarboxylic acid catabolic process (GO:0043649)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|peroxisome fission (GO:0016559)|small molecule metabolic process (GO:0044281)|unsaturated fatty acid metabolic process (GO:0033559)|viral process (GO:0016032)	mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)	acyl-CoA hydrolase activity (GO:0047617)|carboxylic ester hydrolase activity (GO:0052689)|choloyl-CoA hydrolase activity (GO:0033882)|medium-chain acyl-CoA hydrolase activity (GO:0052815)|palmitoyl-CoA hydrolase activity (GO:0016290)|receptor binding (GO:0005102)			kidney(2)|large_intestine(3)|lung(4)|skin(1)	10		Myeloproliferative disorder(115;0.0122)				CAGCTTCGGGTCCCCTGCAGT	0.567																																					p.D89G		Atlas-SNP	.											.	ACOT8	29	.	0			c.A266G						.						59.0	55.0	56.0					20																	44477311		2203	4300	6503	SO:0001583	missense	10005	exon3			TTCGGGTCCCCTG	AF014404	CCDS13378.1	20q13.12	2012-05-16	2005-09-19	2005-09-19	ENSG00000101473	ENSG00000101473	3.1.2.27	"""Acyl CoA thioesterases"""	15919	protein-coding gene	gene with protein product	"""choloyl-CoA hydrolase"""	608123	"""peroxisomal acyl-CoA thioesterase"", ""peroxisomal acyl-CoA thioesterase 1"""	PTE1		10092594, 9153233, 16103133, 16940157	Standard	NM_005469		Approved	hACTE-III, hTE, PTE-2	uc002xqa.2	O14734	OTTHUMG00000033045	ENST00000217455.4:c.266A>G	chr20.hg19:g.44477311T>C	ENSP00000217455:p.Asp89Gly	74.0	0.0		56.0	5.0	NM_005469	O15261|Q17RX4	Missense_Mutation	SNP	ENST00000217455.4	hg19	CCDS13378.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.54|14.54	2.566117|2.566117	0.45694|0.45694	.|.	.|.	ENSG00000101473|ENSG00000101473	ENST00000217455|ENST00000487205	.|.	.|.	.|.	5.38|5.38	5.38|5.38	0.77491|0.77491	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.88577|0.88577	0.6474|0.6474	H|H	0.98218|0.98218	4.175|4.175	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	1.0;1.0;0.999|.	D;D;D|.	0.91635|.	0.99;0.999;0.99|.	D|D	0.92746|0.92746	0.6212|0.6212	9|6	0.87932|0.87932	D|D	0|0	.|.	15.566|15.566	0.76294|0.76294	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	89;36;89|.	B4DLF4;A8K8X9;O14734|.	.;.;ACOT8_HUMAN|.	G|A	89|44	.|.	ENSP00000217455:D89G|ENSP00000433923:T110A	D|T	-|-	2|1	0|0	ACOT8|ACOT8	43910718|43910718	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.955000|0.955000	0.61496|0.61496	7.326000|7.326000	0.79133|0.79133	2.254000|2.254000	0.74563|0.74563	0.533000|0.533000	0.62120|0.62120	GAC|ACC	.	.		0.567	ACOT8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080338.2	NM_183386	
SLC2A4RG	56731	hgsc.bcm.edu	37	20	62373698	62373698	+	Silent	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr20:62373698A>G	ENST00000266077.2	+	6	742	c.690A>G	c.(688-690)gcA>gcG	p.A230A	RP4-583P15.10_ENST00000447343.2_RNA|SLC2A4RG_ENST00000493772.1_3'UTR	NM_020062.3	NP_064446.2	Q9NR83	S2A4R_HUMAN	SLC2A4 regulator	230					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|kidney(1)|lung(2)|prostate(2)|skin(1)	7	all_cancers(38;1.13e-12)|all_epithelial(29;2.64e-14)|Lung NSC(23;4.79e-10)|all_lung(23;1.7e-09)					GGAGGCAGGCAGAGCCTGAGC	0.662																																					p.A230A		Atlas-SNP	.											.	SLC2A4RG	20	.	0			c.A690G						.						45.0	31.0	36.0					20																	62373698		2199	4300	6499	SO:0001819	synonymous_variant	56731	exon6			GCAGGCAGAGCCT	AF249267	CCDS13537.1	20q13.33	2010-03-11			ENSG00000125520	ENSG00000125520			15930	protein-coding gene	gene with protein product	"""GLUT4 enhancer factor"", ""Huntington's disease gene regulatory region-binding protein 1"""	609493				10825161	Standard	NM_020062		Approved	GEF, HDBP1, Si-1-2, Si-1-2-19	uc002ygq.3	Q9NR83	OTTHUMG00000032997	ENST00000266077.2:c.690A>G	chr20.hg19:g.62373698A>G		189.0	0.0		140.0	6.0	NM_020062	Q2PHL5|Q6F6I6|Q6F6I7|Q6GTK5|Q8TAH5|Q8WVW7|Q96QD3|Q9BV85	Silent	SNP	ENST00000266077.2	hg19	CCDS13537.1																																																																																			.	.		0.662	SLC2A4RG-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080202.1	NM_020062	
USP16	10600	hgsc.bcm.edu	37	21	30409650	30409650	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr21:30409650A>G	ENST00000334352.4	+	7	733	c.502A>G	c.(502-504)Agt>Ggt	p.S168G	USP16_ENST00000399976.2_Missense_Mutation_p.S168G|USP16_ENST00000535828.1_Intron|USP16_ENST00000399975.3_Missense_Mutation_p.S167G	NM_001032410.1	NP_001027582.1			ubiquitin specific peptidase 16											breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(12)|ovary(2)|pancreas(1)|prostate(2)	34						AGAAAAAGAGAGTAAGAATGA	0.303																																					p.S168G	Melanoma(92;625 1444 27493 34101 44971)	Atlas-SNP	.											.	USP16	65	.	0			c.A502G						.						72.0	79.0	77.0					21																	30409650		2203	4300	6503	SO:0001583	missense	10600	exon6			AAAGAGAGTAAGA	AF126736	CCDS13583.1, CCDS42912.1	21q21	2008-04-11	2005-08-08		ENSG00000156256	ENSG00000156256		"""Ubiquitin-specific peptidases"""	12614	protein-coding gene	gene with protein product		604735	"""ubiquitin specific protease 16"""			12838346	Standard	NM_006447		Approved	Ubp-M	uc002ymy.3	Q9Y5T5	OTTHUMG00000078802	ENST00000334352.4:c.502A>G	chr21.hg19:g.30409650A>G	ENSP00000334808:p.Ser168Gly	98.0	0.0		75.0	5.0	NM_006447		Missense_Mutation	SNP	ENST00000334352.4	hg19	CCDS13583.1	.	.	.	.	.	.	.	.	.	.	A	11.94	1.787301	0.31593	.	.	ENSG00000156256	ENST00000399975;ENST00000399976;ENST00000334352	T;T;T	0.06849	3.25;3.26;3.26	5.9	5.9	0.94986	.	0.495710	0.27176	N	0.020565	T	0.06508	0.0167	L	0.27053	0.805	0.80722	D	1	B;B;B	0.31548	0.328;0.163;0.102	B;B;B	0.26310	0.045;0.068;0.031	T	0.46133	-0.9213	10	0.22706	T	0.39	.	12.7923	0.57541	0.8636:0.1364:0.0:0.0	.	153;167;168	Q9Y5T5-3;Q9Y5T5-2;Q9Y5T5	.;.;UBP16_HUMAN	G	167;168;168	ENSP00000382857:S167G;ENSP00000382858:S168G;ENSP00000334808:S168G	ENSP00000334808:S168G	S	+	1	0	USP16	29331521	0.997000	0.39634	1.000000	0.80357	0.992000	0.81027	4.180000	0.58296	2.251000	0.74343	0.528000	0.53228	AGT	.	.		0.303	USP16-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000171847.1		
MRPS6	64968	hgsc.bcm.edu	37	21	35497667	35497667	+	Silent	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr21:35497667T>C	ENST00000399312.2	+	2	250	c.72T>C	c.(70-72)cgT>cgC	p.R24R	MRPS6_ENST00000482679.1_3'UTR|AP000320.7_ENST00000362077.4_RNA	NM_032476.3	NP_115865.1	P82932	RT06_HUMAN	mitochondrial ribosomal protein S6	24					translation (GO:0006412)	mitochondrion (GO:0005739)|small ribosomal subunit (GO:0015935)	rRNA binding (GO:0019843)|structural constituent of ribosome (GO:0003735)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|pancreas(1)|skin(1)	6						CTTTGAAACGTACGATAGAGG	0.423																																					p.R24R		Atlas-SNP	.											.	MRPS6	18	.	0			c.T72C						.						140.0	147.0	144.0					21																	35497667		2203	4300	6503	SO:0001819	synonymous_variant	64968	exon2			GAAACGTACGATA	AB051347	CCDS33548.1	21q22.11	2012-09-13	2002-06-20		ENSG00000243927	ENSG00000243927		"""Mitochondrial ribosomal proteins / small subunits"""	14051	protein-coding gene	gene with protein product		611973	"""chromosome 21 open reading frame 101"""	C21orf101			Standard	NM_032476		Approved	MRP-S6, RPMS6	uc002ytp.2	P82932	OTTHUMG00000065820	ENST00000399312.2:c.72T>C	chr21.hg19:g.35497667T>C		103.0	0.0		87.0	4.0	NM_032476	B2R573|Q96Q64|Q9BSK8|Q9BW89	Silent	SNP	ENST00000399312.2	hg19	CCDS33548.1																																																																																			.	.		0.423	MRPS6-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000141033.1	NM_032476	
DOPEY2	9980	hgsc.bcm.edu	37	21	37603030	37603030	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr21:37603030T>C	ENST00000399151.3	+	14	2033	c.1948T>C	c.(1948-1950)Tca>Cca	p.S650P		NM_005128.2	NP_005119.2	Q9Y3R5	DOP2_HUMAN	dopey family member 2	650					cognition (GO:0050890)|endoplasmic reticulum organization (GO:0007029)|Golgi to endosome transport (GO:0006895)|multicellular organismal development (GO:0007275)|protein transport (GO:0015031)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)				autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(6)|lung(25)|ovary(2)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58						GCTGACAGCGTCAGGAGAAGA	0.537																																					p.S650P		Atlas-SNP	.											.	DOPEY2	184	.	0			c.T1948C						.						58.0	59.0	59.0					21																	37603030		2203	4300	6503	SO:0001583	missense	9980	exon14			ACAGCGTCAGGAG	AJ237839	CCDS13643.1	21q22.2	2013-03-05	2006-02-02	2006-02-02	ENSG00000142197	ENSG00000142197			1291	protein-coding gene	gene with protein product		604803	"""chromosome 21 open reading frame 5"""	C21orf5		16301316, 16303751, 10931277	Standard	NM_005128		Approved	KIAA0933	uc002yvg.3	Q9Y3R5	OTTHUMG00000086619	ENST00000399151.3:c.1948T>C	chr21.hg19:g.37603030T>C	ENSP00000382104:p.Ser650Pro	162.0	0.0		137.0	6.0	NM_005128	D3DSG5|Q6PJQ7|Q9UEZ3	Missense_Mutation	SNP	ENST00000399151.3	hg19	CCDS13643.1	.	.	.	.	.	.	.	.	.	.	T	3.739	-0.053918	0.07362	.	.	ENSG00000142197	ENST00000399151	T	0.12039	2.72	5.43	-0.204	0.13200	.	0.807665	0.11689	N	0.539140	T	0.08044	0.0201	L	0.35414	1.06	0.09310	N	1	B;B	0.09022	0.002;0.001	B;B	0.11329	0.006;0.003	T	0.37430	-0.9706	10	0.30078	T	0.28	.	1.4164	0.02302	0.1209:0.2628:0.2478:0.3685	.	650;650	Q9Y3R5-2;Q9Y3R5	.;DOP2_HUMAN	P	650	ENSP00000382104:S650P	ENSP00000382104:S650P	S	+	1	0	DOPEY2	36524900	0.000000	0.05858	0.002000	0.10522	0.113000	0.19764	0.027000	0.13621	0.095000	0.17434	0.402000	0.26972	TCA	.	.		0.537	DOPEY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194636.1	NM_005128	
SLC37A1	54020	hgsc.bcm.edu	37	21	43999901	43999901	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr21:43999901A>G	ENST00000352133.2	+	19	2559	c.1577A>G	c.(1576-1578)gAc>gGc	p.D526G	SLC37A1_ENST00000398341.3_Missense_Mutation_p.D526G			P57057	GLPT_HUMAN	solute carrier family 37 (glucose-6-phosphate transporter), member 1	526					carbohydrate transport (GO:0008643)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	transporter activity (GO:0005215)			breast(1)|endometrium(6)|kidney(1)|large_intestine(2)|liver(2)|lung(3)	15						GCTACGGGGGACCAAGTTCCG	0.582																																					p.D526G		Atlas-SNP	.											.	SLC37A1	48	.	0			c.A1577G						.						67.0	54.0	59.0					21																	43999901		2203	4300	6503	SO:0001583	missense	54020	exon20			CGGGGGACCAAGT	AJ269529	CCDS13689.1	21q22.3	2013-07-17	2013-07-17		ENSG00000160190	ENSG00000160190		"""Solute carriers"""	11024	protein-coding gene	gene with protein product		608094	"""solute carrier family 37 (glycerol-3-phosphate transporter), member 1"""			11112347	Standard	NM_018964		Approved		uc002zbi.3	P57057	OTTHUMG00000086803	ENST00000352133.2:c.1577A>G	chr21.hg19:g.43999901A>G	ENSP00000344648:p.Asp526Gly	100.0	0.0		60.0	4.0	NM_018964	D3DSJ7|Q9HAQ1	Missense_Mutation	SNP	ENST00000352133.2	hg19	CCDS13689.1	.	.	.	.	.	.	.	.	.	.	A	13.26	2.183825	0.38609	.	.	ENSG00000160190	ENST00000398341;ENST00000352133	T;T	0.22743	1.94;1.94	4.86	-0.408	0.12381	.	1.249670	0.05359	N	0.533344	T	0.13884	0.0336	L	0.29908	0.895	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.30475	-0.9977	10	0.30078	T	0.28	-9.898	3.5469	0.07832	0.5668:0.0:0.266:0.1672	.	526	P57057	GLPT_HUMAN	G	526	ENSP00000381383:D526G;ENSP00000344648:D526G	ENSP00000344648:D526G	D	+	2	0	SLC37A1	42872970	0.494000	0.26043	0.026000	0.17262	0.470000	0.32858	0.519000	0.22862	-0.240000	0.09696	0.379000	0.24179	GAC	.	.		0.582	SLC37A1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195377.1		
CBS	875	hgsc.bcm.edu	37	21	44479032	44479032	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr21:44479032T>C	ENST00000398165.3	-	14	1529	c.1270A>G	c.(1270-1272)Acc>Gcc	p.T424A	CBS_ENST00000398158.1_Missense_Mutation_p.T424A|CBS_ENST00000544202.1_Missense_Mutation_p.T336A|CBS_ENST00000398168.1_Missense_Mutation_p.T424A|CBS_ENST00000359624.3_Missense_Mutation_p.T424A|CBS_ENST00000352178.5_Missense_Mutation_p.T424A	NM_000071.2	NP_000062.1	P35520	CBS_HUMAN	cystathionine-beta-synthase	424	CBS. {ECO:0000255|PROSITE- ProRule:PRU00703}.				cellular nitrogen compound metabolic process (GO:0034641)|cysteine biosynthetic process from serine (GO:0006535)|cysteine biosynthetic process via cystathionine (GO:0019343)|homocysteine catabolic process (GO:0043418)|homocysteine metabolic process (GO:0050667)|hydrogen sulfide biosynthetic process (GO:0070814)|L-cysteine catabolic process (GO:0019448)|L-serine catabolic process (GO:0006565)|L-serine metabolic process (GO:0006563)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|transsulfuration (GO:0019346)	cytosol (GO:0005829)|nucleus (GO:0005634)	adenyl nucleotide binding (GO:0030554)|cystathionine beta-synthase activity (GO:0004122)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|modified amino acid binding (GO:0072341)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)|ubiquitin protein ligase binding (GO:0031625)			endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(8)	17					L-Cysteine(DB00151)|L-Serine(DB00133)|S-Adenosylmethionine(DB00118)	GGGAGCACGGTCAGCGGGGCT	0.657																																					p.T424A		Atlas-SNP	.											.	CBS	85	.	0			c.A1270G						.						36.0	31.0	32.0					21																	44479032		2177	4291	6468	SO:0001583	missense	875	exon14			GCACGGTCAGCGG	L14577	CCDS13693.1	21q22.3	2014-09-17			ENSG00000160200	ENSG00000160200	4.2.1.22		1550	protein-coding gene	gene with protein product		613381				9790750	Standard	NM_000071		Approved	HIP4	uc002zcv.2	P35520	OTTHUMG00000086834	ENST00000398165.3:c.1270A>G	chr21.hg19:g.44479032T>C	ENSP00000381231:p.Thr424Ala	105.0	0.0		88.0	5.0	NM_000071	B2R993|D3DSK4|Q99425|Q9BWC5	Missense_Mutation	SNP	ENST00000398165.3	hg19	CCDS13693.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	T|T|T	15.44|15.44|15.44	2.835561|2.835561|2.835561	0.50951|0.50951|0.50951	.|.|.	.|.|.	ENSG00000160200|ENSG00000160200|ENSG00000160200	ENST00000451248|ENST00000398158;ENST00000398165;ENST00000359624;ENST00000352178;ENST00000398168;ENST00000539520;ENST00000544202|ENST00000458223;ENST00000430013	.|D;D;D;D;D;D|.	.|0.95001|.	.|-3.58;-3.58;-3.58;-3.58;-3.58;-3.58|.	4.71|4.71|4.71	4.71|4.71|4.71	0.59529|0.59529|0.59529	.|Cystathionine beta-synthase, core (3);|.	.|0.165190|.	.|0.53938|.	.|D|.	.|0.000055|.	T|T|.	0.77665|0.77665|.	0.4164|0.4164|.	M|M|M	0.85462|0.85462|0.85462	2.755|2.755|2.755	0.54753|0.54753|0.54753	D|D|D	0.99998|0.99998|0.99998	.|B;B;B|.	.|0.28552|.	.|0.215;0.037;0.167|.	.|B;B;B|.	.|0.38327|.	.|0.202;0.088;0.271|.	T|T|.	0.80694|0.80694|.	-0.1268|-0.1268|.	5|10|.	.|0.38643|.	.|T|.	.|0.18|.	-22.9848|-22.9848|-22.9848	13.9291|13.9291|13.9291	0.63983|0.63983|0.63983	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.|.	.|424;424;381|.	.|P35520-2;P35520;B7Z2D6|.	.|.;CBS_HUMAN;.|.	G|A|W	7|424;424;424;424;424;381;336|11;77	.|ENSP00000381225:T424A;ENSP00000381231:T424A;ENSP00000352643:T424A;ENSP00000344460:T424A;ENSP00000381234:T424A;ENSP00000439332:T336A|.	.|ENSP00000344460:T424A|.	D|T|X	-|-|-	2|1|3	0|0|0	CBS|CBS|CBS	43352101|43352101|43352101	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	0.955000|0.955000|0.955000	0.39395|0.39395|0.39395	0.025000|0.025000|0.025000	0.11179|0.11179|0.11179	5.792000|5.792000|5.792000	0.69052|0.69052|0.69052	1.781000|1.781000|1.781000	0.52344|0.52344|0.52344	0.456000|0.456000|0.456000	0.33151|0.33151|0.33151	GAC|ACC|TGA	.	.		0.657	CBS-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195525.1	NM_000071	
C21orf33	8209	hgsc.bcm.edu	37	21	45556049	45556049	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr21:45556049A>G	ENST00000291577.6	+	3	395	c.302A>G	c.(301-303)gAg>gGg	p.E101G	C21orf33_ENST00000493883.1_3'UTR|C21orf33_ENST00000427803.2_Missense_Mutation_p.E101G|C21orf33_ENST00000348499.5_Missense_Mutation_p.E101G	NM_004649.6	NP_004640	P30042	ES1_HUMAN	chromosome 21 open reading frame 33	101						mitochondrion (GO:0005739)				NS(1)|endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|skin(1)	8				STAD - Stomach adenocarcinoma(101;0.168)|Colorectal(79;0.191)		TCCGAAGGCGAGAGCAGGTGT	0.557																																					p.E101G		Atlas-SNP	.											.	C21orf33	23	.	0			c.A302G						.						71.0	64.0	66.0					21																	45556049		2203	4300	6503	SO:0001583	missense	8209	exon3			AAGGCGAGAGCAG	Y07572	CCDS33580.1, CCDS33581.1	21q22.3	2008-07-29			ENSG00000160221	ENSG00000160221			1273	protein-coding gene	gene with protein product		601659				9150728, 8975701	Standard	NM_004649		Approved	KNP-Ia, GT335, ES1, HES1, D21S2048E, KNPI, KNPH, KNP-I	uc002zec.4	P30042	OTTHUMG00000086916	ENST00000291577.6:c.302A>G	chr21.hg19:g.45556049A>G	ENSP00000291577:p.Glu101Gly	190.0	0.0		133.0	6.0	NM_198155	A6NFJ6|A6NJY7|O00650|O00660|O15011|O15012|P55346|P78474|Q92505|Q92507	Missense_Mutation	SNP	ENST00000291577.6	hg19	CCDS33580.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	21.7|21.7	4.186014|4.186014	0.78789|0.78789	.|.	.|.	ENSG00000248354;ENSG00000160221;ENSG00000160221;ENSG00000160221;ENSG00000160221|ENSG00000160221	ENST00000433711;ENST00000291577;ENST00000427803;ENST00000348499;ENST00000389690|ENST00000419699	T;T;T;T|.	0.81247|.	-1.47;-1.47;1.36;-1.47|.	4.93|4.93	3.78|3.78	0.43462|0.43462	ThiJ/PfpI (1);|.	0.052417|.	0.64402|.	D|.	0.000001|.	T|T	0.80808|0.80808	0.4694|0.4694	M|M	0.93150|0.93150	3.385|3.385	0.80722|0.80722	D|D	1|1	D;D|.	0.59767|.	0.986;0.979|.	P;P|.	0.62298|.	0.839;0.9|.	D|D	0.83439|0.83439	0.0042|0.0042	10|5	0.87932|.	D|.	0|.	-21.7287|-21.7287	10.689|10.689	0.45860|0.45860	0.9243:0.0:0.0757:0.0|0.9243:0.0:0.0757:0.0	.|.	101;101|.	P30042-2;P30042|.	.;ES1_HUMAN|.	G|G	80;101;101;101;74|17	ENSP00000291577:E101G;ENSP00000396655:E101G;ENSP00000344901:E101G;ENSP00000374340:E74G|.	ENSP00000415634:E80G|.	E|R	+|+	2|1	0|2	C21orf33;AP001055.7|C21orf33	44380477|44380477	1.000000|1.000000	0.71417|0.71417	0.012000|0.012000	0.15200|0.15200	0.034000|0.034000	0.12701|0.12701	4.610000|4.610000	0.61155|0.61155	0.841000|0.841000	0.35020|0.35020	0.533000|0.533000	0.62120|0.62120	GAG|AGA	.	.		0.557	C21orf33-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000195824.1	NM_004649	
MCM3AP	8888	hgsc.bcm.edu	37	21	47674393	47674393	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr21:47674393T>C	ENST00000397708.1	-	20	4303	c.4049A>G	c.(4048-4050)cAc>cGc	p.H1350R	MCM3AP-AS1_ENST00000455567.1_RNA|AP001469.9_ENST00000447037.1_RNA|MCM3AP_ENST00000291688.1_Missense_Mutation_p.H1350R|MCM3AP_ENST00000467026.1_5'UTR|AP001469.9_ENST00000430259.1_RNA|MCM3AP-AS1_ENST00000590829.1_RNA|MCM3AP-AS1_ENST00000414659.1_RNA			O60318	GANP_HUMAN	minichromosome maintenance complex component 3 associated protein	1350					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)					CCCAGGGAGGTGCTCAGCCAC	0.597																																					p.H1350R		Atlas-SNP	.											.	MCM3AP	146	.	0			c.A4049G						.						78.0	65.0	69.0					21																	47674393		2203	4300	6503	SO:0001583	missense	8888	exon19			GGGAGGTGCTCAG	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.4049A>G	chr21.hg19:g.47674393T>C	ENSP00000380820:p.His1350Arg	91.0	0.0		100.0	4.0	NM_003906	C9JL56|Q2M3C1|Q6PJP6|Q9BSY5|Q9UMT4	Missense_Mutation	SNP	ENST00000397708.1	hg19	CCDS13734.1	.	.	.	.	.	.	.	.	.	.	T	14.27	2.484361	0.44147	.	.	ENSG00000160294	ENST00000397708;ENST00000291688	T;T	0.51817	0.69;0.69	5.22	5.22	0.72569	.	0.148969	0.64402	D	0.000014	T	0.49541	0.1563	M	0.68317	2.08	0.35939	D	0.833051	P	0.49961	0.93	B	0.42319	0.383	T	0.66368	-0.5941	10	0.59425	D	0.04	-16.395	15.1243	0.72469	0.0:0.0:0.0:1.0	.	1350	O60318	MCM3A_HUMAN	R	1350	ENSP00000380820:H1350R;ENSP00000291688:H1350R	ENSP00000291688:H1350R	H	-	2	0	MCM3AP	46498821	1.000000	0.71417	0.970000	0.41538	0.216000	0.24613	3.476000	0.53143	1.974000	0.57490	0.533000	0.62120	CAC	.	.		0.597	MCM3AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207254.1	NM_003906	
MYO18B	84700	hgsc.bcm.edu	37	22	26176036	26176036	+	Silent	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr22:26176036A>G	ENST00000407587.2	+	9	2251	c.2082A>G	c.(2080-2082)cgA>cgG	p.R694R	MYO18B_ENST00000536101.1_Silent_p.R694R|MYO18B_ENST00000335473.7_Silent_p.R694R			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	694	Myosin motor.					cytoplasm (GO:0005737)|nucleus (GO:0005634)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(6)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(27)|liver(2)|lung(60)|ovary(7)|prostate(8)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	146						AGAAGATCCGAGCCACCTTCA	0.627																																					p.R694R		Atlas-SNP	.											.	MYO18B	322	.	0			c.A2082G						.						19.0	24.0	22.0					22																	26176036		2080	4194	6274	SO:0001819	synonymous_variant	84700	exon9			GATCCGAGCCACC	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.2082A>G	chr22.hg19:g.26176036A>G		88.0	0.0		60.0	4.0	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Silent	SNP	ENST00000407587.2	hg19																																																																																				.	.		0.627	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608	
DRG1	4733	hgsc.bcm.edu	37	22	31796695	31796695	+	Silent	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr22:31796695T>C	ENST00000331457.4	+	2	293	c.132T>C	c.(130-132)acT>acC	p.T44T	DRG1_ENST00000433341.1_3'UTR	NM_004147.3	NP_004138.1	Q9Y295	DRG1_HUMAN	developmentally regulated GTP binding protein 1	44					multicellular organismal development (GO:0007275)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|polysome (GO:0005844)	GTP binding (GO:0005525)|identical protein binding (GO:0042802)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(1)|prostate(1)|urinary_tract(1)	11						AACTCATTACTCCAAAGGGTG	0.428																																					p.T44T		Atlas-SNP	.											.	DRG1	28	.	0			c.T132C						.						83.0	77.0	79.0					22																	31796695		2203	4300	6503	SO:0001819	synonymous_variant	4733	exon2			CATTACTCCAAAG	AJ005940	CCDS13897.1	22q12.2	2010-02-26	2001-11-28		ENSG00000185721	ENSG00000185721			3029	protein-coding gene	gene with protein product		603952	"""developmentally regulated GTP-binding protein 1"""	NEDD3		7929244, 1449490	Standard	NM_004147		Approved		uc003aku.3	Q9Y295	OTTHUMG00000030792	ENST00000331457.4:c.132T>C	chr22.hg19:g.31796695T>C		113.0	0.0		87.0	4.0	NM_004147	B2RDS8|Q6FGP8|Q8WW69|Q9UGF2	Silent	SNP	ENST00000331457.4	hg19	CCDS13897.1																																																																																			.	.		0.428	DRG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075680.5	NM_004147	
FBXO7	25793	hgsc.bcm.edu	37	22	32871071	32871071	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr22:32871071T>C	ENST00000266087.7	+	1	409	c.82T>C	c.(82-84)Tcg>Ccg	p.S28P	FBXO7_ENST00000397426.1_5'Flank|FBXO7_ENST00000382058.3_5'Flank	NM_012179.3	NP_036311.3	Q9Y3I1	FBX7_HUMAN	F-box protein 7	28	Ubiquitin-like.				cell death (GO:0008219)|mitochondrion degradation (GO:0000422)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of lymphocyte differentiation (GO:0045620)|protein targeting to mitochondrion (GO:0006626)|protein ubiquitination (GO:0016567)|regulation of protein stability (GO:0031647)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						GCATTTGCGCTCGCACCTGAG	0.736																																					p.S28P		Atlas-SNP	.											.	FBXO7	131	.	0			c.T82C						.						7.0	9.0	8.0					22																	32871071		1905	3746	5651	SO:0001583	missense	25793	exon1			TTGCGCTCGCACC	AF129537	CCDS13907.1, CCDS58806.1	22q12.3	2013-09-19	2004-06-15		ENSG00000100225	ENSG00000100225		"""F-boxes /  ""other"""", ""Parkinson disease"""	13586	protein-coding gene	gene with protein product		605648	"""F-box only protein 7"""			10531035, 10531037, 19038853	Standard	NM_001257990		Approved	FBX7, Fbx, PARK15	uc003amq.3	Q9Y3I1	OTTHUMG00000030674	ENST00000266087.7:c.82T>C	chr22.hg19:g.32871071T>C	ENSP00000266087:p.Ser28Pro	178.0	0.0		97.0	4.0	NM_012179	B4DNB3|B4DWX5|Q5TGC4|Q5TI86|Q96HM6|Q9UF21|Q9UKT2	Missense_Mutation	SNP	ENST00000266087.7	hg19	CCDS13907.1	.	.	.	.	.	.	.	.	.	.	T	10.91	1.484048	0.26598	.	.	ENSG00000100225	ENST00000266087	T	0.39787	1.06	4.14	-0.609	0.11608	.	.	.	.	.	T	0.18676	0.0448	N	0.08118	0	0.80722	D	1	B	0.20550	0.046	B	0.17722	0.019	T	0.03993	-1.0986	9	0.44086	T	0.13	0.6075	4.7956	0.13270	0.1653:0.0:0.5365:0.2983	.	28	Q9Y3I1	FBX7_HUMAN	P	28	ENSP00000266087:S28P	ENSP00000266087:S28P	S	+	1	0	FBXO7	31201071	0.974000	0.33945	0.775000	0.31657	0.022000	0.10575	1.334000	0.33827	-0.097000	0.12307	-1.585000	0.00851	TCG	.	.		0.736	FBXO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129001.1		
FBXO7	25793	hgsc.bcm.edu	37	22	32887083	32887083	+	Silent	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr22:32887083A>G	ENST00000266087.7	+	6	1209	c.882A>G	c.(880-882)gtA>gtG	p.V294V	FBXO7_ENST00000397426.1_Silent_p.V180V|FBXO7_ENST00000382058.3_Silent_p.V215V	NM_012179.3	NP_036311.3	Q9Y3I1	FBX7_HUMAN	F-box protein 7	294	Important for dimerization and interaction with PSMF1.				cell death (GO:0008219)|mitochondrion degradation (GO:0000422)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of lymphocyte differentiation (GO:0045620)|protein targeting to mitochondrion (GO:0006626)|protein ubiquitination (GO:0016567)|regulation of protein stability (GO:0031647)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						GGGAAAATGTAGCCAACATAT	0.363																																					p.V294V		Atlas-SNP	.											.	FBXO7	131	.	0			c.A882G						.						73.0	78.0	77.0					22																	32887083		2203	4300	6503	SO:0001819	synonymous_variant	25793	exon6			AAATGTAGCCAAC	AF129537	CCDS13907.1, CCDS58806.1	22q12.3	2013-09-19	2004-06-15		ENSG00000100225	ENSG00000100225		"""F-boxes /  ""other"""", ""Parkinson disease"""	13586	protein-coding gene	gene with protein product		605648	"""F-box only protein 7"""			10531035, 10531037, 19038853	Standard	NM_001257990		Approved	FBX7, Fbx, PARK15	uc003amq.3	Q9Y3I1	OTTHUMG00000030674	ENST00000266087.7:c.882A>G	chr22.hg19:g.32887083A>G		104.0	0.0		79.0	5.0	NM_012179	B4DNB3|B4DWX5|Q5TGC4|Q5TI86|Q96HM6|Q9UF21|Q9UKT2	Silent	SNP	ENST00000266087.7	hg19	CCDS13907.1																																																																																			.	.		0.363	FBXO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129001.1		
SH3BP1	23616	hgsc.bcm.edu	37	22	38035826	38035826	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr22:38035826A>G	ENST00000357436.4	+	1	345	c.32A>G	c.(31-33)cAg>cGg	p.Q11R	SH3BP1_ENST00000336738.5_Missense_Mutation_p.Q11R|SH3BP1_ENST00000599616.1_5'Flank|Z83844.1_ENST00000456099.1_RNA|SH3BP1_ENST00000442465.2_Missense_Mutation_p.Q11R	NM_018957.3	NP_061830.3	Q9Y3L3	3BP1_HUMAN	SH3-domain binding protein 1	11					signal transduction (GO:0007165)	cytoplasm (GO:0005737)	GTPase activator activity (GO:0005096)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(5)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13	Melanoma(58;0.0574)					CGCATGCGGCAGCTGGCCCAG	0.711																																					p.Q11R		Atlas-SNP	.											.	SH3BP1	41	.	0			c.A32G						.						5.0	7.0	7.0					22																	38035826		1942	3910	5852	SO:0001583	missense	23616	exon1			TGCGGCAGCTGGC		CCDS13952.2	22q13.1	2011-07-04			ENSG00000100092	ENSG00000100092		"""Rho GTPase activating proteins"""	10824	protein-coding gene	gene with protein product						10591208, 12029088	Standard	NM_018957		Approved	ARHGAP43	uc003ati.3	Q9Y3L3	OTTHUMG00000030996	ENST00000357436.4:c.32A>G	chr22.hg19:g.38035826A>G	ENSP00000350018:p.Gln11Arg	203.0	0.0		114.0	5.0	NM_018957	Q5R3N0|Q6IBZ2|Q6ZVL9|Q96HQ5|Q9NSQ9	Missense_Mutation	SNP	ENST00000357436.4	hg19	CCDS13952.2	.	.	.	.	.	.	.	.	.	.	A	25.7	4.668614	0.88348	.	.	ENSG00000100092	ENST00000357436;ENST00000336738;ENST00000442465	T;T;T	0.70869	-0.52;-0.52;-0.52	3.95	3.95	0.45737	BAR (1);	0.000000	0.44097	D	0.000487	T	0.74673	0.3747	L	0.56199	1.76	0.38041	D	0.93545	D;D	0.63880	0.98;0.993	P;P	0.57620	0.759;0.824	T	0.76121	-0.3075	10	0.36615	T	0.2	.	11.4711	0.50268	1.0:0.0:0.0:0.0	.	11;11	F5GZA8;Q9Y3L3	.;3BP1_HUMAN	R	11	ENSP00000350018:Q11R;ENSP00000337213:Q11R;ENSP00000395126:Q11R	ENSP00000337213:Q11R	Q	+	2	0	SH3BP1	36365772	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.948000	0.70249	1.774000	0.52232	0.496000	0.49642	CAG	.	.		0.711	SH3BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075884.4	NM_018957	
RPL3	6122	hgsc.bcm.edu	37	22	39711388	39711388	+	Missense_Mutation	SNP	C	C	T			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr22:39711388C>T	ENST00000216146.4	-	5	847	c.674G>A	c.(673-675)gGc>gAc	p.G225D	RPL3_ENST00000401609.1_Missense_Mutation_p.G173D|SNORD83A_ENST00000386747.1_RNA|SNORD83B_ENST00000386745.1_RNA|RPL3_ENST00000465618.1_5'UTR	NM_000967.3|NM_001033853.1	NP_000958.1|NP_001029025.1	P39023	RL3_HUMAN	ribosomal protein L3	225					cellular protein metabolic process (GO:0044267)|cellular response to interleukin-4 (GO:0071353)|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)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			breast(1)|kidney(4)|large_intestine(2)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	12	Melanoma(58;0.04)				Homoharringtonine(DB04865)	GTAGCCTTTGCCCTTGGTCAC	0.567																																					p.G225D		Atlas-SNP	.											.	RPL3	29	.	0			c.G674A						.						124.0	111.0	115.0					22																	39711388		2203	4300	6503	SO:0001583	missense	6122	exon5			CCTTTGCCCTTGG	AB007166	CCDS13988.1	22q13	2011-04-06			ENSG00000100316	ENSG00000100316		"""L ribosomal proteins"""	10332	protein-coding gene	gene with protein product		604163				2891103, 9582194	Standard	NM_000967		Approved	L3	uc003axi.3	P39023	OTTHUMG00000151079	ENST00000216146.4:c.674G>A	chr22.hg19:g.39711388C>T	ENSP00000346001:p.Gly225Asp	271.0	0.0		148.0	6.0	NM_000967	B2RDV9|Q15548|Q5I0G0	Missense_Mutation	SNP	ENST00000216146.4	hg19	CCDS13988.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.173817	0.78452	.	.	ENSG00000100316	ENST00000401609;ENST00000216146;ENST00000402527;ENST00000453303	D;D;D;D	0.81739	-1.53;-1.53;-1.53;-1.53	5.09	5.09	0.68999	Ribosomal protein L3, conserved site (1);Translation elongation/initiation factor/Ribosomal, beta-barrel (1);	0.000000	0.85682	D	0.000000	D	0.92169	0.7517	M	0.93898	3.47	0.80722	D	1	B;P;B;P	0.39131	0.356;0.607;0.049;0.661	B;P;B;P	0.57548	0.432;0.71;0.226;0.823	D	0.93593	0.6923	10	0.87932	D	0	.	18.4787	0.90802	0.0:1.0:0.0:0.0	.	196;173;225;176	Q8TBW1;G5E9G0;P39023;B3KS36	.;.;RL3_HUMAN;.	D	173;225;173;252	ENSP00000386101:G173D;ENSP00000346001:G225D;ENSP00000385762:G173D;ENSP00000415198:G252D	ENSP00000346001:G225D	G	-	2	0	RPL3	38041334	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.726000	0.84824	2.384000	0.81235	0.462000	0.41574	GGC	.	.		0.567	RPL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321196.1	NM_000967	
TNRC6B	23112	hgsc.bcm.edu	37	22	40657900	40657900	+	Silent	SNP	A	A	G	rs376736908		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr22:40657900A>G	ENST00000454349.2	+	4	391	c.180A>G	c.(178-180)ccA>ccG	p.P60P	TNRC6B_ENST00000335727.9_Silent_p.P60P|TNRC6B_ENST00000402203.1_Silent_p.P96P|TNRC6B_ENST00000301923.9_Silent_p.P96P	NM_001162501.1	NP_001155973.1	Q9UPQ9	TNR6B_HUMAN	trinucleotide repeat containing 6B	60	Interaction with argonaute proteins.				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)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of translation (GO:0006417)	cytosol (GO:0005829)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)	1						GCAGCTCTCCATCGCCACCAG	0.582																																					p.P96P		Atlas-SNP	.											.	TNRC6B	195	.	0			c.A288G						.	A	,,	2,3814		0,2,1906	22.0	26.0	25.0		288,180,180	5.9	1.0	22		25	0,8162		0,0,4081	no	coding-synonymous,coding-synonymous,coding-synonymous	TNRC6B	NM_001024843.1,NM_001162501.1,NM_015088.2	,,	0,2,5987	GG,GA,AA		0.0,0.0524,0.0167	,,	96/1030,60/1834,60/1724	40657900	2,11976	1908	4081	5989	SO:0001819	synonymous_variant	23112	exon7			CTCTCCATCGCCA	AB029016	CCDS46712.1, CCDS46713.1, CCDS54533.1	22q13	2006-08-22			ENSG00000100354	ENSG00000100354		"""Trinucleotide (CAG) repeat containing"""	29190	protein-coding gene	gene with protein product		610740					Standard	NM_015088		Approved	KIAA1093	uc011aor.2	Q9UPQ9	OTTHUMG00000151114	ENST00000454349.2:c.180A>G	chr22.hg19:g.40657900A>G		248.0	0.0		181.0	69.0	NM_001024843	B0QY73|B0QY78|B4DGC0|Q5TH52|Q8TBX2	Silent	SNP	ENST00000454349.2	hg19	CCDS54533.1																																																																																			.	.		0.582	TNRC6B-202	KNOWN	basic|CCDS	protein_coding	protein_coding			
SMC1B	27127	hgsc.bcm.edu	37	22	45767392	45767392	+	Silent	SNP	G	G	T			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr22:45767392G>T	ENST00000357450.4	-	14	2271	c.2272C>A	c.(2272-2274)Cga>Aga	p.R758R	SMC1B_ENST00000404354.3_Silent_p.R758R	NM_148674.3	NP_683515.3	Q8NDV3	SMC1B_HUMAN	structural maintenance of chromosomes 1B	758			R -> Q (in dbSNP:rs9614653).		meiotic nuclear division (GO:0007126)|sister chromatid cohesion (GO:0007062)	chromosome, centromeric region (GO:0000775)|lateral element (GO:0000800)|meiotic cohesin complex (GO:0030893)|nuclear meiotic cohesin complex (GO:0034991)	ATP binding (GO:0005524)|DNA binding (GO:0003677)			breast(2)|endometrium(4)|kidney(3)|large_intestine(6)|lung(15)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	37		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)		CTTCGTTGTCGTTCCTTGATT	0.284																																					p.R758R		Atlas-SNP	.											SMC1B_ENST00000357450,rectum,carcinoma,0,2	SMC1B	215	.	0			c.C2272A						.						102.0	92.0	95.0					22																	45767392		1814	4070	5884	SO:0001819	synonymous_variant	27127	exon14			GTTGTCGTTCCTT	AJ504806	CCDS43027.1, CCDS74876.1	22q13	2006-07-06	2006-07-06	2006-07-06	ENSG00000077935	ENSG00000077935		"""Structural maintenance of chromosomes proteins"""	11112	protein-coding gene	gene with protein product		608685	"""SMC1 (structural maintenance of chromosomes 1, yeast)-like 1"", ""SMC1 structural maintenance of chromosomes 1-like 2 (yeast)"""	SMC1L2		10591208, 11564881	Standard	XM_005261566		Approved	bK268H5	uc003bgc.3	Q8NDV3	OTTHUMG00000151334	ENST00000357450.4:c.2272C>A	chr22.hg19:g.45767392G>T		272.0	0.0		126.0	0.0	NM_148674	A0AV46|B0QY23|B0QY24|Q5TIC3|Q6ZUF9|Q9Y3G5	Silent	SNP	ENST00000357450.4	hg19	CCDS43027.1																																																																																			.	.		0.284	SMC1B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322256.2	NM_148674	
PPP6R2	9701	hgsc.bcm.edu	37	22	50876270	50876270	+	Splice_Site	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr22:50876270A>G	ENST00000216061.5	+	18	2151		c.e18-1		PPP6R2_ENST00000359139.3_Splice_Site|PPP6R2_ENST00000395744.3_Splice_Site|PPP6R2_ENST00000395741.3_Splice_Site			O75170	PP6R2_HUMAN	protein phosphatase 6, regulatory subunit 2							cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)				NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|liver(1)|lung(6)|ovary(2)|skin(1)|urinary_tract(1)	22						TTGCTCTTGCAGTGCCCCGTT	0.632																																					.		Atlas-SNP	.											.	PPP6R2	71	.	0			c.1704-2A>G						.						62.0	44.0	50.0					22																	50876270		2161	4209	6370	SO:0001630	splice_region_variant	9701	exon16			TCTTGCAGTGCCC	AB014585	CCDS33681.1, CCDS56235.1, CCDS56236.1, CCDS74881.1	22q13.33	2012-04-17	2010-06-28	2010-06-28	ENSG00000100239	ENSG00000100239		"""Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits"""	19253	protein-coding gene	gene with protein product		610877	"""KIAA0685"", ""SAPS domain family, member 2"""	KIAA0685, SAPS2		16769727	Standard	NM_014678		Approved	dJ579N16.1, SAP190	uc003blc.3	O75170	OTTHUMG00000150199	ENST00000216061.5:c.1782-1A>G	chr22.hg19:g.50876270A>G		208.0	0.0		69.0	4.0	NM_001242899	A6PVG3|B7Z7T3|Q5U5P3|Q7Z2L2|Q7Z5G5|Q7Z731|Q9UGB9	Splice_Site	SNP	ENST00000216061.5	hg19		.	.	.	.	.	.	.	.	.	.	A	18.73	3.686966	0.68157	.	.	ENSG00000100239	ENST00000359139;ENST00000395741;ENST00000395744;ENST00000216061	.	.	.	5.58	5.58	0.84498	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.7234	0.69326	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	PPP6R2	49223136	1.000000	0.71417	0.566000	0.28421	0.207000	0.24258	8.374000	0.90133	2.129000	0.65627	0.260000	0.18958	.	.	.		0.632	PPP6R2-004	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000316809.1	NM_014678	Intron
SBF1	6305	hgsc.bcm.edu	37	22	50893474	50893474	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr22:50893474A>G	ENST00000390679.3	-	33	4758	c.4574T>C	c.(4573-4575)cTc>cCc	p.L1525P	SBF1_ENST00000348911.6_Missense_Mutation_p.L1526P|SBF1_ENST00000380817.3_Missense_Mutation_p.L1551P|SBF1_ENST00000476293.1_5'Flank			O95248	MTMR5_HUMAN	SET binding factor 1	1525	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.				cell death (GO:0008219)|positive regulation of Rab GTPase activity (GO:0032851)|protein dephosphorylation (GO:0006470)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	protein tyrosine/serine/threonine phosphatase activity (GO:0008138)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|central_nervous_system(2)|endometrium(6)|kidney(8)|large_intestine(3)|lung(18)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	43		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.206)|LUAD - Lung adenocarcinoma(64;0.247)		GTCAGAGTCGAGCAGGAAGGT	0.612																																					p.L1551P		Atlas-SNP	.											.	SBF1	211	.	0			c.T4652C						.						45.0	51.0	49.0					22																	50893474		2091	4216	6307	SO:0001583	missense	6305	exon34			GAGTCGAGCAGGA	U93181	CCDS14091.1, CCDS14091.2	22q13.33	2013-01-10			ENSG00000100241	ENSG00000100241		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"", ""DENN/MADD domain containing"", ""Pleckstrin homology (PH) domain containing"""	10542	protein-coding gene	gene with protein product	"""myotubularin related 5"", ""DENN/MADD domain containing 7A"""	603560				9537414, 9736772	Standard	NM_002972		Approved	MTMR5, DENND7A	uc003blh.3	O95248	OTTHUMG00000150204	ENST00000390679.3:c.4574T>C	chr22.hg19:g.50893474A>G	ENSP00000375097:p.Leu1525Pro	191.0	0.0		79.0	4.0	NM_002972	A6PVG9|O60228|Q5JXD8|Q5PPM2|Q96GR9|Q9UGB8	Missense_Mutation	SNP	ENST00000390679.3	hg19		.	.	.	.	.	.	.	.	.	.	A	21.2	4.109351	0.77096	.	.	ENSG00000100241	ENST00000380817;ENST00000348911;ENST00000337034;ENST00000390679	D;D;D	0.90732	-2.72;-2.72;-2.72	3.74	3.74	0.42951	Myotubularin phosphatase domain (1);	0.170909	0.37219	N	0.002200	D	0.93903	0.8049	M	0.66939	2.045	0.80722	D	1	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.91635	0.998;0.997;0.999	D	0.94240	0.7484	10	0.72032	D	0.01	.	12.5669	0.56314	1.0:0.0:0.0:0.0	.	1525;1551;84	O95248;O95248-4;A6PVG7	MTMR5_HUMAN;.;.	P	1551;1526;1561;1525	ENSP00000370196:L1551P;ENSP00000252027:L1526P;ENSP00000375097:L1525P	ENSP00000336522:L1561P	L	-	2	0	SBF1	49240340	1.000000	0.71417	0.997000	0.53966	0.996000	0.88848	8.702000	0.91338	1.701000	0.51217	0.379000	0.24179	CTC	.	.		0.612	SBF1-201	KNOWN	basic	protein_coding	protein_coding			
ARSE	415	hgsc.bcm.edu	37	X	2861192	2861192	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:2861192A>G	ENST00000381134.3	-	8	1106	c.1040T>C	c.(1039-1041)cTc>cCc	p.L347P	ARSE_ENST00000540563.1_Missense_Mutation_p.L302P|ARSE_ENST00000545496.1_Missense_Mutation_p.L372P	NM_000047.2	NP_000038.2	P51690	ARSE_HUMAN	arylsulfatase E (chondrodysplasia punctata 1)	347					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		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)				AAAATAAATGAGGGTGCTGTT	0.448																																					p.L347P		Atlas-SNP	.											.	ARSE	43	.	0			c.T1040C						.						84.0	74.0	77.0					X																	2861192		2203	4300	6503	SO:0001583	missense	415	exon8			TAAATGAGGGTGC	X83573	CCDS14122.1, CCDS75948.1, CCDS75949.1	Xp22.33	2013-02-14			ENSG00000157399	ENSG00000157399		"""Arylsulfatase family"""	719	protein-coding gene	gene with protein product		300180		CDPX, CDPX1		7720070	Standard	NM_000047		Approved		uc004crc.4	P51690	OTTHUMG00000137358	ENST00000381134.3:c.1040T>C	chrX.hg19:g.2861192A>G	ENSP00000370526:p.Leu347Pro	107.0	0.0		80.0	4.0	NM_000047	Q53FT2|Q53FU8	Missense_Mutation	SNP	ENST00000381134.3	hg19	CCDS14122.1	.	.	.	.	.	.	.	.	.	.	A	12.74	2.028353	0.35797	.	.	ENSG00000157399	ENST00000540563;ENST00000545496;ENST00000381134	D;D;D	0.95342	-3.68;-3.68;-3.68	3.66	3.66	0.41972	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.070336	0.64402	D	0.000020	D	0.98327	0.9445	H	0.99197	4.465	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.98109	1.0419	10	0.87932	D	0	.	11.073	0.48014	1.0:0.0:0.0:0.0	.	302;372;347	F5H324;F5GYY5;P51690	.;.;ARSE_HUMAN	P	302;372;347	ENSP00000438198:L302P;ENSP00000441417:L372P;ENSP00000370526:L347P	ENSP00000370526:L347P	L	-	2	0	ARSE	2871192	0.921000	0.31238	0.024000	0.17045	0.007000	0.05969	7.154000	0.77437	1.301000	0.44836	0.486000	0.48141	CTC	.	.		0.448	ARSE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055643.1	NM_000047	
AMELX	265	hgsc.bcm.edu	37	X	11316394	11316394	+	Silent	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:11316394A>G	ENST00000380714.3	+	4	209	c.141A>G	c.(139-141)ccA>ccG	p.P47P	ARHGAP6_ENST00000380736.1_Intron|ARHGAP6_ENST00000380718.1_Intron|ARHGAP6_ENST00000337414.4_Intron|ARHGAP6_ENST00000380732.3_Intron|AMELX_ENST00000380712.3_Silent_p.P61P|AMELX_ENST00000348912.4_Silent_p.P31P|ARHGAP6_ENST00000413512.3_Intron	NM_001142.2	NP_001133.1	Q99217	AMELX_HUMAN	amelogenin, X-linked	47					biomineral tissue development (GO:0031214)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|chondrocyte differentiation (GO:0002062)|enamel mineralization (GO:0070166)|epithelial to mesenchymal transition (GO:0001837)|ion homeostasis (GO:0050801)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of tooth mineralization (GO:0070172)|signal transduction (GO:0007165)|tooth mineralization (GO:0034505)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)	growth factor activity (GO:0008083)|hydroxyapatite binding (GO:0046848)|identical protein binding (GO:0042802)|structural constituent of tooth enamel (GO:0030345)			endometrium(3)|kidney(2)|large_intestine(1)|lung(9)	15						GCATAAGGCCACCGGTATGTA	0.348																																					p.P61P		Atlas-SNP	.											.	AMELX	31	.	0			c.A183G						.						191.0	191.0	191.0					X																	11316394		2203	4300	6503	SO:0001819	synonymous_variant	265	exon5			AAGGCCACCGGTA		CCDS14144.1, CCDS14145.1, CCDS14146.1	Xp22.31-p22.1	2010-04-20	2010-04-20		ENSG00000125363	ENSG00000125363			461	protein-coding gene	gene with protein product	"""amelogenesis imperfecta 1"""	300391	"""amelogenin (X chromosome, amelogenesis imperfecta 1)"""	AMG, AIH1		1734713	Standard	NM_182680		Approved		uc004cus.3	Q99217	OTTHUMG00000021130	ENST00000380714.3:c.141A>G	chrX.hg19:g.11316394A>G		69.0	0.0		71.0	4.0	NM_182680	Q96NW6|Q9UCA7	Silent	SNP	ENST00000380714.3	hg19	CCDS14144.1																																																																																			.	.		0.348	AMELX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055746.1	NM_001142	
FIGF	2277	hgsc.bcm.edu	37	X	15365316	15365316	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:15365316T>C	ENST00000297904.3	-	6	1337	c.908A>G	c.(907-909)aAg>aGg	p.K303R	FIGF_ENST00000488351.1_5'UTR	NM_004469.4	NP_004460.1	O43915	VEGFD_HUMAN	c-fos induced growth factor (vascular endothelial growth factor D)	303	4 X 16 AA repeats of C-X(10)-C-X-C- X(1,3)-C.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|induction of positive chemotaxis (GO:0050930)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive chemotaxis (GO:0050918)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of mast cell chemotaxis (GO:0060754)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|platelet alpha granule lumen (GO:0031093)	chemoattractant activity (GO:0042056)|platelet-derived growth factor receptor binding (GO:0005161)|vascular endothelial growth factor receptor binding (GO:0005172)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|skin(1)	17	Hepatocellular(33;0.183)					TAGCTTGTGCTTCTGGCAGCA	0.443																																					p.K303R		Atlas-SNP	.											.	FIGF	39	.	0			c.A908G						.						160.0	149.0	152.0					X																	15365316		2203	4300	6503	SO:0001583	missense	2277	exon6			TTGTGCTTCTGGC	AJ000185	CCDS14166.1	Xp22.31	2008-02-05			ENSG00000165197	ENSG00000165197			3708	protein-coding gene	gene with protein product		300091		VEGFD		9479493	Standard	NM_004469		Approved	VEGF-D	uc004cwt.2	O43915	OTTHUMG00000021175	ENST00000297904.3:c.908A>G	chrX.hg19:g.15365316T>C	ENSP00000297904:p.Lys303Arg	115.0	0.0		83.0	4.0	NM_004469	B2R7Z3	Missense_Mutation	SNP	ENST00000297904.3	hg19	CCDS14166.1	.	.	.	.	.	.	.	.	.	.	T	15.20	2.763705	0.49574	.	.	ENSG00000165197	ENST00000297904	.	.	.	5.16	5.16	0.70880	.	0.446510	0.24713	N	0.036220	T	0.45895	0.1365	M	0.64997	1.995	0.34381	D	0.693098	P	0.38597	0.639	B	0.27380	0.079	T	0.63413	-0.6643	9	0.44086	T	0.13	-20.9609	13.3791	0.60757	0.0:0.0:0.0:1.0	.	303	O43915	VEGFD_HUMAN	R	303	.	ENSP00000297904:K303R	K	-	2	0	FIGF	15275237	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	5.461000	0.66699	1.822000	0.53115	0.486000	0.48141	AAG	.	.		0.443	FIGF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055859.1	NM_004469	
MAP7D2	256714	hgsc.bcm.edu	37	X	20031688	20031688	+	Splice_Site	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:20031688T>C	ENST00000379651.3	-	12	1700	c.1682A>G	c.(1681-1683)aAg>aGg	p.K561R	MAP7D2_ENST00000379643.5_Splice_Site_p.K602R|MAP7D2_ENST00000543767.1_Splice_Site_p.K446R|MAP7D2_ENST00000443379.3_Splice_Site_p.K516R|MAP7D2_ENST00000452324.3_Splice_Site_p.K509R	NM_152780.3	NP_689993.2	Q96T17	MA7D2_HUMAN	MAP7 domain containing 2	561					microtubule cytoskeleton organization (GO:0000226)	microtubule (GO:0005874)				NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(13)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	37						AATTCCTACCTTCACTTGTGG	0.328																																					p.K602R		Atlas-SNP	.											.	MAP7D2	165	.	0			c.A1805G						.						208.0	171.0	183.0					X																	20031688		2203	4299	6502	SO:0001630	splice_region_variant	256714	exon13			CCTACCTTCACTT	BC089400	CCDS14195.1, CCDS55384.1, CCDS55385.1, CCDS55386.1	Xp22.12	2008-02-05			ENSG00000184368	ENSG00000184368			25899	protein-coding gene	gene with protein product						12477932	Standard	NM_152780		Approved	FLJ14503	uc010nfo.2	Q96T17	OTTHUMG00000021228	ENST00000379651.3:c.1683+1A>G	chrX.hg19:g.20031688T>C		152.0	0.0		100.0	4.0	NM_001168465	B7Z2J8|B7Z3S7|B9EGC7|C9JMA4|C9JYW0|Q5EBN1|Q5JPS7|Q6PIC7|Q8N792	Missense_Mutation	SNP	ENST00000379651.3	hg19	CCDS14195.1	.	.	.	.	.	.	.	.	.	.	T	24.3	4.516929	0.85495	.	.	ENSG00000184368	ENST00000379651;ENST00000379643;ENST00000543767;ENST00000443379;ENST00000544957;ENST00000452324	T;T;T;T;T	0.26810	1.71;1.71;1.71;1.71;1.71	5.83	5.83	0.93111	.	0.000000	0.85682	D	0.000000	T	0.53270	0.1786	M	0.81497	2.545	0.49915	D	0.99983	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;0.997	D;D;D;D;D	0.87578	0.997;0.995;0.995;0.998;0.981	T	0.56571	-0.7957	10	0.49607	T	0.09	-24.7971	14.2709	0.66152	0.0:0.0:0.0:1.0	.	516;509;602;561;446	B7Z3S7;C9JYW0;Q96T17-2;Q96T17;F5GYC2	.;.;.;MA7D2_HUMAN;.	R	561;602;446;516;244;509	ENSP00000368972:K561R;ENSP00000368964:K602R;ENSP00000440691:K446R;ENSP00000388239:K516R;ENSP00000413301:K509R	ENSP00000368964:K602R	K	-	2	0	MAP7D2	19941609	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	6.067000	0.71193	1.968000	0.57251	0.483000	0.47432	AAG	.	.		0.328	MAP7D2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000056001.1	NM_152780	Missense_Mutation
PCYT1B	9468	hgsc.bcm.edu	37	X	24605386	24605386	+	Silent	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:24605386A>G	ENST00000379144.2	-	5	667	c.537T>C	c.(535-537)gaT>gaC	p.D179D	PCYT1B_ENST00000379145.1_Silent_p.D161D|PCYT1B_ENST00000356768.4_Silent_p.D179D	NM_004845.4	NP_004836.2	Q9Y5K3	PCY1B_HUMAN	phosphate cytidylyltransferase 1, choline, beta	179					CDP-choline pathway (GO:0006657)|glycerophospholipid biosynthetic process (GO:0046474)|ovarian follicle development (GO:0001541)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)	choline-phosphate cytidylyltransferase activity (GO:0004105)			breast(2)|kidney(1)|large_intestine(5)|lung(8)|ovary(1)	17					Choline(DB00122)	TGTAAACATCATCAGAGCCAG	0.463																																					p.D179D		Atlas-SNP	.											.	PCYT1B	88	.	0			c.T537C						.						165.0	110.0	129.0					X																	24605386		2203	4300	6503	SO:0001819	synonymous_variant	9468	exon5			AACATCATCAGAG	AF052510	CCDS14213.1, CCDS55391.1, CCDS55392.1	Xp22	2008-02-05	2005-09-05		ENSG00000102230	ENSG00000102230	2.7.7.15		8755	protein-coding gene	gene with protein product		604926	"""phosphate cytidylyltransferase 1, choline, beta isoform"""			9593753	Standard	NM_004845		Approved	CCT-beta, CTB	uc004dbi.3	Q9Y5K3	OTTHUMG00000021270	ENST00000379144.2:c.537T>C	chrX.hg19:g.24605386A>G		69.0	0.0		59.0	4.0	NM_004845	A8IX00|B2RCX8|B4DK10|E9PD84|O60621|Q86XC9	Silent	SNP	ENST00000379144.2	hg19	CCDS14213.1																																																																																			.	.		0.463	PCYT1B-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056103.1	NM_004845	
CASK	8573	hgsc.bcm.edu	37	X	41495868	41495868	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:41495868T>C	ENST00000378163.1	-	9	1352	c.878A>G	c.(877-879)gAg>gGg	p.E293G	CASK_ENST00000378166.4_Missense_Mutation_p.E293G|CASK_ENST00000442742.2_Missense_Mutation_p.E293G|CASK_ENST00000378158.1_Missense_Mutation_p.E293G|CASK_ENST00000421587.2_Missense_Mutation_p.E293G|RN7SL406P_ENST00000582021.1_RNA|CASK_ENST00000318588.9_Missense_Mutation_p.E293G|CASK_ENST00000378154.1_Missense_Mutation_p.E293G|CASK_ENST00000361962.4_Missense_Mutation_p.E293G			O14936	CSKP_HUMAN	calcium/calmodulin-dependent serine protein kinase (MAGUK family)	293					calcium ion import (GO:0070509)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cellular response to growth factor stimulus (GO:0090288)|negative regulation of keratinocyte proliferation (GO:0010839)|negative regulation of wound healing (GO:0061045)|nucleotide phosphorylation (GO:0046939)|positive regulation of calcium ion import (GO:0090280)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	actin cytoskeleton (GO:0015629)|basement membrane (GO:0005604)|basolateral plasma membrane (GO:0016323)|cell-cell junction (GO:0005911)|ciliary membrane (GO:0060170)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|nuclear lamina (GO:0005652)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	ATP binding (GO:0005524)|guanylate kinase activity (GO:0004385)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|endometrium(5)|kidney(1)|large_intestine(6)|liver(1)|lung(11)|ovary(3)|prostate(1)|stomach(1)	32						CCTCAGCTGCTCTACTGTTTC	0.338																																					p.E293G	NSCLC(42;104 1086 3090 27189 35040)	Atlas-SNP	.											.	CASK	93	.	0			c.A878G						.						192.0	163.0	173.0					X																	41495868		2203	4300	6503	SO:0001583	missense	8573	exon9			AGCTGCTCTACTG	AF035582	CCDS14257.1, CCDS48094.1, CCDS48095.1	Xp11.4	2010-02-09			ENSG00000147044	ENSG00000147044			1497	protein-coding gene	gene with protein product		300172	"""trinucleotide repeat containing 8"""	TNRC8		9722958	Standard	NM_003688		Approved	LIN2, CAGH39, FGS4	uc004dfl.4	O14936	OTTHUMG00000021378	ENST00000378163.1:c.878A>G	chrX.hg19:g.41495868T>C	ENSP00000367405:p.Glu293Gly	136.0	0.0		116.0	5.0	NM_001126054	A6NES1|B7ZKY0|O43215|Q17RI4|Q59HA0|Q5VT16|Q5VT17|Q5VT18|Q5VT19|Q66T42|Q9BYH6|Q9NYB2|Q9NYB3	Missense_Mutation	SNP	ENST00000378163.1	hg19		.	.	.	.	.	.	.	.	.	.	T	27.1	4.798453	0.90538	.	.	ENSG00000147044	ENST00000421587;ENST00000318588;ENST00000361962;ENST00000378163;ENST00000378158;ENST00000378166;ENST00000442742;ENST00000378154	T;T;T;T;T;T;T;T	0.70631	-0.48;-0.48;-0.48;-0.48;-0.48;-0.48;-0.47;-0.5	5.78	5.78	0.91487	Protein kinase-like domain (1);	0.000000	0.64402	D	0.000015	T	0.82029	0.4948	M	0.64997	1.995	0.80722	D	1	D;D;D;D	0.89917	1.0;0.964;0.993;0.993	D;P;P;P	0.81914	0.995;0.902;0.791;0.812	D	0.83803	0.0237	10	0.72032	D	0.01	.	14.9334	0.70935	0.0:0.0:0.0:1.0	.	293;293;293;293	O14936-3;O14936-4;O14936-2;O14936	.;.;.;CSKP_HUMAN	G	293	ENSP00000400526:E293G;ENSP00000322727:E293G;ENSP00000354641:E293G;ENSP00000367405:E293G;ENSP00000367400:E293G;ENSP00000367408:E293G;ENSP00000398007:E293G;ENSP00000367396:E293G	ENSP00000322727:E293G	E	-	2	0	CASK	41380812	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.294000	0.78760	2.056000	0.61249	0.441000	0.28932	GAG	.	.		0.338	CASK-007	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000056285.1	NM_003688	
CXorf36	79742	hgsc.bcm.edu	37	X	45051113	45051113	+	Silent	SNP	C	C	T			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:45051113C>T	ENST00000398000.2	-	2	455	c.381G>A	c.(379-381)agG>agA	p.R127R	RP11-342D14.1_ENST00000438181.1_RNA|RP11-342D14.1_ENST00000450527.1_RNA|CXorf36_ENST00000477281.1_5'UTR|CXorf36_ENST00000377934.4_Silent_p.R127R	NM_176819.3	NP_789789.2	Q9H7Y0	DIA1R_HUMAN	chromosome X open reading frame 36	127						extracellular region (GO:0005576)				endometrium(1)|large_intestine(2)|lung(4)	7						CACAGATTCTCCTGTCTGAGA	0.493																																					p.R127R		Atlas-SNP	.											.	CXorf36	53	.	0			c.G381A						.						89.0	84.0	86.0					X																	45051113		2203	4300	6503	SO:0001819	synonymous_variant	79742	exon2			GATTCTCCTGTCT	AF289581	CCDS14266.1, CCDS48096.1	Xp11.3-p11.23	2012-08-03			ENSG00000147113	ENSG00000147113			25866	protein-coding gene	gene with protein product						11944989, 21283809	Standard	NM_176819		Approved	FLJ14103, DIA1R	uc004dgg.2	Q9H7Y0	OTTHUMG00000021403	ENST00000398000.2:c.381G>A	chrX.hg19:g.45051113C>T		121.0	0.0		84.0	4.0	NM_176819	A8MUU5|B2RPN7|Q6UWJ5	Silent	SNP	ENST00000398000.2	hg19	CCDS48096.1																																																																																			.	.		0.493	CXorf36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056333.2	NM_024689	
JADE3	9767	hgsc.bcm.edu	37	X	46884293	46884293	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:46884293T>C	ENST00000218343.4	+	5	750	c.452T>C	c.(451-453)cTc>cCc	p.L151P	PHF16_ENST00000397189.1_Missense_Mutation_p.L151P	NM_014735.3	NP_055550.1														NS(2)|endometrium(8)|kidney(4)|large_intestine(5)|lung(12)|upper_aerodigestive_tract(2)	33						CTTCAGGAACTCAATGAAGAC	0.413																																					p.L151P		Atlas-SNP	.											.	PHF16	72	.	0			c.T452C						.						125.0	101.0	109.0					X																	46884293		2203	4300	6503	SO:0001583	missense	9767	exon5			AGGAACTCAATGA																												ENST00000218343.4:c.452T>C	chrX.hg19:g.46884293T>C	ENSP00000218343:p.Leu151Pro	92.0	0.0		67.0	4.0	NM_001077445		Missense_Mutation	SNP	ENST00000218343.4	hg19	CCDS14271.1	.	.	.	.	.	.	.	.	.	.	T	20.4	3.977923	0.74360	.	.	ENSG00000102221	ENST00000424392;ENST00000397189;ENST00000218343	T;T;T	0.49139	0.79;0.79;0.79	5.99	5.99	0.97316	Enhancer of polycomb-like, N-terminal (1);	0.341890	0.31156	N	0.008142	T	0.61689	0.2367	M	0.71581	2.175	0.80722	D	1	P	0.47762	0.9	P	0.56163	0.793	T	0.65697	-0.6105	10	0.72032	D	0.01	.	11.3736	0.49715	0.0:0.0:0.149:0.851	.	151	Q92613	JADE3_HUMAN	P	151	ENSP00000391009:L151P;ENSP00000380373:L151P;ENSP00000218343:L151P	ENSP00000218343:L151P	L	+	2	0	PHF16	46769237	1.000000	0.71417	0.995000	0.50966	0.988000	0.76386	3.809000	0.55606	2.014000	0.59158	0.486000	0.48141	CTC	.	.		0.413	PHF16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056376.1		
SYN1	6853	hgsc.bcm.edu	37	X	47466556	47466556	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:47466556T>C	ENST00000295987.7	-	2	543	c.419A>G	c.(418-420)gAc>gGc	p.D140G	SYN1_ENST00000340666.4_Missense_Mutation_p.D140G	NM_006950.3	NP_008881.2	P17600	SYN1_HUMAN	synapsin I	140	C; actin-binding and synaptic-vesicle binding.				neurotransmitter secretion (GO:0007269)|regulation of neurotransmitter secretion (GO:0046928)|regulation of synaptic vesicle exocytosis (GO:2000300)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytosol (GO:0005829)|dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|synaptic vesicle (GO:0008021)	ATP binding (GO:0005524)|catalytic activity (GO:0003824)|protein kinase binding (GO:0019901)|transporter activity (GO:0005215)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|large_intestine(6)|lung(6)|ovary(1)	21						TACTTTAATGTCAATTTCTCC	0.413																																					p.D140G		Atlas-SNP	.											.	SYN1	84	.	0			c.A419G						.						228.0	189.0	202.0					X																	47466556		2203	4300	6503	SO:0001583	missense	6853	exon2			TTAATGTCAATTT		CCDS14280.1, CCDS35233.1	Xp11.2	2012-10-02			ENSG00000008056	ENSG00000008056			11494	protein-coding gene	gene with protein product		313440					Standard	NM_133499		Approved		uc004die.3	P17600	OTTHUMG00000021454	ENST00000295987.7:c.419A>G	chrX.hg19:g.47466556T>C	ENSP00000295987:p.Asp140Gly	106.0	0.0		99.0	5.0	NM_006950	B1AJQ1|O75825|Q5H9A9	Missense_Mutation	SNP	ENST00000295987.7	hg19	CCDS14280.1	.	.	.	.	.	.	.	.	.	.	T	22.5	4.298744	0.81025	.	.	ENSG00000008056	ENST00000295987;ENST00000340666	T;T	0.36340	1.71;1.26	5.96	5.96	0.96718	Pre-ATP-grasp fold (1);PreATP-grasp-like fold (1);Synapsin, pre-ATP-grasp domain (1);	0.000000	0.85682	D	0.000000	T	0.57902	0.2085	M	0.69248	2.105	0.80722	D	1	D;D	0.76494	0.984;0.999	P;D	0.79108	0.866;0.992	T	0.61662	-0.7017	10	0.87932	D	0	-19.8199	13.1508	0.59488	0.0:0.0:0.0:1.0	.	140;140	P17600;P17600-2	SYN1_HUMAN;.	G	140	ENSP00000295987:D140G;ENSP00000343206:D140G	ENSP00000295987:D140G	D	-	2	0	SYN1	47351500	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.319000	0.65835	2.014000	0.59158	0.481000	0.45027	GAC	.	.		0.413	SYN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056445.1	NM_006950	
HDAC6	10013	hgsc.bcm.edu	37	X	48672876	48672876	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:48672876A>G	ENST00000334136.5	+	11	1014	c.836A>G	c.(835-837)gAg>gGg	p.E279G	HDAC6_ENST00000444343.2_Missense_Mutation_p.E293G|HDAC6_ENST00000413163.2_Missense_Mutation_p.E224G|HDAC6_ENST00000376619.2_Missense_Mutation_p.E279G			Q9UBN7	HDAC6_HUMAN	histone deacetylase 6	279	Histone deacetylase 1.				aggresome assembly (GO:0070842)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to misfolded protein (GO:0071218)|cellular response to topologically incorrect protein (GO:0035967)|histone deacetylation (GO:0016575)|Hsp90 deacetylation (GO:0070846)|intracellular protein transport (GO:0006886)|lysosome localization (GO:0032418)|macroautophagy (GO:0016236)|misfolded or incompletely synthesized protein catabolic process (GO:0006515)|negative regulation of hydrogen peroxide metabolic process (GO:0010727)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of oxidoreductase activity (GO:0051354)|negative regulation of protein complex disassembly (GO:0043242)|negative regulation of proteolysis (GO:0045861)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-lysine deacetylation (GO:0034983)|polyubiquitinated misfolded protein transport (GO:0070845)|positive regulation of chaperone-mediated protein complex assembly (GO:0090035)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of hydrogen peroxide-mediated programmed cell death (GO:1901300)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of signal transduction (GO:0009967)|protein complex disassembly (GO:0043241)|protein deacetylation (GO:0006476)|protein polyubiquitination (GO:0000209)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of establishment of protein localization (GO:0070201)|regulation of gene expression, epigenetic (GO:0040029)|regulation of microtubule-based movement (GO:0060632)|regulation of receptor activity (GO:0010469)|response to growth factor (GO:0070848)|response to misfolded protein (GO:0051788)|response to organic substance (GO:0010033)|response to toxic substance (GO:0009636)|transcription, DNA-templated (GO:0006351)|tubulin deacetylation (GO:0090042)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	aggresome (GO:0016235)|axon (GO:0030424)|caveola (GO:0005901)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|dendrite (GO:0030425)|histone deacetylase complex (GO:0000118)|inclusion body (GO:0016234)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)|perikaryon (GO:0043204)|perinuclear region of cytoplasm (GO:0048471)	alpha-tubulin binding (GO:0043014)|beta-catenin binding (GO:0008013)|core promoter binding (GO:0001047)|dynein complex binding (GO:0070840)|enzyme binding (GO:0019899)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|Hsp90 protein binding (GO:0051879)|microtubule binding (GO:0008017)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|polyubiquitin binding (GO:0031593)|tau protein binding (GO:0048156)|tubulin deacetylase activity (GO:0042903)|zinc ion binding (GO:0008270)			breast(2)|endometrium(6)|kidney(5)|large_intestine(8)|lung(9)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	40					Vorinostat(DB02546)	CACCGCTACGAGCAGGGTAGG	0.537																																					p.E279G	Pancreas(112;205 1675 2305 8976 15959)	Atlas-SNP	.											.	HDAC6	111	.	0			c.A836G						.						115.0	104.0	107.0					X																	48672876		2203	4300	6503	SO:0001583	missense	10013	exon11			GCTACGAGCAGGG	AF132609	CCDS14306.1	Xp11.23	2014-06-12			ENSG00000094631	ENSG00000094631			14064	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 90"""	300272				10220385, 10048485	Standard	NM_006044		Approved	KIAA0901, JM21, HD6, FLJ16239, PPP1R90	uc004dks.1	Q9UBN7	OTTHUMG00000034496	ENST00000334136.5:c.836A>G	chrX.hg19:g.48672876A>G	ENSP00000334061:p.Glu279Gly	64.0	0.0		55.0	4.0	NM_006044	O94975|Q6NT75|Q7L3E5|Q96CY0	Missense_Mutation	SNP	ENST00000334136.5	hg19	CCDS14306.1	.	.	.	.	.	.	.	.	.	.	A	17.65	3.441641	0.63067	.	.	ENSG00000094631	ENST00000444343;ENST00000334136;ENST00000376619;ENST00000436813;ENST00000413163	T;T;T;T	0.65364	-0.02;-0.01;-0.01;-0.15	5.05	5.05	0.67936	Histone deacetylase domain (2);	0.136762	0.46442	D	0.000293	T	0.75708	0.3886	M	0.66297	2.02	0.58432	D	0.999998	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.81914	0.99;0.995;0.99	T	0.78355	-0.2236	10	0.87932	D	0	-18.4327	11.7749	0.51981	1.0:0.0:0.0:0.0	.	269;224;279	B4DZN1;E7EUZ1;Q9UBN7	.;.;HDAC6_HUMAN	G	293;279;279;279;224	ENSP00000398566:E293G;ENSP00000334061:E279G;ENSP00000365804:E279G;ENSP00000398801:E224G	ENSP00000334061:E279G	E	+	2	0	HDAC6	48557820	1.000000	0.71417	0.978000	0.43139	0.282000	0.26991	5.552000	0.67281	1.682000	0.51000	0.430000	0.28490	GAG	.	.		0.537	HDAC6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083394.2	NM_006044	
HDAC6	10013	hgsc.bcm.edu	37	X	48675759	48675759	+	Silent	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:48675759T>C	ENST00000334136.5	+	20	1996	c.1818T>C	c.(1816-1818)cgT>cgC	p.R606R	HDAC6_ENST00000444343.2_Silent_p.R620R|HDAC6_ENST00000376619.2_Silent_p.R606R			Q9UBN7	HDAC6_HUMAN	histone deacetylase 6	606	Histone deacetylase 2.				aggresome assembly (GO:0070842)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to misfolded protein (GO:0071218)|cellular response to topologically incorrect protein (GO:0035967)|histone deacetylation (GO:0016575)|Hsp90 deacetylation (GO:0070846)|intracellular protein transport (GO:0006886)|lysosome localization (GO:0032418)|macroautophagy (GO:0016236)|misfolded or incompletely synthesized protein catabolic process (GO:0006515)|negative regulation of hydrogen peroxide metabolic process (GO:0010727)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of oxidoreductase activity (GO:0051354)|negative regulation of protein complex disassembly (GO:0043242)|negative regulation of proteolysis (GO:0045861)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-lysine deacetylation (GO:0034983)|polyubiquitinated misfolded protein transport (GO:0070845)|positive regulation of chaperone-mediated protein complex assembly (GO:0090035)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of hydrogen peroxide-mediated programmed cell death (GO:1901300)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of signal transduction (GO:0009967)|protein complex disassembly (GO:0043241)|protein deacetylation (GO:0006476)|protein polyubiquitination (GO:0000209)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of establishment of protein localization (GO:0070201)|regulation of gene expression, epigenetic (GO:0040029)|regulation of microtubule-based movement (GO:0060632)|regulation of receptor activity (GO:0010469)|response to growth factor (GO:0070848)|response to misfolded protein (GO:0051788)|response to organic substance (GO:0010033)|response to toxic substance (GO:0009636)|transcription, DNA-templated (GO:0006351)|tubulin deacetylation (GO:0090042)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	aggresome (GO:0016235)|axon (GO:0030424)|caveola (GO:0005901)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|dendrite (GO:0030425)|histone deacetylase complex (GO:0000118)|inclusion body (GO:0016234)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)|perikaryon (GO:0043204)|perinuclear region of cytoplasm (GO:0048471)	alpha-tubulin binding (GO:0043014)|beta-catenin binding (GO:0008013)|core promoter binding (GO:0001047)|dynein complex binding (GO:0070840)|enzyme binding (GO:0019899)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|Hsp90 protein binding (GO:0051879)|microtubule binding (GO:0008017)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|polyubiquitin binding (GO:0031593)|tau protein binding (GO:0048156)|tubulin deacetylase activity (GO:0042903)|zinc ion binding (GO:0008270)			breast(2)|endometrium(6)|kidney(5)|large_intestine(8)|lung(9)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	40					Vorinostat(DB02546)	CTGTGGTGCGTCCCCCAGGAC	0.527																																					p.R606R	Pancreas(112;205 1675 2305 8976 15959)	Atlas-SNP	.											.	HDAC6	111	.	0			c.T1818C						.						81.0	61.0	67.0					X																	48675759		2203	4300	6503	SO:0001819	synonymous_variant	10013	exon20			GGTGCGTCCCCCA	AF132609	CCDS14306.1	Xp11.23	2014-06-12			ENSG00000094631	ENSG00000094631			14064	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 90"""	300272				10220385, 10048485	Standard	NM_006044		Approved	KIAA0901, JM21, HD6, FLJ16239, PPP1R90	uc004dks.1	Q9UBN7	OTTHUMG00000034496	ENST00000334136.5:c.1818T>C	chrX.hg19:g.48675759T>C		108.0	0.0		103.0	5.0	NM_006044	O94975|Q6NT75|Q7L3E5|Q96CY0	Silent	SNP	ENST00000334136.5	hg19	CCDS14306.1																																																																																			.	.		0.527	HDAC6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083394.2	NM_006044	
PPP1R3F	89801	hgsc.bcm.edu	37	X	49138448	49138448	+	Silent	SNP	G	G	A			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:49138448G>A	ENST00000055335.6	+	3	1081	c.1065G>A	c.(1063-1065)gaG>gaA	p.E355E	PPP1R3F_ENST00000376188.1_Splice_Site_p.E9E|PPP1R3F_ENST00000438316.1_Splice_Site_p.E26E|PPP1R3F_ENST00000495799.1_Splice_Site_p.E9E|PPP1R3F_ENST00000466508.1_Splice_Site_p.E9E	NM_033215.4	NP_149992.3	Q6ZSY5	PPR3F_HUMAN	protein phosphatase 1, regulatory subunit 3F	355					regulation of glycogen (starch) synthase activity (GO:2000465)|regulation of glycogen biosynthetic process (GO:0005979)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	glycogen binding (GO:2001069)|protein phosphatase binding (GO:0019903)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|skin(4)	27	Ovarian(276;0.236)					CTCTAGCAGAGCATCCTGATG	0.527																																					p.E355E		Atlas-SNP	.											.	PPP1R3F	56	.	0			c.G1065A						.						136.0	96.0	109.0					X																	49138448		2203	4300	6503	SO:0001819	synonymous_variant	89801	exon3			AGCAGAGCATCCT		CCDS35254.1, CCDS55415.1	Xp11.23	2012-04-17	2011-10-04		ENSG00000049769	ENSG00000049769		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	14944	protein-coding gene	gene with protein product			"""protein phosphatase 1, regulatory (inhibitor) subunit 3F"""			11948623	Standard	NM_033215		Approved	Hb2E	uc004dnh.2	Q6ZSY5	OTTHUMG00000024139	ENST00000055335.6:c.1065G>A	chrX.hg19:g.49138448G>A		93.0	0.0		71.0	4.0	NM_033215	A2VDJ8|B3KPW2|E9PCM3	Silent	SNP	ENST00000055335.6	hg19	CCDS35254.1	.	.	.	.	.	.	.	.	.	.	G	2.675	-0.276732	0.05679	.	.	ENSG00000049769	ENST00000471261	.	.	.	3.81	-5.82	0.02333	.	.	.	.	.	T	0.19604	0.0471	.	.	.	0.21553	N	0.999645	.	.	.	.	.	.	T	0.17992	-1.0351	4	.	.	.	-0.0275	4.3718	0.11251	0.3969:0.0:0.2789:0.3242	.	.	.	.	N	105	.	.	S	+	2	0	PPP1R3F	49025392	0.000000	0.05858	0.000000	0.03702	0.241000	0.25554	-1.873000	0.01637	-2.363000	0.00608	-1.225000	0.01585	AGC	.	.		0.527	PPP1R3F-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060819.2	NM_033215	
HUWE1	10075	hgsc.bcm.edu	37	X	53630379	53630379	+	Silent	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:53630379A>G	ENST00000342160.3	-	26	3283	c.2826T>C	c.(2824-2826)tgT>tgC	p.C942C	HUWE1_ENST00000218328.8_Silent_p.C942C|HUWE1_ENST00000262854.6_Silent_p.C942C			Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1, E3 ubiquitin protein ligase	942					base-excision repair (GO:0006284)|cell differentiation (GO:0030154)|histone ubiquitination (GO:0016574)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(15)|central_nervous_system(1)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|liver(2)|lung(52)|ovary(11)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	153						ACACCAGGGAACAGTATAACT	0.458																																					p.C942C		Atlas-SNP	.											.	HUWE1	724	.	0			c.T2826C						.						106.0	82.0	90.0					X																	53630379		2203	4300	6503	SO:0001819	synonymous_variant	10075	exon27			CAGGGAACAGTAT	AB071605	CCDS35301.1	Xp11.22	2014-06-09	2012-02-23		ENSG00000086758	ENSG00000086758			30892	protein-coding gene	gene with protein product		300697	"""HECT, UBA and WWE domain containing 1"""			9205841, 10998601	Standard	NM_031407		Approved	Ib772, KIAA0312, UREB1	uc004dsp.4	Q7Z6Z7	OTTHUMG00000021617	ENST00000342160.3:c.2826T>C	chrX.hg19:g.53630379A>G		125.0	0.0		94.0	4.0	NM_031407	O15029|Q4G2Z2|Q5H961|Q6P4D0|Q8NG67|Q9BUI0|Q9HCJ4|Q9NSL6|Q9P0A9	Silent	SNP	ENST00000342160.3	hg19	CCDS35301.1																																																																																			.	.		0.458	HUWE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056766.1	XM_497119	
DGAT2L6	347516	hgsc.bcm.edu	37	X	69424364	69424364	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:69424364T>C	ENST00000333026.3	+	6	957	c.857T>C	c.(856-858)gTt>gCt	p.V286A		NM_198512.1	NP_940914.1	Q6ZPD8	DG2L6_HUMAN	diacylglycerol O-acyltransferase 2-like 6	286					lipid metabolic process (GO:0006629)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	transferase activity, transferring acyl groups other than amino-acyl groups (GO:0016747)			breast(1)|endometrium(2)|large_intestine(3)|lung(5)|ovary(1)	12						ATTACCACTGTTGGTGAGCTT	0.502																																					p.V286A		Atlas-SNP	.											.	DGAT2L6	40	.	0			c.T857C						.						68.0	63.0	65.0					X																	69424364		2203	4300	6503	SO:0001583	missense	347516	exon6			CCACTGTTGGTGA	AK129500	CCDS14397.1	Xq13.1	2008-02-05			ENSG00000184210	ENSG00000184210			23250	protein-coding gene	gene with protein product		300926				15671038	Standard	NM_198512		Approved	DC3, FLJ25989	uc004dxx.1	Q6ZPD8	OTTHUMG00000021774	ENST00000333026.3:c.857T>C	chrX.hg19:g.69424364T>C	ENSP00000328036:p.Val286Ala	134.0	0.0		83.0	4.0	NM_198512	Q6IEE2	Missense_Mutation	SNP	ENST00000333026.3	hg19	CCDS14397.1	.	.	.	.	.	.	.	.	.	.	T	24.9	4.580714	0.86748	.	.	ENSG00000184210	ENST00000333026	T	0.25579	1.79	4.98	4.98	0.66077	.	0.000000	0.64402	D	0.000009	T	0.53997	0.1831	M	0.88842	2.985	0.58432	D	0.999992	D	0.71674	0.998	D	0.67382	0.951	T	0.62877	-0.6761	10	0.87932	D	0	-7.6613	11.5384	0.50653	0.0:0.0:0.0:1.0	.	286	Q6ZPD8	DG2L6_HUMAN	A	286	ENSP00000328036:V286A	ENSP00000328036:V286A	V	+	2	0	DGAT2L6	69341089	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	7.102000	0.77005	1.852000	0.53769	0.486000	0.48141	GTT	.	.		0.502	DGAT2L6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057067.1	NM_198512	
TEX11	56159	hgsc.bcm.edu	37	X	70072999	70072999	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:70072999A>G	ENST00000395889.2	-	8	610	c.455T>C	c.(454-456)cTg>cCg	p.L152P	TEX11_ENST00000374333.2_Missense_Mutation_p.L137P|TEX11_ENST00000344304.3_Missense_Mutation_p.L152P	NM_001003811.1	NP_001003811.1	Q8IYF3	TEX11_HUMAN	testis expressed 11	152					chiasma assembly (GO:0051026)|fertilization (GO:0009566)|male gonad development (GO:0008584)|male meiosis chromosome segregation (GO:0007060)|meiotic gene conversion (GO:0006311)|negative regulation of apoptotic process (GO:0043066)|reciprocal meiotic recombination (GO:0007131)|resolution of meiotic recombination intermediates (GO:0000712)|synaptonemal complex assembly (GO:0007130)	central element (GO:0000801)				breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(12)|lung(13)|ovary(3)|prostate(3)|skin(3)	48	Renal(35;0.156)					TAATTGCTCCAGACTCTGGAA	0.398																																					p.L152P		Atlas-SNP	.											.	TEX11	132	.	0			c.T455C						.						72.0	60.0	64.0					X																	70072999		2203	4300	6503	SO:0001583	missense	56159	exon8			TGCTCCAGACTCT	AF285594	CCDS35323.1, CCDS43968.1	Xp11	2008-02-05	2007-03-13		ENSG00000120498	ENSG00000120498			11733	protein-coding gene	gene with protein product		300311	"""testis expressed sequence 11"""			11279525	Standard	NM_001003811		Approved	TSGA3, TGC1	uc004dyl.3	Q8IYF3	OTTHUMG00000021782	ENST00000395889.2:c.455T>C	chrX.hg19:g.70072999A>G	ENSP00000379226:p.Leu152Pro	98.0	0.0		62.0	4.0	NM_001003811	A8K8V6|Q5JQQ8|Q96LZ4|Q96M47|Q9BXU6	Missense_Mutation	SNP	ENST00000395889.2	hg19	CCDS35323.1	.	.	.	.	.	.	.	.	.	.	A	12.05	1.822596	0.32237	.	.	ENSG00000120498	ENST00000374333;ENST00000395889;ENST00000344304	T;T;T	0.39056	1.1;1.12;1.12	4.56	4.56	0.56223	Tetratricopeptide-like helical (1);	0.197085	0.33980	N	0.004373	T	0.55049	0.1896	L	0.49778	1.585	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.79108	0.992;0.982	T	0.53215	-0.8470	9	.	.	.	-3.7026	11.0541	0.47907	1.0:0.0:0.0:0.0	.	137;152	Q8IYF3-3;Q8IYF3	.;TEX11_HUMAN	P	137;152;152	ENSP00000363453:L137P;ENSP00000379226:L152P;ENSP00000340995:L152P	.	L	-	2	0	TEX11	69989724	1.000000	0.71417	0.937000	0.37676	0.044000	0.14063	4.476000	0.60216	1.810000	0.52873	0.432000	0.28606	CTG	.	.		0.398	TEX11-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359072.1		
OGT	8473	hgsc.bcm.edu	37	X	70775862	70775862	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:70775862A>G	ENST00000373719.3	+	8	1200	c.983A>G	c.(982-984)gAc>gGc	p.D328G	OGT_ENST00000373701.3_Missense_Mutation_p.D318G	NM_181672.2|NM_181673.2	NP_858058.1|NP_858059.1	O15294	OGT1_HUMAN	O-linked N-acetylglucosamine (GlcNAc) transferase	328					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)					ACCCATGCAGACTCTCTGAAT	0.408																																					p.D328G		Atlas-SNP	.											.	OGT	207	.	0			c.A983G						.						155.0	128.0	137.0					X																	70775862		2203	4300	6503	SO:0001583	missense	8473	exon8			ATGCAGACTCTCT	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.983A>G	chrX.hg19:g.70775862A>G	ENSP00000362824:p.Asp328Gly	162.0	0.0		119.0	5.0	NM_181672	Q7Z3K0|Q8WWM8|Q96CC1|Q9UG57	Missense_Mutation	SNP	ENST00000373719.3	hg19	CCDS14414.1	.	.	.	.	.	.	.	.	.	.	A	26.6	4.756306	0.89843	.	.	ENSG00000147162	ENST00000373719;ENST00000373701	T;T	0.60299	0.2;0.2	5.16	5.16	0.70880	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.000000	0.85682	D	0.000000	T	0.77103	0.4081	M	0.83312	2.635	0.80722	D	1	D;D;D	0.71674	0.997;0.998;0.99	D;D;D	0.87578	0.998;0.996;0.993	T	0.80115	-0.1517	10	0.54805	T	0.06	-16.8643	14.1095	0.65113	1.0:0.0:0.0:0.0	.	202;318;328	Q548W1;O15294-3;O15294	.;.;OGT1_HUMAN	G	328;318	ENSP00000362824:D328G;ENSP00000362805:D318G	ENSP00000362805:D318G	D	+	2	0	OGT	70692587	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.081000	0.94049	1.907000	0.55213	0.486000	0.48141	GAC	.	.		0.408	OGT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000081829.3	NM_003605, NM_181672	
NHSL2	340527	hgsc.bcm.edu	37	X	71359404	71359404	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:71359404T>C	ENST00000373677.1	+	2	2170	c.908T>C	c.(907-909)gTt>gCt	p.V303A	NHSL2_ENST00000535692.1_Missense_Mutation_p.V303A|NHSL2_ENST00000540800.1_Missense_Mutation_p.V669A|NHSL2_ENST00000510661.1_Missense_Mutation_p.V438A			Q5HYW2	NHSL2_HUMAN	NHS-like 2	303	Ser-rich.									NS(1)|breast(3)|endometrium(4)|kidney(2)|large_intestine(10)|lung(7)|stomach(1)	28	Renal(35;0.156)					TGCACCCAAGTTCAGGGCAGC	0.557																																					p.V669A		Atlas-SNP	.											.	NHSL2	148	.	0			c.T2006C						.						74.0	58.0	63.0					X																	71359404		2203	4300	6503	SO:0001583	missense	340527	exon6			CCCAAGTTCAGGG			Xq13.1	2009-02-18			ENSG00000204131	ENSG00000204131			33737	protein-coding gene	gene with protein product							Standard	NM_001013627		Approved		uc011mqa.2	Q5HYW2	OTTHUMG00000021807	ENST00000373677.1:c.908T>C	chrX.hg19:g.71359404T>C	ENSP00000362781:p.Val303Ala	159.0	0.0		136.0	6.0	NM_001013627	B2RN94	Missense_Mutation	SNP	ENST00000373677.1	hg19		.	.	.	.	.	.	.	.	.	.	T	2.270	-0.367112	0.05069	.	.	ENSG00000204131	ENST00000540800;ENST00000373677;ENST00000510661;ENST00000535692	T;T;T;T	0.49139	1.44;0.86;0.79;0.86	5.77	3.39	0.38822	.	0.068183	0.64402	D	0.000018	T	0.31451	0.0797	L	0.45581	1.43	0.40595	D	0.981525	B;B;B	0.25809	0.126;0.135;0.041	B;B;B	0.20767	0.031;0.031;0.019	T	0.08207	-1.0733	10	0.12766	T	0.61	-8.9314	3.6473	0.08189	0.0:0.1771:0.1944:0.6285	.	669;438;303	F5H593;D6RBM4;Q5HYW2	.;.;NHSL2_HUMAN	A	669;303;438;303	ENSP00000444617:V669A;ENSP00000362781:V303A;ENSP00000424079:V438A;ENSP00000444914:V303A	ENSP00000362781:V303A	V	+	2	0	NHSL2	71276129	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	2.238000	0.43070	0.800000	0.34041	-0.354000	0.07668	GTT	.	.		0.557	NHSL2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000057170.1	NM_001013627	
KIAA2022	340533	hgsc.bcm.edu	37	X	73960376	73960376	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:73960376T>C	ENST00000055682.6	-	3	4627	c.4016A>G	c.(4015-4017)gAg>gGg	p.E1339G		NM_001008537.2	NP_001008537.1	Q5QGS0	K2022_HUMAN	KIAA2022	1339					base-excision repair, gap-filling (GO:0006287)|DNA replication proofreading (GO:0045004)|DNA replication, removal of RNA primer (GO:0043137)|nervous system development (GO:0007399)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleotide-excision repair, DNA gap filling (GO:0006297)|regulation of mitotic cell cycle (GO:0007346)	delta DNA polymerase complex (GO:0043625)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|DNA-directed DNA polymerase activity (GO:0003887)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(23)|liver(1)|lung(41)|ovary(7)|pancreas(2)|prostate(4)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(3)	109						CCAAAGGGGCTCTATGGAGGC	0.473																																					p.E1339G		Atlas-SNP	.											.	KIAA2022	262	.	0			c.A4016G						.						76.0	72.0	74.0					X																	73960376		2203	4300	6503	SO:0001583	missense	340533	exon3			AGGGGCTCTATGG		CCDS35337.1	Xq13.3	2014-02-19			ENSG00000050030	ENSG00000050030			29433	protein-coding gene	gene with protein product	"""XLMR-related protein, neurite extension"""	300524				15466006, 23615299	Standard	NM_001008537		Approved	XPN, MRX98	uc004eby.3	Q5QGS0	OTTHUMG00000021860	ENST00000055682.6:c.4016A>G	chrX.hg19:g.73960376T>C	ENSP00000055682:p.Glu1339Gly	144.0	0.0		113.0	5.0	NM_001008537	A7YY87|Q5JUX9|Q8IVE9	Missense_Mutation	SNP	ENST00000055682.6	hg19	CCDS35337.1	.	.	.	.	.	.	.	.	.	.	T	17.84	3.487508	0.63962	.	.	ENSG00000050030	ENST00000373468;ENST00000055682	T;T	0.33654	1.4;1.4	5.55	5.55	0.83447	.	0.206474	0.50627	D	0.000112	T	0.49898	0.1584	L	0.34521	1.04	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.53151	-0.8479	10	0.87932	D	0	-15.4889	14.7048	0.69183	0.0:0.0:0.0:1.0	.	1339	Q5QGS0	K2022_HUMAN	G	1339	ENSP00000362567:E1339G;ENSP00000055682:E1339G	ENSP00000055682:E1339G	E	-	2	0	KIAA2022	73877101	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.698000	0.84413	1.853000	0.53794	0.441000	0.28932	GAG	.	.		0.473	KIAA2022-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057270.2	NM_001008537	
SH3BGRL	6451	hgsc.bcm.edu	37	X	80532637	80532637	+	Missense_Mutation	SNP	C	C	T			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:80532637C>T	ENST00000373212.5	+	2	458	c.200C>T	c.(199-201)cCt>cTt	p.P67L	SH3BGRL_ENST00000481106.1_3'UTR	NM_003022.2	NP_003013.1	O75368	SH3L1_HUMAN	SH3 domain binding glutamate-rich protein like	67					positive regulation of signal transduction (GO:0009967)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	SH3/SH2 adaptor activity (GO:0005070)			endometrium(1)|lung(2)|ovary(1)	4		all_lung(315;5.94e-05)				CCCCTGCCACCTCAGATTTTC	0.388																																					p.P67L		Atlas-SNP	.											.	SH3BGRL	23	.	0			c.C200T						.						58.0	54.0	55.0					X																	80532637		2203	4300	6503	SO:0001583	missense	6451	exon2			TGCCACCTCAGAT	AF042081	CCDS14449.1	Xq13.3	2014-02-19	2014-02-19		ENSG00000131171	ENSG00000131171			10823	protein-coding gene	gene with protein product		300190	"""SH3 domain binding glutamic acid-rich protein like"""			9642120	Standard	NM_003022		Approved	MGC117402	uc004eef.3	O75368	OTTHUMG00000021910	ENST00000373212.5:c.200C>T	chrX.hg19:g.80532637C>T	ENSP00000362308:p.Pro67Leu	141.0	0.0		92.0	4.0	NM_003022	Q3SYL1|Q5JT50|Q6FIE8|Q9H0N8	Missense_Mutation	SNP	ENST00000373212.5	hg19	CCDS14449.1	.	.	.	.	.	.	.	.	.	.	C	25.4	4.634414	0.87660	.	.	ENSG00000131171	ENST00000373212	D	0.96265	-3.96	5.7	5.7	0.88788	Thioredoxin-like fold (2);	0.000000	0.85682	D	0.000000	D	0.98654	0.9549	M	0.93638	3.44	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;1.0	D	0.99734	1.1013	10	0.87932	D	0	-4.2429	17.6307	0.88106	0.0:1.0:0.0:0.0	.	19;66;67	B0AZV6;D3DTE6;O75368	.;.;SH3L1_HUMAN	L	67	ENSP00000362308:P67L	ENSP00000362308:P67L	P	+	2	0	SH3BGRL	80419293	1.000000	0.71417	1.000000	0.80357	0.744000	0.42396	7.182000	0.77689	2.380000	0.81148	0.600000	0.82982	CCT	.	.		0.388	SH3BGRL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057350.1	NM_003022	
TCEAL6	158931	hgsc.bcm.edu	37	X	101395774	101395774	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:101395774T>C	ENST00000372774.3	-	3	779	c.530A>G	c.(529-531)gAc>gGc	p.D177G	TCEAL6_ENST00000372773.1_Missense_Mutation_p.D177G	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						CACCCCGTTGTCCCCTTGGGC	0.507																																					p.D177G		Atlas-SNP	.											.	TCEAL6	27	.	0			c.A530G						.						19.0	18.0	19.0					X																	101395774		2197	4274	6471	SO:0001583	missense	158931	exon3			CCGTTGTCCCCTT	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.530A>G	chrX.hg19:g.101395774T>C	ENSP00000361860:p.Asp177Gly	108.0	0.0		170.0	12.0	NM_001006938	Q5H9J8	Missense_Mutation	SNP	ENST00000372774.3	hg19	CCDS43978.1	.	.	.	.	.	.	.	.	.	.	A	0.755	-0.771235	0.02951	.	.	ENSG00000204071	ENST00000372774;ENST00000372773	T;T	0.23147	1.92;1.92	2.82	-3.23	0.05109	.	0.272209	0.20313	N	0.094788	T	0.11836	0.0288	N	0.24115	0.695	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.08186	-1.0734	10	0.48119	T	0.1	.	3.3698	0.07216	0.1211:0.4969:0.222:0.1599	.	177	Q6IPX3-2	.	G	177	ENSP00000361860:D177G;ENSP00000361859:D177G	ENSP00000361859:D177G	D	-	2	0	TCEAL6	101282430	0.001000	0.12720	0.010000	0.14722	0.828000	0.46876	-1.039000	0.03550	-1.000000	0.03438	-0.742000	0.03525	GAC	.	.		0.507	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-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	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	108.0	0.0		164.0	23.0	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	
GPRASP2	114928	hgsc.bcm.edu	37	X	101971961	101971961	+	Missense_Mutation	SNP	G	G	A			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:101971961G>A	ENST00000535209.1	+	4	2995	c.2164G>A	c.(2164-2166)Ggg>Agg	p.G722R	GPRASP2_ENST00000543253.1_Missense_Mutation_p.G722R|GPRASP2_ENST00000332262.5_Missense_Mutation_p.G722R			Q96D09	GASP2_HUMAN	G protein-coupled receptor associated sorting protein 2	722						cytoplasm (GO:0005737)	beta-amyloid binding (GO:0001540)			breast(3)|endometrium(5)|kidney(2)|large_intestine(6)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)	30						CTATATGTCCGGGTTTCTCTC	0.413																																					p.G722R		Atlas-SNP	.											.	GPRASP2	89	.	0			c.G2164A						.						103.0	93.0	97.0					X																	101971961		2203	4300	6503	SO:0001583	missense	114928	exon4			ATGTCCGGGTTTC	AK094646	CCDS14501.1	Xq22.1	2014-03-21			ENSG00000158301	ENSG00000158301		"""Armadillo repeat containing"""	25169	protein-coding gene	gene with protein product						15086532, 16221301	Standard	NM_138437		Approved	GASP2, FLJ37327		Q96D09	OTTHUMG00000022059	ENST00000535209.1:c.2164G>A	chrX.hg19:g.101971961G>A	ENSP00000437394:p.Gly722Arg	215.0	0.0		167.0	138.0	NM_138437	D3DXA0|Q8NAB4	Missense_Mutation	SNP	ENST00000535209.1	hg19	CCDS14501.1	.	.	.	.	.	.	.	.	.	.	G	11.37	1.619652	0.28801	.	.	ENSG00000158301	ENST00000543253;ENST00000535209;ENST00000332262	T;T;T	0.28666	1.6;1.6;1.6	4.31	4.31	0.51392	Armadillo-like helical (1);Armadillo-type fold (1);	0.150817	0.31279	N	0.007934	T	0.49541	0.1563	M	0.69823	2.125	0.24777	N	0.992834	D	0.89917	1.0	D	0.73708	0.981	T	0.35051	-0.9804	10	0.28530	T	0.3	.	11.1272	0.48325	0.0:0.0:1.0:0.0	.	722	Q96D09	GASP2_HUMAN	R	722	ENSP00000437872:G722R;ENSP00000437394:G722R;ENSP00000339057:G722R	ENSP00000339057:G722R	G	+	1	0	GPRASP2	101858617	0.940000	0.31905	0.596000	0.28811	0.313000	0.28021	3.680000	0.54641	2.394000	0.81467	0.513000	0.50165	GGG	.	.		0.413	GPRASP2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057626.2	NM_138437	
NUP62CL	54830	hgsc.bcm.edu	37	X	106396417	106396417	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:106396417T>C	ENST00000372466.4	-	7	766	c.515A>G	c.(514-516)gAg>gGg	p.E172G	NUP62CL_ENST00000372461.3_3'UTR	NM_017681.2	NP_060151.2	Q9H1M0	N62CL_HUMAN	nucleoporin 62kDa C-terminal like	172					protein transport (GO:0015031)	nuclear pore (GO:0005643)	structural constituent of nuclear pore (GO:0017056)			lung(4)	4						CACATGCTCCTCATCTGCATC	0.433																																					p.E172G		Atlas-SNP	.											.	NUP62CL	10	.	0			c.A515G						.						188.0	204.0	198.0					X																	106396417		2203	4300	6503	SO:0001583	missense	54830	exon7			TGCTCCTCATCTG	AK000137	CCDS14527.1	Xq22.3	2008-02-05			ENSG00000198088	ENSG00000198088			25960	protein-coding gene	gene with protein product						12477932	Standard	NM_017681		Approved	FLJ20130	uc004ena.3	Q9H1M0	OTTHUMG00000022159	ENST00000372466.4:c.515A>G	chrX.hg19:g.106396417T>C	ENSP00000361544:p.Glu172Gly	202.0	0.0		139.0	6.0	NM_017681	D3DUX4|Q8WVL6|Q9NXP2	Missense_Mutation	SNP	ENST00000372466.4	hg19	CCDS14527.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	13.76|13.76	2.332145|2.332145	0.41297|0.41297	.|.	.|.	ENSG00000198088|ENSG00000198088	ENST00000372466;ENST00000372465|ENST00000432145	T|.	0.78126|.	-1.15|.	5.44|5.44	1.48|1.48	0.22813|0.22813	Nucleoporin, NSP1-like, C-terminal (2);|.	0.287377|.	0.38778|.	N|.	0.001567|.	T|.	0.58380|.	0.2118|.	M|M	0.63428|0.63428	1.95|1.95	0.80722|0.80722	D|D	1|1	P|.	0.41188|.	0.741|.	P|.	0.53809|.	0.735|.	T|.	0.49844|.	-0.8896|.	10|.	0.33141|.	T|.	0.24|.	-0.0266|-0.0266	6.5555|6.5555	0.22458|0.22458	0.1472:0.0:0.3004:0.5524|0.1472:0.0:0.3004:0.5524	.|.	172|.	Q9H1M0|.	N62CL_HUMAN|.	G|W	172|103	ENSP00000361544:E172G|.	ENSP00000361543:E172G|.	E|X	-|-	2|3	0|0	NUP62CL|NUP62CL	106283073|106283073	1.000000|1.000000	0.71417|0.71417	0.001000|0.001000	0.08648|0.08648	0.195000|0.195000	0.23768|0.23768	3.221000|3.221000	0.51215|0.51215	-0.079000|-0.079000	0.12707|0.12707	-0.761000|-0.761000	0.03458|0.03458	GAG|TGA	.	.		0.433	NUP62CL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057828.1	NM_017681	
NUP62CL	54830	hgsc.bcm.edu	37	X	106410964	106410964	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:106410964T>C	ENST00000372466.4	-	4	360	c.109A>G	c.(109-111)Aca>Gca	p.T37A	NUP62CL_ENST00000372461.3_Missense_Mutation_p.T37A	NM_017681.2	NP_060151.2	Q9H1M0	N62CL_HUMAN	nucleoporin 62kDa C-terminal like	37	Thr-rich.				protein transport (GO:0015031)	nuclear pore (GO:0005643)	structural constituent of nuclear pore (GO:0017056)			lung(4)	4						Ctggtgattgtggtagtagtg	0.363																																					p.T37A		Atlas-SNP	.											.	NUP62CL	10	.	0			c.A109G						.						251.0	213.0	226.0					X																	106410964		2203	4300	6503	SO:0001583	missense	54830	exon4			TGATTGTGGTAGT	AK000137	CCDS14527.1	Xq22.3	2008-02-05			ENSG00000198088	ENSG00000198088			25960	protein-coding gene	gene with protein product						12477932	Standard	NM_017681		Approved	FLJ20130	uc004ena.3	Q9H1M0	OTTHUMG00000022159	ENST00000372466.4:c.109A>G	chrX.hg19:g.106410964T>C	ENSP00000361544:p.Thr37Ala	142.0	0.0		96.0	4.0	NM_017681	D3DUX4|Q8WVL6|Q9NXP2	Missense_Mutation	SNP	ENST00000372466.4	hg19	CCDS14527.1	.	.	.	.	.	.	.	.	.	.	T	2.105	-0.405143	0.04832	.	.	ENSG00000198088	ENST00000372466;ENST00000372465;ENST00000372461;ENST00000421752	T;T;T	0.59083	0.9;0.29;0.49	3.84	3.84	0.44239	Nucleoporin, NSP1-like, C-terminal (1);	0.756327	0.12760	N	0.441437	T	0.50803	0.1637	N	0.24115	0.695	0.09310	N	1	P	0.52842	0.956	P	0.50659	0.647	T	0.39522	-0.9610	10	0.87932	D	0	-0.9739	8.1143	0.30933	0.0:0.0:0.0:1.0	.	37	Q9H1M0	N62CL_HUMAN	A	37	ENSP00000361544:T37A;ENSP00000361539:T37A;ENSP00000405906:T37A	ENSP00000361539:T37A	T	-	1	0	NUP62CL	106297620	0.760000	0.28428	0.059000	0.19551	0.429000	0.31625	2.945000	0.49043	1.732000	0.51606	0.486000	0.48141	ACA	.	.		0.363	NUP62CL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057828.1	NM_017681	
CAPN6	827	hgsc.bcm.edu	37	X	110496327	110496327	+	Silent	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:110496327A>G	ENST00000324068.1	-	4	582	c.415T>C	c.(415-417)Ttg>Ctg	p.L139L	CAPN6_ENST00000541758.1_5'UTR	NM_014289.3	NP_055104.2	Q9Y6Q1	CAN6_HUMAN	calpain 6	139	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.				microtubule bundle formation (GO:0001578)|proteolysis (GO:0006508)|regulation of cytoskeleton organization (GO:0051493)	perinuclear region of cytoplasm (GO:0048471)|spindle microtubule (GO:0005876)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|microtubule binding (GO:0008017)			cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(25)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)	47						GTGGGCAACAAGTCATCAATC	0.428																																					p.L139L		Atlas-SNP	.											.	CAPN6	120	.	0			c.T415C						.						155.0	131.0	139.0					X																	110496327		2203	4300	6503	SO:0001819	synonymous_variant	827	exon4			GCAACAAGTCATC	AF029232	CCDS14555.1	Xq23	2008-07-29			ENSG00000077274	ENSG00000077274			1483	protein-coding gene	gene with protein product		300146				9503024, 9339374	Standard	NM_014289		Approved	CAPNX, CalpM, CANPX	uc004epc.2	Q9Y6Q1	OTTHUMG00000022203	ENST00000324068.1:c.415T>C	chrX.hg19:g.110496327A>G		111.0	0.0		86.0	4.0	NM_014289	D3DUY7|Q9UEQ1|Q9UJA8	Silent	SNP	ENST00000324068.1	hg19	CCDS14555.1																																																																																			.	.		0.428	CAPN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057922.1		
KIAA1210	57481	hgsc.bcm.edu	37	X	118221022	118221022	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:118221022T>C	ENST00000402510.2	-	11	4170	c.4171A>G	c.(4171-4173)Agc>Ggc	p.S1391G		NM_020721.1	NP_065772.1	Q9ULL0	K1210_HUMAN	KIAA1210	1391										breast(3)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(31)|ovary(4)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	64						TCAGAATTGCTCTCAAAAACA	0.453																																					p.S1391G		Atlas-SNP	.											.	KIAA1210	171	.	0			c.A4171G						.						126.0	122.0	124.0					X																	118221022		1908	4113	6021	SO:0001583	missense	57481	exon11			AATTGCTCTCAAA	AB033036	CCDS48156.1	Xq24	2012-10-04			ENSG00000250423	ENSG00000250423			29218	protein-coding gene	gene with protein product						10574462	Standard	NM_020721		Approved		uc004era.4	Q9ULL0	OTTHUMG00000162980	ENST00000402510.2:c.4171A>G	chrX.hg19:g.118221022T>C	ENSP00000384670:p.Ser1391Gly	79.0	0.0		71.0	4.0	NM_020721	B7ZCI8|Q5JPN4	Missense_Mutation	SNP	ENST00000402510.2	hg19	CCDS48156.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	6.643|6.643	0.487077|0.487077	0.12641|0.12641	.|.	.|.	ENSG00000248857|ENSG00000250423	ENST00000440399|ENST00000402510	.|T	.|0.10763	.|2.84	4.18|4.18	-1.1|-1.1	0.09872|0.09872	.|.	.|.	.|.	.|.	.|.	T|T	0.05227|0.05227	0.0139|0.0139	N|N	0.12182|0.12182	0.205|0.205	0.09310|0.09310	N|N	1|1	.|B	.|0.11235	.|0.004	.|B	.|0.11329	.|0.006	T|T	0.45644|0.45644	-0.9247|-0.9247	6|8	0.62326|.	D|.	0.03|.	.|.	7.3501|7.3501	0.26686|0.26686	0.0:0.4538:0.0:0.5462|0.0:0.4538:0.0:0.5462	.|.	.|1391	.|Q9ULL0	.|K1210_HUMAN	G|G	797|1391	.|ENSP00000384670:S1391G	ENSP00000393550:E797G|.	E|S	-|-	2|1	0|0	KIAA1210|RP13-347D8.6	118105050|118105050	0.001000|0.001000	0.12720|0.12720	0.001000|0.001000	0.08648|0.08648	0.008000|0.008000	0.06430|0.06430	-0.225000|-0.225000	0.09151|0.09151	-0.307000|-0.307000	0.08804|0.08804	0.417000|0.417000	0.27973|0.27973	GAG|AGC	.	.		0.453	KIAA1210-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371251.2	NM_020721	
STAG2	10735	hgsc.bcm.edu	37	X	123195126	123195126	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:123195126A>G	ENST00000371160.1	+	16	1759	c.1469A>G	c.(1468-1470)gAg>gGg	p.E490G	STAG2_ENST00000354548.5_Missense_Mutation_p.E421G|STAG2_ENST00000469481.1_Intron|STAG2_ENST00000218089.9_Missense_Mutation_p.E490G|STAG2_ENST00000371157.3_Missense_Mutation_p.E490G|STAG2_ENST00000371144.3_Missense_Mutation_p.E490G|STAG2_ENST00000371145.3_Missense_Mutation_p.E490G	NM_001282418.1	NP_001269347.1	Q8N3U4	STAG2_HUMAN	stromal antigen 2	490					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						TGTGCTACTGAGCTGCTGAAA	0.383																																					p.E490G		Atlas-SNP	.											.	STAG2	309	.	0			c.A1469G						.						205.0	174.0	185.0					X																	123195126		2203	4300	6503	SO:0001583	missense	10735	exon16			CTACTGAGCTGCT	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.1469A>G	chrX.hg19:g.123195126A>G	ENSP00000360202:p.Glu490Gly	114.0	0.0		87.0	5.0	NM_001042749	B1AMT5|D3DTF5|O00540|Q5JTI6|Q68DE9|Q9H1N8	Missense_Mutation	SNP	ENST00000371160.1	hg19	CCDS14607.1	.	.	.	.	.	.	.	.	.	.	A	17.57	3.423389	0.62733	.	.	ENSG00000101972	ENST00000218089;ENST00000455404;ENST00000354548;ENST00000371160;ENST00000371157;ENST00000371145;ENST00000371144	T;T;T;T;T;T;T	0.47869	1.8;0.83;1.41;1.4;1.4;1.8;1.4	5.28	5.28	0.74379	Armadillo-type fold (1);	0.049098	0.85682	D	0.000000	T	0.43853	0.1266	L	0.49455	1.56	0.58432	D	0.999999	B;B	0.21821	0.002;0.061	B;B	0.23150	0.004;0.044	T	0.30238	-0.9985	10	0.33141	T	0.24	-3.1734	14.4184	0.67165	1.0:0.0:0.0:0.0	.	490;490	Q8N3U4-2;Q8N3U4	.;STAG2_HUMAN	G	490;490;421;490;490;490;490	ENSP00000218089:E490G;ENSP00000397265:E490G;ENSP00000346555:E421G;ENSP00000360202:E490G;ENSP00000360199:E490G;ENSP00000360187:E490G;ENSP00000360186:E490G	ENSP00000218089:E490G	E	+	2	0	STAG2	123022807	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.283000	0.95860	1.853000	0.53794	0.441000	0.28932	GAG	.	.		0.383	STAG2-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000156159.2	NM_006603	
FHL1	2273	hgsc.bcm.edu	37	X	135288588	135288588	+	5'UTR	SNP	C	C	T			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:135288588C>T	ENST00000345434.3	+	0	78				FHL1_ENST00000477080.1_3'UTR|FHL1_ENST00000535737.1_5'UTR|FHL1_ENST00000370676.3_Silent_p.G15G|FHL1_ENST00000394153.2_5'UTR|FHL1_ENST00000543669.1_5'UTR|FHL1_ENST00000394155.2_5'UTR|FHL1_ENST00000539015.1_Silent_p.G28G|FHL1_ENST00000370690.3_5'UTR|FHL1_ENST00000370683.1_Silent_p.G15G			Q13642	FHL1_HUMAN	four and a half LIM domains 1						cell differentiation (GO:0030154)|muscle organ development (GO:0007517)|negative regulation of cell growth (GO:0030308)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of G2/M transition of mitotic cell cycle (GO:0010972)|organ morphogenesis (GO:0009887)|positive regulation of potassium ion transport (GO:0043268)|regulation of membrane depolarization (GO:0003254)|regulation of potassium ion transmembrane transporter activity (GO:1901016)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ion channel binding (GO:0044325)|zinc ion binding (GO:0008270)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)	19	Acute lymphoblastic leukemia(192;0.000127)					ACAAGGTGGGCACCATGGCGG	0.582																																					p.G28G		Atlas-SNP	.											.	FHL1	114	.	0			c.C84T						.						121.0	111.0	115.0					X																	135288588		2203	4300	6503	SO:0001623	5_prime_UTR_variant	2273	exon2			GGTGGGCACCATG	U60115	CCDS14655.1, CCDS55505.1, CCDS55506.1, CCDS55507.1, CCDS76036.1	Xq26.3	2014-09-17			ENSG00000022267	ENSG00000022267			3702	protein-coding gene	gene with protein product	"""Four-and-a-half LIM domains 1"", ""LIM protein SLIMMER"""	300163				8753811, 9714789	Standard	NM_001449		Approved	SLIM1, KYO-T, bA535K18.1, FHL1B, XMPMA, FLH1A, MGC111107	uc004ezo.3	Q13642	OTTHUMG00000022504	ENST00000345434.3:c.-4C>T	chrX.hg19:g.135288588C>T		161.0	0.0		119.0	7.0	NM_001159701	B7Z5T4|B7Z793|O95212|Q13230|Q13645|Q5JXI7|Q5M7Y6|Q6IB30|Q9NZ40|Q9UKZ8|Q9Y630	Silent	SNP	ENST00000345434.3	hg19	CCDS55507.1																																																																																			.	.		0.582	FHL1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058461.1	NM_001449	
L1CAM	3897	hgsc.bcm.edu	37	X	153132510	153132510	+	Splice_Site	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:153132510T>C	ENST00000370060.1	-	18	2396	c.2207A>G	c.(2206-2208)aAg>aGg	p.K736R	L1CAM_ENST00000361981.3_Splice_Site_p.K731R|L1CAM_ENST00000538883.1_Splice_Site_p.K738R|L1CAM_ENST00000361699.4_Splice_Site_p.K736R|L1CAM_ENST00000543994.1_Splice_Site_p.K738R|L1CAM_ENST00000370055.1_Splice_Site_p.K731R|L1CAM_ENST00000370057.3_Splice_Site_p.K736R	NM_001278116.1	NP_001265045.1	P32004	L1CAM_HUMAN	L1 cell adhesion molecule	736	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell death (GO:0008219)|cell surface receptor signaling pathway (GO:0007166)|cell-cell adhesion mediated by integrin (GO:0033631)|chemotaxis (GO:0006935)|heterophilic cell-cell adhesion (GO:0007157)|homophilic cell adhesion (GO:0007156)|homotypic cell-cell adhesion (GO:0034109)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|nervous system development (GO:0007399)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of cell-cell adhesion (GO:0022409)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	sialic acid binding (GO:0033691)			NS(1)|breast(4)|central_nervous_system(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|liver(1)|lung(31)|ovary(13)|pancreas(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	81	all_cancers(53;6.72e-15)|all_epithelial(53;3.19e-09)|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)					GACTCTCACCTTCCACGTGAT	0.542																																					p.K736R		Atlas-SNP	.											.	L1CAM	189	.	0			c.A2207G						.						336.0	270.0	292.0					X																	153132510		2203	4300	6503	SO:0001630	splice_region_variant	3897	exon17			CTCACCTTCCACG	M74387	CCDS14733.1, CCDS14734.1, CCDS48192.1	Xq28	2014-09-17	2003-04-07		ENSG00000198910	ENSG00000198910		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	6470	protein-coding gene	gene with protein product		308840	"""antigen identified by monoclonal antibody R1"""	HSAS1, SPG1, HSAS, MASA, MIC5, S10			Standard	NM_001278116		Approved	CD171	uc031tks.1	P32004	OTTHUMG00000024221	ENST00000370060.1:c.2208+1A>G	chrX.hg19:g.153132510T>C		202.0	0.0		157.0	7.0	NM_000425	A0AV65|A4ZYW4|B2RMU7|G3XAF4|Q8TA87	Missense_Mutation	SNP	ENST00000370060.1	hg19	CCDS14733.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	16.11|16.11	3.029383|3.029383	0.54790|0.54790	.|.	.|.	ENSG00000198910|ENSG00000198910	ENST00000370060;ENST00000543994;ENST00000370057;ENST00000538883;ENST00000361981;ENST00000370055;ENST00000361699|ENST00000455590	T;T;T;T;T;T;T|.	0.58358|.	0.34;0.34;0.34;0.34;0.34;0.34;0.34|.	5.77|5.77	5.77|5.77	0.91146|0.91146	Fibronectin, type III (4);Immunoglobulin-like fold (1);|.	0.080367|.	0.50627|.	D|.	0.000102|.	T|T	0.63070|0.63070	0.2480|0.2480	L|L	0.58302|0.58302	1.8|1.8	0.58432|0.58432	D|D	0.999993|0.999993	P;P;P|.	0.41710|.	0.717;0.563;0.76|.	B;B;B|.	0.44133|.	0.315;0.233;0.442|.	T|T	0.62590|0.62590	-0.6822|-0.6822	10|5	0.46703|.	T|.	0.11|.	.|.	10.4958|10.4958	0.44777|0.44777	0.0:0.0:0.1602:0.8397|0.0:0.0:0.1602:0.8397	.|.	731;736;736|.	G3XAF4;P32004-2;P32004|.	.;.;L1CAM_HUMAN|.	R|G	736;738;736;738;731;731;736|157	ENSP00000359077:K736R;ENSP00000438430:K738R;ENSP00000359074:K736R;ENSP00000439645:K738R;ENSP00000354712:K731R;ENSP00000359072:K731R;ENSP00000355380:K736R|.	ENSP00000355380:K736R|.	K|S	-|-	2|1	0|0	L1CAM|L1CAM	152785704|152785704	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.233000|0.233000	0.25261|0.25261	3.813000|3.813000	0.55636|0.55636	1.941000|1.941000	0.56285|0.56285	0.430000|0.430000	0.28490|0.28490	AAG|AGC	.	.		0.542	L1CAM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061094.2	NM_024003	Missense_Mutation
ZFY	7544	hgsc.bcm.edu	37	Y	2846064	2846064	+	Silent	SNP	C	C	T			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrY:2846064C>T	ENST00000155093.3	+	7	1486	c.1165C>T	c.(1165-1167)Ctg>Ttg	p.L389L	ZFY_ENST00000383052.1_Silent_p.L389L|ZFY-AS1_ENST00000417305.1_RNA|ZFY_ENST00000431102.1_Silent_p.L198L|ZFY_ENST00000449237.1_Silent_p.L312L|ZFY_ENST00000478783.1_3'UTR	NM_003411.3	NP_003402.2	P08048	ZFY_HUMAN	zinc finger protein, Y-linked	389					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			biliary_tract(1)|kidney(3)|large_intestine(1)|lung(3)	8						CCTTGGCAGACTGGCTAAACA	0.443																																					p.L389L		Atlas-SNP	.											.	ZFY	20	.	0			c.C1165T						.																																			SO:0001819	synonymous_variant	7544	exon7			GGCAGACTGGCTA	L10393	CCDS14774.1, CCDS48200.1, CCDS48201.1	Yp11.3	2013-01-08			ENSG00000067646	ENSG00000067646		"""Zinc fingers, C2H2-type"""	12870	protein-coding gene	gene with protein product		490000				2497060	Standard	NM_001145275		Approved	ZNF911	uc004fqj.3	P08048	OTTHUMG00000036159	ENST00000155093.3:c.1165C>T	chrY.hg19:g.2846064C>T		152.0	0.0		99.0	4.0	NM_003411	B4DVF7|Q14021|Q15558|Q1RME9|Q24JR0|Q96TF3	Silent	SNP	ENST00000155093.3	hg19	CCDS14774.1																																																																																			.	.		0.443	ZFY-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088063.1	NM_003411	
KDM5D	8284	hgsc.bcm.edu	37	Y	21870223	21870223	+	Silent	SNP	T	T	C			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrY:21870223T>C	ENST00000317961.4	-	22	3439	c.3168A>G	c.(3166-3168)agA>agG	p.R1056R	KDM5D_ENST00000541639.1_Silent_p.R1087R|KDM5D_ENST00000382806.2_Silent_p.R999R	NM_004653.4	NP_004644.2	Q9BY66	KDM5D_HUMAN	lysine (K)-specific demethylase 5D	1056					histone H3-K4 demethylation (GO:0034720)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (H3-K4 specific) (GO:0032453)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|zinc ion binding (GO:0008270)			kidney(1)|large_intestine(9)|lung(6)|skin(1)	17					Vitamin C(DB00126)	GCTCTAGCTGTCTCAGCTCTT	0.547																																					p.R1087R		Atlas-SNP	.											.	KDM5D	40	.	0			c.A3261G						.						36.0	40.0	39.0					Y																	21870223		576	1907	2483	SO:0001819	synonymous_variant	8284	exon23			TAGCTGTCTCAGC	U52191	CCDS14794.1, CCDS55554.1, CCDS55555.1	Yq11	2013-01-28	2009-04-06	2009-04-06	ENSG00000012817	ENSG00000012817		"""Chromatin-modifying enzymes / K-demethylases"", ""Zinc fingers, PHD-type"""	11115	protein-coding gene	gene with protein product		426000	"""Jumonji, AT rich interactive domain 1D (RBP2-like)"", ""Smcy homolog, Y-linked (mouse)"", ""jumonji, AT rich interactive domain 1D"""	HYA, HY, SMCY, JARID1D		795123, 8841177	Standard	NM_001146705		Approved	KIAA0234	uc011naz.2	Q9BY66	OTTHUMG00000036508	ENST00000317961.4:c.3168A>G	chrY.hg19:g.21870223T>C		121.0	0.0		90.0	4.0	NM_001146705	A2RU19|A6H8V7|B7ZLX1|Q92509|Q92809|Q9HCU1	Silent	SNP	ENST00000317961.4	hg19	CCDS14794.1																																																																																			.	.		0.547	KDM5D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088790.1	NM_004653	
F8A3	474384	hgsc.bcm.edu	37	X	154687164	154687164	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:154687164delG	ENST00000369445.2	-	1	1112	c.1098delC	c.(1096-1098)cccfs	p.P366fs	MIR1184-3_ENST00000408676.1_RNA	NM_001007524.1	NP_001007525.1	P23610	F8I2_HUMAN	coagulation factor VIII-associated 3	366						nucleus (GO:0005634)						all_cancers(53;7.19e-17)|all_epithelial(53;9.83e-11)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					CCTGTCCTGAGGGGGAGATGG	0.537																																					p.S367fs		Atlas-INDEL	.											.	.	.	.	0			c.1099delT						.						0.0	1.0	1.0					X																	154687164		0	2	2	SO:0001589	frameshift_variant	474383	exon1			.		CCDS35463.1	Xq28	2011-04-13	2011-04-13		ENSG00000185990	ENSG00000277150			31850	protein-coding gene	gene with protein product			"""coagulation factor VIII-associated (intronic transcript) 3"""				Standard	NM_001007524		Approved			P23610	OTTHUMG00000034289	ENST00000369445.2:c.1098delC	chrX.hg19:g.154687164delG	ENSP00000358454:p.Pro366fs	488.0	0.0		388.0	28.0	NM_001007523	Q5HY66|Q8IXP3	Frame_Shift_Del	DEL	ENST00000369445.2	hg19	CCDS35463.1																																																																																			.	.		0.537	F8A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082833.1	NM_001007524	
SRCAP	10847	hgsc.bcm.edu	37	16	30745026	30745026	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:30745026delT	ENST00000262518.4	+	29	6786	c.6401delT	c.(6400-6402)gttfs	p.V2134fs	SRCAP_ENST00000395059.2_Frame_Shift_Del_p.V2072fs|SRCAP_ENST00000344771.4_Frame_Shift_Del_p.V1976fs	NM_006662.2	NP_006653.2	Q6ZRS2	SRCAP_HUMAN	Snf2-related CREBBP activator protein	2134	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				histone acetylation (GO:0016573)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)			NS(1)|breast(3)|cervix(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(22)|liver(3)|lung(62)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5)	136			Colorectal(24;0.198)			GACACTGTTGTTTTTTATGAC	0.517																																					p.V2134fs		Atlas-INDEL	.											.	SRCAP	298	.	0			c.6400delG						.						115.0	115.0	115.0					16																	30745026		2197	4300	6497	SO:0001589	frameshift_variant	10847	exon29			.	AB002307	CCDS10689.2	16p11.2	2009-08-06			ENSG00000080603	ENSG00000080603			16974	protein-coding gene	gene with protein product	"""Swi2/Snf2-related ATPase homolog (S. cerevisiae)"", ""domino homolog 1 (Drosophila)"""	611421				10347196, 9205841	Standard	NM_006662		Approved	KIAA0309, EAF1, SWR1, DOMO1	uc002dze.1	Q6ZRS2	OTTHUMG00000132393	ENST00000262518.4:c.6401delT	chr16.hg19:g.30745026delT	ENSP00000262518:p.Val2134fs	155.0	0.0		171.0	13.0	NM_006662	B0JZA6|O15026|Q7Z744|Q9Y5L9	Frame_Shift_Del	DEL	ENST00000262518.4	hg19	CCDS10689.2																																																																																			.	.		0.517	SRCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255523.1	NM_006662	
MYCBP2	23077	hgsc.bcm.edu	37	13	77636737	77636737	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr13:77636737delT	ENST00000544440.2	-	74	12671	c.12654delA	c.(12652-12654)aaafs	p.K4218fs	MYCBP2_ENST00000407578.2_Frame_Shift_Del_p.K4256fs|MYCBP2_ENST00000357337.6_Frame_Shift_Del_p.K4218fs					MYC binding protein 2, E3 ubiquitin protein ligase											NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(51)|ovary(5)|pancreas(2)|prostate(5)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	118		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.22)		GBM - Glioblastoma multiforme(99;0.109)		TTACCATTTGTTTTTGTTGTC	0.393																																					p.Q4257fs		Atlas-INDEL	.											MYCBP2_ENST00000407578,NS,carcinoma,0,2	MYCBP2	1029	.	0			c.12769delC						.						198.0	170.0	179.0					13																	77636737		2203	4300	6503	SO:0001589	frameshift_variant	23077	exon74			.	AB020723		13q22	2012-02-23	2012-02-23		ENSG00000005810	ENSG00000005810			23386	protein-coding gene	gene with protein product		610392	"""MYC binding protein 2"""			9689053, 15057823	Standard	NM_015057		Approved	PAM, KIAA0916, FLJ10106	uc021rks.1	O75592	OTTHUMG00000017105	ENST00000544440.2:c.12654delA	chr13.hg19:g.77636737delT	ENSP00000444596:p.Lys4218fs	217.0	0.0		173.0	13.0	NM_015057		Frame_Shift_Del	DEL	ENST00000544440.2	hg19																																																																																				.	.		0.393	MYCBP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045326.1	NM_015057	
SLC28A1	9154	hgsc.bcm.edu	37	15	85431063	85431063	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:85431063delG	ENST00000286749.3	+	2	162	c.72delG	c.(70-72)atgfs	p.M24fs	SLC28A1_ENST00000537624.1_Frame_Shift_Del_p.M24fs|SLC28A1_ENST00000338602.2_Frame_Shift_Del_p.M24fs|SLC28A1_ENST00000538177.1_Frame_Shift_Del_p.M24fs|SLC28A1_ENST00000537703.1_5'UTR|SLC28A1_ENST00000537216.1_Frame_Shift_Del_p.M24fs|SLC28A1_ENST00000394573.1_Frame_Shift_Del_p.M24fs			O00337	S28A1_HUMAN	solute carrier family 28 (concentrative nucleoside transporter), member 1	24					nucleobase-containing compound metabolic process (GO:0006139)|nucleoside transmembrane transport (GO:1901642)|nucleoside transport (GO:0015858)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	nucleoside binding (GO:0001882)|nucleoside transmembrane transporter activity (GO:0005337)|nucleoside:sodium symporter activity (GO:0005415)			breast(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)	41			BRCA - Breast invasive adenocarcinoma(143;0.0587)		Gemcitabine(DB00441)|Stavudine(DB00649)|Zidovudine(DB00495)	TGGAGAACATGGGGGCTGATT	0.567																																					p.M24fs		Atlas-INDEL	.											.	SLC28A1	118	.	0			c.71delT						.						172.0	155.0	161.0					15																	85431063		2203	4299	6502	SO:0001589	frameshift_variant	9154	exon3			.	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.72delG	chr15.hg19:g.85431063delG	ENSP00000286749:p.Met24fs	231.0	0.0		156.0	11.0	NM_201651	A0AV42|A8K7I2|O00335|O00336|Q5U5S6|Q5U648|Q9UEZ9	Frame_Shift_Del	DEL	ENST00000286749.3	hg19	CCDS10334.1																																																																																			.	.		0.567	SLC28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308998.2		
NCKAP1	10787	hgsc.bcm.edu	37	2	183822266	183822266	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:183822266delT	ENST00000361354.4	-	19	2312	c.1940delA	c.(1939-1941)aagfs	p.K647fs	NCKAP1_ENST00000360982.2_Frame_Shift_Del_p.K653fs	NM_013436.3	NP_038464.1	Q9Y2A7	NCKP1_HUMAN	NCK-associated protein 1	647					apical protein localization (GO:0045176)|apoptotic process (GO:0006915)|basal protein localization (GO:0045175)|central nervous system development (GO:0007417)|embryonic body morphogenesis (GO:0010172)|embryonic foregut morphogenesis (GO:0048617)|embryonic heart tube development (GO:0035050)|endoderm development (GO:0007492)|establishment or maintenance of actin cytoskeleton polarity (GO:0030950)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|lamellipodium assembly (GO:0030032)|mesodermal cell migration (GO:0008078)|neural tube closure (GO:0001843)|notochord morphogenesis (GO:0048570)|paraxial mesoderm morphogenesis (GO:0048340)|positive regulation of Arp2/3 complex-mediated actin nucleation (GO:2000601)|positive regulation of lamellipodium assembly (GO:0010592)|protein stabilization (GO:0050821)|Rac protein signal transduction (GO:0016601)|regulation of protein localization (GO:0032880)|somitogenesis (GO:0001756)|zygotic determination of anterior/posterior axis, embryo (GO:0007354)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|SCAR complex (GO:0031209)	protein complex binding (GO:0032403)			breast(3)|cervix(2)|endometrium(3)|kidney(4)|large_intestine(11)|lung(16)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)	45			OV - Ovarian serous cystadenocarcinoma(117;0.0942)|Epithelial(96;0.209)			ACCAGTCTGCTTTTTTGATTT	0.378																																					p.K653fs		Atlas-INDEL	.											.	NCKAP1	105	.	0			c.1959delG						.						172.0	154.0	160.0					2																	183822266		2203	4300	6503	SO:0001589	frameshift_variant	10787	exon20			.	AB014509	CCDS2287.1, CCDS2288.1	2q32	2009-08-14			ENSG00000061676	ENSG00000061676			7666	protein-coding gene	gene with protein product		604891				10673335, 12181570, 9344857	Standard	NM_013436		Approved	Nap1, HEM2, NAP125	uc002upb.4	Q9Y2A7	OTTHUMG00000132623	ENST00000361354.4:c.1940delA	chr2.hg19:g.183822266delT	ENSP00000355348:p.Lys647fs	243.0	0.0		190.0	14.0	NM_205842	O60329|Q53QN5|Q53S94|Q53Y35	Frame_Shift_Del	DEL	ENST00000361354.4	hg19	CCDS2287.1																																																																																			.	.		0.378	NCKAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255867.2	NM_205842	
IL13RA2	3598	hgsc.bcm.edu	37	X	114248379	114248379	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:114248379delT	ENST00000371936.1	-	6	723	c.474delA	c.(472-474)aaafs	p.K158fs	IL13RA2_ENST00000468224.1_5'Flank|IL13RA2_ENST00000243213.1_Frame_Shift_Del_p.K158fs			Q14627	I13R2_HUMAN	interleukin 13 receptor, alpha 2	158	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cytokine-mediated signaling pathway (GO:0019221)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	cytokine receptor activity (GO:0004896)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(6)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	23						CTATGCCAGGTTTCCAAGAAC	0.308																																					p.P159fs		Atlas-INDEL	.											.	IL13RA2	66	.	0			c.475delC						.						76.0	68.0	71.0					X																	114248379		2203	4299	6502	SO:0001589	frameshift_variant	3598	exon5			.	X95302	CCDS14565.1	Xq23	2014-01-21			ENSG00000123496	ENSG00000123496		"""Interleukins and interleukin receptors"", ""CD molecules"""	5975	protein-coding gene	gene with protein product	"""cancer/testis antigen 19"""	300130				8663118, 9083087	Standard	NM_000640		Approved	IL-13R, IL13BP, CD213a2, CT19	uc004epx.3	Q14627	OTTHUMG00000022229	ENST00000371936.1:c.474delA	chrX.hg19:g.114248379delT	ENSP00000361004:p.Lys158fs	275.0	0.0		199.0	12.0	NM_000640	A8K7E2|O00667	Frame_Shift_Del	DEL	ENST00000371936.1	hg19	CCDS14565.1																																																																																			.	.		0.308	IL13RA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057966.1	NM_000640	
TFDP1	7027	hgsc.bcm.edu	37	13	114240158	114240158	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr13:114240158delA	ENST00000375370.5	+	2	218	c.6delA	c.(4-6)gcafs	p.A2fs	TFDP1_ENST00000544902.1_5'UTR|TFDP1_ENST00000538138.1_5'UTR|TFDP1_ENST00000465174.1_3'UTR	NM_007111.4	NP_009042.1	Q14186	TFDP1_HUMAN	transcription factor Dp-1	2					anoikis (GO:0043276)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|epidermis development (GO:0008544)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|intrinsic apoptotic signaling pathway (GO:0097193)|mitotic cell cycle (GO:0000278)|Notch signaling pathway (GO:0007219)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of DNA biosynthetic process (GO:2000278)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(4)|lung(10)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	26	Lung NSC(43;0.0113)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.132)|all_epithelial(44;0.0731)|all_lung(25;0.149)|Breast(118;0.153)	all cancers(43;0.0576)			GTAACATGGCAAAAGATGTAA	0.348										TSP Lung(29;0.18)																											p.A2fs		Atlas-INDEL	.											.	TFDP1	70	.	0			c.5delC						.						137.0	122.0	127.0					13																	114240158		2203	4300	6503	SO:0001589	frameshift_variant	7027	exon2			.	BC011685	CCDS9538.1	13q34	2008-07-18			ENSG00000198176	ENSG00000198176			11749	protein-coding gene	gene with protein product		189902				8413592, 9027491	Standard	NM_007111		Approved	Dp-1, DRTF1, DP1	uc001vtw.3	Q14186	OTTHUMG00000017388	ENST00000375370.5:c.6delA	chr13.hg19:g.114240158delA	ENSP00000364519:p.Ala2fs	167.0	0.0		123.0	12.0	NM_007111	B4DLQ9|Q5JSB4|Q8IZL5	Frame_Shift_Del	DEL	ENST00000375370.5	hg19	CCDS9538.1																																																																																			.	.		0.348	TFDP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045918.3	NM_007111	
PRMT5	10419	hgsc.bcm.edu	37	14	23398414	23398414	+	Intron	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr14:23398414delC	ENST00000324366.8	-	1	334				RP11-298I3.1_ENST00000548819.1_RNA|PRMT5_ENST00000553897.1_Intron|PRMT5-AS1_ENST00000599580.2_RNA|RP11-298I3.1_ENST00000548322.1_RNA|PRMT5-AS1_ENST00000590290.1_RNA|PRMT5_ENST00000538452.1_5'UTR|PRMT5_ENST00000397440.4_Frame_Shift_Del_p.G7fs|PRMT5-AS1_ENST00000595662.1_RNA|PRMT5_ENST00000216350.8_Frame_Shift_Del_p.G7fs|PRMT5_ENST00000397441.2_Frame_Shift_Del_p.G7fs|PRMT5-AS1_ENST00000587245.2_RNA|PRMT5_ENST00000553641.1_Intron	NM_006109.3	NP_006100.2	O14744	ANM5_HUMAN	protein arginine methyltransferase 5						cell proliferation (GO:0008283)|circadian regulation of gene expression (GO:0032922)|endothelial cell activation (GO:0042118)|gene expression (GO:0010467)|histone H4-R3 methylation (GO:0043985)|ncRNA metabolic process (GO:0034660)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|peptidyl-arginine methylation (GO:0018216)|peptidyl-arginine methylation, to symmetrical-dimethyl arginine (GO:0019918)|peptidyl-arginine N-methylation (GO:0035246)|regulation of mitosis (GO:0007088)|regulation of transcription, DNA-templated (GO:0006355)|RNA metabolic process (GO:0016070)|spliceosomal snRNP assembly (GO:0000387)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|methylosome (GO:0034709)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|core promoter sequence-specific DNA binding (GO:0001046)|histone-arginine N-methyltransferase activity (GO:0008469)|methyltransferase activity (GO:0008168)|protein-arginine omega-N symmetric methyltransferase activity (GO:0035243)|ribonucleoprotein complex binding (GO:0043021)|transcription corepressor activity (GO:0003714)			endometrium(4)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	25	all_cancers(95;2.76e-05)			GBM - Glioblastoma multiforme(265;0.0126)		CCTTCTCCGTCCCCGAGTTCG	0.627																																					p.T8fs		Atlas-INDEL	.											.	PRMT5	101	.	0			c.22delA						.						67.0	72.0	71.0					14																	23398414		2203	4300	6503	SO:0001627	intron_variant	10419	exon1			.	AF015913	CCDS9579.1, CCDS41922.1, CCDS61394.1, CCDS61395.1, CCDS61396.1	14q11.2	2014-06-12	2006-02-16	2006-02-16	ENSG00000100462	ENSG00000100462	2.1.1.125	"""Protein arginine methyltransferases"""	10894	protein-coding gene	gene with protein product		604045	"""skb1 (S. pombe) homolog"", ""SKB1 homolog (S. pombe)"""	HRMT1L5, SKB1		9843966	Standard	NM_001282955		Approved	SKB1Hs	uc001whm.1	O14744	OTTHUMG00000028709	ENST00000324366.8:c.110+46G>-	chr14.hg19:g.23398414delC		188.0	0.0		180.0	12.0	NM_001039619	A8MTP3|A8MZ91|B4DX49|B4DY30|B5BU10|D3DS33|E2QRE7|Q6IBR1|Q9UKH1	Frame_Shift_Del	DEL	ENST00000324366.8	hg19	CCDS9579.1																																																																																			.	.		0.627	PRMT5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071674.3		
CREG2	200407	hgsc.bcm.edu	37	2	102000039	102000039	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:102000039delG	ENST00000324768.5	-	2	704	c.567delC	c.(565-567)cccfs	p.P189fs	CREG2_ENST00000495455.1_5'UTR	NM_153836.3	NP_722578.1	Q8IUH2	CREG2_HUMAN	cellular repressor of E1A-stimulated genes 2	189						endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)	FMN binding (GO:0010181)|oxidoreductase activity (GO:0016491)			endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|skin(1)	10						GCGAGGCCATGGGGTTCTTCA	0.552																																					p.M190fs		Atlas-INDEL	.											.	CREG2	21	.	0			c.568delA						.						71.0	68.0	69.0					2																	102000039		2203	4300	6503	SO:0001589	frameshift_variant	200407	exon2			.	AB046109	CCDS2052.1	2q12.1	2007-08-01			ENSG00000175874	ENSG00000175874			14272	protein-coding gene	gene with protein product						12408961	Standard	NM_153836		Approved		uc002tba.2	Q8IUH2	OTTHUMG00000130692	ENST00000324768.5:c.567delC	chr2.hg19:g.102000039delG	ENSP00000315203:p.Pro189fs	130.0	0.0		89.0	10.0	NM_153836	Q86X03|Q8N540|Q8N9E3	Frame_Shift_Del	DEL	ENST00000324768.5	hg19	CCDS2052.1																																																																																			.	.		0.552	CREG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253188.2	NM_153836	
PLXNB1	5364	hgsc.bcm.edu	37	3	48457527	48457527	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:48457527delC	ENST00000358536.4	-	18	3799	c.3530delG	c.(3529-3531)ggcfs	p.G1177fs	PLXNB1_ENST00000465117.1_5'Flank|PLXNB1_ENST00000296440.6_Frame_Shift_Del_p.G1177fs|PLXNB1_ENST00000456774.1_Frame_Shift_Del_p.G994fs|PLXNB1_ENST00000448774.2_Intron|PLXNB1_ENST00000358459.4_Frame_Shift_Del_p.G994fs	NM_002673.4	NP_002664.2	O43157	PLXB1_HUMAN	plexin B1	1177	IPT/TIG 2.				axon guidance (GO:0007411)|cell migration (GO:0016477)|intracellular signal transduction (GO:0035556)|negative regulation of cell adhesion (GO:0007162)|negative regulation of osteoblast proliferation (GO:0033689)|neuron projection morphogenesis (GO:0048812)|ossification involved in bone maturation (GO:0043931)|positive regulation of axonogenesis (GO:0050772)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell shape (GO:0008360)|regulation of cytoskeleton organization (GO:0051493)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in bone trabecula morphogenesis (GO:1900220)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	GTPase activating protein binding (GO:0032794)|receptor activity (GO:0004872)|semaphorin receptor activity (GO:0017154)|semaphorin receptor binding (GO:0030215)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(10)|ovary(3)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	47				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		GAGACGGGTGCCCCCAGCTCT	0.622																																					p.G1177fs		Atlas-INDEL	.											.	PLXNB1	150	.	0			c.3531delC						.						20.0	22.0	21.0					3																	48457527		2197	4298	6495	SO:0001589	frameshift_variant	5364	exon18			.	X87904	CCDS2765.1	3p21.31	2008-07-18			ENSG00000164050	ENSG00000164050		"""Plexins"""	9103	protein-coding gene	gene with protein product		601053		PLXN5		8570614, 11035813	Standard	XM_005265234		Approved	SEP, KIAA0407	uc003csw.2	O43157	OTTHUMG00000133527	ENST00000358536.4:c.3530delG	chr3.hg19:g.48457527delC	ENSP00000351338:p.Gly1177fs	260.0	0.0		182.0	13.0	NM_001130082	A6H8Y2|Q6NY20|Q9UIV7|Q9UJ92|Q9UJ93	Frame_Shift_Del	DEL	ENST00000358536.4	hg19	CCDS2765.1																																																																																			.	.		0.622	PLXNB1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344454.1	NM_002673	
CDHR3	222256	hgsc.bcm.edu	37	7	105658335	105658335	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:105658335delC	ENST00000317716.9	+	12	1550	c.1470delC	c.(1468-1470)ctcfs	p.L490fs	CDHR3_ENST00000470188.1_Intron|CDHR3_ENST00000542731.1_Frame_Shift_Del_p.L490fs|CDHR3_ENST00000343407.5_Intron|CDHR3_ENST00000478080.1_Frame_Shift_Del_p.L402fs	NM_152750.4	NP_689963.2	Q6ZTQ4	CDHR3_HUMAN	cadherin-related family member 3	490	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(3)|endometrium(1)|kidney(1)|large_intestine(1)|lung(15)|ovary(1)	23						ATAAAGACCTCCCCCAGAGCA	0.517																																					p.L490fs		Atlas-INDEL	.											.	CDHR3	153	.	0			c.1469delT						.						33.0	36.0	35.0					7																	105658335		1888	4103	5991	SO:0001589	frameshift_variant	222256	exon12			.	AK126338	CCDS47684.1, CCDS75651.1	7q22.2	2011-07-01			ENSG00000128536	ENSG00000128536		"""Cadherins / Cadherin-related"""	26308	protein-coding gene	gene with protein product		615610					Standard	NM_152750		Approved	FLJ44366, FLJ23834, CDH28	uc003vdl.4	Q6ZTQ4	OTTHUMG00000157520	ENST00000317716.9:c.1470delC	chr7.hg19:g.105658335delC	ENSP00000325954:p.Leu490fs	141.0	0.0		135.0	11.0	NM_152750	Q8TCI7	Frame_Shift_Del	DEL	ENST00000317716.9	hg19	CCDS47684.1																																																																																			.	.		0.517	CDHR3-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349025.2	NM_152750	
TNXB	7148	hgsc.bcm.edu	37	6	32038147	32038147	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:32038147delC	ENST00000375244.3	-	14	5236	c.5035delG	c.(5035-5037)gagfs	p.E1679fs	TNXB_ENST00000375247.2_Frame_Shift_Del_p.E1679fs			P22105	TENX_HUMAN	tenascin XB	1761	Fibronectin type-III 9. {ECO:0000255|PROSITE-ProRule:PRU00316}.				actin cytoskeleton organization (GO:0030036)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|fatty acid metabolic process (GO:0006631)|regulation of JUN kinase activity (GO:0043506)|single organismal cell-cell adhesion (GO:0016337)|triglyceride metabolic process (GO:0006641)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						ACCCACAGCTCCCCAAGGCGG	0.582																																					p.E1679fs		Atlas-INDEL	.											.	TNXB	553	.	0			c.5036delA						.						15.0	17.0	16.0					6																	32038147		1915	4106	6021	SO:0001589	frameshift_variant	7148	exon14			.	X71923	CCDS4736.1	6p21.3	2013-02-11			ENSG00000168477	ENSG00000168477		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	11976	protein-coding gene	gene with protein product		600985		TNXB1, TNXB2		8530023	Standard	NM_019105		Approved	TNXBS, XBS, XB	uc021yvf.2	P22105	OTTHUMG00000031088	ENST00000375244.3:c.5035delG	chr6.hg19:g.32038147delC	ENSP00000364393:p.Glu1679fs	186.0	0.0		179.0	11.0	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Frame_Shift_Del	DEL	ENST00000375244.3	hg19																																																																																				.	.		0.582	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105	
SETD6	79918	hgsc.bcm.edu	37	16	58550759	58550759	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:58550759delC	ENST00000219315.4	+	5	769	c.719delC	c.(718-720)tccfs	p.S240fs	SETD6_ENST00000394266.4_Frame_Shift_Del_p.S171fs|SETD6_ENST00000310682.2_Frame_Shift_Del_p.S216fs|SETD6_ENST00000418480.1_3'UTR			Q8TBK2	SETD6_HUMAN	SET domain containing 6	240	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				negative regulation of NF-kappaB transcription factor activity (GO:0032088)|peptidyl-lysine monomethylation (GO:0018026)|regulation of inflammatory response (GO:0050727)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	NF-kappaB binding (GO:0051059)|protein-lysine N-methyltransferase activity (GO:0016279)	p.S216C(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|skin(1)	7						GAGCCCAACTCCCCCGTGATG	0.532																																					p.S240fs		Atlas-INDEL	.											.	SETD6	27	.	1	Substitution - Missense(1)	kidney(1)	c.718delT						.						192.0	192.0	192.0					16																	58550759		2198	4300	6498	SO:0001589	frameshift_variant	79918	exon5			.	AK024801	CCDS10798.1, CCDS54013.1	16q21	2008-02-05			ENSG00000103037	ENSG00000103037			26116	protein-coding gene	gene with protein product						12477932	Standard	NM_024860		Approved	FLJ21148	uc002ens.3	Q8TBK2	OTTHUMG00000150276	ENST00000219315.4:c.719delC	chr16.hg19:g.58550759delC	ENSP00000219315:p.Ser240fs	197.0	0.0		164.0	10.0	NM_001160305	A8K380|B5ME38|Q9H787	Frame_Shift_Del	DEL	ENST00000219315.4	hg19	CCDS54013.1																																																																																			.	.		0.532	SETD6-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000317274.2	NM_024860	
NASP	4678	hgsc.bcm.edu	37	1	46073041	46073041	+	Frame_Shift_Del	DEL	A	A	-	rs35351400		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:46073041delA	ENST00000350030.3	+	6	545	c.458delA	c.(457-459)gaafs	p.E153fs	NASP_ENST00000372052.4_Intron|NASP_ENST00000402363.3_Frame_Shift_Del_p.E155fs|NASP_ENST00000537798.1_Frame_Shift_Del_p.E89fs|NASP_ENST00000351223.3_Intron	NM_002482.3	NP_002473.2	P49321	NASP_HUMAN	nuclear autoantigenic sperm protein (histone-binding)	153	Glu-rich (acidic).				blastocyst development (GO:0001824)|cell cycle (GO:0007049)|cell proliferation (GO:0008283)|DNA replication (GO:0006260)|DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|histone exchange (GO:0043486)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)	Hsp90 protein binding (GO:0051879)			breast(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|prostate(3)|skin(1)	17	Acute lymphoblastic leukemia(166;0.155)|Lung SC(450;0.211)					GCCATGGGAGAAAAAGAAGAA	0.393																																					p.E153fs		Atlas-INDEL	.											.	NASP	77	.	0			c.457delG						.						56.0	55.0	56.0					1																	46073041		2203	4300	6503	SO:0001589	frameshift_variant	4678	exon6			.	M97856	CCDS524.1, CCDS525.1, CCDS55597.1	1p34.1	2013-01-10			ENSG00000132780	ENSG00000132780		"""Tetratricopeptide (TTC) repeat domain containing"""	7644	protein-coding gene	gene with protein product		603185				1426632	Standard	NM_002482		Approved	FLB7527, FLJ31599, FLJ35510, MGC19722, MGC20372, MGC2297, DKFZp547F162, PRO1999	uc001coi.2	P49321	OTTHUMG00000007826	ENST00000350030.3:c.458delA	chr1.hg19:g.46073041delA	ENSP00000255120:p.Glu153fs	165.0	0.0		146.0	10.0	NM_002482	A8K6H2|B4DQP3|D3DQ07|F5H3J2|Q53GW5|Q5T622|Q5T625|Q96A69|Q9BTW2	Frame_Shift_Del	DEL	ENST00000350030.3	hg19	CCDS524.1																																																																																			.	.		0.393	NASP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000021533.2	NM_002482	
OR4A15	81328	hgsc.bcm.edu	37	11	55135387	55135387	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:55135387delT	ENST00000314706.3	+	1	28	c.28delT	c.(28-30)tttfs	p.F10fs		NM_001005275.1	NP_001005275.1	Q8NGL6	O4A15_HUMAN	olfactory receptor, family 4, subfamily A, member 15	10						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|breast(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(48)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	71						TAATCTCAAATTTATCACTGA	0.413																																					p.K9fs		Atlas-INDEL	.											.	OR4A15	161	.	0			c.27delA						.						54.0	47.0	49.0					11																	55135387		2201	4296	6497	SO:0001589	frameshift_variant	81328	exon1			.	AB065776	CCDS31500.1	11q11	2012-08-09			ENSG00000181958	ENSG00000181958		"""GPCR / Class A : Olfactory receptors"""	15152	protein-coding gene	gene with protein product							Standard	NM_001005275		Approved		uc010rif.2	Q8NGL6	OTTHUMG00000166711	ENST00000314706.3:c.28delT	chr11.hg19:g.55135387delT	ENSP00000325065:p.Phe10fs	188.0	0.0		156.0	10.0	NM_001005275	Q6IFL4|Q96R65	Frame_Shift_Del	DEL	ENST00000314706.3	hg19	CCDS31500.1																																																																																			.	.		0.413	OR4A15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391161.1	NM_001005275	
FANCE	2178	hgsc.bcm.edu	37	6	35425715	35425715	+	Frame_Shift_Del	DEL	C	C	-	rs587778337		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:35425715delC	ENST00000229769.2	+	4	1108	c.923delC	c.(922-924)gccfs	p.A308fs		NM_021922.2	NP_068741.1	Q9HB96	FANCE_HUMAN	Fanconi anemia, complementation group E	308	Interaction with FANCC.				DNA repair (GO:0006281)	Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(3)|ovary(1)|skin(2)	13						TTGGAGGATGCCCCCCCAGTT	0.542			"""N, F, S"""			"""AML, leukemia"""		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.A308fs		Atlas-INDEL	.	yes	Rec		Fanconi anaemia E	6	6p21-p22	2178	"""Fanconi anemia, complementation group E"""		L	.,2	FANCE	45	.	0			c.922delG						.						77.0	74.0	75.0					6																	35425715		2203	4300	6503	SO:0001589	frameshift_variant	2178	exon4	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	.	AF265210	CCDS4805.1	6p22-p21	2014-09-17			ENSG00000112039	ENSG00000112039		"""Fanconi anemia, complementation groups"""	3586	protein-coding gene	gene with protein product		613976		FACE		7662964, 11001585	Standard	XM_005248885		Approved	FAE	uc003oko.1	Q9HB96	OTTHUMG00000014565	ENST00000229769.2:c.923delC	chr6.hg19:g.35425715delC	ENSP00000229769:p.Ala308fs	173.0	0.0		150.0	10.0	NM_021922	A8K907|Q4ZGH2	Frame_Shift_Del	DEL	ENST00000229769.2	hg19	CCDS4805.1																																																																																			.	.		0.542	FANCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040282.1		
MUC13	56667	hgsc.bcm.edu	37	3	124646629	124646629	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:124646629delG	ENST00000311075.3	-	2	299	c.261delC	c.(259-261)cccfs	p.P87fs	MUC13_ENST00000497378.1_5'Flank	NM_033049.3	NP_149038	Q9H3R2	MUC13_HUMAN	mucin 13, cell surface associated	88	Thr-rich.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(6)|lung(5)|prostate(1)|skin(1)|stomach(1)	18						TACTAATTATGGGGGGAGCAG	0.438																																					p.I88X		Atlas-INDEL	.											.	MUC13	57	.	0			c.262delA						.						229.0	231.0	230.0					3																	124646629		2203	4300	6503	SO:0001589	frameshift_variant	56667	exon2			.	AF286113		3q21.2	2007-01-17	2006-03-14		ENSG00000173702	ENSG00000173702		"""Mucins"""	7511	protein-coding gene	gene with protein product		612181	"""down-regulated in colon cancer 1"", ""mucin 13, epithelial transmembrane"""	DRCC1		11278439	Standard	NM_033049		Approved		uc003ehq.2	Q9H3R2	OTTHUMG00000159484	ENST00000311075.3:c.261delC	chr3.hg19:g.124646629delG	ENSP00000312235:p.Pro87fs	257.0	0.0		244.0	15.0	NM_033049	Q6UWD9|Q9NXT5	Frame_Shift_Del	DEL	ENST00000311075.3	hg19																																																																																				.	.		0.438	MUC13-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000355714.1	NM_033049	
SLC4A7	9497	hgsc.bcm.edu	37	3	27439766	27439766	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:27439766delA	ENST00000295736.5	-	17	2549	c.2479delT	c.(2479-2481)tggfs	p.W827fs	SLC4A7_ENST00000454389.1_Frame_Shift_Del_p.W836fs|SLC4A7_ENST00000428386.1_Frame_Shift_Del_p.W703fs|SLC4A7_ENST00000445684.1_Frame_Shift_Del_p.W823fs|SLC4A7_ENST00000435667.2_Frame_Shift_Del_p.W712fs|SLC4A7_ENST00000455077.1_Frame_Shift_Del_p.W708fs|SLC4A7_ENST00000437179.1_Frame_Shift_Del_p.W708fs|SLC4A7_ENST00000388777.4_Frame_Shift_Del_p.W377fs|SLC4A7_ENST00000425128.2_3'UTR|SLC4A7_ENST00000446700.1_Frame_Shift_Del_p.W819fs|SLC4A7_ENST00000440156.1_Frame_Shift_Del_p.W823fs	NM_003615.4	NP_003606.3	Q9Y6M7	S4A7_HUMAN	solute carrier family 4, sodium bicarbonate cotransporter, member 7	827					auditory receptor cell development (GO:0060117)|bicarbonate transport (GO:0015701)|cochlear nucleus development (GO:0021747)|ion transport (GO:0006811)|retina vasculature morphogenesis in camera-type eye (GO:0061299)|retinal cell programmed cell death (GO:0046666)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|sodium:bicarbonate symporter activity (GO:0008510)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(12)|lung(9)|ovary(4)|skin(1)	38					Sodium bicarbonate(DB01390)	ATGACACACCAAAAGAGCACA	0.368																																					p.W827fs		Atlas-INDEL	.											.	SLC4A7	119	.	0			c.2480delG						.						116.0	117.0	117.0					3																	27439766		2203	4300	6503	SO:0001589	frameshift_variant	9497	exon17			.	AB012130	CCDS33721.1, CCDS58819.1, CCDS58820.1	3p24.1	2013-05-22			ENSG00000033867	ENSG00000033867		"""Solute carriers"""	11033	protein-coding gene	gene with protein product		603353		SLC4A6		10198178, 9610397	Standard	NM_003615		Approved	NBC3, SBC2	uc003cdv.4	Q9Y6M7	OTTHUMG00000155679	ENST00000295736.5:c.2479delT	chr3.hg19:g.27439766delA	ENSP00000295736:p.Trp827fs	241.0	0.0		183.0	11.0	NM_003615	A6NIA8|B2CI53|B5M449|B5M451|B5M452|B5M453|B6DY52|B6DY53|C9JST9|D3K174|D3K175|O60350|Q6AHZ9|Q9HC88|Q9UIB9	Frame_Shift_Del	DEL	ENST00000295736.5	hg19	CCDS33721.1																																																																																			.	.		0.368	SLC4A7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000341230.2	NM_003615	
RFC1	5981	hgsc.bcm.edu	37	4	39322284	39322284	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:39322284delT	ENST00000381897.1	-	9	947	c.814delA	c.(814-816)acafs	p.T272fs	RFC1_ENST00000418436.1_5'UTR|RFC1_ENST00000349703.2_Frame_Shift_Del_p.T272fs	NM_001204747.1|NM_002913.4	NP_001191676.1|NP_002904.3	P35251	RFC1_HUMAN	replication factor C (activator 1) 1, 145kDa	272					DNA repair (GO:0006281)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA-dependent DNA replication (GO:0006261)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|positive regulation of catalytic activity (GO:0043085)|positive regulation of transcription, DNA-templated (GO:0045893)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|telomere maintenance via telomerase (GO:0007004)|transcription, DNA-templated (GO:0006351)|transcription-coupled nucleotide-excision repair (GO:0006283)	cell junction (GO:0030054)|DNA replication factor C complex (GO:0005663)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA clamp loader activity (GO:0003689)|double-stranded DNA binding (GO:0003690)|enzyme activator activity (GO:0008047)|sequence-specific DNA binding (GO:0043565)			haematopoietic_and_lymphoid_tissue(2)|large_intestine(9)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	16						ACTTGTGCTGTTTTTACTAGG	0.323																																					p.T272fs	Colon(109;59 1555 12203 17579 39824)|Esophageal Squamous(18;360 542 16186 28570 51157)	Atlas-INDEL	.											.	RFC1	114	.	0			c.815delC						.						82.0	78.0	80.0					4																	39322284		2203	4298	6501	SO:0001589	frameshift_variant	5981	exon9			.	L23320	CCDS3450.1, CCDS56329.1	4p14-p13	2010-04-21	2002-08-29		ENSG00000035928	ENSG00000035928		"""ATPases / AAA-type"""	9969	protein-coding gene	gene with protein product		102579	"""replication factor C (activator 1) 1 (145kD)"""			8114700	Standard	NM_002913		Approved	A1, PO-GA, RFC140, MHCBFB	uc003gty.2	P35251	OTTHUMG00000099363	ENST00000381897.1:c.814delA	chr4.hg19:g.39322284delT	ENSP00000371321:p.Thr272fs	191.0	0.0		150.0	10.0	NM_002913	A8K6E7|Q5XKF5|Q6PKU0|Q86V41|Q86V46	Frame_Shift_Del	DEL	ENST00000381897.1	hg19	CCDS56329.1																																																																																			.	.		0.323	RFC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216808.1	NM_002913	
SLC30A1	7779	hgsc.bcm.edu	37	1	211751711	211751711	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:211751711delC	ENST00000367001.4	-	1	373	c.244delG	c.(244-246)gctfs	p.A82fs		NM_021194.2	NP_067017.2	Q9Y6M5	ZNT1_HUMAN	solute carrier family 30 (zinc transporter), member 1	82					cadmium ion transmembrane transport (GO:0070574)|calcium ion import (GO:0070509)|cellular calcium ion homeostasis (GO:0006874)|cellular zinc ion homeostasis (GO:0006882)|detoxification of cadmium ion (GO:0071585)|in utero embryonic development (GO:0001701)|negative regulation of calcium ion import (GO:0090281)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of zinc ion transmembrane import (GO:0071584)|transmembrane transport (GO:0055085)|zinc ion transport (GO:0006829)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)	calcium channel inhibitor activity (GO:0019855)|zinc ion transmembrane transporter activity (GO:0005385)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|liver(1)|lung(1)|ovary(3)|prostate(1)	11				OV - Ovarian serous cystadenocarcinoma(81;0.00535)|GBM - Glioblastoma multiforme(131;0.051)|all cancers(67;0.0604)|Epithelial(68;0.0978)		TTCACCAGAGCCCCCATTACC	0.667																																					p.A82fs		Atlas-INDEL	.											.	SLC30A1	27	.	0			c.245delC						.						39.0	48.0	45.0					1																	211751711		2203	4300	6503	SO:0001589	frameshift_variant	7779	exon1			.	AF323590	CCDS1499.1	1q32.3	2013-05-22			ENSG00000170385	ENSG00000170385		"""Solute carriers"""	11012	protein-coding gene	gene with protein product		609521		ZNT1			Standard	NM_021194		Approved	ZRC1	uc001hio.1	Q9Y6M5	OTTHUMG00000036995	ENST00000367001.4:c.244delG	chr1.hg19:g.211751711delC	ENSP00000355968:p.Ala82fs	152.0	0.0		166.0	10.0	NM_021194	Q0VAK9|Q9BZF6	Frame_Shift_Del	DEL	ENST00000367001.4	hg19	CCDS1499.1																																																																																			.	.		0.667	SLC30A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104738.2		
KMT2A	4297	hgsc.bcm.edu	37	11	118342966	118342966	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:118342966delA	ENST00000389506.5	+	3	1092	c.1092delA	c.(1090-1092)tcafs	p.S364fs	KMT2A_ENST00000354520.4_Frame_Shift_Del_p.S364fs|KMT2A_ENST00000534358.1_Frame_Shift_Del_p.S364fs			Q03164	KMT2A_HUMAN	lysine (K)-specific methyltransferase 2A	364					anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|DNA methylation (GO:0006306)|embryonic hemopoiesis (GO:0035162)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|histone H4-K16 acetylation (GO:0043984)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cellular response to drug (GO:2001040)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transporter activity (GO:0032411)|protein complex assembly (GO:0006461)|regulation of histone H3-K4 methylation (GO:0051569)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|histone methyltransferase complex (GO:0035097)|MLL1 complex (GO:0071339)|nucleus (GO:0005634)	AT DNA binding (GO:0003680)|chromatin binding (GO:0003682)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|identical protein binding (GO:0042802)|lysine-acetylated histone binding (GO:0070577)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|unmethylated CpG binding (GO:0045322)|zinc ion binding (GO:0008270)										TTCCTTCTTCAAAAAGGACAG	0.423																																					p.S364X		Atlas-INDEL	.											.	MLL	548	.	0			c.1091delC						.						65.0	67.0	66.0					11																	118342966		2200	4296	6496	SO:0001589	frameshift_variant	4297	exon3			.	L04284	CCDS31686.1, CCDS55791.1	11q23	2014-09-17	2013-05-09	2013-05-09	ENSG00000118058	ENSG00000118058		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	7132	protein-coding gene	gene with protein product		159555	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog)"", ""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila)"""	MLL		1720549	Standard	NM_001197104		Approved	TRX1, HRX, ALL-1, HTRX1, CXXC7, MLL1A		Q03164	OTTHUMG00000166337	ENST00000389506.5:c.1092delA	chr11.hg19:g.118342966delA	ENSP00000374157:p.Ser364fs	346.0	0.0		249.0	15.0	NM_001197104	E9PQG7|Q13743|Q13744|Q14845|Q16364|Q59FF2|Q6UBD1|Q9HBJ3|Q9UD94|Q9UMA3	Frame_Shift_Del	DEL	ENST00000389506.5	hg19	CCDS31686.1																																																																																			.	.		0.423	KMT2A-015	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399085.2	NM_005933	
MOG	4340	hgsc.bcm.edu	37	6	29640726	29640726	+	IGR	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:29640726delG	ENST00000376917.3	+	0	2160				ZFP57_ENST00000488757.1_Frame_Shift_Del_p.H388fs|ZFP57_ENST00000376883.1_Frame_Shift_Del_p.H368fs|ZFP57_ENST00000376881.3_Frame_Shift_Del_p.H368fs	NM_002433.4|NM_206809.3	NP_002424.3|NP_996532.2	Q16653	MOG_HUMAN	myelin oligodendrocyte glycoprotein						cell adhesion (GO:0007155)|central nervous system development (GO:0007417)|positive regulation of MyD88-dependent toll-like receptor signaling pathway (GO:0034126)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(8)|ovary(1)|skin(2)	19						AAAGAACAATGGGGGCAACAG	0.517																																					p.H388fs		Atlas-INDEL	.											.	ZFP57	80	.	0			c.1163delA						.						325.0	353.0	344.0					6																	29640726		1267	2556	3823	SO:0001628	intergenic_variant	346171	exon4			.		CCDS4667.1, CCDS34366.1, CCDS34367.1, CCDS34368.1, CCDS34369.1, CCDS34370.1, CCDS47394.1, CCDS47395.1, CCDS47395.2, CCDS54977.1	6p22.1	2014-01-16			ENSG00000204655	ENSG00000204655		"""Immunoglobulin superfamily / V-set domain containing"", ""Butyrophilins"""	7197	protein-coding gene	gene with protein product		159465					Standard	NM_002433		Approved	BTN6, BTNL11	uc003nne.3	Q16653	OTTHUMG00000031099		chr6.hg19:g.29640726delG		232.0	0.0		160.0	11.0	NM_001109809	A6NDR4|A6NNJ9|A8MY31|B0UZR9|E9PGF0|F8W9D5|O00713|O00714|O00715|Q13054|Q13055|Q14855|Q29ZN8|Q56UY0|Q5JNX7|Q5JNY1|Q5JNY2|Q5JNY4|Q5SSB5|Q5SSB6|Q5STL9|Q5STM0|Q5STM1|Q5STM2|Q5STM5|Q5SUK5|Q5SUK7|Q5SUK8|Q5SUK9|Q5SUL0|Q5SUL1|Q8IYG5|Q92891|Q92892|Q92893|Q92894|Q92895|Q93053|Q96KU9|Q96KV0|Q96KV1|Q99605	Frame_Shift_Del	DEL	ENST00000376917.3	hg19	CCDS34370.1																																																																																			.	.		0.517	MOG-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076160.3	NM_002433	
RAB10	10890	hgsc.bcm.edu	37	2	26350743	26350743	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:26350743delT	ENST00000264710.4	+	5	941	c.442delT	c.(442-444)tttfs	p.F149fs	RAB10_ENST00000462003.1_3'UTR	NM_016131.4	NP_057215.3	P61026	RAB10_HUMAN	RAB10, member RAS oncogene family	149					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)					TGGTATTAGGTTTTTTGAGAC	0.348																																					p.R147fs		Atlas-INDEL	.											.	RAB10	14	.	0			c.441delG						.						168.0	161.0	163.0					2																	26350743		2203	4300	6503	SO:0001589	frameshift_variant	10890	exon5			.	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.442delT	chr2.hg19:g.26350743delT	ENSP00000264710:p.Phe149fs	199.0	0.0		166.0	11.0	NM_016131	D6W538|O88386|Q6IA52|Q9D7X6|Q9H0T3	Frame_Shift_Del	DEL	ENST00000264710.4	hg19	CCDS1720.1																																																																																			.	.		0.348	RAB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211610.1	NM_016131	
AKNAD1	254268	hgsc.bcm.edu	37	1	109395035	109395035	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:109395035delT	ENST00000370001.3	-	2	520	c.252delA	c.(250-252)aaafs	p.K84fs	AKNAD1_ENST00000369995.3_Frame_Shift_Del_p.K84fs|AKNAD1_ENST00000369994.1_Frame_Shift_Del_p.K84fs|AKNAD1_ENST00000357393.4_Intron	NM_152763.4	NP_689976.2	Q5T1N1	AKND1_HUMAN	AKNA domain containing 1	84						cytoplasm (GO:0005737)				breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(10)|ovary(3)|prostate(6)|skin(3)|stomach(2)	32						CTTTCTCGTCTTTTTTGTTGG	0.403																																					p.D85fs		Atlas-INDEL	.											.,1	AKNAD1	83	.	0			c.253delG						.						122.0	117.0	118.0					1																	109395035		2203	4300	6503	SO:0001589	frameshift_variant	254268	exon2			.	AK095517	CCDS791.2	1p13.3	2009-10-29	2009-10-29	2009-10-29	ENSG00000162641	ENSG00000162641			28398	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 62"""	C1orf62			Standard	NM_152763		Approved	MGC26989	uc001dwa.4	Q5T1N1	OTTHUMG00000011231	ENST00000370001.3:c.252delA	chr1.hg19:g.109395035delT	ENSP00000359018:p.Lys84fs	271.0	0.0		198.0	13.0	NM_152763	B9EK62|Q5T1N0|Q8N990|Q8NCN9	Frame_Shift_Del	DEL	ENST00000370001.3	hg19	CCDS791.2																																																																																			.	.		0.403	AKNAD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030923.2	NM_152763	
KIAA0319	9856	hgsc.bcm.edu	37	6	24596508	24596508	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:24596508delC	ENST00000378214.3	-	3	918	c.394delG	c.(394-396)gacfs	p.D132fs	KIAA0319_ENST00000430948.2_Frame_Shift_Del_p.D87fs|KIAA0319_ENST00000535378.1_Frame_Shift_Del_p.D123fs|KIAA0319_ENST00000543707.1_Frame_Shift_Del_p.D132fs|KIAA0319_ENST00000537886.1_Frame_Shift_Del_p.D132fs	NM_001168375.1|NM_014809.3	NP_001161847.1|NP_055624.2	Q5VV43	K0319_HUMAN	KIAA0319	132					negative regulation of dendrite development (GO:2000171)|neuron migration (GO:0001764)	early endosome (GO:0005769)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(3)|endometrium(6)|kidney(3)|large_intestine(11)|lung(19)|ovary(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)	53						TCAGGTGAGTCCCCCCAGATC	0.547																																					p.D132fs		Atlas-INDEL	.											.	KIAA0319	117	.	0			c.395delA						.						70.0	77.0	75.0					6																	24596508		2203	4300	6503	SO:0001589	frameshift_variant	9856	exon3			.	AB002317	CCDS34348.1, CCDS54969.1, CCDS54970.1, CCDS54971.1, CCDS75409.1	6p22.3	2013-12-13			ENSG00000137261	ENSG00000137261			21580	protein-coding gene	gene with protein product	"""neuronal migration"""	609269				9205841, 15514892	Standard	NM_014809		Approved	NMIG	uc003neh.1	Q5VV43	OTTHUMG00000014358	ENST00000378214.3:c.394delG	chr6.hg19:g.24596508delC	ENSP00000367459:p.Asp132fs	140.0	0.0		124.0	10.0	NM_001168375	A7MD37|B2RTU7|B4DHA7|B4DK75|B7ZML3|F5H123|Q9UJC8|Q9Y4G7	Frame_Shift_Del	DEL	ENST00000378214.3	hg19	CCDS34348.1																																																																																			.	.		0.547	KIAA0319-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040009.1	NM_014809	
APBB1IP	54518	hgsc.bcm.edu	37	10	26802473	26802473	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:26802473delT	ENST00000376236.4	+	8	1152	c.697delT	c.(697-699)tttfs	p.F234fs		NM_019043.3	NP_061916.3	Q7Z5R6	AB1IP_HUMAN	amyloid beta (A4) precursor protein-binding, family B, member 1 interacting protein	234	Ras-associating. {ECO:0000255|PROSITE- ProRule:PRU00166}.				blood coagulation (GO:0007596)|platelet activation (GO:0030168)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(27)|skin(7)|upper_aerodigestive_tract(1)	45						ATCAGAGAGGTTTTTTGAAGA	0.343																																					p.R232fs		Atlas-INDEL	.											.	APBB1IP	117	.	0			c.696delG						.						67.0	72.0	70.0					10																	26802473		2203	4300	6503	SO:0001589	frameshift_variant	54518	exon8			.	AB085852	CCDS31167.1	10p12.1	2013-01-10			ENSG00000077420	ENSG00000077420		"""Pleckstrin homology (PH) domain containing"""	17379	protein-coding gene	gene with protein product	"""Rap1-GTP-interacting adaptor molecule"""	609036				9407065	Standard	NM_019043		Approved	INAG1, RIAM	uc001iss.3	Q7Z5R6	OTTHUMG00000017841	ENST00000376236.4:c.697delT	chr10.hg19:g.26802473delT	ENSP00000365411:p.Phe234fs	270.0	0.0		156.0	10.0	NM_019043	Q8IWS8|Q8IYL7|Q8IZZ7	Frame_Shift_Del	DEL	ENST00000376236.4	hg19	CCDS31167.1																																																																																			.	.		0.343	APBB1IP-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047270.1	NM_019043	
FYN	2534	hgsc.bcm.edu	37	6	112021336	112021336	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:112021336delC	ENST00000354650.3	-	9	1439	c.833delG	c.(832-834)ggafs	p.G278fs	FYN_ENST00000229471.4_Intron|FYN_ENST00000368667.2_Frame_Shift_Del_p.G278fs|FYN_ENST00000538466.1_Intron|FYN_ENST00000476769.2_5'UTR|FYN_ENST00000229470.5_Intron|FYN_ENST00000368678.4_Intron|FYN_ENST00000368682.3_Intron|FYN_ENST00000356013.2_Intron	NM_002037.5	NP_002028.1	P06241	FYN_HUMAN	FYN proto-oncogene, Src family tyrosine kinase	278	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activated T cell proliferation (GO:0050798)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|cellular response to peptide hormone stimulus (GO:0071375)|dendrite morphogenesis (GO:0048813)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|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)|feeding behavior (GO:0007631)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain development (GO:0030900)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|learning (GO:0007612)|leukocyte migration (GO:0050900)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of gene expression (GO:0010629)|negative regulation of protein catabolic process (GO:0042177)|neuron migration (GO:0001764)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein localization to nucleus (GO:1900182)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cell shape (GO:0008360)|regulation of defense response to virus by virus (GO:0050690)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	cytosol (GO:0005829)|endosome (GO:0005768)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	ATP binding (GO:0005524)|ephrin receptor binding (GO:0046875)|glycoprotein binding (GO:0001948)|growth factor receptor binding (GO:0070851)|metal ion binding (GO:0046872)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(17)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	30		all_cancers(87;1.37e-05)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.00125)|Colorectal(196;0.0211)		all cancers(137;0.0451)|OV - Ovarian serous cystadenocarcinoma(136;0.0476)|Epithelial(106;0.102)	Dasatinib(DB01254)	CTGCCCATTTCCCAGTCTCTT	0.478																																					p.G278fs		Atlas-INDEL	.											.	FYN	108	.	0			c.834delA						.						137.0	138.0	138.0					6																	112021336		2203	4300	6503	SO:0001589	frameshift_variant	2534	exon9			.	AK056699	CCDS5094.1, CCDS5095.1, CCDS5096.1	6q21	2014-06-25	2014-06-25		ENSG00000010810	ENSG00000010810		"""SH2 domain containing"""	4037	protein-coding gene	gene with protein product		137025	"""FYN oncogene related to SRC, FGR, YES"""			3526330	Standard	NM_002037		Approved	SYN, SLK, MGC45350	uc003pvh.3	P06241	OTTHUMG00000016305	ENST00000354650.3:c.833delG	chr6.hg19:g.112021336delC	ENSP00000346671:p.Gly278fs	193.0	0.0		169.0	12.0	NM_002037	B5BU57|E1P557|H0UI48|Q16248|Q5R3A6|Q5R3A7|Q8N5D7	Frame_Shift_Del	DEL	ENST00000354650.3	hg19	CCDS5094.1																																																																																			.	.		0.478	FYN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043655.1		
ERAL1	26284	hgsc.bcm.edu	37	17	27182148	27182148	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:27182148delT	ENST00000254928.5	+	1	193	c.96delT	c.(94-96)cctfs	p.P32fs	FAM222B_ENST00000583953.1_5'Flank|ERAL1_ENST00000578001.1_3'UTR	NM_005702.2	NP_005693.1	O75616	ERAL1_HUMAN	Era-like 12S mitochondrial rRNA chaperone 1	32					ribosomal small subunit assembly (GO:0000028)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)|poly(A) RNA binding (GO:0044822)|ribosomal small subunit binding (GO:0043024)|rRNA binding (GO:0019843)			endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|skin(2)	11	all_cancers(5;2.12e-15)|all_epithelial(6;3.44e-19)|Lung NSC(42;0.01)		Epithelial(11;1.12e-05)|all cancers(11;5.32e-05)|BRCA - Breast invasive adenocarcinoma(11;0.000272)|OV - Ovarian serous cystadenocarcinoma(11;0.105)			GGGTGATCCCTTTTTCCTCAC	0.627																																					p.P32fs		Atlas-INDEL	.											ERAL1,NS,carcinoma,0,1	ERAL1	28	.	0			c.95delC						.						89.0	77.0	81.0					17																	27182148		2203	4300	6503	SO:0001589	frameshift_variant	26284	exon1			.	AF082657	CCDS11244.1	17q11.2	2013-05-22	2013-05-22		ENSG00000132591	ENSG00000132591			3424	protein-coding gene	gene with protein product		607435	"""Era (E. coli G-protein homolog)-like 1"", ""Era G-protein-like 1 (E. coli)"""			10945472, 20604745	Standard	NM_005702		Approved	HERA-B	uc002hcy.1	O75616	OTTHUMG00000132675	ENST00000254928.5:c.96delT	chr17.hg19:g.27182148delT	ENSP00000254928:p.Pro32fs	214.0	0.0		175.0	13.0	NM_005702	B3KN21|C9JEC6|O75617|Q8WUY4|Q96LE2|Q96TC0	Frame_Shift_Del	DEL	ENST00000254928.5	hg19	CCDS11244.1																																																																																			.	.		0.627	ERAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255937.2		
RNF111	54778	hgsc.bcm.edu	37	15	59383348	59383348	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:59383348delA	ENST00000557998.1	+	12	3021	c.2734delA	c.(2734-2736)aaafs	p.K913fs	RNF111_ENST00000434298.1_Frame_Shift_Del_p.K922fs|RNF111_ENST00000348370.4_Frame_Shift_Del_p.K913fs|RNF111_ENST00000559209.1_Frame_Shift_Del_p.K922fs|RNF111_ENST00000561186.1_Frame_Shift_Del_p.K922fs	NM_001270530.1	NP_001257459.1	Q6ZNA4	RN111_HUMAN	ring finger protein 111	913					gene expression (GO:0010467)|pattern specification process (GO:0007389)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|protein polyubiquitination (GO:0000209)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent SMAD protein catabolic process (GO:0030579)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	ligase activity (GO:0016874)|SUMO polymer binding (GO:0032184)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(11)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35				all cancers(107;0.194)		ACATAAATACAAAAAGGTAAG	0.333																																					p.Y920X	NSCLC(72;983 1365 10746 34387 47081)	Atlas-INDEL	.											.	RNF111	179	.	0			c.2760delC						.						88.0	93.0	91.0					15																	59383348		2192	4291	6483	SO:0001589	frameshift_variant	54778	exon12			.	AL157474	CCDS10169.1, CCDS58365.1, CCDS58366.1	15q21	2013-01-09			ENSG00000157450	ENSG00000157450		"""RING-type (C3HC4) zinc fingers"""	17384	protein-coding gene	gene with protein product		605840				11298452	Standard	NM_017610		Approved	ARK, Arkadia, FLJ38008, DKFZP761D081	uc002aft.4	Q6ZNA4	OTTHUMG00000132716	ENST00000557998.1:c.2734delA	chr15.hg19:g.59383348delA	ENSP00000452732:p.Lys913fs	248.0	0.0		204.0	13.0	NM_001270528	C9JUS4|H0YN55|Q6P9A4|Q6ZMU2|Q7L428|Q7Z346|Q8N1P9|Q8WUA3|Q9NSR1	Frame_Shift_Del	DEL	ENST00000557998.1	hg19	CCDS58366.1																																																																																			.	.		0.333	RNF111-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000416012.1	NM_017610	
EXOSC9	5393	hgsc.bcm.edu	37	4	122723068	122723068	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:122723068delA	ENST00000243498.5	+	2	261	c.153delA	c.(151-153)ggafs	p.G51fs	EXOSC9_ENST00000379663.3_Frame_Shift_Del_p.G51fs|EXOSC9_ENST00000512454.1_Frame_Shift_Del_p.G35fs|EXOSC9_ENST00000509980.1_3'UTR	NM_005033.2	NP_005024.2	Q06265	EXOS9_HUMAN	exosome component 9	51	ARE binding.				exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|immune response (GO:0006955)|mRNA metabolic process (GO:0016071)|nuclear mRNA surveillance (GO:0071028)|nuclear polyadenylation-dependent rRNA catabolic process (GO:0071035)|nuclear-transcribed mRNA catabolic process (GO:0000956)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|positive regulation of cell growth (GO:0030307)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|exosome (RNase complex) (GO:0000178)|intermediate filament cytoskeleton (GO:0045111)|nuclear exosome (RNase complex) (GO:0000176)|nucleolus (GO:0005730)|nucleus (GO:0005634)	3'-5'-exoribonuclease activity (GO:0000175)|AU-rich element binding (GO:0017091)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(4)|urinary_tract(1)	16						TGGAACTTGGAAAAACAAGGT	0.388																																					p.G51fs		Atlas-INDEL	.											.	EXOSC9	51	.	0			c.152delG						.						103.0	93.0	96.0					4																	122723068		2203	4300	6503	SO:0001589	frameshift_variant	5393	exon2			.	M58460	CCDS3722.2, CCDS34057.1	4q27	2010-05-07	2004-06-16	2004-06-18	ENSG00000123737	ENSG00000123737	3.1.13.-		9137	protein-coding gene	gene with protein product	"""polymyositis/scleroderma autoantigen 1 (75kD)"""	606180	"""polymyositis/scleroderma autoantigen 1, 75kDa"""	PMSCL1			Standard	XR_427545		Approved	PM/Scl-75, Rrp45p, RRP45, p5, p6	uc003idz.3	Q06265	OTTHUMG00000128783	ENST00000243498.5:c.153delA	chr4.hg19:g.122723068delA	ENSP00000243498:p.Gly51fs	293.0	0.0		180.0	11.0	NM_001034194	Q12883|Q4W5P5|Q86Y41|Q86Y48	Frame_Shift_Del	DEL	ENST00000243498.5	hg19	CCDS3722.2																																																																																			.	.		0.388	EXOSC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250708.2	NM_005033	
COL11A1	1301	hgsc.bcm.edu	37	1	103461421	103461421	+	Splice_Site	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:103461421delT	ENST00000370096.3	-	28	2651	c.2339delA	c.(2338-2340)aag>ag	p.K780fs	COL11A1_ENST00000353414.4_Splice_Site_p.K741fs|COL11A1_ENST00000512756.1_Splice_Site_p.K664fs|COL11A1_ENST00000358392.2_Splice_Site_p.K792fs	NM_001854.3	NP_001845.3	P12107	COBA1_HUMAN	collagen, type XI, alpha 1	780	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)		AAATTTTACCTTTTCACCTTT	0.269																																					p.K792fs		Atlas-INDEL	.											.	COL11A1	972	.	0			c.2376delG						.						68.0	76.0	73.0					1																	103461421		2202	4290	6492	SO:0001630	splice_region_variant	1301	exon28			.	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.2340+1A>-	chr1.hg19:g.103461421delT		232.0	0.0		163.0	10.0	NM_080629	B1ASK7|D3DT73|E9PCU0|Q14034|Q149N0|Q9UIT4|Q9UIT5|Q9UIT6	Frame_Shift_Del	DEL	ENST00000370096.3	hg19	CCDS778.1																																																																																			.	.		0.269	COL11A1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029997.1	NM_080630	Frame_Shift_Del
TUBA3D	113457	hgsc.bcm.edu	37	2	132238225	132238225	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:132238225delG	ENST00000321253.6	+	4	1066	c.959delG	c.(958-960)aggfs	p.R320fs		NM_080386.3	NP_525125.2	Q13748	TBA3C_HUMAN	tubulin, alpha 3d	320					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|microtubule-based process (GO:0007017)|protein folding (GO:0006457)|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)			breast(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(18)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	32				BRCA - Breast invasive adenocarcinoma(221;0.13)		ATGTTGTACAGGGGGGACGTG	0.567																																					p.R320fs	Ovarian(137;2059 2432 35543 39401)	Atlas-INDEL	.											.	TUBA3D	60	.	0			c.958delA						.						126.0	130.0	129.0					2																	132238225		2203	4300	6503	SO:0001589	frameshift_variant	113457	exon4			.	K03460	CCDS33290.1	2q21.1	2007-03-16			ENSG00000075886	ENSG00000075886		"""Tubulins"""	24071	protein-coding gene	gene with protein product	"""alpha-tubulin isotype H2-alpha"""					3785200	Standard	NM_080386		Approved	H2-ALPHA	uc002tsu.4	Q13748	OTTHUMG00000153600	ENST00000321253.6:c.959delG	chr2.hg19:g.132238225delG	ENSP00000326042:p.Arg320fs	418.0	0.0		243.0	15.0	NM_080386	A6NJQ0|Q5W099|Q6PEY3|Q96F18	Frame_Shift_Del	DEL	ENST00000321253.6	hg19	CCDS33290.1																																																																																			.	.		0.567	TUBA3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331800.2	NM_080386	
C12orf40	283461	hgsc.bcm.edu	37	12	40041671	40041671	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:40041671delT	ENST00000324616.5	+	6	616	c.462delT	c.(460-462)tctfs	p.S154fs	C12orf40_ENST00000405531.3_Frame_Shift_Del_p.S154fs|C12orf40_ENST00000398716.1_Frame_Shift_Del_p.S77fs	NM_001031748.2	NP_001026918.2	Q86WS4	CL040_HUMAN	chromosome 12 open reading frame 40	154										breast(4)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(14)|ovary(6)|prostate(1)|skin(2)	38						CTCCATCATCTTTTTCAGTGG	0.363																																					p.S154fs		Atlas-INDEL	.											.	C12orf40	118	.	0			c.461delC						.						90.0	86.0	88.0					12																	40041671		1836	4093	5929	SO:0001589	frameshift_variant	283461	exon6			.	AK097445	CCDS41770.1	12q12	2008-08-04			ENSG00000180116	ENSG00000180116			26846	protein-coding gene	gene with protein product						12477932	Standard	XM_005268806		Approved	FLJ40126	uc001rmc.3	Q86WS4	OTTHUMG00000133567	ENST00000324616.5:c.462delT	chr12.hg19:g.40041671delT	ENSP00000317671:p.Ser154fs	310.0	0.0		221.0	15.0	NM_001031748	B7WNU1|Q8IXY6|Q8N818|V9HW02	Frame_Shift_Del	DEL	ENST00000324616.5	hg19	CCDS41770.1																																																																																			.	.		0.363	C12orf40-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257664.2	NM_173599	
CIC	23152	hgsc.bcm.edu	37	19	42794469	42794469	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:42794469delC	ENST00000575354.2	+	10	1589	c.1549delC	c.(1549-1551)cccfs	p.P518fs	CIC_ENST00000160740.3_Frame_Shift_Del_p.P518fs|CIC_ENST00000572681.2_Frame_Shift_Del_p.P1427fs	NM_015125.3	NP_055940.3	Q96RK0	CIC_HUMAN	capicua transcriptional repressor	518	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.P518fs*5(1)		autonomic_ganglia(1)|breast(5)|central_nervous_system(32)|endometrium(10)|kidney(2)|large_intestine(7)|lung(9)|ovary(7)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	82		Prostate(69;0.00682)				GCCCCCAGGGCCCCCGGATCC	0.627			"""Mis, F, S"""		oligodendroglioma																																p.G516fs		Atlas-INDEL	.		Rec	yes		19	19q13.2	23152	capicua homolog		O	.	CIC	249	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1548delG						.						64.0	64.0	64.0					19																	42794469		2203	4300	6503	SO:0001589	frameshift_variant	23152	exon10			.	AB002304	CCDS12601.1	19q13.2	2013-03-15	2013-03-15		ENSG00000079432	ENSG00000079432			14214	protein-coding gene	gene with protein product		612082	"""capicua (Drosophila) homolog"", ""capicua homolog (Drosophila)"""			12393275, 15981098	Standard	NM_015125		Approved	KIAA0306	uc002otf.1	Q96RK0		ENST00000575354.2:c.1549delC	chr19.hg19:g.42794469delC	ENSP00000458663:p.Pro518fs	270.0	0.0		222.0	14.0	NM_015125	Q7LGI1|Q9UEG5|Q9Y6T1	Frame_Shift_Del	DEL	ENST00000575354.2	hg19	CCDS12601.1																																																																																			.	.		0.627	CIC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438532.2		
VPS37C	55048	hgsc.bcm.edu	37	11	60899827	60899827	+	Frame_Shift_Del	DEL	G	G	-	rs199606009		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:60899827delG	ENST00000301765.5	-	5	765	c.533delC	c.(532-534)ccgfs	p.P178fs		NM_017966.4	NP_060436.4	A5D8V6	VP37C_HUMAN	vacuolar protein sorting 37 homolog C (S. cerevisiae)	178	Pro-rich.				endosomal transport (GO:0016197)|intracellular transport of virus (GO:0075733)|membrane organization (GO:0061024)|protein transport (GO:0015031)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	endosome membrane (GO:0010008)|ESCRT I complex (GO:0000813)|extracellular vesicular exosome (GO:0070062)				breast(1)|kidney(1)|large_intestine(3)|lung(1)|skin(1)	7						TGGGCGCACCGGGGGTGGTGG	0.682																																					p.P178fs		Atlas-INDEL	.											.	VPS37C	30	.	0			c.534delG						.						12.0	15.0	14.0					11																	60899827		2196	4283	6479	SO:0001589	frameshift_variant	55048	exon5			.	AK097326	CCDS31573.1	11q12.2	2008-02-05	2006-04-04			ENSG00000167987			26097	protein-coding gene	gene with protein product		610038	"""vacuolar protein sorting 37C (yeast)"""			15509564	Standard	XM_005274077		Approved	FLJ20847	uc001nqv.1	A5D8V6		ENST00000301765.5:c.533delC	chr11.hg19:g.60899827delG	ENSP00000301765:p.Pro178fs	206.0	0.0		196.0	12.0	NM_017966	Q8N3K4	Frame_Shift_Del	DEL	ENST00000301765.5	hg19	CCDS31573.1																																																																																			.	.		0.682	VPS37C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396467.1	NM_017966	
WDR78	79819	hgsc.bcm.edu	37	1	67292680	67292680	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:67292680delA	ENST00000371026.3	-	15	2217	c.2162delT	c.(2161-2163)ttafs	p.L721fs	WDR78_ENST00000431318.1_Frame_Shift_Del_p.L434fs|RP11-342H21.2_ENST00000456389.1_RNA	NM_024763.4	NP_079039.4	Q5VTH9	WDR78_HUMAN	WD repeat domain 78	721					hematopoietic progenitor cell differentiation (GO:0002244)					NS(1)|endometrium(3)|kidney(6)|large_intestine(6)|lung(10)|ovary(3)|skin(3)	32						AGAACAGCTTAAAAATACATC	0.328																																					p.L721fs		Atlas-INDEL	.											.	WDR78	102	.	0			c.2163delA						.						130.0	133.0	132.0					1																	67292680		2203	4300	6503	SO:0001589	frameshift_variant	79819	exon15			.	BX648840	CCDS635.1, CCDS44157.1	1p31.2	2014-02-21	2013-02-19	2013-02-19	ENSG00000152763	ENSG00000152763		"""WD repeat domain containing"""	26252	protein-coding gene	gene with protein product						21953912	Standard	NM_207014		Approved	DIC4, FLJ23129	uc001dcx.3	Q5VTH9	OTTHUMG00000009165	ENST00000371026.3:c.2162delT	chr1.hg19:g.67292680delA	ENSP00000360065:p.Leu721fs	461.0	0.0		360.0	24.0	NM_024763	A8K9W5|B5MDT3|H7BY80|Q5VTI0|Q8N5G5|Q9H5R9|Q9UF44	Frame_Shift_Del	DEL	ENST00000371026.3	hg19	CCDS635.1																																																																																			.	.		0.328	WDR78-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025404.1	NM_024763	
ZNF200	7752	hgsc.bcm.edu	37	16	3274133	3274133	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:3274133delT	ENST00000431561.3	-	5	1559	c.947delA	c.(946-948)aacfs	p.N316fs	ZNF200_ENST00000414144.2_Frame_Shift_Del_p.N316fs|ZNF200_ENST00000396868.3_Frame_Shift_Del_p.N315fs|ZNF200_ENST00000575948.1_Frame_Shift_Del_p.N315fs|ZNF200_ENST00000396870.4_Frame_Shift_Del_p.N315fs|ZNF200_ENST00000396871.4_Frame_Shift_Del_p.N315fs|AJ003147.9_ENST00000576468.1_RNA	NM_001145447.1|NM_003454.3	NP_001138919.1|NP_003445.2	P98182	ZN200_HUMAN	zinc finger protein 200	316					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(2)|kidney(2)|large_intestine(4)|lung(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	17						CTGACGGAAGTTTTTTCCACA	0.388																																					p.N316fs		Atlas-INDEL	.											.	ZNF200	36	.	0			c.948delC						.						112.0	111.0	111.0					16																	3274133		2197	4300	6497	SO:0001589	frameshift_variant	7752	exon5			.	AF060866	CCDS10497.1, CCDS42112.1, CCDS45395.1	16p13.3	2013-01-08			ENSG00000010539	ENSG00000010539		"""Zinc fingers, C2H2-type"""	12993	protein-coding gene	gene with protein product		603231				9288094, 9787081	Standard	NM_003454		Approved		uc002cuk.2	P98182	OTTHUMG00000129317	ENST00000431561.3:c.947delA	chr16.hg19:g.3274133delT	ENSP00000395723:p.Asn316fs	221.0	0.0		175.0	11.0	NM_003454	D3DUB7|D3DUB8|O15361|Q5XKM5|Q7Z5V1	Frame_Shift_Del	DEL	ENST00000431561.3	hg19	CCDS10497.1																																																																																			.	.		0.388	ZNF200-005	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000437545.1		
COPS2	9318	hgsc.bcm.edu	37	15	49436467	49436467	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:49436467delC	ENST00000388901.5	-	3	276	c.203delG	c.(202-204)ggafs	p.G68fs	COPS2_ENST00000542928.1_Intron|COPS2_ENST00000299259.6_Frame_Shift_Del_p.G68fs	NM_001143887.1|NM_004236.3	NP_001137359.1|NP_004227.1	P61201	CSN2_HUMAN	COP9 signalosome subunit 2	68					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)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(8)|prostate(1)|skin(2)	18		all_lung(180;0.0428)		all cancers(107;1.34e-07)|GBM - Glioblastoma multiforme(94;3.02e-05)		TGCTTTAAATCCCCATTCTCC	0.284																																					p.G68fs	NSCLC(36;322 1063 10349 30082 48062)|Esophageal Squamous(122;685 1633 15569 21293 52803)	Atlas-INDEL	.											.	COPS2	41	.	0			c.204delA						.						71.0	71.0	71.0					15																	49436467		2194	4277	6471	SO:0001589	frameshift_variant	9318	exon3			.	AF212227	CCDS32235.1, CCDS45257.1	15q21.2	2013-03-14	2013-03-14						30747	protein-coding gene	gene with protein product		604508	"""COP9 constitutive photomorphogenic homolog subunit 2 (Arabidopsis)"""			7776974, 9535219	Standard	NM_004236		Approved	TRIP15, ALIEN, CSN2	uc001zxh.3	P61201		ENST00000388901.5:c.203delG	chr15.hg19:g.49436467delC	ENSP00000373553:p.Gly68fs	238.0	0.0		149.0	12.0	NM_004236	O88950|Q15647|Q6FGP4|Q9BY54|Q9R249|Q9UNI2|Q9UNQ5	Frame_Shift_Del	DEL	ENST00000388901.5	hg19	CCDS32235.1																																																																																			.	.		0.284	COPS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417840.1	NM_004236	
BIN1	274	hgsc.bcm.edu	37	2	127821169	127821169	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:127821169delT	ENST00000316724.5	-	9	1163	c.752delA	c.(751-753)aacfs	p.N251fs	BIN1_ENST00000352848.3_Frame_Shift_Del_p.N220fs|BIN1_ENST00000393040.3_Frame_Shift_Del_p.N220fs|BIN1_ENST00000409400.1_Frame_Shift_Del_p.N220fs|BIN1_ENST00000346226.3_Frame_Shift_Del_p.N220fs|BIN1_ENST00000393041.3_Frame_Shift_Del_p.N220fs|BIN1_ENST00000376113.2_Frame_Shift_Del_p.N220fs|BIN1_ENST00000466111.1_5'UTR|BIN1_ENST00000357970.3_Frame_Shift_Del_p.N251fs|BIN1_ENST00000259238.4_Frame_Shift_Del_p.N220fs|BIN1_ENST00000348750.4_Frame_Shift_Del_p.N220fs|BIN1_ENST00000351659.3_Frame_Shift_Del_p.N251fs	NM_139343.2	NP_647593.1	O00499	BIN1_HUMAN	bridging integrator 1	251	BAR. {ECO:0000255|PROSITE- ProRule:PRU00361}.				cell proliferation (GO:0008283)|endocytosis (GO:0006897)|lipid tube assembly (GO:0060988)|muscle cell differentiation (GO:0042692)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of endocytosis (GO:0045807)|positive regulation of GTPase activity (GO:0043547)|regulation of cell cycle arrest (GO:0071156)|regulation of neuron differentiation (GO:0045664)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|axon initial segment (GO:0043194)|axon terminus (GO:0043679)|cerebellar mossy fiber (GO:0044300)|cytoplasm (GO:0005737)|I band (GO:0031674)|lipid tube (GO:0060987)|node of Ranvier (GO:0033268)|nucleus (GO:0005634)|synaptic vesicle (GO:0008021)|T-tubule (GO:0030315)|varicosity (GO:0043196)|Z disc (GO:0030018)	identical protein binding (GO:0042802)|tau protein binding (GO:0048156)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(3)|lung(6)|ovary(3)|prostate(3)|skin(3)	24	Colorectal(110;0.0831)			BRCA - Breast invasive adenocarcinoma(221;0.073)		CTTGTGGAAGTTTTCCTCCAG	0.632																																					p.N251fs		Atlas-INDEL	.											.	BIN1	85	.	0			c.753delC						.						94.0	70.0	78.0					2																	127821169		2203	4300	6503	SO:0001589	frameshift_variant	274	exon9			.	U68485	CCDS2137.1, CCDS2138.1, CCDS2139.1, CCDS2140.1, CCDS2141.1, CCDS2142.1, CCDS2143.1, CCDS42743.1, CCDS42744.1, CCDS46403.1	2q14	2014-09-17			ENSG00000136717	ENSG00000136717			1052	protein-coding gene	gene with protein product	"""amphiphysin II"""	601248		AMPHL		8725406, 8782822, 17676042	Standard	NM_004305		Approved	SH3P9, AMPH2	uc002tns.2	O00499	OTTHUMG00000131465	ENST00000316724.5:c.752delA	chr2.hg19:g.127821169delT	ENSP00000316779:p.Asn251fs	198.0	0.0		155.0	10.0	NM_139343	O00297|O00545|O43867|O60552|O60553|O60554|O60555|O75514|O75515|O75516|O75517|O75518|Q659B7|Q92944|Q99688	Frame_Shift_Del	DEL	ENST00000316724.5	hg19	CCDS2138.1																																																																																			.	.		0.632	BIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254298.2	NM_139343	
XCR1	2829	hgsc.bcm.edu	37	3	46062566	46062566	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:46062566delC	ENST00000309285.3	-	2	1230	c.874delG	c.(874-876)gtcfs	p.V292fs	XCR1_ENST00000542109.1_Frame_Shift_Del_p.V292fs	NM_001024644.1	NP_001019815.1	P46094	XCR1_HUMAN	chemokine (C motif) receptor 1	292					chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|inflammatory response (GO:0006954)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|release of sequestered calcium ion into cytosol (GO:0051209)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	chemokine receptor activity (GO:0004950)			NS(2)|endometrium(2)|kidney(2)|large_intestine(1)|lung(3)|ovary(1)|pancreas(1)|prostate(2)	14				BRCA - Breast invasive adenocarcinoma(193;0.00113)|KIRC - Kidney renal clear cell carcinoma(197;0.0172)|Kidney(197;0.0203)		CGGAACTTGACCCCCACGAAG	0.607																																					p.V292fs		Atlas-INDEL	.											.	XCR1	51	.	0			c.875delT						.						75.0	78.0	77.0					3																	46062566		2203	4300	6503	SO:0001589	frameshift_variant	2829	exon2			.		CCDS2736.1	3p21.3-p21.1	2012-11-19	2006-01-13	2002-08-23	ENSG00000173578	ENSG00000173578		"""GPCR / Class A : Chemokine receptors : X-C motif"""	1625	protein-coding gene	gene with protein product		600552	"""chemokine (C motif) XC receptor 1"""	GPR5, CCXCR1		7832990, 10400311	Standard	NM_005283		Approved		uc003cpf.3	P46094	OTTHUMG00000133449	ENST00000309285.3:c.874delG	chr3.hg19:g.46062566delC	ENSP00000310405:p.Val292fs	428.0	0.0		263.0	18.0	NM_001024644		Frame_Shift_Del	DEL	ENST00000309285.3	hg19	CCDS2736.1																																																																																			.	.		0.607	XCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257322.2		
DNAJC7	7266	hgsc.bcm.edu	37	17	40141477	40141477	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:40141477delA	ENST00000457167.4	-	7	934	c.698delT	c.(697-699)ttcfs	p.F233fs	DNAJC7_ENST00000426588.3_Frame_Shift_Del_p.F177fs|DNAJC7_ENST00000316603.7_Frame_Shift_Del_p.F177fs	NM_003315.3	NP_003306.3	Q99615	DNJC7_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 7	233					chaperone cofactor-dependent protein refolding (GO:0070389)|protein folding (GO:0006457)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	heat shock protein binding (GO:0031072)			endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)	9		all_cancers(22;0.00273)|Breast(137;0.00104)|all_epithelial(22;0.0305)				AGCCTGTACGAAAAACTGAAC	0.463																																					p.F233fs	Colon(63;618 1117 8600 10857 19751)	Atlas-INDEL	.											.	DNAJC7	51	.	0			c.699delC						.						151.0	142.0	145.0					17																	40141477		1909	4128	6037	SO:0001589	frameshift_variant	7266	exon7			.	U46571	CCDS45677.1, CCDS45678.1	17q11.2	2013-01-10				ENSG00000168259		"""Heat shock proteins / DNAJ (HSP40)"", ""Tetratricopeptide (TTC) repeat domain containing"""	12392	protein-coding gene	gene with protein product		601964		TTC2		8836031, 11147971	Standard	NR_029431		Approved	TPR2	uc002hyo.3	Q99615		ENST00000457167.4:c.698delT	chr17.hg19:g.40141477delA	ENSP00000406463:p.Phe233fs	240.0	0.0		170.0	11.0	NM_003315	Q7Z784	Frame_Shift_Del	DEL	ENST00000457167.4	hg19	CCDS45677.1																																																																																			.	.		0.463	DNAJC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453366.2		
NPHP1	4867	hgsc.bcm.edu	37	2	110881425	110881425	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:110881425delA	ENST00000393272.3	-	20	2239	c.2142delT	c.(2140-2142)tttfs	p.F714fs	NPHP1_ENST00000417665.1_Frame_Shift_Del_p.F693fs|NPHP1_ENST00000445609.2_Frame_Shift_Del_p.F659fs|AC013268.1_ENST00000390802.1_RNA|NPHP1_ENST00000316534.4_Frame_Shift_Del_p.F715fs|NPHP1_ENST00000355301.4_Frame_Shift_Del_p.F596fs	NM_000272.3|NM_207181.2	NP_000263.2|NP_997064.2	O15259	NPHP1_HUMAN	nephronophthisis 1 (juvenile)	714					actin cytoskeleton organization (GO:0030036)|cell projection organization (GO:0030030)|cellular protein localization (GO:0034613)|excretion (GO:0007588)|photoreceptor cell outer segment organization (GO:0035845)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|spermatid differentiation (GO:0048515)|visual behavior (GO:0007632)	cell-cell junction (GO:0005911)|ciliary transition zone (GO:0035869)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|membrane (GO:0016020)|motile cilium (GO:0031514)|photoreceptor connecting cilium (GO:0032391)|tight junction (GO:0005923)	structural molecule activity (GO:0005198)	p.F715L(1)		autonomic_ganglia(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(10)|ovary(2)	24						CTGAAAGGTCAAAAGGTTCAT	0.502																																					p.D716fs		Atlas-INDEL	.											.	NPHP1	68	.	1	Substitution - Missense(1)	lung(1)	c.2146delG						.						105.0	93.0	97.0					2																	110881425		2203	4300	6503	SO:0001589	frameshift_variant	4867	exon20			.	AF023674	CCDS2086.1, CCDS46384.1, CCDS46385.1, CCDS46386.1	2q13	2014-01-28			ENSG00000144061	ENSG00000144061			7905	protein-coding gene	gene with protein product	"""nephrocystin-1"""	607100		NPH1			Standard	NM_000272		Approved	JBTS4, SLSN1	uc002tfm.4	O15259	OTTHUMG00000131195	ENST00000393272.3:c.2142delT	chr2.hg19:g.110881425delA	ENSP00000376953:p.Phe714fs	248.0	0.0		157.0	10.0	NM_000272	O14837	Frame_Shift_Del	DEL	ENST00000393272.3	hg19	CCDS46385.1																																																																																			.	.		0.502	NPHP1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253919.3	NM_000272	
CCNT2	905	hgsc.bcm.edu	37	2	135712007	135712007	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:135712007delT	ENST00000264157.5	+	9	2012	c.1982delT	c.(1981-1983)gttfs	p.V661fs	CCNT2_ENST00000295238.6_Intron|CCNT2_ENST00000537343.1_Intron	NM_001241.3|NM_058241.2	NP_001232.1|NP_490595.1	O60583	CCNT2_HUMAN	cyclin T2	661					cell cycle (GO:0007049)|cell division (GO:0051301)|gene expression (GO:0010467)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)				endometrium(2)|kidney(3)|large_intestine(10)|lung(6)|ovary(2)|prostate(1)|skin(1)	25				BRCA - Breast invasive adenocarcinoma(221;0.107)		CACAACTCTGTTTTTAACCAT	0.483																																					p.V661fs		Atlas-INDEL	.											.	CCNT2	98	.	0			c.1981delG						.						188.0	176.0	180.0					2																	135712007		2203	4300	6503	SO:0001589	frameshift_variant	905	exon9			.	AF048731	CCDS2174.1, CCDS2175.1	2q21.3	2010-11-15			ENSG00000082258	ENSG00000082258			1600	protein-coding gene	gene with protein product		603862				9499409, 10465067	Standard	NM_001241		Approved		uc002tuc.2	O60583	OTTHUMG00000131712	ENST00000264157.5:c.1982delT	chr2.hg19:g.135712007delT	ENSP00000264157:p.Val661fs	263.0	0.0		207.0	14.0	NM_058241	A8KA48|D3DP73|D3DP74|O60582|Q29R66|Q53SR4|Q5I1Y0	Frame_Shift_Del	DEL	ENST00000264157.5	hg19	CCDS2174.1																																																																																			.	.		0.483	CCNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254629.1	NM_058241	
XDH	7498	hgsc.bcm.edu	37	2	31588960	31588960	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:31588960delT	ENST00000379416.3	-	22	2386	c.2338delA	c.(2338-2340)atgfs	p.M780fs		NM_000379.3	NP_000370.2	P47989	XDH_HUMAN	xanthine dehydrogenase	780					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)	ACCCCCAACATTTTTGCAACA	0.507																																					p.M780fs	Colon(66;682 1445 30109 40147)	Atlas-INDEL	.											.	XDH	191	.	0			c.2339delT						.						127.0	122.0	124.0					2																	31588960		2203	4300	6503	SO:0001589	frameshift_variant	7498	exon22			.	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.2338delA	chr2.hg19:g.31588960delT	ENSP00000368727:p.Met780fs	181.0	0.0		134.0	10.0	NM_000379	Q16681|Q16712|Q4PJ16	Frame_Shift_Del	DEL	ENST00000379416.3	hg19	CCDS1775.1																																																																																			.	.		0.507	XDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216840.1	NM_000379	
RAD50	10111	hgsc.bcm.edu	37	5	131977933	131977933	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:131977933delT	ENST00000265335.6	+	25	4203	c.3816delT	c.(3814-3816)gatfs	p.D1272fs	AC004041.2_ENST00000457489.1_RNA|AC004041.2_ENST00000435042.1_RNA|RAD50_ENST00000378823.3_Frame_Shift_Del_p.D1133fs|AC004041.2_ENST00000458509.1_RNA|AC004041.2_ENST00000417516.1_RNA			Q92878	RAD50_HUMAN	RAD50 homolog (S. cerevisiae)	1272					cellular response to DNA damage stimulus (GO:0006974)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|positive regulation of kinase activity (GO:0033674)|positive regulation of protein autophosphorylation (GO:0031954)|reciprocal meiotic recombination (GO:0007131)|regulation of mitotic recombination (GO:0000019)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)	membrane (GO:0016020)|Mre11 complex (GO:0030870)|nuclear chromosome, telomeric region (GO:0000784)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|pronucleus (GO:0045120)|site of double-strand break (GO:0035861)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|nuclease activity (GO:0004518)|protein binding, bridging (GO:0030674)|zinc ion binding (GO:0008270)			breast(3)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(10)|liver(1)|lung(8)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	36		all_cancers(142;0.0368)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			ATGATGAAGATTTTGTGGAGC	0.363								Homologous recombination																													p.D1272fs		Atlas-INDEL	.											.	RAD50	246	.	0			c.3815delA						.						111.0	111.0	111.0					5																	131977933		2203	4300	6503	SO:0001589	frameshift_variant	10111	exon25			.	Z75311	CCDS34233.1	5q23-q31	2008-05-30	2001-11-28		ENSG00000113522	ENSG00000113522			9816	protein-coding gene	gene with protein product		604040	"""RAD50 (S. cerevisiae) homolog"""			8756642, 9705271	Standard	NM_005732		Approved	hRad50, RAD50-2	uc003kxi.3	Q92878	OTTHUMG00000059613	ENST00000265335.6:c.3816delT	chr5.hg19:g.131977933delT	ENSP00000265335:p.Asp1272fs	270.0	0.0		185.0	12.0	NM_005732	B9EGF5|O43254|Q6GMT7|Q6P5X3|Q9UP86	Frame_Shift_Del	DEL	ENST00000265335.6	hg19	CCDS34233.1																																																																																			.	.		0.363	RAD50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132566.5	NM_005732	
PDIA4	9601	hgsc.bcm.edu	37	7	148702444	148702444	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:148702444delT	ENST00000286091.4	-	9	1543	c.1311delA	c.(1309-1311)aaafs	p.K437fs		NM_004911.4	NP_004902.1	P13667	PDIA4_HUMAN	protein disulfide isomerase family A, member 4	437					cell redox homeostasis (GO:0045454)|chaperone-mediated protein folding (GO:0061077)|protein folding (GO:0006457)|protein secretion (GO:0009306)|response to endoplasmic reticulum stress (GO:0034976)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)	poly(A) RNA binding (GO:0044822)|protein disulfide isomerase activity (GO:0003756)			large_intestine(6)|lung(15)|ovary(2)|prostate(1)	24	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00385)			CCTCTAGGACTTTGCTCCGCC	0.582											OREG0018420	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V438fs		Atlas-INDEL	.											.	PDIA4	57	.	0			c.1312delG						.						92.0	81.0	85.0					7																	148702444		2203	4300	6503	SO:0001589	frameshift_variant	9601	exon9			.	BC001928	CCDS5893.1	7q35	2009-11-20	2005-06-29		ENSG00000155660	ENSG00000155660	5.3.4.1	"""Protein disulfide isomerases"""	30167	protein-coding gene	gene with protein product			"""protein disulfide isomerase-associated 4"""			2549034, 2002068	Standard	NM_004911		Approved	ERP70, ERP72	uc003wff.2	P13667	OTTHUMG00000150248	ENST00000286091.4:c.1311delA	chr7.hg19:g.148702444delT	ENSP00000286091:p.Lys437fs	145.0	0.0	1719	154.0	10.0	NM_004911	A8K4K6|Q549T6	Frame_Shift_Del	DEL	ENST00000286091.4	hg19	CCDS5893.1																																																																																			.	.		0.582	PDIA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317077.1	NM_004911	
HACE1	57531	hgsc.bcm.edu	37	6	105198277	105198277	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:105198277delA	ENST00000262903.4	-	20	2558	c.2282delT	c.(2281-2283)ttafs	p.L761fs	HACE1_ENST00000517995.1_5'UTR|HACE1_ENST00000369125.2_Frame_Shift_Del_p.L546fs	NM_020771.3	NP_065822.2	Q8IYU2	HACE1_HUMAN	HECT domain and ankyrin repeat containing E3 ubiquitin protein ligase 1	761	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				cell cycle (GO:0007049)|Golgi organization (GO:0007030)|membrane fusion (GO:0061025)|protein K48-linked ubiquitination (GO:0070936)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|Rac protein signal transduction (GO:0016601)|regulation of cell migration (GO:0030334)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|nucleus (GO:0005634)	ligase activity (GO:0016874)|Rab GTPase binding (GO:0017137)|Rac GTPase binding (GO:0048365)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|lung(17)|ovary(5)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	44		all_cancers(87;6.89e-05)|Acute lymphoblastic leukemia(125;1.9e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0216)|Colorectal(196;0.202)		BRCA - Breast invasive adenocarcinoma(108;0.122)|Epithelial(106;0.204)		AAAGCCCTGTAAAAAAGCATT	0.383																																					p.L761fs		Atlas-INDEL	.											.	HACE1	96	.	0			c.2283delA						.						110.0	104.0	106.0					6																	105198277		2203	4300	6503	SO:0001589	frameshift_variant	57531	exon20			.	BC034982	CCDS5050.1	6q21	2013-01-10	2012-02-23		ENSG00000085382	ENSG00000085382		"""Ankyrin repeat domain containing"""	21033	protein-coding gene	gene with protein product		610876				10718198	Standard	NM_020771		Approved	KIAA1320	uc003pqu.1	Q8IYU2	OTTHUMG00000015287	ENST00000262903.4:c.2282delT	chr6.hg19:g.105198277delA	ENSP00000262903:p.Leu761fs	245.0	0.0		146.0	10.0	NM_020771	A8K6U5|B3KY89|B4DFM6|B4DTQ4|B7Z9X6|E9PGP0|Q5VU99|Q5VUA0|Q8ND12|Q9P2M6	Frame_Shift_Del	DEL	ENST00000262903.4	hg19	CCDS5050.1																																																																																			.	.		0.383	HACE1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041643.2	XM_045095	
USP9X	8239	hgsc.bcm.edu	37	X	41043827	41043827	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:41043827delA	ENST00000324545.8	+	23	4090	c.3457delA	c.(3457-3459)aaafs	p.K1153fs	USP9X_ENST00000378308.2_Frame_Shift_Del_p.K1153fs	NM_001039590.2|NM_001039591.2	NP_001034679.2|NP_001034680.2	Q93008	USP9X_HUMAN	ubiquitin specific peptidase 9, X-linked	1153					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						CAATGCTCTTAAAATAGCCAA	0.473																																					p.L1152fs	Ovarian(172;1807 2695 35459 49286)	Atlas-INDEL	.											.	USP9X	385	.	0			c.3456delT						.						94.0	86.0	89.0					X																	41043827		2172	4280	6452	SO:0001589	frameshift_variant	8239	exon23			.	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.3457delA	chrX.hg19:g.41043827delA	ENSP00000316357:p.Lys1153fs	160.0	0.0		143.0	10.0	NM_001039591	O75550|Q8WWT3|Q8WX12	Frame_Shift_Del	DEL	ENST00000324545.8	hg19	CCDS43930.1																																																																																			.	.		0.473	USP9X-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000056250.4	NM_004652	
ARAP2	116984	hgsc.bcm.edu	37	4	36148950	36148950	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:36148950delT	ENST00000303965.4	-	19	3720	c.3231delA	c.(3229-3231)aaafs	p.K1077fs		NM_015230.3	NP_056045.2	Q8WZ64	ARAP2_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 2	1077	PH 4. {ECO:0000255|PROSITE- ProRule:PRU00145}.				regulation of ARF GTPase activity (GO:0032312)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|liver(1)|lung(32)|ovary(2)|pancreas(1)|prostate(3)|skin(7)|urinary_tract(1)	82						AAACATCCAGTTTTTCCCCAT	0.348																																					p.L1078fs		Atlas-INDEL	.											.	ARAP2	210	.	0			c.3232delC						.						97.0	109.0	105.0					4																	36148950		2202	4298	6500	SO:0001589	frameshift_variant	116984	exon19			.	AF411982	CCDS3441.1	4p15.1	2013-01-11	2008-09-22	2008-09-22	ENSG00000047365	ENSG00000047365		"""ADP-ribosylation factor GTPase activating proteins"", ""Sterile alpha motif (SAM) domain containing"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	16924	protein-coding gene	gene with protein product		606645	"""centaurin, delta 1"""	CENTD1			Standard	NM_015230		Approved	PARX	uc003gsq.2	Q8WZ64	OTTHUMG00000097811	ENST00000303965.4:c.3231delA	chr4.hg19:g.36148950delT	ENSP00000302895:p.Lys1077fs	252.0	0.0		225.0	16.0	NM_015230	Q4W5D2|Q7Z2L5|Q96L70|Q96P49|Q9Y4E4	Frame_Shift_Del	DEL	ENST00000303965.4	hg19	CCDS3441.1																																																																																			.	.		0.348	ARAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215074.2	NM_015230	
ZNF331	55422	hgsc.bcm.edu	37	19	54079990	54079990	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:54079990delA	ENST00000253144.9	+	7	1509	c.176delA	c.(175-177)gaafs	p.E59fs	ZNF331_ENST00000449416.1_Frame_Shift_Del_p.E59fs|ZNF331_ENST00000511154.1_Frame_Shift_Del_p.E59fs|ZNF331_ENST00000513265.1_Frame_Shift_Del_p.E59fs|ZNF331_ENST00000513999.1_Frame_Shift_Del_p.E59fs|ZNF331_ENST00000512387.1_Frame_Shift_Del_p.E59fs|ZNF331_ENST00000511593.2_Frame_Shift_Del_p.E59fs|ZNF331_ENST00000411977.2_Frame_Shift_Del_p.E59fs	NM_001253801.1|NM_018555.5	NP_001240730.1|NP_061025.5	Q9NQX6	ZN331_HUMAN	zinc finger protein 331	59	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.			E -> K (in Ref. 3; AAH09433). {ECO:0000305}.	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)|large_intestine(1)|lung(1)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	10				GBM - Glioblastoma multiforme(134;0.00555)		TTACCTACAGAAAAAAACATT	0.368			T	?	follicular thyroid adenoma																																p.E59fs		Atlas-INDEL	.		Dom	yes		19	19q13.3-q13.4	55422	zinc finger protein 331		E	.	ZNF331	66	.	0			c.175delG						.						42.0	45.0	44.0					19																	54079990		2203	4300	6503	SO:0001589	frameshift_variant	55422	exon5			.	AF251515	CCDS33102.1	19q13	2013-12-10				ENSG00000130844		"""Zinc fingers, C2H2-type"", ""-"""	15489	protein-coding gene	gene with protein product	"""rearranged in thyroid adenomas"""	606043					Standard	NM_001079906		Approved	RITA, ZNF463, ZNF361	uc021uzh.1	Q9NQX6		ENST00000253144.9:c.176delA	chr19.hg19:g.54079990delA	ENSP00000253144:p.Glu59fs	221.0	0.0		180.0	13.0	NM_001253801	Q96GJ4	Frame_Shift_Del	DEL	ENST00000253144.9	hg19	CCDS33102.1																																																																																			.	.		0.368	ZNF331-008	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371366.1	NM_018555	
GREB1L	80000	hgsc.bcm.edu	37	18	19100709	19100709	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr18:19100709delT	ENST00000580732.2	+	32	5914	c.5533delT	c.(5533-5535)tttfs	p.F1846fs	GREB1L_ENST00000424526.1_Frame_Shift_Del_p.F1846fs|GREB1L_ENST00000269218.6_Frame_Shift_Del_p.F1737fs|GREB1L_ENST00000400483.4_3'UTR			Q9C091	GRB1L_HUMAN	growth regulation by estrogen in breast cancer-like	1846						integral component of membrane (GO:0016021)				breast(5)|endometrium(4)|kidney(6)|lung(1)|skin(1)	17						TGAAGGGGTGTTTTTCAGTGG	0.393																																					p.V1844fs		Atlas-INDEL	.											.	GREB1L	69	.	0			c.5532delG						.						165.0	136.0	145.0					18																	19100709		692	1591	2283	SO:0001589	frameshift_variant	80000	exon32			.	AK023749	CCDS45836.1	18q11.2	2009-09-08	2009-09-08	2009-09-08					31042	protein-coding gene	gene with protein product			"""KIAA1772"""	KIAA1772		11214970	Standard	NM_001142966		Approved	FLJ13687, C18orf6	uc010xam.2	Q9C091		ENST00000580732.2:c.5533delT	chr18.hg19:g.19100709delT	ENSP00000464162:p.Phe1846fs	225.0	0.0		171.0	12.0	NM_001142966	A4QN17|Q9H8F1	Frame_Shift_Del	DEL	ENST00000580732.2	hg19	CCDS45836.1																																																																																			.	.		0.393	GREB1L-003	KNOWN	not_organism_supported|upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443782.2	NM_024935	
KIF21B	23046	hgsc.bcm.edu	37	1	200974546	200974546	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:200974546delC	ENST00000422435.2	-	5	938	c.622delG	c.(622-624)gccfs	p.A208fs	KIF21B_ENST00000332129.2_Frame_Shift_Del_p.A208fs|KIF21B_ENST00000461742.2_Frame_Shift_Del_p.A208fs|KIF21B_ENST00000360529.5_Frame_Shift_Del_p.A208fs	NM_001252100.1	NP_001239029.1	O75037	KI21B_HUMAN	kinesin family member 21B	208	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(4)|large_intestine(8)|liver(1)|lung(27)|ovary(3)|pancreas(1)|prostate(5)|skin(8)|stomach(2)|urinary_tract(2)	83						CGGGACAGGGCCCCCTGCTTC	0.622																																					p.A208fs		Atlas-INDEL	.											.	KIF21B	208	.	0			c.623delC						.						103.0	94.0	97.0					1																	200974546		2203	4300	6503	SO:0001589	frameshift_variant	23046	exon5			.	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.622delG	chr1.hg19:g.200974546delC	ENSP00000411831:p.Ala208fs	137.0	0.0		212.0	14.0	NM_017596	B2RP62|B7ZMI0|Q5T4J3	Frame_Shift_Del	DEL	ENST00000422435.2	hg19	CCDS58056.1																																																																																			.	.		0.622	KIF21B-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382635.1	XM_371332	
CACUL1	143384	hgsc.bcm.edu	37	10	120514243	120514243	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:120514243delC	ENST00000369151.3	-	1	515	c.32delG	c.(31-33)ggcfs	p.G11fs	CACUL1_ENST00000340214.4_Frame_Shift_Del_p.G11fs	NM_153810.4	NP_722517.3	Q86Y37	CACL1_HUMAN	CDK2-associated, cullin domain 1	11					G1/S transition of mitotic cell cycle (GO:0000082)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein kinase activity (GO:0045860)|ubiquitin-dependent protein catabolic process (GO:0006511)	cullin-RING ubiquitin ligase complex (GO:0031461)	protein kinase binding (GO:0019901)										CTCGTAGCTGCCCCCCTCCTC	0.711																																					p.G11fs		Atlas-INDEL	.											.	.	.	.	0			c.33delC						.						58.0	69.0	66.0					10																	120514243		2033	4172	6205	SO:0001589	frameshift_variant	143384	exon1			.	AK097728	CCDS41570.1	10q26.13	2012-06-12	2012-06-12	2012-06-12	ENSG00000151893	ENSG00000151893			23727	protein-coding gene	gene with protein product	"""Cdk-Associated Cullin1"""		"""chromosome 10 open reading frame 46"""	C10orf46		19829063	Standard	NM_153810		Approved	FLJ40409, MGC33215, CAC1	uc001lds.1	Q86Y37	OTTHUMG00000019138	ENST00000369151.3:c.32delG	chr10.hg19:g.120514243delC	ENSP00000358147:p.Gly11fs	477.0	0.0		285.0	19.0	NM_153810	Q5XPL7|Q8IY11|Q8N7S4	Frame_Shift_Del	DEL	ENST00000369151.3	hg19	CCDS41570.1																																																																																			.	.		0.711	CACUL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050612.2	NM_153810	
EPS8L2	64787	hgsc.bcm.edu	37	11	721655	721655	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:721655delA	ENST00000533256.1	+	11	1234	c.859delA	c.(859-861)aaafs	p.K288fs	EPS8L2_ENST00000318562.8_Frame_Shift_Del_p.K288fs|EPS8L2_ENST00000530636.1_Frame_Shift_Del_p.K288fs|AP006621.9_ENST00000527021.2_RNA|EPS8L2_ENST00000526198.1_Frame_Shift_Del_p.K304fs			Q9H6S3	ES8L2_HUMAN	EPS8-like 2	288					positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of ruffle assembly (GO:1900029)|regulation of Rho protein signal transduction (GO:0035023)|Rho protein signal transduction (GO:0007266)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)|vesicle (GO:0031982)	actin binding (GO:0003779)	p.K290fs*22(1)		NS(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|pancreas(1)|prostate(2)|soft_tissue(1)|urinary_tract(1)	13		all_cancers(49;1.24e-08)|all_epithelial(84;1.87e-05)|Breast(177;0.000286)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.106)|all_lung(207;0.136)		all cancers(45;4.37e-27)|Epithelial(43;2.81e-26)|OV - Ovarian serous cystadenocarcinoma(40;1.33e-20)|BRCA - Breast invasive adenocarcinoma(625;4.29e-05)|Lung(200;0.0582)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GAACCAGCGGAAAAAGGGGAA	0.652																																					p.R286fs		Atlas-INDEL	.											.,1	EPS8L2	42	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.858delG						.						33.0	44.0	40.0					11																	721655		2196	4288	6484	SO:0001589	frameshift_variant	64787	exon10			.	AF318331	CCDS31328.1	11p15.5	2008-02-05				ENSG00000177106			21296	protein-coding gene	gene with protein product		614988				12620401	Standard	NM_022772		Approved	FLJ21935, FLJ22171, MGC3088	uc001lqt.3	Q9H6S3		ENST00000533256.1:c.859delA	chr11.hg19:g.721655delA	ENSP00000435585:p.Lys288fs	312.0	0.0		248.0	15.0	NM_022772	B3KSX1|B7ZKL3|Q53GM8|Q8WYW7|Q96K06|Q9H6K9	Frame_Shift_Del	DEL	ENST00000533256.1	hg19	CCDS31328.1																																																																																			.	.		0.652	EPS8L2-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382344.1	NM_022772	
TTN	7273	hgsc.bcm.edu	37	2	179485563	179485563	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:179485563delT	ENST00000591111.1	-	197	41075	c.40851delA	c.(40849-40851)aaafs	p.K13617fs	TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342992.6_Frame_Shift_Del_p.K12690fs|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000359218.5_Frame_Shift_Del_p.K6318fs|TTN-AS1_ENST00000604956.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN_ENST00000460472.2_Frame_Shift_Del_p.K6193fs|TTN_ENST00000589042.1_Frame_Shift_Del_p.K15258fs|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000342175.6_Frame_Shift_Del_p.K6385fs|TTN-AS1_ENST00000590807.1_RNA			Q8WZ42	TITIN_HUMAN	titin	13617	Ig-like 92.				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)			AGACTAGGTCTTTTTGGAGAA	0.368																																					p.D15259fs		Atlas-INDEL	.											.	TTN	18412	.	0			c.45775delG						.						172.0	167.0	168.0					2																	179485563		1870	4093	5963	SO:0001589	frameshift_variant	7273	exon247			.	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.40851delA	chr2.hg19:g.179485563delT	ENSP00000465570:p.Lys13617fs	244.0	0.0		154.0	10.0	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																																																																																				.	.		0.368	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
GLS	2744	hgsc.bcm.edu	37	2	191769844	191769844	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:191769844delA	ENST00000320717.3	+	6	1188	c.930delA	c.(928-930)ggafs	p.G310fs	GLS_ENST00000338435.4_Frame_Shift_Del_p.G310fs	NM_014905.4	NP_055720.3	O94925	GLSK_HUMAN	glutaminase	310					cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|glutamate biosynthetic process (GO:0006537)|glutamate secretion (GO:0014047)|glutamine catabolic process (GO:0006543)|neurotransmitter secretion (GO:0007269)|protein homotetramerization (GO:0051289)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|small molecule metabolic process (GO:0044281)|suckling behavior (GO:0001967)|synaptic transmission (GO:0007268)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	glutaminase activity (GO:0004359)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|lung(9)|ovary(1)|skin(1)|urinary_tract(1)	16			OV - Ovarian serous cystadenocarcinoma(117;0.00625)|Epithelial(96;0.0744)|all cancers(119;0.181)		L-Glutamine(DB00130)	GATATGTTGGAAAAGAGCCGA	0.338																																					p.G310fs		Atlas-INDEL	.											.	GLS	47	.	0			c.929delG						.						125.0	124.0	124.0					2																	191769844		2203	4300	6503	SO:0001589	frameshift_variant	2744	exon6			.	AB020645	CCDS2308.1, CCDS58744.1	2q32-q34	2013-01-10			ENSG00000115419	ENSG00000115419	3.5.1.2	"""Ankyrin repeat domain containing"""	4331	protein-coding gene	gene with protein product		138280				10048485	Standard	NM_014905		Approved	KIAA0838, GLS1	uc002usf.3	O94925	OTTHUMG00000132701	ENST00000320717.3:c.930delA	chr2.hg19:g.191769844delA	ENSP00000317379:p.Gly310fs	222.0	0.0		147.0	11.0	NM_001256310	Q9UL05|Q9UL06|Q9UL07|Q9UN40	Frame_Shift_Del	DEL	ENST00000320717.3	hg19	CCDS2308.1																																																																																			.	.		0.338	GLS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255999.2		
RPL23	9349	hgsc.bcm.edu	37	17	37008859	37008859	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:37008859delT	ENST00000479035.2	-	3	356	c.224delA	c.(223-225)aagfs	p.K75fs	RPL23_ENST00000394333.1_Frame_Shift_Del_p.K75fs|RPL23_ENST00000245857.5_Frame_Shift_Del_p.K16fs|SNORA21_ENST00000362423.1_RNA|RPL23_ENST00000577407.1_Frame_Shift_Del_p.K75fs|RPL23_ENST00000394332.1_Frame_Shift_Del_p.K75fs|SNORA21_ENST00000516890.1_RNA	NM_000978.3	NP_000969.1	P62829	RL23_HUMAN	ribosomal protein L23	75					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)|ribosomal protein import into nucleus (GO:0006610)|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)|membrane (GO:0016020)|nucleolus (GO:0005730)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			endometrium(2)|large_intestine(1)	3						TTACTCACCCTTTTTTCTGAG	0.488																																					p.K75fs		Atlas-INDEL	.											.	RPL23	7	.	0			c.225delG						.						138.0	111.0	120.0					17																	37008859		2203	4300	6503	SO:0001589	frameshift_variant	9349	exon3			.	X52839	CCDS11330.1	17q12	2011-04-06			ENSG00000125691	ENSG00000125691		"""L ribosomal proteins"""	10316	protein-coding gene	gene with protein product		603662				1861993	Standard	NM_000978		Approved	rpL17, L23	uc002hqx.1	P62829	OTTHUMG00000133118	ENST00000479035.2:c.224delA	chr17.hg19:g.37008859delT	ENSP00000420311:p.Lys75fs	292.0	0.0		211.0	14.0	NM_000978	P23131|P24048|Q29246|Q3SWV7|Q6P5S1	Frame_Shift_Del	DEL	ENST00000479035.2	hg19	CCDS11330.1																																																																																			.	.		0.488	RPL23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256785.3	NM_000978	
SKP2	6502	hgsc.bcm.edu	37	5	36170455	36170455	+	Frame_Shift_Del	DEL	A	A	-	rs142374565	byFrequency	TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:36170455delA	ENST00000274255.6	+	6	877	c.681delA	c.(679-681)gcafs	p.A227fs	SKP2_ENST00000508514.1_Intron|SKP2_ENST00000546211.1_Frame_Shift_Del_p.A13fs|SKP2_ENST00000274254.5_Frame_Shift_Del_p.A227fs	NM_005983.3	NP_005974.2	Q13309	SKP2_HUMAN	S-phase kinase-associated protein 2, E3 ubiquitin protein ligase	227					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|cellular response to cell-matrix adhesion (GO:0071460)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of smooth muscle cell proliferation (GO:0048661)|protein polyubiquitination (GO:0000209)|regulation of cell cycle (GO:0051726)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SCF ubiquitin ligase complex (GO:0019005)	identical protein binding (GO:0042802)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|central_nervous_system(2)|ovary(1)	4	all_lung(31;5.63e-05)		Epithelial(62;0.0396)|Lung(74;0.111)|all cancers(62;0.115)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			GTACTCTCGCAAAAAACTCAA	0.398																																					p.A227fs		Atlas-INDEL	.											.	SKP2	70	.	0			c.680delC						.						126.0	120.0	122.0					5																	36170455		2203	4299	6502	SO:0001589	frameshift_variant	6502	exon6			.	U33761	CCDS3915.1, CCDS3916.1, CCDS58944.1	5p13	2012-02-23	2012-02-23		ENSG00000145604	ENSG00000145604		"""F-boxes / Leucine-rich repeats"""	10901	protein-coding gene	gene with protein product		601436	"""S-phase kinase-associated protein 2 (p45)"""			8646875	Standard	NM_005983		Approved	FBXL1, FBL1, p45	uc003jkc.2	Q13309	OTTHUMG00000131106	ENST00000274255.6:c.681delA	chr5.hg19:g.36170455delA	ENSP00000274255:p.Ala227fs	239.0	0.0		195.0	12.0	NM_032637	A8K5E0|B4DJT4|Q8TDZ0|Q8TDZ1|Q9BV69	Frame_Shift_Del	DEL	ENST00000274255.6	hg19	CCDS3916.1																																																																																			.	.		0.398	SKP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253769.2	NM_005983	
TMEM232	642987	hgsc.bcm.edu	37	5	109973983	109973983	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:109973983delA	ENST00000455884.2	-	5	467	c.417delT	c.(415-417)tttfs	p.F139fs	TMEM232_ENST00000515518.2_5'UTR|TMEM232_ENST00000429839.2_Frame_Shift_Del_p.F139fs			C9JQI7	TM232_HUMAN	transmembrane protein 232	139						integral component of membrane (GO:0016021)				breast(1)|kidney(2)	3						ATTCCGCAACAAAAAATAAGG	0.323																																					p.V140fs		Atlas-INDEL	.											.	TMEM232	57	.	0			c.418delG						.						143.0	125.0	130.0					5																	109973983		692	1591	2283	SO:0001589	frameshift_variant	642987	exon5			.	AK125070	CCDS47253.1, CCDS47253.2	5q22.1	2014-02-12	2009-10-02		ENSG00000186952	ENSG00000186952			37270	protein-coding gene	gene with protein product							Standard	NM_001039763		Approved	FLJ43080	uc011cvh.2	C9JQI7	OTTHUMG00000163297	ENST00000455884.2:c.417delT	chr5.hg19:g.109973983delA	ENSP00000401477:p.Phe139fs	365.0	0.0		303.0	19.0	NM_001039763	B4DKF4	Frame_Shift_Del	DEL	ENST00000455884.2	hg19	CCDS47253.2																																																																																			.	.		0.323	TMEM232-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372488.2	NM_001039763	
T	6862	hgsc.bcm.edu	37	6	166580213	166580213	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:166580213delC	ENST00000296946.2	-	3	806	c.338delG	c.(337-339)ggcfs	p.G113fs	T_ENST00000366871.3_Frame_Shift_Del_p.G113fs	NM_003181.3	NP_003172.1	O15178	BRAC_HUMAN	T, brachyury homolog (mouse)	113					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)		CTCCGGCTTGCCCCCCGGCAC	0.657									Chordoma, Familial Clustering of																												p.G113fs		Atlas-INDEL	.											.	T	77	.	0			c.339delC						.						46.0	48.0	47.0					6																	166580213		2203	4300	6503	SO:0001589	frameshift_variant	6862	exon3	Familial Cancer Database		.	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.338delG	chr6.hg19:g.166580213delC	ENSP00000296946:p.Gly113fs	188.0	0.0		143.0	10.0	NM_001270484	E7ERD6|Q4KMP4	Frame_Shift_Del	DEL	ENST00000296946.2	hg19	CCDS5290.1																																																																																			.	.		0.657	T-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043037.2	NM_003181	
FSD1L	83856	hgsc.bcm.edu	37	9	108234293	108234293	+	Intron	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:108234293delA	ENST00000481272.1	+	5	560				FSD1L_ENST00000539376.1_Intron|FSD1L_ENST00000374716.4_Frame_Shift_Del_p.K118fs|FSD1L_ENST00000484973.1_Intron|FSD1L_ENST00000374710.3_Intron|FSD1L_ENST00000480279.1_Intron|FSD1L_ENST00000394926.3_Intron|FSD1L_ENST00000495708.1_Intron	NM_001145313.1	NP_001138785.1	Q9BXM9	FSD1L_HUMAN	fibronectin type III and SPRY domain containing 1-like											NS(1)|endometrium(1)	2						AAAGGTACACAAAAACTGCAT	0.294																																					p.H117fs		Atlas-INDEL	.											.	FSD1L	31	.	0			c.351delC						.						71.0	64.0	66.0					9																	108234293		692	1586	2278	SO:0001627	intron_variant	83856	exon4			.	AF316830	CCDS6765.2, CCDS47999.1, CCDS6765.3, CCDS75870.1	9q31	2013-02-11	2006-03-10	2006-03-10	ENSG00000106701	ENSG00000106701		"""Fibronectin type III domain containing"""	13753	protein-coding gene	gene with protein product		609829	"""cystatin and DUF19 domain containing 1"", ""coiled-coil domain containing 10"""	CSDUFD1, CCDC10, FSD1NL, FSD1CL		11267680	Standard	XM_005252254		Approved		uc004bcq.2	Q9BXM9	OTTHUMG00000020426	ENST00000481272.1:c.441+7A>-	chr9.hg19:g.108234293delA		288.0	0.0		232.0	15.0	NM_031919	A2A338|A6NKH7|B7Z5S6|B7Z5W3|Q5T879|Q5T880	Frame_Shift_Del	DEL	ENST00000481272.1	hg19	CCDS47999.1																																																																																			.	.		0.294	FSD1L-007	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000349935.1	NM_207647	
MBTPS1	8720	hgsc.bcm.edu	37	16	84118656	84118656	+	Frame_Shift_Del	DEL	C	C	-	rs145922793		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:84118656delC	ENST00000343411.3	-	10	1713	c.1218delG	c.(1216-1218)gggfs	p.G406fs	MBTPS1_ENST00000569770.1_5'UTR	NM_003791.2	NP_003782.1	Q14703	MBTP1_HUMAN	membrane-bound transcription factor peptidase, site 1	406	Peptidase S8.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|cholesterol metabolic process (GO:0008203)|endoplasmic reticulum unfolded protein response (GO:0030968)|lipid metabolic process (GO:0006629)|lysosome organization (GO:0007040)|proteolysis (GO:0006508)|regulation of transcription factor import into nucleus (GO:0042990)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)	serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|lung(10)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41						GGGCCCGGCACCCCCCTTTCA	0.582											OREG0023982	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.C407fs		Atlas-INDEL	.											.	MBTPS1	85	.	0			c.1219delT						.						82.0	71.0	75.0					16																	84118656		2200	4300	6500	SO:0001589	frameshift_variant	8720	exon10			.	D42053	CCDS10941.1	16q24	2008-08-04	2005-08-17		ENSG00000140943	ENSG00000140943			15456	protein-coding gene	gene with protein product		603355	"""membrane-bound transcription factor protease, site 1"""			9809072, 10944850	Standard	NM_003791		Approved	S1P, KIAA0091, SKI-1, PCSK8	uc002fhi.3	Q14703	OTTHUMG00000137639	ENST00000343411.3:c.1218delG	chr16.hg19:g.84118656delC	ENSP00000344223:p.Gly406fs	301.0	0.0	1226	212.0	13.0	NM_003791	A8K6V8|Q24JQ2|Q9UF67	Frame_Shift_Del	DEL	ENST00000343411.3	hg19	CCDS10941.1																																																																																			.	.		0.582	MBTPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269080.2	NM_003791	
CC2D1B	200014	hgsc.bcm.edu	37	1	52822693	52822693	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:52822693delT	ENST00000371586.2	-	16	2014	c.1876delA	c.(1876-1878)atgfs	p.M626fs	CC2D1B_ENST00000438831.1_Start_Codon_Del|CC2D1B_ENST00000460261.1_5'UTR|CC2D1B_ENST00000284376.3_Frame_Shift_Del_p.M620fs	NM_032449.2	NP_115825.1	Q5T0F9	C2D1B_HUMAN	coiled-coil and C2 domain containing 1B	626						nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)			breast(1)|large_intestine(6)|lung(13)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	27						TCCAGAAGCATTTTTTGCAGC	0.592																																					p.M626fs		Atlas-INDEL	.											.	CC2D1B	73	.	0			c.1877delT						.						76.0	73.0	74.0					1																	52822693		2191	4294	6485	SO:0001589	frameshift_variant	200014	exon16			.	AB058739	CCDS30714.1	1p32.3	2008-02-05			ENSG00000154222	ENSG00000154222			29386	protein-coding gene	gene with protein product						11347906	Standard	NM_032449		Approved	KIAA1836	uc001ctq.2	Q5T0F9	OTTHUMG00000008102	ENST00000371586.2:c.1876delA	chr1.hg19:g.52822693delT	ENSP00000360642:p.Met626fs	282.0	0.0		214.0	13.0	NM_032449	Q49AE8|Q5T0F8|Q5T0G0|Q6ZNQ1|Q96AP3|Q96I04|Q96JJ1	Frame_Shift_Del	DEL	ENST00000371586.2	hg19	CCDS30714.1																																																																																			.	.		0.592	CC2D1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000022189.1	NM_032449	
MAB21L2	10586	hgsc.bcm.edu	37	4	151505172	151505172	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:151505172delC	ENST00000317605.4	+	1	2096	c.991delC	c.(991-993)cccfs	p.P331fs	RP11-1336O20.2_ENST00000507934.1_RNA|LRBA_ENST00000503716.1_5'Flank|LRBA_ENST00000507224.1_Intron|LRBA_ENST00000357115.3_Intron|LRBA_ENST00000510413.1_Intron|LRBA_ENST00000535741.1_Intron	NM_006439.4	NP_006430.1	Q9Y586	MB212_HUMAN	mab-21-like 2 (C. elegans)	331					camera-type eye development (GO:0043010)|embryonic body morphogenesis (GO:0010172)|eye development (GO:0001654)|nervous system development (GO:0007399)|positive regulation of cell proliferation (GO:0008284)	nucleus (GO:0005634)				breast(2)|endometrium(6)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|skin(2)	21	all_hematologic(180;0.151)			GBM - Glioblastoma multiforme(119;0.159)		TCAGGGCAAGCCCCATTCGGC	0.607																																					p.K330fs		Atlas-INDEL	.											.	MAB21L2	53	.	0			c.990delG						.						52.0	50.0	51.0					4																	151505172		2203	4300	6503	SO:0001589	frameshift_variant	10586	exon1			.	AF155219	CCDS3774.1	4q31.3	2013-10-22	2001-11-28		ENSG00000181541	ENSG00000181541			6758	protein-coding gene	gene with protein product		604357	"""mab-21 (C. elegans)-like 2"""				Standard	NM_006439		Approved		uc003ilw.3	Q9Y586	OTTHUMG00000161442	ENST00000317605.4:c.991delC	chr4.hg19:g.151505172delC	ENSP00000324701:p.Pro331fs	183.0	0.0		129.0	10.0	NM_006439	B3KP37|Q9HBA7	Frame_Shift_Del	DEL	ENST00000317605.4	hg19	CCDS3774.1																																																																																			.	.		0.607	MAB21L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364937.1	NM_006439	
RRP7A	27341	hgsc.bcm.edu	37	22	42911202	42911202	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr22:42911202delG	ENST00000323013.6	-	4	430	c.415delC	c.(415-417)ctgfs	p.L140fs	SERHL_ENST00000359906.2_RNA	NM_015703.4	NP_056518.2	Q9Y3A4	RRP7A_HUMAN	ribosomal RNA processing 7 homolog A (S. cerevisiae)	140							nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|liver(2)|lung(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	10						GACACCAGCAGGGGGCCCTTC	0.602																																					p.L139fs		Atlas-INDEL	.											.	RRP7A	25	.	0			c.416delT						.						4.0	8.0	7.0					22																	42911202		1658	3948	5606	SO:0001589	frameshift_variant	27341	exon4			.	BC035992	CCDS14036.1	22q13.2	2008-08-08			ENSG00000189306	ENSG00000189306			24286	protein-coding gene	gene with protein product						10810093, 12087473	Standard	NM_015703		Approved	CGI-96	uc003bcq.3	Q9Y3A4	OTTHUMG00000150891	ENST00000323013.6:c.415delC	chr22.hg19:g.42911202delG	ENSP00000321449:p.Leu140fs	225.0	0.0		168.0	12.0	NM_015703	A4FTX2|B2RBG4|Q0VAD0|Q5JZ94|Q6P4B5|Q8IVR9|Q8IVY0|Q8N5Q3|Q8NEY6|Q9Y3H5	Frame_Shift_Del	DEL	ENST00000323013.6	hg19	CCDS14036.1																																																																																			.	.		0.602	RRP7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320451.1	NM_015703	
GPBP1L1	60313	hgsc.bcm.edu	37	1	46120968	46120968	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:46120968delT	ENST00000290795.3	-	4	1305	c.84delA	c.(82-84)aaafs	p.K28fs	GPBP1L1_ENST00000355105.3_Frame_Shift_Del_p.K28fs			Q9HC44	GPBL1_HUMAN	GC-rich promoter binding protein 1-like 1	28					positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)		GPBP1L1/MAST2_ENST00000361297(2)	breast(1)|endometrium(2)|large_intestine(4)|lung(10)|ovary(1)|skin(2)|stomach(1)	21	Acute lymphoblastic leukemia(166;0.155)					GCTCTCCGTGTTTTTCGAAGG	0.428																																					p.H29fs		Atlas-INDEL	.											.	GPBP1L1	43	.	0			c.85delC						.						143.0	138.0	140.0					1																	46120968		2203	4300	6503	SO:0001589	frameshift_variant	60313	exon5			.		CCDS528.1	1p34.1	2008-02-05			ENSG00000159592	ENSG00000159592			28843	protein-coding gene	gene with protein product						12477932	Standard	NM_021639		Approved	SP192	uc001coq.3	Q9HC44	OTTHUMG00000040990	ENST00000290795.3:c.84delA	chr1.hg19:g.46120968delT	ENSP00000290795:p.Lys28fs	325.0	0.0		238.0	15.0	NM_021639	D3DQ10|Q9H751	Frame_Shift_Del	DEL	ENST00000290795.3	hg19	CCDS528.1																																																																																			.	.		0.428	GPBP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098375.1	NM_021639	
ABCB7	22	hgsc.bcm.edu	37	X	74282215	74282215	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:74282215delG	ENST00000373394.3	-	14	1890	c.1883delC	c.(1882-1884)ccafs	p.P628fs	ABCB7_ENST00000253577.3_Frame_Shift_Del_p.P629fs|ABCB7_ENST00000339447.4_Frame_Shift_Del_p.P588fs|ABCB7_ENST00000534570.1_5'Flank			O75027	ABCB7_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 7	628	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.				cellular iron ion homeostasis (GO:0006879)|heme transport (GO:0015886)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|heme transporter activity (GO:0015232)			breast(1)|endometrium(5)|large_intestine(5)|lung(6)|ovary(2)|prostate(1)	20						GAGTATGACTGGGGGGTCCTT	0.348																																					p.P629fs		Atlas-INDEL	.											.	ABCB7	69	.	0			c.1887delA						.						101.0	90.0	94.0					X																	74282215		2203	4300	6503	SO:0001589	frameshift_variant	22	exon14			.	AF038950	CCDS14428.1, CCDS65290.1, CCDS65291.1, CCDS75994.1	Xq13.3	2012-03-14			ENSG00000131269	ENSG00000131269		"""ATP binding cassette transporters / subfamily B"""	48	protein-coding gene	gene with protein product		300135		ABC7		9143506	Standard	NM_004299		Approved	EST140535, Atm1p, ASAT	uc004ebz.4	O75027	OTTHUMG00000021862	ENST00000373394.3:c.1883delC	chrX.hg19:g.74282215delG	ENSP00000362492:p.Pro628fs	225.0	0.0		179.0	13.0	NM_004299	G3XAC4|O75345|Q5VWY7|Q5VWY8|Q9BRE1|Q9UND1|Q9UP01	Frame_Shift_Del	DEL	ENST00000373394.3	hg19																																																																																				.	.		0.348	ABCB7-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000057274.1	NM_004299	
ZCCHC6	79670	hgsc.bcm.edu	37	9	88960648	88960648	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:88960648delA	ENST00000375963.3	-	4	927	c.755delT	c.(754-756)ttafs	p.L252fs	ZCCHC6_ENST00000375961.2_Frame_Shift_Del_p.L252fs|ZCCHC6_ENST00000375948.1_5'Flank|ZCCHC6_ENST00000375947.1_Frame_Shift_Del_p.L85fs|ZCCHC6_ENST00000277141.6_5'UTR|ZCCHC6_ENST00000375960.2_Frame_Shift_Del_p.L252fs	NM_001185059.1|NM_024617.3	NP_001171988.1|NP_078893.2	Q5VYS8	TUT7_HUMAN	zinc finger, CCHC domain containing 6	252					RNA 3'-end processing (GO:0031123)		poly(A) RNA binding (GO:0044822)|RNA uridylyltransferase activity (GO:0050265)|zinc ion binding (GO:0008270)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|liver(1)|lung(14)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	46						GGATTCAATTAAAACATCACA	0.353																																					p.L252fs		Atlas-INDEL	.											.	ZCCHC6	105	.	0			c.756delA						.						184.0	169.0	174.0					9																	88960648		2203	4300	6503	SO:0001589	frameshift_variant	79670	exon4			.	AL832026	CCDS35057.1, CCDS55323.1	9q21	2014-03-05			ENSG00000083223	ENSG00000083223		"""Zinc fingers, CCHC domain containing"""	25817	protein-coding gene	gene with protein product	"""TUTase7"""					11214970	Standard	NM_001185059		Approved	KIAA1711, FLJ13409, PAPD6, TUT7	uc004aoq.3	Q5VYS8	OTTHUMG00000020137	ENST00000375963.3:c.755delT	chr9.hg19:g.88960648delA	ENSP00000365130:p.Leu252fs	255.0	0.0		169.0	11.0	NM_024617	Q5H9T0|Q5VYS5|Q5VYS7|Q658Z9|Q659A2|Q6MZJ3|Q8N5F0|Q96N57|Q96NE8|Q9C0F2|Q9H8M6	Frame_Shift_Del	DEL	ENST00000375963.3	hg19	CCDS35057.1																																																																																			.	.		0.353	ZCCHC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052918.1	NM_024617	
PBX4	80714	hgsc.bcm.edu	37	19	19681606	19681606	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	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	198.0	0.0		136.0	11.0	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		
NR1H4	9971	hgsc.bcm.edu	37	12	100904639	100904639	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:100904639delC	ENST00000551379.1	+	2	221	c.193delC	c.(193-195)cccfs	p.P65fs	NR1H4_ENST00000549996.1_Frame_Shift_Del_p.P55fs|NR1H4_ENST00000392986.3_Frame_Shift_Del_p.P55fs|NR1H4_ENST00000188403.7_Frame_Shift_Del_p.P65fs|NR1H4_ENST00000548884.1_Frame_Shift_Del_p.P55fs			Q96RI1	NR1H4_HUMAN	nuclear receptor subfamily 1, group H, member 4	65					bile acid metabolic process (GO:0008206)|cellular response to acid chemical (GO:0071229)|cellular response to organonitrogen compound (GO:0071417)|digestive tract development (GO:0048565)|gene expression (GO:0010467)|intracellular bile acid receptor signaling pathway (GO:0038185)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of bile acid biosynthetic process (GO:0070858)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nitrogen catabolite activation of transcription from RNA polymerase II promoter (GO:0001080)|positive regulation of ammonia assimilation cycle (GO:2001250)|positive regulation of glutamate metabolic process (GO:2000213)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of bile acid biosynthetic process (GO:0070857)|regulation of carbohydrate metabolic process (GO:0006109)|regulation of cholesterol metabolic process (GO:0090181)|regulation of urea metabolic process (GO:0034255)|response to glucose (GO:0009749)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)	bile acid binding (GO:0032052)|bile acid receptor activity (GO:0038181)|chenodeoxycholic acid binding (GO:1902122)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|ligand-dependent nuclear receptor binding (GO:0016922)|peptide binding (GO:0042277)|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 (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|thyroid hormone receptor activity (GO:0004887)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(23)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	44					Chenodeoxycholic acid(DB06777)	TGTTCAGTTTCCCCAAGTTCA	0.458																																					p.F64fs		Atlas-INDEL	.											.	NR1H4	145	.	0			c.192delT						.						94.0	84.0	87.0					12																	100904639		2203	4300	6503	SO:0001589	frameshift_variant	9971	exon2			.	U68233	CCDS9078.1, CCDS55873.1, CCDS55874.1, CCDS55875.1, CCDS55876.1	12q23.1	2013-01-16				ENSG00000012504		"""Nuclear hormone receptors"""	7967	protein-coding gene	gene with protein product		603826				7774010, 9223286	Standard	NM_001206977		Approved	FXR, RIP14, HRR1, HRR-1	uc001tht.2	Q96RI1	OTTHUMG00000170359	ENST00000551379.1:c.193delC	chr12.hg19:g.100904639delC	ENSP00000447149:p.Pro65fs	403.0	0.0		258.0	17.0	NM_001206992	A1L4K5|B7Z412|B7ZM06|F8VYG8|Q8NFP5|Q8NFP6|Q92943	Frame_Shift_Del	DEL	ENST00000551379.1	hg19	CCDS55876.1																																																																																			.	.		0.458	NR1H4-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409140.1	NM_005123	
HYLS1	219844	hgsc.bcm.edu	37	11	125769979	125769979	+	Frame_Shift_Del	DEL	G	G	-	rs372527418		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:125769979delG	ENST00000425380.2	+	3	1497	c.716delG	c.(715-717)tggfs	p.W239fs	PUS3_ENST00000227474.3_Intron|HYLS1_ENST00000526028.1_Frame_Shift_Del_p.W239fs|HYLS1_ENST00000356438.3_Frame_Shift_Del_p.W239fs	NM_001134793.1	NP_001128265.1	Q96M11	HYLS1_HUMAN	hydrolethalus syndrome 1	239						centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|endometrium(1)|large_intestine(3)|skin(3)|upper_aerodigestive_tract(1)	9	all_hematologic(175;0.177)	Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.131)|all_lung(97;0.139)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0446)		GAATTACGCTGGGGTGTCCGA	0.473																																					p.W239fs	Esophageal Squamous(172;2590 2636 8884 10471)	Atlas-INDEL	.											.	HYLS1	25	.	0			c.715delT						.						84.0	76.0	78.0					11																	125769979		2201	4299	6500	SO:0001589	frameshift_variant	219844	exon3			.	AK057477	CCDS8467.1	11q24	2014-06-18				ENSG00000198331			26558	protein-coding gene	gene with protein product		610693				15843405	Standard	NM_145014		Approved	FLJ32915	uc009zbv.3	Q96M11		ENST00000425380.2:c.716delG	chr11.hg19:g.125769979delG	ENSP00000414884:p.Trp239fs	181.0	0.0		128.0	10.0	NM_001134793	B3KXI8|Q96BX9	Frame_Shift_Del	DEL	ENST00000425380.2	hg19	CCDS8467.1																																																																																			.	.		0.473	HYLS1-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386733.1	NM_145014	
LLGL2	3993	hgsc.bcm.edu	37	17	73560534	73560534	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:73560534delT	ENST00000392550.3	+	10	1099	c.982delT	c.(982-984)ttcfs	p.F328fs	LLGL2_ENST00000167462.5_Frame_Shift_Del_p.F328fs|LLGL2_ENST00000375227.4_Frame_Shift_Del_p.F328fs|LLGL2_ENST00000578363.1_Frame_Shift_Del_p.F328fs|LLGL2_ENST00000577200.1_Frame_Shift_Del_p.F328fs	NM_001031803.1	NP_001026973.1	Q6P1M3	L2GL2_HUMAN	lethal giant larvae homolog 2 (Drosophila)	328					cell cycle (GO:0007049)|cell division (GO:0051301)|exocytosis (GO:0006887)|regulation of establishment or maintenance of cell polarity (GO:0032878)	cytoplasm (GO:0005737)	PDZ domain binding (GO:0030165)			NS(1)|breast(3)|cervix(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	all_cancers(13;3.15e-09)|all_epithelial(9;5.78e-10)|Breast(9;5.8e-10)|all_lung(278;0.246)		all cancers(21;1.8e-07)|Epithelial(20;1.38e-06)|Lung(188;0.0696)|LUSC - Lung squamous cell carcinoma(166;0.112)			GGCCTTCGACTTCACCTCCCG	0.632																																					p.D327fs		Atlas-INDEL	.											.	LLGL2	155	.	0			c.981delC						.						66.0	62.0	63.0					17																	73560534		2203	4300	6503	SO:0001589	frameshift_variant	3993	exon10			.	X87342	CCDS11725.1, CCDS32733.1, CCDS45776.1	17q25.1	2013-01-10	2001-11-28			ENSG00000073350		"""WD repeat domain containing"""	6629	protein-coding gene	gene with protein product			"""lethal giant larvae (Drosophila) homolog 2"""				Standard	XR_243659		Approved	HGL	uc002joh.3	Q6P1M3		ENST00000392550.3:c.982delT	chr17.hg19:g.73560534delT	ENSP00000376333:p.Phe328fs	180.0	0.0		182.0	11.0	NM_001015002	Q14521|Q9BR62	Frame_Shift_Del	DEL	ENST00000392550.3	hg19	CCDS32733.1																																																																																			.	.		0.632	LLGL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447633.1	NM_004524	
RBFOX1	54715	hgsc.bcm.edu	37	16	7568215	7568215	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:7568215delC	ENST00000550418.1	+	5	1082	c.94delC	c.(94-96)cccfs	p.P33fs	RBFOX1_ENST00000311745.5_Frame_Shift_Del_p.P53fs|RBFOX1_ENST00000422070.4_Frame_Shift_Del_p.P76fs|RBFOX1_ENST00000436368.2_Frame_Shift_Del_p.P53fs|RBFOX1_ENST00000355637.4_Frame_Shift_Del_p.P53fs|RBFOX1_ENST00000535565.2_Frame_Shift_Del_p.P69fs|RBFOX1_ENST00000340209.4_Frame_Shift_Del_p.P38fs|RBFOX1_ENST00000547372.1_Frame_Shift_Del_p.P76fs|RBFOX1_ENST00000553186.1_Frame_Shift_Del_p.P33fs|RBFOX1_ENST00000552089.1_Frame_Shift_Del_p.P69fs|RBFOX1_ENST00000547338.1_Frame_Shift_Del_p.P33fs	NM_018723.3	NP_061193.2	Q9NWB1	RFOX1_HUMAN	RNA binding protein, fox-1 homolog (C. elegans) 1	33					mRNA processing (GO:0006397)|neuromuscular process controlling balance (GO:0050885)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)|RNA transport (GO:0050658)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	nucleotide binding (GO:0000166)|protein C-terminus binding (GO:0008022)|RNA binding (GO:0003723)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(11)|lung(17)|ovary(1)|pancreas(1)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)	55						CCAGTTTGCTCCCCCGCAGAA	0.587																																					p.A51fs	Ovarian(157;934 2567 15163 39509)	Atlas-INDEL	.											.	RBFOX1	341	.	0			c.153delT						.						130.0	130.0	130.0					16																	7568215		2197	4300	6497	SO:0001589	frameshift_variant	54715	exon2			.	AF107203	CCDS10531.1, CCDS10532.1, CCDS45405.1, CCDS55983.1, CCDS55984.1	16p13.3	2013-02-12			ENSG00000078328	ENSG00000078328		"""RNA binding motif (RRM) containing"""	18222	protein-coding gene	gene with protein product	"""ataxin 2-binding protein 1"", ""hexaribonucleotide binding protein 1"""	605104				10814712, 16260614	Standard	NM_018723		Approved	A2BP1, FOX-1, HRNBP1	uc002cyy.2	Q9NWB1	OTTHUMG00000129551	ENST00000550418.1:c.94delC	chr16.hg19:g.7568215delC	ENSP00000450031:p.Pro33fs	194.0	0.0		160.0	11.0	NM_145891	Q7Z7I7|Q8TAE3|Q8TAF2|Q8WYB2|Q9NS20	Frame_Shift_Del	DEL	ENST00000550418.1	hg19	CCDS55983.1																																																																																			.	.		0.587	RBFOX1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409492.2	NM_145891	
FBP1	2203	hgsc.bcm.edu	37	9	97369188	97369188	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:97369188delT	ENST00000375326.4	-	5	810	c.614delA	c.(613-615)aagfs	p.K206fs	FBP1_ENST00000415431.1_Frame_Shift_Del_p.K206fs	NM_000507.3	NP_000498.2	P09467	F16P1_HUMAN	fructose-1,6-bisphosphatase 1	206					carbohydrate metabolic process (GO:0005975)|cellular response to drug (GO:0035690)|cellular response to magnesium ion (GO:0071286)|dephosphorylation (GO:0016311)|fructose 6-phosphate metabolic process (GO:0006002)|fructose metabolic process (GO:0006000)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|negative regulation of cell growth (GO:0030308)|negative regulation of glycolytic process (GO:0045820)|negative regulation of Ras protein signal transduction (GO:0046580)|protein homotetramerization (GO:0051289)|regulation of gluconeogenesis (GO:0006111)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	AMP binding (GO:0016208)|fructose 1,6-bisphosphate 1-phosphatase activity (GO:0042132)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|monosaccharide binding (GO:0048029)			kidney(1)|liver(1)|lung(1)	3		Acute lymphoblastic leukemia(62;0.136)			Adenosine monophosphate(DB00131)	TTTACCTTTCTTTTTTATCTT	0.502																																					p.K205fs	Ovarian(142;590 2466 25593 44496)	Atlas-INDEL	.											.	FBP1	13	.	0			c.615delG						.						148.0	137.0	141.0					9																	97369188		2203	4300	6503	SO:0001589	frameshift_variant	2203	exon5			.	M19922	CCDS6712.1	9q22.3	2012-08-13			ENSG00000165140	ENSG00000165140	3.1.3.11		3606	protein-coding gene	gene with protein product		611570		FBP		8387495	Standard	NM_000507		Approved		uc004auw.4	P09467	OTTHUMG00000020268	ENST00000375326.4:c.614delA	chr9.hg19:g.97369188delT	ENSP00000364475:p.Lys206fs	326.0	0.0		216.0	15.0	NM_000507	O75571|Q53F94|Q96E46	Frame_Shift_Del	DEL	ENST00000375326.4	hg19	CCDS6712.1																																																																																			.	.		0.502	FBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053187.1	NM_000507	
MEIS1	4211	hgsc.bcm.edu	37	2	66667704	66667704	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:66667704delA	ENST00000272369.9	+	4	849	c.392delA	c.(391-393)gaafs	p.E131fs	MEIS1_ENST00000407092.2_Frame_Shift_Del_p.E131fs|MEIS1_ENST00000488550.1_Frame_Shift_Del_p.E131fs|MEIS1_ENST00000444274.2_Frame_Shift_Del_p.E99fs|MEIS1_ENST00000398506.2_Frame_Shift_Del_p.E129fs|MEIS1-AS1_ENST00000454595.1_RNA|MEIS1_ENST00000560281.2_Frame_Shift_Del_p.E131fs|MEIS1_ENST00000495021.2_Frame_Shift_Del_p.E66fs|MEIS1-AS2_ENST00000439433.1_RNA	NM_002398.2	NP_002389.1	O00470	MEIS1_HUMAN	Meis homeobox 1	131					angiogenesis (GO:0001525)|definitive hemopoiesis (GO:0060216)|lens morphogenesis in camera-type eye (GO:0002089)|megakaryocyte development (GO:0035855)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of neuron differentiation (GO:0045665)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)			breast(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(10)|prostate(2)|skin(1)|urinary_tract(1)	24						ATTCGCGCAGAAAAACCTCTA	0.493																																					p.E131fs		Atlas-INDEL	.											.	MEIS1	52	.	0			c.391delG						.						87.0	88.0	87.0					2																	66667704		1801	4064	5865	SO:0001589	frameshift_variant	4211	exon4			.		CCDS46309.1	2p14	2011-06-20	2007-02-15		ENSG00000143995	ENSG00000143995		"""Homeoboxes / TALE class"""	7000	protein-coding gene	gene with protein product		601739	"""Meis1 (mouse) homolog"", ""Meis1, myeloid ecotropic viral integration site 1 homolog (mouse)"""			7565694	Standard	NM_002398		Approved		uc002sdu.3	O00470	OTTHUMG00000150714	ENST00000272369.9:c.392delA	chr2.hg19:g.66667704delA	ENSP00000272369:p.Glu131fs	345.0	0.0		256.0	18.0	NM_002398	A8MV50	Frame_Shift_Del	DEL	ENST00000272369.9	hg19	CCDS46309.1																																																																																			.	.		0.493	MEIS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319725.4	NM_002398	
PIK3R3	8503	hgsc.bcm.edu	37	1	46531807	46531807	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:46531807delT	ENST00000262741.5	-	5	1229	c.540delA	c.(538-540)aaafs	p.K180fs	PIK3R3_ENST00000340332.6_Frame_Shift_Del_p.K144fs|PIK3R3_ENST00000420542.1_Frame_Shift_Del_p.K180fs|PIK3R3_ENST00000540385.1_Frame_Shift_Del_p.K226fs|PIK3R3_ENST00000354242.4_Frame_Shift_Del_p.K180fs|PIK3R3_ENST00000423209.1_Frame_Shift_Del_p.K180fs|PIK3R3_ENST00000372006.1_Frame_Shift_Del_p.K180fs	NM_003629.3	NP_003620.3	Q92569	P55G_HUMAN	phosphoinositide-3-kinase, regulatory subunit 3 (gamma)	180					insulin receptor signaling pathway (GO:0008286)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphatidylinositol 3-kinase complex (GO:0005942)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|phosphatidylinositol 3-kinase regulator activity (GO:0035014)			endometrium(1)|large_intestine(5)|lung(6)|prostate(2)	14	Acute lymphoblastic leukemia(166;0.155)				Isoprenaline(DB01064)	ATTCTTGCAGTTTTTTACCTA	0.318																																					p.L181fs		Atlas-INDEL	.											.	PIK3R3	41	.	0			c.541delC						.						149.0	133.0	138.0					1																	46531807		2201	4296	6497	SO:0001589	frameshift_variant	8503	exon5			.	BC021622	CCDS529.1	1p34.1	2013-02-14	2008-02-04		ENSG00000117461	ENSG00000117461		"""SH2 domain containing"""	8981	protein-coding gene	gene with protein product		606076				9524259	Standard	NM_003629		Approved	p55	uc001cpb.4	Q92569	OTTHUMG00000008096	ENST00000262741.5:c.540delA	chr1.hg19:g.46531807delT	ENSP00000262741:p.Lys180fs	259.0	0.0		187.0	14.0	NM_003629	B2R9C1|D3DQ12|O60482|Q5T4P1|Q5T4P2	Frame_Shift_Del	DEL	ENST00000262741.5	hg19	CCDS529.1																																																																																			.	.		0.318	PIK3R3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022171.1	NM_003629	
CALML6	163688	hgsc.bcm.edu	37	1	1848432	1848432	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:1848432delG	ENST00000307786.3	+	5	872	c.418delG	c.(418-420)gggfs	p.G140fs	CALML6_ENST00000462293.1_3'UTR	NM_138705.2	NP_619650.2	Q8TD86	CALL6_HUMAN	calmodulin-like 6	140	EF-hand 3. {ECO:0000255|PROSITE- ProRule:PRU00448}.					cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(1)|kidney(1)|lung(1)|prostate(2)	7	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;5.61e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;1.94e-37)|OV - Ovarian serous cystadenocarcinoma(86;2.83e-23)|GBM - Glioblastoma multiforme(42;3.23e-08)|Colorectal(212;3.98e-05)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00229)|BRCA - Breast invasive adenocarcinoma(365;0.00437)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.034)|Lung(427;0.199)		AATGAACGCAGGGGAGCCCCT	0.667																																					p.A139fs		Atlas-INDEL	.											.	CALML6	18	.	0			c.417delA						.						72.0	62.0	65.0					1																	1848432		2203	4298	6501	SO:0001589	frameshift_variant	163688	exon5			.	AF490905	CCDS30566.1	1p36.33	2013-01-10			ENSG00000169885	ENSG00000169885		"""EF-hand domain containing"""	24193	protein-coding gene	gene with protein product		610171					Standard	NM_138705		Approved	CAGLP	uc001aih.1	Q8TD86	OTTHUMG00000000943	ENST00000307786.3:c.418delG	chr1.hg19:g.1848432delG	ENSP00000304643:p.Gly140fs	146.0	0.0		126.0	10.0	NM_138705	A2A2M3|Q6Q2C4	Frame_Shift_Del	DEL	ENST00000307786.3	hg19	CCDS30566.1																																																																																			.	.		0.667	CALML6-004	KNOWN	mRNA_start_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276929.1	NM_138705	
CLCA1	1179	hgsc.bcm.edu	37	1	86957003	86957003	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:86957003delT	ENST00000234701.3	+	10	1764	c.1413delT	c.(1411-1413)gctfs	p.A471fs	CLCA1_ENST00000394711.1_Frame_Shift_Del_p.A471fs			A8K7I4	CLCA1_HUMAN	chloride channel accessory 1	471	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				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)		TCATTGATGCTTTTGGGGCCC	0.388																																					p.A471fs		Atlas-INDEL	.											.	CLCA1	109	.	0			c.1412delC						.						126.0	124.0	124.0					1																	86957003		2203	4300	6503	SO:0001589	frameshift_variant	1179	exon9			.		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.1413delT	chr1.hg19:g.86957003delT	ENSP00000234701:p.Ala471fs	242.0	0.0		169.0	13.0	NM_001285	B2RAV5|O95151|Q5TDF4|Q9UNF6|Q9UPC6	Frame_Shift_Del	DEL	ENST00000234701.3	hg19	CCDS709.1																																																																																			.	.		0.388	CLCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028277.1	NM_001285	
ZNF200	7752	hgsc.bcm.edu	37	16	3283724	3283724	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:3283724delG	ENST00000431561.3	-	2	644	c.32delC	c.(31-33)ccafs	p.P11fs	ZNF200_ENST00000414144.2_Frame_Shift_Del_p.P11fs|ZNF200_ENST00000396868.3_Frame_Shift_Del_p.P11fs|ZNF200_ENST00000575948.1_Frame_Shift_Del_p.P11fs|ZNF200_ENST00000396870.4_Frame_Shift_Del_p.P11fs|ZNF200_ENST00000396871.4_Frame_Shift_Del_p.P11fs	NM_001145447.1|NM_003454.3	NP_001138919.1|NP_003445.2	P98182	ZN200_HUMAN	zinc finger protein 200	11					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(2)|kidney(2)|large_intestine(4)|lung(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	17						CTTTGGCTTTGGGGGCATAGG	0.552																																					p.P11fs		Atlas-INDEL	.											.	ZNF200	36	.	0			c.33delA						.						140.0	133.0	136.0					16																	3283724		2197	4300	6497	SO:0001589	frameshift_variant	7752	exon2			.	AF060866	CCDS10497.1, CCDS42112.1, CCDS45395.1	16p13.3	2013-01-08			ENSG00000010539	ENSG00000010539		"""Zinc fingers, C2H2-type"""	12993	protein-coding gene	gene with protein product		603231				9288094, 9787081	Standard	NM_003454		Approved		uc002cuk.2	P98182	OTTHUMG00000129317	ENST00000431561.3:c.32delC	chr16.hg19:g.3283724delG	ENSP00000395723:p.Pro11fs	234.0	0.0		156.0	12.0	NM_003454	D3DUB7|D3DUB8|O15361|Q5XKM5|Q7Z5V1	Frame_Shift_Del	DEL	ENST00000431561.3	hg19	CCDS10497.1																																																																																			.	.		0.552	ZNF200-005	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000437545.1		
YAP1	10413	hgsc.bcm.edu	37	11	102094405	102094405	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:102094405delA	ENST00000282441.5	+	7	1473	c.1085delA	c.(1084-1086)caafs	p.Q362fs	YAP1_ENST00000537274.1_Frame_Shift_Del_p.Q350fs|YAP1_ENST00000531439.1_Frame_Shift_Del_p.Q346fs|YAP1_ENST00000526343.1_Frame_Shift_Del_p.Q308fs|YAP1_ENST00000345877.2_Frame_Shift_Del_p.Q312fs|YAP1_ENST00000524575.1_Frame_Shift_Del_p.Q184fs	NM_001130145.2|NM_001282101.1	NP_001123617.1|NP_001269030.1	P46937	YAP1_HUMAN	Yes-associated protein 1	362	Transactivation domain.				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)		GGTGGGACTCAAAATCCAGTG	0.433																																					p.Q362fs	Colon(50;247 1103 7861 28956)	Atlas-INDEL	.											.	YAP1	45	.	0			c.1084delC						.						105.0	95.0	99.0					11																	102094405		2203	4299	6502	SO:0001589	frameshift_variant	10413	exon7			.		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.1085delA	chr11.hg19:g.102094405delA	ENSP00000282441:p.Gln362fs	247.0	0.0		165.0	11.0	NM_001130145	B4DTY1|B7ZA01|E3WEB5|E3WEB6|E9PRV2|F5H202|K0KQ18|K0KYZ8|K0L195|K0L1G3|Q7Z574|Q8IUY9	Frame_Shift_Del	DEL	ENST00000282441.5	hg19	CCDS44716.1																																																																																			.	.		0.433	YAP1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000394151.1	NM_006106	
ENO1	2023	hgsc.bcm.edu	37	1	8926380	8926380	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:8926380delC	ENST00000234590.4	-	7	744	c.625delG	c.(625-627)gatfs	p.D209fs		NM_001428.3	NP_001419.1	P06733	ENOA_HUMAN	enolase 1, (alpha)	209	Required for repression of c-myc promoter activity.				carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|negative regulation of cell growth (GO:0030308)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|response to virus (GO:0009615)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|phosphopyruvate hydratase complex (GO:0000015)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|magnesium ion binding (GO:0000287)|phosphopyruvate hydratase activity (GO:0004634)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)	10	Ovarian(185;0.0661)|all_lung(157;0.127)	all_epithelial(116;2.54e-20)|all_lung(118;2.99e-06)|Lung NSC(185;6.25e-06)|Renal(390;0.000147)|Breast(348;0.00086)|Colorectal(325;0.00205)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;2.42e-07)|COAD - Colon adenocarcinoma(227;2.78e-05)|Kidney(185;0.000249)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|STAD - Stomach adenocarcinoma(132;0.00177)|BRCA - Breast invasive adenocarcinoma(304;0.00185)|READ - Rectum adenocarcinoma(331;0.0642)		CCGCCTTCATCCCCCACATTG	0.542																																					p.D209fs	Esophageal Squamous(21;302 608 19946 22210 33560)	Atlas-INDEL	.											.	ENO1	38	.	0			c.626delA						.						116.0	111.0	113.0					1																	8926380		2203	4300	6503	SO:0001589	frameshift_variant	2023	exon7			.	BC022545	CCDS97.1	1p36.2	2010-03-11			ENSG00000074800	ENSG00000074800	4.2.1.11		3350	protein-coding gene	gene with protein product		172430		ENO1L1, MPB1		9653645, 9691177	Standard	NM_001428		Approved	PPH, MBP-1	uc001apj.2	P06733	OTTHUMG00000001773	ENST00000234590.4:c.625delG	chr1.hg19:g.8926380delC	ENSP00000234590:p.Asp209fs	190.0	0.0		118.0	10.0	NM_001428	B2RD59|P22712|Q16704|Q4TUS4|Q53FT9|Q53HR3|Q658M5|Q6GMP2|Q71V37|Q7Z3V6|Q8WU71|Q96GV1|Q9BT62|Q9UCH6|Q9UM55	Frame_Shift_Del	DEL	ENST00000234590.4	hg19	CCDS97.1																																																																																			.	.		0.542	ENO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004945.1	NM_001428	
NHSL1	57224	hgsc.bcm.edu	37	6	138817355	138817355	+	Splice_Site	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:138817355delC	ENST00000427025.2	-	2	984		c.e2+1		NHSL1_ENST00000479393.2_Splice_Site|NHSL1_ENST00000343505.5_Splice_Site	NM_020464.1	NP_065197.1	Q5SYE7	NHSL1_HUMAN	NHS-like 1											breast(2)|endometrium(4)|kidney(1)	7						TGCCATCTTACCCCTCAGTAC	0.463																																					.		Atlas-INDEL	.											.	NHSL1	99	.	0			c.355+2G>-						.						133.0	126.0	128.0					6																	138817355		692	1591	2283	SO:0001630	splice_region_variant	57224	exon3			.	AB037778	CCDS47487.1, CCDS55063.1	6q23.3	2009-02-18	2004-10-07	2004-10-07	ENSG00000135540	ENSG00000135540			21021	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 63"""	C6orf63			Standard	NM_001144060		Approved	bA43P8.1, KIAA1357	uc011edp.2	Q5SYE7	OTTHUMG00000016321	ENST00000427025.2:c.355+1G>-	chr6.hg19:g.138817355delC		181.0	0.0		175.0	11.0	NM_020464	Q3ZCS5|Q5SYE8|Q9P2J0	Splice_Site	DEL	ENST00000427025.2	hg19	CCDS55063.1																																																																																			.	.		0.463	NHSL1-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043700.2	XM_050421	Intron
APOH	350	hgsc.bcm.edu	37	17	64212962	64212962	+	Frame_Shift_Del	DEL	G	G	-	rs142113711		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:64212962delG	ENST00000205948.6	-	6	765	c.728delC	c.(727-729)ccgfs	p.P243fs		NM_000042.2	NP_000033.2	P02749	APOH_HUMAN	apolipoprotein H (beta-2-glycoprotein I)	243	Sushi 4. {ECO:0000255|PROSITE- ProRule:PRU00302}.				blood coagulation, intrinsic pathway (GO:0007597)|negative regulation of angiogenesis (GO:0016525)|negative regulation of blood coagulation (GO:0030195)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of myeloid cell apoptotic process (GO:0033033)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|plasminogen activation (GO:0031639)|positive regulation of blood coagulation (GO:0030194)|positive regulation of lipoprotein lipase activity (GO:0051006)|regulation of fibrinolysis (GO:0051917)|triglyceride metabolic process (GO:0006641)|triglyceride transport (GO:0034197)	cell surface (GO:0009986)|chylomicron (GO:0042627)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)|very-low-density lipoprotein particle (GO:0034361)	glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|lipid binding (GO:0008289)|lipoprotein lipase activator activity (GO:0060230)|phospholipid binding (GO:0005543)			central_nervous_system(1)|kidney(3)|large_intestine(5)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	17			BRCA - Breast invasive adenocarcinoma(6;9.74e-08)			TATTTCTTCCGGGCCATCCAG	0.418																																					p.P243fs	Melanoma(155;624 1882 16869 48804 51309)	Atlas-INDEL	.											.	APOH	45	.	0			c.729delG						.						156.0	152.0	153.0					17																	64212962		2203	4300	6503	SO:0001589	frameshift_variant	350	exon6			.		CCDS11663.1	17q24.2	2013-01-24				ENSG00000091583		"""Apolipoproteins"""	616	protein-coding gene	gene with protein product	"""beta-2-glycoprotein I"""	138700		B2G1		1582254	Standard	NM_000042		Approved	BG	uc002jfn.4	P02749		ENST00000205948.6:c.728delC	chr17.hg19:g.64212962delG	ENSP00000205948:p.Pro243fs	196.0	0.0		199.0	12.0	NM_000042	B2R9M3|Q9UCN7	Frame_Shift_Del	DEL	ENST00000205948.6	hg19	CCDS11663.1																																																																																			.	.		0.418	APOH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446926.1	NM_000042	
SBDS	51119	hgsc.bcm.edu	37	7	66458407	66458407	+	Intron	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:66458407delA	ENST00000246868.2	-	3	442					NM_016038.2	NP_057122.2	Q9Y3A5	SBDS_HUMAN	Shwachman-Bodian-Diamond syndrome						bone marrow development (GO:0048539)|bone mineralization (GO:0030282)|cell proliferation (GO:0008283)|inner cell mass cell proliferation (GO:0001833)|leukocyte chemotaxis (GO:0030595)|mature ribosome assembly (GO:0042256)|mitotic spindle stabilization (GO:0043148)|ribosomal large subunit biogenesis (GO:0042273)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|spindle pole (GO:0000922)	microtubule binding (GO:0008017)|poly(A) RNA binding (GO:0044822)|ribosome binding (GO:0043022)|rRNA binding (GO:0019843)			cervix(1)|endometrium(1)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	7						GTCAAAATCTAAAAAAATGCC	0.323			Gene Conversion			"""AML, MDS"""			Shwachman-Diamond syndrome																												.		Atlas-INDEL	.	yes	Rec		Schwachman-Diamond syndrome	7	7q11	51119	Shwachman-Bodian-Diamond syndrome protein		L	.	SBDS	20	.	0			c.259-2T>-						.						114.0	100.0	105.0					7																	66458407		2203	4300	6503	SO:0001627	intron_variant	51119	exon4	Familial Cancer Database	Shwachman syndrome, Shwachman-Bodian syndrome, Congenital Lipomatosis of the Pancreas	.	AF151855	CCDS5537.1	7q11.22	2014-09-17			ENSG00000126524	ENSG00000126524			19440	protein-coding gene	gene with protein product		607444				12496757	Standard	NM_016038		Approved	CGI-97, FLJ10917, SDS, SWDS	uc003tvm.1	Q9Y3A5	OTTHUMG00000023165	ENST00000246868.2:c.259-3T>-	chr7.hg19:g.66458407delA		140.0	0.0		172.0	11.0	NM_016038	A8K0P4|Q96FX0|Q9NV53	Splice_Site	DEL	ENST00000246868.2	hg19	CCDS5537.1																																																																																			.	.		0.323	SBDS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251746.2	NM_016038	
CLSTN3	9746	hgsc.bcm.edu	37	12	7301639	7301639	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:7301639delC	ENST00000266546.6	+	13	2369	c.1919delC	c.(1918-1920)gccfs	p.A640fs	CLSTN3_ENST00000537408.1_Frame_Shift_Del_p.A652fs	NM_014718.3	NP_055533.2	Q9BQT9	CSTN3_HUMAN	calsyntenin 3	640					homophilic cell adhesion (GO:0007156)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)	calcium ion binding (GO:0005509)			NS(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(7)|prostate(1)|skin(1)	33						CAGCCTGACGCCCCCCAGATC	0.567																																					p.A640fs		Atlas-INDEL	.											CLSTN3,NS,adenocarcinoma,0,1	CLSTN3	84	.	0			c.1918delG						.						89.0	70.0	76.0					12																	7301639		2203	4300	6503	SO:0001589	frameshift_variant	9746	exon13			.	AB018269	CCDS8575.1	12p13.31	2011-07-01			ENSG00000139182	ENSG00000139182		"""Cadherins / Cadherin-related"""	18371	protein-coding gene	gene with protein product	"""cadherin-related family member 14"""	611324				12498782	Standard	NM_014718		Approved	CSTN3, KIAA0726, CDHR14	uc001qsr.3	Q9BQT9	OTTHUMG00000168167	ENST00000266546.6:c.1919delC	chr12.hg19:g.7301639delC	ENSP00000266546:p.Ala640fs	163.0	0.0		141.0	11.0	NM_014718	D3DUT6|O94831|Q2T9J5|Q5UE57	Frame_Shift_Del	DEL	ENST00000266546.6	hg19	CCDS8575.1																																																																																			.	.		0.567	CLSTN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398560.2	NM_014718	
FAM120B	84498	hgsc.bcm.edu	37	6	170639584	170639584	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:170639584delG	ENST00000476287.1	+	4	2071	c.1963delG	c.(1963-1965)gggfs	p.G655fs	MIR4644_ENST00000579929.1_RNA|FAM120B_ENST00000537664.1_Frame_Shift_Del_p.G678fs|FAM120B_ENST00000540480.1_Frame_Shift_Del_p.G667fs|FAM120B_ENST00000252510.9_5'UTR	NM_032448.1	NP_115824.1	Q96EK7	F120B_HUMAN	family with sequence similarity 120B	655					cell differentiation (GO:0030154)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(11)|liver(1)|lung(15)|ovary(1)|prostate(2)|skin(2)	44		Breast(66;0.000338)|Esophageal squamous(34;0.241)		OV - Ovarian serous cystadenocarcinoma(33;3.94e-22)|BRCA - Breast invasive adenocarcinoma(81;6.47e-06)|GBM - Glioblastoma multiforme(31;0.0899)		TGTGTATCCTGGGAACCCACT	0.522																																					p.P654fs		Atlas-INDEL	.											.	FAM120B	108	.	0			c.1962delT						.						155.0	141.0	146.0					6																	170639584		2203	4300	6503	SO:0001589	frameshift_variant	84498	exon4			.	AB058741	CCDS5314.1, CCDS75555.1	6q27	2011-04-13	2006-07-04	2006-07-04	ENSG00000112584	ENSG00000112584			21109	protein-coding gene	gene with protein product	"""PPARgamma constitutive coactivator 1"", ""constitutive coactivator of PPAR-gamma"""	612266	"""KIAA1838"""	KIAA1838		14585507	Standard	NM_032448		Approved	PGCC1, CCPG	uc003qxp.3	Q96EK7	OTTHUMG00000016080	ENST00000476287.1:c.1963delG	chr6.hg19:g.170639584delG	ENSP00000417970:p.Gly655fs	342.0	0.0		222.0	14.0	NM_032448	B4DL34|Q86V68|Q96JI9	Frame_Shift_Del	DEL	ENST00000476287.1	hg19	CCDS5314.1																																																																																			.	.		0.522	FAM120B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000043259.2	NM_032448	
CFDP1	10428	hgsc.bcm.edu	37	16	75445767	75445767	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:75445767delT	ENST00000283882.3	-	4	618	c.486delA	c.(484-486)aaafs	p.K162fs	RP11-77K12.1_ENST00000561887.1_5'Flank|SNORA76_ENST00000516313.1_RNA|CFDP1_ENST00000564286.1_5'UTR	NM_006324.2	NP_006315.1	Q9UEE9	CFDP1_HUMAN	craniofacial development protein 1	162					cell adhesion (GO:0007155)|multicellular organismal development (GO:0007275)|negative regulation of fibroblast apoptotic process (GO:2000270)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)					endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)	5						TGATTTTAACTTTTTCTGTTT	0.338																																					p.V163fs		Atlas-INDEL	.											.	CFDP1	17	.	0			c.487delG						.						123.0	110.0	115.0					16																	75445767		2198	4299	6497	SO:0001589	frameshift_variant	10428	exon4			.	AB009285	CCDS10916.1	16q22.2-q22.3	2011-08-12			ENSG00000153774	ENSG00000153774			1873	protein-coding gene	gene with protein product	"""Bucentaur"", ""centromere protein 29"""	608108				9602175, 9006920, 11992732	Standard	NM_006324		Approved	BCNT, p97, CP27, SWC5, Yeti, CENP-29	uc002fdy.3	Q9UEE9	OTTHUMG00000137615	ENST00000283882.3:c.486delA	chr16.hg19:g.75445767delT	ENSP00000283882:p.Lys162fs	205.0	0.0		140.0	10.0	NM_006324	O00393|O00404|Q9UEF0|Q9UEF1|Q9UEF8	Frame_Shift_Del	DEL	ENST00000283882.3	hg19	CCDS10916.1																																																																																			.	.		0.338	CFDP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269031.2	NM_006324	
DNAH5	1767	hgsc.bcm.edu	37	5	13864702	13864702	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:13864702delA	ENST00000265104.4	-	28	4504	c.4400delT	c.(4399-4401)ttgfs	p.L1467fs	CTB-51A17.1_ENST00000503244.1_RNA	NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	1467	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					CTTCAGGTCCAAAAAAGCCTG	0.498									Kartagener syndrome																												p.L1467fs		Atlas-INDEL	.											.	DNAH5	868	.	0			c.4401delG						.						57.0	57.0	57.0					5																	13864702		2203	4300	6503	SO:0001589	frameshift_variant	1767	exon28	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	.	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"""Axonemal dyneins"""	2950	protein-coding gene	gene with protein product	"""dynein heavy chain 5"""	603335	"""dynein, axonemal, heavy polypeptide 5"""			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.4400delT	chr5.hg19:g.13864702delA	ENSP00000265104:p.Leu1467fs	215.0	0.0		152.0	10.0	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Frame_Shift_Del	DEL	ENST00000265104.4	hg19	CCDS3882.1																																																																																			.	.		0.498	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369	
TMEM132C	92293	hgsc.bcm.edu	37	12	129178468	129178468	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:129178468delC	ENST00000435159.2	+	6	1544	c.1544delC	c.(1543-1545)gccfs	p.A515fs	TMEM132C_ENST00000315208.8_Frame_Shift_Del_p.A131fs|TMEM132C_ENST00000537538.1_5'UTR	NM_001136103.2	NP_001129575.2	Q8N3T6	T132C_HUMAN	transmembrane protein 132C	515						integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|lung(2)|prostate(2)|skin(1)	13						TACCTGAGCGCCCCCCTGTGT	0.567																																					p.A515fs		Atlas-INDEL	.											.	TMEM132C	142	.	0			c.1543delG						.						51.0	49.0	49.0					12																	129178468		692	1591	2283	SO:0001589	frameshift_variant	92293	exon6			.	AK126715		12q24.32	2014-06-13				ENSG00000181234			25436	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 152"""						Standard	NM_001136103		Approved	DKFZp761O2018, PPP1R152	uc021rgn.1	Q8N3T6		ENST00000435159.2:c.1544delC	chr12.hg19:g.129178468delC	ENSP00000410852:p.Ala515fs	254.0	0.0		216.0	14.0	NM_001136103	Q69YX8	Frame_Shift_Del	DEL	ENST00000435159.2	hg19																																																																																				.	.		0.567	TMEM132C-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		XM_044062	
KMT2D	8085	hgsc.bcm.edu	37	12	49420553	49420554	+	Frame_Shift_Del	DEL	AC	AC	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	AC	AC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:49420553_49420554delAC	ENST00000301067.7	-	48	15194_15195	c.15195_15196delGT	c.(15193-15198)tggtccfs	p.WS5065fs		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	5065					chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)										ACCTCCGTGGACCAAAGGGCAC	0.619																																					p.5066_5066del		Atlas-Indel,Pindel	.											.	MLL2	1173	.	0			c.15196_15197del						.																																			SO:0001589	frameshift_variant	8085	exon48			.	AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	7133	protein-coding gene	gene with protein product		602113	"""trinucleotide repeat containing 21"", ""myeloid/lymphoid or mixed-lineage leukemia 2"""	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.15195_15196delGT	chr12.hg19:g.49420553_49420554delAC	ENSP00000301067:p.Trp5065fs	108.0	0.0		87.0	31.0	NM_003482	O14687	Frame_Shift_Del	DEL	ENST00000301067.7	hg19	CCDS44873.1																																																																																			.	.		0.619	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2		
SCN10A	6336	hgsc.bcm.edu	37	3	38793861	38793861	+	Frame_Shift_Del	DEL	C	C	-	rs556526024		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:38793861delC	ENST00000449082.2	-	11	1603	c.1604delG	c.(1603-1605)ggcfs	p.G535fs		NM_006514.2	NP_006505.2	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha subunit	535					AV node cell to bundle of His cell communication (GO:0086067)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of cardiac muscle contraction (GO:0055117)|regulation of heart rate (GO:0002027)|regulation of ion transmembrane transport (GO:0034765)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(5)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(14)|kidney(5)|large_intestine(33)|lung(54)|ovary(5)|pancreas(1)|prostate(5)|skin(13)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	150				KIRC - Kidney renal clear cell carcinoma(284;0.0769)|Kidney(284;0.0945)	Benzocaine(DB01086)|Bupivacaine(DB00297)|Chloroprocaine(DB01161)|Cinchocaine(DB00527)|Cocaine(DB00907)|Dyclonine(DB00645)|Hexylcaine(DB00473)|Lacosamide(DB06218)|Levobupivacaine(DB01002)|Lidocaine(DB00281)|Mepivacaine(DB00961)|Orphenadrine(DB01173)|Oxybuprocaine(DB00892)|Procaine(DB00721)|Proparacaine(DB00807)|Ropivacaine(DB00296)|Valproic Acid(DB00313)	CAGCAGAGAGCCCCGATGGCT	0.597																																					p.G535fs		Atlas-INDEL	.											.	SCN10A	359	.	0			c.1605delC						.						62.0	68.0	66.0					3																	38793861		2203	4300	6503	SO:0001589	frameshift_variant	6336	exon11			.	AF117907	CCDS33736.1	3p22.2	2012-02-26	2007-01-23		ENSG00000185313	ENSG00000185313		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10582	protein-coding gene	gene with protein product		604427	"""sodium channel, voltage-gated, type X, alpha polypeptide"""			9839820, 10198179, 16382098	Standard	NM_006514		Approved	Nav1.8, hPN3, SNS, PN3	uc003ciq.3	Q9Y5Y9	OTTHUMG00000048245	ENST00000449082.2:c.1604delG	chr3.hg19:g.38793861delC	ENSP00000390600:p.Gly535fs	193.0	0.0		127.0	10.0	NM_006514	A6NDQ1	Frame_Shift_Del	DEL	ENST00000449082.2	hg19	CCDS33736.1																																																																																			.	.		0.597	SCN10A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109745.3	NM_006514	
ARID1A	8289	hgsc.bcm.edu	37	1	27092724	27092724	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:27092724delC	ENST00000324856.7	+	9	3116	c.2745delC	c.(2743-2745)tacfs	p.Y915fs	ARID1A_ENST00000457599.2_Frame_Shift_Del_p.Y915fs|ARID1A_ENST00000374152.2_Frame_Shift_Del_p.Y532fs|RN7SL501P_ENST00000578818.1_RNA	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	915					androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)		ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		CGCCAGGCTACCCCAATATGA	0.473			"""Mis, N, F, S, D"""		"""clear cell ovarian carcinoma, RCC"""																																p.Y915fs		Atlas-INDEL	.		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	.	ARID1A	842	.	0			c.2744delA						.						82.0	81.0	81.0					1																	27092724		2203	4300	6503	SO:0001589	frameshift_variant	8289	exon9			.	AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"""-"""	11110	protein-coding gene	gene with protein product		603024	"""SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1"", ""AT rich interactive domain 1A (SWI- like)"""	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.2745delC	chr1.hg19:g.27092724delC	ENSP00000320485:p.Tyr915fs	207.0	0.0		146.0	10.0	NM_006015	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Frame_Shift_Del	DEL	ENST00000324856.7	hg19	CCDS285.1																																																																																			.	.		0.473	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135	
PLA2G4D	283748	hgsc.bcm.edu	37	15	42377319	42377319	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:42377319delT	ENST00000290472.3	-	6	540	c.446delA	c.(445-447)aacfs	p.N149fs		NM_178034.3	NP_828848.3	Q86XP0	PA24D_HUMAN	phospholipase A2, group IVD (cytosolic)	149					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid catabolic process (GO:0009395)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|membrane (GO:0016020)	metal ion binding (GO:0046872)|phospholipase A2 activity (GO:0004623)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(4)|lung(7)|ovary(1)|skin(2)|stomach(1)	27		all_cancers(109;6.37e-17)|all_epithelial(112;3.78e-15)|Lung NSC(122;5.01e-09)|all_lung(180;2.24e-08)|Melanoma(134;0.019)|Ovarian(310;0.143)|Colorectal(260;0.245)		OV - Ovarian serous cystadenocarcinoma(18;4.9e-17)|GBM - Glioblastoma multiforme(94;1.02e-06)		GGTGATGAGGTTTTCTGGGCG	0.592																																					p.N149fs		Atlas-INDEL	.											.	PLA2G4D	72	.	0			c.447delC						.						132.0	120.0	124.0					15																	42377319		2203	4299	6502	SO:0001589	frameshift_variant	283748	exon6			.	AB090876	CCDS32203.1	15q14	2008-09-19				ENSG00000159337	3.1.1.4		30038	protein-coding gene	gene with protein product		612864				14709560	Standard	NM_178034		Approved	cPLA2delta	uc001zox.3	Q86XP0		ENST00000290472.3:c.446delA	chr15.hg19:g.42377319delT	ENSP00000290472:p.Asn149fs	137.0	0.0		116.0	12.0	NM_178034	Q8N176	Frame_Shift_Del	DEL	ENST00000290472.3	hg19	CCDS32203.1																																																																																			.	.		0.592	PLA2G4D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419317.1	NM_178034	
C1orf131	128061	hgsc.bcm.edu	37	1	231362561	231362561	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:231362561delT	ENST00000366649.2	-	5	642	c.617delA	c.(616-618)aagfs	p.K206fs	C1orf131_ENST00000366651.3_Frame_Shift_Del_p.K205fs|C1orf131_ENST00000318906.2_Frame_Shift_Del_p.K206fs			Q8NDD1	CA131_HUMAN	chromosome 1 open reading frame 131	206	Lys-rich.						poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(2)|skin(1)	8	Breast(184;0.0871)	all_cancers(173;0.2)|Prostate(94;0.183)				CACATAACTCTTTTTAGGAGG	0.373																																					p.K206fs		Atlas-INDEL	.											.	C1orf131	30	.	0			c.618delG						.						125.0	131.0	129.0					1																	231362561		2203	4300	6503	SO:0001589	frameshift_variant	128061	exon5			.	BC062353	CCDS1591.2, CCDS73049.1	1q42.2	2012-06-27			ENSG00000143633	ENSG00000143633			25332	protein-coding gene	gene with protein product						12975309	Standard	XM_005273051		Approved	DKFZp547B1713	uc001hul.3	Q8NDD1	OTTHUMG00000038023	ENST00000366649.2:c.617delA	chr1.hg19:g.231362561delT	ENSP00000355609:p.Lys206fs	123.0	0.0		214.0	16.0	NM_152379	Q5TBI0|Q5TBI1|Q6P6B4|Q7Z6H5|Q8N432|Q96NM6	Frame_Shift_Del	DEL	ENST00000366649.2	hg19	CCDS1591.2																																																																																			.	.		0.373	C1orf131-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000092864.1	NM_152379	
PRR12	57479	hgsc.bcm.edu	37	19	50123635	50123635	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:50123635delA	ENST00000418929.2	+	10	5536	c.5524delA	c.(5524-5526)aaafs	p.K1842fs		NM_020719.1	NP_065770.1	Q9ULL5	PRR12_HUMAN	proline rich 12	1021							DNA binding (GO:0003677)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|pancreas(1)|prostate(2)	11		all_lung(116;2.45e-07)|Lung NSC(112;1.24e-06)|Ovarian(192;0.0728)|all_neural(266;0.0887)		OV - Ovarian serous cystadenocarcinoma(262;0.00319)|GBM - Glioblastoma multiforme(134;0.0132)		GCGTCTGCTCAAAACCAGGGC	0.577																																					p.L1841fs		Atlas-INDEL	.											.	PRR12	157	.	0			c.5523delC						.						45.0	49.0	48.0					19																	50123635		2114	4233	6347	SO:0001589	frameshift_variant	57479	exon10			.	AB033031	CCDS46143.1	19q13.33	2008-07-02	2006-02-06	2006-02-06		ENSG00000126464			29217	protein-coding gene	gene with protein product			"""KIAA1205"""	KIAA1205		10574462	Standard	NM_020719		Approved		uc002poo.4	Q9ULL5		ENST00000418929.2:c.5524delA	chr19.hg19:g.50123635delA	ENSP00000394510:p.Lys1842fs	218.0	0.0		185.0	12.0	NM_020719	E9PB06|Q8N4J6	Frame_Shift_Del	DEL	ENST00000418929.2	hg19	CCDS46143.1																																																																																			.	.		0.577	PRR12-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465915.1	NM_020719	
KLF9	687	hgsc.bcm.edu	37	9	73028126	73028126	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:73028126delC	ENST00000377126.2	-	1	1414	c.154delG	c.(154-156)gacfs	p.D52fs		NM_001206.2	NP_001197.1	Q13886	KLF9_HUMAN	Kruppel-like factor 9	52					cellular response to thyroid hormone stimulus (GO:0097067)|embryo implantation (GO:0007566)|progesterone receptor signaling pathway (GO:0050847)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(3)|lung(1)|prostate(2)|urinary_tract(1)	9						TTCCAGGTGTCCCCCGGGTCA	0.647																																					p.D52fs		Atlas-INDEL	.											.	KLF9	16	.	0			c.155delA						.						75.0	56.0	62.0					9																	73028126		2203	4300	6503	SO:0001589	frameshift_variant	687	exon1			.	BC069431	CCDS6633.1	9q21.11	2013-01-08	2004-11-29	2004-12-01	ENSG00000119138	ENSG00000119138		"""Kruppel-like transcription factors"", ""Zinc fingers, C2H2-type"""	1123	protein-coding gene	gene with protein product		602902	"""basic transcription element binding protein 1"""	BTEB1		1356762	Standard	NM_001206		Approved		uc004aht.3	Q13886	OTTHUMG00000019991	ENST00000377126.2:c.154delG	chr9.hg19:g.73028126delC	ENSP00000366330:p.Asp52fs	245.0	0.0		150.0	11.0	NM_001206	B2R943|Q16196	Frame_Shift_Del	DEL	ENST00000377126.2	hg19	CCDS6633.1																																																																																			.	.		0.647	KLF9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052602.1	NM_001206	
FHAD1	114827	hgsc.bcm.edu	37	1	15684625	15684625	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:15684625delA	ENST00000375998.4	+	19	2516	c.2516delA	c.(2515-2517)caafs	p.Q839fs	FHAD1_ENST00000417793.1_Frame_Shift_Del_p.Q803fs|FHAD1_ENST00000358897.4_Frame_Shift_Del_p.Q839fs|FHAD1_ENST00000314740.8_Frame_Shift_Del_p.Q92fs|FHAD1_ENST00000375999.3_Frame_Shift_Del_p.Q839fs|FHAD1_ENST00000471347.1_3'UTR			B1AJZ9	FHAD1_HUMAN	forkhead-associated (FHA) phosphopeptide binding domain 1	839										skin(1)|stomach(1)	2						TTAAAAGAGCAAAAAGAGGAC	0.383																																					p.Q839fs		Atlas-INDEL	.											.	FHAD1	78	.	0			c.2515delC						.						38.0	36.0	37.0					1																	15684625		692	1591	2283	SO:0001589	frameshift_variant	114827	exon20			.	AK093300		1p36.21	2012-04-19			ENSG00000142621	ENSG00000142621			29408	protein-coding gene	gene with protein product						11572484	Standard	NM_052929		Approved	KIAA1937	uc001awb.2	B1AJZ9	OTTHUMG00000002088	ENST00000375998.4:c.2516delA	chr1.hg19:g.15684625delA	ENSP00000365166:p.Gln839fs	214.0	0.0		164.0	10.0	NM_052929	Q0P6F5|Q8N8D3|Q8N9T6|Q8NA05	Frame_Shift_Del	DEL	ENST00000375998.4	hg19																																																																																				.	.		0.383	FHAD1-026	PUTATIVE	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000393400.2	NM_052929	
FAM69C	125704	hgsc.bcm.edu	37	18	72113977	72113977	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr18:72113977delC	ENST00000343998.6	-	2	748	c.740delG	c.(739-741)ggtfs	p.G248fs	FAM69C_ENST00000400291.2_Intron	NM_001044369.2	NP_001037834.2	Q0P6D2	FA69C_HUMAN	family with sequence similarity 69, member C	248						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	transferase activity, transferring phosphorus-containing groups (GO:0016772)			breast(1)|large_intestine(2)|ovary(2)	5						GGCCTGGCCACCCCCAGGGGC	0.647																																					p.G247fs		Atlas-INDEL	.											.	FAM69C	45	.	0			c.741delT						.						92.0	88.0	90.0					18																	72113977		692	1591	2283	SO:0001589	frameshift_variant	125704	exon2			.	BC019628	CCDS42445.2	18q22.3	2012-08-03	2009-07-23	2009-07-23	ENSG00000187773	ENSG00000187773			31729	protein-coding gene	gene with protein product		614544	"""chromosome 18 open reading frame 51"""	C18orf51		21334309	Standard	NM_001044369		Approved		uc002llk.3	Q0P6D2	OTTHUMG00000156984	ENST00000343998.6:c.740delG	chr18.hg19:g.72113977delC	ENSP00000344331:p.Gly248fs	223.0	0.0		131.0	10.0	NM_001044369		Frame_Shift_Del	DEL	ENST00000343998.6	hg19	CCDS42445.2																																																																																			.	.		0.647	FAM69C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346971.2	XM_058931	
SZT2	23334	hgsc.bcm.edu	37	1	43912809	43912809	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:43912809delC	ENST00000562955.1	+	65	9085	c.9085delC	c.(9085-9087)cccfs	p.P3029fs	SZT2-AS1_ENST00000396885.2_RNA|SZT2_ENST00000372442.1_Frame_Shift_Del_p.P2187fs	NM_015284.3	NP_056099.3	Q5T011	SZT2_HUMAN	seizure threshold 2 homolog (mouse)	3086					central nervous system development (GO:0007417)|corpus callosum morphogenesis (GO:0021540)|embryo development (GO:0009790)|pigmentation (GO:0043473)|post-embryonic development (GO:0009791)|regulation of superoxide dismutase activity (GO:1901668)	extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)				NS(2)|breast(9)|central_nervous_system(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(19)|lung(39)|ovary(4)|pancreas(3)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	113						CCCTGACGGACCCCACTTTGG	0.607																																					p.G3028fs		Atlas-INDEL	.											.	SZT2	383	.	0			c.9084delA						.						106.0	76.0	86.0					1																	43912809		2203	4300	6503	SO:0001589	frameshift_variant	23334	exon65			.	AB007936	CCDS30694.1, CCDS30694.2	1p34.2	2012-11-19	2011-06-10	2011-06-10	ENSG00000198198	ENSG00000198198			29040	protein-coding gene	gene with protein product	"""seizure threshold 2 homolog A (mouse)"", ""seizure threshold 2 homolog B (mouse)"""	615463	"""chromosome 1 open reading frame 84"", ""KIAA0467"""	C1orf84, KIAA0467		9455484	Standard	NM_015284		Approved	FLJ10387, SZT2B, RP11-506B15.1, FLJ34502, SZT2A	uc001cjk.3	Q5T011	OTTHUMG00000007423	ENST00000562955.1:c.9085delC	chr1.hg19:g.43912809delC	ENSP00000457168:p.Pro3029fs	278.0	0.0		211.0	14.0	NM_015284	A0PJK5|A7E2X4|O75055|Q5JUY7|Q5T012|Q5XKC7|Q6ZNI8|Q6ZT24|Q7Z636|Q8NAY9|Q9H5H7|Q9UFQ8	Frame_Shift_Del	DEL	ENST00000562955.1	hg19	CCDS30694.2																																																																																			.	.		0.607	SZT2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019517.3	NM_015284	
EXOC2	55770	hgsc.bcm.edu	37	6	564874	564874	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:564874delT	ENST00000230449.4	-	14	1634	c.1499delA	c.(1498-1500)aatfs	p.N500fs	EXOC2_ENST00000448181.3_Frame_Shift_Del_p.N95fs	NM_018303.5	NP_060773.3	Q96KP1	EXOC2_HUMAN	exocyst complex component 2	500					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)		CTTAAAATCATTTTGTCTTTG	0.328																																					p.N500fs		Atlas-INDEL	.											.	EXOC2	81	.	0			c.1500delT						.						203.0	193.0	196.0					6																	564874		2203	4300	6503	SO:0001589	frameshift_variant	55770	exon14			.	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.1499delA	chr6.hg19:g.564874delT	ENSP00000230449:p.Asn500fs	375.0	0.0		261.0	16.0	NM_018303	B2RBE6|Q5JPC8|Q96AN6|Q9NUZ8|Q9UJM7	Frame_Shift_Del	DEL	ENST00000230449.4	hg19	CCDS34327.1																																																																																			.	.		0.328	EXOC2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039627.1	NM_018303	
MAPK10	5602	hgsc.bcm.edu	37	4	86985490	86985490	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:86985490delT	ENST00000359221.3	-	11	1565	c.1039delA	c.(1039-1041)agafs	p.R347fs	MAPK10_ENST00000449047.2_Frame_Shift_Del_p.R202fs|MAPK10_ENST00000361569.2_Frame_Shift_Del_p.R347fs|MAPK10_ENST00000395161.2_Frame_Shift_Del_p.R347fs|MAPK10_ENST00000395160.3_Frame_Shift_Del_p.R202fs|MAPK10_ENST00000395169.3_Frame_Shift_Del_p.R309fs|MAPK10_ENST00000395157.3_Frame_Shift_Del_p.R202fs|MAPK10_ENST00000395166.1_Frame_Shift_Del_p.R309fs			P53779	MK10_HUMAN	mitogen-activated protein kinase 10	347	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|JUN phosphorylation (GO:0007258)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|JUN kinase activity (GO:0004705)|MAP kinase kinase activity (GO:0004708)			breast(1)|central_nervous_system(1)|stomach(1)	3		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.243)		OV - Ovarian serous cystadenocarcinoma(123;0.002)		ACTGATATTCTTTTTGCTGGG	0.433																																					p.R347fs		Atlas-INDEL	.											.	MAPK10	106	.	0			c.1040delG						.						175.0	160.0	165.0					4																	86985490		2203	4300	6503	SO:0001589	frameshift_variant	5602	exon11			.	U07620	CCDS3612.1, CCDS3613.1, CCDS34026.1, CCDS43247.1	4q22-q23	2011-06-09			ENSG00000109339	ENSG00000109339	2.7.11.1	"""Mitogen-activated protein kinase cascade / Kinases"""	6872	protein-coding gene	gene with protein product		602897		PRKM10		8654373, 12436199	Standard	NM_002753		Approved	JNK3, p493F12, p54bSAPK	uc003hpt.3	P53779	OTTHUMG00000130604	ENST00000359221.3:c.1039delA	chr4.hg19:g.86985490delT	ENSP00000352157:p.Arg347fs	225.0	0.0		176.0	11.0	NM_138982	A6NFS3|A6NG28|B3KQ94|Q15707|Q49AP1	Frame_Shift_Del	DEL	ENST00000359221.3	hg19	CCDS34026.1																																																																																			.	.		0.433	MAPK10-012	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000361363.2		
URGCP	55665	hgsc.bcm.edu	37	7	43917420	43917420	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:43917420delC	ENST00000453200.1	-	6	2135	c.1642delG	c.(1642-1644)gtgfs	p.V548fs	URGCP_ENST00000447717.3_Frame_Shift_Del_p.V505fs|URGCP_ENST00000223341.7_Frame_Shift_Del_p.V505fs|URGCP-MRPS24_ENST00000603700.1_Intron|URGCP_ENST00000443736.1_Frame_Shift_Del_p.V505fs|URGCP_ENST00000336086.6_Frame_Shift_Del_p.V505fs|URGCP_ENST00000402306.3_Frame_Shift_Del_p.V539fs|URGCP_ENST00000497914.1_5'UTR			Q8TCY9	URGCP_HUMAN	upregulator of cell proliferation	548					cell cycle (GO:0007049)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	GTP binding (GO:0005525)			breast(3)|endometrium(4)|kidney(2)|large_intestine(3)|liver(1)|lung(13)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						AACTCCTGCACCCCCGAGGAG	0.652																																					p.V548fs		Atlas-INDEL	.											.	URGCP	170	.	0			c.1643delT						.						34.0	39.0	37.0					7																	43917420		2038	4172	6210	SO:0001589	frameshift_variant	55665	exon6			.		CCDS43572.1, CCDS47577.1, CCDS47578.1	7p13	2010-02-17			ENSG00000106608	ENSG00000106608			30890	protein-coding gene	gene with protein product	"""up-regulated gene 4"""	610337				10819331, 12082552	Standard	NM_017920		Approved	URG4, KIAA1507, FLJ20654, DKFZp666G166, DKFZp686O0457	uc003tiw.3	Q8TCY9	OTTHUMG00000155245	ENST00000453200.1:c.1642delG	chr7.hg19:g.43917420delC	ENSP00000396918:p.Val548fs	182.0	0.0		197.0	12.0	NM_001077663	E9PFF6|Q658M4|Q68DH6|Q6MZZ5|Q8WV98|Q9NWR7|Q9P221	Frame_Shift_Del	DEL	ENST00000453200.1	hg19	CCDS47578.1																																																																																			.	.		0.652	URGCP-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338995.1	NM_001077664	
VARS2	57176	hgsc.bcm.edu	37	6	30890972	30890972	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:30890972delT	ENST00000321897.5	+	23	2909	c.2277delT	c.(2275-2277)gctfs	p.A759fs	VARS2_ENST00000541562.1_Frame_Shift_Del_p.A789fs|VARS2_ENST00000416670.2_Frame_Shift_Del_p.A759fs|VARS2_ENST00000476162.1_3'UTR|VARS2_ENST00000542001.1_Frame_Shift_Del_p.A619fs			Q5ST30	SYVM_HUMAN	valyl-tRNA synthetase 2, mitochondrial	759					gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)|valyl-tRNA aminoacylation (GO:0006438)	mitochondrion (GO:0005739)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|valine-tRNA ligase activity (GO:0004832)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(15)|ovary(3)|prostate(3)|skin(4)|urinary_tract(1)	46						TCCTCAATGCTTTAGGGGAGA	0.532																																					p.A789fs		Atlas-INDEL	.											.	VARS2	60	.	0			c.2366delC						.						108.0	121.0	116.0					6																	30890972		1510	2708	4218	SO:0001589	frameshift_variant	57176	exon24			.	AB067472	CCDS34387.1, CCDS54980.1	6p21.33	2012-10-26	2012-10-26	2007-02-23	ENSG00000137411	ENSG00000137411	6.1.1.9	"""Aminoacyl tRNA synthetases / Class I"""	21642	protein-coding gene	gene with protein product	"""valine tRNA ligase 2, mitochondrial"""	612802	"""valyl-tRNA synthetase 2-like"", ""valyl-tRNA synthetase like"", ""valyl-tRNA synthetase 2, mitochondrial (putative)"""	VARS2L, VARSL		1898367, 11572484, 18400783	Standard	NM_001167734		Approved	DKFZP434L1435, KIAA1885, G7a	uc011dmz.2	Q5ST30	OTTHUMG00000031263	ENST00000321897.5:c.2277delT	chr6.hg19:g.30890972delT	ENSP00000316092:p.Ala759fs	261.0	0.0		159.0	12.0	NM_001167734	A2ABL7|B4DET4|B4E3P5|F5GXJ0|F5H323|Q2M2A0|Q59FI1|Q5SQ96|Q5SS98|Q6DKJ5|Q6ZV24|Q96GN2|Q96H77|Q96Q02|Q9H6R2|Q9UFH7	Frame_Shift_Del	DEL	ENST00000321897.5	hg19	CCDS34387.1																																																																																			.	.		0.532	VARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076566.2	NM_020442	
PSD4	23550	hgsc.bcm.edu	37	2	113950863	113950863	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:113950863delG	ENST00000245796.6	+	8	2143	c.1948delG	c.(1948-1950)gggfs	p.G650fs	PSD4_ENST00000441564.3_Frame_Shift_Del_p.G622fs	NM_012455.2	NP_036587.2	Q8NDX1	PSD4_HUMAN	pleckstrin and Sec7 domain containing 4	650	SEC7. {ECO:0000255|PROSITE- ProRule:PRU00189}.				neuron differentiation (GO:0030182)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|phospholipid binding (GO:0005543)			cervix(1)|endometrium(2)|large_intestine(4)|lung(13)|ovary(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						GGTGCTCAGTGGGGAGACTCA	0.617																																					p.S649fs		Atlas-INDEL	.											.	PSD4	74	.	0			c.1947delT						.						62.0	67.0	66.0					2																	113950863		2203	4300	6503	SO:0001589	frameshift_variant	23550	exon8			.	U63127	CCDS33276.1	2q13	2013-01-10			ENSG00000125637	ENSG00000125637		"""Pleckstrin homology (PH) domain containing"""	19096	protein-coding gene	gene with protein product		614442				12082148	Standard	XM_005263634		Approved	TIC, EFA6B	uc002tjc.3	Q8NDX1	OTTHUMG00000153339	ENST00000245796.6:c.1948delG	chr2.hg19:g.113950863delG	ENSP00000245796:p.Gly650fs	182.0	0.0		165.0	10.0	NM_012455	A6NEG7|A8K1Y0|O95621|Q4ZG34|Q6GPH8|Q8IYP4	Frame_Shift_Del	DEL	ENST00000245796.6	hg19	CCDS33276.1																																																																																			.	.		0.617	PSD4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000330789.1	NM_012455	
KIT	3815	hgsc.bcm.edu	37	4	55565881	55565881	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:55565881delA	ENST00000288135.5	+	4	802	c.705delA	c.(703-705)atafs	p.I235fs		NM_000222.2|NM_001093772.1	NP_000213.1|NP_001087241.1	P10721	KIT_HUMAN	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	235	Ig-like C2-type 3.				actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cellular response to thyroid hormone stimulus (GO:0097067)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell cytokine production (GO:0002371)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|digestive tract development (GO:0048565)|ectopic germ cell programmed cell death (GO:0035234)|embryonic hemopoiesis (GO:0035162)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation (GO:0050673)|erythrocyte differentiation (GO:0030218)|erythropoietin-mediated signaling pathway (GO:0038162)|Fc receptor signaling pathway (GO:0038093)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell migration (GO:0008354)|glycosphingolipid metabolic process (GO:0006687)|hemopoiesis (GO:0030097)|immature B cell differentiation (GO:0002327)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|Kit signaling pathway (GO:0038109)|lamellipodium assembly (GO:0030032)|lymphoid progenitor cell differentiation (GO:0002320)|male gonad development (GO:0008584)|mast cell chemotaxis (GO:0002551)|mast cell cytokine production (GO:0032762)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|mast cell proliferation (GO:0070662)|megakaryocyte development (GO:0035855)|melanocyte adhesion (GO:0097326)|melanocyte differentiation (GO:0030318)|melanocyte migration (GO:0097324)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of programmed cell death (GO:0043069)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|pigmentation (GO:0043473)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of developmental pigmentation (GO:0048070)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|stem cell differentiation (GO:0048863)|stem cell maintenance (GO:0019827)|T cell differentiation (GO:0030217)|visual learning (GO:0008542)	acrosomal vesicle (GO:0001669)|cell-cell junction (GO:0005911)|cytoplasmic side of plasma membrane (GO:0009898)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|stem cell factor receptor activity (GO:0005020)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(8)|autonomic_ganglia(1)|bone(21)|breast(2)|central_nervous_system(4)|endometrium(10)|eye(12)|genital_tract(18)|haematopoietic_and_lymphoid_tissue(1820)|kidney(17)|large_intestine(17)|lung(27)|ovary(23)|pancreas(4)|prostate(1)|salivary_gland(15)|skin(228)|soft_tissue(4117)|stomach(3)|testis(55)|thymus(7)|upper_aerodigestive_tract(1)	6411	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	CGTGCACAATAAAAGATGTGT	0.428		1	"""Mis, O"""		"""GIST, AML, TGCT, mastocytosis, mucosal melanoma"""	"""GIST, epithelioma"""	Piebald trait		Piebaldism;Mast Cell disease, Familial Clustering of;Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Gastrointestinal Stromal Tumors																												p.I235fs		Atlas-INDEL	.	yes	Dom	yes	Familial gastrointestinal stromal tumour	4	4q12	3815	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	yes	"""L, M, O, E"""	.	KIT	7396	.	0			c.704delT						.						185.0	171.0	176.0					4																	55565881		2203	4300	6503	SO:0001589	frameshift_variant	3815	exon4	Familial Cancer Database	Piebald trait;incl.: Familial Cutaneous Mastocytosis (Urticaria Pigmentosum);Sporadic Multiple GIST;Familial GIST, incl. Multiple Familial Gastrointestinal Autonomic Nerve Tumors (GANT)	.	S67773	CCDS3496.1, CCDS47058.1	4q12	2014-09-17			ENSG00000157404	ENSG00000157404		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6342	protein-coding gene	gene with protein product		164920	"""piebald trait"""	PBT		9027509	Standard	NM_001093772		Approved	CD117, SCFR, C-Kit	uc010igr.3	P10721	OTTHUMG00000128713	ENST00000288135.5:c.705delA	chr4.hg19:g.55565881delA	ENSP00000288135:p.Ile235fs	227.0	0.0		151.0	10.0	NM_000222	B5A956|D5LXN2|D5M931|F5H8F8|Q6IQ28|Q99662|Q9UM99	Frame_Shift_Del	DEL	ENST00000288135.5	hg19	CCDS3496.1																																																																																			.	.		0.428	KIT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250618.1		
ZNF311	282890	hgsc.bcm.edu	37	6	28963809	28963809	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:28963809delT	ENST00000377179.3	-	7	1482	c.970delA	c.(970-972)accfs	p.T324fs	ZNF311_ENST00000483450.1_5'UTR	NM_001010877.2	NP_001010877.2	Q5JNZ3	ZN311_HUMAN	zinc finger protein 311	324					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(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(11)|skin(3)|upper_aerodigestive_tract(2)	28						CCACTGTGGGTTTTTTTATGT	0.507																																					p.T324fs		Atlas-INDEL	.											.	ZNF311	59	.	0			c.971delC						.						72.0	62.0	66.0					6																	28963809		1511	2709	4220	SO:0001589	frameshift_variant	282890	exon7			.	AL833166	CCDS34357.1	6p21.33	2013-01-08			ENSG00000197935	ENSG00000197935		"""Zinc fingers, C2H2-type"", ""-"""	13847	protein-coding gene	gene with protein product							Standard	XM_006715067		Approved		uc003nlu.2	Q5JNZ3	OTTHUMG00000031292	ENST00000377179.3:c.970delA	chr6.hg19:g.28963809delT	ENSP00000366384:p.Thr324fs	239.0	0.0		174.0	13.0	NM_001010877	A2BFK5|B0S7Y4|Q92971	Frame_Shift_Del	DEL	ENST00000377179.3	hg19	CCDS34357.1																																																																																			.	.		0.507	ZNF311-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076631.3	XM_212581	
TMEM62	80021	hgsc.bcm.edu	37	15	43461843	43461843	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:43461843delT	ENST00000260403.2	+	11	1628	c.1349delT	c.(1348-1350)attfs	p.I450fs	TMEM62_ENST00000569369.1_3'UTR	NM_024956.3	NP_079232.3	Q0P6H9	TMM62_HUMAN	transmembrane protein 62	450						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)		ATTCTCATTATTTTTAGATAT	0.388																																					p.I450fs		Atlas-INDEL	.											.	TMEM62	47	.	0			c.1348delA						.						127.0	125.0	126.0					15																	43461843		2203	4299	6502	SO:0001589	frameshift_variant	80021	exon11			.	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.1349delT	chr15.hg19:g.43461843delT	ENSP00000260403:p.Ile450fs	186.0	0.0		163.0	12.0	NM_024956	Q6I9Y5|Q9H5J6	Frame_Shift_Del	DEL	ENST00000260403.2	hg19	CCDS32210.1																																																																																			.	.		0.388	TMEM62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432227.1	NM_024956	
COL24A1	255631	hgsc.bcm.edu	37	1	86196292	86196292	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:86196292delT	ENST00000370571.2	-	60	5448	c.5082delA	c.(5080-5082)aaafs	p.K1694fs	COL24A1_ENST00000436319.1_Frame_Shift_Del_p.K1673fs	NM_152890.5	NP_690850.2	Q17RW2	COOA1_HUMAN	collagen, type XXIV, alpha 1	1694	Fibrillar collagen NC1. {ECO:0000255|PROSITE-ProRule:PRU00793}.				extracellular matrix organization (GO:0030198)|hematopoietic progenitor cell differentiation (GO:0002244)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)			NS(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(9)|liver(1)|lung(56)|ovary(4)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	101				all cancers(265;0.0627)|Epithelial(280;0.0689)		GATGAGGAAGTTTTTGTACTT	0.383																																					p.L1695fs		Atlas-INDEL	.											.	COL24A1	202	.	0			c.5083delC						.						144.0	135.0	138.0					1																	86196292		1864	4096	5960	SO:0001589	frameshift_variant	255631	exon60			.	AF410793	CCDS41353.1	1p22.3-p22.2	2013-01-16			ENSG00000171502	ENSG00000171502		"""Collagens"""	20821	protein-coding gene	gene with protein product		610025					Standard	NM_152890		Approved		uc001dlj.3	Q17RW2	OTTHUMG00000010629	ENST00000370571.2:c.5082delA	chr1.hg19:g.86196292delT	ENSP00000359603:p.Lys1694fs	204.0	0.0		164.0	10.0	NM_152890	C9J1X6|Q14BD7|Q59EX5|Q5VY50|Q7Z5L5	Frame_Shift_Del	DEL	ENST00000370571.2	hg19	CCDS41353.1																																																																																			.	.		0.383	COL24A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029335.4	NM_152890	
ROCK1	6093	hgsc.bcm.edu	37	18	18690859	18690859	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr18:18690859delC	ENST00000399799.2	-	1	953	c.13delG	c.(13-15)gacfs	p.D5fs		NM_005406.2	NP_005397.1	Q13464	ROCK1_HUMAN	Rho-associated, coiled-coil containing protein kinase 1	5					actin cytoskeleton organization (GO:0030036)|apical constriction (GO:0003383)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|bleb assembly (GO:0032060)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)|membrane to membrane docking (GO:0022614)|myoblast migration (GO:0051451)|negative regulation of angiogenesis (GO:0016525)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of focal adhesion assembly (GO:0051894)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of establishment of cell polarity (GO:2000114)|regulation of focal adhesion assembly (GO:0051893)|regulation of keratinocyte differentiation (GO:0045616)|regulation of stress fiber assembly (GO:0051492)|Rho protein signal transduction (GO:0007266)|signal transduction (GO:0007165)|smooth muscle contraction (GO:0006939)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(4)|central_nervous_system(1)|large_intestine(8)|lung(2)	16	Melanoma(1;0.165)					TCAAAACTGTCCCCAGTCGAC	0.517																																					p.D5fs		Atlas-INDEL	.											.	ROCK1	162	.	0			c.14delA						.						164.0	147.0	152.0					18																	18690859		2203	4300	6503	SO:0001589	frameshift_variant	6093	exon1			.		CCDS11870.2	18q11.2	2013-01-10			ENSG00000067900	ENSG00000067900	2.7.11.1	"""Pleckstrin homology (PH) domain containing"""	10251	protein-coding gene	gene with protein product		601702				8617235	Standard	NM_005406		Approved	p160ROCK	uc002kte.3	Q13464	OTTHUMG00000131723	ENST00000399799.2:c.13delG	chr18.hg19:g.18690859delC	ENSP00000382697:p.Asp5fs	174.0	0.0		143.0	10.0	NM_005406	B0YJ91|Q2KHM4|Q59GZ4	Frame_Shift_Del	DEL	ENST00000399799.2	hg19	CCDS11870.2																																																																																			.	.		0.517	ROCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254641.2	NM_005406	
NOL6	65083	hgsc.bcm.edu	37	9	33469208	33469208	+	Frame_Shift_Del	DEL	C	C	-	rs192128071	byFrequency	TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:33469208delC	ENST00000379471.2	-	6	946	c.859delG	c.(859-861)gatfs	p.D287fs	NOL6_ENST00000455041.2_Frame_Shift_Del_p.D227fs|NOL6_ENST00000464829.1_5'UTR			Q9H6R4	NOL6_HUMAN	nucleolar protein 6 (RNA-associated)	287					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)		TGCTCACCATCCCCTGCAGGA	0.612																																					p.D287fs		Atlas-INDEL	.											.	NOL6	85	.	0			c.860delA						.						102.0	100.0	101.0					9																	33469208		2203	4300	6503	SO:0001589	frameshift_variant	65083	exon6			.	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.859delG	chr9.hg19:g.33469208delC	ENSP00000368784:p.Asp287fs	211.0	0.0		165.0	10.0	NM_022917	Q5T5M3|Q5T5M4|Q7L4G6|Q8N6I0|Q8TEY9|Q8TEZ0|Q8TEZ1|Q9H675	Frame_Shift_Del	DEL	ENST00000379471.2	hg19																																																																																				.	.		0.612	NOL6-005	NOVEL	non_canonical_TEC|basic	protein_coding	protein_coding	OTTHUMT00000001019.2	NM_022917	
OR1N2	138882	hgsc.bcm.edu	37	9	125316423	125316423	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:125316423delA	ENST00000373688.2	+	1	1033	c.975delA	c.(973-975)ggafs	p.G325fs		NM_001004457.1	NP_001004457.1	Q8NGR9	OR1N2_HUMAN	olfactory receptor, family 1, subfamily N, member 2	325						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|large_intestine(6)|lung(10)|ovary(2)|skin(3)|stomach(3)	26						TTGTCAGTGGAAAAACATTCT	0.388																																					p.G325fs		Atlas-INDEL	.											.	OR1N2	51	.	0			c.974delG						.						84.0	86.0	85.0					9																	125316423		2202	4300	6502	SO:0001589	frameshift_variant	138882	exon1			.		CCDS35123.1	9q33.2	2013-09-20			ENSG00000171501	ENSG00000171501		"""GPCR / Class A : Olfactory receptors"""	15111	protein-coding gene	gene with protein product							Standard	NM_001004457		Approved		uc011lyx.2	Q8NGR9	OTTHUMG00000020607	ENST00000373688.2:c.975delA	chr9.hg19:g.125316423delA	ENSP00000362792:p.Gly325fs	223.0	0.0		159.0	10.0	NM_001004457	A3KFM2|B2RNY4|Q6IF17|Q96RA3	Frame_Shift_Del	DEL	ENST00000373688.2	hg19	CCDS35123.1																																																																																			.	.		0.388	OR1N2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053937.2		
TNIK	23043	hgsc.bcm.edu	37	3	170801981	170801981	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:170801981delT	ENST00000436636.2	-	26	3476	c.3132delA	c.(3130-3132)aaafs	p.K1044fs	TNIK_ENST00000470834.1_Frame_Shift_Del_p.K1007fs|TNIK_ENST00000538048.1_Frame_Shift_Del_p.K996fs|TNIK_ENST00000460047.1_Frame_Shift_Del_p.K981fs|TNIK_ENST00000284483.8_Frame_Shift_Del_p.K1036fs|TNIK_ENST00000488470.1_Frame_Shift_Del_p.K989fs|TNIK_ENST00000341852.6_Frame_Shift_Del_p.K960fs|TNIK_ENST00000475336.1_Frame_Shift_Del_p.K952fs|TNIK_ENST00000357327.5_Frame_Shift_Del_p.K1015fs|TNIK_ENST00000369326.5_Frame_Shift_Del_p.K1022fs	NM_015028.2	NP_055843.1	Q9UKE5	TNIK_HUMAN	TRAF2 and NCK interacting kinase	1044	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)			AGTTGAATCGTTTCTTGTATT	0.373																																					p.R1045fs		Atlas-INDEL	.											TNIK_ENST00000436636,NS,carcinoma,0,2	TNIK	313	.	0			c.3133delC						.						105.0	96.0	99.0					3																	170801981		1845	4082	5927	SO:0001589	frameshift_variant	23043	exon26			.	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.3132delA	chr3.hg19:g.170801981delT	ENSP00000399511:p.Lys1044fs	230.0	0.0		203.0	13.0	NM_015028	A7E2A3|A8K4U1|D3DNQ6|O60298|Q8WUY7|Q9UKD8|Q9UKD9|Q9UKE0|Q9UKE1|Q9UKE2|Q9UKE3|Q9UKE4	Frame_Shift_Del	DEL	ENST00000436636.2	hg19	CCDS46956.1																																																																																			.	.		0.373	TNIK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352973.2	XM_039796	
CRYBG3	131544	hgsc.bcm.edu	37	3	97596406	97596406	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:97596406delT	ENST00000182096.4	+	1	588	c.524delT	c.(523-525)gttfs	p.V175fs		NM_153605.3	NP_705833.3	Q68DQ2	CRBG3_HUMAN	beta-gamma crystallin domain containing 3	2123							carbohydrate binding (GO:0030246)			breast(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(10)|stomach(1)|upper_aerodigestive_tract(2)	32						TCCTCTTCTGTTTTATCCCTT	0.473																																					p.V2123fs		Atlas-INDEL	.											.	CRYBG3	86	.	0			c.6367delG						.						57.0	57.0	57.0					3																	97596406		1983	4174	6157	SO:0001589	frameshift_variant	131544	exon4			.			3q11.2	2008-09-30			ENSG00000080200	ENSG00000080200			34427	protein-coding gene	gene with protein product							Standard	NM_153605		Approved	DKFZp667G2110	uc021xbn.2	Q68DQ2	OTTHUMG00000159187	ENST00000182096.4:c.524delT	chr3.hg19:g.97596406delT	ENSP00000182096:p.Val175fs	173.0	0.0		154.0	10.0	NM_153605	B4DLE8|F6VHI2|Q4G0V8|Q7Z4R9|Q86VD0|Q8N262|Q8N7F1|Q8NDQ8	Frame_Shift_Del	DEL	ENST00000182096.4	hg19																																																																																				.	.		0.473	CRYBG3-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000353751.1	NM_153605	
CUL7	9820	hgsc.bcm.edu	37	6	43015994	43015994	+	Intron	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:43015994delG	ENST00000265348.3	-	9	2149				CUL7_ENST00000478630.1_5'Flank|CUL7_ENST00000535468.1_Intron			Q14999	CUL7_HUMAN	cullin 7						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)|epithelial to mesenchymal transition (GO:0001837)|Golgi organization (GO:0007030)|microtubule cytoskeleton organization (GO:0000226)|mitotic cytokinesis (GO:0000281)|placenta development (GO:0001890)|positive regulation of dendrite morphogenesis (GO:0050775)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of mitosis (GO:0007088)|ubiquitin-dependent protein catabolic process (GO:0006511)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	3M complex (GO:1990393)|anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|Cul7-RING ubiquitin ligase complex (GO:0031467)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)				breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(8)|liver(1)|lung(11)|ovary(3)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	49			all cancers(41;0.00231)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|OV - Ovarian serous cystadenocarcinoma(102;0.0442)|KIRC - Kidney renal clear cell carcinoma(15;0.133)|Kidney(15;0.188)			TCAGGATTCTGGGGGCAGAGA	0.627																																					.		Atlas-INDEL	.											CUL7,colon,carcinoma,0,1	CUL7	133	.	0			c.2064-2C>-						.						78.0	80.0	80.0					6																	43015994		2203	4300	6503	SO:0001627	intron_variant	9820	exon10			.	BC033647	CCDS4881.1, CCDS55003.1	6p21.1	2011-05-24	2004-03-22	2004-03-22	ENSG00000044090	ENSG00000044090			21024	protein-coding gene	gene with protein product		609577	"""KIAA0076"""	KIAA0076		12481031, 12904573	Standard	NM_014780		Approved	dJ20C7.5	uc011dvb.2	Q14999	OTTHUMG00000014718	ENST00000265348.3:c.2064-3C>-	chr6.hg19:g.43015994delG		171.0	0.0		134.0	10.0	NM_014780	B4DYZ0|F5H0L1|Q5T654	Splice_Site	DEL	ENST00000265348.3	hg19	CCDS4881.1																																																																																			.	.		0.627	CUL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040575.1	NM_014780	
PIK3C2G	5288	hgsc.bcm.edu	37	12	18716360	18716360	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:18716360delA	ENST00000266497.5	+	26	3745	c.3707delA	c.(3706-3708)gaafs	p.E1236fs	PIK3C2G_ENST00000433979.1_Frame_Shift_Del_p.E1236fs|PIK3C2G_ENST00000538779.1_Frame_Shift_Del_p.E1277fs			O75747	P3C2G_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 gamma	1236	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				chemotaxis (GO:0006935)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|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 binding (GO:0035091)|phosphatidylinositol phosphate kinase activity (GO:0016307)			breast(5)|central_nervous_system(6)|endometrium(2)|kidney(4)|large_intestine(8)|lung(31)|ovary(2)|prostate(1)|skin(2)|stomach(4)|upper_aerodigestive_tract(1)	66		Hepatocellular(102;0.194)				AGCCTGACAGAAAAATCATTT	0.403																																					p.E1236fs		Atlas-INDEL	.											.	PIK3C2G	315	.	0			c.3706delG						.						69.0	64.0	66.0					12																	18716360		1860	4113	5973	SO:0001589	frameshift_variant	5288	exon27			.	AJ000008	CCDS44839.1, CCDS73452.1	12p12	2012-07-13	2012-07-13		ENSG00000139144	ENSG00000139144	2.7.1.154		8973	protein-coding gene	gene with protein product		609001	"""phosphoinositide-3-kinase, class 2, gamma polypeptide"""			9878262	Standard	XM_005253393		Approved		uc001rdt.3	O75747	OTTHUMG00000168841	ENST00000266497.5:c.3707delA	chr12.hg19:g.18716360delA	ENSP00000266497:p.Glu1236fs	162.0	0.0		131.0	10.0	NM_004570	A1L3U0	Frame_Shift_Del	DEL	ENST00000266497.5	hg19	CCDS44839.1																																																																																			.	.		0.403	PIK3C2G-002	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401316.1	NM_004570	
EDC4	23644	hgsc.bcm.edu	37	16	67917535	67917535	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:67917535delT	ENST00000358933.5	+	28	4153	c.3914delT	c.(3913-3915)gttfs	p.V1305fs	NRN1L_ENST00000576147.1_5'Flank|NRN1L_ENST00000339176.3_5'Flank|CTC-479C5.10_ENST00000572067.1_lincRNA	NM_014329.4	NP_055144.3	Q6P2E9	EDC4_HUMAN	enhancer of mRNA decapping 4	1305					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(3)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(4)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	41		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0042)|Epithelial(162;0.0185)|all cancers(182;0.121)		CCAGCCCAGGTTTTTGGGCAG	0.562											OREG0023890	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V1305fs		Atlas-INDEL	.											.	EDC4	101	.	0			c.3913delG						.						150.0	157.0	154.0					16																	67917535		2198	4300	6498	SO:0001589	frameshift_variant	23644	exon28			.	U17474	CCDS10849.1	16q22.1	2008-02-05			ENSG00000038358	ENSG00000038358			17157	protein-coding gene	gene with protein product		606030				9067524	Standard	NM_014329		Approved	RCD-8, Ge-1, HEDLS	uc002eur.3	Q6P2E9	OTTHUMG00000137543	ENST00000358933.5:c.3914delT	chr16.hg19:g.67917535delT	ENSP00000351811:p.Val1305fs	172.0	0.0	1103	147.0	11.0	NM_014329	A6NGM1|A8K4T4|Q13025|Q13826|Q6ZR12|Q7Z6H7	Frame_Shift_Del	DEL	ENST00000358933.5	hg19	CCDS10849.1																																																																																			.	.		0.562	EDC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268874.2	NM_014329	
LGALS3BP	3959	hgsc.bcm.edu	37	17	76968422	76968422	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:76968422delC	ENST00000262776.3	-	6	1302	c.994delG	c.(994-996)gagfs	p.E332fs	LGALS3BP_ENST00000591778.1_3'UTR	NM_005567.3	NP_005558.1	Q08380	LG3BP_HUMAN	lectin, galactoside-binding, soluble, 3 binding protein	332	BACK.				cell adhesion (GO:0007155)|cellular defense response (GO:0006968)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	scavenger receptor activity (GO:0005044)			NS(1)|breast(1)|central_nervous_system(5)|endometrium(3)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	17			BRCA - Breast invasive adenocarcinoma(99;0.0677)|OV - Ovarian serous cystadenocarcinoma(97;0.139)			GAGGCACGCTCCCCCCAGCTC	0.642																																					p.E332fs	GBM(89;1105 1755 18102 21513)	Atlas-INDEL	.											.	LGALS3BP	47	.	0			c.995delA						.						46.0	48.0	47.0					17																	76968422		2203	4300	6503	SO:0001589	frameshift_variant	3959	exon6			.	L13210	CCDS11759.1	17q25	2014-07-09				ENSG00000108679		"""BTB/POZ domain containing"", ""Endogenous ligands"""	6564	protein-coding gene	gene with protein product	"""L3 antigen"", ""Mac-2-binding protein"", ""serum protein 90K"", ""transport and golgi organization 10 homolog B (Drosophila)"""	600626				7698018, 8034587, 8390986	Standard	NM_005567		Approved	MAC-2-BP, 90K, BTBD17B, TANGO10B, M2BP, gp90, CyCAP	uc002jwh.3	Q08380		ENST00000262776.3:c.994delG	chr17.hg19:g.76968422delC	ENSP00000262776:p.Glu332fs	101.0	0.0		143.0	11.0	NM_005567	Q7M4S0|Q9UCH8|Q9UCH9|Q9UCI0	Frame_Shift_Del	DEL	ENST00000262776.3	hg19	CCDS11759.1																																																																																			.	.		0.642	LGALS3BP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437785.3	NM_005567	
CERKL	375298	hgsc.bcm.edu	37	2	182430832	182430832	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:182430832delC	ENST00000339098.5	-	4	629	c.630delG	c.(628-630)gggfs	p.G210fs	CERKL_ENST00000479558.1_5'UTR|CERKL_ENST00000374969.2_Intron|CERKL_ENST00000374970.2_Intron|CERKL_ENST00000410087.3_Frame_Shift_Del_p.G210fs|CERKL_ENST00000409440.3_Frame_Shift_Del_p.G166fs			Q49MI3	CERKL_HUMAN	ceramide kinase-like	210	DAGKc. {ECO:0000255|PROSITE- ProRule:PRU00783}.			G -> E (in Ref. 2; CAG26977). {ECO:0000305}.	negative regulation of apoptotic process (GO:0043066)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951)			NS(1)|breast(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(13)|ovary(3)|skin(3)	32			OV - Ovarian serous cystadenocarcinoma(117;0.088)			ACAGAGCGTGCCCTTCATATT	0.308																																					p.H211fs		Atlas-INDEL	.											.	CERKL	138	.	0			c.631delC						.						82.0	77.0	79.0					2																	182430832		1830	4098	5928	SO:0001589	frameshift_variant	375298	exon4			.	BC020465	CCDS33340.1, CCDS33341.1, CCDS42789.1, CCDS46466.1, CCDS54425.1	2q31.3	2005-01-04			ENSG00000188452	ENSG00000188452			21699	protein-coding gene	gene with protein product			"""retinitis pigmentosa 26 (autosomal recessive)"""	RP26		14681825	Standard	NR_027689		Approved		uc002uny.3	Q49MI3	OTTHUMG00000154315	ENST00000339098.5:c.630delG	chr2.hg19:g.182430832delC	ENSP00000341159:p.Gly210fs	318.0	0.0		265.0	17.0	NM_001030311	B2RPL2|B4DEY1|Q49MH9|Q49MI0|Q49MI1|Q49MI2|Q5DVJ2|Q5DVJ4|Q5DVJ5|Q6UZF6|Q6ZP59	Frame_Shift_Del	DEL	ENST00000339098.5	hg19	CCDS42789.1																																																																																			.	.		0.308	CERKL-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334811.1		
HNRNPH1	3187	hgsc.bcm.edu	37	5	179044644	179044644	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:179044644delA	ENST00000356731.5	-	8	2463	c.928delT	c.(928-930)tcafs	p.S310fs	HNRNPH1_ENST00000511300.2_Frame_Shift_Del_p.S40fs|HNRNPH1_ENST00000393432.4_Frame_Shift_Del_p.S310fs|HNRNPH1_ENST00000510411.1_Frame_Shift_Del_p.S310fs|HNRNPH1_ENST00000329433.6_Frame_Shift_Del_p.S310fs|HNRNPH1_ENST00000442819.2_Frame_Shift_Del_p.S310fs|HNRNPH1_ENST00000524180.1_5'Flank			P31943	HNRH1_HUMAN	heterogeneous nuclear ribonucleoprotein H1 (H)	310	2 X 16 AA Gly-rich approximate repeats.|RRM 3. {ECO:0000255|PROSITE- ProRule:PRU00176}.				gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|regulation of RNA splicing (GO:0043484)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(4)|skin(1)	14						TTGAGCGGTGAAAAAAACTAC	0.383																																					p.S310fs		Atlas-INDEL	.											.	HNRNPH1	62	.	0			c.929delC						.						80.0	79.0	80.0					5																	179044644		2203	4300	6503	SO:0001589	frameshift_variant	3187	exon9			.	BC001348	CCDS4446.1	5q35.3	2013-02-12		2008-04-18	ENSG00000169045	ENSG00000169045		"""RNA binding motif (RRM) containing"""	5041	protein-coding gene	gene with protein product		601035		HNRPH1		7499401	Standard	NM_005520		Approved	hnRNPH	uc003mkf.5	P31943	OTTHUMG00000130908	ENST00000356731.5:c.928delT	chr5.hg19:g.179044644delA	ENSP00000349168:p.Ser310fs	280.0	0.0		204.0	15.0	NM_001257293	B3KW86|D3DWQ2|Q6IBM4	Frame_Shift_Del	DEL	ENST00000356731.5	hg19	CCDS4446.1																																																																																			.	.		0.383	HNRNPH1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253497.3	NM_005520	
SLC6A4	6532	hgsc.bcm.edu	37	17	28544272	28544272	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:28544272delC	ENST00000401766.2	-	5	1261	c.749delG	c.(748-750)ggcfs	p.G250fs	SLC6A4_ENST00000261707.3_Frame_Shift_Del_p.G250fs			P31645	SC6A4_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 4	250					brain morphogenesis (GO:0048854)|cellular response to cGMP (GO:0071321)|cellular response to retinoic acid (GO:0071300)|circadian rhythm (GO:0007623)|memory (GO:0007613)|monoamine transport (GO:0015844)|negative regulation of cerebellar granule cell precursor proliferation (GO:0021941)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of organ growth (GO:0046621)|negative regulation of synaptic transmission, dopaminergic (GO:0032227)|positive regulation of cell cycle (GO:0045787)|positive regulation of gene expression (GO:0010628)|protein homooligomerization (GO:0051260)|protein oligomerization (GO:0051259)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to hypoxia (GO:0001666)|response to nutrient (GO:0007584)|response to toxic substance (GO:0009636)|serotonin transport (GO:0006837)|serotonin uptake (GO:0051610)|social behavior (GO:0035176)|sperm ejaculation (GO:0042713)|thalamus development (GO:0021794)|vasoconstriction (GO:0042310)	cytosol (GO:0005829)|endomembrane system (GO:0012505)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|cocaine binding (GO:0019811)|monoamine transmembrane transporter activity (GO:0008504)|Rab GTPase binding (GO:0017137)|serotonin transmembrane transporter activity (GO:0015222)|serotonin:sodium symporter activity (GO:0005335)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(4)	25					Amitriptyline(DB00321)|Amoxapine(DB00543)|Amphetamine(DB00182)|Atomoxetine(DB00289)|Chlorphenamine(DB01114)|Citalopram(DB00215)|Clomipramine(DB01242)|Cocaine(DB00907)|Desipramine(DB01151)|Desvenlafaxine(DB06700)|Dexfenfluramine(DB01191)|Dexmethylphenidate(DB06701)|Dextromethorphan(DB00514)|Dopamine(DB00988)|Doxepin(DB01142)|Duloxetine(DB00476)|Ephedra(DB01363)|Escitalopram(DB01175)|Fluoxetine(DB00472)|Fluvoxamine(DB00176)|Imipramine(DB00458)|Levomilnacipran(DB08918)|Loxapine(DB00408)|Mazindol(DB00579)|Methamphetamine(DB01577)|Methylphenidate(DB00422)|Mianserin(DB06148)|Milnacipran(DB04896)|Minaprine(DB00805)|Mirtazapine(DB00370)|Nefazodone(DB01149)|Nortriptyline(DB00540)|Paroxetine(DB00715)|Pethidine(DB00454)|Phentermine(DB00191)|Protriptyline(DB00344)|Pseudoephedrine(DB00852)|Sertraline(DB01104)|Sibutramine(DB01105)|Tapentadol(DB06204)|Tramadol(DB00193)|Trazodone(DB00656)|Trimipramine(DB00726)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vilazodone(DB06684)	CCAGCTGATGCCCCCCAGGTC	0.582																																					p.G250fs		Atlas-INDEL	.											SLC6A4,NS,carcinoma,0,1	SLC6A4	60	.	0			c.750delC						.						79.0	80.0	79.0					17																	28544272		2203	4300	6503	SO:0001589	frameshift_variant	6532	exon6			.	L05568	CCDS11256.1	17q11.2	2014-01-30	2013-07-19		ENSG00000108576	ENSG00000108576		"""Solute carriers"""	11050	protein-coding gene	gene with protein product	"""serotonin transporter 1"""	182138	"""solute carrier family 6 (neurotransmitter transporter, serotonin), member 4"", ""5-hydroxytryptamine (serotonin) transporter"", ""obsessive-compulsive disorder 1"""	HTT, OCD1		7681602, 19806148	Standard	NM_001045		Approved	5-HTT, SERT1	uc002hey.5	P31645	OTTHUMG00000132751	ENST00000401766.2:c.749delG	chr17.hg19:g.28544272delC	ENSP00000385822:p.Gly250fs	212.0	0.0		169.0	12.0	NM_001045	Q5EE02	Frame_Shift_Del	DEL	ENST00000401766.2	hg19	CCDS11256.1																																																																																			.	.		0.582	SLC6A4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256115.3	NM_001045	
ISM2	145501	hgsc.bcm.edu	37	14	77942048	77942048	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr14:77942048delC	ENST00000342219.4	-	7	1662	c.1606delG	c.(1606-1608)gacfs	p.D536fs	ISM2_ENST00000412904.1_Frame_Shift_Del_p.D455fs|ISM2_ENST00000493585.1_3'UTR|ISM2_ENST00000393684.3_Frame_Shift_Del_p.D448fs|ISM2_ENST00000429906.1_Frame_Shift_Del_p.D455fs	NM_199296.2	NP_954993.1	Q6H9L7	ISM2_HUMAN	isthmin 2	536	AMOP. {ECO:0000255|PROSITE- ProRule:PRU00347}.					extracellular region (GO:0005576)				endometrium(3)|large_intestine(4)|lung(11)|prostate(1)|skin(1)|urinary_tract(1)	21						CGGCTCCAGTCCCCCTTGCAC	0.637																																					p.D536fs		Atlas-INDEL	.											.	ISM2	68	.	0			c.1607delA						.						89.0	84.0	86.0					14																	77942048		2203	4300	6503	SO:0001589	frameshift_variant	145501	exon7			.	AK056709	CCDS9864.1, CCDS45143.1	14q24.3	2013-05-15	2013-05-15	2008-12-23	ENSG00000100593	ENSG00000100593			23176	protein-coding gene	gene with protein product	"""thrombospondin and AMOP containing isthmin-like 1"""	612684	"""thrombospondin, type I domain-containing 3"", ""thrombospondin, type I, domain containing 3"", ""isthmin 2 homolog (zebrafish)"""	THSD3		15194193	Standard	NM_199296		Approved	FLJ32147, TAIL1	uc001xtz.3	Q6H9L7	OTTHUMG00000158563	ENST00000342219.4:c.1606delG	chr14.hg19:g.77942048delC	ENSP00000341490:p.Asp536fs	230.0	0.0		166.0	10.0	NM_199296	A8K6D5|O95432|Q495U5|Q68CN3|Q86TQ7|Q86TW3|Q86TW4|Q8N501|Q8NBL0	Frame_Shift_Del	DEL	ENST00000342219.4	hg19	CCDS9864.1																																																																																			.	.		0.637	ISM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000351309.1	NM_182509	
ANO7	50636	hgsc.bcm.edu	37	2	242129532	242129532	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:242129532delC	ENST00000274979.8	+	2	319	c.216delC	c.(214-216)agcfs	p.S72fs	ANO7_ENST00000402430.3_Frame_Shift_Del_p.S72fs|ANO7_ENST00000402530.3_Frame_Shift_Del_p.S72fs	NM_001001891.3	NP_001001891.2	Q6IWH7	ANO7_HUMAN	anoctamin 7	72					calcium activated galactosylceramide scrambling (GO:0061591)|calcium activated phosphatidylcholine scrambling (GO:0061590)|calcium activated phosphatidylserine scrambling (GO:0061589)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)|phospholipid scramblase activity (GO:0017128)			NS(1)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(14)|pancreas(2)|prostate(1)|skin(3)|urinary_tract(2)	32						TCGATGTGAGCCCCCCTGAGG	0.662																																					p.S72fs		Atlas-INDEL	.											.	ANO7	136	.	0			c.215delG						.						36.0	34.0	35.0					2																	242129532		2199	4287	6486	SO:0001589	frameshift_variant	50636	exon2			.	AY617079	CCDS33423.1, CCDS46563.1	2q37.3	2014-04-09	2008-08-28	2008-08-28	ENSG00000146205	ENSG00000146205		"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	31677	protein-coding gene	gene with protein product		605096	"""transmembrane protein 16G"""	PCANAP5, TMEM16G		14981236, 15375614, 24692353	Standard	NM_001001891		Approved	NGEP, PCANAP5L, IPCA-5	uc002wax.2	Q6IWH7	OTTHUMG00000151702	ENST00000274979.8:c.216delC	chr2.hg19:g.242129532delC	ENSP00000274979:p.Ser72fs	319.0	0.0		231.0	14.0	NM_001001666	Q6IWH6	Frame_Shift_Del	DEL	ENST00000274979.8	hg19	CCDS33423.1																																																																																			.	.		0.662	ANO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323509.1	NM_001001891	
PRKG2	5593	hgsc.bcm.edu	37	4	82027025	82027025	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:82027025delT	ENST00000395578.1	-	16	2121	c.2005delA	c.(2005-2007)atgfs	p.M669fs	PRKG2_ENST00000264399.1_Frame_Shift_Del_p.M669fs|PRKG2_ENST00000418486.2_Frame_Shift_Del_p.M640fs|PRKG2_ENST00000509169.1_5'UTR|PRKG2_ENST00000545647.1_Frame_Shift_Del_p.M249fs			Q13237	KGP2_HUMAN	protein kinase, cGMP-dependent, type II	669	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				blood coagulation (GO:0007596)|circadian regulation of gene expression (GO:0032922)|nitric oxide metabolic process (GO:0046209)|protein phosphorylation (GO:0006468)|regulation of nitric-oxide synthase activity (GO:0050999)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cGMP binding (GO:0030553)|cGMP-dependent protein kinase activity (GO:0004692)|protein kinase activity (GO:0004672)			NS(1)|breast(4)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(7)|lung(14)|ovary(1)|skin(2)	37						GGAAAATCCATTTTTTCAATT	0.413																																					p.M669fs		Atlas-INDEL	.											.	PRKG2	195	.	0			c.2006delT						.						129.0	123.0	125.0					4																	82027025		2203	4300	6503	SO:0001589	frameshift_variant	5593	exon15			.	X94612	CCDS3589.1, CCDS75150.1	4q13.1-q21.1	2009-07-10			ENSG00000138669	ENSG00000138669	2.7.11.1		9416	protein-coding gene	gene with protein product		601591				7498513	Standard	XM_005263126		Approved	cGKII, PRKGR2	uc003hmh.2	Q13237	OTTHUMG00000130296	ENST00000395578.1:c.2005delA	chr4.hg19:g.82027025delT	ENSP00000378945:p.Met669fs	227.0	0.0		164.0	10.0	NM_006259	B4DMX3|E7EPE6|O00125|O60916	Frame_Shift_Del	DEL	ENST00000395578.1	hg19	CCDS3589.1																																																																																			.	.		0.413	PRKG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252639.1	NM_006259	
ERN2	10595	hgsc.bcm.edu	37	16	23717673	23717673	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:23717673delG	ENST00000457008.2	-	7	605	c.567delC	c.(565-567)cccfs	p.P189fs	ERN2_ENST00000256797.4_Frame_Shift_Del_p.P237fs					endoplasmic reticulum to nucleus signaling 2											large_intestine(2)|lung(2)|ovary(2)	6				GBM - Glioblastoma multiforme(48;0.0156)		AGCCATCCATGGGGGGCGCTG	0.587																																					p.M238fs		Atlas-INDEL	.											.	ERN2	131	.	0			c.712delA						.						39.0	34.0	36.0					16																	23717673		2196	4298	6494	SO:0001589	frameshift_variant	10595	exon7			.	AA527544	CCDS32407.1	16p12.2	2008-02-05	2007-08-14			ENSG00000134398			16942	protein-coding gene	gene with protein product		604034	"""ER to nucleus signalling 2"""			9755171, 11175748	Standard	NM_033266		Approved	IRE1b	uc002dma.4	Q76MJ5		ENST00000457008.2:c.567delC	chr16.hg19:g.23717673delG	ENSP00000413812:p.Pro189fs	210.0	0.0		166.0	12.0	NM_033266		Frame_Shift_Del	DEL	ENST00000457008.2	hg19																																																																																				.	.		0.587	ERN2-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000434886.1		
GCNT2	2651	hgsc.bcm.edu	37	6	10586407	10586407	+	Intron	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:10586407delA	ENST00000379597.3	+	2	1481				GCNT2_ENST00000495262.1_Intron|GCNT2_ENST00000316170.3_Intron|GCNT2_ENST00000397423.2_Intron|GCNT2_ENST00000265012.4_Frame_Shift_Del_p.E62fs|GCNT2_ENST00000410107.1_Intron			Q8N0V5	GNT2A_HUMAN	glucosaminyl (N-acetyl) transferase 2, I-branching enzyme (I blood group)						maintenance of lens transparency (GO:0036438)|negative regulation of cell-substrate adhesion (GO:0010812)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of protein kinase B signaling (GO:0051897)|posttranscriptional regulation of gene expression (GO:0010608)|protein glycosylation (GO:0006486)|transforming growth factor beta receptor signaling pathway (GO:0007179)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	N-acetyllactosaminide beta-1,6-N-acetylglucosaminyltransferase activity (GO:0008109)			endometrium(2)|kidney(1)|large_intestine(5)|lung(2)|ovary(2)	12	Ovarian(93;0.107)|Breast(50;0.148)	all_hematologic(90;0.107)		KIRC - Kidney renal clear cell carcinoma(1;0.099)|Kidney(1;0.119)		TTTTTGTGGGAAAATATATTA	0.438																																					p.E62fs		Atlas-INDEL	.											.	GCNT2	123	.	0			c.184delG						.						163.0	161.0	162.0					6																	10586407		2203	4300	6503	SO:0001627	intron_variant	2651	exon1			.	L41605	CCDS4512.1, CCDS4513.1, CCDS34338.1	6p24.2	2014-07-18	2006-02-23		ENSG00000111846	ENSG00000111846	2.4.1.150	"""Blood group antigens"", ""Glucosaminyl (N-acetyl) transferase and xylosyltransferase family"""	4204	protein-coding gene	gene with protein product	"""Ii blood group"", ""unassigned linkage group 3"""	600429	"""glucosaminyl (N-acetyl) transferase 5"", ""glucosaminyl (N-acetyl) transferase 2, I-branching enzyme"", ""glucosaminyl (N-acetyl) transferase 2, I-branching enzyme (Ii blood group)"", ""cataract, congenital"""	NACGT1, II, GCNT5, CCAT		8449405, 9915862	Standard	NM_145649		Approved	IGNT, NAGCT1, bA421M1.1, bA360O19.2, ULG3	uc003mze.3	Q06430	OTTHUMG00000014244	ENST00000379597.3:c.926-35177A>-	chr6.hg19:g.10586407delA		247.0	0.0		158.0	10.0	NM_145655		Frame_Shift_Del	DEL	ENST00000379597.3	hg19	CCDS34338.1																																																																																			.	.		0.438	GCNT2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327912.3	NM_145649	
ZNF324	25799	hgsc.bcm.edu	37	19	58983203	58983203	+	Frame_Shift_Del	DEL	G	G	-	rs536947978	byFrequency	TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:58983203delG	ENST00000536459.2	+	4	2053	c.1344delG	c.(1342-1344)acgfs	p.T448fs	ZNF324_ENST00000196482.3_Frame_Shift_Del_p.T448fs|ZNF324_ENST00000535298.1_Frame_Shift_Del_p.T225fs|ZNF446_ENST00000596341.1_5'Flank			O75467	Z324A_HUMAN	zinc finger protein 324	448					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)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|liver(1)|lung(2)|prostate(2)|urinary_tract(2)	16		all_cancers(17;1.81e-17)|all_epithelial(17;1.21e-12)|Lung NSC(17;2.8e-05)|all_lung(17;0.000139)|Colorectal(82;0.000147)|Renal(17;0.00528)|all_neural(62;0.0133)|Ovarian(87;0.156)|Medulloblastoma(540;0.232)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0164)|Lung(386;0.179)		TCCTGCACACGGGCGAGCGGC	0.692																																					p.T448fs		Atlas-INDEL	.											.	ZNF324	46	.	0			c.1343delC						.						44.0	47.0	46.0					19																	58983203		2203	4298	6501	SO:0001589	frameshift_variant	25799	exon4			.	AF060503	CCDS12981.1	19q13.43	2013-01-08				ENSG00000083812		"""Zinc fingers, C2H2-type"", ""-"""	14096	protein-coding gene	gene with protein product							Standard	NM_014347		Approved	ZF5128, ZNF324A	uc002qsw.2	O75467		ENST00000536459.2:c.1344delG	chr19.hg19:g.58983203delG	ENSP00000444812:p.Thr448fs	219.0	0.0		153.0	11.0	NM_014347	B3KRX1	Frame_Shift_Del	DEL	ENST00000536459.2	hg19	CCDS12981.1																																																																																			.	.		0.692	ZNF324-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467044.1	NM_014347	
UBR1	197131	hgsc.bcm.edu	37	15	43363019	43363019	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:43363019delT	ENST00000290650.4	-	5	711	c.633delA	c.(631-633)aaafs	p.K211fs	UBR1_ENST00000382177.2_Frame_Shift_Del_p.K211fs	NM_174916.2	NP_777576.1	Q8IWV7	UBR1_HUMAN	ubiquitin protein ligase E3 component n-recognin 1	211					cellular response to leucine (GO:0071233)|negative regulation of TOR signaling (GO:0032007)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|proteasome complex (GO:0000502)|ubiquitin ligase complex (GO:0000151)	leucine binding (GO:0070728)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(2)|endometrium(2)|kidney(7)|large_intestine(12)|lung(25)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	58		all_cancers(109;4.32e-15)|all_epithelial(112;4.05e-13)|Lung NSC(122;1.75e-08)|all_lung(180;2e-07)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;4.08e-07)|COAD - Colon adenocarcinoma(120;0.185)|Colorectal(105;0.214)		GAGGCAGTTCTTTTTCCTCTT	0.378																																					p.E212fs		Atlas-INDEL	.											UBR1,NS,carcinoma,0,1	UBR1	124	.	0			c.634delG						.						180.0	171.0	174.0					15																	43363019		2203	4299	6502	SO:0001589	frameshift_variant	197131	exon5			.		CCDS10091.1	15q13	2008-06-23			ENSG00000159459	ENSG00000159459		"""Ubiquitin protein ligase E3 component n-recognins"""	16808	protein-coding gene	gene with protein product		605981				9653112	Standard	NM_174916		Approved		uc001zqq.3	Q8IWV7	OTTHUMG00000130702	ENST00000290650.4:c.633delA	chr15.hg19:g.43363019delT	ENSP00000290650:p.Lys211fs	121.0	0.0		130.0	10.0	NM_174916	O60708|O75492|Q14D45|Q68DN9|Q8IWY6|Q96JY4	Frame_Shift_Del	DEL	ENST00000290650.4	hg19	CCDS10091.1																																																																																			.	.		0.378	UBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253202.1	NM_174916	
RNASE12	493901	hgsc.bcm.edu	37	14	21058692	21058692	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr14:21058692delT	ENST00000556526.1	-	1	290	c.191delA	c.(190-192)aagfs	p.K64fs	RNASE11_ENST00000553849.1_5'Flank|RNASE11_ENST00000398008.2_5'Flank|RP11-14J7.6_ENST00000556487.1_RNA|RP11-14J7.6_ENST00000554529.1_RNA|RNASE11_ENST00000398009.2_5'Flank|RP11-14J7.6_ENST00000553604.1_RNA|RNASE11_ENST00000432835.2_5'Flank|RNASE11_ENST00000555283.1_Intron|RP11-14J7.6_ENST00000554993.1_RNA|RP11-14J7.6_ENST00000554006.1_RNA|RNASE11_ENST00000555841.1_5'Flank|RNASE11_ENST00000610205.1_5'Flank	NM_001024822.2	NP_001019993.1	Q5GAN4	RNS12_HUMAN	ribonuclease, RNase A family, 12 (non-active)	64						extracellular region (GO:0005576)	nucleic acid binding (GO:0003676)			kidney(1)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	8	all_cancers(95;0.00238)		Epithelial(56;1.85e-06)|all cancers(55;1.46e-05)	GBM - Glioblastoma multiforme(265;0.013)		GACATGCTCCTTTTTACAAGT	0.448																																					p.K64fs		Atlas-INDEL	.											.	RNASE12	19	.	0			c.192delG						.						146.0	123.0	131.0					14																	21058692		2203	4300	6503	SO:0001589	frameshift_variant	493901	exon1			.		CCDS32037.1	14q11.1	2012-10-05			ENSG00000258436	ENSG00000258436		"""Ribonucleases, RNase A"""	24211	protein-coding gene	gene with protein product							Standard	NM_001024822		Approved		uc001vxt.3	Q5GAN4	OTTHUMG00000170991	ENST00000556526.1:c.191delA	chr14.hg19:g.21058692delT	ENSP00000450580:p.Lys64fs	192.0	0.0		165.0	11.0	NM_001024822		Frame_Shift_Del	DEL	ENST00000556526.1	hg19	CCDS32037.1																																																																																			.	.		0.448	RNASE12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411107.1		
C9orf84	158401	hgsc.bcm.edu	37	9	114453859	114453859	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:114453859delA	ENST00000318737.4	-	25	4334	c.4206delT	c.(4204-4206)tttfs	p.F1402fs	C9orf84_ENST00000394777.4_Frame_Shift_Del_p.F1328fs|C9orf84_ENST00000374287.3_Frame_Shift_Del_p.F1402fs|C9orf84_ENST00000394779.3_Frame_Shift_Del_p.F1363fs	NM_173521.3	NP_775792.3	Q5VXU9	CI084_HUMAN	chromosome 9 open reading frame 84	1402										breast(1)|cervix(1)|endometrium(3)|kidney(7)|large_intestine(10)|liver(1)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	35						CTCCTGAGTTAAATGAAGATT	0.303																																					p.N1403fs		Atlas-INDEL	.											.	C9orf84	207	.	0			c.4207delA						.						88.0	89.0	89.0					9																	114453859		2203	4300	6503	SO:0001589	frameshift_variant	158401	exon25			.	AL833535	CCDS6781.3, CCDS43863.1	9q32	2012-03-16			ENSG00000165181	ENSG00000165181			26535	protein-coding gene	gene with protein product							Standard	XM_005251738		Approved	FLJ32779	uc004bfr.3	Q5VXU9	OTTHUMG00000020495	ENST00000318737.4:c.4206delT	chr9.hg19:g.114453859delA	ENSP00000322108:p.Phe1402fs	228.0	0.0		172.0	11.0	NM_173521	A2A2V3|Q2M1H8|Q96M73	Frame_Shift_Del	DEL	ENST00000318737.4	hg19	CCDS6781.3																																																																																			.	.		0.303	C9orf84-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053656.2	NM_173521	
TNRC6A	27327	hgsc.bcm.edu	37	16	24802560	24802560	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:24802560delG	ENST00000395799.3	+	6	2726	c.2597delG	c.(2596-2598)tggfs	p.W866fs	TNRC6A_ENST00000315183.7_Frame_Shift_Del_p.W866fs	NM_014494.2	NP_055309.2	Q8NDV7	TNR6A_HUMAN	trinucleotide repeat containing 6A	866	Interaction with argonaute family proteins.|Sufficient for interaction with AGO1 and AGO4.				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)	p.W866L(1)		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)		AATAACCATTGGGGTGAGGCC	0.463																																					p.W866fs		Atlas-INDEL	.											.	TNRC6A	171	.	1	Substitution - Missense(1)	lung(1)	c.2596delT						.						83.0	80.0	81.0					16																	24802560		2197	4300	6497	SO:0001589	frameshift_variant	27327	exon6			.	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.2597delG	chr16.hg19:g.24802560delG	ENSP00000379144:p.Trp866fs	306.0	0.0		227.0	15.0	NM_014494	C9JAR8|O15408|Q658L5|Q6NVB5|Q8NEZ0|Q8TBT8|Q8TCR0|Q9NV59|Q9P268	Frame_Shift_Del	DEL	ENST00000395799.3	hg19	CCDS10624.2																																																																																			.	.		0.463	TNRC6A-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214081.1	NM_020847	
DISC1	27185	hgsc.bcm.edu	37	1	232099236	232099236	+	Intron	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:232099236delC	ENST00000439617.2	+	10	2095				DISC1_ENST00000535983.1_Intron|DISC1_ENST00000427560.1_Intron|DISC1_ENST00000537876.1_Intron|DISC1_ENST00000366637.3_Intron	NM_001164537.1|NM_001164540.1|NM_018662.2	NP_001158009.1|NP_001158012.1|NP_061132.2	Q9NRI5	DISC1_HUMAN	disrupted in schizophrenia 1						canonical Wnt signaling pathway (GO:0060070)|cell proliferation in forebrain (GO:0021846)|cellular protein localization (GO:0034613)|cerebral cortex radially oriented cell migration (GO:0021799)|microtubule cytoskeleton organization (GO:0000226)|mitochondrial calcium ion homeostasis (GO:0051560)|neuron migration (GO:0001764)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of neuron projection development (GO:0010975)|regulation of synapse maturation (GO:0090128)|TOR signaling (GO:0031929)	cell junction (GO:0030054)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|postsynaptic membrane (GO:0045211)				breast(1)|cervix(1)|kidney(1)|large_intestine(1)|liver(2)|lung(6)|skin(2)|upper_aerodigestive_tract(1)	15		all_cancers(173;0.0208)|Prostate(94;0.0975)				TGCTCCCCCACCCCTCTGCAT	0.542																																					.		Atlas-INDEL	.											.	.	.	.	0			.						.																																			SO:0001627	intron_variant	0	.			.	AF222980	CCDS31055.1, CCDS31056.1, CCDS53482.1, CCDS53483.1, CCDS53484.1, CCDS59205.1, CCDS59206.1, CCDS59207.1	1q42.1	2008-02-05			ENSG00000162946	ENSG00000162946			2888	protein-coding gene	gene with protein product		605210				10814723	Standard	NM_001164550		Approved		uc010pxh.2	Q9NRI5	OTTHUMG00000037835	ENST00000439617.2:c.2042+4602C>-	chr1.hg19:g.232099236delC		137.0	0.0		199.0	14.0	.	A6NLH2|C4P091|C4P095|C4P0A1|C4P0A3|C4P0B3|C4P0B6|C4P0C1|C9J6D0|O75045|Q5VT44|Q5VT45|Q8IXJ0|Q8IXJ1|Q9BX19|Q9NRI3|Q9NRI4	RNA	DEL	ENST00000439617.2	hg19																																																																																				.	.		0.542	DISC1-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000092351.2	NM_018662	
ZFYVE20	64145	hgsc.bcm.edu	37	3	15132024	15132024	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:15132024delT	ENST00000253699.3	-	5	784	c.171delA	c.(169-171)aaafs	p.K57fs	ZFYVE20_ENST00000476527.2_Frame_Shift_Del_p.K57fs|ZFYVE20_ENST00000449964.2_5'UTR|ZFYVE20_ENST00000435849.3_Frame_Shift_Del_p.K57fs	NM_022340.2	NP_071735.2	Q9H1K0	RBNS5_HUMAN	zinc finger, FYVE domain containing 20	57					blood coagulation (GO:0007596)|endosomal transport (GO:0016197)|protein transport (GO:0015031)	endosome (GO:0005768)|endosome membrane (GO:0010008)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)			NS(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(10)|skin(3)|stomach(1)|urinary_tract(2)	26						TGTCCTTTGCTTTTTTAGCCT	0.408																																					p.A58fs		Atlas-INDEL	.											.	ZFYVE20	61	.	0			c.172delG						.						181.0	155.0	164.0					3																	15132024		2203	4300	6503	SO:0001589	frameshift_variant	64145	exon5			.	AY009133	CCDS2623.1	3p25.1	2014-01-15			ENSG00000131381	ENSG00000131381		"""Zinc fingers, FYVE domain containing"""	20759	protein-coding gene	gene with protein product		609511				11062261	Standard	XR_427283		Approved	Rabenosyn-5	uc003bzm.1	Q9H1K0	OTTHUMG00000129860	ENST00000253699.3:c.171delA	chr3.hg19:g.15132024delT	ENSP00000253699:p.Lys57fs	219.0	0.0		184.0	13.0	NM_022340	B4DWY8|C9J4P5|Q3KP30|Q59EY8|Q8NAQ1	Frame_Shift_Del	DEL	ENST00000253699.3	hg19	CCDS2623.1																																																																																			.	.		0.408	ZFYVE20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252102.2	NM_022340	
BMP2K	55589	hgsc.bcm.edu	37	4	79768365	79768365	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:79768365delC	ENST00000335016.5	+	6	858	c.692delC	c.(691-693)gccfs	p.A231fs	BMP2K_ENST00000502871.1_Frame_Shift_Del_p.A231fs	NM_198892.1	NP_942595.1	Q9NSY1	BMP2K_HUMAN	BMP2 inducible kinase	231	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				regulation of bone mineralization (GO:0030500)	nucleus (GO:0005634)	ATP binding (GO:0005524)|phosphatase regulator activity (GO:0019208)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|endometrium(4)|large_intestine(2)|lung(3)|prostate(1)|urinary_tract(1)	13						TCATACAGAGCCCCTGAAATG	0.378																																					p.A231fs		Atlas-INDEL	.											.	BMP2K	169	.	0			c.691delG						.						51.0	51.0	51.0					4																	79768365		2202	4300	6502	SO:0001589	frameshift_variant	55589	exon6			.	AB015331	CCDS34019.1, CCDS47083.1	4q21.21	2008-05-15			ENSG00000138756	ENSG00000138756			18041	protein-coding gene	gene with protein product							Standard	NM_017593		Approved	DKFZp434K0614, BIKe	uc003hlk.3	Q9NSY1	OTTHUMG00000160900	ENST00000335016.5:c.692delC	chr4.hg19:g.79768365delC	ENSP00000334836:p.Ala231fs	245.0	0.0		159.0	14.0	NM_017593	O94791|Q4W5H2|Q8IYF2|Q8N2G7|Q8NHG9|Q9NTG8	Frame_Shift_Del	DEL	ENST00000335016.5	hg19	CCDS47083.1																																																																																			.	.		0.378	BMP2K-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_017593	
FOXI1	2299	hgsc.bcm.edu	37	5	169533034	169533034	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:169533034delC	ENST00000306268.6	+	1	134	c.73delC	c.(73-75)cccfs	p.P26fs	FOXI1_ENST00000449804.2_Frame_Shift_Del_p.P26fs			Q12951	FOXI1_HUMAN	forkhead box I1	26	Pro-rich.				embryo development (GO:0009790)|inner ear morphogenesis (GO:0042472)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding, bending (GO:0008301)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(3)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(7)|lung(16)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	35	Renal(175;0.000159)|Lung NSC(126;0.0267)|all_lung(126;0.04)	Medulloblastoma(196;0.0109)|all_neural(177;0.0298)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CGGCCAGGAGCCCCCCGAGAT	0.697									Pendred syndrome																												p.E24fs		Atlas-INDEL	.											.	FOXI1	70	.	0			c.72delG						.						24.0	28.0	26.0					5																	169533034		2203	4298	6501	SO:0001589	frameshift_variant	2299	exon1	Familial Cancer Database	Goiter-Deafness syndrome	.	BC029778	CCDS4372.1, CCDS47337.1	5q34	2008-02-05			ENSG00000168269	ENSG00000168269		"""Forkhead boxes"""	3815	protein-coding gene	gene with protein product		601093		FKHL10		7957066, 8825632	Standard	NM_144769		Approved	FREAC6	uc003mai.4	Q12951	OTTHUMG00000130436	ENST00000306268.6:c.73delC	chr5.hg19:g.169533034delC	ENSP00000304286:p.Pro26fs	411.0	0.0		283.0	17.0	NM_012188	Q14518|Q66SR7|Q8N6L8	Frame_Shift_Del	DEL	ENST00000306268.6	hg19	CCDS4372.1																																																																																			.	.		0.697	FOXI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252827.2	NM_144769, NM_012188	
PRMT5	10419	hgsc.bcm.edu	37	14	23391406	23391406	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr14:23391406delA	ENST00000324366.8	-	16	1963	c.1740delT	c.(1738-1740)tttfs	p.F580fs	PRMT5_ENST00000553897.1_Frame_Shift_Del_p.F536fs|PRMT5-AS1_ENST00000599580.2_RNA|PRMT5-AS1_ENST00000590290.1_RNA|PRMT5_ENST00000538452.1_Frame_Shift_Del_p.F474fs|PRMT5-AS1_ENST00000457443.2_RNA|PRMT5_ENST00000397440.4_Frame_Shift_Del_p.F409fs|PRMT5-AS1_ENST00000595662.1_RNA|PRMT5_ENST00000216350.8_Frame_Shift_Del_p.F519fs|PRMT5_ENST00000397441.2_Frame_Shift_Del_p.F563fs|PRMT5-AS1_ENST00000587245.2_RNA|PRMT5-AS1_ENST00000609885.1_RNA|PRMT5-AS1_ENST00000424245.2_RNA	NM_006109.3	NP_006100.2	O14744	ANM5_HUMAN	protein arginine methyltransferase 5	580	Beta barrel. {ECO:0000269|PubMed:23071334}.|SAM-dependent MTase PRMT-type. {ECO:0000255|PROSITE-ProRule:PRU01015}.				cell proliferation (GO:0008283)|circadian regulation of gene expression (GO:0032922)|endothelial cell activation (GO:0042118)|gene expression (GO:0010467)|histone H4-R3 methylation (GO:0043985)|ncRNA metabolic process (GO:0034660)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|peptidyl-arginine methylation (GO:0018216)|peptidyl-arginine methylation, to symmetrical-dimethyl arginine (GO:0019918)|peptidyl-arginine N-methylation (GO:0035246)|regulation of mitosis (GO:0007088)|regulation of transcription, DNA-templated (GO:0006355)|RNA metabolic process (GO:0016070)|spliceosomal snRNP assembly (GO:0000387)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|methylosome (GO:0034709)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|core promoter sequence-specific DNA binding (GO:0001046)|histone-arginine N-methyltransferase activity (GO:0008469)|methyltransferase activity (GO:0008168)|protein-arginine omega-N symmetric methyltransferase activity (GO:0035243)|ribonucleoprotein complex binding (GO:0043021)|transcription corepressor activity (GO:0003714)			endometrium(4)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	25	all_cancers(95;2.76e-05)			GBM - Glioblastoma multiforme(265;0.0126)		AGAGGATGGGAAACCATGAGA	0.443																																					p.P581fs		Atlas-INDEL	.											.	PRMT5	101	.	0			c.1741delC						.						176.0	172.0	173.0					14																	23391406		2203	4300	6503	SO:0001589	frameshift_variant	10419	exon16			.	AF015913	CCDS9579.1, CCDS41922.1, CCDS61394.1, CCDS61395.1, CCDS61396.1	14q11.2	2014-06-12	2006-02-16	2006-02-16	ENSG00000100462	ENSG00000100462	2.1.1.125	"""Protein arginine methyltransferases"""	10894	protein-coding gene	gene with protein product		604045	"""skb1 (S. pombe) homolog"", ""SKB1 homolog (S. pombe)"""	HRMT1L5, SKB1		9843966	Standard	NM_001282955		Approved	SKB1Hs	uc001whm.1	O14744	OTTHUMG00000028709	ENST00000324366.8:c.1740delT	chr14.hg19:g.23391406delA	ENSP00000319169:p.Phe580fs	193.0	0.0		135.0	12.0	NM_006109	A8MTP3|A8MZ91|B4DX49|B4DY30|B5BU10|D3DS33|E2QRE7|Q6IBR1|Q9UKH1	Frame_Shift_Del	DEL	ENST00000324366.8	hg19	CCDS9579.1																																																																																			.	.		0.443	PRMT5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071674.3		
ENTPD6	955	hgsc.bcm.edu	37	20	25203522	25203522	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr20:25203522delA	ENST00000376652.4	+	12	1257	c.1094delA	c.(1093-1095)caafs	p.Q365fs	ENTPD6_ENST00000360031.2_Frame_Shift_Del_p.Q364fs|ENTPD6_ENST00000485936.1_3'UTR|ENTPD6_ENST00000433259.2_Frame_Shift_Del_p.Q331fs|ENTPD6_ENST00000354989.5_Frame_Shift_Del_p.Q348fs			O75354	ENTP6_HUMAN	ectonucleoside triphosphate diphosphohydrolase 6 (putative)	365					response to calcium ion (GO:0051592)|response to magnesium ion (GO:0032026)	cell surface (GO:0009986)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	guanosine-5'-triphosphate,3'-diphosphate diphosphatase activity (GO:0008894)|nucleoside-triphosphatase activity (GO:0017111)|uridine-diphosphatase activity (GO:0045134)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(16)|prostate(1)|skin(1)	27						GAGGTCCTTCAAAACAGAGTG	0.577																																					p.Q365fs		Atlas-INDEL	.											.	ENTPD6	57	.	0			c.1093delC						.						176.0	145.0	156.0					20																	25203522		2203	4300	6503	SO:0001589	frameshift_variant	955	exon12			.	AF039916	CCDS13170.1, CCDS46586.1	20p11.21	2010-06-24	2010-06-24		ENSG00000197586	ENSG00000197586			3368	protein-coding gene	gene with protein product		603160	"""interleukin 6 signal transducer-2"""	CD39L2, IL6ST2		9676430	Standard	NM_001247		Approved	NTPDase-6, dJ738P15.3	uc002wuj.2	O75354	OTTHUMG00000032116	ENST00000376652.4:c.1094delA	chr20.hg19:g.25203522delA	ENSP00000365840:p.Gln365fs	227.0	0.0		151.0	10.0	NM_001247	A6NCX6|D3DW49|Q5QPJ2|Q5QPJ5|Q7Z5B5|Q8N3H3|Q8TAS7|Q9UJD1	Frame_Shift_Del	DEL	ENST00000376652.4	hg19	CCDS13170.1																																																																																			.	.		0.577	ENTPD6-020	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078414.2		
DSP	1832	hgsc.bcm.edu	37	6	7585185	7585185	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:7585185delA	ENST00000379802.3	+	24	8031	c.7690delA	c.(7690-7692)aaafs	p.K2564fs	DSP_ENST00000418664.2_Frame_Shift_Del_p.K1965fs	NM_004415.2	NP_004406.2	P15924	DESP_HUMAN	desmoplakin	2564	Globular 2.				adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|desmosome organization (GO:0002934)|epidermis development (GO:0008544)|intermediate filament organization (GO:0045109)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|protein localization to adherens junction (GO:0071896)|regulation of heart rate by cardiac conduction (GO:0086091)|single organismal cell-cell adhesion (GO:0016337)|ventricular cardiac muscle cell action potential (GO:0086005)|ventricular compact myocardium morphogenesis (GO:0003223)|wound healing (GO:0042060)	basolateral plasma membrane (GO:0016323)|cornified envelope (GO:0001533)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)|protein kinase C binding (GO:0005080)|scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			biliary_tract(1)|breast(6)|central_nervous_system(7)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|liver(2)|lung(27)|ovary(4)|prostate(1)|skin(8)|stomach(3)|upper_aerodigestive_tract(7)|urinary_tract(5)	101	Ovarian(93;0.0584)	all_hematologic(90;0.236)		OV - Ovarian serous cystadenocarcinoma(45;0.000508)		GATCTCCTTGAAAAATGGTGT	0.478																																					p.L2563fs		Atlas-INDEL	.											.	DSP	306	.	0			c.7689delG						.						95.0	92.0	93.0					6																	7585185		2203	4300	6503	SO:0001589	frameshift_variant	1832	exon24			.	J05211	CCDS4501.1, CCDS47368.1	6p24.3	2014-09-17	2003-05-20		ENSG00000096696	ENSG00000096696			3052	protein-coding gene	gene with protein product		125647	"""desmoplakin (DPI, DPII)"""			1889810	Standard	NM_004415		Approved	KPPS2, PPKS2, DPI, DPII	uc003mxp.1	P15924	OTTHUMG00000014212	ENST00000379802.3:c.7690delA	chr6.hg19:g.7585185delA	ENSP00000369129:p.Lys2564fs	211.0	0.0		186.0	13.0	NM_004415	B2RTT2|D7RX09|O75993|Q14189|Q9UHN4	Frame_Shift_Del	DEL	ENST00000379802.3	hg19	CCDS4501.1																																																																																			.	.		0.478	DSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039786.2	NM_004415	
CNTN6	27255	hgsc.bcm.edu	37	3	1427450	1427450	+	Frame_Shift_Del	DEL	C	C	-	rs201612169		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:1427450delC	ENST00000446702.2	+	20	3300	c.2673delC	c.(2671-2673)agcfs	p.S891fs	CNTN6_ENST00000350110.2_Frame_Shift_Del_p.S891fs|CNTN6_ENST00000539053.1_Frame_Shift_Del_p.S819fs			Q9UQ52	CNTN6_HUMAN	contactin 6	891	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|central nervous system development (GO:0007417)|Notch signaling pathway (GO:0007219)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				breast(6)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(34)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	90		all_cancers(2;0.000164)|all_epithelial(2;0.107)		Epithelial(13;0.000233)|all cancers(10;0.0013)|OV - Ovarian serous cystadenocarcinoma(96;0.0139)		GGCCCTCAAGCCCCCCAGTCA	0.453																																					p.S891fs		Atlas-INDEL	.											.,1	CNTN6	245	.	0			c.2672delG						.						144.0	143.0	144.0					3																	1427450		2203	4300	6503	SO:0001589	frameshift_variant	27255	exon20			.	AB003592	CCDS2557.1	3p26-p25	2013-02-11			ENSG00000134115	ENSG00000134115		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	2176	protein-coding gene	gene with protein product	"""neural adhesion molecule"""	607220				9486763	Standard	NM_014461		Approved	NB-3	uc003bpa.3	Q9UQ52	OTTHUMG00000119030	ENST00000446702.2:c.2673delC	chr3.hg19:g.1427450delC	ENSP00000407822:p.Ser891fs	203.0	0.0		150.0	11.0	NM_014461	Q2KHM2	Frame_Shift_Del	DEL	ENST00000446702.2	hg19	CCDS2557.1																																																																																			.	.		0.453	CNTN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239235.2	NM_014461	
ZMIZ2	83637	hgsc.bcm.edu	37	7	44806215	44806215	+	Frame_Shift_Del	DEL	C	C	-	rs199813267		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:44806215delC	ENST00000309315.4	+	18	2731	c.2608delC	c.(2608-2610)cccfs	p.P871fs	ZMIZ2_ENST00000413916.1_Frame_Shift_Del_p.P813fs|ZMIZ2_ENST00000433667.1_Frame_Shift_Del_p.P839fs|ZMIZ2_ENST00000463931.1_3'UTR|ZMIZ2_ENST00000265346.7_Frame_Shift_Del_p.P845fs|ZMIZ2_ENST00000441627.1_Frame_Shift_Del_p.P871fs	NM_031449.3	NP_113637.3	Q8NF64	ZMIZ2_HUMAN	zinc finger, MIZ-type containing 2	871	Pro-rich.				positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	mitochondrion (GO:0005739)|nuclear replication fork (GO:0043596)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|zinc ion binding (GO:0008270)			breast(3)|endometrium(2)|kidney(3)|large_intestine(6)|lung(10)|ovary(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35						CGTGATGGGGCCCCCCAGCAT	0.672																																					p.G869fs	NSCLC(20;604 852 1948 16908 50522)	Atlas-INDEL	.											ZMIZ2,colon,carcinoma,0,1	ZMIZ2	82	.	0			c.2607delG						.						29.0	34.0	32.0					7																	44806215		1852	4090	5942	SO:0001589	frameshift_variant	83637	exon18			.	AK090415	CCDS43576.1, CCDS43577.1, CCDS75591.1	7p13	2009-11-06			ENSG00000122515	ENSG00000122515		"""Zinc fingers, MIZ-type"""	22229	protein-coding gene	gene with protein product		611196					Standard	XM_005249866		Approved	KIAA1886, hZIMP7, ZIMP7, DKFZp761I2123, NET27	uc003tlr.3	Q8NF64	OTTHUMG00000155817	ENST00000309315.4:c.2608delC	chr7.hg19:g.44806215delC	ENSP00000311778:p.Pro871fs	109.0	0.0		170.0	12.0	NM_031449	A4D2K7|D3DVL1|O94790|Q0VGB4|Q659A8|Q6JKL5|Q8WTX8|Q96Q01|Q9BQH7	Frame_Shift_Del	DEL	ENST00000309315.4	hg19	CCDS43576.1																																																																																			.	.		0.672	ZMIZ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341790.1	NM_031449	
HELQ	113510	hgsc.bcm.edu	37	4	84358058	84358058	+	Frame_Shift_Del	DEL	A	A	-	rs375051270		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:84358058delA	ENST00000295488.3	-	9	2163	c.2001delT	c.(1999-2001)tttfs	p.F667fs	HELQ_ENST00000510985.1_Frame_Shift_Del_p.F600fs	NM_133636.2	NP_598375	Q8TDG4	HELQ_HUMAN	helicase, POLQ-like	667	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				double-strand break repair via homologous recombination (GO:0000724)	nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(10)|lung(17)|ovary(2)|skin(2)	38						ATGTGCAGGTAAAAAGACAGA	0.478								Other identified genes with known or suspected DNA repair function																													p.T668fs		Atlas-INDEL	.											.	HELQ	95	.	0			c.2002delA						.						99.0	93.0	95.0					4																	84358058		2203	4300	6503	SO:0001589	frameshift_variant	113510	exon9			.	AF436845	CCDS3603.1, CCDS75158.1	4q21.23	2009-02-26			ENSG00000163312	ENSG00000163312			18536	protein-coding gene	gene with protein product		606769				11751861	Standard	XM_005262711		Approved	Hel308	uc003hom.3	Q8TDG4	OTTHUMG00000130423	ENST00000295488.3:c.2001delT	chr4.hg19:g.84358058delA	ENSP00000295488:p.Phe667fs	234.0	0.0		163.0	10.0	NM_133636	Q05DF9|Q502W9|Q659B8|Q6ZQX4|Q6ZTS4|Q96EX7	Frame_Shift_Del	DEL	ENST00000295488.3	hg19	CCDS3603.1																																																																																			.	.		0.478	HELQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252810.1	NM_133636	
FBN1	2200	hgsc.bcm.edu	37	15	48748935	48748935	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:48748935delG	ENST00000316623.5	-	44	5776	c.5321delC	c.(5320-5322)ccafs	p.P1774fs		NM_000138.4	NP_000129	P35555	FBN1_HUMAN	fibrillin 1	1774	EGF-like 29; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|kidney development (GO:0001822)|sequestering of BMP in extracellular matrix (GO:0035582)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|skeletal system development (GO:0001501)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(5)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|liver(1)|lung(49)|ovary(4)|pancreas(1)|prostate(9)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	139		all_lung(180;0.00279)		all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05)		ACAGACCCCTGGGATCTCCCG	0.458																																					p.P1774fs		Atlas-INDEL	.											.	FBN1	310	.	0			c.5322delA						.						113.0	100.0	105.0					15																	48748935		2198	4296	6494	SO:0001589	frameshift_variant	2200	exon44			.	X63556	CCDS32232.1	15q21.1	2014-09-17	2006-04-25			ENSG00000166147			3603	protein-coding gene	gene with protein product	"""Marfan syndrome"""	134797	"""fibrillin 1 (Marfan syndrome)"""	FBN, MFS1, WMS		10036187, 12525539	Standard	NM_000138		Approved	MASS, OCTD, SGS	uc001zwx.2	P35555		ENST00000316623.5:c.5321delC	chr15.hg19:g.48748935delG	ENSP00000325527:p.Pro1774fs	205.0	0.0		157.0	11.0	NM_000138	B2RUU0|D2JYH6|Q15972|Q75N87	Frame_Shift_Del	DEL	ENST00000316623.5	hg19	CCDS32232.1																																																																																			.	.		0.458	FBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417355.1		
ACP1	52	hgsc.bcm.edu	37	2	277054	277054	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:277054delA	ENST00000272065.5	+	5	461	c.368delA	c.(367-369)caafs	p.Q123fs	ACP1_ENST00000484464.1_3'UTR|ACP1_ENST00000272067.6_Frame_Shift_Del_p.Q123fs	NM_004300.3	NP_004291.1	P24666	PPAC_HUMAN	acid phosphatase 1, soluble	123						cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|extracellular vesicular exosome (GO:0070062)	acid phosphatase activity (GO:0003993)|non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)			endometrium(1)|large_intestine(3)|lung(6)|prostate(1)|skin(1)	12	all_hematologic(175;0.0429)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.00175)|Lung NSC(108;0.216)|all_epithelial(98;0.236)		all cancers(51;0.000391)|Epithelial(75;0.00281)|OV - Ovarian serous cystadenocarcinoma(76;0.00542)|GBM - Glioblastoma multiforme(21;0.127)	Adenine(DB00173)	TATGATCCACAAAAACAACTT	0.303																																					p.Q123fs		Atlas-INDEL	.											.	ACP1	42	.	0			c.367delC						.						70.0	72.0	72.0					2																	277054		2203	4300	6503	SO:0001589	frameshift_variant	52	exon5			.	M87546	CCDS1639.1, CCDS1640.1, CCDS46217.1	2p25	2011-06-09			ENSG00000143727	ENSG00000143727	3.1.3.2	"""Protein tyrosine phosphatases / Class II Cys-based PTPs"""	122	protein-coding gene	gene with protein product		171500					Standard	NM_001040649		Approved		uc002qwf.3	P24666	OTTHUMG00000086933	ENST00000272065.5:c.368delA	chr2.hg19:g.277054delA	ENSP00000272065:p.Gln123fs	279.0	0.0		171.0	11.0	NM_007099	A8K1L9|B5MCC7|P24667|Q16035|Q16036|Q16725|Q3KQX8|Q53RU0	Frame_Shift_Del	DEL	ENST00000272065.5	hg19	CCDS1639.1																																																																																			.	.		0.303	ACP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000195862.3		
C5orf42	65250	hgsc.bcm.edu	37	5	37153894	37153894	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:37153894delT	ENST00000508244.1	-	40	8252	c.8159delA	c.(8158-8160)aacfs	p.N2720fs	C5orf42_ENST00000425232.2_Frame_Shift_Del_p.N2720fs|C5orf42_ENST00000274258.7_Frame_Shift_Del_p.N1618fs			Q9H799	CE042_HUMAN	chromosome 5 open reading frame 42	2720						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)			CTGTTCTATGTTTTCAGCAAT	0.398																																					p.N2720fs		Atlas-INDEL	.											.	C5orf42	422	.	0			c.8160delC						.						98.0	89.0	92.0					5																	37153894		2203	4300	6503	SO:0001589	frameshift_variant	65250	exon41			.		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.8159delA	chr5.hg19:g.37153894delT	ENSP00000421690:p.Asn2720fs	179.0	0.0		164.0	10.0	NM_023073	A8MUB7|B7ZLV7|Q4G174|Q6DK46|Q8N8L4|Q9H5T1|Q9H8T9	Frame_Shift_Del	DEL	ENST00000508244.1	hg19	CCDS34146.2																																																																																			.	.		0.398	C5orf42-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360806.1	NM_023073	
MAN1B1	11253	hgsc.bcm.edu	37	9	139994268	139994268	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:139994268delG	ENST00000371589.4	+	6	924	c.851delG	c.(850-852)tggfs	p.W284fs	MAN1B1_ENST00000474902.1_5'UTR	NM_016219.4	NP_057303.2	Q9UKM7	MA1B1_HUMAN	mannosidase, alpha, class 1B, member 1	284					cellular protein metabolic process (GO:0044267)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|oligosaccharide metabolic process (GO:0009311)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum quality control compartment (GO:0044322)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|vesicle (GO:0031982)	calcium ion binding (GO:0005509)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)			autonomic_ganglia(1)|central_nervous_system(2)|kidney(1)|large_intestine(2)|liver(2)|lung(4)|ovary(2)	14	all_cancers(76;0.0926)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.0878)	OV - Ovarian serous cystadenocarcinoma(145;3.08e-05)|Epithelial(140;0.000513)		TTCAGTGAGTGGTTTGGCCTC	0.572																																					p.W284fs		Atlas-INDEL	.											.	MAN1B1	40	.	0			c.850delT						.						219.0	171.0	187.0					9																	139994268		2203	4300	6503	SO:0001589	frameshift_variant	11253	exon6			.	AF145732	CCDS7029.1	9q34.3	2014-05-27			ENSG00000177239	ENSG00000177239			6823	protein-coding gene	gene with protein product	"""endoplasmic reticulum alpha-mannosidase 1"", ""alpha 1,2-mannosidase"", ""endoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha-mannosidase 1"", ""ER alpha 1,2-mannosidase"", ""Man9GlcNAc2-specific processing alpha-mannosidase"""	604346				10409699, 10521544	Standard	NM_016219		Approved	MANA-ER, MRT15	uc004cld.3	Q9UKM7	OTTHUMG00000020978	ENST00000371589.4:c.851delG	chr9.hg19:g.139994268delG	ENSP00000360645:p.Trp284fs	207.0	0.0		174.0	11.0	NM_016219	Q5VSG3|Q9BRS9|Q9Y5K7	Frame_Shift_Del	DEL	ENST00000371589.4	hg19	CCDS7029.1																																																																																			.	.		0.572	MAN1B1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055294.2	NM_016219	
NEUROD6	63974	hgsc.bcm.edu	37	7	31378032	31378032	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:31378032delT	ENST00000297142.3	-	2	1173	c.851delA	c.(850-852)aatfs	p.N284fs		NM_022728.2	NP_073565.2	Q96NK8	NDF6_HUMAN	neuronal differentiation 6	284					cell differentiation (GO:0030154)|dentate gyrus development (GO:0021542)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(18)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	32						GTAATTGTAATTTTTACCATA	0.502																																					p.N284fs		Atlas-INDEL	.											.	NEUROD6	84	.	0			c.852delT						.						93.0	93.0	93.0					7																	31378032		2203	4300	6503	SO:0001589	frameshift_variant	63974	exon2			.	AF248954	CCDS5434.1	7p15.1	2013-05-21	2012-02-22		ENSG00000164600	ENSG00000164600		"""Basic helix-loop-helix proteins"""	13804	protein-coding gene	gene with protein product		611513	"""neurogenic differentiation 6"""			12357074	Standard	NM_022728		Approved	Atoh2, NEX1M, Math-2, bHLHa2, Nex1	uc003tch.4	Q96NK8	OTTHUMG00000022865	ENST00000297142.3:c.851delA	chr7.hg19:g.31378032delT	ENSP00000297142:p.Asn284fs	121.0	0.0		157.0	10.0	NM_022728	Q548T9|Q9H3H6	Frame_Shift_Del	DEL	ENST00000297142.3	hg19	CCDS5434.1																																																																																			.	.		0.502	NEUROD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215050.1	NM_022728	
KAT6A	7994	hgsc.bcm.edu	37	8	41791683	41791683	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:41791683delA	ENST00000396930.3	-	18	4598	c.4055delT	c.(4054-4056)ttafs	p.L1352fs	KAT6A_ENST00000265713.2_Frame_Shift_Del_p.L1352fs|KAT6A_ENST00000406337.1_Frame_Shift_Del_p.L1352fs	NM_001099412.1	NP_001092882.1	Q92794	KAT6A_HUMAN	K(lysine) acetyltransferase 6A	1352					aorta morphogenesis (GO:0035909)|cellular senescence (GO:0090398)|chromatin organization (GO:0006325)|DNA packaging (GO:0006323)|embryonic hemopoiesis (GO:0035162)|face morphogenesis (GO:0060325)|heart morphogenesis (GO:0003007)|histone acetylation (GO:0016573)|histone H3 acetylation (GO:0043966)|myeloid cell differentiation (GO:0030099)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of transcription, DNA-templated (GO:0045893)|protein acetylation (GO:0006473)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	Golgi apparatus (GO:0005794)|MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|PML body (GO:0016605)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)										ATTAGCATCTAAAAAAGACTC	0.493																																					p.L1352fs		Atlas-INDEL	.											.	.	.	.	0			c.4056delA						.						149.0	152.0	151.0					8																	41791683		2203	4300	6503	SO:0001589	frameshift_variant	7994	exon17			.	U47742	CCDS6124.1	8p11	2013-01-28	2011-07-21	2011-07-21	ENSG00000083168	ENSG00000083168		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Zinc fingers, C2HC-type containing"", ""Zinc fingers, PHD-type"""	13013	protein-coding gene	gene with protein product	"""Monocytic leukemia zinc finger protein"""	601408	"""runt-related transcription factor binding protein 2"", ""MYST histone acetyltransferase (monocytic leukemia) 3"""	ZNF220, RUNXBP2, MYST3		8849440, 8782817	Standard	NM_001099412		Approved	MOZ, ZC2HC6A	uc003xon.4	Q92794	OTTHUMG00000150453	ENST00000396930.3:c.4055delT	chr8.hg19:g.41791683delA	ENSP00000380136:p.Leu1352fs	217.0	0.0		155.0	10.0	NM_006766	Q76L81	Frame_Shift_Del	DEL	ENST00000396930.3	hg19	CCDS6124.1																																																																																			.	.		0.493	KAT6A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318163.1	NM_006766	
LUC7L3	51747	hgsc.bcm.edu	37	17	48814327	48814327	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:48814327delA	ENST00000505658.1	+	2	295	c.106delA	c.(106-108)aaafs	p.K36fs	LUC7L3_ENST00000240304.1_Frame_Shift_Del_p.K36fs|LUC7L3_ENST00000393227.2_Frame_Shift_Del_p.K36fs|LUC7L3_ENST00000544170.1_Intron|LUC7L3_ENST00000311571.3_Frame_Shift_Del_p.K36fs			O95232	LC7L3_HUMAN	LUC7-like 3 (S. cerevisiae)	36					mRNA splice site selection (GO:0006376)|RNA splicing (GO:0008380)	focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|U1 snRNP (GO:0005685)	DNA binding (GO:0003677)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)	12						CTAGGTTTGTAAATATTATCT	0.299																																					p.C35X		Atlas-INDEL	.											.	LUC7L3	32	.	0			c.105delT						.						108.0	102.0	104.0					17																	48814327		2203	4297	6500	SO:0001589	frameshift_variant	51747	exon2			.		CCDS11573.1	17q21.33	2010-02-17			ENSG00000108848	ENSG00000108848			24309	protein-coding gene	gene with protein product	"""cisplatin resistance associated overexpressed protein"", ""CRE-associated protein"""	609434				10631324, 12565863	Standard	NM_016424		Approved	LUC7A, CROP, OA48-18, CREAP-1, FLJ11063, CRA, hLuc7A	uc002iss.3	O95232	OTTHUMG00000162257	ENST00000505658.1:c.106delA	chr17.hg19:g.48814327delA	ENSP00000425092:p.Lys36fs	209.0	0.0		165.0	11.0	NM_006107	B3KN54|D3DTY1|Q6PHR9|Q9NUY0|Q9P2S7	Frame_Shift_Del	DEL	ENST00000505658.1	hg19	CCDS11573.1																																																																																			.	.		0.299	LUC7L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368205.2	NM_016424	
COG2	22796	hgsc.bcm.edu	37	1	230800279	230800279	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	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	173.0	0.0		269.0	18.0	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	
ATXN1	6310	hgsc.bcm.edu	37	6	16327823	16327823	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:16327823delG	ENST00000244769.4	-	8	1655	c.719delC	c.(718-720)ccafs	p.P241fs	ATXN1_ENST00000436367.1_Frame_Shift_Del_p.P241fs	NM_000332.3	NP_000323.2	P54253	ATX1_HUMAN	ataxin 1	241					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)				CTGGGCTGGTGGGGGGGACCC	0.677																																					p.P240fs		Atlas-INDEL	.											.	ATXN1	117	.	0			c.720delA						.																																			SO:0001589	frameshift_variant	6310	exon8			.	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.719delC	chr6.hg19:g.16327823delG	ENSP00000244769:p.Pro241fs	187.0	0.0		179.0	11.0	NM_000332	Q17S02|Q9UJG2|Q9Y4J1	Frame_Shift_Del	DEL	ENST00000244769.4	hg19	CCDS34342.1																																																																																			.	.		0.677	ATXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039943.3	NM_000332	
YIPF4	84272	hgsc.bcm.edu	37	2	32503243	32503243	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:32503243delC	ENST00000238831.4	+	1	265	c.19delC	c.(19-21)cccfs	p.P8fs		NM_032312.3	NP_115688.1	Q9BSR8	YIPF4_HUMAN	Yip1 domain family, member 4	8						endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)				kidney(2)|lung(3)|prostate(3)|skin(1)	9	Acute lymphoblastic leukemia(172;0.155)					TCCGGGCCCGCCCCCGGCCTA	0.716																																					p.P6fs		Atlas-INDEL	.											.,1	YIPF4	23	.	0			c.18delG						.						7.0	8.0	8.0					2																	32503243		2162	4234	6396	SO:0001589	frameshift_variant	84272	exon1			.	AK098486	CCDS1781.1	2p22.3	2008-02-05			ENSG00000119820	ENSG00000119820		"""Yip1 domain family"""	28145	protein-coding gene	gene with protein product						12477932	Standard	NM_032312		Approved	MGC11061, FinGER4	uc002rok.3	Q9BSR8	OTTHUMG00000128452	ENST00000238831.4:c.19delC	chr2.hg19:g.32503243delC	ENSP00000238831:p.Pro8fs	184.0	0.0		124.0	10.0	NM_032312		Frame_Shift_Del	DEL	ENST00000238831.4	hg19	CCDS1781.1																																																																																			.	.		0.716	YIPF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250250.3	NM_032312	
EHBP1	23301	hgsc.bcm.edu	37	2	62991489	62991489	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:62991489delT	ENST00000263991.5	+	4	733	c.251delT	c.(250-252)cttfs	p.L84fs	EHBP1_ENST00000405289.1_Frame_Shift_Del_p.L84fs|EHBP1_ENST00000431489.1_Frame_Shift_Del_p.L84fs|EHBP1_ENST00000405015.3_Frame_Shift_Del_p.L84fs|EHBP1_ENST00000354487.3_Frame_Shift_Del_p.L84fs	NM_015252.3	NP_056067.2	Q8NDI1	EHBP1_HUMAN	EH domain binding protein 1	84						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)			ACTGTAACACTTTTTAAGGTA	0.348																																					p.L84fs		Atlas-INDEL	.											.	EHBP1	127	.	0			c.250delC						.						106.0	103.0	104.0					2																	62991489		2203	4300	6503	SO:0001589	frameshift_variant	23301	exon4			.	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.251delT	chr2.hg19:g.62991489delT	ENSP00000263991:p.Leu84fs	262.0	0.0		164.0	10.0	NM_001142616	O94977|Q53TG7|Q53TV6|Q580X2|Q6NX72|Q6PIT3|Q6QNV2|Q9NWI9	Frame_Shift_Del	DEL	ENST00000263991.5	hg19	CCDS1872.1																																																																																			.	.		0.348	EHBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251616.1	NM_015252	
TPCN2	219931	hgsc.bcm.edu	37	11	68839465	68839465	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:68839465delG	ENST00000294309.3	+	11	1136	c.1035delG	c.(1033-1035)gtgfs	p.V345fs	TPCN2_ENST00000542467.1_Frame_Shift_Del_p.V345fs|TPCN2_ENST00000442692.2_3'UTR	NM_139075.3	NP_620714.2	Q8NHX9	TPC2_HUMAN	two pore segment channel 2	345					calcium ion transport (GO:0006816)|cellular calcium ion homeostasis (GO:0006874)|ion transmembrane transport (GO:0034220)|membrane depolarization during action potential (GO:0086010)|release of sequestered calcium ion into cytosol (GO:0051209)|smooth muscle contraction (GO:0006939)|transmembrane transport (GO:0055085)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|NAADP-sensitive calcium-release channel activity (GO:0072345)|protein kinase binding (GO:0019901)|voltage-gated calcium channel activity (GO:0005245)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(17)|prostate(2)|skin(1)|urinary_tract(1)	32			STAD - Stomach adenocarcinoma(18;0.0208)|LUAD - Lung adenocarcinoma(13;0.0713)			CCTCCATGGTGGGGGAGGGAG	0.627																																					p.V345fs		Atlas-INDEL	.											.	TPCN2	63	.	0			c.1034delT						.						54.0	58.0	57.0					11																	68839465		2200	4294	6494	SO:0001589	frameshift_variant	219931	exon11			.	AK023366	CCDS8189.1	11q13.1	2011-07-05			ENSG00000162341	ENSG00000162341		"""Voltage-gated ion channels / Two-pore channels"""	20820	protein-coding gene	gene with protein product		612163				16382101	Standard	NM_139075		Approved	TPC2	uc001oos.2	Q8NHX9	OTTHUMG00000167898	ENST00000294309.3:c.1035delG	chr11.hg19:g.68839465delG	ENSP00000294309:p.Val345fs	123.0	0.0		102.0	10.0	NM_139075	Q9NT82	Frame_Shift_Del	DEL	ENST00000294309.3	hg19	CCDS8189.1																																																																																			.	.		0.627	TPCN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396878.2	NM_139075	
SH2D1A	4068	hgsc.bcm.edu	37	X	123504064	123504064	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:123504064delA	ENST00000371139.4	+	3	539	c.240delA	c.(238-240)atafs	p.I80fs	STAG2_ENST00000469481.1_Intron|SH2D1A_ENST00000360027.4_Frame_Shift_Del_p.I80fs|SH2D1A_ENST00000491950.1_3'UTR|SH2D1A_ENST00000477673.2_Intron	NM_001114937.2|NM_002351.4	NP_001108409.1|NP_002342.1	O60880	SH21A_HUMAN	SH2 domain containing 1A	80	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				cell-cell signaling (GO:0007267)|cellular defense response (GO:0006968)|humoral immune response (GO:0006959)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|positive regulation of signal transduction (GO:0009967)	cytoplasm (GO:0005737)	SH3/SH2 adaptor activity (GO:0005070)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	10						TCCGGAAAATAAAAAATCTCA	0.368																																					p.I80fs		Atlas-INDEL	.											.	SH2D1A	23	.	0			c.239delT						.						104.0	103.0	103.0					X																	123504064		2203	4300	6503	SO:0001589	frameshift_variant	4068	exon3			.	AL023657	CCDS14608.1, CCDS48162.1	Xq25	2014-09-17	2010-04-21		ENSG00000183918	ENSG00000183918		"""SH2 domain containing"""	10820	protein-coding gene	gene with protein product	"""Duncan's disease"""	300490	"""lymphoproliferative syndrome"", ""SH2 domain protein 1A"""	IMD5, LYP		9771704, 9774102	Standard	NM_001114937		Approved	XLP, MTCP1, DSHP, XLPD, EBVS, SAP	uc004euf.4	O60880	OTTHUMG00000022344	ENST00000371139.4:c.240delA	chrX.hg19:g.123504064delA	ENSP00000360181:p.Ile80fs	283.0	0.0		209.0	15.0	NM_001114937	A8MSW0|O95383|O95384|O95385|O95386|Q6FGS6|Q9UNR0	Frame_Shift_Del	DEL	ENST00000371139.4	hg19	CCDS14608.1																																																																																			.	.		0.368	SH2D1A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058174.1	NM_002351	
KLHDC9	126823	hgsc.bcm.edu	37	1	161068399	161068399	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:161068399delT	ENST00000368011.4	+	1	216	c.74delT	c.(73-75)cttfs	p.L26fs	KLHDC9_ENST00000490724.2_Intron|PFDN2_ENST00000468311.1_5'Flank|KLHDC9_ENST00000392192.2_Frame_Shift_Del_p.L26fs	NM_152366.4	NP_689579.3	Q8NEP7	KLDC9_HUMAN	kelch domain containing 9	26										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)			CGGGACGCGCTTTTGGCTAGA	0.692																																					p.L25fs		Atlas-INDEL	.											.	KLHDC9	16	.	0			c.73delC						.						25.0	25.0	25.0					1																	161068399		2203	4300	6503	SO:0001589	frameshift_variant	126823	exon1			.	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.74delT	chr1.hg19:g.161068399delT	ENSP00000356990:p.Leu26fs	209.0	0.0		224.0	15.0	NM_152366	Q5SY56|Q6NXT9|Q6PKN4|Q8N5E1|Q8NA16	Frame_Shift_Del	DEL	ENST00000368011.4	hg19	CCDS30919.1																																																																																			.	.		0.692	KLHDC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077092.1	NM_152366	
CD40	958	hgsc.bcm.edu	37	20	44747014	44747014	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr20:44747014delG	ENST00000372285.3	+	1	104	c.32delG	c.(31-33)tggfs	p.W11fs	CD40_ENST00000372276.3_Frame_Shift_Del_p.W11fs|CD40_ENST00000489304.1_3'UTR	NM_001250.4	NP_001241.1	P25942	TNR5_HUMAN	CD40 molecule, TNF receptor superfamily member 5	11					B cell proliferation (GO:0042100)|cellular calcium ion homeostasis (GO:0006874)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to mechanical stimulus (GO:0071260)|defense response to virus (GO:0051607)|immune response-regulating cell surface receptor signaling pathway (GO:0002768)|inflammatory response (GO:0006954)|platelet activation (GO:0030168)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of Cdc42 GTPase activity (GO:0043089)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of isotype switching to IgG isotypes (GO:0048304)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein kinase C signaling (GO:0090037)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|protein complex assembly (GO:0006461)|regulation of immune response (GO:0050776)|regulation of immunoglobulin secretion (GO:0051023)	CD40 receptor complex (GO:0035631)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|enzyme binding (GO:0019899)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)|ubiquitin protein ligase binding (GO:0031625)			endometrium(2)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10		Myeloproliferative disorder(115;0.0122)				TGCGTCCTCTGGGGCTGCTTG	0.632									Immune Deficiency with Hyper-IgM																												p.W11fs		Atlas-INDEL	.											.	CD40	33	.	0			c.31delT						.						70.0	59.0	62.0					20																	44747014		2203	4300	6503	SO:0001589	frameshift_variant	958	exon1	Familial Cancer Database	Hypogammaglobulinemia with Hyper-IgM, HIGM type I-V, XLHIGM	.	X60592	CCDS13393.1, CCDS13394.1	20q12-q13.2	2014-09-17	2006-03-28	2005-01-14	ENSG00000101017	ENSG00000101017		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11919	protein-coding gene	gene with protein product		109535	"""tumor necrosis factor receptor superfamily, member 5"""	TNFRSF5		7687385, 2998589	Standard	XM_005260617		Approved	p50, Bp50	uc002xrg.1	P25942	OTTHUMG00000033053	ENST00000372285.3:c.32delG	chr20.hg19:g.44747014delG	ENSP00000361359:p.Trp11fs	244.0	0.0		171.0	11.0	NM_152854	E1P5S9|Q53GN5|Q5JY15|Q5U007|Q7M4Q8|Q86YK5|Q9BYU0	Frame_Shift_Del	DEL	ENST00000372285.3	hg19	CCDS13393.1																																																																																			.	.		0.632	CD40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080376.1	NM_001250	
HCK	3055	hgsc.bcm.edu	37	20	30640230	30640230	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr20:30640230delG	ENST00000375852.2	+	1	167	c.3delG	c.(1-3)ctgfs	p.L1fs	HCK_ENST00000538448.1_5'UTR|HCK_ENST00000518730.1_5'UTR|RNA5SP482_ENST00000391269.1_RNA|HCK_ENST00000375862.2_Frame_Shift_Del_p.L1fs|HCK_ENST00000534862.1_5'UTR|HCK_ENST00000520553.1_5'UTR			P08631	HCK_HUMAN	HCK proto-oncogene, Src family tyrosine kinase	1					cell adhesion (GO:0007155)|cytokine-mediated signaling pathway (GO:0019221)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|innate immune response-activating signal transduction (GO:0002758)|integrin-mediated signaling pathway (GO:0007229)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte degranulation (GO:0043299)|leukocyte migration involved in immune response (GO:0002522)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|mesoderm development (GO:0007498)|negative regulation of apoptotic process (GO:0043066)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell proliferation (GO:0008284)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cell shape (GO:0008360)|regulation of defense response to virus by virus (GO:0050690)|regulation of inflammatory response (GO:0050727)|regulation of phagocytosis (GO:0050764)|regulation of podosome assembly (GO:0071801)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|respiratory burst after phagocytosis (GO:0045728)|viral process (GO:0016032)	caveola (GO:0005901)|cell projection (GO:0042995)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|lysosome (GO:0005764)|nucleus (GO:0005634)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)	p.R4fs*38(1)		NS(1)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(18)|ovary(2)|pancreas(1)|prostate(2)|skin(4)	36			UCEC - Uterine corpus endometrioid carcinoma (5;0.0241)		Bosutinib(DB06616)	CTGCCGAGCTGGGGGGGCGCT	0.721																																					p.L1fs		Atlas-INDEL	.											.,1	HCK	181	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.2delT						.		,,,,,	10,1862		2,6,928	1.0	2.0	2.0		,,,,,	3.0	1.0	20		2	30,4280		11,8,2136	no	frameshift,utr-5,utr-5,utr-5,frameshift,utr-5	HCK	NM_002110.3,NM_001172133.1,NM_001172132.1,NM_001172131.1,NM_001172130.1,NM_001172129.1	,,,,,	13,14,3064	A1A1,A1R,RR		0.6961,0.5342,0.647	,,,,,	,,,,,	30640230	40,6142	1158	2568	3726	SO:0001589	frameshift_variant	3055	exon1			.	AK026432	CCDS33460.1, CCDS54453.1, CCDS54455.1, CCDS54456.1	20q11-q12	2014-06-25	2014-06-25		ENSG00000101336	ENSG00000101336		"""SH2 domain containing"""	4840	protein-coding gene	gene with protein product		142370	"""hemopoietic cell kinase"""			3496523	Standard	NM_002110		Approved	JTK9	uc002wxh.3	P08631	OTTHUMG00000032204	ENST00000375852.2:c.3delG	chr20.hg19:g.30640230delG	ENSP00000365012:p.Leu1fs	299.0	0.0		197.0	13.0	NM_001172130	A8K1I1|B4DQB6|E1P5M2|Q29RX1|Q2VPE2|Q504R5|Q5T7K1|Q5T7K2|Q96CC0|Q9H5Y5|Q9NUA4|Q9UMJ5	Frame_Shift_Del	DEL	ENST00000375852.2	hg19	CCDS33460.1																																																																																			.	.		0.721	HCK-001	KNOWN	NAGNAG_splice_site|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000078603.4		
ELMO1	9844	hgsc.bcm.edu	37	7	37172765	37172765	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:37172765delA	ENST00000310758.4	-	14	1808	c.1161delT	c.(1159-1161)tttfs	p.F387fs	ELMO1_ENST00000442504.1_Frame_Shift_Del_p.F387fs|ELMO1_ENST00000448602.1_Frame_Shift_Del_p.F387fs|ELMO1_ENST00000341056.3_Frame_Shift_Del_p.F89fs	NM_001206480.1|NM_014800.10	NP_001193409.1|NP_055615.8	Q92556	ELMO1_HUMAN	engulfment and cell motility 1	387	ELMO. {ECO:0000255|PROSITE- ProRule:PRU00664}.				actin cytoskeleton organization (GO:0030036)|apoptotic process (GO:0006915)|cellular component movement (GO:0006928)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|phagocytosis, engulfment (GO:0006911)|Rac protein signal transduction (GO:0016601)|regulation of defense response to virus by virus (GO:0050690)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	SH3 domain binding (GO:0017124)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(11)|liver(2)|lung(28)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	58						GGTGCTTGGCAAAGTACAGCA	0.438																																					p.A388fs		Atlas-INDEL	.											.	ELMO1	141	.	0			c.1162delG						.						169.0	143.0	152.0					7																	37172765		2203	4300	6503	SO:0001589	frameshift_variant	9844	exon14			.	AF398885	CCDS5449.1, CCDS5450.1	7p14.1	2012-07-10	2006-01-20		ENSG00000155849	ENSG00000155849		"""Engulfment and cell motility proteins"""	16286	protein-coding gene	gene with protein product		606420	"""engulfment and cell motility 1 (ced-12 homolog, C. elegans)"""			11595183	Standard	NM_001039459		Approved	KIAA0281, CED12, ELMO-1, CED-12	uc003tfk.2	Q92556	OTTHUMG00000023701	ENST00000310758.4:c.1161delT	chr7.hg19:g.37172765delA	ENSP00000312185:p.Phe387fs	141.0	0.0		175.0	11.0	NM_014800	A4D1X6|Q29R79|Q6ZTJ0|Q96PB0|Q9H0I1	Frame_Shift_Del	DEL	ENST00000310758.4	hg19	CCDS5449.1																																																																																			.	.		0.438	ELMO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219830.4	NM_130442	
GAD1	2571	hgsc.bcm.edu	37	2	171715334	171715334	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:171715334delT	ENST00000358196.3	+	16	2092	c.1542delT	c.(1540-1542)tgtfs	p.C514fs		NM_000817.2	NP_000808.2	Q99259	DCE1_HUMAN	glutamate decarboxylase 1 (brain, 67kDa)	514					gamma-aminobutyric acid biosynthetic process (GO:0009449)|glutamate catabolic process (GO:0006538)|glutamate decarboxylation to succinate (GO:0006540)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter secretion (GO:0007269)|protein-pyridoxal-5-phosphate linkage (GO:0018352)|response to drug (GO:0042493)|synaptic transmission (GO:0007268)	clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|vesicle membrane (GO:0012506)	glutamate binding (GO:0016595)|glutamate decarboxylase activity (GO:0004351)|pyridoxal phosphate binding (GO:0030170)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|lung(15)|ovary(1)|urinary_tract(2)	35						CAAACGTCTGTTTTTGGTATA	0.428																																					p.C514fs		Atlas-INDEL	.											.	GAD1	79	.	0			c.1541delG						.						85.0	85.0	85.0					2																	171715334		2203	4300	6503	SO:0001589	frameshift_variant	2571	exon16			.		CCDS2239.1, CCDS2240.1	2q31	2008-02-05	2002-08-29		ENSG00000128683	ENSG00000128683	4.1.1.15		4092	protein-coding gene	gene with protein product		605363	"""glutamate decarboxylase 1 (brain, 67kD)"""	GAD		1549570	Standard	XM_005246443		Approved		uc002ugi.3	Q99259	OTTHUMG00000044175	ENST00000358196.3:c.1542delT	chr2.hg19:g.171715334delT	ENSP00000350928:p.Cys514fs	242.0	0.0		182.0	12.0	NM_000817	Q49AK1|Q53TQ7|Q9BU91|Q9UHH4	Frame_Shift_Del	DEL	ENST00000358196.3	hg19	CCDS2239.1																																																																																			.	.		0.428	GAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102664.2		
AKIP1	56672	hgsc.bcm.edu	37	11	8938845	8938845	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:8938845delA	ENST00000309377.4	+	5	510	c.420delA	c.(418-420)agafs	p.R140fs	AKIP1_ENST00000525005.1_Frame_Shift_Del_p.R140fs|AKIP1_ENST00000396648.2_Frame_Shift_Del_p.R113fs|AKIP1_ENST00000299576.5_Frame_Shift_Del_p.R113fs|AKIP1_ENST00000529876.1_Frame_Shift_Del_p.R113fs|AKIP1_ENST00000534506.1_Frame_Shift_Del_p.R113fs|AKIP1_ENST00000309357.4_Intron|AKIP1_ENST00000534147.1_Frame_Shift_Del_p.R140fs	NM_020642.3	NP_065693.2	Q9NQ31	AKIP1_HUMAN	A kinase (PRKA) interacting protein 1	140					substrate adhesion-dependent cell spreading (GO:0034446)	nucleus (GO:0005634)				kidney(1)|large_intestine(2)|lung(2)	5						GAAAAGACAGAAAAAAGACAT	0.443																																					p.R140fs		Atlas-INDEL	.											.	AKIP1	9	.	0			c.419delG						.						91.0	77.0	82.0					11																	8938845		2201	4296	6497	SO:0001589	frameshift_variant	56672	exon5			.	AF512007	CCDS7793.1, CCDS55743.1, CCDS55744.1	11p15.3	2011-04-18	2011-04-18	2011-04-18	ENSG00000166452	ENSG00000166452			1170	protein-coding gene	gene with protein product		609191	"""chromosome 11 open reading frame 17"""	C11orf17		20562110, 18178962, 15630084	Standard	NM_020642		Approved	BCA3	uc001mgx.3	Q9NQ31	OTTHUMG00000165653	ENST00000309377.4:c.420delA	chr11.hg19:g.8938845delA	ENSP00000310459:p.Arg140fs	210.0	0.0		163.0	11.0	NM_020642	Q8NBS2|Q8TAC6|Q8TAD3|Q8TAE0	Frame_Shift_Del	DEL	ENST00000309377.4	hg19	CCDS7793.1																																																																																			.	.		0.443	AKIP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000385615.1	NM_020642	
KMT2B	9757	hgsc.bcm.edu	37	19	36212560	36212560	+	Frame_Shift_Del	DEL	C	C	-	rs531978572	byFrequency	TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:36212560delC	ENST00000222270.7	+	3	2311	c.2311delC	c.(2311-2313)cccfs	p.P771fs	KMT2B_ENST00000607650.1_RNA|KMT2B_ENST00000420124.1_Frame_Shift_Del_p.P771fs	NM_014727.1	NP_055542.1	Q9UMN6	KMT2B_HUMAN	lysine (K)-specific methyltransferase 2B	771	Pro-rich.				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)										GCAGATGCCTCCCCTGGAAAA	0.622																																					p.P770fs		Atlas-INDEL	.											.	MLL4	229	.	0			c.2310delT						.						26.0	35.0	32.0					19																	36212560		2102	4245	6347	SO:0001589	frameshift_variant	8085	exon3			.	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.2311delC	chr19.hg19:g.36212560delC	ENSP00000222270:p.Pro771fs	135.0	0.0		103.0	10.0	NM_014727	O15022|O95836|Q96GP2|Q96IP3|Q9UK25|Q9Y668|Q9Y669	Frame_Shift_Del	DEL	ENST00000222270.7	hg19	CCDS46055.1																																																																																			.	.		0.622	KMT2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014727	
RP11-402P6.11	0	hgsc.bcm.edu	37	X	70984231	70984231	+	lincRNA	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:70984231delG	ENST00000439926.1	-	0	0				CXorf49B_ENST00000542739.1_lincRNA																							GAAGATGGCCGGGGGGAAGAA	0.692																																					p.A319fs		Atlas-INDEL	.											.	.	.	.	0			c.957delC						.																																					100130361	exon1			.																													chrX.hg19:g.70984231delG		194.0	0.0		197.0	12.0	NM_001145140		Frame_Shift_Del	DEL	ENST00000439926.1	hg19																																																																																				.	.		0.692	RP11-402P6.11-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000057168.1		
SAMD15	161394	hgsc.bcm.edu	37	14	77845359	77845359	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr14:77845359delA	ENST00000216471.4	+	1	1884	c.1598delA	c.(1597-1599)gaafs	p.E533fs	TMED8_ENST00000216468.7_5'Flank|SAMD15_ENST00000533095.2_Intron	NM_001010860.1	NP_001010860.1	Q9P1V8	SAM15_HUMAN	sterile alpha motif domain containing 15	533										breast(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|pancreas(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						ACCCAGCCAGAAAAAGGGACT	0.428																																					p.E533fs		Atlas-INDEL	.											.	SAMD15	60	.	0			c.1597delG						.						76.0	73.0	74.0					14																	77845359		2203	4300	6503	SO:0001589	frameshift_variant	161394	exon1			.	AK093282	CCDS32126.1	14q24.3	2013-01-10	2010-10-20	2010-10-20	ENSG00000100583	ENSG00000100583		"""Sterile alpha motif (SAM) domain containing"""	18631	protein-coding gene	gene with protein product			"""family with sequence similarity 15, member A"", ""chromosome 14 open reading frame 174"""	FAM15A, C14orf174			Standard	XM_006720069		Approved	FLJ35963	uc001xtq.1	Q9P1V8		ENST00000216471.4:c.1598delA	chr14.hg19:g.77845359delA	ENSP00000216471:p.Glu533fs	278.0	0.0		191.0	12.0	NM_001010860	Q2M3P3	Frame_Shift_Del	DEL	ENST00000216471.4	hg19	CCDS32126.1																																																																																			.	.		0.428	SAMD15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394587.2	NM_001010860	
C2CD4C	126567	hgsc.bcm.edu	37	19	408210	408210	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:408210delA	ENST00000332235.6	-	2	325	c.152delT	c.(151-153)ttcfs	p.F51fs		NM_001136263.1	NP_001129735.1	Q8TF44	C2C4C_HUMAN	C2 calcium-dependent domain containing 4C	51										large_intestine(1)|pancreas(1)	2						GGGGGGGATGAAAAAGTCGGG	0.711																																					p.F51fs		Atlas-INDEL	.											.	C2CD4C	13	.	0			c.153delC						.						25.0	32.0	30.0					19																	408210		692	1589	2281	SO:0001589	frameshift_variant	126567	exon2			.	AB075837	CCDS45890.1	19p13.3	2009-09-28	2009-09-28	2009-09-28		ENSG00000183186			29417	protein-coding gene	gene with protein product	"""nuclear localized factor 3"""	610336	"""KIAA1957"", ""family with sequence similarity 148, member C"""	KIAA1957, FAM148C		11853319	Standard	NM_001136263		Approved	NLF3	uc002loo.3	Q8TF44		ENST00000332235.6:c.152delT	chr19.hg19:g.408210delA	ENSP00000328677:p.Phe51fs	310.0	0.0		298.0	19.0	NM_001136263	Q8N3H7	Frame_Shift_Del	DEL	ENST00000332235.6	hg19	CCDS45890.1																																																																																			.	.		0.711	C2CD4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451789.2	XM_065166	
RIN1	9610	hgsc.bcm.edu	37	11	66103273	66103273	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:66103273delG	ENST00000311320.4	-	3	468	c.342delC	c.(340-342)cccfs	p.P114fs	RIN1_ENST00000424433.2_Frame_Shift_Del_p.P9fs|RIN1_ENST00000530056.1_Frame_Shift_Del_p.P9fs|RIN1_ENST00000524804.1_5'Flank|RP11-867G23.12_ENST00000526655.1_RNA	NM_004292.2	NP_004283.2	Q13671	RIN1_HUMAN	Ras and Rab interactor 1	114	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				associative learning (GO:0008306)|endocytosis (GO:0006897)|memory (GO:0007613)|negative regulation of synaptic plasticity (GO:0031914)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)			breast(1)|central_nervous_system(3)|haematopoietic_and_lymphoid_tissue(1)|lung(8)|ovary(1)	14						AGACGAAGGAGGGGCCACTGG	0.647																																					p.S115fs		Atlas-INDEL	.											.	RIN1	64	.	0			c.343delT						.						32.0	37.0	35.0					11																	66103273		2200	4295	6495	SO:0001589	frameshift_variant	9610	exon3			.	L36463	CCDS31614.1	11q13.2	2005-09-18				ENSG00000174791			18749	protein-coding gene	gene with protein product		605965				9144171, 1849280	Standard	NM_004292		Approved		uc001ohn.1	Q13671		ENST00000311320.4:c.342delC	chr11.hg19:g.66103273delG	ENSP00000310406:p.Pro114fs	161.0	0.0		120.0	10.0	NM_004292	O15010|Q00427|Q96CC8	Frame_Shift_Del	DEL	ENST00000311320.4	hg19	CCDS31614.1																																																																																			.	.		0.647	RIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392980.2	NM_004292	
ATXN2	6311	hgsc.bcm.edu	37	12	111926535	111926535	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:111926535delT	ENST00000377617.3	-	15	2626	c.2465delA	c.(2464-2466)aatfs	p.N822fs	AC002395.1_ENST00000581907.1_RNA|ATXN2_ENST00000535949.1_Frame_Shift_Del_p.N533fs|ATXN2_ENST00000389153.4_Frame_Shift_Del_p.N557fs|ATXN2_ENST00000542287.2_Frame_Shift_Del_p.N557fs|ATXN2_ENST00000608853.1_Frame_Shift_Del_p.N662fs|ATXN2_ENST00000550104.1_Frame_Shift_Del_p.N822fs	NM_002973.3	NP_002964.3	Q99700	ATX2_HUMAN	ataxin 2	822					cell death (GO:0008219)|cerebellar Purkinje cell differentiation (GO:0021702)|cytoplasmic mRNA processing body assembly (GO:0033962)|homeostasis of number of cells (GO:0048872)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of receptor internalization (GO:0002091)|neuromuscular process (GO:0050905)|neuron projection morphogenesis (GO:0048812)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA transport (GO:0050658)|stress granule assembly (GO:0034063)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|polysome (GO:0005844)|ribonucleoprotein complex (GO:0030529)|trans-Golgi network (GO:0005802)	epidermal growth factor receptor binding (GO:0005154)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|RNA binding (GO:0003723)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(5)|large_intestine(8)|lung(6)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	37						TCCCTCTCTATTTTTGTTTAG	0.308																																					p.N822fs		Atlas-INDEL	.											.	ATXN2	99	.	0			c.2466delT						.						43.0	42.0	42.0					12																	111926535		2203	4300	6503	SO:0001589	frameshift_variant	6311	exon15			.	U80749	CCDS31902.1	12q23-q24.1	2014-09-17	2004-08-12	2004-08-13	ENSG00000204842	ENSG00000204842		"""Ataxins"""	10555	protein-coding gene	gene with protein product	"""trinucleotide repeat containing 13"""	601517	"""spinocerebellar ataxia 2 (olivopontocerebellar ataxia 2, autosomal dominant, ataxin 2)"""	SCA2, TNRC13		8358438, 9225980	Standard	NM_002973		Approved	ATX2	uc001tsj.3	Q99700	OTTHUMG00000133475	ENST00000377617.3:c.2465delA	chr12.hg19:g.111926535delT	ENSP00000366843:p.Asn822fs	172.0	0.0		162.0	10.0	NM_002973	A6NLD4|Q6ZQZ7|Q99493	Frame_Shift_Del	DEL	ENST00000377617.3	hg19	CCDS31902.1																																																																																			.	.		0.308	ATXN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257351.3	NM_002973	
PLEKHA3	65977	hgsc.bcm.edu	37	2	179363984	179363984	+	Intron	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:179363984delA	ENST00000234453.5	+	6	1061					NM_019091.3	NP_061964.3	Q9HB20	PKHA3_HUMAN	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 3							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)			TCAGAGAGGTAAAAGAACCTT	0.368																																					.		Atlas-INDEL	.											.	PLEKHA3	25	.	0			c.659+2A>-						.						89.0	88.0	88.0					2																	179363984		2203	4300	6503	SO:0001627	intron_variant	65977	exon6			.	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.659+3A>-	chr2.hg19:g.179363984delA		264.0	0.0		166.0	10.0	NM_019091	Q4ZG69|Q86TQ1|Q9NXT3	Splice_Site	DEL	ENST00000234453.5	hg19	CCDS33336.1																																																																																			.	.		0.368	PLEKHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335241.2	NM_019091	
TIMM44	10469	hgsc.bcm.edu	37	19	8002975	8002975	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:8002975delT	ENST00000270538.3	-	3	517	c.249delA	c.(247-249)aaafs	p.K83fs		NM_006351.3	NP_006342.2	O43615	TIM44_HUMAN	translocase of inner mitochondrial membrane 44 homolog (yeast)	83					cellular protein metabolic process (GO:0044267)|protein targeting to mitochondrion (GO:0006626)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|P-P-bond-hydrolysis-driven protein transmembrane transporter activity (GO:0015450)			NS(1)|endometrium(3)|kidney(3)|large_intestine(2)|liver(2)|lung(2)|ovary(2)|skin(1)|urinary_tract(1)	17						CGTCACGGAATTTTTTTATAC	0.413																																					p.F84fs		Atlas-INDEL	.											.	TIMM44	47	.	0			c.250delT						.						243.0	241.0	242.0					19																	8002975		2203	4300	6503	SO:0001589	frameshift_variant	10469	exon3			.	AF026030	CCDS12192.1	19p13.3-p13.2	2008-07-04				ENSG00000104980			17316	protein-coding gene	gene with protein product		605058				10848612, 10339406	Standard	NM_006351		Approved	TIM44	uc002miz.3	O43615		ENST00000270538.3:c.249delA	chr19.hg19:g.8002975delT	ENSP00000270538:p.Lys83fs	204.0	0.0		191.0	13.0	NM_006351	A8K0R9|D6W664|Q8N193	Frame_Shift_Del	DEL	ENST00000270538.3	hg19	CCDS12192.1																																																																																			.	.		0.413	TIMM44-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461596.3		
APBB1	322	hgsc.bcm.edu	37	11	6416867	6416867	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:6416867delG	ENST00000609360.1	-	15	2129	c.2030delC	c.(2029-2031)cctfs	p.P677fs	APBB1_ENST00000609331.1_Frame_Shift_Del_p.P442fs|APBB1_ENST00000608394.1_Frame_Shift_Del_p.P418fs|APBB1_ENST00000299402.6_Frame_Shift_Del_p.P675fs|APBB1_ENST00000311051.3_Frame_Shift_Del_p.P675fs|APBB1_ENST00000389906.2_Frame_Shift_Del_p.P677fs|APBB1_ENST00000608704.1_Frame_Shift_Del_p.P418fs|APBB1_ENST00000530885.1_Frame_Shift_Del_p.P455fs|APBB1_ENST00000526240.1_5'UTR|APBB1_ENST00000608655.1_Frame_Shift_Del_p.P457fs|APBB1_ENST00000608645.1_Frame_Shift_Del_p.P418fs|APBB1_ENST00000529519.1_Frame_Shift_Del_p.P202fs	NM_001164.3	NP_001155.1	O00213	APBB1_HUMAN	amyloid beta (A4) precursor protein-binding, family B, member 1 (Fe65)	677	PID 2. {ECO:0000255|PROSITE- ProRule:PRU00148}.				apoptotic process (GO:0006915)|axonogenesis (GO:0007409)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|histone H4 acetylation (GO:0043967)|negative regulation of cell growth (GO:0030308)|negative regulation of thymidylate synthase biosynthetic process (GO:0050760)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synapse (GO:0045202)	beta-amyloid binding (GO:0001540)|chromatin binding (GO:0003682)|histone binding (GO:0042393)|proline-rich region binding (GO:0070064)|transcription factor binding (GO:0008134)			breast(4)|endometrium(3)|kidney(1)|large_intestine(7)|lung(5)|prostate(2)|skin(1)|urinary_tract(1)	24		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;6.49e-08)|BRCA - Breast invasive adenocarcinoma(625;0.194)		AGACTCAGCAGGGGGTGCTGG	0.662																																					p.P677fs	GBM(147;1810 2556 5672 39622)	Atlas-INDEL	.											.	APBB1	73	.	0			c.2031delT						.						33.0	32.0	32.0					11																	6416867		2201	4295	6496	SO:0001589	frameshift_variant	322	exon14			.	L77864	CCDS31410.1, CCDS58114.1, CCDS66015.1, CCDS66016.1, CCDS66017.1, CCDS66018.1	11p15	2008-02-01				ENSG00000166313			581	protein-coding gene	gene with protein product		602709		RIR		8955346, 8894693	Standard	NM_001164		Approved	Fe65	uc001mcy.1	O00213		ENST00000609360.1:c.2030delC	chr11.hg19:g.6416867delG	ENSP00000477213:p.Pro677fs	166.0	0.0		139.0	11.0	NM_001164	A1E379|A6NH82|A6NL69|B7Z1J5|B7Z1J6|B7Z2Y0|D3DQT2|Q7Z324|Q96A93|V9GYK0|V9GYT4	Frame_Shift_Del	DEL	ENST00000609360.1	hg19																																																																																				.	.		0.662	APBB1-023	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000471831.1	NM_001164	
JAK1	3716	hgsc.bcm.edu	37	1	65309771	65309771	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:65309771delG	ENST00000342505.4	-	17	2627	c.2379delC	c.(2377-2379)cccfs	p.P793fs	JAK1_ENST00000465376.1_5'UTR	NM_002227.2	NP_002218.2	P23458	JAK1_HUMAN	Janus kinase 1	793	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cytokine-mediated signaling pathway (GO:0019221)|enzyme linked receptor protein signaling pathway (GO:0007167)|interferon-gamma-mediated signaling pathway (GO:0060333)|interleukin-2-mediated signaling pathway (GO:0038110)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to antibiotic (GO:0046677)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)			breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(48)|kidney(3)|large_intestine(8)|liver(2)|lung(19)|ovary(1)|prostate(12)|skin(1)|soft_tissue(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	120				BRCA - Breast invasive adenocarcinoma(111;0.0485)	Ruxolitinib(DB08877)|Tofacitinib(DB08895)	TGTCTTTCAAGGGGATCTCGC	0.557			Mis		ALL																																p.L794X		Atlas-INDEL	.		Dom	yes		1	1p32.3-p31.3	3716	Janus kinase 1		L	.	JAK1	209	.	0			c.2380delT						.						128.0	131.0	130.0					1																	65309771		2030	4203	6233	SO:0001589	frameshift_variant	3716	exon17			.	M64174	CCDS41346.1	1p32.3-p31.3	2009-07-10	2009-04-23		ENSG00000162434	ENSG00000162434	2.7.10.1		6190	protein-coding gene	gene with protein product		147795		JAK1B		1848670, 7698020	Standard	NM_002227		Approved	JAK1A, JTK3	uc001dbu.1	P23458	OTTHUMG00000009310	ENST00000342505.4:c.2379delC	chr1.hg19:g.65309771delG	ENSP00000343204:p.Pro793fs	241.0	0.0		150.0	10.0	NM_002227	Q59GQ2|Q9UD26	Frame_Shift_Del	DEL	ENST00000342505.4	hg19	CCDS41346.1																																																																																			.	.		0.557	JAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025791.1	NM_002227	
TSPAN19	144448	hgsc.bcm.edu	37	12	85421730	85421730	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:85421730delA	ENST00000532498.2	-	4	291	c.211delT	c.(211-213)tgtfs	p.C71fs	TSPAN19_ENST00000547403.2_Intron	NM_001100917.1	NP_001094387.1	P0C672	TSN19_HUMAN	tetraspanin 19	71						integral component of membrane (GO:0016021)				ovary(1)	1						CCCAATAGACAAAAAAGAACA	0.289																																					p.C71fs		Atlas-INDEL	.											.	TSPAN19	23	.	0			c.212delG						.						60.0	56.0	57.0					12																	85421730		1810	4063	5873	SO:0001589	frameshift_variant	144448	exon4			.		CCDS44949.1	12q21.31	2013-02-14			ENSG00000231738	ENSG00000231738		"""Tetraspanins"""	31886	protein-coding gene	gene with protein product							Standard	NM_001100917		Approved		uc009zsj.3	P0C672	OTTHUMG00000166181	ENST00000532498.2:c.211delT	chr12.hg19:g.85421730delA	ENSP00000433816:p.Cys71fs	206.0	0.0		171.0	14.0	NM_001100917		Frame_Shift_Del	DEL	ENST00000532498.2	hg19	CCDS44949.1																																																																																			.	.		0.289	TSPAN19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388240.2	NM_001100917	
SLC6A14	11254	hgsc.bcm.edu	37	X	115577930	115577930	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:115577930delC	ENST00000371900.4	+	7	901	c.813delC	c.(811-813)ttcfs	p.F271fs		NM_007231.3	NP_009162.1	Q9UN76	S6A14_HUMAN	solute carrier family 6 (amino acid transporter), member 14	271					amino acid transmembrane transport (GO:0003333)|amino acid transport (GO:0006865)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|response to toxic substance (GO:0009636)|transmembrane transport (GO:0055085)|transport (GO:0006810)	brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	amino acid transmembrane transporter activity (GO:0015171)|neurotransmitter:sodium symporter activity (GO:0005328)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	23					L-Proline(DB00172)|Valaciclovir(DB00577)|Valganciclovir(DB01610)	CAGCTCTTTTCCCCTATGTGG	0.338																																					p.F271fs		Atlas-INDEL	.											.	SLC6A14	56	.	0			c.812delT						.						105.0	104.0	104.0					X																	115577930		2203	4299	6502	SO:0001589	frameshift_variant	11254	exon7			.	AF151978	CCDS14570.1	Xq23	2013-05-22			ENSG00000087916	ENSG00000268104		"""Solute carriers"""	11047	protein-coding gene	gene with protein product		300444	"""solute carrier family 6 (neurotransmitter transporter), member 14"""			10446133	Standard	NM_007231		Approved		uc004eqi.3	Q9UN76	OTTHUMG00000022245	ENST00000371900.4:c.813delC	chrX.hg19:g.115577930delC	ENSP00000360967:p.Phe271fs	205.0	0.0		160.0	10.0	NM_007231	Q5H942	Frame_Shift_Del	DEL	ENST00000371900.4	hg19	CCDS14570.1																																																																																			.	.		0.338	SLC6A14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057986.1		
DACH1	1602	hgsc.bcm.edu	37	13	72147000	72147000	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr13:72147000delG	ENST00000359684.2	-	5	1432	c.1433delC	c.(1432-1434)ccafs	p.P478fs	DACH1_ENST00000313174.7_Intron|DACH1_ENST00000354591.4_Intron|DACH1_ENST00000305425.4_Frame_Shift_Del_p.P426fs			Q9UI36	DACH1_HUMAN	dachshund family transcription factor 1	478					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)			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)		AACTCTGGATGGGGGACTCTG	0.423																																					p.P426fs		Atlas-INDEL	.											.	DACH1	123	.	0			c.1278delA						.						96.0	97.0	97.0					13																	72147000		2027	4202	6229	SO:0001589	frameshift_variant	1602	exon4			.	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.1433delC	chr13.hg19:g.72147000delG	ENSP00000352712:p.Pro478fs	208.0	0.0		150.0	10.0	NM_080759	D0FY35|D0FY36|O75523|O75687|Q5VYY3|Q5VYY4|Q96SG3|Q96SG4|Q9H524|Q9UMH4	Frame_Shift_Del	DEL	ENST00000359684.2	hg19																																																																																				.	.		0.423	DACH1-002	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000045240.1	NM_004392	
BCAP31	10134	hgsc.bcm.edu	37	X	152967544	152967544	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:152967544delT	ENST00000345046.6	-	7	1027	c.620delA	c.(619-621)aacfs	p.N207fs	BCAP31_ENST00000458587.2_Frame_Shift_Del_p.N274fs|BCAP31_ENST00000441714.1_Frame_Shift_Del_p.N207fs	NM_001256447.1	NP_001243376.1	P51572	BAP31_HUMAN	B-cell receptor-associated protein 31	207					antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|negative regulation of endoplasmic reticulum calcium ion concentration (GO:0032471)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial calcium ion concentration (GO:0051561)|protein localization to endoplasmic reticulum exit site (GO:0070973)|spermatogenesis (GO:0007283)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lipid particle (GO:0005811)|membrane (GO:0016020)				endometrium(2)|large_intestine(2)|lung(2)|prostate(1)	7	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					CAGAACCTGGTTTTCAGCTTT	0.502																																					p.N274fs		Atlas-INDEL	.											.	BCAP31	33	.	0			c.822delC						.						43.0	38.0	39.0					X																	152967544		2203	4297	6500	SO:0001589	frameshift_variant	10134	exon7			.	X81109	CCDS14727.1, CCDS48191.1	Xq28	2005-10-11			ENSG00000185825	ENSG00000185825			16695	protein-coding gene	gene with protein product		300398					Standard	NM_001139441		Approved	DXS1357E, BAP31, 6C6-Ag, CDM	uc011mza.1	P51572	OTTHUMG00000024218	ENST00000345046.6:c.620delA	chrX.hg19:g.152967544delT	ENSP00000343458:p.Asn207fs	214.0	0.0		145.0	10.0	NM_001139457	B3KQ79|D3DWV5|Q13836|Q96CF0	Frame_Shift_Del	DEL	ENST00000345046.6	hg19	CCDS14727.1																																																																																			.	.		0.502	BCAP31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061071.1	NM_005745	
INADL	10207	hgsc.bcm.edu	37	1	62586958	62586958	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:62586958delA	ENST00000371158.2	+	38	5110	c.4996delA	c.(4996-4998)aaafs	p.K1666fs	INADL_ENST00000472512.1_3'UTR	NM_176877.2	NP_795352	Q8NI35	INADL_HUMAN	InaD-like (Drosophila)	1666					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						TCCTTCCCAGAAAAATTCAGG	0.408																																					p.Q1665fs		Atlas-INDEL	.											.	INADL	179	.	0			c.4995delG						.			1,3747		0,1,1873	66.0	69.0	68.0			-5.0	0.0	1		69	0,7928		0,0,3964	no	frameshift	INADL	NM_176877.2		0,1,5837	A1A1,A1R,RR		0.0,0.0267,0.0086			62586958	1,11675	1946	4153	6099	SO:0001589	frameshift_variant	10207	exon38			.	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.4996delA	chr1.hg19:g.62586958delA	ENSP00000360200:p.Lys1666fs	219.0	0.0		159.0	11.0	NM_176877	O15249|O43742|O60833|Q5VUA5|Q5VUA6|Q5VUA7|Q5VUA8|Q5VUA9|Q5VUB0|Q8WU78|Q9H3N9	Frame_Shift_Del	DEL	ENST00000371158.2	hg19	CCDS617.2																																																																																			.	.		0.408	INADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023639.2	NM_170605	
HAMP	57817	hgsc.bcm.edu	37	19	35775716	35775716	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:35775716delC	ENST00000598398.1	+	3	411	c.115delC	c.(115-117)cccfs	p.P39fs	HAMP_ENST00000222304.3_Frame_Shift_Del_p.P39fs	NM_021175.2	NP_066998.1	P81172	HEPC_HUMAN	hepcidin antimicrobial peptide	39					cellular iron ion homeostasis (GO:0006879)|defense response to bacterium (GO:0042742)|defense response to fungus (GO:0050832)|immune response (GO:0006955)|killing of cells of other organism (GO:0031640)	apical cortex (GO:0045179)|extracellular region (GO:0005576)				breast(1)|central_nervous_system(1)|large_intestine(1)|lung(1)	4	all_lung(56;2.37e-08)|Lung NSC(56;3.66e-08)|Esophageal squamous(110;0.162)		Epithelial(14;7.4e-20)|OV - Ovarian serous cystadenocarcinoma(14;6.47e-19)|all cancers(14;4.17e-17)|LUSC - Lung squamous cell carcinoma(66;0.0417)			AGAGCTGCAACCCCAGGACAG	0.637																																					p.Q38fs		Atlas-INDEL	.											.	HAMP	14	.	0			c.114delA						.						87.0	85.0	85.0					19																	35775716		2203	4300	6503	SO:0001589	frameshift_variant	57817	exon2			.	AF309489	CCDS12454.1	19q13.1	2014-09-17				ENSG00000105697			15598	protein-coding gene	gene with protein product		606464				11034317, 11113132	Standard	NM_021175		Approved	LEAP-1, HEPC, HFE2B, LEAP1	uc002nyw.3	P81172		ENST00000598398.1:c.115delC	chr19.hg19:g.35775716delC	ENSP00000471894:p.Pro39fs	205.0	0.0		156.0	14.0	NM_021175	Q1HE14|Q9BY68	Frame_Shift_Del	DEL	ENST00000598398.1	hg19	CCDS12454.1																																																																																			.	.		0.637	HAMP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466067.1	NM_021175	
NEK5	341676	hgsc.bcm.edu	37	13	52650224	52650224	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	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	162.0	0.0		171.0	11.0	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	
ILF3	3609	hgsc.bcm.edu	37	19	10798146	10798146	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:10798146delA	ENST00000590261.1	+	17	2184	c.2184delA	c.(2182-2184)ccafs	p.P728fs	ILF3_ENST00000449870.1_Frame_Shift_Del_p.P732fs|ILF3_ENST00000318511.3_Frame_Shift_Del_p.P728fs|ILF3_ENST00000588657.1_Frame_Shift_Del_p.P732fs			Q12906	ILF3_HUMAN	interleukin enhancer binding factor 3, 90kDa	728	Interaction with PRMT1.				defense response to virus (GO:0051607)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translation (GO:0017148)|negative regulation of viral genome replication (GO:0045071)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(9)|ovary(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	31			Epithelial(33;6.86e-06)|all cancers(31;1.65e-05)			CGGTGCCCCCAAAACACGCTG	0.647																																					p.P732fs		Atlas-INDEL	.											.	ILF3	99	.	0			c.2195delC						.						32.0	31.0	32.0					19																	10798146		2203	4299	6502	SO:0001589	frameshift_variant	3609	exon18			.	U10324	CCDS12246.1, CCDS12247.1, CCDS45965.1, CCDS45966.1, CCDS45967.1	19p13.2	2012-08-10	2002-08-29		ENSG00000129351	ENSG00000129351			6038	protein-coding gene	gene with protein product	"""M-phase phosphoprotein 4"""	603182	"""interleukin enhancer binding factor 3, 90kD"""			7519613, 8885239	Standard	NM_012218		Approved	NF90, MPHOSPH4, MPP4, DRBP76, NFAR-1	uc002mpo.3	Q12906		ENST00000590261.1:c.2184delA	chr19.hg19:g.10798146delA	ENSP00000468156:p.Pro728fs	182.0	0.0		146.0	11.0	NM_017620	A8K6F2|G5E9M5|O43409|Q6P1X1|Q86XY7|Q99544|Q99545|Q9BZH4|Q9BZH5|Q9NQ95|Q9NQ96|Q9NQ97|Q9NQ98|Q9NQ99|Q9NQA0|Q9NQA1|Q9NQA2|Q9NRN2|Q9NRN3|Q9NRN4|Q9UMZ9|Q9UN00|Q9UN84|Q9UNA2	Frame_Shift_Del	DEL	ENST00000590261.1	hg19	CCDS12246.1																																																																																			.	.		0.647	ILF3-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452074.1		
UBXN4	23190	hgsc.bcm.edu	37	2	136540331	136540331	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:136540331delA	ENST00000272638.9	+	13	1712	c.1401delA	c.(1399-1401)agafs	p.R467fs	UBXN4_ENST00000490163.1_3'UTR	NM_014607.3	NP_055422.1	Q92575	UBXN4_HUMAN	UBX domain protein 4	467					response to unfolded protein (GO:0006986)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleus (GO:0005634)				NS(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	24						AACCAGTGAGAAAAAGAGTGC	0.383																																					p.R467fs		Atlas-INDEL	.											.	UBXN4	54	.	0			c.1400delG						.						167.0	169.0	168.0					2																	136540331		1822	4080	5902	SO:0001589	frameshift_variant	23190	exon13			.	D87684	CCDS42761.1	2q21.3-q22.1	2008-07-25	2008-07-25	2008-07-25	ENSG00000144224	ENSG00000144224		"""UBX domain containing"""	14860	protein-coding gene	gene with protein product	"""erasin"""	611216	"""UBX domain-containing 2"", ""UBX domain containing 2"""	UBXDC1, UBXD2		16968747	Standard	NM_014607		Approved	KIAA0242	uc002tur.3	Q92575	OTTHUMG00000153577	ENST00000272638.9:c.1401delA	chr2.hg19:g.136540331delA	ENSP00000272638:p.Arg467fs	163.0	0.0		128.0	10.0	NM_014607	A8K9W4|Q4ZG56|Q8IYM5	Frame_Shift_Del	DEL	ENST00000272638.9	hg19	CCDS42761.1																																																																																			.	.		0.383	UBXN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331696.1	NM_014607	
CHD6	84181	hgsc.bcm.edu	37	20	40033271	40033271	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr20:40033271delC	ENST00000373233.3	-	37	8287	c.8110delG	c.(8110-8112)gagfs	p.E2704fs	CHD6_ENST00000480022.1_5'UTR	NM_032221.3	NP_115597.3	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6	2704					ATP catabolic process (GO:0006200)|chromatin modification (GO:0016568)|positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0036091)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|transcription cofactor binding (GO:0001221)			breast(8)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(24)|lung(53)|ovary(8)|prostate(5)|skin(8)|stomach(1)|urinary_tract(9)	129		Myeloproliferative disorder(115;0.00425)				AGTGCCCCCTCCCCAGCCTGT	0.493																																					p.E2704fs		Atlas-INDEL	.											.	CHD6	312	.	0			c.8111delA						.						109.0	119.0	116.0					20																	40033271		2203	4300	6503	SO:0001589	frameshift_variant	84181	exon37			.	AF525085	CCDS13317.1	20q12	2003-03-07			ENSG00000124177	ENSG00000124177			19057	protein-coding gene	gene with protein product						11889561	Standard	NM_032221		Approved	KIAA1335, FLJ22369, dJ620E11.1, CHD5, RIGB	uc002xka.1	Q8TD26	OTTHUMG00000032487	ENST00000373233.3:c.8110delG	chr20.hg19:g.40033271delC	ENSP00000362330:p.Glu2704fs	194.0	0.0		152.0	10.0	NM_032221	Q5JYQ0|Q5TGZ9|Q5TH00|Q5TH01|Q8IZR2|Q8WTY0|Q9H4H6|Q9H6D4|Q9NTT7|Q9P2L1	Frame_Shift_Del	DEL	ENST00000373233.3	hg19	CCDS13317.1																																																																																			.	.		0.493	CHD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079270.1		
TOX2	84969	hgsc.bcm.edu	37	20	42694668	42694668	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr20:42694668delC	ENST00000358131.5	+	6	1431	c.1223delC	c.(1222-1224)gccfs	p.A408fs	TOX2_ENST00000435864.2_3'UTR|TOX2_ENST00000341197.4_Frame_Shift_Del_p.A426fs|TOX2_ENST00000372999.1_Frame_Shift_Del_p.A384fs|TOX2_ENST00000423191.2_Frame_Shift_Del_p.A384fs	NM_001098798.1	NP_001092268.1	Q96NM4	TOX2_HUMAN	TOX high mobility group box family member 2	408	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)			ATGTCCCCAGCCCCCCAGCCC	0.682																																					p.A426fs		Atlas-INDEL	.											.	TOX2	158	.	0			c.1276delG						.						16.0	18.0	17.0					20																	42694668		2199	4290	6489	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.1223delC	chr20.hg19:g.42694668delC	ENSP00000350849:p.Ala408fs	276.0	0.0		213.0	16.0	NM_001098797	A8K1J1|E1P5X0|G3XAC7|Q5TE33|Q5TE34|Q5TE35|Q96IC9|Q9BQN5	Frame_Shift_Del	DEL	ENST00000358131.5	hg19	CCDS42875.1																																																																																			.	.		0.682	TOX2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079329.2		
PRPF8	10594	hgsc.bcm.edu	37	17	1554134	1554134	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:1554134delC	ENST00000572621.1	-	42	7235	c.6970delG	c.(6970-6972)gagfs	p.E2324fs	PRPF8_ENST00000304992.6_Frame_Shift_Del_p.E2324fs|RILP_ENST00000301336.6_5'Flank|PRPF8_ENST00000575116.1_5'Flank			Q6P2Q9	PRP8_HUMAN	pre-mRNA processing factor 8	2324	Required for interaction with EFTUD2 and SNRNP200.				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)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|U5 snRNP (GO:0005682)	poly(A) RNA binding (GO:0044822)|U5 snRNA binding (GO:0030623)|U6 snRNA binding (GO:0017070)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(13)|lung(24)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(3)	77				UCEC - Uterine corpus endometrioid carcinoma (25;0.0855)		GAGTAAACCTCCCCCTCCTGC	0.592																																					p.E2324fs		Atlas-INDEL	.											.	PRPF8	169	.	0			c.6971delA						.						137.0	111.0	120.0					17																	1554134		2203	4300	6503	SO:0001589	frameshift_variant	10594	exon43			.	AB007510	CCDS11010.1	17p13.3	2013-07-16	2013-06-10		ENSG00000174231	ENSG00000174231			17340	protein-coding gene	gene with protein product		607300	"""PRP8 pre-mRNA processing factor 8 homolog (yeast)"", ""PRP8 pre-mRNA processing factor 8 homolog (S. cerevisiae)"""	RP13		11468273, 10411133	Standard	NM_006445		Approved	PRPC8, Prp8, hPrp8, SNRNP220	uc002fte.3	Q6P2Q9	OTTHUMG00000090553	ENST00000572621.1:c.6970delG	chr17.hg19:g.1554134delC	ENSP00000460348:p.Glu2324fs	131.0	0.0		126.0	11.0	NM_006445	O14547|O75965	Frame_Shift_Del	DEL	ENST00000572621.1	hg19	CCDS11010.1																																																																																			.	.		0.592	PRPF8-002	NOVEL	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438412.2		
OR4C46	119749	hgsc.bcm.edu	37	11	51515445	51515445	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:51515445delC	ENST00000328188.1	+	1	164	c.164delC	c.(163-165)tccfs	p.S55fs		NM_001004703.1	NP_001004703.1	A6NHA9	O4C46_HUMAN	olfactory receptor, family 4, subfamily C, member 46	55						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(5)|large_intestine(5)|lung(31)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)	48						TCACTGGGGTCCCCCATGTAC	0.448																																					p.S55fs		Atlas-INDEL	.											.	OR4C46	96	.	0			c.163delT						.						232.0	227.0	229.0					11																	51515445		2201	4296	6497	SO:0001589	frameshift_variant	119749	exon1			.		CCDS73288.1	11p11.12	2012-08-09			ENSG00000185926	ENSG00000185926		"""GPCR / Class A : Olfactory receptors"""	31271	protein-coding gene	gene with protein product		614273					Standard	NM_001004703		Approved		uc010ric.2	A6NHA9	OTTHUMG00000166705	ENST00000328188.1:c.164delC	chr11.hg19:g.51515445delC	ENSP00000329056:p.Ser55fs	301.0	0.0		199.0	13.0	NM_001004703		Frame_Shift_Del	DEL	ENST00000328188.1	hg19	CCDS31498.1																																																																																			.	.		0.448	OR4C46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391155.1	NM_001004703	
TMEM102	284114	hgsc.bcm.edu	37	17	7340045	7340045	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:7340045delA	ENST00000323206.1	+	3	1020	c.747delA	c.(745-747)ccafs	p.P249fs	RP11-104H15.9_ENST00000570444.1_RNA|FGF11_ENST00000575235.1_5'Flank|RP11-104H15.7_ENST00000575310.1_RNA|TMEM102_ENST00000396568.1_Frame_Shift_Del_p.P249fs|RP11-104H15.8_ENST00000576615.1_RNA|RP11-104H15.10_ENST00000575331.1_RNA|FGF11_ENST00000293829.4_5'Flank	NM_178518.2	NP_848613.1	Q8N9M5	TM102_HUMAN	transmembrane protein 102	249					apoptotic process (GO:0006915)|positive regulation of cell adhesion (GO:0045785)|positive regulation of T cell chemotaxis (GO:0010820)|positive regulation of T cell migration (GO:2000406)|regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901028)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to cytokine (GO:0034097)|signal transduction (GO:0007165)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|protein complex (GO:0043234)				kidney(1)|lung(3)|skin(1)	5		Prostate(122;0.173)				GCCCAGTCCCAAAGCCGTCGG	0.612																																					p.P249fs		Atlas-INDEL	.											.	TMEM102	11	.	0			c.746delC						.						77.0	80.0	79.0					17																	7340045		2203	4300	6503	SO:0001589	frameshift_variant	284114	exon3			.	AK094197	CCDS11104.1	17p13.1	2008-04-21			ENSG00000181284	ENSG00000181284			26722	protein-coding gene	gene with protein product		613936				12477932	Standard	NM_178518		Approved	FLJ36878	uc002ggx.1	Q8N9M5	OTTHUMG00000132901	ENST00000323206.1:c.747delA	chr17.hg19:g.7340045delA	ENSP00000315387:p.Pro249fs	212.0	0.0		161.0	10.0	NM_178518	D3DTP8	Frame_Shift_Del	DEL	ENST00000323206.1	hg19	CCDS11104.1																																																																																			.	.		0.612	TMEM102-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256405.1	NM_178518	
CC2D1A	54862	hgsc.bcm.edu	37	19	14024365	14024365	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:14024365delC	ENST00000318003.7	+	6	903	c.662delC	c.(661-663)gccfs	p.A221fs	CC2D1A_ENST00000589606.1_Frame_Shift_Del_p.A221fs	NM_017721.4	NP_060191.3	Q6P1N0	C2D1A_HUMAN	coiled-coil and C2 domain containing 1A	221	Pro-rich.				positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(12)|prostate(2)|skin(2)	27			OV - Ovarian serous cystadenocarcinoma(19;3.49e-23)			ATCGCGTCAGCCCCAGAGCCC	0.677																																					p.A221fs		Atlas-INDEL	.											.	CC2D1A	67	.	0			c.661delG						.						30.0	38.0	35.0					19																	14024365		1964	4121	6085	SO:0001589	frameshift_variant	54862	exon6			.	AF536205	CCDS42512.1	19p13.12	2007-01-08				ENSG00000132024			30237	protein-coding gene	gene with protein product	"""mental retardation, nonsyndromic, autosomal recessive, 3"""	610055				12761501, 16033914	Standard	NM_017721		Approved	FLJ20241, MRT3	uc002mxo.2	Q6P1N0		ENST00000318003.7:c.662delC	chr19.hg19:g.14024365delC	ENSP00000313601:p.Ala221fs	217.0	0.0		155.0	10.0	NM_017721	Q7Z435|Q86XV0|Q8NF89|Q9H603|Q9NXI1	Frame_Shift_Del	DEL	ENST00000318003.7	hg19	CCDS42512.1																																																																																			.	.		0.677	CC2D1A-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457954.1	NM_017721	
KATNAL1	84056	hgsc.bcm.edu	37	13	30814622	30814622	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr13:30814622delA	ENST00000380615.3	-	6	868	c.701delT	c.(700-702)ttcfs	p.F234fs	KATNAL1_ENST00000380617.3_Frame_Shift_Del_p.F234fs	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)		AATCCCTTTGAAAAAGTCAGG	0.398																																					p.F234fs		Atlas-INDEL	.											.	KATNAL1	53	.	0			c.702delC						.						114.0	106.0	109.0					13																	30814622		2203	4300	6503	SO:0001589	frameshift_variant	84056	exon6			.	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.701delT	chr13.hg19:g.30814622delA	ENSP00000369989:p.Phe234fs	139.0	0.0		147.0	10.0	NM_001014380		Frame_Shift_Del	DEL	ENST00000380615.3	hg19	CCDS31956.1																																																																																			.	.		0.398	KATNAL1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044346.2	NM_032116	
KCND2	3751	hgsc.bcm.edu	37	7	120372995	120372995	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:120372995delT	ENST00000331113.4	+	2	2119	c.1154delT	c.(1153-1155)attfs	p.I385fs		NM_012281.2	NP_036413.1	Q9NZV8	KCND2_HUMAN	potassium voltage-gated channel, Shal-related subfamily, member 2	385					action potential (GO:0001508)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	dendritic spine (GO:0043197)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	A-type (transient outward) potassium channel activity (GO:0005250)|metal ion binding (GO:0046872)|voltage-gated potassium channel activity (GO:0005249)			NS(2)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(11)|lung(35)|ovary(3)|pancreas(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	75	all_neural(327;0.117)				Amitriptyline(DB00321)|Dalfampridine(DB06637)|Disopyramide(DB00280)|Imipramine(DB00458)	GCAGGGAAGATTTTTGGTTCT	0.398																																					p.I385fs		Atlas-INDEL	.											.	KCND2	194	.	0			c.1153delA						.						177.0	161.0	166.0					7																	120372995		2203	4300	6503	SO:0001589	frameshift_variant	3751	exon2			.	AJ010969	CCDS5776.1	7q31	2012-07-05			ENSG00000184408	ENSG00000184408		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6238	protein-coding gene	gene with protein product		605410				10551270, 16382104	Standard	NM_012281		Approved	Kv4.2, RK5, KIAA1044	uc003vjj.1	Q9NZV8	OTTHUMG00000156989	ENST00000331113.4:c.1154delT	chr7.hg19:g.120372995delT	ENSP00000333496:p.Ile385fs	291.0	0.0		264.0	18.0	NM_012281	O95012|O95021|Q2TBD3|Q9UBY7|Q9UN98|Q9UNH9	Frame_Shift_Del	DEL	ENST00000331113.4	hg19	CCDS5776.1																																																																																			.	.		0.398	KCND2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346996.1	NM_012281	
HERC1	8925	hgsc.bcm.edu	37	15	63999002	63999002	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:63999002delA	ENST00000443617.2	-	25	4700	c.4613delT	c.(4612-4614)ttgfs	p.L1538fs	RP11-317G6.1_ENST00000559303.2_RNA	NM_003922.3	NP_003913.3	Q15751	HERC1_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	1538					cerebellar Purkinje cell differentiation (GO:0021702)|negative regulation of autophagy (GO:0010507)|neuromuscular process controlling balance (GO:0050885)|neuron projection development (GO:0031175)|positive regulation of GTPase activity (GO:0043547)|transport (GO:0006810)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(3)|breast(9)|central_nervous_system(4)|endometrium(23)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(22)|liver(1)|lung(36)|ovary(7)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	132						AGATGCTGCCAAATCCAAATC	0.274																																					p.L1538fs		Atlas-INDEL	.											.	HERC1	624	.	0			c.4614delG						.						33.0	30.0	31.0					15																	63999002		1775	3950	5725	SO:0001589	frameshift_variant	8925	exon25			.	U50078	CCDS45277.1	15q22	2013-01-10	2012-02-23			ENSG00000103657		"""WD repeat domain containing"""	4867	protein-coding gene	gene with protein product		605109	"""hect (homologous to the E6-AP (UBE3A) carboxyl terminus) domain and RCC1 (CHC1)-like domain (RLD) 1"""			8861955, 9233772	Standard	NM_003922		Approved	p532, p619	uc002amp.3	Q15751		ENST00000443617.2:c.4613delT	chr15.hg19:g.63999002delA	ENSP00000390158:p.Leu1538fs	189.0	0.0		198.0	12.0	NM_003922	Q8IW65	Frame_Shift_Del	DEL	ENST00000443617.2	hg19	CCDS45277.1																																																																																			.	.		0.274	HERC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418523.1	NM_003922	
OR52B6	340980	hgsc.bcm.edu	37	11	5602667	5602667	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:5602667delT	ENST00000345043.2	+	1	561	c.561delT	c.(559-561)tatfs	p.Y187fs	HBG2_ENST00000380259.2_Intron|AC015691.13_ENST00000394793.2_RNA	NM_001005162.2	NP_001005162.2	Q8NGF0	O52B6_HUMAN	olfactory receptor, family 52, subfamily B, member 6	187						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(2)|lung(7)|ovary(1)|prostate(1)	12		Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)		Epithelial(150;3.56e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		ACCTGCACTATTGCCAGATCA	0.478																																					p.Y187fs		Atlas-INDEL	.											.	OR52B6	37	.	0			c.560delA						.						196.0	201.0	199.0					11																	5602667		2185	4289	6474	SO:0001589	frameshift_variant	340980	exon1			.	AB065858	CCDS41611.1	11p15.4	2012-08-09			ENSG00000187747	ENSG00000187747		"""GPCR / Class A : Olfactory receptors"""	15211	protein-coding gene	gene with protein product							Standard	NM_001005162		Approved		uc010qzi.2	Q8NGF0	OTTHUMG00000066906	ENST00000345043.2:c.561delT	chr11.hg19:g.5602667delT	ENSP00000341581:p.Tyr187fs	201.0	0.0		152.0	10.0	NM_001005162	Q6IFI7	Frame_Shift_Del	DEL	ENST00000345043.2	hg19	CCDS41611.1																																																																																			.	.		0.478	OR52B6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143397.1	NM_001005162	
TACC2	10579	hgsc.bcm.edu	37	10	123985931	123985931	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:123985931delT	ENST00000369005.1	+	13	7999	c.7659delT	c.(7657-7659)actfs	p.T2553fs	TACC2_ENST00000369000.1_Frame_Shift_Del_p.T253fs|TACC2_ENST00000368999.1_Frame_Shift_Del_p.T643fs|TACC2_ENST00000358010.1_Frame_Shift_Del_p.T699fs|TACC2_ENST00000360561.3_Frame_Shift_Del_p.T631fs|TACC2_ENST00000515603.1_Frame_Shift_Del_p.T2508fs|TACC2_ENST00000369001.1_Frame_Shift_Del_p.T257fs|TACC2_ENST00000334433.3_Frame_Shift_Del_p.T2553fs|TACC2_ENST00000369004.3_Frame_Shift_Del_p.T643fs|TACC2_ENST00000513429.1_Frame_Shift_Del_p.T699fs|TACC2_ENST00000453444.2_Frame_Shift_Del_p.T2557fs|TACC2_ENST00000515273.1_Frame_Shift_Del_p.T2557fs|TACC2_ENST00000260733.3_Frame_Shift_Del_p.T631fs	NM_206862.2	NP_996744.2	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing protein 2	2553					astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of microtubule-based process (GO:0032886)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	nuclear hormone receptor binding (GO:0035257)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(15)|lung(27)|ovary(6)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	83		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)				TGTTTGACACTTCTCAGGAGA	0.522																																					p.T2553fs		Atlas-INDEL	.											.	TACC2	271	.	0			c.7658delC						.						160.0	124.0	136.0					10																	123985931		2203	4300	6503	SO:0001589	frameshift_variant	10579	exon13			.	AF095791	CCDS7625.1, CCDS7626.1, CCDS7627.1, CCDS7628.1	10q26	2008-07-29			ENSG00000138162	ENSG00000138162			11523	protein-coding gene	gene with protein product		605302				14767476	Standard	XM_005269388		Approved	AZU-1	uc001lfv.3	O95359	OTTHUMG00000019181	ENST00000369005.1:c.7659delT	chr10.hg19:g.123985931delT	ENSP00000358001:p.Thr2553fs	224.0	0.0		145.0	10.0	NM_206862	Q4VXL0|Q4VXL3|Q4VXL6|Q4VXL7|Q5U5T7|Q86WG6|Q86WG7|Q8TCK9|Q9BVQ1|Q9NZ41|Q9NZR5	Frame_Shift_Del	DEL	ENST00000369005.1	hg19	CCDS7626.1																																																																																			.	.		0.522	TACC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090004.1		
UBE3B	89910	hgsc.bcm.edu	37	12	109921448	109921448	+	Frame_Shift_Del	DEL	G	G	-	rs139172208		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:109921448delG	ENST00000342494.3	+	3	687	c.92delG	c.(91-93)cggfs	p.R31fs	UBE3B_ENST00000434735.2_Frame_Shift_Del_p.R31fs|UBE3B_ENST00000536398.1_Frame_Shift_Del_p.R31fs|UBE3B_ENST00000537063.1_Frame_Shift_Del_p.R31fs|UBE3B_ENST00000280774.5_Frame_Shift_Del_p.R31fs|UBE3B_ENST00000540230.1_Frame_Shift_Del_p.R31fs|UBE3B_ENST00000340074.5_Frame_Shift_Del_p.R31fs	NM_130466.3	NP_569733.2	Q7Z3V4	UBE3B_HUMAN	ubiquitin protein ligase E3B	31	IQ. {ECO:0000255|PROSITE- ProRule:PRU00116}.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.R31Q(1)		NS(1)|breast(3)|endometrium(6)|kidney(4)|large_intestine(7)|lung(20)|ovary(2)|urinary_tract(2)	45						GAACGGGAGCGGGCAGCTGTT	0.532																																					p.R31fs		Atlas-INDEL	.											.	UBE3B	116	.	1	Substitution - Missense(1)	endometrium(1)	c.91delC						.						161.0	151.0	155.0					12																	109921448		2203	4300	6503	SO:0001589	frameshift_variant	89910	exon3			.	BC032301	CCDS9129.1, CCDS58277.1	12q24.12	2004-03-02			ENSG00000151148	ENSG00000151148			13478	protein-coding gene	gene with protein product		608047					Standard	NM_130466		Approved		uc001toq.4	Q7Z3V4	OTTHUMG00000169254	ENST00000342494.3:c.92delG	chr12.hg19:g.109921448delG	ENSP00000340596:p.Arg31fs	191.0	0.0		208.0	13.0	NM_001270451	A5D8Z3|Q05BX9|Q659F7|Q7Z7Q1|Q9BXZ4	Frame_Shift_Del	DEL	ENST00000342494.3	hg19	CCDS9129.1																																																																																			.	.		0.532	UBE3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403119.1	NM_183415	
ATP2C1	27032	hgsc.bcm.edu	37	3	130694322	130694322	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:130694322delG	ENST00000510168.1	+	18	2110	c.1560delG	c.(1558-1560)gcgfs	p.A520fs	ATP2C1_ENST00000508532.1_Frame_Shift_Del_p.A520fs|ATP2C1_ENST00000507488.2_Frame_Shift_Del_p.A504fs|ATP2C1_ENST00000504948.1_Frame_Shift_Del_p.A504fs|ATP2C1_ENST00000328560.8_Frame_Shift_Del_p.A520fs|ATP2C1_ENST00000422190.2_Frame_Shift_Del_p.A520fs|ATP2C1_ENST00000359644.3_Frame_Shift_Del_p.A520fs|ATP2C1_ENST00000513801.1_Frame_Shift_Del_p.A504fs|ATP2C1_ENST00000533801.2_Frame_Shift_Del_p.A515fs|ATP2C1_ENST00000393221.4_Frame_Shift_Del_p.A554fs|ATP2C1_ENST00000504381.1_Frame_Shift_Del_p.A465fs|ATP2C1_ENST00000428331.2_Frame_Shift_Del_p.A520fs|ATP2C1_ENST00000505330.1_Frame_Shift_Del_p.A504fs			P98194	AT2C1_HUMAN	ATPase, Ca++ transporting, type 2C, member 1	520					actin cytoskeleton reorganization (GO:0031532)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|calcium-dependent cell-cell adhesion (GO:0016339)|cellular calcium ion homeostasis (GO:0006874)|cellular manganese ion homeostasis (GO:0030026)|epidermis development (GO:0008544)|Golgi calcium ion homeostasis (GO:0032468)|Golgi calcium ion transport (GO:0032472)|ion transmembrane transport (GO:0034220)|manganese ion transmembrane transport (GO:0071421)|manganese ion transport (GO:0006828)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)|transmembrane transport (GO:0055085)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calcium-transporting ATPase activity (GO:0005388)|manganese ion binding (GO:0030145)|manganese-transporting ATPase activity (GO:0015410)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(15)|prostate(2)|skin(2)|urinary_tract(1)	39					Desflurane(DB01189)|Enflurane(DB00228)|Halothane(DB01159)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)	TGGGCTCAGCGGGACTCAGAG	0.478									Hailey-Hailey disease																												p.A554fs	Esophageal Squamous(99;456 1443 27647 34099 42636)	Atlas-INDEL	.											.	ATP2C1	94	.	0			c.1661delC						.						89.0	78.0	82.0					3																	130694322		2203	4300	6503	SO:0001589	frameshift_variant	27032	exon17	Familial Cancer Database	HHD, Familial Benign Chronic Pemphigus, Benign Familial Pemphigus	.	AF181120	CCDS33856.1, CCDS46912.1, CCDS46913.1, CCDS46914.1, CCDS56278.1, CCDS56279.1, CCDS56280.1, CCDS56281.1, CCDS75006.1	3q21.3	2012-10-22			ENSG00000017260	ENSG00000017260	3.6.3.8	"""ATPases / P-type"""	13211	protein-coding gene	gene with protein product	"""secretory pathway Ca2+/Mn2+ ATPase 1"", ""calcium-transporting ATPase type 2C member 1"""	604384	"""benign chronic pemphigus (Hailey-Hailey disease)"""	BCPM		10615129, 10767338	Standard	NM_001001485		Approved	KIAA1347, ATP2C1A, PMR1, SPCA1	uc011bli.2	P98194	OTTHUMG00000136802	ENST00000510168.1:c.1560delG	chr3.hg19:g.130694322delG	ENSP00000427461:p.Ala520fs	296.0	0.0		178.0	11.0	NM_001199181	B2RAT7|B4DSW3|B7Z3X9|G3XAH8|G8JLN9|O76005|Q86V72|Q86V73|Q8N6V1|Q8NCJ7	Frame_Shift_Del	DEL	ENST00000510168.1	hg19	CCDS46914.1																																																																																			.	.		0.478	ATP2C1-008	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356648.2	NM_001001486	
MR1	3140	hgsc.bcm.edu	37	1	181003146	181003146	+	Start_Codon_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:181003146delG	ENST00000367580.5	+	0	8				MR1_ENST00000367579.3_Start_Codon_Del|MR1_ENST00000434571.2_Start_Codon_Del|MR1_ENST00000438435.2_3'UTR|MR1_ENST00000282990.6_Start_Codon_Del	NM_001531.2	NP_001522.1	Q95460	HMR1_HUMAN	major histocompatibility complex, class I-related						antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|innate immune response (GO:0045087)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|signal transduction (GO:0007165)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|MHC class I protein complex (GO:0042612)	MHC class I receptor activity (GO:0032393)|peptide antigen binding (GO:0042605)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(2)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	18					Antithymocyte globulin(DB00098)	GAAGGACTATGGGGGAACTGA	0.488																																					p.M1fs	Colon(174;1412 1962 45296 46549 47110)	Atlas-INDEL	.											.	MR1	46	.	0			c.2delT						.						116.0	101.0	106.0					1																	181003146		2203	4300	6503	SO:0001582	initiator_codon_variant	3140	exon2			.	AF010446	CCDS1342.1, CCDS53440.1, CCDS53441.1, CCDS53442.1	1q25.3	2013-01-11	2003-03-05	2003-03-07	ENSG00000153029	ENSG00000153029		"""Immunoglobulin superfamily / C1-set domain containing"""	4975	protein-coding gene	gene with protein product		600764	"""major histocompatibility complex, class I-like sequence"""	HLALS		7624800, 9784382	Standard	NM_001194999		Approved		uc001goq.2	Q95460	OTTHUMG00000035175		chr1.hg19:g.181003146delG		174.0	0.0		173.0	13.0	NM_001195035	A8K2V9|B4E3B1|O97985|O97986|Q53GM1|Q95HB8|Q9MY23|Q9NPL2|Q9TQB3|Q9TQB9|Q9TQK3	Frame_Shift_Del	DEL	ENST00000367580.5	hg19	CCDS1342.1																																																																																			.	.		0.488	MR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085134.2	NM_001531	
OVOL2	58495	hgsc.bcm.edu	37	20	18022253	18022253	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr20:18022253delT	ENST00000278780.6	-	3	678	c.436delA	c.(436-438)agafs	p.R146fs	OVOL2_ENST00000483661.1_5'UTR	NM_021220.2	NP_067043.2	Q9BRP0	OVOL2_HUMAN	ovo-like zinc finger 2	146					angiogenesis (GO:0001525)|dorsal/ventral pattern formation (GO:0009953)|embryonic digestive tract morphogenesis (GO:0048557)|endocardium formation (GO:0060214)|heart looping (GO:0001947)|heart trabecula formation (GO:0060347)|labyrinthine layer blood vessel development (GO:0060716)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of keratinocyte differentiation (GO:0045617)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of transcription by competitive promoter binding (GO:0010944)|negative regulation of transcription, DNA-templated (GO:0045892)|neural crest cell migration (GO:0001755)|neural fold formation (GO:0001842)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell cycle (GO:0051726)|regulation of keratinocyte proliferation (GO:0010837)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|transcription regulatory region DNA binding (GO:0044212)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(3)	6						CACAGGTGTCTTTTCACCTGG	0.592																																					p.R146fs		Atlas-INDEL	.											.	OVOL2	18	.	0			c.437delG						.						148.0	93.0	112.0					20																	18022253		2203	4300	6503	SO:0001589	frameshift_variant	58495	exon3			.	AK022284	CCDS13132.1	20p11.23	2013-10-17	2013-10-17	2005-05-31	ENSG00000125850	ENSG00000125850		"""Zinc fingers, C2H2-type"""	15804	protein-coding gene	gene with protein product			"""zinc finger protein 339"", ""ovo-like 2 (Drosophila)"""	ZNF339			Standard	NM_021220		Approved	bA504H3.3, HOVO2	uc002wqi.1	Q9BRP0	OTTHUMG00000031960	ENST00000278780.6:c.436delA	chr20.hg19:g.18022253delT	ENSP00000278780:p.Arg146fs	189.0	0.0		145.0	10.0	NM_021220	Q5T8B4|Q9BX22|Q9HA54|Q9Y4M0	Frame_Shift_Del	DEL	ENST00000278780.6	hg19	CCDS13132.1																																																																																			.	.		0.592	OVOL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078148.5	NM_021220	
STOX1	219736	hgsc.bcm.edu	37	10	70646243	70646243	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:70646243delC	ENST00000298596.6	+	3	2774	c.2691delC	c.(2689-2691)ttcfs	p.F897fs	STOX1_ENST00000421961.2_Frame_Shift_Del_p.F787fs|STOX1_ENST00000399169.4_Frame_Shift_Del_p.F897fs|STOX1_ENST00000399162.2_Intron|STOX1_ENST00000399165.4_Intron	NM_152709.4	NP_689922.3	Q6ZVD7	STOX1_HUMAN	storkhead box 1	897						cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(5)|endometrium(2)|kidney(2)|large_intestine(5)|liver(2)|lung(8)|prostate(1)|skin(3)	28						GAAAACATTTCCCACAAAAGT	0.428																																					p.F897fs		Atlas-INDEL	.											.	STOX1	75	.	0			c.2690delT						.						65.0	68.0	67.0					10																	70646243		2082	4252	6334	SO:0001589	frameshift_variant	219736	exon3			.	AK057891	CCDS41535.1, CCDS44416.1, CCDS44417.1	10q22.1	2005-11-29	2005-04-04	2005-04-04	ENSG00000165730	ENSG00000165730			23508	protein-coding gene	gene with protein product		609397	"""chromosome 10 open reading frame 24"""	C10orf24			Standard	NM_152709		Approved	FLJ25162	uc001joq.3	Q6ZVD7	OTTHUMG00000018367	ENST00000298596.6:c.2691delC	chr10.hg19:g.70646243delC	ENSP00000298596:p.Phe897fs	135.0	0.0		112.0	10.0	NM_152709	A2A3Q9|A5D6Y7|B0QZA4|B0QZA5|B0QZA6|Q4F8Q6|Q5I946|Q5I947|Q5I948|Q5VX38|Q5VX39|Q6ZRY3|Q96LR3|Q96LS0	Frame_Shift_Del	DEL	ENST00000298596.6	hg19	CCDS41535.1																																																																																			.	.		0.428	STOX1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276849.3	NM_152709	
HS3ST5	222537	hgsc.bcm.edu	37	6	114378787	114378787	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:114378787delT	ENST00000312719.5	-	5	1863	c.675delA	c.(673-675)aaafs	p.K225fs	RP3-399L15.3_ENST00000519270.1_RNA|HS3ST5_ENST00000411826.1_Frame_Shift_Del_p.K225fs|RP3-399L15.3_ENST00000523087.1_RNA|RP3-399L15.3_ENST00000519104.1_RNA			Q8IZT8	HS3S5_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 5	225					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process, enzymatic modification (GO:0015015)|negative regulation of coagulation (GO:0050819)|protein sulfation (GO:0006477)|regulation of viral entry into host cell (GO:0046596)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	3'-phosphoadenosine 5'-phosphosulfate binding (GO:0050656)|[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity (GO:0008467)			breast(4)|endometrium(2)|kidney(1)|large_intestine(7)|lung(17)|ovary(1)|pancreas(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)	41		all_cancers(87;0.0587)|Colorectal(196;0.0676)|all_epithelial(87;0.154)		OV - Ovarian serous cystadenocarcinoma(136;0.00937)|all cancers(137;0.0117)|Epithelial(106;0.0274)|GBM - Glioblastoma multiforme(226;0.143)		CTGCTTTGTATTTTGTGTTCA	0.413																																					p.Y226fs		Atlas-INDEL	.											.	HS3ST5	80	.	0			c.676delT						.						285.0	284.0	284.0					6																	114378787		2203	4300	6503	SO:0001589	frameshift_variant	222537	exon2			.	AF503292	CCDS34517.1	6q21	2011-11-16			ENSG00000249853	ENSG00000249853		"""Sulfotransferases, membrane-bound"""	19419	protein-coding gene	gene with protein product		609407				12138164	Standard	NM_153612		Approved	3-OST-5	uc003pwg.4	Q8IZT8	OTTHUMG00000015412	ENST00000312719.5:c.675delA	chr6.hg19:g.114378787delT	ENSP00000427888:p.Lys225fs	401.0	0.0		330.0	21.0	NM_153612	A8K1J2|Q52LI2|Q8N285	Frame_Shift_Del	DEL	ENST00000312719.5	hg19	CCDS34517.1																																																																																			.	.		0.413	HS3ST5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041911.2	NM_153612	
NIN	51199	hgsc.bcm.edu	37	14	51233604	51233604	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr14:51233604delT	ENST00000382041.3	-	13	1629	c.1439delA	c.(1438-1440)aacfs	p.N480fs	NIN_ENST00000389868.3_Frame_Shift_Del_p.N480fs|NIN_ENST00000530997.2_Frame_Shift_Del_p.N480fs|NIN_ENST00000382043.4_Frame_Shift_Del_p.N480fs|NIN_ENST00000324330.9_Frame_Shift_Del_p.N480fs|NIN_ENST00000453196.1_Frame_Shift_Del_p.N480fs|NIN_ENST00000245441.5_Frame_Shift_Del_p.N480fs	NM_016350.4|NM_182946.1	NP_057434.4|NP_891991	Q8N4C6	NIN_HUMAN	ninein (GSK3B interacting protein)	480					centrosome localization (GO:0051642)|centrosome-templated microtubule nucleation (GO:0090222)|microtubule anchoring at centrosome (GO:0034454)	centriole (GO:0005814)|centrosome (GO:0005813)|microtubule (GO:0005874)|nucleolus (GO:0005730)|spindle pole (GO:0000922)	calcium ion binding (GO:0005509)|GTP binding (GO:0005525)			breast(4)|central_nervous_system(1)|cervix(2)|endometrium(10)|kidney(5)|large_intestine(13)|lung(16)|ovary(1)|pancreas(1)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5)	71	all_epithelial(31;0.00244)|Breast(41;0.127)					CAGACGACTGTTTTCCTGAAC	0.338			T	PDGFRB	MPD																																p.N480fs		Atlas-INDEL	.		Dom	yes		14	14q24	51199	ninein (GSK3B interacting protein)		L	.	NIN	475	.	0			c.1440delC						.						120.0	116.0	117.0					14																	51233604		2203	4298	6501	SO:0001589	frameshift_variant	51199	exon13			.	AF212162	CCDS32078.1, CCDS32079.1, CCDS32078.2	14q21-q22	2013-01-10			ENSG00000100503	ENSG00000100503		"""EF-hand domain containing"""	14906	protein-coding gene	gene with protein product		608684				11004522, 11162463	Standard	NM_020921		Approved		uc001wyi.3	Q8N4C6	OTTHUMG00000029569	ENST00000382041.3:c.1439delA	chr14.hg19:g.51233604delT	ENSP00000371472:p.Asn480fs	168.0	0.0		113.0	10.0	NM_020921	A6NDB8|B7WPA3|C9JSB6|C9JSG2|C9JXL2|Q5BKU3|Q6P0P6|Q9BWU6|Q9C012|Q9C013|Q9C014|Q9H5I6|Q9HAT7|Q9HBY5|Q9HCK7|Q9UH61	Frame_Shift_Del	DEL	ENST00000382041.3	hg19	CCDS32079.1																																																																																			.	.		0.338	NIN-016	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395207.2	NM_182946	
DNAH12	201625	hgsc.bcm.edu	37	3	57456205	57456205	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:57456205delA	ENST00000351747.2	-	16	2250	c.2070delT	c.(2068-2070)tttfs	p.F690fs	snoU13_ENST00000459308.1_RNA|DNAH12_ENST00000389536.4_Frame_Shift_Del_p.F690fs	NM_178504.4	NP_848599.3	Q6ZR08	DYH12_HUMAN	dynein, axonemal, heavy chain 12	690	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(3)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(4)|lung(7)|pancreas(1)|prostate(1)|skin(1)	25						AAACAAAATTAAAAAACTTCT	0.274																																					p.N691fs		Atlas-INDEL	.											.	DNAH12	182	.	0			c.2071delA						.						66.0	53.0	57.0					3																	57456205		692	1585	2277	SO:0001589	frameshift_variant	201625	exon16			.	U53532, AK126276	CCDS33771.1	3p21.1	2009-02-04	2006-09-04		ENSG00000174844	ENSG00000174844		"""Axonemal dyneins"""	2943	protein-coding gene	gene with protein product		603340	"""dynein, axonemal, heavy polypeptide 12"", ""dynein heavy chain domain 2"", ""dynein heavy domain 2"", ""dynein, axonemal, heavy chain 12-like"", ""dynein, axonemal, heavy chain 7-like"""	DNHD2, DNAH12L, DNAH7L		8812413, 8666668	Standard	NM_198564		Approved	DLP12, Dnahc3, HL-19, hdhc3, DHC3, FLJ40427, FLJ44290	uc003dit.2	Q6ZR08	OTTHUMG00000158598	ENST00000351747.2:c.2070delT	chr3.hg19:g.57456205delA	ENSP00000295937:p.Phe690fs	262.0	0.0		228.0	14.0	NM_178504	A6NGI2|Q6ZTR8|Q8N7R9|Q8WXK2|Q92816	Frame_Shift_Del	DEL	ENST00000351747.2	hg19																																																																																				.	.		0.274	DNAH12-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_178504	
TTC14	151613	hgsc.bcm.edu	37	3	180326508	180326508	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:180326508delA	ENST00000296015.4	+	11	1442	c.1310delA	c.(1309-1311)gaafs	p.E437fs	TTC14_ENST00000382584.4_Frame_Shift_Del_p.E437fs|TTC14_ENST00000412756.2_3'UTR|TTC14_ENST00000465625.1_3'UTR	NM_133462.3	NP_597719.1	Q96N46	TTC14_HUMAN	tetratricopeptide repeat domain 14	437							RNA binding (GO:0003723)			endometrium(3)|kidney(5)|large_intestine(9)|lung(24)|ovary(2)|pancreas(1)|skin(1)	45	all_cancers(143;9.31e-15)|Ovarian(172;0.0212)		OV - Ovarian serous cystadenocarcinoma(80;5.62e-23)|GBM - Glioblastoma multiforme(14;0.000558)			GAATTAAGAGAAAAACAAGCT	0.323																																					p.E437fs		Atlas-INDEL	.											.	TTC14	112	.	0			c.1309delG						.						20.0	21.0	20.0					3																	180326508		2198	4284	6482	SO:0001589	frameshift_variant	151613	exon11			.	AB075860	CCDS3237.1, CCDS46963.1, CCDS75055.1	3q27.2	2013-01-10			ENSG00000163728	ENSG00000163728		"""Tetratricopeptide (TTC) repeat domain containing"""	24697	protein-coding gene	gene with protein product						11853319	Standard	NM_001042601		Approved	FLJ00166, KIAA1980	uc003fkk.3	Q96N46	OTTHUMG00000157859	ENST00000296015.4:c.1310delA	chr3.hg19:g.180326508delA	ENSP00000296015:p.Glu437fs	239.0	0.0		183.0	11.0	NM_133462	G5E9X0|Q6UWJ7|Q8TF22	Frame_Shift_Del	DEL	ENST00000296015.4	hg19	CCDS3237.1																																																																																			.	.		0.323	TTC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349786.1	NM_133462	
KIF26B	55083	hgsc.bcm.edu	37	1	245775272	245775272	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:245775272delG	ENST00000407071.2	+	9	2532	c.2092delG	c.(2092-2094)gggfs	p.G699fs	KIF26B_ENST00000366518.4_Frame_Shift_Del_p.G318fs|RP11-522M21.2_ENST00000418402.1_RNA	NM_018012.3	NP_060482.2	Q2KJY2	KI26B_HUMAN	kinesin family member 26B	699	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				establishment of cell polarity (GO:0030010)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|ureteric bud invasion (GO:0072092)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(21)|ovary(4)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	51	all_cancers(71;3.86e-05)|all_epithelial(71;0.000121)|Ovarian(71;0.0412)|all_lung(81;0.0498)|Lung NSC(105;0.0708)|Breast(184;0.127)		OV - Ovarian serous cystadenocarcinoma(106;0.022)			GAGCGGGAAAGGGGGAAGTAA	0.577																																					p.K697fs		Atlas-INDEL	.											.	KIF26B	343	.	0			c.2091delA						.						52.0	60.0	57.0					1																	245775272		2074	4192	6266	SO:0001589	frameshift_variant	55083	exon9			.	AK001019	CCDS44342.1	1q44	2008-02-05			ENSG00000162849	ENSG00000162849		"""Kinesins"""	25484	protein-coding gene	gene with protein product		614026					Standard	NM_018012		Approved	FLJ10157	uc001ibf.1	Q2KJY2	OTTHUMG00000040079	ENST00000407071.2:c.2092delG	chr1.hg19:g.245775272delG	ENSP00000385545:p.Gly699fs	122.0	0.0		200.0	12.0	NM_018012	Q6ZQR9|Q6ZUZ0|Q8IUN3|Q8IVR1|Q9NWB4	Frame_Shift_Del	DEL	ENST00000407071.2	hg19	CCDS44342.1																																																																																			.	.		0.577	KIF26B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381037.1	XM_371354	
HIATL1	84641	hgsc.bcm.edu	37	9	97213759	97213759	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:97213759delA	ENST00000375344.3	+	8	1134	c.865delA	c.(865-867)aaafs	p.K289fs	HIATL1_ENST00000428393.2_Frame_Shift_Del_p.K224fs	NM_032558.2	NP_115947.2	Q5SR56	HIAL1_HUMAN	hippocampus abundant transcript-like 1	289					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			endometrium(1)|large_intestine(2)|lung(5)|ovary(2)|pancreas(1)	11		Acute lymphoblastic leukemia(62;0.136)				TGGATCTGTTAAAATTGCAGC	0.254																																					p.V288fs	Pancreas(77;1260 1915 1973 10423)	Atlas-INDEL	.											.	HIATL1	31	.	0			c.864delT						.						82.0	86.0	85.0					9																	97213759		2203	4300	6503	SO:0001589	frameshift_variant	84641	exon8			.	AK027659	CCDS6710.2	9q22.32	2009-12-04			ENSG00000148110	ENSG00000148110			23376	protein-coding gene	gene with protein product							Standard	XM_005252277		Approved	FLJ14753	uc004aur.3	Q5SR56	OTTHUMG00000020265	ENST00000375344.3:c.865delA	chr9.hg19:g.97213759delA	ENSP00000364493:p.Lys289fs	193.0	0.0		154.0	12.0	NM_032558	B4DUE6|E9PD58|Q3KQT4|Q53GU5|Q8WU95|Q96SM4	Frame_Shift_Del	DEL	ENST00000375344.3	hg19	CCDS6710.2																																																																																			.	.		0.254	HIATL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053184.1	NM_032558	
DENND2C	163259	hgsc.bcm.edu	37	1	115144134	115144134	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:115144134delA	ENST00000393274.1	-	13	2435	c.1810delT	c.(1810-1812)tcafs	p.S604fs	DENND2C_ENST00000393277.1_Frame_Shift_Del_p.S604fs|DENND2C_ENST00000481894.1_5'UTR|DENND2C_ENST00000393276.3_Frame_Shift_Del_p.S547fs	NM_001256404.1	NP_001243333.1	Q68D51	DEN2C_HUMAN	DENN/MADD domain containing 2C	604	DENN. {ECO:0000255|PROSITE- ProRule:PRU00304}.				positive regulation of Rab GTPase activity (GO:0032851)		Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(2)|breast(2)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(10)|pancreas(1)|skin(3)	37	all_epithelial(7;9.54e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		CTCACCTTTGAAAAAAGATTG	0.388																																					p.S604X		Atlas-INDEL	.											.	DENND2C	105	.	0			c.1811delC						.						215.0	230.0	225.0					1																	115144134		2203	4300	6503	SO:0001589	frameshift_variant	163259	exon13			.		CCDS875.1, CCDS58018.1	1p13.2-p13.1	2012-10-03			ENSG00000175984	ENSG00000175984		"""DENN/MADD domain containing"""	24748	protein-coding gene	gene with protein product							Standard	NM_198459		Approved	FLJ37099, DKFZp686G0351, DKFZp779P1149, dJ1156J9.1, RP5-1156J9.1	uc001efd.1	Q68D51	OTTHUMG00000011893	ENST00000393274.1:c.1810delT	chr1.hg19:g.115144134delA	ENSP00000376955:p.Ser604fs	374.0	0.0		259.0	16.0	NM_001256404	B1AL26|Q5TCX6|Q6P3R3	Frame_Shift_Del	DEL	ENST00000393274.1	hg19	CCDS58018.1																																																																																			.	.		0.388	DENND2C-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000314822.1	NM_198459	
CDC20B	166979	hgsc.bcm.edu	37	5	54424346	54424346	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:54424346delT	ENST00000381375.2	-	7	942	c.797delA	c.(796-798)aacfs	p.N266fs	CDC20B_ENST00000322374.6_Frame_Shift_Del_p.N266fs|CDC20B_ENST00000334206.5_Frame_Shift_Del_p.N266fs|CDC20B_ENST00000296733.1_Frame_Shift_Del_p.N266fs			Q86Y33	CD20B_HUMAN	cell division cycle 20B	266										kidney(1)|large_intestine(5)|lung(7)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	19		Lung NSC(810;0.000744)|Breast(144;0.159)|Prostate(74;0.194)	LUSC - Lung squamous cell carcinoma(15;0.225)			TAAGTCTATGTTTTCAATCCC	0.448																																					p.N266fs		Atlas-INDEL	.											.	CDC20B	61	.	0			c.798delC						.						160.0	162.0	161.0					5																	54424346		2203	4300	6503	SO:0001589	frameshift_variant	166979	exon7			.	AB086378	CCDS3966.1, CCDS47207.1, CCDS54852.1	5q11.2	2013-01-17	2013-01-17		ENSG00000164287	ENSG00000164287		"""WD repeat domain containing"""	24222	protein-coding gene	gene with protein product			"""CDC20 cell division cycle 20 homolog B (S. cerevisiae)"", ""cell division cycle 20 homolog B (S. cerevisiae)"""				Standard	NM_152623		Approved	FLJ37927	uc003jpo.2	Q86Y33	OTTHUMG00000131185	ENST00000381375.2:c.797delA	chr5.hg19:g.54424346delT	ENSP00000370781:p.Asn266fs	262.0	0.0		171.0	11.0	NM_001145734	B7WNV8|B9EGL8|C9J6X8|C9JHE9|C9JKL5|Q86Y31|Q86Y32|Q8IUZ8|Q8N1S1|Q8NG56	Frame_Shift_Del	DEL	ENST00000381375.2	hg19	CCDS54852.1																																																																																			.	.		0.448	CDC20B-004	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369715.1	NM_152623	
FAM160A2	84067	hgsc.bcm.edu	37	11	6245706	6245706	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:6245706delC	ENST00000449352.2	-	2	304	c.41delG	c.(40-42)ggcfs	p.G14fs	FAM160A2_ENST00000265978.4_Frame_Shift_Del_p.G14fs|FAM160A2_ENST00000524416.1_Frame_Shift_Del_p.G14fs			Q8N612	F16A2_HUMAN	family with sequence similarity 160, member A2	14					early endosome to late endosome transport (GO:0045022)|endosome organization (GO:0007032)|endosome to lysosome transport (GO:0008333)|lysosome organization (GO:0007040)|protein transport (GO:0015031)	FHF complex (GO:0070695)				NS(1)|endometrium(3)|kidney(2)|large_intestine(7)|liver(1)|lung(14)|ovary(2)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						GTGCCCAGGGCCCCGGGAGGC	0.597																																					p.G14fs		Atlas-INDEL	.											.	FAM160A2	100	.	0			c.42delC						.						72.0	68.0	69.0					11																	6245706		2201	4296	6497	SO:0001589	frameshift_variant	84067	exon2			.		CCDS7760.1, CCDS44530.1	11p15.4	2008-06-05	2008-06-05	2008-06-05	ENSG00000051009	ENSG00000051009			25378	protein-coding gene	gene with protein product			"""chromosome 11 open reading frame 56"""	C11orf56		11230166, 11214970	Standard	NM_001098794		Approved	FLJ22665, KIAA1759, DKFZP566M1046	uc001mck.4	Q8N612	OTTHUMG00000133379	ENST00000449352.2:c.41delG	chr11.hg19:g.6245706delC	ENSP00000416918:p.Gly14fs	209.0	0.0		160.0	11.0	NM_032127	Q9C0A4|Q9H0N3|Q9H624	Frame_Shift_Del	DEL	ENST00000449352.2	hg19	CCDS44530.1																																																																																			.	.		0.597	FAM160A2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000383759.1	NM_032127	
OSCP1	127700	hgsc.bcm.edu	37	1	36888410	36888410	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:36888410delA	ENST00000356637.5	-	7	801	c.738delT	c.(736-738)tttfs	p.F246fs	OSCP1_ENST00000495222.1_5'UTR|OSCP1_ENST00000433045.2_Frame_Shift_Del_p.F191fs|OSCP1_ENST00000235532.5_Frame_Shift_Del_p.F236fs|OSCP1_ENST00000315643.9_Frame_Shift_Del_p.F246fs			Q8WVF1	OSCP1_HUMAN	organic solute carrier partner 1	246					transport (GO:0006810)	plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|stomach(2)|urinary_tract(1)	22						CATAAAGTTCAAAAGAACCTT	0.388																																					p.E237fs		Atlas-INDEL	.											.	OSCP1	48	.	0			c.709delG						.						139.0	126.0	131.0					1																	36888410		2203	4300	6503	SO:0001589	frameshift_variant	127700	exon6			.		CCDS409.1, CCDS410.1, CCDS409.2	1p34.3	2009-07-06	2009-07-06	2009-07-06	ENSG00000116885	ENSG00000116885			29971	protein-coding gene	gene with protein product	"""oxidored nitro domain containing protein"""	608854	"""chromosome 1 open reading frame 102"""	C1orf102		12477932	Standard	NM_145047		Approved	NOR1	uc001caq.3	Q8WVF1	OTTHUMG00000008139	ENST00000356637.5:c.738delT	chr1.hg19:g.36888410delA	ENSP00000349052:p.Phe246fs	243.0	0.0		197.0	12.0	NM_145047	A6NHM5|A6NHS9|A6NIN9|Q4AEJ0|Q8N7G2|Q8TDF1	Frame_Shift_Del	DEL	ENST00000356637.5	hg19																																																																																				.	.		0.388	OSCP1-010	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000389759.1	NM_145047	
CDV3	55573	hgsc.bcm.edu	37	3	133306780	133306780	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:133306780delA	ENST00000264993.3	+	5	982	c.667delA	c.(667-669)aaafs	p.K223fs	CDV3_ENST00000508481.1_Frame_Shift_Del_p.K121fs|CDV3_ENST00000420115.2_3'UTR|CDV3_ENST00000515421.1_Intron	NM_001134422.1|NM_001282763.1|NM_017548.4	NP_001127894.1|NP_001269692.1|NP_060018.1	Q9UKY7	CDV3_HUMAN	CDV3 homolog (mouse)	223					cell proliferation (GO:0008283)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)				kidney(3)|lung(1)|prostate(1)	5						AGTAAGACACAAAAATAGAGG	0.358																																					p.H222fs		Atlas-INDEL	.											.	CDV3	22	.	0			c.666delC						.						75.0	83.0	81.0					3																	133306780		2201	4300	6501	SO:0001589	frameshift_variant	55573	exon5			.	AK096865	CCDS3079.1, CCDS46917.1, CCDS46918.1, CCDS75013.1, CCDS75014.1, CCDS75015.1	3q22.1	2008-02-05			ENSG00000091527	ENSG00000091527			26928	protein-coding gene	gene with protein product						10497265	Standard	NM_017548		Approved	H41	uc003epq.3	Q9UKY7	OTTHUMG00000159764	ENST00000264993.3:c.667delA	chr3.hg19:g.133306780delA	ENSP00000264993:p.Lys223fs	328.0	0.0		267.0	17.0	NM_017548	B3KUC2|Q96IP9	Frame_Shift_Del	DEL	ENST00000264993.3	hg19	CCDS3079.1																																																																																			.	.		0.358	CDV3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357203.1	NM_017548	
IGSF10	285313	hgsc.bcm.edu	37	3	151164709	151164709	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:151164709delC	ENST00000282466.3	-	4	3059	c.3060delG	c.(3058-3060)gggfs	p.G1020fs		NM_001178145.1|NM_001178146.1|NM_178822.4	NP_001171616.1|NP_001171617.1|NP_849144.2	Q6WRI0	IGS10_HUMAN	immunoglobulin superfamily, member 10	1020					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)	extracellular region (GO:0005576)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(24)|liver(4)|lung(43)|ovary(8)|prostate(4)|skin(9)|stomach(1)|urinary_tract(3)	116			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			TGATAATCCGCCCCCTTCCGC	0.473																																					p.R1021fs		Atlas-INDEL	.											.	IGSF10	279	.	0			c.3061delC						.						75.0	77.0	77.0					3																	151164709		2203	4300	6503	SO:0001589	frameshift_variant	285313	exon4			.	AY273815	CCDS3160.1	3q25.1	2013-01-11			ENSG00000152580	ENSG00000152580		"""Immunoglobulin superfamily / I-set domain containing"""	26384	protein-coding gene	gene with protein product						12477932	Standard	NM_178822		Approved	FLJ25972, CMF608	uc011bod.2	Q6WRI0	OTTHUMG00000159856	ENST00000282466.3:c.3060delG	chr3.hg19:g.151164709delC	ENSP00000282466:p.Gly1020fs	157.0	0.0		149.0	10.0	NM_178822	Q86YJ9|Q8N772|Q8NA84	Frame_Shift_Del	DEL	ENST00000282466.3	hg19	CCDS3160.1																																																																																			.	.		0.473	IGSF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357782.1	NM_178822	
PLEKHH3	79990	hgsc.bcm.edu	37	17	40823012	40823012	+	Splice_Site	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:40823012delT	ENST00000591022.1	-	9	1808	c.1421delA	c.(1420-1422)aac>ac	p.N474fs	PLEKHH3_ENST00000412503.1_Intron|PLEKHH3_ENST00000293349.6_Intron|PLEKHH3_ENST00000456950.2_Intron	NM_024927.4	NP_079203	Q7Z736	PKHH3_HUMAN	pleckstrin homology domain containing, family H (with MyTH4 domain) member 3	474	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				signal transduction (GO:0007165)	cytoskeleton (GO:0005856)|extracellular space (GO:0005615)				endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|prostate(2)|skin(2)	13		Breast(137;0.00116)		BRCA - Breast invasive adenocarcinoma(366;0.14)		GGACATTTACTTCTCAAACCT	0.632																																					.		Atlas-INDEL	.											.	PLEKHH3	49	.	0			c.1421+1A>-						.						56.0	64.0	61.0					17																	40823012		2125	4233	6358	SO:0001630	splice_region_variant	79990	exon10			.	BC052978	CCDS11434.1	17q21.2	2013-01-11				ENSG00000068137		"""Pleckstrin homology (PH) domain containing"""	26105	protein-coding gene	gene with protein product						12477932	Standard	NM_024927		Approved	FLJ21019	uc002iau.3	Q7Z736		ENST00000591022.1:c.1421+1A>-	chr17.hg19:g.40823012delT		193.0	0.0		159.0	10.0	NM_024927	C9JQ76|Q59H20|Q96B28|Q9H7D6|Q9NT18	Splice_Site	DEL	ENST00000591022.1	hg19	CCDS11434.1																																																																																			.	.		0.632	PLEKHH3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452332.1	NM_024927	Frame_Shift_Del
KIF15	56992	hgsc.bcm.edu	37	3	44816769	44816769	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:44816769delT	ENST00000326047.4	+	3	235	c.86delT	c.(85-87)gttfs	p.V29fs		NM_020242.2	NP_064627.1	Q9NS87	KIF15_HUMAN	kinesin family member 15	29	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic nuclear division (GO:0007067)	centrosome (GO:0005813)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|plus-end kinesin complex (GO:0005873)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|liver(2)|lung(9)|ovary(1)|prostate(4)|urinary_tract(5)	36				BRCA - Breast invasive adenocarcinoma(193;0.0099)|KIRC - Kidney renal clear cell carcinoma(197;0.0564)|Kidney(197;0.0707)		GCCATCAAAGTTTTTGTGCGA	0.418																																					p.V29fs		Atlas-INDEL	.											.	KIF15	103	.	0			c.85delG						.						146.0	133.0	137.0					3																	44816769		2203	4300	6503	SO:0001589	frameshift_variant	56992	exon3			.	AB035898	CCDS33744.1	3p21.31	2008-03-03	2005-03-15	2005-03-17	ENSG00000163808	ENSG00000163808		"""Kinesins"""	17273	protein-coding gene	gene with protein product			"""kinesin-like 7"""	KNSL7		10878014	Standard	NM_020242		Approved	HKLP2, NY-BR-62	uc003cnx.4	Q9NS87	OTTHUMG00000156307	ENST00000326047.4:c.86delT	chr3.hg19:g.44816769delT	ENSP00000324020:p.Val29fs	212.0	0.0		167.0	11.0	NM_020242	Q17RV9|Q69YL6|Q96JX7|Q9H280	Frame_Shift_Del	DEL	ENST00000326047.4	hg19	CCDS33744.1																																																																																			.	.		0.418	KIF15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343831.2		
HERC3	8916	hgsc.bcm.edu	37	4	89601295	89601295	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:89601295delT	ENST00000402738.1	+	20	2487	c.2248delT	c.(2248-2250)tttfs	p.F751fs	HERC3_ENST00000264345.3_Frame_Shift_Del_p.F751fs|HERC3_ENST00000543130.1_Frame_Shift_Del_p.F195fs	NM_001271602.1|NM_014606.1	NP_001258531.1|NP_055421.1	Q15034	HERC3_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase 3	751					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasmic vesicle (GO:0031410)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(10)|lung(14)|prostate(2)|skin(2)	45				OV - Ovarian serous cystadenocarcinoma(123;0.000319)		TACAAAGGAATTTTTTCTTTT	0.343																																					p.E749fs		Atlas-INDEL	.											.	HERC3	82	.	0			c.2247delA						.						102.0	106.0	105.0					4																	89601295		2203	4300	6503	SO:0001589	frameshift_variant	8916	exon20			.	D25215	CCDS34028.1	4q21	2012-02-23	2012-02-23		ENSG00000138641	ENSG00000138641			4876	protein-coding gene	gene with protein product		605200	"""hect domain and RLD 3"""			10702688	Standard	NM_014606		Approved	KIAA0032	uc003hrw.2	Q15034	OTTHUMG00000150436	ENST00000402738.1:c.2248delT	chr4.hg19:g.89601295delT	ENSP00000385684:p.Phe751fs	124.0	0.0		99.0	13.0	NM_014606	A8K1S5|Q8IXX3	Frame_Shift_Del	DEL	ENST00000402738.1	hg19	CCDS34028.1																																																																																			.	.		0.343	HERC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318081.2	NM_014606	
USP48	84196	hgsc.bcm.edu	37	1	22056297	22056297	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:22056297delT	ENST00000308271.9	-	10	1848	c.1200delA	c.(1198-1200)aaafs	p.K400fs	USP48_ENST00000529637.1_Frame_Shift_Del_p.K399fs|USP48_ENST00000400301.1_Frame_Shift_Del_p.K400fs|USP48_ENST00000421625.2_Frame_Shift_Del_p.K400fs	NM_032236.5	NP_115612.4	Q86UV5	UBP48_HUMAN	ubiquitin specific peptidase 48	400	USP.				ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ubiquitin-specific protease activity (GO:0004843)			NS(1)|endometrium(6)|kidney(2)|large_intestine(11)|lung(14)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42		Colorectal(325;3.46e-05)|all_lung(284;4.29e-05)|Lung NSC(340;4.66e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|OV - Ovarian serous cystadenocarcinoma(117;4.74e-26)|COAD - Colon adenocarcinoma(152;1.3e-05)|GBM - Glioblastoma multiforme(114;1.86e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000614)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(1967;0.00711)|Lung(427;0.0327)|READ - Rectum adenocarcinoma(331;0.0657)|LUSC - Lung squamous cell carcinoma(448;0.0753)		CACACTTGGGTTTACGTGTCT	0.403																																					p.P401fs		Atlas-INDEL	.											.	USP48	91	.	0			c.1201delC						.						186.0	173.0	178.0					1																	22056297		2203	4300	6503	SO:0001589	frameshift_variant	84196	exon10			.	AF502942	CCDS30623.1, CCDS44084.1	1p36.12	2008-02-05	2005-08-08	2004-04-07	ENSG00000090686	ENSG00000090686		"""Ubiquitin-specific peptidases"""	18533	protein-coding gene	gene with protein product			"""ubiquitin specific protease 31"", ""ubiquitin specific protease 48"""	USP31		12838346	Standard	XM_005246009		Approved	FLJ23277, FLJ11328, FLJ20103, FLJ23054, MGC14879	uc001bfb.3	Q86UV5	OTTHUMG00000007798	ENST00000308271.9:c.1200delA	chr1.hg19:g.22056297delT	ENSP00000309262:p.Lys400fs	214.0	0.0		152.0	10.0	NM_001032730	B7ZKS7|Q2M3I4|Q5SZI4|Q5T3T5|Q6NX53|Q8N3F6|Q96F64|Q96IQ3|Q9H5N3|Q9H5T7|Q9NUJ6|Q9NXR0	Frame_Shift_Del	DEL	ENST00000308271.9	hg19	CCDS30623.1																																																																																			.	.		0.403	USP48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021372.1	NM_032236	
LCA5L	150082	hgsc.bcm.edu	37	21	40782217	40782217	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr21:40782217delT	ENST00000358268.2	-	8	1665	c.1137delA	c.(1135-1137)aaafs	p.K379fs	LCA5L_ENST00000380671.2_Frame_Shift_Del_p.K379fs|WRB_ENST00000541890.1_Intron|LCA5L_ENST00000495240.1_5'UTR|LCA5L_ENST00000288350.3_Frame_Shift_Del_p.K379fs			O95447	LCA5L_HUMAN	Leber congenital amaurosis 5-like	379										breast(1)|cervix(1)|endometrium(3)|large_intestine(8)|lung(4)|pancreas(2)|prostate(2)|skin(2)|urinary_tract(1)	24		Prostate(19;1.2e-06)				GAACATCTGATTTTTGGGTTC	0.368																																					p.S380fs		Atlas-INDEL	.											.	LCA5L	57	.	0			c.1138delT						.						232.0	223.0	227.0					21																	40782217		2203	4300	6503	SO:0001589	frameshift_variant	150082	exon8			.	AF121781	CCDS13665.1	21q22.2	2007-12-18	2007-12-18	2007-12-18	ENSG00000157578	ENSG00000157578			1255	protein-coding gene	gene with protein product			"""chromosome 21 open reading frame 13"""	C21orf13			Standard	XM_005260926		Approved	MGC33295	uc002yxu.3	O95447	OTTHUMG00000066280	ENST00000358268.2:c.1137delA	chr21.hg19:g.40782217delT	ENSP00000351008:p.Lys379fs	223.0	0.0		152.0	10.0	NM_152505	D3DSI0|Q3ZCT0	Frame_Shift_Del	DEL	ENST00000358268.2	hg19	CCDS13665.1																																																																																			.	.		0.368	LCA5L-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141807.2	NM_152505	
FBXO11	80204	hgsc.bcm.edu	37	2	48066828	48066828	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:48066828delT	ENST00000403359.3	-	2	385	c.313delA	c.(313-315)actfs	p.T105fs	FBXO11_ENST00000480038.1_5'UTR|FBXO11_ENST00000316377.4_Frame_Shift_Del_p.T21fs|FBXO11_ENST00000378314.3_5'UTR|FBXO11_ENST00000402508.1_Frame_Shift_Del_p.T21fs	NM_001190274.1	NP_001177203.1	Q86XK2	FBX11_HUMAN	F-box protein 11	105					cellular protein modification process (GO:0006464)|peptidyl-arginine N-methylation (GO:0035246)|protein ubiquitination (GO:0016567)|sensory perception of sound (GO:0007605)|ubiquitin-dependent protein catabolic process (GO:0006511)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	protein-arginine N-methyltransferase activity (GO:0016274)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.0?(2)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	26		Acute lymphoblastic leukemia(82;0.0299)|all_hematologic(82;0.0358)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			GGCAAAAGAGTTTTTCTACGA	0.368			"""Mis, F, D"""		DLBCL																																p.T105fs		Atlas-INDEL	.		Rec	yes		2	2p16.3	80204	F-box protein 11		L	.	FBXO11	127	.	2	Whole gene deletion(2)	haematopoietic_and_lymphoid_tissue(2)	c.314delC						.						133.0	124.0	127.0					2																	48066828		2203	4300	6503	SO:0001589	frameshift_variant	80204	exon2			.	AF174599	CCDS1837.1, CCDS54357.1	2p16.3	2014-01-29	2008-06-23	2008-06-23	ENSG00000138081	ENSG00000138081		"""Ubiquitin protein ligase E3 component n-recognins"", ""F-boxes /  ""other"""""	13590	protein-coding gene	gene with protein product	"""ubiquitin protein ligase E3 component n-recognin 6"""	607871	"""F-box only protein 11"""			10531035, 16487488, 18162545	Standard	NM_025133		Approved	FBX11, UBR6	uc002rwe.3	Q86XK2	OTTHUMG00000129130	ENST00000403359.3:c.313delA	chr2.hg19:g.48066828delT	ENSP00000384823:p.Thr105fs	185.0	0.0		128.0	10.0	NM_001190274	A1L491|Q52ZP1|Q53EP7|Q53RT5|Q8IXG3|Q96E90|Q9H6V8|Q9H9L1|Q9NR14|Q9UFK1|Q9UHI1|Q9UKC2	Frame_Shift_Del	DEL	ENST00000403359.3	hg19	CCDS54357.1																																																																																			.	.		0.368	FBXO11-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251181.3	NM_012167, NM_018693, NM_025133	
SLCO1C1	53919	hgsc.bcm.edu	37	12	20885884	20885884	+	Frame_Shift_Del	DEL	G	G	-	rs368038819		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:20885884delG	ENST00000266509.2	+	10	1596	c.1228delG	c.(1228-1230)gggfs	p.G411fs	SLCO1C1_ENST00000545604.1_Frame_Shift_Del_p.G411fs|SLCO1C1_ENST00000540354.1_Frame_Shift_Del_p.G362fs|SLCO1C1_ENST00000545102.1_Frame_Shift_Del_p.G293fs|SLCO1C1_ENST00000381552.1_Frame_Shift_Del_p.G411fs	NM_017435.4	NP_059131.1	Q9NYB5	SO1C1_HUMAN	solute carrier organic anion transporter family, member 1C1	411					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)	AATATTCTCTGGGGGGATAGT	0.383																																					p.S409fs		Atlas-INDEL	.											.	SLCO1C1	216	.	0			c.1227delT						.						104.0	101.0	102.0					12																	20885884		2203	4300	6503	SO:0001589	frameshift_variant	53919	exon10			.	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.1228delG	chr12.hg19:g.20885884delG	ENSP00000266509:p.Gly411fs	201.0	0.0		151.0	11.0	NM_017435	B7Z251|B7Z3Q3|B7Z8P1|F5GZD6|Q5JPA4	Frame_Shift_Del	DEL	ENST00000266509.2	hg19	CCDS8683.1																																																																																			.	.		0.383	SLCO1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401765.1	NM_017435	
SLC8A2	6543	hgsc.bcm.edu	37	19	47944446	47944446	+	Intron	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:47944446delG	ENST00000236877.6	-	6	2263				SLC8A2_ENST00000542837.1_Intron|SLC8A2_ENST00000539381.1_Intron|SLC8A2_ENST00000601757.1_Intron	NM_015063.2	NP_055878.1	Q9UPR5	NAC2_HUMAN	solute carrier family 8 (sodium/calcium exchanger), member 2						blood coagulation (GO:0007596)|cell communication (GO:0007154)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium:sodium antiporter activity (GO:0005432)	p.?(1)		breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(10)|ovary(2)|prostate(2)|skin(5)|stomach(1)	31		all_cancers(25;3.05e-07)|all_lung(116;4.19e-06)|Lung NSC(112;7.16e-06)|all_epithelial(76;7.65e-06)|all_neural(266;0.0652)|Ovarian(192;0.086)|Breast(70;0.173)		OV - Ovarian serous cystadenocarcinoma(262;0.000501)|all cancers(93;0.00058)|Epithelial(262;0.0181)|GBM - Glioblastoma multiforme(486;0.0457)		TAGCAGAGCTGGGGAGAGACA	0.592																																					.		Atlas-INDEL	.											.	SLC8A2	77	.	1	Unknown(1)	lung(1)	c.1868-2C>-						.						96.0	93.0	94.0					19																	47944446		2203	4300	6503	SO:0001627	intron_variant	6543	exon7			.	AB029010	CCDS33065.1	19q13.32	2013-07-15	2008-09-02		ENSG00000118160	ENSG00000118160		"""Solute carriers"""	11069	protein-coding gene	gene with protein product		601901				8021246	Standard	NM_015063		Approved	NCX2, KIAA1087	uc002pgx.3	Q9UPR5	OTTHUMG00000183529	ENST00000236877.6:c.1868-3C>-	chr19.hg19:g.47944446delG		172.0	0.0		139.0	10.0	NM_015063	B4DYQ9	Splice_Site	DEL	ENST00000236877.6	hg19	CCDS33065.1																																																																																			.	.		0.592	SLC8A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466997.1		
ALPK3	57538	hgsc.bcm.edu	37	15	85406007	85406007	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:85406007delC	ENST00000258888.5	+	10	5044	c.4877delC	c.(4876-4878)tccfs	p.S1626fs		NM_020778.4	NP_065829.3	Q96L96	ALPK3_HUMAN	alpha-kinase 3	1626	Alpha-type protein kinase. {ECO:0000255|PROSITE-ProRule:PRU00501}.				heart development (GO:0007507)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(3)|breast(2)|central_nervous_system(2)|endometrium(12)|kidney(4)|large_intestine(9)|lung(27)|ovary(3)|prostate(5)|skin(8)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	81			BRCA - Breast invasive adenocarcinoma(143;0.0587)			CGGAAGGCCTCCCAGGCCAAG	0.627																																					p.S1626fs		Atlas-INDEL	.											.	ALPK3	289	.	0			c.4876delT						.						88.0	85.0	86.0					15																	85406007		2203	4299	6502	SO:0001589	frameshift_variant	57538	exon10			.	AY044449	CCDS10333.1	15q25.2	2013-01-29			ENSG00000136383	ENSG00000136383		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	17574	protein-coding gene	gene with protein product	"""myocyte induction differentiation originator"", ""muscle alpha-kinase"""					10021370	Standard	NM_020778		Approved	MAK, KIAA1330, Midori	uc002ble.3	Q96L96	OTTHUMG00000148667	ENST00000258888.5:c.4877delC	chr15.hg19:g.85406007delC	ENSP00000258888:p.Ser1626fs	227.0	0.0		176.0	11.0	NM_020778	Q9P2L6	Frame_Shift_Del	DEL	ENST00000258888.5	hg19	CCDS10333.1																																																																																			.	.		0.627	ALPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308997.1	NM_020778	
ZBTB3	79842	hgsc.bcm.edu	37	11	62520953	62520953	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:62520953delC	ENST00000394807.3	-	2	459	c.334delG	c.(334-336)gatfs	p.D112fs		NM_024784.3	NP_079060.1	Q9H5J0	ZBTB3_HUMAN	zinc finger and BTB domain containing 3	112	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)			breast(4)|endometrium(3)|kidney(1)|large_intestine(2)|liver(1)|lung(9)|ovary(2)|prostate(2)	24						CACACCAGATCCCTCTTGTCC	0.547																																					p.D112fs		Atlas-INDEL	.											.	ZBTB3	47	.	0			c.335delA						.						90.0	87.0	88.0					11																	62520953		2202	4299	6501	SO:0001589	frameshift_variant	79842	exon2			.	AK027045	CCDS8034.1	11q12.3	2013-01-09				ENSG00000185670		"""-"", ""BTB/POZ domain containing"", ""Zinc fingers, C2H2-type"""	22918	protein-coding gene	gene with protein product							Standard	NM_024784		Approved	FLJ23392	uc001nuz.3	Q9H5J0		ENST00000394807.3:c.334delG	chr11.hg19:g.62520953delC	ENSP00000378286:p.Asp112fs	239.0	0.0		180.0	11.0	NM_024784		Frame_Shift_Del	DEL	ENST00000394807.3	hg19	CCDS8034.1																																																																																			.	.		0.547	ZBTB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395342.1	NM_024784	
ARAF	369	hgsc.bcm.edu	37	X	47426094	47426094	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:47426094delC	ENST00000377045.4	+	7	808	c.614delC	c.(613-615)gccfs	p.A205fs	ARAF_ENST00000290277.6_Intron	NM_001256196.1|NM_001654.4	NP_001243125.1|NP_001645.1	P10398	ARAF_HUMAN	A-Raf proto-oncogene, serine/threonine kinase	205					cellular protein modification process (GO:0006464)|negative regulation of apoptotic process (GO:0043066)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|regulation of TOR signaling (GO:0032006)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein activity (GO:0005057)	p.L207fs*85(1)		biliary_tract(1)|endometrium(4)|large_intestine(7)|liver(2)|lung(11)|ovary(2)|skin(1)|urinary_tract(1)	29					Adenosine triphosphate(DB00171)	CCAGCCAATGCCCCCCTACAG	0.632																																					p.A208fs		Atlas-INDEL	.											.	ARAF	67	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.622delG						.						49.0	39.0	43.0					X																	47426094		2203	4300	6503	SO:0001589	frameshift_variant	369	exon7			.	X04790	CCDS35232.1, CCDS59164.1, CCDS75970.1	Xp11.3-p11.23	2014-06-26	2014-06-26	2005-01-19	ENSG00000078061	ENSG00000078061			646	protein-coding gene	gene with protein product		311010	"""v-raf murine sarcoma 3611 viral oncogene homolog 1"""	ARAF1			Standard	NM_001654		Approved		uc004dic.2	P10398	OTTHUMG00000021446	ENST00000377045.4:c.614delC	chrX.hg19:g.47426094delC	ENSP00000366244:p.Ala205fs	383.0	0.0		263.0	17.0	NM_001256196	P07557|Q5H9B2|Q5H9B3	Frame_Shift_Del	DEL	ENST00000377045.4	hg19	CCDS35232.1																																																																																			.	.		0.632	ARAF-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056418.1		
ATP6AP1L	92270	hgsc.bcm.edu	37	5	81613888	81613888	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:81613888delT	ENST00000380167.4	+	10	1769	c.444delT	c.(442-444)gctfs	p.A148fs	ATP6AP1L_ENST00000508366.1_Intron|ATP6AP1L_ENST00000439350.1_Frame_Shift_Del_p.A148fs			Q52LC2	VAS1L_HUMAN	ATPase, H+ transporting, lysosomal accessory protein 1-like	148					ATP hydrolysis coupled proton transport (GO:0015991)	integral component of membrane (GO:0016021)|proton-transporting V-type ATPase, V1 domain (GO:0033180)	proton-transporting ATP synthase activity, rotational mechanism (GO:0046933)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(4)|urinary_tract(1)	12						TCTCGCCAGCTTTTCTGATCG	0.537																																					p.A148fs		Atlas-INDEL	.											.	ATP6AP1L	29	.	0			c.443delC						.						96.0	84.0	88.0					5																	81613888		2203	4300	6503	SO:0001589	frameshift_variant	92270	exon4			.	AK022625	CCDS34196.1	5q14.2	2010-03-10				ENSG00000205464			28091	protein-coding gene	gene with protein product							Standard	XR_112744		Approved		uc003khw.3	Q52LC2		ENST00000380167.4:c.444delT	chr5.hg19:g.81613888delT	ENSP00000369513:p.Ala148fs	236.0	0.0		159.0	10.0	NM_001017971		Frame_Shift_Del	DEL	ENST00000380167.4	hg19	CCDS34196.1																																																																																			.	.		0.537	ATP6AP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369562.3	NM_001017971	
MSH2	4436	hgsc.bcm.edu	37	2	47630437	47630437	+	Frame_Shift_Del	DEL	T	T	-	rs63751056		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:47630437delT	ENST00000233146.2	+	1	330	c.107delT	c.(106-108)cttfs	p.L36fs	MSH2_ENST00000406134.1_Frame_Shift_Del_p.L36fs|MSH2_ENST00000543555.1_Intron	NM_000251.2	NP_000242.1	P43246	MSH2_HUMAN	mutS homolog 2	36					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)			ACAGTGCGCCTTTTCGACCGG	0.667			"""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																												p.L36fs		Atlas-INDEL	.	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.106delC						.						14.0	15.0	15.0					2																	47630437		2196	4294	6490	SO:0001589	frameshift_variant	4436	exon1	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	.	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.107delT	chr2.hg19:g.47630437delT	ENSP00000233146:p.Leu36fs	239.0	0.0		206.0	13.0	NM_000251	B4E2Z2|O75488	Frame_Shift_Del	DEL	ENST00000233146.2	hg19	CCDS1834.1																																																																																			.	.		0.667	MSH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250805.3		
COL28A1	340267	hgsc.bcm.edu	37	7	7480482	7480482	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:7480482delC	ENST00000399429.3	-	21	1801	c.1661delG	c.(1660-1662)ggcfs	p.G554fs		NM_001037763.2	NP_001032852.2	Q2UY09	COSA1_HUMAN	collagen, type XXVIII, alpha 1	554	Collagen-like 5.				cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.G554V(1)		cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(23)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	42		Ovarian(82;0.0789)		UCEC - Uterine corpus endometrioid carcinoma (126;0.228)		CCCTTTCTTGCCTTCGTCACC	0.443																																					p.G554fs		Atlas-INDEL	.											.	COL28A1	113	.	1	Substitution - Missense(1)	lung(1)	c.1662delC						.						150.0	141.0	144.0					7																	7480482		1845	4094	5939	SO:0001589	frameshift_variant	340267	exon21			.	AJ890451	CCDS43553.1	7p21.3	2013-01-16			ENSG00000215018	ENSG00000215018		"""Collagens"""	22442	protein-coding gene	gene with protein product		609996				16330543	Standard	NM_001037763		Approved		uc003src.1	Q2UY09	OTTHUMG00000150034	ENST00000399429.3:c.1661delG	chr7.hg19:g.7480482delC	ENSP00000382356:p.Gly554fs	77.0	0.0		154.0	10.0	NM_001037763	A4D101|A4D106|A4D107|A8MVR2|B9EGX9|Q2UY07|Q2UY08	Frame_Shift_Del	DEL	ENST00000399429.3	hg19	CCDS43553.1																																																																																			.	.		0.443	COL28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315899.1	NM_001037763	
ASCC3	10973	hgsc.bcm.edu	37	6	100960741	100960741	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:100960741delT	ENST00000369162.2	-	40	6473	c.6129delA	c.(6127-6129)aaafs	p.K2043fs		NM_006828.2	NP_006819.2	Q8N3C0	ASCC3_HUMAN	activating signal cointegrator 1 complex subunit 3	2043	SEC63 2.				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)		CCCACGAGCCTTTAACACTTA	0.373																																					p.G2044fs		Atlas-INDEL	.											.	ASCC3	205	.	0			c.6130delG						.						119.0	98.0	105.0					6																	100960741		2203	4300	6503	SO:0001589	frameshift_variant	10973	exon40			.	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.6129delA	chr6.hg19:g.100960741delT	ENSP00000358159:p.Lys2043fs	196.0	0.0		172.0	11.0	NM_006828	E7EW23|O43738|Q4G1A0|Q5VTN2|Q9H1I9|Q9H5A2|Q9NTR0	Frame_Shift_Del	DEL	ENST00000369162.2	hg19	CCDS5046.1																																																																																			.	.		0.373	ASCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041632.2	NM_006828	
GSDMA	284110	hgsc.bcm.edu	37	17	38132221	38132221	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:38132221delA	ENST00000301659.4	+	11	1184	c.1066delA	c.(1066-1068)aaafs	p.K357fs		NM_178171.4	NP_835465.2	Q96QA5	GSDMA_HUMAN	gasdermin A	357					apoptotic process (GO:0006915)	perinuclear region of cytoplasm (GO:0048471)				NS(1)|endometrium(2)|large_intestine(3)|lung(1)	7						ATCCATGGAGAAAAAGATCCT	0.517																																					p.E355fs		Atlas-INDEL	.											.	GSDMA	26	.	0			c.1065delG						.						53.0	54.0	54.0					17																	38132221		1900	4143	6043	SO:0001589	frameshift_variant	284110	exon11			.	AB093591	CCDS45669.1	17q21.2	2008-07-31	2008-07-31	2008-07-31		ENSG00000167914			13311	protein-coding gene	gene with protein product		611218	"""gasdermin"", ""gasdermin 1"""	GSDM, GSDM1		12883658, 15010812, 17350798	Standard	NM_178171		Approved	FLJ39120	uc002htl.1	Q96QA5		ENST00000301659.4:c.1066delA	chr17.hg19:g.38132221delA	ENSP00000301659:p.Lys357fs	325.0	0.0		217.0	15.0	NM_178171	Q32MC5|Q86VE7|Q8N1M6	Frame_Shift_Del	DEL	ENST00000301659.4	hg19	CCDS45669.1																																																																																			.	.		0.517	GSDMA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446847.1	NM_178171	
SSPO	23145	hgsc.bcm.edu	37	7	149489415	149489415	+	RNA	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:149489415delG	ENST00000378016.2	+	0	5568							A2VEC9	SSPO_HUMAN	SCO-spondin						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	peptidase inhibitor activity (GO:0030414)					Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			GGCAGGTGCTGGGCAGCGAGG	0.692																																					p.L1856fs		Atlas-INDEL	.											.	.	.	.	0			c.5567delT						.						12.0	19.0	17.0					7																	149489415		2021	4180	6201			23145	exon37			.	AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"""subcommissural organ spondin"", ""SCO protein, thrombospondin domain containing"""		"""SCO-spondin homolog (Bos taurus)"""			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		chr7.hg19:g.149489415delG		129.0	0.0		169.0	11.0	NM_198455	Q76B61	Frame_Shift_Del	DEL	ENST00000378016.2	hg19																																																																																				.	.		0.692	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
XRCC6	2547	hgsc.bcm.edu	37	22	42033647	42033647	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr22:42033647delG	ENST00000359308.4	+	5	1280	c.625delG	c.(625-627)gggfs	p.G210fs	XRCC6_ENST00000405878.1_Frame_Shift_Del_p.G210fs|XRCC6_ENST00000405506.1_Frame_Shift_Del_p.G160fs|XRCC6_ENST00000402580.3_Frame_Shift_Del_p.G169fs|XRCC6_ENST00000360079.3_Frame_Shift_Del_p.G210fs|XRCC6_ENST00000428575.2_Frame_Shift_Del_p.G77fs			P12956	XRCC6_HUMAN	X-ray repair complementing defective repair in Chinese hamster cells 6	210					brain development (GO:0007420)|cellular hyperosmotic salinity response (GO:0071475)|cellular response to X-ray (GO:0071481)|DNA duplex unwinding (GO:0032508)|DNA ligation (GO:0006266)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via nonhomologous end joining (GO:0006303)|establishment of integrated proviral latency (GO:0075713)|innate immune response (GO:0045087)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of neurogenesis (GO:0050769)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|telomere maintenance (GO:0000723)|transcription, DNA-templated (GO:0006351)|V(D)J recombination (GO:0033151)|viral process (GO:0016032)	cytosol (GO:0005829)|Ku70:Ku80 complex (GO:0043564)|membrane (GO:0016020)|nonhomologous end joining complex (GO:0070419)|nuclear telomere cap complex (GO:0000783)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	5'-deoxyribose-5-phosphate lyase activity (GO:0051575)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|telomeric DNA binding (GO:0042162)|transcription regulatory region DNA binding (GO:0044212)			central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(4)|liver(2)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	31						GAAGAAACCTGGGGGCTTTGA	0.443								Non-homologous end-joining																													p.P208fs		Atlas-INDEL	.											.	XRCC6	64	.	0			c.624delT						.						32.0	28.0	29.0					22																	42033647		2203	4300	6503	SO:0001589	frameshift_variant	2547	exon6			.	J04607	CCDS14021.1, CCDS74870.1, CCDS74871.1	22q13.2	2011-09-12	2008-07-31	2005-05-06	ENSG00000196419	ENSG00000196419			4055	protein-coding gene	gene with protein product	"""Ku autoantigen, 70kDa"""	152690	"""thyroid autoantigen 70kD (Ku antigen)"", ""thyroid autoantigen 70kDa (Ku antigen)"""	G22P1		9200330, 9223317	Standard	NM_001469		Approved	D22S731, D22S671, KU70, ML8	uc003bao.1	P12956	OTTHUMG00000151190	ENST00000359308.4:c.625delG	chr22.hg19:g.42033647delG	ENSP00000352257:p.Gly210fs	301.0	0.0		249.0	15.0	NM_001469	B1AHC8|Q6FG89|Q9UCQ2|Q9UCQ3	Frame_Shift_Del	DEL	ENST00000359308.4	hg19	CCDS14021.1																																																																																			.	.		0.443	XRCC6-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321688.1	NM_001469	
KMT2E	55904	hgsc.bcm.edu	37	7	104745930	104745930	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:104745930delA	ENST00000311117.3	+	18	2786	c.2241delA	c.(2239-2241)ggafs	p.G747fs	KMT2E_ENST00000334877.4_Frame_Shift_Del_p.G747fs|CTB-152G17.6_ENST00000607968.1_RNA|KMT2E_ENST00000257745.4_Frame_Shift_Del_p.G747fs|KMT2E_ENST00000334914.7_5'UTR	NM_182931.2	NP_891847.1	Q8IZD2	KMT2E_HUMAN	lysine (K)-specific methyltransferase 2E	747					cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|DNA methylation (GO:0006306)|erythrocyte differentiation (GO:0030218)|histone H3-K4 methylation (GO:0051568)|neutrophil activation (GO:0042119)|neutrophil mediated immunity (GO:0002446)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of transcription, DNA-templated (GO:0045893)|retinoic acid receptor signaling pathway (GO:0048384)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|MLL5-L complex (GO:0070688)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)										AGAAGACAGGAAAACCTTCAG	0.378																																					p.G747fs		Atlas-INDEL	.											.	MLL5	173	.	0			c.2240delG						.						89.0	90.0	90.0					7																	104745930		2203	4300	6503	SO:0001589	frameshift_variant	55904	exon18			.	AF067804	CCDS34723.1	7q22.1	2013-05-09	2013-05-09	2013-05-09	ENSG00000005483	ENSG00000005483		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	18541	protein-coding gene	gene with protein product		608444	"""myeloid/lymphoid or mixed-lineage leukemia 5 (trithorax homolog, Drosophila)"""	MLL5		9218106, 7672722	Standard	XM_005250493		Approved	HDCMC04P		Q8IZD2	OTTHUMG00000157403	ENST00000311117.3:c.2241delA	chr7.hg19:g.104745930delA	ENSP00000312379:p.Gly747fs	106.0	0.0		132.0	10.0	NM_182931	B6ZDE4|B6ZDM3|M4K8J3|Q6P5Y2|Q6PKG4|Q6T316|Q86TI3|Q86W12|Q86WG0|Q86WL2|Q8IV78|Q8IWR5|Q8NFF8|Q9NWE7	Frame_Shift_Del	DEL	ENST00000311117.3	hg19	CCDS34723.1																																																																																			.	.		0.378	KMT2E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348697.1		
SRP54	6729	hgsc.bcm.edu	37	14	35497334	35497334	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr14:35497334delA	ENST00000556994.1	+	16	1765	c.1368delA	c.(1366-1368)gcafs	p.A456fs	SRP54_ENST00000216774.6_Frame_Shift_Del_p.A456fs|SRP54_ENST00000546080.1_Frame_Shift_Del_p.A407fs|SRP54_ENST00000555557.1_Frame_Shift_Del_p.A392fs			P61011	SRP54_HUMAN	signal recognition particle 54kDa	456	M-domain.				cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|GTP catabolic process (GO:0006184)|protein targeting to ER (GO:0045047)|response to drug (GO:0042493)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition (GO:0006617)|SRP-dependent cotranslational protein targeting to membrane, translocation (GO:0006616)|translation (GO:0006412)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleus (GO:0005634)|signal recognition particle, endoplasmic reticulum targeting (GO:0005786)	7S RNA binding (GO:0008312)|drug binding (GO:0008144)|endoplasmic reticulum signal peptide binding (GO:0030942)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|ribonucleoprotein complex binding (GO:0043021)			NS(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	14	Breast(36;0.0545)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(48;2.48e-05)|Lung(238;3.13e-05)|Epithelial(34;0.0314)|all cancers(34;0.0797)|BRCA - Breast invasive adenocarcinoma(188;0.243)	GBM - Glioblastoma multiforme(112;0.0396)		CACAGATGGCAAAATTGAACC	0.383																																					p.A456fs		Atlas-INDEL	.											.	SRP54	38	.	0			c.1367delC						.						134.0	115.0	122.0					14																	35497334		2203	4300	6503	SO:0001589	frameshift_variant	6729	exon15			.	X86373	CCDS9652.1, CCDS53893.1	14q13.2	2014-06-02	2002-08-29		ENSG00000100883	ENSG00000100883			11301	protein-coding gene	gene with protein product		604857	"""signal recognition particle 54kD"""			8722571	Standard	NM_003136		Approved		uc001wso.3	P61011	OTTHUMG00000140214	ENST00000556994.1:c.1368delA	chr14.hg19:g.35497334delA	ENSP00000451818:p.Ala456fs	161.0	0.0		158.0	11.0	NM_003136	B2R759|B4DUW6|P13624	Frame_Shift_Del	DEL	ENST00000556994.1	hg19	CCDS9652.1																																																																																			.	.		0.383	SRP54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276643.2	NM_003136	
TRIM66	9866	hgsc.bcm.edu	37	11	8662474	8662474	+	Frame_Shift_Del	DEL	G	G	-	rs552975454	byFrequency	TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:8662474delG	ENST00000299550.6	-	9	1207	c.1013delC	c.(1012-1014)ccafs	p.P339fs	TRIM66_ENST00000402157.2_Frame_Shift_Del_p.P337fs	NM_014818.1	NP_055633.1	O15016	TRI66_HUMAN	tripartite motif containing 66	339						aggresome (GO:0016235)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(4)|kidney(1)|lung(1)|skin(2)	9						TATGCTGGGTGGGGGGACCTG	0.637																																					p.P338fs		Atlas-INDEL	.											.	TRIM66	45	.	0			c.1014delA						.						23.0	25.0	25.0					11																	8662474		692	1591	2283	SO:0001589	frameshift_variant	9866	exon9			.	AB002296		11p15.4	2013-01-28	2011-01-25		ENSG00000166436	ENSG00000166436		"""Tripartite motif containing / Tripartite motif containing"", ""Zinc fingers, PHD-type"""	29005	protein-coding gene	gene with protein product		612000	"""chromosome 11 open reading frame 29"", ""tripartite motif-containing 66"""	C11orf29		9205841	Standard	NM_014818		Approved	KIAA0298, TIF1D	uc010rbo.2	O15016	OTTHUMG00000150481	ENST00000299550.6:c.1013delC	chr11.hg19:g.8662474delG	ENSP00000299550:p.Pro339fs	140.0	0.0		155.0	10.0	NM_014818	Q9BQQ4	Frame_Shift_Del	DEL	ENST00000299550.6	hg19																																																																																				.	.		0.637	TRIM66-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_084529	
PHKB	5257	hgsc.bcm.edu	37	16	47630338	47630338	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:47630338delA	ENST00000323584.5	+	13	1283	c.1259delA	c.(1258-1260)gaafs	p.E420fs	PHKB_ENST00000455779.1_Frame_Shift_Del_p.E413fs|PHKB_ENST00000566044.1_Frame_Shift_Del_p.E413fs|PHKB_ENST00000299167.8_Frame_Shift_Del_p.E420fs	NM_000293.2	NP_000284.1	Q93100	KPBB_HUMAN	phosphorylase kinase, beta	420					carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|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)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|liver(1)|lung(18)|ovary(1)|skin(1)	41		all_cancers(37;0.00447)|all_lung(18;0.00616)|Lung NSC(13;0.0418)|Breast(268;0.203)				GTAGAATATGAAAAAAATAAC	0.338																																					p.E420fs		Atlas-INDEL	.											.	PHKB	298	.	0			c.1258delG						.						89.0	95.0	93.0					16																	47630338		2201	4300	6501	SO:0001589	frameshift_variant	5257	exon13			.		CCDS10729.1, CCDS42161.1	16q12-q13	2009-07-10			ENSG00000102893	ENSG00000102893	2.7.11.19		8927	protein-coding gene	gene with protein product		172490					Standard	NM_000293		Approved		uc002eev.4	Q93100	OTTHUMG00000133102	ENST00000323584.5:c.1259delA	chr16.hg19:g.47630338delA	ENSP00000313504:p.Glu420fs	114.0	0.0		131.0	11.0	NM_000293	Q8N4T5	Frame_Shift_Del	DEL	ENST00000323584.5	hg19	CCDS10729.1																																																																																			.	.		0.338	PHKB-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000430413.1		
CD302	9936	hgsc.bcm.edu	37	2	160628476	160628476	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:160628476delT	ENST00000259053.4	-	6	628	c.585delA	c.(583-585)aaafs	p.K195fs	LY75-CD302_ENST00000504764.1_Frame_Shift_Del_p.K1836fs|CD302_ENST00000429078.2_Frame_Shift_Del_p.K137fs|LY75-CD302_ENST00000505052.1_Frame_Shift_Del_p.K1780fs|LY75_ENST00000554112.1_Frame_Shift_Del_p.K1836fs|LY75_ENST00000553424.1_Frame_Shift_Del_p.K1780fs|CD302_ENST00000480212.1_5'UTR	NM_001198764.1|NM_014880.4	NP_001185693.1|NP_055695.2	Q8IX05	CD302_HUMAN	CD302 molecule	195					phagocytosis (GO:0006909)	cell cortex (GO:0005938)|filopodium (GO:0030175)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)			endometrium(1)|kidney(2)|large_intestine(3)|lung(3)|prostate(1)|skin(1)	11						AATCAGAATGTTTTTTGTACA	0.368																																					p.H1837fs		Atlas-INDEL	.											.	.	.	.	0			c.5509delC						.						104.0	107.0	106.0					2																	160628476		2203	4300	6503	SO:0001589	frameshift_variant	100526664	exon39			.	AY314007	CCDS33308.1, CCDS56139.1, CCDS74595.1	2q24.2	2011-08-30	2006-03-28		ENSG00000241399	ENSG00000241399		"""CD molecules"", ""C-type lectin domain containing"""	30843	protein-coding gene	gene with protein product	"""C-type lectin domain family 13, member A"""	612246	"""CD302 antigen"""			7584026, 7584028	Standard	NM_014880		Approved	DCL-1, KIAA0022, BIMLEC, CLEC13A		Q8IX05	OTTHUMG00000154080	ENST00000259053.4:c.585delA	chr2.hg19:g.160628476delT	ENSP00000259053:p.Lys195fs	230.0	0.0		189.0	12.0	NM_001198759	A8K5G4|B4E2T9|Q15009	Frame_Shift_Del	DEL	ENST00000259053.4	hg19	CCDS33308.1																																																																																			.	.		0.368	CD302-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333760.1	NM_014880	
SHISA2	387914	hgsc.bcm.edu	37	13	26620702	26620702	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr13:26620702delG	ENST00000319420.3	-	2	892	c.837delC	c.(835-837)cccfs	p.P279fs		NM_001007538.1	NP_001007539.1	Q6UWI4	SHSA2_HUMAN	shisa family member 2	279					multicellular organismal development (GO:0007275)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(2)|skin(1)	17						TGTGAGGGAAGGGGGACTGAA	0.572																																					p.F280fs		Atlas-Indel,Pindel	.											.	SHISA2	43	.	0			c.838delT						.						103.0	91.0	95.0					13																	26620702		2203	4300	6503	SO:0001589	frameshift_variant	387914	exon2			.		CCDS31951.1	13q12.13	2013-07-31	2013-07-31	2008-04-01	ENSG00000180730	ENSG00000180730		"""Shisa homologs"""	20366	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 13"", ""transmembrane protein 46"", ""shisa homolog 2 (Xenopus laevis)"""	C13orf13, TMEM46			Standard	NM_001007538		Approved	bA398O19.2, PRO28631, WGAR9166, hShisa	uc001uqm.1	Q6UWI4	OTTHUMG00000016612	ENST00000319420.3:c.837delC	chr13.hg19:g.26620702delG	ENSP00000313079:p.Pro279fs	95.0	0.0		90.0	27.0	NM_001007538	B9EH70|Q5W0G8	Frame_Shift_Del	DEL	ENST00000319420.3	hg19	CCDS31951.1																																																																																			.	.		0.572	SHISA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044239.2	NM_001007538	
SV2B	9899	hgsc.bcm.edu	37	15	91811750	91811750	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:91811750delT	ENST00000394232.1	+	9	1758	c.1288delT	c.(1288-1290)tttfs	p.F431fs	SV2B_ENST00000330276.4_Frame_Shift_Del_p.F431fs|SV2B_ENST00000545111.2_Frame_Shift_Del_p.F280fs	NM_014848.4	NP_055663.1	Q7L1I2	SV2B_HUMAN	synaptic vesicle glycoprotein 2B	431					neurotransmitter transport (GO:0006836)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|synaptic vesicle (GO:0008021)	transmembrane transporter activity (GO:0022857)			NS(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(17)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	42	Lung NSC(78;0.0987)|all_lung(78;0.172)		BRCA - Breast invasive adenocarcinoma(143;0.0895)			AATGAAGGTGTTTTTTGGTGA	0.408																																					p.V429fs		Atlas-INDEL	.											.	SV2B	98	.	0			c.1287delG						.						170.0	162.0	165.0					15																	91811750		2198	4298	6496	SO:0001589	frameshift_variant	9899	exon10			.	AB018278	CCDS10370.1, CCDS53972.1	15q26.1	2005-01-10			ENSG00000185518	ENSG00000185518			16874	protein-coding gene	gene with protein product		185861				9872452, 7681585	Standard	NM_014848		Approved	KIAA0735, HsT19680	uc002bqv.3	Q7L1I2	OTTHUMG00000149833	ENST00000394232.1:c.1288delT	chr15.hg19:g.91811750delT	ENSP00000377779:p.Phe431fs	262.0	0.0		166.0	11.0	NM_014848	B4DH30|C6G489|O94840|Q6IAR8	Frame_Shift_Del	DEL	ENST00000394232.1	hg19	CCDS10370.1																																																																																			.	.		0.408	SV2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313494.3	NM_014848	
PNPT1	87178	hgsc.bcm.edu	37	2	55887311	55887311	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:55887311delT	ENST00000447944.2	-	15	1351	c.1265delA	c.(1264-1266)aatfs	p.N422fs		NM_033109.3	NP_149100.2	Q8TCS8	PNPT1_HUMAN	polyribonucleotide nucleotidyltransferase 1	422					cellular response to interferon-beta (GO:0035458)|cellular response to oxidative stress (GO:0034599)|mitochondrial mRNA catabolic process (GO:0000958)|mitochondrial mRNA polyadenylation (GO:0097222)|mitochondrial RNA 3'-end processing (GO:0000965)|mitochondrial RNA 5'-end processing (GO:0000964)|mitochondrial RNA catabolic process (GO:0000957)|mitochondrion morphogenesis (GO:0070584)|mitotic cell cycle arrest (GO:0071850)|mRNA catabolic process (GO:0006402)|negative regulation of growth (GO:0045926)|nuclear polyadenylation-dependent mRNA catabolic process (GO:0071042)|positive regulation of miRNA catabolic process (GO:2000627)|positive regulation of mitochondrial RNA catabolic process (GO:0000962)|positive regulation of mRNA catabolic process (GO:0061014)|protein homooligomerization (GO:0051260)|protein homotrimerization (GO:0070207)|regulation of cellular respiration (GO:0043457)|regulation of cellular senescence (GO:2000772)|RNA catabolic process (GO:0006401)|RNA import into mitochondrion (GO:0035927)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|RNA polyadenylation (GO:0043631)|rRNA import into mitochondrion (GO:0035928)	cytoplasm (GO:0005737)|membrane (GO:0016020)|mitochondrial degradosome (GO:0045025)|mitochondrial intermembrane space (GO:0005758)|mitochondrion (GO:0005739)	3'-5'-exoribonuclease activity (GO:0000175)|miRNA binding (GO:0035198)|poly(A) RNA binding (GO:0044822)|poly(G) binding (GO:0034046)|poly(U) RNA binding (GO:0008266)|polyribonucleotide nucleotidyltransferase activity (GO:0004654)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(10)|lung(9)|skin(2)|urinary_tract(1)	27			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			CAGCATGAAATTTTTATCTTT	0.284																																					p.N422fs		Atlas-INDEL	.											.	PNPT1	68	.	0			c.1266delT						.						16.0	17.0	17.0					2																	55887311		2157	4260	6417	SO:0001589	frameshift_variant	87178	exon15			.	BC053660	CCDS1856.1	2p15	2013-01-08			ENSG00000138035	ENSG00000138035			23166	protein-coding gene	gene with protein product	"""polynucleotide phosphorylase"", ""3'-5' RNA exonuclease"""	610316	"""deafness, autosomal recessive 70"""	DFNB70		12419256	Standard	NM_033109		Approved	PNPase, OLD35, old-35	uc002rzf.3	Q8TCS8	OTTHUMG00000129335	ENST00000447944.2:c.1265delA	chr2.hg19:g.55887311delT	ENSP00000400646:p.Asn422fs	123.0	0.0		155.0	10.0	NM_033109	Q53SU0|Q68CN1|Q7Z7D1|Q8IWX1|Q96T05|Q9BRU3|Q9BVX0	Frame_Shift_Del	DEL	ENST00000447944.2	hg19	CCDS1856.1																																																																																			.	.		0.284	PNPT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251481.2	NM_033109	
EP400NL	347918	hgsc.bcm.edu	37	12	132589038	132589038	+	Frame_Shift_Del	DEL	A	A	-	rs371896558		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:132589038delA	ENST00000376625.4	+	1	499	c.473delA	c.(472-474)gacfs	p.D158fs	EP400NL_ENST00000392352.1_Intron|EP400NL_ENST00000389560.2_Frame_Shift_Del_p.D89fs|EP400NL_ENST00000443539.2_Intron|EP400NL_ENST00000361109.5_Intron			Q6ZTU2	E400N_HUMAN	EP400 N-terminal like	158										endometrium(1)|lung(1)|prostate(2)|urinary_tract(1)	5						CCTACAGGGGACTTCGTGGAT	0.667																																					.		Atlas-INDEL	.											.	EP400NL	29	.	0			.						.						58.0	84.0	76.0					12																	132589038		640	1586	2226	SO:0001589	frameshift_variant	347918	.			.	AK091234		12q24.33	2013-02-15			ENSG00000185684	ENSG00000185684			26602	protein-coding gene	gene with protein product						12477932	Standard	NR_003290		Approved	FLJ33915	uc009zyq.3	Q6ZTU2	OTTHUMG00000168251	ENST00000376625.4:c.473delA	chr12.hg19:g.132589038delA	ENSP00000365812:p.Asp158fs	29.0	0.0		32.0	10.0	.	A6NLB7|A8K0Z5|B3KQY2|Q6NXP1|Q8N253|Q8N7S7|Q9UFJ3	RNA	DEL	ENST00000376625.4	hg19																																																																																				.	.		0.667	EP400NL-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_182613	
PREX1	57580	hgsc.bcm.edu	37	20	47253224	47253224	+	Intron	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr20:47253224delG	ENST00000371941.3	-	32	3969				PREX1_ENST00000396220.1_Intron	NM_020820.3	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1						actin filament polymerization (GO:0030041)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|neutrophil activation (GO:0042119)|neutrophil chemotaxis (GO:0030593)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of actin filament polymerization (GO:0030833)|regulation of dendrite development (GO:0050773)|superoxide metabolic process (GO:0006801)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(27)|lung(53)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	110			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)			CTCCGTGTCTGGGGGCAGAGG	0.701																																					.		Atlas-INDEL	.											.	PREX1	441	.	0			c.3947-2C>-						.						8.0	9.0	9.0					20																	47253224		2128	4193	6321	SO:0001627	intron_variant	57580	exon33			.	AB037836	CCDS13410.1	20q13.13	2013-01-10	2008-09-15		ENSG00000124126	ENSG00000124126		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	32594	protein-coding gene	gene with protein product		606905				11955434, 15545267, 16301320	Standard	NM_020820		Approved	KIAA1415, P-REX1	uc002xtw.1	Q8TCU6	OTTHUMG00000032685	ENST00000371941.3:c.3947-3C>-	chr20.hg19:g.47253224delG		227.0	0.0		150.0	11.0	NM_020820	E1P5X9|Q5JS95|Q5JS96|Q69YL2|Q7Z2L9|Q9BQH0|Q9BX55|Q9H4Q6|Q9P2D2|Q9UGQ4	Splice_Site	DEL	ENST00000371941.3	hg19	CCDS13410.1																																																																																			.	.		0.701	PREX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079623.1	NM_020820	
KCNK7	10089	hgsc.bcm.edu	37	11	65363236	65363236	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:65363236delC	ENST00000340313.4	-	1	231	c.8delG	c.(7-9)ggtfs	p.G3fs	KCNK7_ENST00000342202.4_Frame_Shift_Del_p.G3fs|KCNK7_ENST00000394216.2_Frame_Shift_Del_p.G3fs|KCNK7_ENST00000394217.2_Frame_Shift_Del_p.G3fs	NM_033347.1	NP_203133.1	Q9Y2U2	KCNK7_HUMAN	potassium channel, subfamily K, member 7	3					potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)			endometrium(1)|liver(1)|lung(1)	3						GGGCCTTAGACCCCCCATGGC	0.711																																					p.G3fs		Atlas-INDEL	.											.	KCNK7	22	.	0			c.9delT						.						7.0	9.0	8.0					11																	65363236		2147	4242	6389	SO:0001589	frameshift_variant	10089	exon1			.	AF110522	CCDS8106.1, CCDS31608.1, CCDS41673.1	11q13	2012-03-07			ENSG00000173338	ENSG00000173338		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Two-P"""	6282	protein-coding gene	gene with protein product		603940				10206991, 11256078, 16382106	Standard	NM_033347		Approved	K2p7.1	uc001oes.3	Q9Y2U2	OTTHUMG00000166528	ENST00000340313.4:c.8delG	chr11.hg19:g.65363236delC	ENSP00000344820:p.Gly3fs	399.0	0.0		275.0	17.0	NM_005714	Q3SYI2|Q9Y2U3|Q9Y2U4	Frame_Shift_Del	DEL	ENST00000340313.4	hg19	CCDS31608.1																																																																																			.	.		0.711	KCNK7-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390206.1	NM_005714	
TCEAL4	79921	hgsc.bcm.edu	37	X	102841623	102841623	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:102841623delA	ENST00000472745.1	+	3	572	c.20delA	c.(19-21)gaafs	p.E7fs	TCEAL4_ENST00000415568.2_Frame_Shift_Del_p.E7fs|TCEAL4_ENST00000494801.1_Frame_Shift_Del_p.E7fs|TCEAL4_ENST00000468024.1_Frame_Shift_Del_p.E7fs|TCEAL4_ENST00000472484.1_Frame_Shift_Del_p.E7fs|TCEAL4_ENST00000372629.4_Frame_Shift_Del_p.E150fs			Q96EI5	TCAL4_HUMAN	transcription elongation factor A (SII)-like 4	7	Glu-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(2)|skin(2)	6						CTCTACAGTGAAAATGAAGGA	0.463																																					p.E7fs		Atlas-INDEL	.											.	TCEAL4	18	.	0			c.19delG						.						75.0	73.0	73.0					X																	102841623		2181	4286	6467	SO:0001589	frameshift_variant	79921	exon3			.	AF314542	CCDS14510.2, CCDS76004.1	Xq22.2	2014-03-21			ENSG00000133142	ENSG00000133142			26121	protein-coding gene	gene with protein product						14702039, 16221301	Standard	XM_005262192		Approved	FLJ21174, WEX7	uc004ekn.3	Q96EI5	OTTHUMG00000022103	ENST00000472745.1:c.20delA	chrX.hg19:g.102841623delA	ENSP00000424314:p.Glu7fs	208.0	0.0		150.0	11.0	NM_001006935	Q8WY12|Q9H2H1|Q9H775	Frame_Shift_Del	DEL	ENST00000472745.1	hg19	CCDS14510.2																																																																																			.	.		0.463	TCEAL4-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252339.2	NM_024863	
TMEM50A	23585	hgsc.bcm.edu	37	1	25683316	25683316	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:25683316delT	ENST00000374358.4	+	6	953	c.400delT	c.(400-402)tttfs	p.F135fs	TMEM50A_ENST00000480937.1_3'UTR	NM_014313.3	NP_055128.1	O95807	TM50A_HUMAN	transmembrane protein 50A	135						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|large_intestine(3)|lung(1)	6		Colorectal(325;3.46e-05)|Lung NSC(340;0.000245)|all_lung(284;0.000335)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0101)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0936)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0422)|OV - Ovarian serous cystadenocarcinoma(117;3.47e-27)|Colorectal(126;1.1e-08)|COAD - Colon adenocarcinoma(152;7.48e-07)|STAD - Stomach adenocarcinoma(196;0.00035)|BRCA - Breast invasive adenocarcinoma(304;0.00047)|KIRC - Kidney renal clear cell carcinoma(1967;0.000755)|GBM - Glioblastoma multiforme(114;0.00106)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.204)		AATTGCTGTATTTTTCCAGAA	0.274																																					p.V133fs		Atlas-INDEL	.											.	TMEM50A	17	.	0			c.399delA						.						158.0	142.0	147.0					1																	25683316		2201	4298	6499	SO:0001589	frameshift_variant	23585	exon6			.	AY071927	CCDS264.1	1p36.11	2008-02-05			ENSG00000183726	ENSG00000183726			30590	protein-coding gene	gene with protein product	"""small membrane protein 1"""	605348				10938938, 10845894	Standard	NM_014313		Approved	SMP1	uc001bke.3	O95807	OTTHUMG00000007651	ENST00000374358.4:c.400delT	chr1.hg19:g.25683316delT	ENSP00000363478:p.Phe135fs	185.0	0.0		170.0	11.0	NM_014313		Frame_Shift_Del	DEL	ENST00000374358.4	hg19	CCDS264.1																																																																																			.	.		0.274	TMEM50A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020313.1		
GPANK1	7918	hgsc.bcm.edu	37	6	31630338	31630338	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:31630338delC	ENST00000375906.1	-	4	1460	c.776delG	c.(775-777)ggcfs	p.G259fs	GPANK1_ENST00000375895.2_Frame_Shift_Del_p.G259fs|CSNK2B_ENST00000375885.4_5'Flank|GPANK1_ENST00000375900.4_Frame_Shift_Del_p.G259fs|C6orf47_ENST00000375911.1_5'Flank|GPANK1_ENST00000375893.2_Frame_Shift_Del_p.G259fs|GPANK1_ENST00000375896.4_Frame_Shift_Del_p.G259fs|C6orf47-AS1_ENST00000422049.1_RNA|Y_RNA_ENST00000364337.1_RNA	NM_001199237.1	NP_001186166.1	O95872	GPAN1_HUMAN	G patch domain and ankyrin repeats 1	259	G-patch. {ECO:0000255|PROSITE- ProRule:PRU00092}.						nucleic acid binding (GO:0003676)			central_nervous_system(1)|kidney(2)|large_intestine(2)|lung(7)	12						CAGTTTGAAGCCCGGGCTGGA	0.647																																					p.G259fs		Atlas-INDEL	.											.	GPANK1	19	.	0			c.777delC						.						39.0	48.0	45.0					6																	31630338		1511	2708	4219	SO:0001589	frameshift_variant	7918	exon4			.		CCDS4711.1	6p21.3	2013-01-28	2010-11-24	2010-11-24	ENSG00000204438	ENSG00000204438		"""Ankyrin repeat domain containing"", ""G patch domain containing"""	13920	protein-coding gene	gene with protein product	"""G patch domain containing 10"", ""ankyrin repeat domain 59"""	142610	"""HLA-B associated transcript 4"""	BAT4		2911734, 2813433	Standard	NM_001199237		Approved	G5, D6S54E, GPATCH10, ANKRD59	uc021yuu.1	O95872	OTTHUMG00000031174	ENST00000375906.1:c.776delG	chr6.hg19:g.31630338delC	ENSP00000365071:p.Gly259fs	225.0	0.0		167.0	11.0	NM_001199238	A6NG25|B0UXA2|Q5SQ49	Frame_Shift_Del	DEL	ENST00000375906.1	hg19	CCDS4711.1																																																																																			.	.		0.647	GPANK1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000144445.2	NM_033177	
PAN3	255967	hgsc.bcm.edu	37	13	28748431	28748431	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr13:28748431delT	ENST00000380958.3	+	2	605	c.453delT	c.(451-453)gctfs	p.A151fs	PAN3_ENST00000399613.1_Frame_Shift_Del_p.A5fs	NM_175854.7	NP_787050.6			PAN3 poly(A) specific ribonuclease subunit											endometrium(1)|kidney(3)|large_intestine(7)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	24	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)	Colorectal(13;0.000334)	all cancers(112;0.0102)|Epithelial(112;0.0803)|GBM - Glioblastoma multiforme(144;0.121)|OV - Ovarian serous cystadenocarcinoma(117;0.13)|Lung(94;0.174)		ATGGAGGTGCTTTAACTGATA	0.368																																					p.A151fs		Atlas-INDEL	.											.	PAN3	123	.	0			c.452delC						.						100.0	97.0	98.0					13																	28748431		2203	4300	6503	SO:0001589	frameshift_variant	255967	exon2			.	AK091307	CCDS9329.1, CCDS9329.2	13q12.2	2014-03-27	2014-03-27		ENSG00000152520	ENSG00000152520			29991	protein-coding gene	gene with protein product			"""PAN3 poly(A) specific ribonuclease subunit homolog (S. cerevisiae)"""			14583602	Standard	NM_175854		Approved		uc001urz.3	Q58A45	OTTHUMG00000016645	ENST00000380958.3:c.453delT	chr13.hg19:g.28748431delT	ENSP00000370345:p.Ala151fs	187.0	0.0		149.0	10.0	NM_175854		Frame_Shift_Del	DEL	ENST00000380958.3	hg19	CCDS9329.2																																																																																			.	.		0.368	PAN3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044318.4	NM_175854	
BRSK2	9024	hgsc.bcm.edu	37	11	1477640	1477640	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:1477640delG	ENST00000528841.1	+	17	2115	c.1731delG	c.(1729-1731)acgfs	p.T577fs	BRSK2_ENST00000526678.1_Frame_Shift_Del_p.T599fs|BRSK2_ENST00000528710.1_Frame_Shift_Del_p.T517fs|BRSK2_ENST00000382179.1_Frame_Shift_Del_p.T623fs|BRSK2_ENST00000308230.5_Frame_Shift_Del_p.T599fs|BRSK2_ENST00000544817.1_Frame_Shift_Del_p.T272fs|BRSK2_ENST00000531197.1_Frame_Shift_Del_p.T577fs|BRSK2_ENST00000308219.9_Frame_Shift_Del_p.T577fs			Q8IWQ3	BRSK2_HUMAN	BR serine/threonine kinase 2	577					actin cytoskeleton reorganization (GO:0031532)|axonogenesis (GO:0007409)|establishment of cell polarity (GO:0030010)|exocytosis (GO:0006887)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|mitotic nuclear division (GO:0007067)|neuron differentiation (GO:0030182)|peptidyl-serine phosphorylation (GO:0018105)|protein phosphorylation (GO:0006468)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)|tau-protein kinase activity (GO:0050321)			endometrium(4)|large_intestine(1)|lung(5)	10		all_epithelial(84;4.17e-05)|Breast(177;0.000307)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00144)|Lung(200;0.0713)|LUSC - Lung squamous cell carcinoma(625;0.0842)		ACAAGGCCACGGGGGGGCCAG	0.622																																					p.T623fs		Atlas-INDEL	.											.,2	BRSK2	97	.	0			c.1868delC						.																																			SO:0001589	frameshift_variant	9024	exon17			.	AF020089	CCDS41590.1, CCDS58106.1, CCDS58107.1, CCDS58108.1, CCDS60696.1	11p15.5	2008-02-05	2003-09-11	2005-01-27	ENSG00000174672	ENSG00000174672			11405	protein-coding gene	gene with protein product	"""serine/threonine kinase 29"""	609236	"""chromsosome 11 open reading frame 7"""	C11orf7, STK29		9852686, 9929968	Standard	NM_001256629		Approved	PEN11B	uc001ltm.4	Q8IWQ3	OTTHUMG00000167089	ENST00000528841.1:c.1731delG	chr11.hg19:g.1477640delG	ENSP00000432000:p.Thr577fs	209.0	0.0		147.0	10.0	NM_001256630	B3KVE9|E9PLM7|O60843|O95099|Q5J5B4|Q6ZMQ4|Q8TB60	Frame_Shift_Del	DEL	ENST00000528841.1	hg19	CCDS58107.1																																																																																			.	.		0.622	BRSK2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000393033.1	NM_003957	
CD83	9308	hgsc.bcm.edu	37	6	14131848	14131848	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:14131848delC	ENST00000379153.3	+	3	422	c.251delC	c.(250-252)gccfs	p.A84fs		NM_001040280.1|NM_001251901.1|NM_004233.3	NP_001035370.1|NP_001238830.1|NP_004224.1	Q01151	CD83_HUMAN	CD83 molecule	84	Ig-like V-type.				defense response (GO:0006952)|humoral immune response (GO:0006959)|negative regulation of interleukin-4 production (GO:0032713)|positive regulation of CD4-positive, alpha-beta T cell differentiation (GO:0043372)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-2 production (GO:0032743)|response to organic cyclic compound (GO:0014070)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				breast(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)	12	Breast(50;0.00245)|Ovarian(93;0.137)	all_hematologic(90;0.117)				TCTTTCGACGCCCCCAATGAA	0.547																																					p.A84fs		Atlas-INDEL	.											CD83,NS,carcinoma,-1,1	CD83	23	.	0			c.250delG						.						130.0	121.0	124.0					6																	14131848		2203	4300	6503	SO:0001589	frameshift_variant	9308	exon3			.	Z11697	CCDS4532.1, CCDS75403.1	6p23	2013-01-11	2006-03-31		ENSG00000112149	ENSG00000112149		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	1703	protein-coding gene	gene with protein product		604534	"""CD83 antigen (activated B lymphocytes, immunoglobulin superfamily)"", ""CD83 molecule """			1378080, 8422464	Standard	NM_001251901		Approved	HB15, BL11	uc003nbi.3	Q01151	OTTHUMG00000014283	ENST00000379153.3:c.251delC	chr6.hg19:g.14131848delC	ENSP00000368450:p.Ala84fs	209.0	0.0		144.0	11.0	NM_004233	Q5THX9	Frame_Shift_Del	DEL	ENST00000379153.3	hg19	CCDS4532.1																																																																																			.	.		0.547	CD83-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039916.1		
UBAC2	337867	hgsc.bcm.edu	37	13	99896772	99896772	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr13:99896772delT	ENST00000403766.3	+	4	418	c.283delT	c.(283-285)tttfs	p.F95fs	UBAC2_ENST00000376440.2_Intron	NM_001144072.1	NP_001137544.1	Q8NBM4	UBAC2_HUMAN	UBA domain containing 2	95					protein localization to endoplasmic reticulum (GO:0070972)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				breast(1)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(2)	10	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					TTTGTAGTCCTTTTTGCTGGG	0.368																																					p.S94fs		Atlas-INDEL	.											.	UBAC2	23	.	0			c.282delC						.						152.0	122.0	131.0					13																	99896772		1566	3582	5148	SO:0001589	frameshift_variant	337867	exon4			.	AK055110	CCDS9490.1, CCDS45064.1	13q32.3	2012-02-01	2007-04-20	2007-04-20	ENSG00000134882	ENSG00000134882			20486	protein-coding gene	gene with protein product			"""phosphoglycerate dehydrogenase like 1"""	PHGDHL1			Standard	NM_177967		Approved	FLJ30548, RP11-178C10.1	uc001voa.4	Q8NBM4	OTTHUMG00000017267	ENST00000403766.3:c.283delT	chr13.hg19:g.99896772delT	ENSP00000383911:p.Phe95fs	196.0	0.0		145.0	10.0	NM_001144072	B3KNV7|Q0VAB5|Q5W0W6|Q5W0W9|Q6GQR2|Q6P4B0|Q8N2E8|Q96NW2	Frame_Shift_Del	DEL	ENST00000403766.3	hg19	CCDS45064.1																																																																																			.	.		0.368	UBAC2-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045588.1	NM_177967	
GPR162	27239	hgsc.bcm.edu	37	12	6936291	6936291	+	Frame_Shift_Del	DEL	G	G	-	rs139203738	byFrequency	TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:6936291delG	ENST00000311268.3	+	5	2476	c.1689delG	c.(1687-1689)acgfs	p.T563fs	LEPREL2_ENST00000251761.8_RNA|LEPREL2_ENST00000606935.1_RNA|GPR162_ENST00000382315.3_Frame_Shift_Del_p.T259fs|GPR162_ENST00000428545.2_Frame_Shift_Del_p.T279fs|LEPREL2_ENST00000396725.2_RNA	NM_019858.1	NP_062832.1	Q16538	GP162_HUMAN	G protein-coupled receptor 162	563						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|ovary(2)|pancreas(2)|skin(1)	18						GCTCCCTGACGGGGGGTGAAG	0.642																																					p.T563fs		Atlas-INDEL	.											.	GPR162	55	.	0			c.1688delC						.						31.0	38.0	35.0					12																	6936291		2163	4204	6367	SO:0001589	frameshift_variant	27239	exon5			.	U47928, U47929, U47924, U47925	CCDS8563.1, CCDS44819.1	12p13	2012-08-21						"""GPCR / Class A : Orphans"""	16693	protein-coding gene	gene with protein product						15777626	Standard	NM_014449		Approved	A-2, GRCA	uc001qqw.1	Q16538		ENST00000311268.3:c.1689delG	chr12.hg19:g.6936291delG	ENSP00000311528:p.Thr563fs	146.0	0.0		153.0	10.0	NM_019858	Q16664|Q59EH5|Q66K56	Frame_Shift_Del	DEL	ENST00000311268.3	hg19	CCDS8563.1																																																																																			.	.		0.642	GPR162-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399478.1	NM_019858	
LYSMD2	256586	hgsc.bcm.edu	37	15	52017185	52017185	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:52017185delT	ENST00000267838.3	-	2	921	c.407delA	c.(406-408)aatfs	p.N136fs	LYSMD2_ENST00000558126.1_Frame_Shift_Del_p.N29fs|LYSMD2_ENST00000560491.1_Frame_Shift_Del_p.N45fs|LYSMD2_ENST00000454181.2_Frame_Shift_Del_p.N45fs	NM_153374.2	NP_699205.1	Q8IV50	LYSM2_HUMAN	LysM, putative peptidoglycan-binding, domain containing 2	136										lung(2)|upper_aerodigestive_tract(1)	3				all cancers(107;0.00258)		AGCAGTTTCATTTTCTGGAGA	0.428																																					p.N136fs		Atlas-INDEL	.											.	LYSMD2	8	.	0			c.408delT						.						93.0	102.0	99.0					15																	52017185		2195	4293	6488	SO:0001589	frameshift_variant	256586	exon2			.	AY125955	CCDS10143.1, CCDS45259.1	15q21.2	2005-08-09			ENSG00000140280	ENSG00000140280			28571	protein-coding gene	gene with protein product						12477932	Standard	NM_153374		Approved	MGC35274	uc002abi.3	Q8IV50	OTTHUMG00000131804	ENST00000267838.3:c.407delA	chr15.hg19:g.52017185delT	ENSP00000267838:p.Asn136fs	234.0	0.0		179.0	11.0	NM_153374	Q5CZ88|Q8WTV3	Frame_Shift_Del	DEL	ENST00000267838.3	hg19	CCDS10143.1																																																																																			.	.		0.428	LYSMD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254741.1	NM_153374	
XRRA1	143570	hgsc.bcm.edu	37	11	74574037	74574037	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:74574037delA	ENST00000340360.6	-	11	1340	c.1009delT	c.(1009-1011)tcafs	p.S337fs	XRRA1_ENST00000321448.8_Frame_Shift_Del_p.S104fs|XRRA1_ENST00000527087.1_Intron	NM_182969.2	NP_892014.1			X-ray radiation resistance associated 1											breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(8)|prostate(3)	20						TCTGAGGTTGAAAATCCAGGG	0.378																																					p.S337X		Atlas-INDEL	.											.	XRRA1	46	.	0			c.1010delC						.						49.0	44.0	45.0					11																	74574037		1861	4098	5959	SO:0001589	frameshift_variant	143570	exon11			.	AK074152	CCDS44680.1, CCDS58159.1, CCDS58160.1	11q13.4	2010-03-19			ENSG00000166435	ENSG00000166435			18868	protein-coding gene	gene with protein product		609788				12908878, 17295261	Standard	NM_182969		Approved	FLJ00225	uc009yub.3	Q6P2D8		ENST00000340360.6:c.1009delT	chr11.hg19:g.74574037delA	ENSP00000339918:p.Ser337fs	233.0	0.0		165.0	10.0	NM_182969		Frame_Shift_Del	DEL	ENST00000340360.6	hg19	CCDS44680.1																																																																																			.	.		0.378	XRRA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384715.1	NM_182969	
THSD7A	221981	hgsc.bcm.edu	37	7	11468622	11468622	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:11468622delT	ENST00000423059.4	-	14	3446	c.3195delA	c.(3193-3195)aaafs	p.K1065fs	AC004538.3_ENST00000445839.1_RNA	NM_015204.2	NP_056019.1	Q9UPZ6	THS7A_HUMAN	thrombospondin, type I, domain containing 7A	1065	TSP type-1 11. {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)		CATTATATGGTTTTTCACGCA	0.478										HNSCC(18;0.044)																											p.P1066fs		Atlas-INDEL	.											.	THSD7A	219	.	0			c.3196delC						.						250.0	243.0	245.0					7																	11468622		2016	4174	6190	SO:0001589	frameshift_variant	221981	exon14			.		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.3195delA	chr7.hg19:g.11468622delT	ENSP00000406482:p.Lys1065fs	282.0	0.0		343.0	21.0	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	
BRCA1	672	hgsc.bcm.edu	37	17	41219686	41219686	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:41219686delT	ENST00000357654.3	-	16	5131	c.5013delA	c.(5011-5013)aaafs	p.K1671fs	BRCA1_ENST00000493795.1_Frame_Shift_Del_p.K1624fs|BRCA1_ENST00000586385.1_Intron|BRCA1_ENST00000471181.2_Frame_Shift_Del_p.K1692fs|BRCA1_ENST00000346315.3_Intron|BRCA1_ENST00000351666.3_Frame_Shift_Del_p.K488fs|BRCA1_ENST00000468300.1_Frame_Shift_Del_p.K567fs|BRCA1_ENST00000352993.3_Frame_Shift_Del_p.K529fs|BRCA1_ENST00000591534.1_Frame_Shift_Del_p.K162fs|BRCA1_ENST00000309486.4_Frame_Shift_Del_p.K1375fs|BRCA1_ENST00000591849.1_Intron|BRCA1_ENST00000491747.2_Frame_Shift_Del_p.K567fs|BRCA1_ENST00000354071.3_Intron	NM_007294.3	NP_009225.1	P38398	BRCA1_HUMAN	breast cancer 1, early onset	1671	BRCT 1. {ECO:0000255|PROSITE- ProRule:PRU00033}.				androgen receptor signaling pathway (GO:0030521)|apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to indole-3-methanol (GO:0071681)|cellular response to tumor necrosis factor (GO:0071356)|chromosome segregation (GO:0007059)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|fatty acid biosynthetic process (GO:0006633)|G2 DNA damage checkpoint (GO:0031572)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of centriole replication (GO:0046600)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of DNA repair (GO:0045739)|positive regulation of gene expression (GO:0010628)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of histone H3-K9 acetylation (GO:2000617)|positive regulation of histone H4-K16 acetylation (GO:2000620)|positive regulation of histone H4-K20 methylation (GO:0070512)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation vascular endothelial growth factor production (GO:0010575)|postreplication repair (GO:0006301)|protein autoubiquitination (GO:0051865)|protein K6-linked ubiquitination (GO:0085020)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|regulation of cell proliferation (GO:0042127)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to estrogen (GO:0043627)|response to ionizing radiation (GO:0010212)	BRCA1-A complex (GO:0070531)|BRCA1-BARD1 complex (GO:0031436)|chromosome (GO:0005694)|cytoplasm (GO:0005737)|gamma-tubulin ring complex (GO:0008274)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ribonucleoprotein complex (GO:0030529)|ubiquitin ligase complex (GO:0000151)	androgen receptor binding (GO:0050681)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligase activity (GO:0016874)|RNA binding (GO:0003723)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|tubulin binding (GO:0015631)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(30)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(28)|ovary(36)|skin(2)|stomach(4)|urinary_tract(2)	120		Breast(137;0.000717)		BRCA - Breast invasive adenocarcinoma(366;0.126)		TGATGTGGTGTTTTCTGGCAA	0.358			"""D, Mis, N, F, S"""		ovarian	"""breast, ovarian"""		Homologous recombination	Hereditary Breast-Ovarian Cancer, BRCA1 type	TCGA Ovarian(2;0.000030)																											p.H1693fs		Atlas-INDEL	.	yes	Rec	yes	Hereditary breast/ovarian cancer	17	17q21	672	familial breast/ovarian cancer gene 1		E	.	BRCA1	304	.	0			c.5077delC						.						131.0	127.0	128.0					17																	41219686		2202	4300	6502	SO:0001589	frameshift_variant	672	exon17	Familial Cancer Database		.	U14680	CCDS11453.1, CCDS11454.1, CCDS11455.1, CCDS11456.1, CCDS11459.1, CCDS11455.2, CCDS11456.2, CCDS11459.2, CCDS11454.2	17q21.31	2014-09-17			ENSG00000012048	ENSG00000012048		"""RING-type (C3HC4) zinc fingers"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	1100	protein-coding gene	gene with protein product	"""BRCA1/BRCA2-containing complex, subunit 1"", ""protein phosphatase 1, regulatory subunit 53"""	113705				1676470	Standard	NM_007300		Approved	RNF53, BRCC1, PPP1R53	uc002ict.3	P38398	OTTHUMG00000157426	ENST00000357654.3:c.5013delA	chr17.hg19:g.41219686delT	ENSP00000350283:p.Lys1671fs	145.0	0.0		116.0	10.0	NM_007300	O15129|Q1RMC1|Q3LRJ0|Q3LRJ6|Q6IN79|Q7KYU9	Frame_Shift_Del	DEL	ENST00000357654.3	hg19	CCDS11453.1																																																																																			.	.		0.358	BRCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348798.2	NM_007294	
CXCL12	6387	hgsc.bcm.edu	37	10	44871433	44871433	+	Intron	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:44871433delT	ENST00000374429.2	-	4	353				AL137026.1_ENST00000593376.1_5'Flank|CXCL12_ENST00000395795.4_Intron|CXCL12_ENST00000374426.2_Frame_Shift_Del_p.K106fs|CXCL12_ENST00000496375.1_5'Flank|CXCL12_ENST00000395793.3_Intron	NM_000609.5|NM_001277990.1	NP_000600.1|NP_001264919.1	P48061	SDF1_HUMAN	chemokine (C-X-C motif) ligand 12						adult locomotory behavior (GO:0008344)|ameboidal cell migration (GO:0001667)|blood circulation (GO:0008015)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cellular calcium ion homeostasis (GO:0006874)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|germ cell development (GO:0007281)|germ cell migration (GO:0008354)|immune response (GO:0006955)|induction of positive chemotaxis (GO:0050930)|motor neuron axon guidance (GO:0008045)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of leukocyte apoptotic process (GO:2000107)|negative regulation of leukocyte tethering or rolling (GO:1903237)|neuron migration (GO:0001764)|organ regeneration (GO:0031100)|patterning of blood vessels (GO:0001569)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of calcium ion import (GO:0090280)|positive regulation of cell adhesion (GO:0045785)|positive regulation of dopamine secretion (GO:0033603)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of monocyte chemotaxis (GO:0090026)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of T cell migration (GO:2000406)|regulation of actin polymerization or depolymerization (GO:0008064)|response to heat (GO:0009408)|response to hypoxia (GO:0001666)|response to mechanical stimulus (GO:0009612)|response to peptide hormone (GO:0043434)|response to radiation (GO:0009314)|response to virus (GO:0009615)|signal transduction (GO:0007165)|T cell proliferation (GO:0042098)|telencephalon cell migration (GO:0022029)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	chemokine activity (GO:0008009)|chemokine receptor binding (GO:0042379)|CXCR chemokine receptor binding (GO:0045236)|receptor binding (GO:0005102)			endometrium(1)|large_intestine(1)|lung(3)|skin(1)	6					Tinzaparin(DB06822)	CTGTCGCTTCTTTTTTCCTAT	0.398																																					p.K105fs		Atlas-INDEL	.											.	CXCL12	37	.	0			c.315delG						.						308.0	316.0	313.0					10																	44871433		2203	4298	6501	SO:0001627	intron_variant	6387	exon4			.	L36033	CCDS7207.1, CCDS31186.1, CCDS44373.1, CCDS53527.1, CCDS60518.1	10q11.1	2013-02-28	2010-05-11	2002-08-23	ENSG00000107562	ENSG00000107562		"""Endogenous ligands"""	10672	protein-coding gene	gene with protein product		600835	"""stromal cell-derived factor 1"""	SDF1A, SDF1B, SDF1		7490086	Standard	NM_001033886		Approved	SCYB12, SDF-1a, SDF-1b, PBSF, TLSF-a, TLSF-b, TPAR1	uc021ppm.1	P48061	OTTHUMG00000018054	ENST00000374429.2:c.267-2642A>-	chr10.hg19:g.44871433delT		301.0	0.0		224.0	15.0	NM_001033886	B2R4G0|E7EVL0|H7BYN8|Q2L985|Q2L986|Q2L988|Q5IT36|Q6ICW0|Q9H554	Frame_Shift_Del	DEL	ENST00000374429.2	hg19	CCDS44373.1																																																																																			.	.		0.398	CXCL12-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047738.2	NM_000609	
LYST	1130	hgsc.bcm.edu	37	1	235887447	235887447	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:235887447delA	ENST00000389794.3	-	39	9370	c.9196delT	c.(9196-9198)tccfs	p.S3066fs	LYST_ENST00000389793.2_Frame_Shift_Del_p.S3066fs|LYST_ENST00000473037.1_5'UTR			Q99698	LYST_HUMAN	lysosomal trafficking regulator	3066					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)			TATGTCCAGGAAAATGATGCT	0.338																																					p.S3066fs		Atlas-INDEL	.											.	LYST	370	.	0			c.9197delC						.						89.0	88.0	88.0					1																	235887447		2203	4300	6503	SO:0001589	frameshift_variant	1130	exon39			.	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.9196delT	chr1.hg19:g.235887447delA	ENSP00000374444:p.Ser3066fs	191.0	0.0		291.0	18.0	NM_000081	O43274|Q5T2U9|Q96TD7|Q96TD8|Q99709|Q9H133	Frame_Shift_Del	DEL	ENST00000389794.3	hg19	CCDS31062.1																																																																																			.	.		0.338	LYST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097533.5		
TRAK2	66008	hgsc.bcm.edu	37	2	202245603	202245603	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:202245603delA	ENST00000332624.3	-	16	2836	c.2408delT	c.(2407-2409)ttgfs	p.L803fs		NM_015049.2	NP_055864.2	O60296	TRAK2_HUMAN	trafficking protein, kinesin binding 2	803					protein O-linked glycosylation (GO:0006493)|protein targeting (GO:0006605)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cytoplasm (GO:0005737)|endosome (GO:0005768)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GABA receptor binding (GO:0050811)|receptor binding (GO:0005102)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(12)|ovary(1)|skin(1)	23						TCGAGAGGCCAAAAAATTTTC	0.512																																					p.L803fs		Atlas-INDEL	.											.	TRAK2	62	.	0			c.2409delG						.						85.0	86.0	86.0					2																	202245603		2203	4300	6503	SO:0001589	frameshift_variant	66008	exon16			.	AB038951	CCDS2347.1	2q33.1	2012-03-05	2005-12-13	2005-12-13	ENSG00000115993	ENSG00000115993			13206	protein-coding gene	gene with protein product	"""gamma-aminobutyric acid(A) receptor-interacting factor"", ""milton homolog 2 (Drosophila)"", ""O-linked N-acetylglucosamine transferase interacting protein 98"""	607334	"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 3"""	ALS2CR3		11161814, 16380713, 20230862	Standard	NM_015049		Approved	CALS-C, KIAA0549, GRIF-1, OIP98, MILT2	uc002uyb.4	O60296	OTTHUMG00000132822	ENST00000332624.3:c.2408delT	chr2.hg19:g.202245603delA	ENSP00000328875:p.Leu803fs	243.0	0.0		156.0	10.0	NM_015049	E7EV21|Q8WVH7|Q96NS2|Q9C0K5|Q9C0K6	Frame_Shift_Del	DEL	ENST00000332624.3	hg19	CCDS2347.1																																																																																			.	.		0.512	TRAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256284.3	NM_015049	
ZNF705A	440077	hgsc.bcm.edu	37	12	8330032	8330032	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:8330032delA	ENST00000359286.4	+	5	845	c.756delA	c.(754-756)ggafs	p.G252fs	FAM66C_ENST00000541558.1_RNA|FAM66C_ENST00000454799.2_RNA|FAM66C_ENST00000544214.1_RNA|FAM66C_ENST00000456135.2_RNA	NM_001004328.2|NM_001278713.1	NP_001004328.1|NP_001265642.1	Q6ZN79	Z705A_HUMAN	zinc finger protein 705A	252					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|skin(3)|stomach(4)	18				Kidney(36;0.0877)		CTCACCTTGGAAAAAAGTGTT	0.388																																					p.G252fs		Atlas-INDEL	.											.	ZNF705A	32	.	0			c.755delG						.						38.0	42.0	41.0					12																	8330032		2194	4289	6483	SO:0001589	frameshift_variant	440077	exon5			.	AK131339	CCDS31737.1	12p13.31	2014-02-12	2005-09-22		ENSG00000196946	ENSG00000196946		"""Zinc fingers, C2H2-type"", ""-"""	32281	protein-coding gene	gene with protein product							Standard	NM_001004328		Approved	FLJ16353	uc001qud.1	Q6ZN79	OTTHUMG00000168635	ENST00000359286.4:c.756delA	chr12.hg19:g.8330032delA	ENSP00000352233:p.Gly252fs	396.0	0.0		275.0	17.0	NM_001004328		Frame_Shift_Del	DEL	ENST00000359286.4	hg19	CCDS31737.1																																																																																			.	.		0.388	ZNF705A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400449.1	NM_001004328	
TCF7L1	83439	hgsc.bcm.edu	37	2	85531091	85531091	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:85531091delC	ENST00000282111.3	+	6	1007	c.732delC	c.(730-732)atcfs	p.I244fs		NM_031283.2	NP_112573.1	Q9HCS4	TF7L1_HUMAN	transcription factor 7-like 1 (T-cell specific, HMG-box)	244	Pro-rich.				anterior/posterior axis specification, embryo (GO:0008595)|axial mesoderm morphogenesis (GO:0048319)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|chromatin organization (GO:0006325)|generation of neurons (GO:0048699)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter during mitosis (GO:0046022)|regulation of stem cell maintenance (GO:2000036)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|regulation of Wnt signaling pathway (GO:0030111)|skin development (GO:0043588)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|skin(4)|upper_aerodigestive_tract(1)	18						TCGGACAAATCCCCCACCCCC	0.632																																					p.I244fs		Atlas-INDEL	.											.	TCF7L1	44	.	0			c.731delT						.						103.0	97.0	99.0					2																	85531091		2203	4300	6503	SO:0001589	frameshift_variant	83439	exon6			.	X62870	CCDS1971.1	2p11.2	2008-02-05			ENSG00000152284	ENSG00000152284			11640	protein-coding gene	gene with protein product		604652		TCF3		1741298, 11085512	Standard	NM_031283		Approved		uc002soy.3	Q9HCS4	OTTHUMG00000130026	ENST00000282111.3:c.732delC	chr2.hg19:g.85531091delC	ENSP00000282111:p.Ile244fs	190.0	0.0		159.0	10.0	NM_031283	Q53R97|Q6PD70|Q9NP00	Frame_Shift_Del	DEL	ENST00000282111.3	hg19	CCDS1971.1																																																																																			.	.		0.632	TCF7L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252301.2	NM_031283	
SGOL2	151246	hgsc.bcm.edu	37	2	201436349	201436349	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:201436349delA	ENST00000357799.4	+	7	1378	c.1280delA	c.(1279-1281)gaafs	p.E427fs		NM_001160033.1|NM_001160046.1|NM_152524.5	NP_001153505.1|NP_001153518.1|NP_689737.4	Q562F6	SGOL2_HUMAN	shugoshin-like 2 (S. pombe)	427					meiotic sister chromatid cohesion, centromeric (GO:0051754)|mitotic cell cycle (GO:0000278)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|kinetochore (GO:0000776)|mitotic cohesin complex (GO:0030892)|nucleus (GO:0005634)				NS(2)|breast(2)|cervix(3)|endometrium(1)|kidney(2)|large_intestine(7)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	46						GATATTGGGGAAAAGATTGAA	0.378																																					p.E427fs		Atlas-INDEL	.											.	SGOL2	126	.	0			c.1279delG						.						79.0	77.0	77.0					2																	201436349		1831	4078	5909	SO:0001589	frameshift_variant	151246	exon7			.	AY094614	CCDS42796.1	2q33.2	2008-02-05			ENSG00000163535	ENSG00000163535			30812	protein-coding gene	gene with protein product		612425					Standard	NM_001160046		Approved	TRIPIN, FLJ25211	uc002uvw.2	Q562F6	OTTHUMG00000154535	ENST00000357799.4:c.1280delA	chr2.hg19:g.201436349delA	ENSP00000350447:p.Glu427fs	216.0	0.0		179.0	11.0	NM_001160046	Q53RR9|Q53T20|Q86XY4|Q8IWK2|Q8IZK1|Q8N1Q5|Q96LQ3	Frame_Shift_Del	DEL	ENST00000357799.4	hg19	CCDS42796.1																																																																																			.	.		0.378	SGOL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335834.1	NM_152524	
LEKR1	389170	hgsc.bcm.edu	37	3	156745953	156745953	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:156745953delA	ENST00000470811.1	+	13	1853	c.518delA	c.(517-519)gaafs	p.E173fs	LEKR1_ENST00000356539.4_Frame_Shift_Del_p.E477fs			Q6ZMV7	LEKR1_HUMAN	leucine, glutamate and lysine rich 1	173										breast(1)|large_intestine(5)|lung(3)|ovary(1)|skin(1)	11			LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)			ACTCTTAAAGAAAAACTTCAC	0.343																																					p.E477fs		Atlas-INDEL	.											LEKR1_ENST00000356539,NS,carcinoma,0,2	LEKR1	66	.	0			c.1429delG						.						59.0	62.0	61.0					3																	156745953		2202	4300	6502	SO:0001589	frameshift_variant	389170	exon12			.	AK131473	CCDS54660.1	3q25.31	2014-02-12	2008-02-21		ENSG00000197980	ENSG00000197980			33765	protein-coding gene	gene with protein product		613536					Standard	NM_001004316		Approved	FLJ16641	uc021xgh.1	Q6ZMV7	OTTHUMG00000160130	ENST00000470811.1:c.518delA	chr3.hg19:g.156745953delA	ENSP00000418214:p.Glu173fs	219.0	0.0		154.0	13.0	NM_001004316		Frame_Shift_Del	DEL	ENST00000470811.1	hg19																																																																																				.	.		0.343	LEKR1-010	KNOWN	upstream_ATG|basic	protein_coding	protein_coding	OTTHUMT00000351625.3	NM_001004316	
PRKD2	25865	hgsc.bcm.edu	37	19	47219519	47219519	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:47219519delG	ENST00000291281.4	-	1	334	c.109delC	c.(109-111)cagfs	p.Q37fs	PRKD2_ENST00000600194.1_5'Flank|PRKD2_ENST00000433867.1_Frame_Shift_Del_p.Q37fs|PRKD2_ENST00000601806.1_Intron|PRKD2_ENST00000595515.1_Frame_Shift_Del_p.Q37fs			Q9BZL6	KPCD2_HUMAN	protein kinase D2	37					angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell death (GO:0008219)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|endothelial tube morphogenesis (GO:0061154)|intracellular signal transduction (GO:0035556)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell adhesion (GO:0045785)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of endothelial cell chemotaxis (GO:2001028)|positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway (GO:0038033)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of histone deacetylase activity (GO:1901727)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of T cell receptor signaling pathway (GO:0050862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|T cell receptor signaling pathway (GO:0050852)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(13)|ovary(2)|prostate(2)|skin(1)|stomach(2)|urinary_tract(1)	41		Ovarian(192;0.0129)|all_neural(266;0.0459)|Breast(70;0.212)		OV - Ovarian serous cystadenocarcinoma(262;0.000189)|all cancers(93;0.000545)|Epithelial(262;0.0219)|GBM - Glioblastoma multiforme(486;0.0353)		GCCGGGATCTGGGGCAGTAGC	0.721																																					p.Q37fs		Atlas-INDEL	.											.	PRKD2	94	.	0			c.110delA						.						18.0	24.0	22.0					19																	47219519		2185	4261	6446	SO:0001589	frameshift_variant	25865	exon1			.	AF151021	CCDS12689.1, CCDS59401.1	19q13.2	2013-01-10				ENSG00000105287		"""Pleckstrin homology (PH) domain containing"""	17293	protein-coding gene	gene with protein product		607074				11042152, 11062248	Standard	NM_001079880		Approved	PKD2, HSPC187, DKFZP586E0820	uc002pfj.3	Q9BZL6		ENST00000291281.4:c.109delC	chr19.hg19:g.47219519delG	ENSP00000291281:p.Gln37fs	218.0	0.0		180.0	11.0	NM_016457	Q8TB08|Q9P0T6|Q9Y3X8	Frame_Shift_Del	DEL	ENST00000291281.4	hg19	CCDS12689.1																																																																																			.	.		0.721	PRKD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466591.1	NM_016457	
MAPK15	225689	hgsc.bcm.edu	37	8	144801240	144801240	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:144801240delC	ENST00000338033.4	+	6	614	c.495delC	c.(493-495)ctcfs	p.L165fs	RP11-429J17.5_ENST00000527908.1_RNA|MAPK15_ENST00000395108.2_Frame_Shift_Del_p.L165fs|MAPK15_ENST00000395107.4_Frame_Shift_Del_p.L182fs	NM_139021.2	NP_620590.2	Q8TD08	MK15_HUMAN	mitogen-activated protein kinase 15	165	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)			TGGGCGACCTCCCCGAGGGGC	0.642																																					p.L165fs		Atlas-INDEL	.											.	MAPK15	32	.	0			c.494delT						.						29.0	28.0	28.0					8																	144801240		2199	4297	6496	SO:0001589	frameshift_variant	225689	exon6			.	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.495delC	chr8.hg19:g.144801240delC	ENSP00000337691:p.Leu165fs	137.0	0.0		143.0	10.0	NM_139021	Q2TCF9|Q8N362	Frame_Shift_Del	DEL	ENST00000338033.4	hg19	CCDS6409.2																																																																																			.	.		0.642	MAPK15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000300348.1	NM_139021	
UNC13D	201294	hgsc.bcm.edu	37	17	73836368	73836368	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:73836368delG	ENST00000207549.4	-	10	1175	c.796delC	c.(796-798)cgcfs	p.R266fs	UNC13D_ENST00000412096.2_Frame_Shift_Del_p.R266fs|UNC13D_ENST00000587504.1_5'UTR	NM_199242.2	NP_954712.1	Q70J99	UN13D_HUMAN	unc-13 homolog D (C. elegans)	266	Interaction with RAB27A.				defense response to virus (GO:0051607)|germinal center formation (GO:0002467)|granuloma formation (GO:0002432)|natural killer cell degranulation (GO:0043320)|phagocytosis (GO:0006909)|positive regulation of exocytosis (GO:0045921)|regulation of mast cell degranulation (GO:0043304)	endosome (GO:0005768)|exocytic vesicle (GO:0070382)|lysosome (GO:0005764)|membrane (GO:0016020)				central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(9)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29			all cancers(21;2.11e-06)|Epithelial(20;2.32e-06)|BRCA - Breast invasive adenocarcinoma(9;0.000618)|LUSC - Lung squamous cell carcinoma(166;0.154)			GTCTCAGTGCGGGGTTCCAGG	0.652									Familial Hemophagocytic Lymphohistiocytosis																												p.R266fs		Atlas-INDEL	.											.	UNC13D	68	.	0			c.797delG						.						51.0	47.0	48.0					17																	73836368		2203	4300	6503	SO:0001589	frameshift_variant	201294	exon10	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	.	AK024474	CCDS11730.1	17q25.3	2014-09-17				ENSG00000092929			23147	protein-coding gene	gene with protein product		608897					Standard	NM_199242		Approved	Munc13-4	uc002jpp.3	Q70J99		ENST00000207549.4:c.796delC	chr17.hg19:g.73836368delG	ENSP00000207549:p.Arg266fs	196.0	0.0		155.0	10.0	NM_199242	B4DWG9|Q9H7K5	Frame_Shift_Del	DEL	ENST00000207549.4	hg19	CCDS11730.1																																																																																			.	.		0.652	UNC13D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448847.2	XM_113950	
PIPSL	266971	hgsc.bcm.edu	37	10	95720247	95720247	+	RNA	DEL	G	G	-	rs187242740	byFrequency	TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:95720247delG	ENST00000480546.1	-	0	1050					NR_002319.2		A2A3N6	PIPSL_HUMAN	PIP5K1A and PSMD4-like, pseudogene							cytoplasm (GO:0005737)	phosphatidylinositol phosphate kinase activity (GO:0016307)										AGAGCCTTTTGGGGGGCTGGT	0.517																																					.		Atlas-INDEL	.											.	.	.	.	0			.						.																																					266971	.			.	BC068549		10q23.33	2010-10-27	2010-10-27	2007-07-06	ENSG00000180764	ENSG00000180764		"""Proteasome (prosome, macropain) subunits"""	23733	pseudogene	pseudogene			"""proteasome (prosome, macropain) 26S subunit, non-ATPase, 4, pseudogene 2"", ""phosphatidylinositol-4-phosphate 5-kinase, type I-like 1"", ""PIP5K1A and PSMD4-like"""	PSMD4P2, PIP5K1L1		16344562	Standard	NR_002319		Approved	PIP5K1A-PSMD4, PIP5K1P3	uc009xuj.2	A2A3N6	OTTHUMG00000137480		chr10.hg19:g.95720247delG		431.0	0.0		347.0	21.0	.	Q6NUK8	RNA	DEL	ENST00000480546.1	hg19																																																																																				.	.		0.517	PIPSL-002	PUTATIVE	basic	processed_transcript	pseudogene	OTTHUMT00000351483.1	NR_002319	
ZRANB2	9406	hgsc.bcm.edu	37	1	71532574	71532574	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:71532574delT	ENST00000370920.3	-	9	1115	c.814delA	c.(814-816)agafs	p.R272fs	ZRANB2_ENST00000254821.6_Frame_Shift_Del_p.R272fs|ZRANB2_ENST00000477096.1_5'UTR|MIR186_ENST00000384988.1_RNA|ZRANB2-AS1_ENST00000450461.1_RNA|ZRANB2-AS1_ENST00000426999.1_RNA	NM_203350.2	NP_976225.1	O95218	ZRAB2_HUMAN	zinc finger, RAN-binding domain containing 2	272	Required for nuclear targeting.				mRNA processing (GO:0006397)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(4)|lung(4)|ovary(2)|stomach(1)	15						GAATAAGATCTTTTTCGTGGG	0.388																																					p.R272fs		Atlas-INDEL	.											ZRANB2_ENST00000370920,colon,carcinoma,0,2	ZRANB2	75	.	0			c.815delG						.						83.0	83.0	83.0					1																	71532574		2203	4300	6503	SO:0001589	frameshift_variant	9406	exon9			.	AF065391	CCDS659.1, CCDS660.1	1p31	2008-02-05	2006-06-28	2006-06-28	ENSG00000132485	ENSG00000132485		"""Zinc fingers, RAN-binding domain containing"""	13058	protein-coding gene	gene with protein product		604347	"""zinc finger protein 265"""	ZNF265		9931435	Standard	NM_005455		Approved	ZIS, ZIS1, ZIS2	uc001dft.3	O95218	OTTHUMG00000009660	ENST00000370920.3:c.814delA	chr1.hg19:g.71532574delT	ENSP00000359958:p.Arg272fs	231.0	0.0		163.0	11.0	NM_005455	D3DQ75|Q53GS3|Q59F92|Q5VV33|Q5VV34|Q8IXN6|Q9UP63	Frame_Shift_Del	DEL	ENST00000370920.3	hg19	CCDS659.1																																																																																			.	.		0.388	ZRANB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026636.1	NM_203350	
MLKL	197259	hgsc.bcm.edu	37	16	74725195	74725195	+	Frame_Shift_Del	DEL	T	T	-	rs56247416	byFrequency	TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:74725195delT	ENST00000308807.7	-	4	1165	c.702delA	c.(700-702)aaafs	p.K234fs	MLKL_ENST00000306247.7_Intron	NM_152649.2	NP_689862.1			mixed lineage kinase domain-like											breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(2)|lung(6)|skin(1)|stomach(2)	19						CAGCCTGGAGTTTTTTGAATA	0.438																																					p.L235fs		Atlas-INDEL	.											.	MLKL	51	.	0			c.703delC						.						255.0	264.0	261.0					16																	74725195		2198	4300	6498	SO:0001589	frameshift_variant	197259	exon4			.	AK091708	CCDS32487.1, CCDS45528.1	16q22.3	2008-02-05				ENSG00000168404			26617	protein-coding gene	gene with protein product		615153				12477932	Standard	NM_152649		Approved	FLJ34389	uc002fdb.2	Q8NB16		ENST00000308807.7:c.702delA	chr16.hg19:g.74725195delT	ENSP00000308351:p.Lys234fs	195.0	0.0		140.0	10.0	NM_152649		Frame_Shift_Del	DEL	ENST00000308807.7	hg19	CCDS32487.1																																																																																			.	.		0.438	MLKL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436403.3	NM_152649	
HIVEP3	59269	hgsc.bcm.edu	37	1	41978825	41978825	+	Frame_Shift_Del	DEL	C	C	-	rs2483689	byFrequency	TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:41978825delC	ENST00000372583.1	-	8	6952	c.6067delG	c.(6067-6069)gctfs	p.A2023fs	HIVEP3_ENST00000372584.1_Frame_Shift_Del_p.A2023fs|HIVEP3_ENST00000247584.5_Frame_Shift_Del_p.A2023fs|HIVEP3_ENST00000460604.1_5'UTR|HIVEP3_ENST00000429157.2_Frame_Shift_Del_p.A2023fs	NM_024503.4	NP_078779.2	Q5T1R4	ZEP3_HUMAN	human immunodeficiency virus type I enhancer binding protein 3	2023			A -> P (in dbSNP:rs2483689). {ECO:0000269|PubMed:10997877, ECO:0000269|PubMed:11161801, ECO:0000269|PubMed:15489334}.		positive regulation of transcription, DNA-templated (GO:0045893)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(3)|central_nervous_system(5)|endometrium(13)|kidney(3)|large_intestine(13)|lung(33)|ovary(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	85	Ovarian(52;0.00769)|all_hematologic(146;0.109)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0367)				CAAGGGAGAGCGCCCATGCCC	0.637																																					p.A2023fs		Atlas-INDEL	.											.	HIVEP3	235	.	0			c.6068delC						.						40.0	47.0	44.0					1																	41978825		2203	4300	6503	SO:0001589	frameshift_variant	59269	exon8			.	AF278765	CCDS463.1, CCDS44124.1	1p34	2013-01-08	2001-11-28		ENSG00000127124	ENSG00000127124		"""Zinc fingers, C2H2-type"""	13561	protein-coding gene	gene with protein product	"""kappabinding protein-1"""	606649	"""human immunodeficiency virus type I enhancer-binding protein 3"""			11161801	Standard	NR_038260		Approved	KRC, KBP1, KBP-1, SHN3, FLJ16752, KIAA1555, ZAS3, Schnurri-3, ZNF40C	uc001cha.4	Q5T1R4	OTTHUMG00000006361	ENST00000372583.1:c.6067delG	chr1.hg19:g.41978825delC	ENSP00000361664:p.Ala2023fs	222.0	0.0		194.0	12.0	NM_024503	A7YY91|Q5T1R5|Q9BZS0|Q9HCL7	Frame_Shift_Del	DEL	ENST00000372583.1	hg19	CCDS463.1																																																																																			.	.		0.637	HIVEP3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000016978.1	NM_024503	
NOTCH2	4853	hgsc.bcm.edu	37	1	120468081	120468081	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:120468081delC	ENST00000256646.2	-	25	4577	c.4358delG	c.(4357-4359)ggtfs	p.G1453fs	NOTCH2_ENST00000493703.1_5'Flank	NM_024408.3	NP_077719.2	Q04721	NOTC2_HUMAN	notch 2	1453	Negative regulatory region (NRR).				apoptotic process (GO:0006915)|atrial septum morphogenesis (GO:0060413)|bone remodeling (GO:0046849)|cell cycle arrest (GO:0007050)|cell fate determination (GO:0001709)|cell growth (GO:0016049)|ciliary body morphogenesis (GO:0061073)|determination of left/right symmetry (GO:0007368)|embryonic limb morphogenesis (GO:0030326)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|humoral immune response (GO:0006959)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|intracellular receptor signaling pathway (GO:0030522)|morphogenesis of an epithelial sheet (GO:0002011)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|placenta blood vessel development (GO:0060674)|positive regulation of apoptotic process (GO:0043065)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Ras protein signal transduction (GO:0046579)|pulmonary valve morphogenesis (GO:0003184)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cilium (GO:0005929)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|ligand-activated RNA polymerase II transcription factor binding transcription factor activity (GO:0038049)|receptor activity (GO:0004872)			breast(4)|central_nervous_system(6)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(9)|kidney(9)|large_intestine(19)|liver(1)|lung(57)|ovary(4)|pancreas(1)|prostate(7)|skin(24)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	158	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)		AGAACAGTCACCCCCATCCCA	0.582			"""N, F, Mis"""		"""marginal zone lymphoma, DLBCL"""				Alagille Syndrome																												p.G1453fs		Atlas-INDEL	.		Dom	yes		1	1p13-p11	4853	Notch homolog 2		L	.	NOTCH2	348	.	0			c.4359delT						.						78.0	77.0	77.0					1																	120468081		2203	4300	6503	SO:0001589	frameshift_variant	4853	exon25	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	.	AF315356	CCDS908.1	1p13-p11	2013-01-10	2010-06-24		ENSG00000134250	ENSG00000134250		"""Ankyrin repeat domain containing"""	7882	protein-coding gene	gene with protein product		600275	"""Notch (Drosophila) homolog 2"", ""Notch homolog 2 (Drosophila)"""			7698746	Standard	NM_001200001		Approved		uc001eik.3	Q04721	OTTHUMG00000012177	ENST00000256646.2:c.4358delG	chr1.hg19:g.120468081delC	ENSP00000256646:p.Gly1453fs	236.0	0.0		151.0	10.0	NM_024408	Q5T3X7|Q99734|Q9H240	Frame_Shift_Del	DEL	ENST00000256646.2	hg19	CCDS908.1																																																																																			.	.		0.582	NOTCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033679.1	NM_024408	
ATF7IP2	80063	hgsc.bcm.edu	37	16	10551340	10551340	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:10551340delA	ENST00000396560.2	+	7	1533	c.1306delA	c.(1306-1308)aaafs	p.K437fs	ATF7IP2_ENST00000543967.1_Intron|ATF7IP2_ENST00000396559.1_Frame_Shift_Del_p.K437fs|ATF7IP2_ENST00000324570.5_Frame_Shift_Del_p.K437fs|ATF7IP2_ENST00000356427.2_Frame_Shift_Del_p.K437fs	NM_024997.3	NP_079273.2	Q5U623	MCAF2_HUMAN	activating transcription factor 7 interacting protein 2	437					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				large_intestine(3)	3						AAAAGGAAGTAAAAAAATTAA	0.294																																					p.S435fs		Atlas-INDEL	.											.	ATF7IP2	40	.	0			c.1305delT						.						93.0	105.0	101.0					16																	10551340		2196	4295	6491	SO:0001589	frameshift_variant	80063	exon7			.	AK022730	CCDS10540.1, CCDS58422.1	16p13.2	2008-02-05			ENSG00000166669	ENSG00000166669			20397	protein-coding gene	gene with protein product		613645					Standard	NM_001256160		Approved	FLJ12668	uc002czu.3	Q5U623	OTTHUMG00000129749	ENST00000396560.2:c.1306delA	chr16.hg19:g.10551340delA	ENSP00000379808:p.Lys437fs	212.0	0.0		186.0	13.0	NM_024997	B2RNR2|Q53EZ7|Q658U2|Q6IS97|Q8N9X8|Q9H9L6	Frame_Shift_Del	DEL	ENST00000396560.2	hg19	CCDS10540.1																																																																																			.	.		0.294	ATF7IP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251961.1	NM_024997	
CAPS2	84698	hgsc.bcm.edu	37	12	75692472	75692472	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:75692472delA	ENST00000409445.3	-	12	1292	c.1096delT	c.(1096-1098)tatfs	p.Y366fs	CAPS2_ENST00000409799.1_Frame_Shift_Del_p.Y284fs|CAPS2_ENST00000393284.3_Frame_Shift_Del_p.Y134fs|CAPS2_ENST00000409004.1_5'UTR|CAPS2_ENST00000442339.2_Intron|RP11-560G2.1_ENST00000534648.2_RNA	NM_032606.3	NP_115995.2	Q9BXY5	CAYP2_HUMAN	calcyphosine 2	366							calcium ion binding (GO:0005509)			endometrium(2)|large_intestine(1)|lung(4)|ovary(2)|skin(1)	10						CTTACAACATAAAAATCACCA	0.383																																					p.Y366fs		Atlas-INDEL	.											.	CAPS2	96	.	0			c.1097delA						.						137.0	134.0	135.0					12																	75692472		2203	4299	6502	SO:0001589	frameshift_variant	84698	exon12			.	AF251056	CCDS9008.2, CCDS66424.1, CCDS73497.1	12q14.1	2013-01-10	2005-05-09		ENSG00000180881	ENSG00000180881		"""EF-hand domain containing"""	16471	protein-coding gene	gene with protein product		607724	"""calcyphosphine 2"""			11846421	Standard	NM_032606		Approved		uc001sxk.4	Q9BXY5	OTTHUMG00000152787	ENST00000409445.3:c.1096delT	chr12.hg19:g.75692472delA	ENSP00000386959:p.Tyr366fs	234.0	0.0		173.0	11.0	NM_032606	Q6PH84|Q8N242|Q8NAY5	Frame_Shift_Del	DEL	ENST00000409445.3	hg19	CCDS9008.2																																																																																			.	.		0.383	CAPS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000327880.2		
MYT1	4661	hgsc.bcm.edu	37	20	62851088	62851088	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr20:62851088delA	ENST00000328439.1	+	13	2358	c.1994delA	c.(1993-1995)gaafs	p.E665fs	MYT1_ENST00000536311.1_Frame_Shift_Del_p.E692fs|MYT1_ENST00000360149.4_Frame_Shift_Del_p.E367fs	NM_004535.2	NP_004526.1	Q99640	PMYT1_HUMAN	myelin transcription factor 1	0					G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of phosphatase activity (GO:0010923)|regulation of cell cycle (GO:0051726)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of mitosis (GO:0007088)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(12)|liver(1)|lung(17)|ovary(5)|prostate(2)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55	all_cancers(38;1.82e-11)|all_epithelial(29;3.3e-13)|Lung NSC(23;5.21e-10)|all_lung(23;1.92e-09)					GAGGTAGACGAAAATGGAACC	0.517																																					p.E665fs	GBM(59;481 1041 20555 21139 33705)	Atlas-INDEL	.											MYT1,caecum,carcinoma,0,2	MYT1	152	.	0			c.1993delG						.						108.0	100.0	103.0					20																	62851088		2203	4300	6503	SO:0001589	frameshift_variant	4661	exon13			.	M96980	CCDS13558.1	20q13.33	2014-03-24			ENSG00000196132	ENSG00000196132		"""Zinc fingers, C2HC-type containing"""	7622	protein-coding gene	gene with protein product	"""neural zinc finger transcription factor 2"""	600379		PLPB1		1280325, 9268380	Standard	NM_004535		Approved	MTF1, MYTI, ZC2HC4A, NZF2	uc002yii.3	Q01538	OTTHUMG00000149988	ENST00000328439.1:c.1994delA	chr20.hg19:g.62851088delA	ENSP00000327465:p.Glu665fs	334.0	0.0		196.0	15.0	NM_004535	B3KUN8|B4DXD4|D3DUA4|F8W164|I3L1V2|O14731|Q7LE24|Q8TCM9	Frame_Shift_Del	DEL	ENST00000328439.1	hg19	CCDS13558.1																																																																																			.	.		0.517	MYT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080297.1	NM_004535	
SSX2IP	117178	hgsc.bcm.edu	37	1	85127951	85127951	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:85127951delT	ENST00000342203.3	-	8	1120	c.857delA	c.(856-858)aagfs	p.K286fs	SSX2IP_ENST00000437941.2_Frame_Shift_Del_p.K259fs|SSX2IP_ENST00000370612.4_Frame_Shift_Del_p.K286fs|SSX2IP_ENST00000605755.1_Frame_Shift_Del_p.K259fs|SSX2IP_ENST00000603677.1_Intron	NM_001166293.1|NM_001166294.1|NM_014021.3	NP_001159765.1|NP_001159766.1|NP_054740.3	Q9Y2D8	ADIP_HUMAN	synovial sarcoma, X breakpoint 2 interacting protein	286					cell adhesion (GO:0007155)|centrosome organization (GO:0051297)|regulation of cell motility (GO:2000145)|regulation of Rac protein signal transduction (GO:0035020)	cell leading edge (GO:0031252)|cell-cell adherens junction (GO:0005913)|centriolar satellite (GO:0034451)|nucleus (GO:0005634)|protein complex (GO:0043234)				endometrium(5)|kidney(1)|large_intestine(4)|lung(6)|ovary(2)|urinary_tract(1)	19				all cancers(265;0.0053)|Epithelial(280;0.0214)|OV - Ovarian serous cystadenocarcinoma(397;0.173)		AATCATTTCCTTTTTCATTTG	0.333																																					p.K286fs		Atlas-INDEL	.											.	SSX2IP	53	.	0			c.858delG						.						156.0	175.0	169.0					1																	85127951		2203	4300	6503	SO:0001589	frameshift_variant	117178	exon8			.		CCDS699.1, CCDS53337.1	1p22.3	2008-02-05			ENSG00000117155	ENSG00000117155			16509	protein-coding gene	gene with protein product		608690					Standard	NM_014021		Approved		uc001dkj.3	Q9Y2D8	OTTHUMG00000009926	ENST00000342203.3:c.857delA	chr1.hg19:g.85127951delT	ENSP00000340279:p.Lys286fs	177.0	0.0		146.0	10.0	NM_001166293	A8K8W0|B4DFE3|D3DT13|J3KR02|Q6P2P8|Q6ULS1|Q7L168|Q9UIX0	Frame_Shift_Del	DEL	ENST00000342203.3	hg19	CCDS699.1																																																																																			.	.		0.333	SSX2IP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027469.1	NM_014021	
XRRA1	143570	hgsc.bcm.edu	37	11	74559430	74559430	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:74559430delG	ENST00000340360.6	-	15	1765	c.1434delC	c.(1432-1434)cccfs	p.P478fs	RN7SL239P_ENST00000490061.2_RNA|XRRA1_ENST00000321448.8_Frame_Shift_Del_p.P203fs|XRRA1_ENST00000527087.1_Frame_Shift_Del_p.P391fs	NM_182969.2	NP_892014.1			X-ray radiation resistance associated 1											breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(8)|prostate(3)	20						TATCCTTTGAGGGAGACTTGG	0.542																																					p.S479fs		Atlas-INDEL	.											.	XRRA1	46	.	0			c.1435delT						.						54.0	60.0	58.0					11																	74559430		2080	4189	6269	SO:0001589	frameshift_variant	143570	exon15			.	AK074152	CCDS44680.1, CCDS58159.1, CCDS58160.1	11q13.4	2010-03-19			ENSG00000166435	ENSG00000166435			18868	protein-coding gene	gene with protein product		609788				12908878, 17295261	Standard	NM_182969		Approved	FLJ00225	uc009yub.3	Q6P2D8		ENST00000340360.6:c.1434delC	chr11.hg19:g.74559430delG	ENSP00000339918:p.Pro478fs	210.0	0.0		155.0	12.0	NM_182969		Frame_Shift_Del	DEL	ENST00000340360.6	hg19	CCDS44680.1																																																																																			.	.		0.542	XRRA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384715.1	NM_182969	
MGAT5	4249	hgsc.bcm.edu	37	2	135107494	135107494	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:135107494delT	ENST00000409645.1	+	10	1483	c.1231delT	c.(1231-1233)tttfs	p.F411fs	MGAT5_ENST00000281923.2_Frame_Shift_Del_p.F411fs			Q09328	MGT5A_HUMAN	mannosyl (alpha-1,6-)-glycoprotein beta-1,6-N-acetyl-glucosaminyltransferase	411					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase activity (GO:0030144)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|liver(1)|lung(18)|ovary(3)|pancreas(1)|skin(3)	36				BRCA - Breast invasive adenocarcinoma(221;0.0964)		CCCTCAGCAGTTTTATACCAT	0.413																																					p.Q410fs		Atlas-INDEL	.											.	MGAT5	84	.	0			c.1230delG						.						135.0	130.0	132.0					2																	135107494		2203	4300	6503	SO:0001589	frameshift_variant	4249	exon9			.	D17716	CCDS2171.1	2q21	2013-02-25			ENSG00000152127	ENSG00000152127	2.4.1.155	"""Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"""	7049	protein-coding gene	gene with protein product		601774				8292036	Standard	NM_002410		Approved	GNT-V	uc002ttw.4	Q09328	OTTHUMG00000131681	ENST00000409645.1:c.1231delT	chr2.hg19:g.135107494delT	ENSP00000386377:p.Phe411fs	198.0	0.0		129.0	11.0	NM_002410	D3DP70	Frame_Shift_Del	DEL	ENST00000409645.1	hg19	CCDS2171.1																																																																																			.	.		0.413	MGAT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254584.3	NM_002410	
IRS1	3667	hgsc.bcm.edu	37	2	227659975	227659975	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:227659975delG	ENST00000305123.5	-	1	4500	c.3480delC	c.(3478-3480)cccfs	p.P1160fs	IRS1_ENST00000498335.1_5'Flank	NM_005544.2	NP_005535.1	P35568	IRS1_HUMAN	insulin receptor substrate 1	1160					cellular response to insulin stimulus (GO:0032869)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose homeostasis (GO:0042593)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lipid catabolic process (GO:0016042)|mammary gland development (GO:0030879)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of insulin secretion (GO:0046676)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fatty acid beta-oxidation (GO:0032000)|positive regulation of glucose import (GO:0046326)|positive regulation of glucose import in response to insulin stimulus (GO:2001275)|positive regulation of glucose metabolic process (GO:0010907)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of insulin receptor signaling pathway (GO:0046628)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|protein kinase B signaling (GO:0043491)|protein localization to nucleus (GO:0034504)|regulation of gene expression (GO:0010468)|response to insulin (GO:0032868)|response to peptide hormone (GO:0043434)|signal transduction (GO:0007165)	caveola (GO:0005901)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|insulin receptor complex (GO:0005899)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	insulin receptor binding (GO:0005158)|insulin-like growth factor receptor binding (GO:0005159)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein kinase C binding (GO:0005080)|SH2 domain binding (GO:0042169)|signal transducer activity (GO:0004871)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)	p.P1160P(1)		autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|endometrium(5)|kidney(4)|large_intestine(10)|lung(33)|ovary(6)|pancreas(1)|prostate(1)|urinary_tract(2)	69		Renal(207;0.023)|all_lung(227;0.0994)|all_hematologic(139;0.118)|Esophageal squamous(248;0.23)		Epithelial(121;3.03e-11)|all cancers(144;2.42e-08)|Lung(261;0.00712)|LUSC - Lung squamous cell carcinoma(224;0.0137)		CTGGCTCCTTGGGGGCTCCCC	0.582																																					p.K1161fs		Atlas-INDEL	.											.	IRS1	141	.	1	Substitution - coding silent(1)	breast(1)	c.3481delA						.						50.0	59.0	56.0					2																	227659975		2203	4300	6503	SO:0001589	frameshift_variant	3667	exon1			.		CCDS2463.1	2q36	2013-01-10			ENSG00000169047	ENSG00000169047		"""Pleckstrin homology (PH) domain containing"""	6125	protein-coding gene	gene with protein product		147545				1648180	Standard	NM_005544		Approved	HIRS-1	uc002voh.4	P35568	OTTHUMG00000133179	ENST00000305123.5:c.3480delC	chr2.hg19:g.227659975delG	ENSP00000304895:p.Pro1160fs	162.0	0.0		112.0	10.0	NM_005544		Frame_Shift_Del	DEL	ENST00000305123.5	hg19	CCDS2463.1																																																																																			.	.		0.582	IRS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256886.3	NM_005544	
MYSM1	114803	hgsc.bcm.edu	37	1	59137586	59137586	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:59137586delT	ENST00000472487.1	-	12	1656	c.1617delA	c.(1615-1617)aaafs	p.K539fs	MYSM1_ENST00000493821.1_5'UTR	NM_001085487.2	NP_001078956.1	Q5VVJ2	MYSM1_HUMAN	Myb-like, SWIRM and MPN domains 1	539					chromatin remodeling (GO:0006338)|monoubiquitinated histone H2A deubiquitination (GO:0035522)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone binding (GO:0042393)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|protein complex binding (GO:0032403)|transcription coactivator activity (GO:0003713)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(6)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	24	all_cancers(7;9.36e-06)					CAGGTCTGCCTTTTTCCTCTT	0.343																																					p.G540fs		Atlas-INDEL	.											.	MYSM1	50	.	0			c.1618delG						.						132.0	120.0	124.0					1																	59137586		1824	4092	5916	SO:0001589	frameshift_variant	114803	exon12			.	AB067502	CCDS41343.1	1p32.1	2009-02-11	2009-02-11		ENSG00000162601	ENSG00000162601			29401	protein-coding gene	gene with protein product		612176				11572484, 17428495, 17707232	Standard	NM_001085487		Approved	KIAA1915	uc009wab.2	Q5VVJ2	OTTHUMG00000009533	ENST00000472487.1:c.1617delA	chr1.hg19:g.59137586delT	ENSP00000418734:p.Lys539fs	277.0	0.0		164.0	10.0	NM_001085487	A8KA54|B3KX65|Q68DD3|Q6AI53|Q7Z3G8|Q96PX3	Frame_Shift_Del	DEL	ENST00000472487.1	hg19	CCDS41343.1																																																																																			.	.		0.343	MYSM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026343.2	XM_055481	
CALD1	800	hgsc.bcm.edu	37	7	134618168	134618168	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:134618168delA	ENST00000361675.2	+	5	877	c.648delA	c.(646-648)acafs	p.T217fs	CALD1_ENST00000422748.1_Intron|CALD1_ENST00000543443.1_Intron|CALD1_ENST00000424922.1_Intron|CALD1_ENST00000361388.2_Intron|CALD1_ENST00000417172.1_Intron|CALD1_ENST00000495522.1_Intron|CALD1_ENST00000361901.2_Intron|CALD1_ENST00000393118.2_Intron			Q05682	CALD1_HUMAN	caldesmon 1	217					cellular component movement (GO:0006928)|muscle contraction (GO:0006936)	actin cap (GO:0030478)|actin cytoskeleton (GO:0015629)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|calmodulin binding (GO:0005516)|tropomyosin binding (GO:0005523)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(15)|lung(10)	43						aagagaaAACAACTGAAAGCC	0.453																																					p.T216fs		Atlas-INDEL	.											.	CALD1	150	.	0			c.647delC						.						81.0	76.0	78.0					7																	134618168		2203	4300	6503	SO:0001589	frameshift_variant	800	exon5			.	M64110	CCDS5834.1, CCDS5835.1, CCDS5836.1, CCDS47716.1, CCDS47717.1, CCDS5836.2	7q33	2007-04-23			ENSG00000122786	ENSG00000122786			1441	protein-coding gene	gene with protein product		114213				1885618	Standard	NM_004342		Approved	CDM, H-CAD, L-CAD	uc003vrz.3	Q05682	OTTHUMG00000155407	ENST00000361675.2:c.648delA	chr7.hg19:g.134618168delA	ENSP00000354826:p.Thr217fs	111.0	0.0		142.0	10.0	NM_033138	A8K0X1|Q13978|Q13979|Q14741|Q14742|Q9UD91	Frame_Shift_Del	DEL	ENST00000361675.2	hg19	CCDS5835.1																																																																																			.	.		0.453	CALD1-005	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339939.1	NM_033138	
CYLD	1540	hgsc.bcm.edu	37	16	50811827	50811827	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:50811827delA	ENST00000427738.3	+	7	1318	c.1113delA	c.(1111-1113)tcafs	p.S371fs	CYLD_ENST00000566206.1_Frame_Shift_Del_p.S368fs|CYLD_ENST00000569418.1_Frame_Shift_Del_p.S368fs|CYLD_ENST00000568704.2_Frame_Shift_Del_p.S368fs|CYLD_ENST00000540145.1_Frame_Shift_Del_p.S371fs|CYLD_ENST00000311559.9_Frame_Shift_Del_p.S371fs|CYLD_ENST00000564326.1_Frame_Shift_Del_p.S368fs|CYLD_ENST00000398568.2_Frame_Shift_Del_p.S368fs			Q9NQC7	CYLD_HUMAN	cylindromatosis (turban tumor syndrome)	371	Interaction with TRIP.				cell cycle (GO:0007049)|innate immune response (GO:0045087)|necroptotic process (GO:0070266)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|protein K63-linked deubiquitination (GO:0070536)|regulation of intrinsic apoptotic signaling pathway (GO:2001242)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of mitotic cell cycle (GO:0007346)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)	centrosome (GO:0005813)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|microtubule (GO:0005874)|nucleus (GO:0005634)	Lys63-specific deubiquitinase activity (GO:0061578)|proline-rich region binding (GO:0070064)|protein kinase binding (GO:0019901)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			central_nervous_system(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(9)|lung(17)|pancreas(1)|skin(22)|upper_aerodigestive_tract(1)	62		all_cancers(37;0.0156)				AATCCAAATCAAAAAATACAT	0.313			"""Mis, N, F, S"""		cylindroma	cylindroma			Multiple Trichoepithelioma, Familial;Familial Cylindromatosis																												p.S371X		Atlas-INDEL	.	yes	Rec	yes	Familial cylindromatosis	16	16q12-q13	1540	familial cylindromatosis gene		E	CYLD,colon,carcinoma,-1,1	CYLD	150	.	0			c.1112delC						.						86.0	80.0	81.0					16																	50811827		1813	4063	5876	SO:0001589	frameshift_variant	1540	exon9	Familial Cancer Database	;FADC, Turban Tumor syndrome, Epithelioma Adenoides Cysticum of Brooke, Hereditary Multiple Benign Cystic Epithelioma, Dermal Eccrine Cylindromatosis, Brooke-Spiegler s.	.	AB020656	CCDS42164.1, CCDS45482.1	16q12-q13	2014-09-17							2584	protein-coding gene	gene with protein product	"""ubiquitin specific peptidase like 2"""	605018		CYLD1		7493027	Standard	NM_015247		Approved	KIAA0849, USPL2	uc002egq.1	Q9NQC7		ENST00000427738.3:c.1113delA	chr16.hg19:g.50811827delA	ENSP00000392025:p.Ser371fs	165.0	0.0		152.0	10.0	NM_015247	O94934|Q7L3N6|Q96EH0|Q9NZX9	Frame_Shift_Del	DEL	ENST00000427738.3	hg19	CCDS45482.1																																																																																			.	.		0.313	CYLD-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000422998.2		
FHOD3	80206	hgsc.bcm.edu	37	18	34320658	34320658	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr18:34320658delA	ENST00000359247.4	+	17	3040	c.3040delA	c.(3040-3042)aaafs	p.K1014fs	FHOD3_ENST00000257209.4_Frame_Shift_Del_p.K1031fs|FHOD3_ENST00000590592.1_Frame_Shift_Del_p.K1206fs|FHOD3_ENST00000591635.1_Frame_Shift_Del_p.K227fs|FHOD3_ENST00000592128.1_Frame_Shift_Del_p.K10fs|FHOD3_ENST00000445677.1_Frame_Shift_Del_p.K993fs	NM_001281739.1	NP_001268668.1	Q2V2M9	FHOD3_HUMAN	formin homology 2 domain containing 3	1014	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				actin filament network formation (GO:0051639)|cardiac myofibril assembly (GO:0055003)|negative regulation of actin filament polymerization (GO:0030837)|sarcomere organization (GO:0045214)	striated muscle thin filament (GO:0005865)				NS(1)|breast(5)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(25)|liver(2)|lung(29)|ovary(3)|prostate(4)|skin(5)|upper_aerodigestive_tract(1)	90		all_epithelial(2;0.0181)|Colorectal(2;0.0195)				GGAGAAGCAGAAAATCCAGGA	0.507																																					p.Q1030fs		Atlas-INDEL	.											.	FHOD3	210	.	0			c.3090delG						.						69.0	62.0	65.0					18																	34320658		2203	4300	6503	SO:0001589	frameshift_variant	80206	exon18			.	AK091899	CCDS32816.1, CCDS62418.1, CCDS62419.1	18q12	2007-08-02				ENSG00000134775			26178	protein-coding gene	gene with protein product		609691				11214970	Standard	NM_025135		Approved	FHOS2, KIAA1695, FLJ22297, FLJ22717	uc021uiv.1	Q2V2M9		ENST00000359247.4:c.3040delA	chr18.hg19:g.34320658delA	ENSP00000352186:p.Lys1014fs	239.0	0.0		190.0	12.0	NM_025135	A8MQT4|E5F5Q0|Q642I2|Q6ZRQ7|Q86TF9|Q8N3A5|Q9C0G8|Q9H604|Q9H6G7	Frame_Shift_Del	DEL	ENST00000359247.4	hg19																																																																																				.	.		0.507	FHOD3-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460884.1	XM_371114	
HP1BP3	50809	hgsc.bcm.edu	37	1	21097452	21097452	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:21097452delT	ENST00000312239.5	-	6	764	c.625delA	c.(625-627)agafs	p.R209fs	HP1BP3_ENST00000375003.2_Frame_Shift_Del_p.R57fs	NM_016287.3	NP_057371.2	Q5SSJ5	HP1B3_HUMAN	heterochromatin protein 1, binding protein 3	209	H15 1. {ECO:0000255|PROSITE- ProRule:PRU00837}.				nucleosome assembly (GO:0006334)	nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(5)|prostate(2)|skin(2)|urinary_tract(1)	16		all_lung(284;6.55e-06)|Lung NSC(340;6.59e-06)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|COAD - Colon adenocarcinoma(152;1.26e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00015)|GBM - Glioblastoma multiforme(114;0.000521)|Kidney(64;0.000529)|STAD - Stomach adenocarcinoma(196;0.00311)|KIRC - Kidney renal clear cell carcinoma(64;0.00687)|READ - Rectum adenocarcinoma(331;0.0655)|Lung(427;0.201)		TTTAATTCTCTTTTCAGTGCT	0.358																																					p.R209fs		Atlas-INDEL	.											.	HP1BP3	47	.	0			c.626delG						.						165.0	157.0	160.0					1																	21097452		2203	4300	6503	SO:0001589	frameshift_variant	50809	exon6			.	BC053327	CCDS30621.1	1p36.12	2008-02-05			ENSG00000127483	ENSG00000127483			24973	protein-coding gene	gene with protein product						12477932	Standard	NM_016287		Approved	HP1-BP74	uc001bdw.1	Q5SSJ5	OTTHUMG00000002622	ENST00000312239.5:c.625delA	chr1.hg19:g.21097452delT	ENSP00000312625:p.Arg209fs	222.0	0.0		133.0	10.0	NM_016287	A6NI71|A8K5D7|B3KMZ8|B4E210|Q05BI0|Q5SSJ6|Q5SWC6|Q6PIM9|Q8NDF0|Q9UHY0	Frame_Shift_Del	DEL	ENST00000312239.5	hg19	CCDS30621.1																																																																																			.	.		0.358	HP1BP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007457.2	NM_016287	
FASTKD1	79675	hgsc.bcm.edu	37	2	170428277	170428277	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:170428277delT	ENST00000453153.2	-	2	609	c.263delA	c.(262-264)aatfs	p.N88fs	FASTKD1_ENST00000453929.2_Frame_Shift_Del_p.N88fs	NM_024622.3	NP_078898.3	Q53R41	FAKD1_HUMAN	FAST kinase domains 1	88					cellular respiration (GO:0045333)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(5)|large_intestine(10)|lung(9)|ovary(4)|prostate(3)	37						ATACTCAGCATTTTTTAACAG	0.343																																					p.N88fs		Atlas-INDEL	.											.	FASTKD1	86	.	0			c.264delT						.						93.0	87.0	89.0					2																	170428277		2203	4300	6503	SO:0001589	frameshift_variant	79675	exon2			.	AL832058	CCDS33318.1, CCDS63051.1	2q31.1	2008-02-05			ENSG00000138399	ENSG00000138399			26150	protein-coding gene	gene with protein product						11347906	Standard	NM_024622		Approved	FLJ21901	uc002uev.4	Q53R41	OTTHUMG00000154953	ENST00000453153.2:c.263delA	chr2.hg19:g.170428277delT	ENSP00000400513:p.Asn88fs	269.0	0.0		227.0	14.0	NM_024622	Q8N583|Q8TEA9|Q96JM5|Q96N71|Q9H6T4	Frame_Shift_Del	DEL	ENST00000453153.2	hg19	CCDS33318.1																																																																																			.	.		0.343	FASTKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337788.2	NM_024622	
PAXIP1	22976	hgsc.bcm.edu	37	7	154768002	154768002	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:154768002delT	ENST00000404141.1	-	6	632	c.478delA	c.(478-480)attfs	p.I160fs	PAXIP1_ENST00000473219.1_5'UTR|PAXIP1_ENST00000397192.1_Frame_Shift_Del_p.I160fs			Q6ZW49	PAXI1_HUMAN	PAX interacting (with transcription-activation domain) protein 1	160	BRCT 2. {ECO:0000255|PROSITE- ProRule:PRU00033}.|Interaction with PAGR1. {ECO:0000250}.				adipose tissue development (GO:0060612)|chorion development (GO:0060717)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|endothelial cell migration (GO:0043542)|histone H3-K4 methylation (GO:0051568)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone H3-K36 methylation (GO:0000416)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of isotype switching (GO:0045830)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|response to ionizing radiation (GO:0010212)|transcription, DNA-templated (GO:0006351)|vasculogenesis (GO:0001570)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)				NS(1)|breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	33	all_neural(206;0.119)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.0296)	UCEC - Uterine corpus endometrioid carcinoma (81;0.178)		GGAGTCACAATTTTAATACTT	0.368																																					p.I160fs		Atlas-INDEL	.											.	PAXIP1	150	.	0			c.479delT						.						79.0	77.0	78.0					7																	154768002		1859	4119	5978	SO:0001589	frameshift_variant	22976	exon6			.	U80735	CCDS47753.1	7q36	2007-07-06	2005-04-05	2005-04-05	ENSG00000157212	ENSG00000157212			8624	protein-coding gene	gene with protein product		608254	"""PAX transcription activation domain interacting protein 1 like"""	PAXIP1L		9225980	Standard	XM_005249539		Approved	CAGF29, CAGF28, TNRC2, PTIP	uc022aqf.1	Q6ZW49	OTTHUMG00000151322	ENST00000404141.1:c.478delA	chr7.hg19:g.154768002delT	ENSP00000384048:p.Ile160fs	195.0	0.0		177.0	12.0	NM_007349	O15404|Q6N099|Q6ZWH9|Q7Z315|Q86UN0|Q8N4P9|Q96HP2	Frame_Shift_Del	DEL	ENST00000404141.1	hg19	CCDS47753.1																																																																																			.	.		0.368	PAXIP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322223.1	NM_007349	
TRNAU1AP	54952	hgsc.bcm.edu	37	1	28906485	28906485	+	IGR	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:28906485delG	ENST00000373830.3	+	0	1793				SNHG12_ENST00000483436.1_RNA|SNHG12_ENST00000384581.1_RNA|SNHG12_ENST00000475441.1_RNA|SNHG12_ENST00000488745.1_RNA|SNHG12_ENST00000384584.1_RNA|SNHG12_ENST00000531126.1_RNA|SNORD99_ENST00000408612.1_RNA|SNHG12_ENST00000384342.1_RNA	NM_017846.4	NP_060316.1	Q9NX07	TSAP1_HUMAN	tRNA selenocysteine 1 associated protein 1						selenocysteine incorporation (GO:0001514)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(2)|large_intestine(2)|ovary(1)|pancreas(1)|skin(1)	8						CAGGAAACTTGGGGGCAACCT	0.507																																					.		Atlas-INDEL	.											.	.	.	.	0			.						.																																			SO:0001628	intergenic_variant	85028	.			.		CCDS324.1	1p35.3	2013-02-12	2008-09-05	2008-09-05	ENSG00000180098	ENSG00000180098		"""RNA binding motif (RRM) containing"""	30813	protein-coding gene	gene with protein product			"""tRNA selenocysteine associated protein 1"""	TRSPAP1		10606267, 16230358	Standard	NM_017846		Approved	SECP43, FLJ20503	uc001bqi.3	Q9NX07	OTTHUMG00000003653		chr1.hg19:g.28906485delG		199.0	0.0		161.0	10.0	.	Q86SU7	RNA	DEL	ENST00000373830.3	hg19	CCDS324.1																																																																																			.	.		0.507	TRNAU1AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010346.1	NM_017846	
PIGW	284098	hgsc.bcm.edu	37	17	34893402	34893402	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:34893402delT	ENST00000592983.1	+	2	1032	c.452delT	c.(451-453)cttfs	p.L151fs	MYO19_ENST00000431794.3_5'Flank|MYO19_ENST00000544606.1_5'Flank|PIGW_ENST00000328396.2_Frame_Shift_Del_p.L151fs|MYO19_ENST00000590081.1_Intron|MYO19_ENST00000268852.9_5'Flank|MYO19_ENST00000586007.1_5'Flank			Q7Z7B1	PIGW_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class W	151					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	transferase activity, transferring acyl groups (GO:0016746)			breast(2)|endometrium(3)|kidney(1)|large_intestine(1)|lung(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13		Breast(25;0.00957)|Ovarian(249;0.17)	Kidney(155;0.104)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		GACTTCCCACTTTTTCCCAGA	0.433																																					p.L151fs		Atlas-INDEL	.											.	PIGW	50	.	0			c.451delC						.						228.0	226.0	227.0					17																	34893402		2203	4300	6503	SO:0001589	frameshift_variant	284098	exon2			.	AB097818	CCDS11313.1	17q21.1	2014-05-06	2006-06-28		ENSG00000184886	ENSG00000277161		"""Phosphatidylinositol glycan anchor biosynthesis"""	23213	protein-coding gene	gene with protein product		610275	"""phosphatidylinositol glycan, class W"""			14517336, 12714589	Standard	XM_005257238		Approved	Gwt1, FLJ37433	uc002hmz.1	Q7Z7B1	OTTHUMG00000188438	ENST00000592983.1:c.452delT	chr17.hg19:g.34893402delT	ENSP00000468778:p.Leu151fs	311.0	0.0		246.0	15.0	NM_178517	Q8N9G3	Frame_Shift_Del	DEL	ENST00000592983.1	hg19	CCDS11313.1																																																																																			.	.		0.433	PIGW-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451318.1	NM_178517	
NEMF	9147	hgsc.bcm.edu	37	14	50267183	50267183	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr14:50267183delT	ENST00000298310.5	-	23	2776	c.2327delA	c.(2326-2328)aatfs	p.N776fs	NEMF_ENST00000546046.1_Frame_Shift_Del_p.N755fs|NEMF_ENST00000545773.1_Frame_Shift_Del_p.N734fs|NEMF_ENST00000556925.1_5'UTR			O60524	NEMF_HUMAN	nuclear export mediator factor	776					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						ATCAGGATAATTTAATGTCTC	0.348																																					p.N776fs		Atlas-INDEL	.											.	NEMF	79	.	0			c.2328delT						.						133.0	117.0	123.0					14																	50267183		2203	4300	6503	SO:0001589	frameshift_variant	9147	exon23			.	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.2327delA	chr14.hg19:g.50267183delT	ENSP00000298310:p.Asn776fs	273.0	0.0		204.0	14.0	NM_004713	A0JLQ3|B3KSK1|B4DDL3|B4DHA9|B4E3F3|Q32Q66|Q8WW70|Q9NWG1	Frame_Shift_Del	DEL	ENST00000298310.5	hg19	CCDS9694.1																																																																																			.	.		0.348	NEMF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410798.1	NM_004713	
MED25	81857	hgsc.bcm.edu	37	19	50339074	50339074	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:50339074delC	ENST00000312865.6	+	16	1890	c.1837delC	c.(1837-1839)cccfs	p.P615fs	PTOV1-AS1_ENST00000596521.1_RNA|MED25_ENST00000538643.1_Frame_Shift_Del_p.P402fs	NM_030973.3	NP_112235.2	Q71SY5	MED25_HUMAN	mediator complex subunit 25	615	Interaction with RARA.|Pro-rich.				cell death (GO:0008219)|gene expression (GO:0010467)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of chromatin binding (GO:0035563)|positive regulation of mediator complex assembly (GO:2001178)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)	retinoic acid receptor binding (GO:0042974)|retinoid X receptor binding (GO:0046965)|transcription factor binding (GO:0008134)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(6)|ovary(1)|stomach(1)|urinary_tract(1)	17		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00822)|GBM - Glioblastoma multiforme(134;0.0122)		TACTGCCCAGCCCCCGCCAGG	0.721																																					p.Q612fs	GBM(51;894 1657 37868)	Atlas-INDEL	.											.	MED25	98	.	0			c.1836delG						.																																			SO:0001589	frameshift_variant	81857	exon16			.	AL136746	CCDS33075.1	19q13.3	2014-09-17	2007-07-30			ENSG00000104973			28845	protein-coding gene	gene with protein product		610197	"""mediator of RNA polymerase II transcription, subunit 25 homolog (S. cerevisiae)"""			9110174, 11230166	Standard	NM_030973		Approved	ARC92, ACID1, TCBAP0758, DKFZp434K0512	uc002ppw.2	Q71SY5		ENST00000312865.6:c.1837delC	chr19.hg19:g.50339074delC	ENSP00000326767:p.Pro615fs	187.0	0.0		147.0	11.0	NM_030973	A8K095|B9TX30|O95783|Q6P143|Q6QMH5|Q707U4|Q8TB55|Q9H0L5|Q9HB34	Frame_Shift_Del	DEL	ENST00000312865.6	hg19	CCDS33075.1																																																																																			.	.		0.721	MED25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465316.1	NM_030973	
FASTKD3	79072	hgsc.bcm.edu	37	5	7867919	7867919	+	Frame_Shift_Del	DEL	T	T	-	rs79525539	byFrequency	TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:7867919delT	ENST00000264669.5	-	2	414	c.278delA	c.(277-279)aatfs	p.N93fs	FASTKD3_ENST00000513658.1_Intron|MTRR_ENST00000341013.6_5'Flank|MTRR_ENST00000440940.2_5'Flank|MTRR_ENST00000502509.1_Intron|MTRR_ENST00000264668.2_5'Flank	NM_024091.3	NP_076996.2	Q14CZ7	FAKD3_HUMAN	FAST kinase domains 3	93					cellular respiration (GO:0045333)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)			breast(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|liver(2)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39						ATTTTTAACATTTTGTTCAAG	0.413																																					p.N93fs		Atlas-INDEL	.											.	FASTKD3	88	.	0			c.279delT						.						67.0	65.0	66.0					5																	7867919		2203	4300	6503	SO:0001589	frameshift_variant	79072	exon2			.	AK026927	CCDS3873.1	5p15.31	2008-02-05			ENSG00000124279	ENSG00000124279			28758	protein-coding gene	gene with protein product						12477932	Standard	NM_024091		Approved	MGC5297, FLJ23274	uc003jeb.3	Q14CZ7	OTTHUMG00000131029	ENST00000264669.5:c.278delA	chr5.hg19:g.7867919delT	ENSP00000264669:p.Asn93fs	196.0	0.0		151.0	10.0	NM_024091	Q9BVD3	Frame_Shift_Del	DEL	ENST00000264669.5	hg19	CCDS3873.1																																																																																			.	.		0.413	FASTKD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253673.1	NM_024091	
ZNF234	10780	hgsc.bcm.edu	37	19	44660629	44660629	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:44660629delA	ENST00000426739.2	+	6	718	c.460delA	c.(460-462)aaafs	p.K155fs	ZNF234_ENST00000592437.1_Frame_Shift_Del_p.K155fs	NM_006630.2	NP_006621.1	Q14588	ZN234_HUMAN	zinc finger protein 234	155					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(11)|ovary(1)|prostate(1)	23		Prostate(69;0.0435)				TGATGAGTACAAAAAATCCTT	0.403																																					p.Y153X		Atlas-INDEL	.											.	ZNF234	132	.	0			c.459delC						.						63.0	68.0	66.0					19																	44660629		2193	4295	6488	SO:0001589	frameshift_variant	10780	exon6			.	X78927	CCDS46101.1	19q13	2013-01-08				ENSG00000263002		"""Zinc fingers, C2H2-type"", ""-"""	13027	protein-coding gene	gene with protein product		604750		ZNF269		7865130	Standard	NM_006630		Approved	HZF4	uc002oyl.4	Q14588		ENST00000426739.2:c.460delA	chr19.hg19:g.44660629delA	ENSP00000400878:p.Lys155fs	300.0	0.0		169.0	11.0	NM_006630	A8K1C8|Q96IR4|Q9NS45|Q9NYT7	Frame_Shift_Del	DEL	ENST00000426739.2	hg19	CCDS46101.1																																																																																			.	.		0.403	ZNF234-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460586.2		
ARHGAP17	55114	hgsc.bcm.edu	37	16	24964264	24964264	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:24964264delG	ENST00000289968.6	-	11	1021	c.952delC	c.(952-954)catfs	p.H318fs	ARHGAP17_ENST00000441763.2_3'UTR|ARHGAP17_ENST00000575975.1_5'Flank|ARHGAP17_ENST00000303665.5_Frame_Shift_Del_p.H318fs	NM_001006634.1	NP_001006635.1	Q68EM7	RHG17_HUMAN	Rho GTPase activating protein 17	318	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	GTPase activator activity (GO:0005096)			breast(2)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(3)|lung(13)|ovary(1)|urinary_tract(2)	30				GBM - Glioblastoma multiforme(48;0.0407)		GCTACAGCATGGGGGTCTGAA	0.507																																					p.H318fs		Atlas-INDEL	.											.	ARHGAP17	138	.	0			c.953delA						.						92.0	91.0	91.0					16																	24964264		2197	4300	6497	SO:0001589	frameshift_variant	55114	exon11			.	AJ306731	CCDS32408.1, CCDS32409.1	16p12.2-p12.1	2011-06-29				ENSG00000140750		"""Rho GTPase activating proteins"""	18239	protein-coding gene	gene with protein product		608293				10967100, 11431473	Standard	XM_005255413		Approved	RICH1, FLJ10308, NADRIN, FLJ13219, WBP15	uc002dnb.3	Q68EM7		ENST00000289968.6:c.952delC	chr16.hg19:g.24964264delG	ENSP00000289968:p.His318fs	236.0	0.0		160.0	10.0	NM_001006634	A8K6M6|Q6ZUS4|Q7Z2F2|Q8NDG2|Q96KS2|Q96KS3|Q96SS8|Q9BVF6|Q9H8U5|Q9NW54	Frame_Shift_Del	DEL	ENST00000289968.6	hg19	CCDS32409.1																																																																																			.	.		0.507	ARHGAP17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436548.3	NM_018054	
CHUK	1147	hgsc.bcm.edu	37	10	101964874	101964874	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:101964874delT	ENST00000370397.7	-	12	1400	c.1314delA	c.(1312-1314)aaafs	p.K438fs		NM_001278.3	NP_001269.3	O15111	IKKA_HUMAN	conserved helix-loop-helix ubiquitous kinase	438					anatomical structure morphogenesis (GO:0009653)|cellular response to tumor necrosis factor (GO:0071356)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell proliferation (GO:0033598)|morphogenesis of an epithelial sheet (GO:0002011)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoclast differentiation (GO:0030316)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|protein phosphorylation (GO:0006468)|response to amino acid (GO:0043200)|response to drug (GO:0042493)|response to hydroperoxide (GO:0033194)|response to lipopolysaccharide (GO:0032496)|response to toxic substance (GO:0009636)|response to virus (GO:0009615)|Rho protein signal transduction (GO:0007266)|skeletal muscle contraction (GO:0003009)|striated muscle cell differentiation (GO:0051146)|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)	CD40 receptor complex (GO:0035631)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|IkappaB kinase complex (GO:0008385)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	ATP binding (GO:0005524)|IkappaB kinase activity (GO:0008384)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|scaffold protein binding (GO:0097110)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(9)|lung(8)|ovary(2)|prostate(1)|skin(1)|stomach(1)	27		Colorectal(252;0.117)		Epithelial(162;2.05e-10)|all cancers(201;1.91e-08)	Acetylcysteine(DB06151)|Aminosalicylic Acid(DB00233)|Mesalazine(DB00244)|Sulfasalazine(DB00795)	TATAGTCTTCTTTTAGTCCAG	0.398																																					p.E439fs	Ovarian(159;52 1904 10536 35305 37148)	Atlas-INDEL	.											.	CHUK	71	.	0			c.1315delG						.						194.0	170.0	178.0					10																	101964874		2203	4300	6503	SO:0001589	frameshift_variant	1147	exon12			.	AF009225	CCDS7488.1	10q24-q25	2008-08-01			ENSG00000213341	ENSG00000213341			1974	protein-coding gene	gene with protein product		600664		TCF16		7558004, 16902410	Standard	XR_246062		Approved	IKK1, IKK-alpha, IkBKA, NFKBIKA, IKKA	uc001kqp.3	O15111	OTTHUMG00000018899	ENST00000370397.7:c.1314delA	chr10.hg19:g.101964874delT	ENSP00000359424:p.Lys438fs	207.0	0.0		174.0	12.0	NM_001278	O14666|Q13132|Q5W0I4|Q92467	Frame_Shift_Del	DEL	ENST00000370397.7	hg19	CCDS7488.1																																																																																			.	.		0.398	CHUK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049836.1	NM_001278	
CCDC178	374864	hgsc.bcm.edu	37	18	30846924	30846924	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr18:30846924delT	ENST00000383096.3	-	14	1547	c.1365delA	c.(1363-1365)aaafs	p.K455fs	CCDC178_ENST00000583930.1_Frame_Shift_Del_p.K455fs|CCDC178_ENST00000579947.1_Frame_Shift_Del_p.K455fs|CCDC178_ENST00000579916.1_Intron|CCDC178_ENST00000406524.2_Frame_Shift_Del_p.K455fs|CCDC178_ENST00000402325.1_Frame_Shift_Del_p.K455fs|CCDC178_ENST00000300227.8_Frame_Shift_Del_p.K455fs|CCDC178_ENST00000403303.1_Frame_Shift_Del_p.K455fs			Q5BJE1	CC178_HUMAN	coiled-coil domain containing 178	455																	CAATCTCAAGTTTTTTATTGT	0.269																																					p.L456fs		Atlas-INDEL	.											.	.	.	.	0			c.1366delC						.						50.0	48.0	49.0					18																	30846924		2201	4285	6486	SO:0001589	frameshift_variant	374864	exon13			.	AK126038	CCDS11906.1, CCDS42424.1	18q12.1	2012-10-15	2012-10-15	2012-10-15	ENSG00000166960	ENSG00000166960			29588	protein-coding gene	gene with protein product			"""chromosome 18 open reading frame 34"""	C18orf34			Standard	NM_198995		Approved	FLJ44050	uc002kxn.2	Q5BJE1	OTTHUMG00000132279	ENST00000383096.3:c.1365delA	chr18.hg19:g.30846924delT	ENSP00000372576:p.Lys455fs	278.0	0.0		225.0	17.0	NM_001105528	A6NDC6|J3KS92|Q6ZP67|Q6ZU20	Frame_Shift_Del	DEL	ENST00000383096.3	hg19	CCDS42424.1																																																																																			.	.		0.269	CCDC178-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255373.2	NM_198995	
MAOB	4129	hgsc.bcm.edu	37	X	43637948	43637948	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:43637948delC	ENST00000378069.4	-	11	1265	c.1118delG	c.(1117-1119)ggtfs	p.G373fs	MAOB_ENST00000538942.1_Frame_Shift_Del_p.G357fs|MAOB_ENST00000536181.1_Frame_Shift_Del_p.G357fs	NM_000898.4	NP_000889.3	P27338	AOFB_HUMAN	monoamine oxidase B	373					negative regulation of serotonin secretion (GO:0014063)|positive regulation of dopamine metabolic process (GO:0045964)|response to aluminum ion (GO:0010044)|response to corticosterone (GO:0051412)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)|xenobiotic metabolic process (GO:0006805)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrial envelope (GO:0005740)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|primary amine oxidase activity (GO:0008131)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(1)|liver(1)|lung(3)|ovary(1)|prostate(2)|skin(5)	21					Amantadine(DB00915)|Amphetamine(DB00182)|Dopamine(DB00988)|Ephedra(DB01363)|Flavin adenine dinucleotide(DB03147)|Furazolidone(DB00614)|Isocarboxazid(DB01247)|Linezolid(DB00601)|Methamphetamine(DB01577)|Moclobemide(DB01171)|Nandrolone decanoate(DB08804)|Nicotine(DB00184)|Pargyline(DB01626)|Phenelzine(DB00780)|Phentermine(DB00191)|Procaine(DB00721)|Rasagiline(DB01367)|Selegiline(DB01037)|Sertraline(DB01104)|Tranylcypromine(DB00752)|Zonisamide(DB00909)	TTCTAGGGAACCCAGAACCTT	0.443																																					p.G373fs		Atlas-INDEL	.											.	MAOB	52	.	0			c.1119delT						.						71.0	58.0	63.0					X																	43637948		2203	4300	6503	SO:0001589	frameshift_variant	4129	exon11			.		CCDS14261.1	Xp11.4-p11.3	2008-02-05			ENSG00000069535	ENSG00000069535	1.4.3.4		6834	protein-coding gene	gene with protein product		309860					Standard	NM_000898		Approved		uc004dfz.4	P27338	OTTHUMG00000021388	ENST00000378069.4:c.1118delG	chrX.hg19:g.43637948delC	ENSP00000367309:p.Gly373fs	257.0	0.0		175.0	12.0	NM_000898	B2R6R3|B7Z5H3|D3DWC3|Q7Z6S2	Frame_Shift_Del	DEL	ENST00000378069.4	hg19	CCDS14261.1																																																																																			.	.		0.443	MAOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056303.1	NM_000898	
FAM118B	79607	hgsc.bcm.edu	37	11	126120425	126120425	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:126120425delT	ENST00000533050.1	+	5	857	c.364delT	c.(364-366)tttfs	p.F123fs	FAM118B_ENST00000525728.1_3'UTR|FAM118B_ENST00000360194.4_Frame_Shift_Del_p.F123fs|FAM118B_ENST00000529731.1_Intron	NM_024556.3	NP_078832.1	Q9BPY3	F118B_HUMAN	family with sequence similarity 118, member B	123										breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|skin(1)	13	all_hematologic(175;0.145)	Breast(109;0.00156)|Lung NSC(97;0.00948)|all_lung(97;0.0101)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.15e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0784)		TCGATCCACATTTTTCAAGGA	0.378																																					p.T121fs		Atlas-INDEL	.											.	FAM118B	29	.	0			c.363delA						.						90.0	90.0	90.0					11																	126120425		2201	4299	6500	SO:0001589	frameshift_variant	79607	exon5			.	BC001340	CCDS8470.1	11q24.2	2014-03-13				ENSG00000197798			26110	protein-coding gene	gene with protein product						24569877	Standard	NM_024556		Approved	FLJ21103	uc001qdf.3	Q9BPY3		ENST00000533050.1:c.364delT	chr11.hg19:g.126120425delT	ENSP00000433343:p.Phe123fs	220.0	0.0		160.0	10.0	NM_024556	Q9H7B0	Frame_Shift_Del	DEL	ENST00000533050.1	hg19	CCDS8470.1																																																																																			.	.		0.378	FAM118B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386346.1	NM_024556	
C10orf55	414236	hgsc.bcm.edu	37	10	75673438	75673438	+	Intron	DEL	G	G	-	rs549461157	byFrequency	TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:75673438delG	ENST00000409178.1	-	3	268				C10orf55_ENST00000412307.2_Intron|PLAU_ENST00000446342.1_Frame_Shift_Del_p.R184fs|PLAU_ENST00000372764.3_Frame_Shift_Del_p.R201fs|PLAU_ENST00000372762.4_Frame_Shift_Del_p.R165fs|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,Pindel	.											.,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		282.0	0.0		215.0	13.0	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	
CASC5	57082	hgsc.bcm.edu	37	15	40913467	40913467	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:40913467delT	ENST00000346991.5	+	11	1473	c.1083delT	c.(1081-1083)aatfs	p.N361fs	CASC5_ENST00000527044.1_3'UTR|CASC5_ENST00000399668.2_Frame_Shift_Del_p.N335fs			Q8NG31	CASC5_HUMAN	cancer susceptibility candidate 5	361	Interaction with BUB1 and BUB1B.				acrosome assembly (GO:0001675)|attachment of spindle microtubules to kinetochore (GO:0008608)|CENP-A containing nucleosome assembly (GO:0034080)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of phosphatase activity (GO:0010923)|nucleosome assembly (GO:0006334)|protein localization to kinetochore (GO:0034501)|spindle assembly checkpoint (GO:0071173)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				NS(1)|breast(7)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(13)|lung(16)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	57		all_cancers(109;2.03e-18)|all_epithelial(112;4.26e-15)|Lung NSC(122;1.12e-10)|all_lung(180;2.59e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;4.99e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0861)|COAD - Colon adenocarcinoma(120;0.211)		CAACAGGTAATTTTTCTGAAA	0.328																																					p.N361fs		Atlas-INDEL	.											CASC5_ENST00000346991,colon,carcinoma,0,2	CASC5	269	.	0			c.1082delA						.						59.0	56.0	57.0					15																	40913467		1823	4082	5905	SO:0001589	frameshift_variant	57082	exon11			.	AF173994	CCDS42023.1, CCDS42024.1	15q14	2013-07-03			ENSG00000137812	ENSG00000137812		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	24054	protein-coding gene	gene with protein product	"""cancer/testis antigen 29"", ""kinetochore null 1 homolog (C. elegans)"", ""blinkin, bub-linking kinetochore protein"", ""protein phosphatase 1, regulatory subunit 55"""	609173				10980622, 10780384, 18045986	Standard	NM_170589		Approved	D40, AF15Q14, CT29, hKNL-1, KNL1, hSpc105, PPP1R55, Spc7	uc010bbt.1	Q8NG31	OTTHUMG00000166532	ENST00000346991.5:c.1083delT	chr15.hg19:g.40913467delT	ENSP00000335463:p.Asn361fs	175.0	0.0		137.0	10.0	NM_170589	Q8NHE1|Q8WXA6|Q9HCK2|Q9NR92	Frame_Shift_Del	DEL	ENST00000346991.5	hg19	CCDS42023.1																																																																																			.	.		0.328	CASC5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390224.2	NM_144508	
CCDC138	165055	hgsc.bcm.edu	37	2	109473308	109473308	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:109473308delA	ENST00000295124.4	+	13	1635	c.1575delA	c.(1573-1575)ggafs	p.G525fs	CCDC138_ENST00000412964.2_Frame_Shift_Del_p.G525fs	NM_144978.1	NP_659415.1	Q96M89	CC138_HUMAN	coiled-coil domain containing 138	525										endometrium(1)|large_intestine(3)|lung(7)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	14						CAGAAGAAGGAAAAACCTTGT	0.373																																					p.G525fs		Atlas-INDEL	.											.	CCDC138	49	.	0			c.1574delG						.						190.0	196.0	194.0					2																	109473308		2203	4300	6503	SO:0001589	frameshift_variant	165055	exon13			.	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.1575delA	chr2.hg19:g.109473308delA	ENSP00000295124:p.Gly525fs	231.0	0.0		137.0	11.0	NM_144978	Q05DF1|Q4ZG07|Q53TE1|Q6ZUY5|Q86VL7	Frame_Shift_Del	DEL	ENST00000295124.4	hg19	CCDS2080.1																																																																																			.	.		0.373	CCDC138-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253593.1	NM_144978	
MAGED1	9500	hgsc.bcm.edu	37	X	51637805	51637806	+	Intron	DEL	TG	TG	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:51637805_51637806delTG	ENST00000375722.1	+	3	297				MAGED1_ENST00000375772.3_Intron|MAGED1_ENST00000326587.7_Intron|MAGED1_ENST00000375695.2_Frame_Shift_Del_p.L43fs|MAGED1_ENST00000494718.1_Intron			Q9Y5V3	MAGD1_HUMAN	melanoma antigen family D, 1						apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|circadian regulation of gene expression (GO:0032922)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of apoptotic process (GO:0042981)|regulation of circadian rhythm (GO:0042752)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	transcription coactivator activity (GO:0003713)			breast(1)|endometrium(4)|large_intestine(10)|lung(13)|ovary(3)|upper_aerodigestive_tract(1)	32	Ovarian(276;0.236)					TTCCCCACTCTGTGCGACCCCC	0.584										Multiple Myeloma(10;0.10)																											p.43_43del		Atlas-Indel,Pindel	.											.	MAGED1	84	.	0			c.127_128del						.																																			SO:0001627	intron_variant	9500	exon3			.	AF124440	CCDS14337.1, CCDS35279.1	Xp11.23	2008-08-01			ENSG00000179222	ENSG00000179222			6813	protein-coding gene	gene with protein product		300224				10409427	Standard	NM_006986		Approved	NRAGE, DLXIN-1	uc004dpn.3	Q9Y5V3	OTTHUMG00000021540	ENST00000375722.1:c.46-343TG>-	chrX.hg19:g.51637807_51637808delTG		223.0	0.0		130.0	85.0	NM_001005333	Q5VSH6|Q8IZ84|Q8WY92|Q9H352|Q9HBT4|Q9UF36	Frame_Shift_Del	DEL	ENST00000375722.1	hg19	CCDS14337.1																																																																																			.	.		0.584	MAGED1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056593.1	NM_001005332	
TPTE2	93492	hgsc.bcm.edu	37	13	20039443	20039443	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr13:20039443delT	ENST00000400230.2	-	9	672	c.628delA	c.(628-630)aggfs	p.R211fs	TPTE2_ENST00000400103.2_Frame_Shift_Del_p.R100fs|TPTE2_ENST00000457266.2_Frame_Shift_Del_p.R100fs|TPTE2_ENST00000255310.6_Frame_Shift_Del_p.R134fs|TPTE2_ENST00000382975.4_Frame_Shift_Del_p.R171fs|TPTE2_ENST00000390680.2_Frame_Shift_Del_p.R134fs|TPTE2_ENST00000382977.4_Frame_Shift_Del_p.R211fs|TPTE2_ENST00000382978.1_Frame_Shift_Del_p.R171fs			Q6XPS3	TPTE2_HUMAN	transmembrane phosphoinositide 3-phosphatase and tensin homolog 2	211	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.				phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(2)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(8)|lung(21)|pancreas(1)|prostate(8)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		all_cancers(29;1.23e-20)|all_lung(29;1.97e-20)|all_epithelial(30;5.86e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;1.73e-05)|Epithelial(112;7.42e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000785)|Lung(94;0.0176)|LUSC - Lung squamous cell carcinoma(192;0.089)		GTGTATCGCCTTTTGTTTTCT	0.313																																					p.R210fs		Atlas-INDEL	.											.	TPTE2	225	.	0			c.629delG						.						182.0	168.0	173.0					13																	20039443		2203	4300	6503	SO:0001589	frameshift_variant	93492	exon10			.	AJ421032	CCDS9285.1, CCDS45013.1, CCDS45014.1	13q12.11	2012-12-10			ENSG00000132958	ENSG00000132958		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"""	17299	protein-coding gene	gene with protein product		606791				11716755, 12717346, 15057823	Standard	NM_130785		Approved	TPIP	uc001umd.3	Q6XPS3	OTTHUMG00000016493	ENST00000400230.2:c.628delA	chr13.hg19:g.20039443delT	ENSP00000383089:p.Arg211fs	253.0	0.0		191.0	12.0	NM_199254	A1A4X0|A1A4X1|A8MX64|B1AQ16|B4DWZ2|Q5VUH2|Q8WWL4|Q8WWL5	Frame_Shift_Del	DEL	ENST00000400230.2	hg19	CCDS45014.1																																																																																			.	.		0.313	TPTE2-205	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_199254	
SLC35F5	80255	hgsc.bcm.edu	37	2	114493428	114493428	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:114493428delA	ENST00000245680.2	-	8	1171	c.758delT	c.(757-759)ttgfs	p.L253fs		NM_025181.2	NP_079457.2	Q8WV83	S35F5_HUMAN	solute carrier family 35, member F5	253	EamA.				transport (GO:0006810)	integral component of membrane (GO:0016021)				endometrium(1)|kidney(4)|large_intestine(2)|lung(7)|ovary(2)|prostate(3)|skin(1)	20						CAAATTTGCCAAAAACCACTA	0.313																																					p.L253fs		Atlas-INDEL	.											.	SLC35F5	60	.	0			c.759delG						.						36.0	36.0	36.0					2																	114493428		2202	4292	6494	SO:0001589	frameshift_variant	80255	exon8			.	AF529364	CCDS2119.1	2q14.1	2013-05-22			ENSG00000115084	ENSG00000115084		"""Solute carriers"""	23617	protein-coding gene	gene with protein product							Standard	XM_005263799		Approved	FLJ22004	uc002tku.1	Q8WV83	OTTHUMG00000131361	ENST00000245680.2:c.758delT	chr2.hg19:g.114493428delA	ENSP00000245680:p.Leu253fs	277.0	0.0		203.0	14.0	NM_025181	Q9H6P8|Q9H7D8	Frame_Shift_Del	DEL	ENST00000245680.2	hg19	CCDS2119.1																																																																																			.	.		0.313	SLC35F5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254150.1	NM_025181	
INTS8	55656	hgsc.bcm.edu	37	8	95877744	95877744	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:95877744delT	ENST00000523731.1	+	17	2220	c.2087delT	c.(2086-2088)cttfs	p.L697fs	INTS8_ENST00000520845.1_Intron|INTS8_ENST00000447247.1_Frame_Shift_Del_p.L697fs	NM_017864.2	NP_060334.2	Q75QN2	INT8_HUMAN	integrator complex subunit 8	697					snRNA processing (GO:0016180)	integrator complex (GO:0032039)				breast(3)|endometrium(3)|kidney(1)|large_intestine(9)|liver(1)|lung(9)|prostate(1)|upper_aerodigestive_tract(1)	28	Breast(36;1.05e-06)					CTTGGACAGCTTTTAGCAGCT	0.398																																					p.L696fs		Atlas-INDEL	.											.	INTS8	92	.	0			c.2086delC						.						99.0	94.0	96.0					8																	95877744		2203	4300	6503	SO:0001589	frameshift_variant	55656	exon17			.	AK091278	CCDS34925.1	8q22.1	2007-05-03	2006-03-15	2006-03-15	ENSG00000164941	ENSG00000164941			26048	protein-coding gene	gene with protein product		611351	"""chromosome 8 open reading frame 52"""	C8orf52		16239144	Standard	NM_017864		Approved	FLJ20530, INT8, MGC131633	uc003yhb.4	Q75QN2	OTTHUMG00000164695	ENST00000523731.1:c.2087delT	chr8.hg19:g.95877744delT	ENSP00000430338:p.Leu697fs	230.0	0.0		291.0	18.0	NM_017864	B2RN92|Q5RKZ3|Q6P1R5|Q7Z314|Q9NVS6|Q9NWY7	Frame_Shift_Del	DEL	ENST00000523731.1	hg19	CCDS34925.1																																																																																			.	.		0.398	INTS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379794.1	NM_017864	
SENP6	26054	hgsc.bcm.edu	37	6	76312282	76312282	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:76312282delT	ENST00000447266.2	+	1	520	c.42delT	c.(40-42)actfs	p.T14fs	SENP6_ENST00000370014.3_Frame_Shift_Del_p.T14fs|SENP6_ENST00000327284.8_Frame_Shift_Del_p.T14fs|SENP6_ENST00000370010.2_Frame_Shift_Del_p.T14fs	NM_015571.2	NP_056386.2	Q9GZR1	SENP6_HUMAN	SUMO1/sentrin specific peptidase 6	14					protein desumoylation (GO:0016926)|protein modification by small protein removal (GO:0070646)|protein sumoylation (GO:0016925)|regulation of kinetochore assembly (GO:0090234)|regulation of spindle assembly (GO:0090169)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	SUMO-specific protease activity (GO:0016929)			breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(2)|lung(12)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		all_hematologic(105;0.189)				GGGAGATTACTTTTCTGGAAG	0.607																																					p.T14fs		Atlas-INDEL	.											.	SENP6	189	.	0			c.41delC						.						32.0	38.0	36.0					6																	76312282		1764	3787	5551	SO:0001589	frameshift_variant	26054	exon1			.		CCDS43483.1, CCDS47454.1	6q13-q14.3	2008-02-05	2005-08-17		ENSG00000112701	ENSG00000112701			20944	protein-coding gene	gene with protein product		605003	"""SUMO1/sentrin specific protease 6"""				Standard	NM_015571		Approved	SUSP1, KIAA0797	uc003pid.4	Q9GZR1	OTTHUMG00000015060	ENST00000447266.2:c.42delT	chr6.hg19:g.76312282delT	ENSP00000402527:p.Thr14fs	204.0	0.0		159.0	10.0	NM_015571	A6NNY9|O94891|Q5VUL3|Q5VUL4|Q8TBY4|Q9UJV5	Frame_Shift_Del	DEL	ENST00000447266.2	hg19	CCDS47454.1																																																																																			.	.		0.607	SENP6-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041272.2	NM_015571	
PCNX	22990	hgsc.bcm.edu	37	14	71500186	71500186	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr14:71500186delT	ENST00000304743.2	+	17	4045	c.3599delT	c.(3598-3600)attfs	p.I1200fs	PCNX_ENST00000439984.3_Frame_Shift_Del_p.I1089fs|PCNX_ENST00000238570.5_Frame_Shift_Del_p.I1200fs	NM_014982.2	NP_055797.2	Q96RV3	PCX1_HUMAN	pecanex homolog (Drosophila)	1200						integral component of membrane (GO:0016021)				NS(2)|biliary_tract(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(14)|liver(2)|lung(40)|ovary(1)|prostate(7)|skin(2)|urinary_tract(1)	87			KIRC - Kidney renal clear cell carcinoma(12;0.206)	all cancers(60;0.00835)|BRCA - Breast invasive adenocarcinoma(234;0.00951)|OV - Ovarian serous cystadenocarcinoma(108;0.0417)		CTTTTCTCCATTTTTTGTGGT	0.338																																					p.I1200fs		Atlas-INDEL	.											.	PCNX	198	.	0			c.3598delA						.						168.0	150.0	156.0					14																	71500186		2203	4300	6503	SO:0001589	frameshift_variant	22990	exon17			.	AF233450, AB018348	CCDS9806.1	14q24.2	2014-07-03							19740	protein-coding gene	gene with protein product			"""pecanex-like 1 (Drosophila)"""	PCNXL1		9244429, 15777640	Standard	NM_014982		Approved	KIAA0995, KIAA0805, pecanex	uc001xmo.2	Q96RV3		ENST00000304743.2:c.3599delT	chr14.hg19:g.71500186delT	ENSP00000304192:p.Ile1200fs	212.0	0.0		163.0	11.0	NM_014982	B2RTR6|O94897|Q96AI7|Q9Y2J9	Frame_Shift_Del	DEL	ENST00000304743.2	hg19	CCDS9806.1																																																																																			.	.		0.338	PCNX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412479.1	NM_014982	
ZNF425	155054	hgsc.bcm.edu	37	7	148800796	148800796	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:148800796delA	ENST00000378061.2	-	4	2299	c.2167delT	c.(2167-2169)tctfs	p.S723fs		NM_001001661.2	NP_001001661.1	Q6IV72	ZN425_HUMAN	zinc finger protein 425	723					negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(6)|endometrium(4)|kidney(3)|large_intestine(11)|lung(20)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	50	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00463)			TCATCACAAGAAAAAGGCCTC	0.577																																					p.S723fs		Atlas-INDEL	.											.	ZNF425	99	.	0			c.2168delC						.						75.0	67.0	70.0					7																	148800796		2203	4300	6503	SO:0001589	frameshift_variant	155054	exon4			.	AK056498	CCDS34773.1	7q36.1	2013-01-08			ENSG00000204947	ENSG00000204947		"""Zinc fingers, C2H2-type"", ""-"""	20690	protein-coding gene	gene with protein product							Standard	NM_001001661		Approved		uc003wfj.3	Q6IV72	OTTHUMG00000158971	ENST00000378061.2:c.2167delT	chr7.hg19:g.148800796delA	ENSP00000367300:p.Ser723fs	173.0	0.0		182.0	11.0	NM_001001661	B3KPM1|Q08AG3	Frame_Shift_Del	DEL	ENST00000378061.2	hg19	CCDS34773.1																																																																																			.	.		0.577	ZNF425-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352726.1	XM_088140	
ZCCHC14	23174	hgsc.bcm.edu	37	16	87445899	87445899	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:87445899delG	ENST00000268616.4	-	12	2234	c.2017delC	c.(2017-2019)cggfs	p.R673fs		NM_015144.2	NP_055959.1	Q8WYQ9	ZCH14_HUMAN	zinc finger, CCHC domain containing 14	673							nucleic acid binding (GO:0003676)|phosphatidylinositol binding (GO:0035091)|zinc ion binding (GO:0008270)	p.R673R(1)		breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	36				BRCA - Breast invasive adenocarcinoma(80;0.0285)		AGAGCAGTCCGGGGGTTTATT	0.512																																					p.R673fs		Atlas-INDEL	.											.	ZCCHC14	87	.	1	Substitution - coding silent(1)	lung(1)	c.2018delG						.						77.0	94.0	88.0					16																	87445899		2197	4290	6487	SO:0001589	frameshift_variant	23174	exon12			.	AB011151	CCDS10961.1	16q24.2	2013-01-10			ENSG00000140948	ENSG00000140948		"""Zinc fingers, CCHC domain containing"", ""Sterile alpha motif (SAM) domain containing"""	24134	protein-coding gene	gene with protein product						9628581	Standard	XM_005255858		Approved	BDG29, MGC14139	uc002fjz.1	Q8WYQ9	OTTHUMG00000137655	ENST00000268616.4:c.2017delC	chr16.hg19:g.87445899delG	ENSP00000268616:p.Arg673fs	243.0	0.0		229.0	15.0	NM_015144	D3DUN1|O60324|Q3MJD8|Q9UFP0	Frame_Shift_Del	DEL	ENST00000268616.4	hg19	CCDS10961.1																																																																																			.	.		0.512	ZCCHC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269107.1	NM_015144	
DYNC2H1	79659	hgsc.bcm.edu	37	11	103090657	103090657	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:103090657delA	ENST00000375735.2	+	56	8990	c.8846delA	c.(8845-8847)caafs	p.Q2949fs	DYNC2H1_ENST00000334267.7_Intron|DYNC2H1_ENST00000398093.3_Frame_Shift_Del_p.Q2949fs	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	2949	Stalk. {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)		GCTAGTGAGCAAAAAACAGAA	0.259																																					p.Q2949fs		Atlas-INDEL	.											.	DYNC2H1	246	.	0			c.8845delC						.						43.0	41.0	42.0					11																	103090657		1788	4046	5834	SO:0001589	frameshift_variant	79659	exon56			.	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.8846delA	chr11.hg19:g.103090657delA	ENSP00000364887:p.Gln2949fs	271.0	0.0		258.0	17.0	NM_001377	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Frame_Shift_Del	DEL	ENST00000375735.2	hg19	CCDS53701.1																																																																																			.	.		0.259	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652	
WNT2	7472	hgsc.bcm.edu	37	7	116962981	116962981	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:116962981delG	ENST00000265441.3	-	1	362	c.63delC	c.(61-63)cccfs	p.P21fs	AC002465.2_ENST00000436097.1_RNA	NM_003391.2	NP_003382.1	P09544	WNT2_HUMAN	wingless-type MMTV integration site family member 2	21					atrial cardiac muscle tissue morphogenesis (GO:0055009)|canonical Wnt signaling pathway (GO:0060070)|cardiac epithelial to mesenchymal transition (GO:0060317)|cell fate commitment (GO:0045165)|cell-cell signaling (GO:0007267)|cellular response to retinoic acid (GO:0071300)|cellular response to transforming growth factor beta stimulus (GO:0071560)|iris morphogenesis (GO:0061072)|labyrinthine layer blood vessel development (GO:0060716)|lens development in camera-type eye (GO:0002088)|lung development (GO:0030324)|lung induction (GO:0060492)|mammary gland epithelium development (GO:0061180)|neuron differentiation (GO:0030182)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	cytokine activity (GO:0005125)|frizzled binding (GO:0005109)|receptor agonist activity (GO:0048018)			breast(2)|central_nervous_system(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|liver(1)|lung(13)|ovary(3)|prostate(1)|skin(2)	31	all_epithelial(6;2.24e-06)|Lung NSC(10;0.000936)|all_lung(10;0.00109)		STAD - Stomach adenocarcinoma(10;0.000512)	LUSC - Lung squamous cell carcinoma(290;0.133)		AGTTGACCTCGGGGGTGAGCC	0.602																																					p.E22fs		Atlas-INDEL	.											.	WNT2	56	.	0			c.64delG						.						79.0	79.0	79.0					7																	116962981		2203	4300	6503	SO:0001589	frameshift_variant	7472	exon1			.	X07876	CCDS5771.1	7q31	2013-02-28			ENSG00000105989	ENSG00000105989		"""Wingless-type MMTV integration sites"", ""Endogenous ligands"""	12780	protein-coding gene	gene with protein product	"""secreted growth factor"""	147870		INT1L1		2971536	Standard	NM_003391		Approved	IRP	uc003viz.3	P09544	OTTHUMG00000023428	ENST00000265441.3:c.63delC	chr7.hg19:g.116962981delG	ENSP00000265441:p.Pro21fs	102.0	0.0		105.0	10.0	NM_003391	A4D0V1|Q75N05|Q9UDP9	Frame_Shift_Del	DEL	ENST00000265441.3	hg19	CCDS5771.1																																																																																			.	.		0.602	WNT2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059749.3	NM_003391	
BCL9L	283149	hgsc.bcm.edu	37	11	118779099	118779099	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:118779099delG	ENST00000334801.3	-	2	1256	c.292delC	c.(292-294)cagfs	p.Q98fs	BCL9L_ENST00000526143.1_5'UTR|MIR4492_ENST00000581627.1_RNA	NM_182557.2	NP_872363.1	Q86UU0	BCL9L_HUMAN	B-cell CLL/lymphoma 9-like	98					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)		ACCCCTGCCTGGGGGTTCTTC	0.642																																					p.Q98fs		Atlas-INDEL	.											.	BCL9L	254	.	0			c.293delA						.						75.0	72.0	73.0					11																	118779099		2200	4295	6495	SO:0001589	frameshift_variant	283149	exon2			.	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.292delC	chr11.hg19:g.118779099delG	ENSP00000335320:p.Gln98fs	276.0	0.0		172.0	11.0	NM_182557	A1A4C1|Q67FY1|Q6ZWJ0|Q6ZWK2	Frame_Shift_Del	DEL	ENST00000334801.3	hg19	CCDS8403.1																																																																																			.	.		0.642	BCL9L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389653.1	NM_182557	
ATAD2B	54454	hgsc.bcm.edu	37	2	24008915	24008915	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:24008915delT	ENST00000238789.5	-	21	3298	c.2955delA	c.(2953-2955)aaafs	p.K985fs	ATAD2B_ENST00000474583.1_5'UTR	NM_001242338.1|NM_017552.2	NP_001229267.1|NP_060022.1	Q9ULI0	ATD2B_HUMAN	ATPase family, AAA domain containing 2B	985	Bromo. {ECO:0000255|PROSITE- ProRule:PRU00035}.					nucleus (GO:0005634)	ATP binding (GO:0005524)|lysine-acetylated histone binding (GO:0070577)			central_nervous_system(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TATCCACCGGTTTGCTGAAGA	0.398																																					p.P986fs		Atlas-INDEL	.											.	ATAD2B	110	.	0			c.2956delC						.						71.0	66.0	68.0					2																	24008915		1878	4104	5982	SO:0001589	frameshift_variant	54454	exon21			.	AB033066	CCDS46227.1	2p24.1-p23.3	2010-04-21		2007-02-08	ENSG00000119778	ENSG00000119778		"""ATPases / AAA-type"""	29230	protein-coding gene	gene with protein product		615347					Standard	XM_005264372		Approved	KIAA1240	uc002rek.4	Q9ULI0	OTTHUMG00000151902	ENST00000238789.5:c.2955delA	chr2.hg19:g.24008915delT	ENSP00000238789:p.Lys985fs	204.0	0.0		182.0	11.0	NM_017552	B9ZVQ5|Q6ZNA6|Q8N9E7	Frame_Shift_Del	DEL	ENST00000238789.5	hg19	CCDS46227.1																																																																																			.	.		0.398	ATAD2B-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324333.1	NM_017552	
MUC6	4588	hgsc.bcm.edu	37	11	1024954	1024954	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:1024954delC	ENST00000421673.2	-	24	3165	c.3115delG	c.(3115-3117)gacfs	p.D1039fs		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1039	VWFD 3. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		AAGCTCACGTCCCCGCACAGC	0.622																																					p.D1039fs		Atlas-INDEL	.											.	MUC6	408	.	0			c.3116delA						.						40.0	48.0	46.0					11																	1024954		2124	4232	6356	SO:0001589	frameshift_variant	4588	exon24			.	U97698, AY312160	CCDS44513.1	11p15.5	2008-02-05	2006-03-14		ENSG00000184956	ENSG00000184956		"""Mucins"""	7517	protein-coding gene	gene with protein product		158374	"""mucin 6, gastric"""			7680650	Standard	NM_005961		Approved		uc001lsw.2	Q6W4X9	OTTHUMG00000165140	ENST00000421673.2:c.3115delG	chr11.hg19:g.1024954delC	ENSP00000406861:p.Asp1039fs	260.0	0.0		199.0	12.0	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Frame_Shift_Del	DEL	ENST00000421673.2	hg19	CCDS44513.1																																																																																			.	.		0.622	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540	
NAA15	80155	hgsc.bcm.edu	37	4	140270718	140270718	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:140270718delA	ENST00000296543.5	+	7	1117	c.794delA	c.(793-795)gaafs	p.E265fs	NAA15_ENST00000398947.1_Frame_Shift_Del_p.E265fs|NAA15_ENST00000480277.2_3'UTR	NM_057175.3	NP_476516.1	Q9BXJ9	NAA15_HUMAN	N(alpha)-acetyltransferase 15, NatA auxiliary subunit	265					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|N-terminal protein amino acid acetylation (GO:0006474)|negative regulation of apoptotic process (GO:0043066)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|NatA complex (GO:0031415)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	N-acetyltransferase activity (GO:0008080)|poly(A) RNA binding (GO:0044822)|ribosome binding (GO:0043022)			NS(1)|endometrium(3)|large_intestine(7)|liver(2)|lung(8)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	29						AAAGGCTTGGAAAAAGCACTC	0.333																																					p.E265fs		Atlas-INDEL	.											.	NAA15	88	.	0			c.793delG						.						49.0	46.0	47.0					4																	140270718		1798	4073	5871	SO:0001589	frameshift_variant	80155	exon7			.	AY039242	CCDS43270.1	4q31.1	2010-01-14	2010-01-14	2010-01-14	ENSG00000164134	ENSG00000164134		"""N(alpha)-acetyltransferase subunits"""	30782	protein-coding gene	gene with protein product		608000	"""NMDA receptor regulated 1"""	NARG1		12140756, 11478804, 19660095	Standard	XM_005263236		Approved	TBDN100, NATH, FLJ13340	uc003ihu.1	Q9BXJ9	OTTHUMG00000137363	ENST00000296543.5:c.794delA	chr4.hg19:g.140270718delA	ENSP00000296543:p.Glu265fs	218.0	0.0		162.0	11.0	NM_057175	D3DNY6|Q52LG9|Q8IWH4|Q8NEV2|Q9H8P6	Frame_Shift_Del	DEL	ENST00000296543.5	hg19	CCDS43270.1																																																																																			.	.		0.333	NAA15-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000267839.2	NM_057175	
MOCOS	55034	hgsc.bcm.edu	37	18	33785127	33785127	+	Frame_Shift_Del	DEL	C	C	-	rs533721204		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr18:33785127delC	ENST00000261326.5	+	6	1127	c.1106delC	c.(1105-1107)gccfs	p.A369fs		NM_017947.2	NP_060417.2			molybdenum cofactor sulfurase											breast(2)|endometrium(5)|kidney(1)|large_intestine(10)|liver(1)|lung(15)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	43						CCCAATGGAGCCCCTGTGGTG	0.488																																					p.A369fs		Atlas-INDEL	.											.	MOCOS	84	.	0			c.1105delG						.						115.0	107.0	110.0					18																	33785127		2203	4300	6503	SO:0001589	frameshift_variant	55034	exon6			.	AK000740	CCDS11919.1	18q12	2003-12-18			ENSG00000075643	ENSG00000075643			18234	protein-coding gene	gene with protein product		613274				11302742	Standard	NM_017947		Approved	HMCS, FLJ20733, MOS	uc002kzq.4	Q96EN8	OTTHUMG00000132590	ENST00000261326.5:c.1106delC	chr18.hg19:g.33785127delC	ENSP00000261326:p.Ala369fs	260.0	0.0		199.0	12.0	NM_017947		Frame_Shift_Del	DEL	ENST00000261326.5	hg19	CCDS11919.1																																																																																			.	.		0.488	MOCOS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255801.1		
ADAMTS3	9508	hgsc.bcm.edu	37	4	73414286	73414286	+	Frame_Shift_Del	DEL	C	C	-	rs788908	byFrequency	TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:73414286delC	ENST00000286657.4	-	3	449	c.413delG	c.(412-414)agafs	p.R138fs	ADAMTS3_ENST00000505193.1_5'UTR	NM_014243.2	NP_055058.2	O15072	ATS3_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 3	138			R -> K (in dbSNP:rs788908). {ECO:0000269|PubMed:11408482, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9205841}.		collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix organization (GO:0030198)|positive regulation of vascular endothelial growth factor signaling pathway (GO:1900748)|protein processing (GO:0016485)|vascular endothelial growth factor production (GO:0010573)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	endopeptidase activity (GO:0004175)|heparin binding (GO:0008201)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(21)|lung(33)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	76			Epithelial(6;4.97e-05)|OV - Ovarian serous cystadenocarcinoma(6;5.66e-05)|all cancers(17;0.000486)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			AGGCTCTGTTCTCCGGATTCT	0.493																																					p.R138fs	NSCLC(168;1941 2048 2918 13048 43078)	Atlas-INDEL	.											.	ADAMTS3	164	.	0			c.414delA						.						227.0	223.0	224.0					4																	73414286		2203	4300	6503	SO:0001589	frameshift_variant	9508	exon3			.	AB002364	CCDS3553.1	4q21	2008-07-29	2005-08-19		ENSG00000156140	ENSG00000156140	3.4.24.-	"""ADAM metallopeptidases with thrombospondin type 1 motif"""	219	protein-coding gene	gene with protein product		605011	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 3"""			10094461	Standard	NM_014243		Approved	KIAA0366, ADAMTS-4	uc003hgk.2	O15072	OTTHUMG00000129912	ENST00000286657.4:c.413delG	chr4.hg19:g.73414286delC	ENSP00000286657:p.Arg138fs	257.0	0.0		173.0	11.0	NM_014243	A1L3U9|Q9BXZ8	Frame_Shift_Del	DEL	ENST00000286657.4	hg19	CCDS3553.1																																																																																			.	.		0.493	ADAMTS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252164.2		
ADAMTS14	140766	hgsc.bcm.edu	37	10	72500743	72500743	+	Splice_Site	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:72500743delC	ENST00000373207.1	+	12	1749	c.1749delC	c.(1747-1749)tcc>tc	p.S583fs	ADAMTS14_ENST00000373208.1_Splice_Site_p.S586fs	NM_080722.3	NP_542453.2	Q8WXS8	ATS14_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 14	583	TSP type-1 1. {ECO:0000255|PROSITE- ProRule:PRU00210}.				collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(15)|ovary(7)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50						TCTGTCCCAGCCCAGCCTATG	0.617																																					.		Atlas-INDEL	.											.	ADAMTS14	148	.	0			c.1758-1C>-						.						54.0	47.0	49.0					10																	72500743		2203	4300	6503	SO:0001630	splice_region_variant	140766	exon12			.	AF358666	CCDS7306.1, CCDS7307.1	10q21	2008-08-01	2005-08-19		ENSG00000138316	ENSG00000138316		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	14899	protein-coding gene	gene with protein product		607506	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 14"""			11779638	Standard	NM_139155		Approved		uc001jrg.3	Q8WXS8	OTTHUMG00000018414	ENST00000373207.1:c.1749-1C>-	chr10.hg19:g.72500743delC		265.0	0.0		162.0	10.0	NM_139155	Q5T4G0|Q5T4G1|Q8TE55|Q8TEY8	Splice_Site	DEL	ENST00000373207.1	hg19	CCDS7306.1																																																																																			.	.		0.617	ADAMTS14-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000048522.1	NM_080722	Frame_Shift_Del
NUP98	4928	hgsc.bcm.edu	37	11	3720389	3720389	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:3720389delT	ENST00000324932.7	-	25	4352	c.3932delA	c.(3931-3933)aacfs	p.N1311fs	NUP98_ENST00000488828.1_5'Flank|NUP98_ENST00000355260.3_Frame_Shift_Del_p.N1311fs|NUP98_ENST00000359171.4_Frame_Shift_Del_p.N1311fs	NM_016320.4|NM_139132.3	NP_057404.2|NP_624358.2	P52948	NUP98_HUMAN	nucleoporin 98kDa	1328					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|DNA replication (GO:0006260)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|nuclear pore organization (GO:0006999)|nucleocytoplasmic transport (GO:0006913)|protein import into nucleus, docking (GO:0000059)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear envelope (GO:0005635)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nuclear pore outer ring (GO:0031080)|nucleoplasm (GO:0005654)	peptide binding (GO:0042277)|structural constituent of nuclear pore (GO:0017056)|transporter activity (GO:0005215)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(13)|liver(1)|lung(15)|ovary(2)|prostate(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	66		Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0403)|LUSC - Lung squamous cell carcinoma(625;0.116)|Lung(200;0.199)		CACAGGGCTGTTTTTTTGGGT	0.512			T	"""HOXA9, NSD1, WHSC1L1, DDX10, TOP1, HOXD13, PMX1, HOXA13, HOXD11, HOXA11, RAP1GDS1, HOXC11"""	AML																																p.N1311fs		Atlas-INDEL	.		Dom	yes		11	11p15	4928	nucleoporin 98kDa		L	.	NUP98	149	.	0			c.3933delC						.						176.0	183.0	180.0					11																	3720389		2201	4298	6499	SO:0001589	frameshift_variant	4928	exon25			.	AF071076, AF231130, BC012906, BG773331	CCDS7746.1, CCDS31347.1, CCDS41605.1, CCDS41606.1	11p15	2008-02-26	2002-08-29		ENSG00000110713	ENSG00000110713			8068	protein-coding gene	gene with protein product		601021	"""nucleoporin 98kD"""			9166830	Standard	NM_139131		Approved	NUP96	uc001lyh.3	P52948	OTTHUMG00000011846	ENST00000324932.7:c.3932delA	chr11.hg19:g.3720389delT	ENSP00000316032:p.Asn1311fs	274.0	0.0		190.0	15.0	NM_016320	Q8IUT2|Q8WYB0|Q96E54|Q9H3Q4|Q9NT02|Q9UF57|Q9UHX0|Q9Y6J4|Q9Y6J5	Frame_Shift_Del	DEL	ENST00000324932.7	hg19	CCDS7746.1																																																																																			.	.		0.512	NUP98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032766.3	NM_016320	
MYH4	4622	hgsc.bcm.edu	37	17	10369889	10369889	+	Frame_Shift_Del	DEL	C	C	-	rs143441825	byFrequency	TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:10369889delC	ENST00000255381.2	-	3	284	c.174delG	c.(172-174)gggfs	p.G58fs	CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA|RP11-799N11.1_ENST00000399342.2_RNA	NM_017533.2	NP_060003.2	Q9Y623	MYH4_HUMAN	myosin, heavy chain 4, skeletal muscle	58					actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|membrane organization (GO:0061024)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|response to activity (GO:0014823)	muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|microfilament motor activity (GO:0000146)			NS(4)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(72)|ovary(10)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	149						CTGTCACCTTCCCCCCTTCCC	0.458																																					p.K59fs		Atlas-INDEL	.											.	MYH4	349	.	0			c.175delA						.						209.0	194.0	199.0					17																	10369889		2203	4300	6503	SO:0001589	frameshift_variant	4622	exon3			.		CCDS11154.1	17p13.1	2013-09-19	2006-09-29		ENSG00000264424	ENSG00000264424		"""Myosins / Myosin superfamily : Class II"""	7574	protein-coding gene	gene with protein product		160742	"""myosin, heavy polypeptide 4, skeletal muscle"""			8518795	Standard	NM_017533		Approved	MYH2B, MyHC-2B, MyHC-IIb	uc002gmn.3	Q9Y623	OTTHUMG00000130365	ENST00000255381.2:c.174delG	chr17.hg19:g.10369889delC	ENSP00000255381:p.Gly58fs	357.0	0.0		261.0	17.0	NM_017533		Frame_Shift_Del	DEL	ENST00000255381.2	hg19	CCDS11154.1																																																																																			.	.		0.458	MYH4-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252731.1	NM_017533	
SLC29A1	2030	hgsc.bcm.edu	37	6	44199193	44199193	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:44199193delA	ENST00000393841.1	+	10	1350	c.859delA	c.(859-861)aaafs	p.K287fs	SLC29A1_ENST00000371713.1_Frame_Shift_Del_p.K287fs|SLC29A1_ENST00000371724.1_Frame_Shift_Del_p.K287fs|SLC29A1_ENST00000472176.1_3'UTR|SLC29A1_ENST00000313248.7_Frame_Shift_Del_p.K366fs|SLC29A1_ENST00000371740.5_Frame_Shift_Del_p.K287fs|SLC29A1_ENST00000371731.1_Frame_Shift_Del_p.K287fs|SLC29A1_ENST00000393844.1_Frame_Shift_Del_p.K287fs|SLC29A1_ENST00000371755.3_Frame_Shift_Del_p.K287fs|SLC29A1_ENST00000427851.2_Frame_Shift_Del_p.K287fs|SLC29A1_ENST00000371708.1_Frame_Shift_Del_p.K287fs	NM_001078177.1	NP_001071645.1	Q99808	S29A1_HUMAN	solute carrier family 29 (equilibrative nucleoside transporter), member 1	287					cellular response to glucose stimulus (GO:0071333)|cellular response to hypoxia (GO:0071456)|lactation (GO:0007595)|nucleobase-containing compound metabolic process (GO:0006139)|nucleoside transmembrane transport (GO:1901642)|nucleoside transport (GO:0015858)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|sleep (GO:0030431)|transmembrane transport (GO:0055085)|uridine transport (GO:0015862)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	nucleoside transmembrane transporter activity (GO:0005337)			endometrium(3)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|skin(2)	17	all_cancers(18;3.19e-06)|Lung NSC(15;0.00108)|all_lung(25;0.00278)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)		Cytarabine(DB00987)|Didanosine(DB00900)|Fludarabine(DB01073)|Fluorouracil(DB00544)|Gemcitabine(DB00441)|Mercaptopurine(DB01033)|Pemetrexed(DB00642)|Ribavirin(DB00811)|Zalcitabine(DB00943)	AGCCATCCTGAAAAATGTACG	0.522																																					p.L286fs		Atlas-INDEL	.											.	SLC29A1	45	.	0			c.858delG						.						106.0	86.0	93.0					6																	44199193		2203	4300	6503	SO:0001589	frameshift_variant	2030	exon10			.	U81375	CCDS4908.1	6p21.1	2013-07-17	2013-07-17		ENSG00000112759	ENSG00000112759		"""Solute carriers"""	11003	protein-coding gene	gene with protein product		602193	"""solute carrier family 29 (nucleoside transporters), member 1"""	ENT1		8986748, 9344680	Standard	NM_004955		Approved		uc003owy.2	Q99808	OTTHUMG00000014759	ENST00000393841.1:c.859delA	chr6.hg19:g.44199193delA	ENSP00000377424:p.Lys287fs	153.0	0.0		173.0	11.0	NM_001078175	B3KQV7|B3KQY5|Q5T9W9|Q9UJY2	Frame_Shift_Del	DEL	ENST00000393841.1	hg19	CCDS4908.1																																																																																			.	.		0.522	SLC29A1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040721.1		
OSMR	9180	hgsc.bcm.edu	37	5	38917660	38917660	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:38917660delC	ENST00000274276.3	+	10	1700	c.1298delC	c.(1297-1299)gccfs	p.A433fs		NM_003999.2	NP_003990.1	Q99650	OSMR_HUMAN	oncostatin M receptor	433	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|oncostatin-M-mediated signaling pathway (GO:0038165)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of cell proliferation (GO:0008284)|response to cytokine (GO:0034097)	oncostatin-M receptor complex (GO:0005900)	growth factor binding (GO:0019838)|oncostatin-M receptor activity (GO:0004924)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(8)|lung(20)|ovary(2)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	46	all_lung(31;0.000365)					CCCTCAGAGGCCCCTGATGTC	0.418																																					p.A433fs		Atlas-INDEL	.											.	OSMR	133	.	0			c.1297delG						.						115.0	114.0	114.0					5																	38917660		2203	4300	6503	SO:0001589	frameshift_variant	9180	exon10			.	U60805	CCDS3928.1, CCDS54847.1	5p13.2	2013-02-11			ENSG00000145623	ENSG00000145623		"""Fibronectin type III domain containing"""	8507	protein-coding gene	gene with protein product		601743				8999038	Standard	NM_001168355		Approved	OSMRB	uc003jln.2	Q99650	OTTHUMG00000090811	ENST00000274276.3:c.1298delC	chr5.hg19:g.38917660delC	ENSP00000274276:p.Ala433fs	228.0	0.0		173.0	11.0	NM_003999	Q6P4E8|Q96QJ6	Frame_Shift_Del	DEL	ENST00000274276.3	hg19	CCDS3928.1																																																																																			.	.		0.418	OSMR-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000207609.2	NM_003999	
PTPRZ1	5803	hgsc.bcm.edu	37	7	121650545	121650545	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:121650545delC	ENST00000393386.2	+	12	1856	c.1445delC	c.(1444-1446)tccfs	p.S482fs	PTPRZ1_ENST00000449182.1_Frame_Shift_Del_p.S482fs	NM_001206838.1|NM_002851.2	NP_001193767.1|NP_002842.2	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type, Z polypeptide 1	482					axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|hematopoietic progenitor cell differentiation (GO:0002244)|learning or memory (GO:0007611)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of oligodendrocyte progenitor proliferation (GO:0070445)	integral component of plasma membrane (GO:0005887)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)	protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(12)|large_intestine(17)|liver(1)|lung(42)|ovary(4)|prostate(5)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	106						ACTAACCGATCCCCAACAAGA	0.413																																					p.S482fs		Atlas-INDEL	.											.	PTPRZ1	605	.	0			c.1444delT						.						126.0	110.0	115.0					7																	121650545		2203	4300	6503	SO:0001589	frameshift_variant	5803	exon12			.	M93426	CCDS34740.1, CCDS56505.1	7q31.3	2013-02-11			ENSG00000106278	ENSG00000106278		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9685	protein-coding gene	gene with protein product		176891		PTPZ, PTPRZ		7736789, 8387522	Standard	NM_001206838		Approved	PTP18, RPTPB, phosphacan	uc003vjy.3	P23471	OTTHUMG00000157057	ENST00000393386.2:c.1445delC	chr7.hg19:g.121650545delC	ENSP00000377047:p.Ser482fs	184.0	0.0		194.0	12.0	NM_001206838	A4D0W5|C9JFM0|O76043|Q9UDR6	Frame_Shift_Del	DEL	ENST00000393386.2	hg19	CCDS34740.1																																																																																			.	.		0.413	PTPRZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347288.1	NM_002851	
MYH15	22989	hgsc.bcm.edu	37	3	108182059	108182059	+	Frame_Shift_Del	DEL	T	T	-	rs202235922		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:108182059delT	ENST00000273353.3	-	17	1879	c.1823delA	c.(1822-1824)aagfs	p.K608fs	MYH15_ENST00000495753.2_5'Flank	NM_014981.1	NP_055796.1	Q9Y2K3	MYH15_HUMAN	myosin, heavy chain 15	608	Myosin motor.					cytoplasm (GO:0005737)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(1)|breast(3)|central_nervous_system(2)|cervix(4)|endometrium(10)|kidney(4)|large_intestine(14)|lung(47)|ovary(5)|pancreas(2)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	105						GTCTTTGTTCTTTTCCAGCCA	0.383																																					p.K608fs		Atlas-INDEL	.											.	MYH15	223	.	0			c.1824delG						.						165.0	155.0	158.0					3																	108182059		1826	4085	5911	SO:0001589	frameshift_variant	22989	exon17			.	AB023217	CCDS43127.1	3q13	2011-09-27	2006-09-29		ENSG00000144821	ENSG00000144821		"""Myosins / Myosin superfamily : Class II"""	31073	protein-coding gene	gene with protein product		609929	"""myosin, heavy polypeptide 15"""			15014174, 15042088	Standard	NM_014981		Approved	KIAA1000	uc003dxa.1	Q9Y2K3	OTTHUMG00000159226	ENST00000273353.3:c.1823delA	chr3.hg19:g.108182059delT	ENSP00000273353:p.Lys608fs	276.0	0.0		191.0	12.0	NM_014981		Frame_Shift_Del	DEL	ENST00000273353.3	hg19	CCDS43127.1																																																																																			.	.		0.383	MYH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353935.1	XM_036988	
CNNM4	26504	hgsc.bcm.edu	37	2	97427712	97427712	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:97427712delT	ENST00000377075.2	+	1	1074	c.976delT	c.(976-978)tttfs	p.F327fs		NM_020184.3	NP_064569.3	Q6P4Q7	CNNM4_HUMAN	cyclin and CBS domain divalent metal cation transport mediator 4	327	DUF21.				biomineral tissue development (GO:0031214)|ion transport (GO:0006811)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	adenyl nucleotide binding (GO:0030554)			breast(2)|endometrium(4)|kidney(1)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)	20						GCTCCTGGACTTTTTTCTGGG	0.512																																					p.D325fs		Atlas-INDEL	.											.	CNNM4	48	.	0			c.975delC						.						94.0	98.0	96.0					2																	97427712		2203	4300	6503	SO:0001589	frameshift_variant	26504	exon1			.	AB046812	CCDS2024.2	2q11.2	2014-08-08	2014-08-07		ENSG00000158158	ENSG00000158158			105	protein-coding gene	gene with protein product		607805	"""cyclin M4"""	ACDP4		21393841, 24194943	Standard	XM_005263914		Approved	KIAA1592	uc002swx.3	Q6P4Q7	OTTHUMG00000130532	ENST00000377075.2:c.976delT	chr2.hg19:g.97427712delT	ENSP00000366275:p.Phe327fs	215.0	0.0		198.0	13.0	NM_020184	B7Z1U0|C7SQM3|C7SQM4|C7SQM5|Q53RE5|Q9H9G3|Q9HCI0|Q9NRN1	Frame_Shift_Del	DEL	ENST00000377075.2	hg19	CCDS2024.2																																																																																			.	.		0.512	CNNM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252954.1	NM_020184	
BRCA1	672	hgsc.bcm.edu	37	17	41251836	41251836	+	Frame_Shift_Del	DEL	T	T	-	rs273901743		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:41251836delT	ENST00000357654.3	-	7	621	c.503delA	c.(502-504)aagfs	p.K168fs	BRCA1_ENST00000493795.1_Frame_Shift_Del_p.K121fs|BRCA1_ENST00000586385.1_Intron|BRCA1_ENST00000471181.2_Frame_Shift_Del_p.K168fs|BRCA1_ENST00000346315.3_Frame_Shift_Del_p.K168fs|BRCA1_ENST00000351666.3_Frame_Shift_Del_p.K168fs|BRCA1_ENST00000468300.1_Frame_Shift_Del_p.K168fs|BRCA1_ENST00000352993.3_Frame_Shift_Del_p.K168fs|BRCA1_ENST00000591534.1_Intron|BRCA1_ENST00000309486.4_5'UTR|BRCA1_ENST00000591849.1_Intron|BRCA1_ENST00000491747.2_Frame_Shift_Del_p.K168fs|BRCA1_ENST00000354071.3_Frame_Shift_Del_p.K168fs	NM_007294.3	NP_009225.1	P38398	BRCA1_HUMAN	breast cancer 1, early onset	168					androgen receptor signaling pathway (GO:0030521)|apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to indole-3-methanol (GO:0071681)|cellular response to tumor necrosis factor (GO:0071356)|chromosome segregation (GO:0007059)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|fatty acid biosynthetic process (GO:0006633)|G2 DNA damage checkpoint (GO:0031572)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of centriole replication (GO:0046600)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of DNA repair (GO:0045739)|positive regulation of gene expression (GO:0010628)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of histone H3-K9 acetylation (GO:2000617)|positive regulation of histone H4-K16 acetylation (GO:2000620)|positive regulation of histone H4-K20 methylation (GO:0070512)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation vascular endothelial growth factor production (GO:0010575)|postreplication repair (GO:0006301)|protein autoubiquitination (GO:0051865)|protein K6-linked ubiquitination (GO:0085020)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|regulation of cell proliferation (GO:0042127)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to estrogen (GO:0043627)|response to ionizing radiation (GO:0010212)	BRCA1-A complex (GO:0070531)|BRCA1-BARD1 complex (GO:0031436)|chromosome (GO:0005694)|cytoplasm (GO:0005737)|gamma-tubulin ring complex (GO:0008274)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ribonucleoprotein complex (GO:0030529)|ubiquitin ligase complex (GO:0000151)	androgen receptor binding (GO:0050681)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligase activity (GO:0016874)|RNA binding (GO:0003723)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|tubulin binding (GO:0015631)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(30)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(28)|ovary(36)|skin(2)|stomach(4)|urinary_tract(2)	120		Breast(137;0.000717)		BRCA - Breast invasive adenocarcinoma(366;0.126)		TATCCGCTGCTTTGTCCTCAG	0.398			"""D, Mis, N, F, S"""		ovarian	"""breast, ovarian"""		Homologous recombination	Hereditary Breast-Ovarian Cancer, BRCA1 type	TCGA Ovarian(2;0.000030)																											p.K168fs		Atlas-INDEL	.	yes	Rec	yes	Hereditary breast/ovarian cancer	17	17q21	672	familial breast/ovarian cancer gene 1		E	.	BRCA1	304	.	0			c.504delG						.						178.0	170.0	173.0					17																	41251836		2203	4300	6503	SO:0001589	frameshift_variant	672	exon6	Familial Cancer Database		.	U14680	CCDS11453.1, CCDS11454.1, CCDS11455.1, CCDS11456.1, CCDS11459.1, CCDS11455.2, CCDS11456.2, CCDS11459.2, CCDS11454.2	17q21.31	2014-09-17			ENSG00000012048	ENSG00000012048		"""RING-type (C3HC4) zinc fingers"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	1100	protein-coding gene	gene with protein product	"""BRCA1/BRCA2-containing complex, subunit 1"", ""protein phosphatase 1, regulatory subunit 53"""	113705				1676470	Standard	NM_007300		Approved	RNF53, BRCC1, PPP1R53	uc002ict.3	P38398	OTTHUMG00000157426	ENST00000357654.3:c.503delA	chr17.hg19:g.41251836delT	ENSP00000350283:p.Lys168fs	236.0	0.0		158.0	11.0	NM_007298	O15129|Q1RMC1|Q3LRJ0|Q3LRJ6|Q6IN79|Q7KYU9	Frame_Shift_Del	DEL	ENST00000357654.3	hg19	CCDS11453.1																																																																																			.	.		0.398	BRCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348798.2	NM_007294	
MSH4	4438	hgsc.bcm.edu	37	1	76269449	76269449	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:76269449delA	ENST00000263187.3	+	2	382	c.278delA	c.(277-279)gaafs	p.E93fs		NM_002440.3	NP_002431.2	O15457	MSH4_HUMAN	mutS homolog 4	93					ATP catabolic process (GO:0006200)|chiasma assembly (GO:0051026)|female gamete generation (GO:0007292)|homologous chromosome segregation (GO:0045143)|mismatch repair (GO:0006298)|ovarian follicle development (GO:0001541)|reciprocal meiotic recombination (GO:0007131)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|mismatched DNA binding (GO:0030983)			breast(1)|endometrium(2)|kidney(4)|large_intestine(9)|lung(26)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	47						GCTTATGCAGAAAACACAGTT	0.303								Mismatch excision repair (MMR)																													p.E93fs		Atlas-INDEL	.											.	MSH4	147	.	0			c.277delG						.						60.0	62.0	61.0					1																	76269449		2203	4300	6503	SO:0001589	frameshift_variant	4438	exon2			.	U89293	CCDS670.1	1p31	2013-09-12	2013-09-12		ENSG00000057468	ENSG00000057468			7327	protein-coding gene	gene with protein product		602105	"""mutS (E. coli) homolog 4"", ""mutS homolog 4 (E. coli)"""			9299235	Standard	NM_002440		Approved		uc001dhd.2	O15457	OTTHUMG00000009788	ENST00000263187.3:c.278delA	chr1.hg19:g.76269449delA	ENSP00000263187:p.Glu93fs	168.0	0.0		147.0	10.0	NM_002440	Q5T4U6|Q8NEB3|Q9UNP8	Frame_Shift_Del	DEL	ENST00000263187.3	hg19	CCDS670.1																																																																																			.	.		0.303	MSH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026983.1	NM_002440	
PTDSS2	81490	hgsc.bcm.edu	37	11	489639	489639	+	Frame_Shift_Del	DEL	C	C	-	rs143446343		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:489639delC	ENST00000308020.5	+	10	1197	c.1021delC	c.(1021-1023)cccfs	p.P342fs		NM_030783.1	NP_110410.1	Q9BVG9	PTSS2_HUMAN	phosphatidylserine synthase 2	342					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylserine biosynthetic process (GO:0006659)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	CDP-diacylglycerol-serine O-phosphatidyltransferase activity (GO:0003882)			autonomic_ganglia(1)|breast(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|skin(1)	9		all_cancers(49;1.59e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;2.76e-26)|Epithelial(43;2.56e-25)|OV - Ovarian serous cystadenocarcinoma(40;7.54e-20)|BRCA - Breast invasive adenocarcinoma(625;8.76e-05)|Lung(200;0.0407)|LUSC - Lung squamous cell carcinoma(625;0.0735)	Phosphatidylserine(DB00144)	GCTGTGGATGCCCCCGGAGCA	0.622																																					p.M340fs		Atlas-INDEL	.											.	PTDSS2	27	.	0			c.1020delG						.																																			SO:0001589	frameshift_variant	81490	exon10			.	BC001210	CCDS7696.1	11p15	2008-05-02			ENSG00000174915	ENSG00000174915			15463	protein-coding gene	gene with protein product		612793				14984733	Standard	NM_030783		Approved	PSS2	uc001lpj.3	Q9BVG9	OTTHUMG00000119087	ENST00000308020.5:c.1021delC	chr11.hg19:g.489639delC	ENSP00000308258:p.Pro342fs	259.0	0.0		179.0	11.0	NM_030783		Frame_Shift_Del	DEL	ENST00000308020.5	hg19	CCDS7696.1																																																																																			.	.		0.622	PTDSS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239301.2		
LCE1E	353135	hgsc.bcm.edu	37	1	152760075	152760075	+	Frame_Shift_Del	DEL	A	A	-	rs201660535	byFrequency	TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:152760075delA	ENST00000368770.3	+	2	353	c.300delA	c.(298-300)tcafs	p.S100fs	LCE1E_ENST00000368771.1_Frame_Shift_Del_p.S100fs	NM_178353.1	NP_848130.1	Q5T753	LCE1E_HUMAN	late cornified envelope 1E	100	Cys-rich.				keratinization (GO:0031424)					lung(5)|stomach(1)	6	Lung NSC(65;3.97e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			GCCAGCCCTCAGGGGGCTCCA	0.642																																					p.S100X		Atlas-INDEL	.											.	LCE1E	26	.	0			c.299delC						.						36.0	52.0	47.0					1																	152760075		2104	4254	6358	SO:0001589	frameshift_variant	353135	exon2			.	BC038391	CCDS1024.1	1q21.3	2008-02-05			ENSG00000186226	ENSG00000186226		"""Late cornified envelopes"""	29466	protein-coding gene	gene with protein product		612607				11698679	Standard	NM_178353		Approved	LEP5	uc001fan.3	Q5T753	OTTHUMG00000012405	ENST00000368770.3:c.300delA	chr1.hg19:g.152760075delA	ENSP00000357759:p.Ser100fs	123.0	0.0		207.0	16.0	NM_178353	D3DV30	Frame_Shift_Del	DEL	ENST00000368770.3	hg19	CCDS1024.1																																																																																			.	.		0.642	LCE1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034525.1	NM_178353	
PCF11	51585	hgsc.bcm.edu	37	11	82882908	82882908	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:82882908delT	ENST00000298281.4	+	9	4161	c.3709delT	c.(3709-3711)tttfs	p.F1237fs		NM_015885.3	NP_056969.2	O94913	PCF11_HUMAN	PCF11 cleavage and polyadenylation factor subunit	1237					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	mRNA cleavage factor complex (GO:0005849)|nucleoplasm (GO:0005654)				cervix(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(22)|ovary(1)|urinary_tract(1)	33						AGGACAACAGTTTTTACCAGT	0.328																																					p.Q1236fs		Atlas-INDEL	.											.	PCF11	220	.	0			c.3708delG						.						144.0	140.0	141.0					11																	82882908		1830	4084	5914	SO:0001589	frameshift_variant	51585	exon9			.	AB020631	CCDS44689.1	11q13	2013-07-02	2013-07-02		ENSG00000165494	ENSG00000165494			30097	protein-coding gene	gene with protein product		608876	"""PCF11, cleavage and polyadenylation factor II subunit, homolog (S. cerevisiae)"", ""PCF11, cleavage and polyadenylation factor subunit, homolog (S. cerevisiae)"""			11060040	Standard	NM_015885		Approved	KIAA0824	uc001ozx.4	O94913	OTTHUMG00000167031	ENST00000298281.4:c.3709delT	chr11.hg19:g.82882908delT	ENSP00000298281:p.Phe1237fs	173.0	0.0		131.0	11.0	NM_015885	A6H8W7|O43671|Q6P0X8	Frame_Shift_Del	DEL	ENST00000298281.4	hg19	CCDS44689.1																																																																																			.	.		0.328	PCF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392548.2	NM_015885	
CEP152	22995	hgsc.bcm.edu	37	15	49061255	49061255	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:49061255delT	ENST00000380950.2	-	14	1993	c.1806delA	c.(1804-1806)aaafs	p.K602fs	CEP152_ENST00000399334.3_Frame_Shift_Del_p.K602fs|CEP152_ENST00000325747.5_Frame_Shift_Del_p.K509fs|CEP152_ENST00000559398.1_5'UTR	NM_001194998.1|NM_014985.3	NP_001181927.1|NP_055800.2	O94986	CE152_HUMAN	centrosomal protein 152kDa	602					cell projection organization (GO:0030030)|centriole replication (GO:0007099)|centrosome duplication (GO:0051298)|de novo centriole assembly (GO:0098535)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytosol (GO:0005829)|deuterosome (GO:0098536)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)			breast(3)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(16)|lung(30)|ovary(1)|prostate(2)|skin(2)	63		all_lung(180;0.0428)		all cancers(107;1.08e-07)|GBM - Glioblastoma multiforme(94;2.32e-06)		GATTCTTTGGTTTTTCTGAGG	0.284																																					p.P603fs		Atlas-INDEL	.											CEP152,caecum,carcinoma,0,1	CEP152	145	.	0			c.1807delC						.						92.0	87.0	89.0					15																	49061255		1787	4051	5838	SO:0001589	frameshift_variant	22995	exon14			.	AB020719	CCDS42033.1, CCDS58361.1	15q21.1	2014-02-20							29298	protein-coding gene	gene with protein product	"""asterless"""	613529	"""microcephaly, primary autosomal recessive 4"""	MCPH4		14654843, 21131973	Standard	NM_014985		Approved	KIAA0912, SCKL5	uc001zwz.3	O94986		ENST00000380950.2:c.1806delA	chr15.hg19:g.49061255delT	ENSP00000370337:p.Lys602fs	144.0	0.0		148.0	10.0	NM_014985	E7ER66|Q17RV1|Q6NTA0	Frame_Shift_Del	DEL	ENST00000380950.2	hg19	CCDS58361.1																																																																																			.	.		0.284	CEP152-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417365.1	NM_014985	
PANK2	80025	hgsc.bcm.edu	37	20	3899427	3899427	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr20:3899427delT	ENST00000316562.4	+	6	1652	c.1646delT	c.(1645-1647)cttfs	p.L549fs	MIR103A2_ENST00000362154.1_RNA|PANK2_ENST00000497424.1_Frame_Shift_Del_p.L258fs|PANK2_ENST00000610179.1_Frame_Shift_Del_p.L426fs	NM_153638.2	NP_705902.2	Q9BZ23	PANK2_HUMAN	pantothenate kinase 2	549					aerobic respiration (GO:0009060)|cell death (GO:0008219)|coenzyme A biosynthetic process (GO:0015937)|coenzyme biosynthetic process (GO:0009108)|mitochondrion morphogenesis (GO:0070584)|pantothenate metabolic process (GO:0015939)|regulation of mitochondrial membrane potential (GO:0051881)|small molecule metabolic process (GO:0044281)|spermatid development (GO:0007286)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial intermembrane space (GO:0005758)	ATP binding (GO:0005524)|pantothenate kinase activity (GO:0004594)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15						TTGAAAGCACTTTTTTCGGAA	0.448																																					p.L549fs		Atlas-INDEL	.											.	PANK2	37	.	0			c.1645delC						.						238.0	234.0	235.0					20																	3899427		2203	4300	6503	SO:0001589	frameshift_variant	80025	exon6			.	AK021791	CCDS13071.2, CCDS13072.1	20p13	2008-07-31	2008-07-31	2002-09-06	ENSG00000125779	ENSG00000125779	2.7.1.33		15894	protein-coding gene	gene with protein product	"""Hallervorden-Spatz syndrome"""	606157	"""neurodegeneration with brain iron accumulation 1 (Hallervorden-Spatz syndrome)"""	C20orf48, NBIA1		8944032, 11479594	Standard	XM_005260835		Approved	HSS, FLJ11729, PKAN, HARP	uc002wkc.3	Q9BZ23	OTTHUMG00000031768	ENST00000316562.4:c.1646delT	chr20.hg19:g.3899427delT	ENSP00000313377:p.Leu549fs	385.0	0.0		250.0	15.0	NM_153638	B1AK33|B2Z3X0|D3DVZ0|Q5T7I2|Q5T7I4|Q7RTX5|Q8N7Q4|Q8TCR5|Q9BYW5|Q9HAF2	Frame_Shift_Del	DEL	ENST00000316562.4	hg19	CCDS13071.2																																																																																			.	.		0.448	PANK2-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077793.2	NM_024960	
SEC16B	89866	hgsc.bcm.edu	37	1	177913790	177913790	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:177913790delA	ENST00000308284.6	-	15	1876	c.1787delT	c.(1786-1788)ttgfs	p.L596fs	RP4-798P15.3_ENST00000354921.3_RNA	NM_033127.2	NP_149118.2	Q96JE7	SC16B_HUMAN	SEC16 homolog B (S. cerevisiae)	596					COPII vesicle coating (GO:0048208)|endoplasmic reticulum organization (GO:0007029)|peroxisome fission (GO:0016559)|peroxisome organization (GO:0007031)|positive regulation of gene expression (GO:0010628)|positive regulation of protein exit from endoplasmic reticulum (GO:0070863)|protein localization to endoplasmic reticulum (GO:0070972)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|intracellular membrane-bounded organelle (GO:0043231)				central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(7)|lung(14)|ovary(3)|skin(1)|stomach(1)	35						TGCAAATTTCAAAAACTCTTG	0.468																																					p.L596fs		Atlas-INDEL	.											.	SEC16B	92	.	0			c.1788delG						.						109.0	112.0	111.0					1																	177913790		1877	4110	5987	SO:0001589	frameshift_variant	89866	exon15			.	AK090411	CCDS44281.1	1q25.2	2012-10-08	2007-06-20	2007-06-20	ENSG00000120341	ENSG00000120341			30301	protein-coding gene	gene with protein product	"""regucalcin gene promotor region related protein"""	612855	"""leucine zipper transcription regulator 2"""	LZTR2		11572484, 11605020	Standard	NM_033127		Approved	RGPR, PGPR-p117	uc001gli.1	Q96JE7	OTTHUMG00000167206	ENST00000308284.6:c.1787delT	chr1.hg19:g.177913790delA	ENSP00000308339:p.Leu596fs	105.0	0.0		131.0	11.0	NM_033127	A3EYF1|Q5HYF6|Q8N7D6|Q96GX6	Frame_Shift_Del	DEL	ENST00000308284.6	hg19	CCDS44281.1																																																																																			.	.		0.468	SEC16B-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084773.16	NM_033127	
CSTF3	1479	hgsc.bcm.edu	37	11	33121158	33121158	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:33121158delT	ENST00000323959.4	-	11	1071	c.932delA	c.(931-933)aagfs	p.K311fs	TCP11L1_ENST00000324357.9_Intron	NM_001326.2	NP_001317.1	Q12996	CSTF3_HUMAN	cleavage stimulation factor, 3' pre-RNA, subunit 3, 77kDa	311					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(2)|endometrium(4)|kidney(1)|large_intestine(5)|lung(4)|prostate(1)|skin(1)|stomach(1)	19						ACTTACTCCCTTTTCTGCGAG	0.388																																					p.K311fs		Atlas-INDEL	.											.	CSTF3	59	.	0			c.933delG						.						75.0	71.0	73.0					11																	33121158		2202	4298	6500	SO:0001589	frameshift_variant	1479	exon11			.	U15782	CCDS7883.1, CCDS44563.1, CCDS44564.1	11p13	2007-01-05	2002-08-29		ENSG00000176102	ENSG00000176102			2485	protein-coding gene	gene with protein product		600367	"""cleavage stimulation factor, 3' pre-RNA, subunit 3, 77kD"""			7984242	Standard	XM_006718154		Approved	CstF-77	uc001muh.3	Q12996	OTTHUMG00000166268	ENST00000323959.4:c.932delA	chr11.hg19:g.33121158delT	ENSP00000315791:p.Lys311fs	324.0	0.0		248.0	16.0	NM_001326	A8K471|D3DR04|E9PB40|Q32P22|Q96FQ8|Q96QD6|Q96QK4	Frame_Shift_Del	DEL	ENST00000323959.4	hg19	CCDS7883.1																																																																																			.	.		0.388	CSTF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388801.1	NM_001326	
NUDT12	83594	hgsc.bcm.edu	37	5	102895020	102895020	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:102895020delT	ENST00000230792.2	-	3	452	c.356delA	c.(355-357)aatfs	p.N119fs	NUDT12_ENST00000507423.1_Frame_Shift_Del_p.N101fs	NM_031438.2	NP_113626.1	Q9BQG2	NUD12_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 12	119					NAD catabolic process (GO:0019677)|NADP catabolic process (GO:0006742)	nucleus (GO:0005634)|peroxisome (GO:0005777)	metal ion binding (GO:0046872)|NAD+ diphosphatase activity (GO:0000210)|NADH pyrophosphatase activity (GO:0035529)			endometrium(1)|kidney(1)|large_intestine(2)|liver(1)|lung(6)|urinary_tract(1)	12		all_cancers(142;6.38e-08)|all_epithelial(76;1.99e-10)|Prostate(80;0.0138)|Lung NSC(167;0.0212)|Colorectal(57;0.0247)|all_lung(232;0.0283)|Ovarian(225;0.0423)		Epithelial(69;9.3e-13)|COAD - Colon adenocarcinoma(37;0.0221)		GCTAAAATAATTTTCACATTC	0.378																																					p.N119fs		Atlas-INDEL	.											.	NUDT12	27	.	0			c.357delT						.						61.0	65.0	63.0					5																	102895020		2202	4299	6501	SO:0001589	frameshift_variant	83594	exon3			.	AL136592	CCDS4096.1, CCDS75284.1	5q15	2013-01-10			ENSG00000112874	ENSG00000112874		"""Nudix motif containing"", ""Ankyrin repeat domain containing"""	18826	protein-coding gene	gene with protein product	"""nucleoside diphosphate linked moiety X-type motif 12"""	609232				11230166	Standard	XM_005272095		Approved	DKFZP761I172	uc003koi.3	Q9BQG2	OTTHUMG00000128739	ENST00000230792.2:c.356delA	chr5.hg19:g.102895020delT	ENSP00000230792:p.Asn119fs	172.0	0.0		164.0	10.0	NM_031438	B3KUW2|Q8TAL7	Frame_Shift_Del	DEL	ENST00000230792.2	hg19	CCDS4096.1																																																																																			.	.		0.378	NUDT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250650.1	NM_031438	
ZDBF2	57683	hgsc.bcm.edu	37	2	207175038	207175038	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:207175038delA	ENST00000374423.3	+	5	6172	c.5786delA	c.(5785-5787)caafs	p.Q1929fs		NM_020923.1	NP_065974.1	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2	1929							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(5)|large_intestine(28)|lung(50)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	95						CCTCCTAAGCAAAAGGGGCGT	0.428																																					p.Q1929fs		Atlas-INDEL	.											.	ZDBF2	531	.	0			c.5785delC						.						69.0	69.0	69.0					2																	207175038		1957	4154	6111	SO:0001589	frameshift_variant	57683	exon5			.	AB046791	CCDS46501.1, CCDS74637.1	2q33.3	2013-01-10			ENSG00000204186	ENSG00000204186		"""Zinc fingers, DBF-type"""	29313	protein-coding gene	gene with protein product						10997877	Standard	XM_005246711		Approved	FLJ45338, KIAA1571	uc002vbp.2	Q9HCK1	OTTHUMG00000154648	ENST00000374423.3:c.5786delA	chr2.hg19:g.207175038delA	ENSP00000363545:p.Gln1929fs	261.0	0.0		177.0	11.0	NM_020923	Q6ZNP7|Q6ZSN8	Frame_Shift_Del	DEL	ENST00000374423.3	hg19	CCDS46501.1																																																																																			.	.		0.428	ZDBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336458.1	NM_020923	
HLA-E	3133	hgsc.bcm.edu	37	6	30458916	30458916	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:30458916delC	ENST00000376630.4	+	4	678	c.613delC	c.(613-615)cccfs	p.P206fs		NM_005516.5	NP_005507.3	P13747	HLAE_HUMAN	major histocompatibility complex, class I, E	206	Alpha-3.|Ig-like C1-type.				antigen processing and presentation of endogenous peptide antigen via MHC class Ib (GO:0002476)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|innate immune response (GO:0045087)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of natural killer cell mediated immunity (GO:0002717)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|protection from natural killer cell mediated cytotoxicity (GO:0042270)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|ER to Golgi transport vesicle membrane (GO:0012507)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	MHC class I protein binding (GO:0042288)|peptide antigen binding (GO:0042605)			breast(2)|central_nervous_system(4)|endometrium(1)|kidney(3)|large_intestine(2)|lung(1)|ovary(3)|skin(1)|urinary_tract(1)	18						CCCCTCAGAGCCCCCAAAGAC	0.552																																					p.E204fs		Atlas-INDEL	.											.	HLA-E	35	.	0			c.612delG						.						115.0	135.0	127.0					6																	30458916		1511	2709	4220	SO:0001589	frameshift_variant	3133	exon4			.	M20022	CCDS34379.1	6p21.3	2013-01-11			ENSG00000204592	ENSG00000204592		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4962	protein-coding gene	gene with protein product		143010				3131426	Standard	NM_005516		Approved		uc003nqg.3	P13747	OTTHUMG00000031155	ENST00000376630.4:c.613delC	chr6.hg19:g.30458916delC	ENSP00000365817:p.Pro206fs	283.0	0.0		174.0	11.0	NM_005516	Q30169|Q9BT83|Q9GIY7|Q9GIY8	Frame_Shift_Del	DEL	ENST00000376630.4	hg19	CCDS34379.1																																																																																			.	.		0.552	HLA-E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076282.2	NM_005516	
SERHL2	253190	hgsc.bcm.edu	37	22	42951001	42951001	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr22:42951001delG	ENST00000327678.5	+	2	182	c.80delG	c.(79-81)tggfs	p.W27fs	SERHL2_ENST00000340239.4_Frame_Shift_Del_p.W27fs|SERHL2_ENST00000335879.5_Intron|Z93241.1_ENST00000580472.1_RNA|SERHL2_ENST00000407614.4_Intron|RRP7B_ENST00000357802.2_RNA	NM_014509.3	NP_055324.2	Q9NQF3	SERHL_HUMAN	serine hydrolase-like 2	27							hydrolase activity (GO:0016787)			breast(1)|endometrium(2)|lung(3)|skin(1)|stomach(1)	8						GCCAAAGCCTGGGGCTCCCTG	0.597																																					p.W27fs		Atlas-INDEL	.											.	SERHL2	23	.	0			c.79delT						.						5.0	5.0	5.0					22																	42951001		1769	3734	5503	SO:0001589	frameshift_variant	253190	exon2			.		CCDS14037.1, CCDS63498.1	22q13	2005-08-09			ENSG00000183569	ENSG00000183569			29446	protein-coding gene	gene with protein product							Standard	NM_014509		Approved		uc003bcr.3	Q9H4I8	OTTHUMG00000150892	ENST00000327678.5:c.80delG	chr22.hg19:g.42951001delG	ENSP00000331376:p.Trp27fs	225.0	0.0		165.0	10.0	NM_014509	Q5JZ95|Q9UH21	Frame_Shift_Del	DEL	ENST00000327678.5	hg19	CCDS14037.1																																																																																			.	.		0.597	SERHL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320454.1	NM_014509	
STK24	8428	hgsc.bcm.edu	37	13	99114125	99114125	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr13:99114125delC	ENST00000376547.3	-	8	1137	c.992delG	c.(991-993)ggcfs	p.G331fs	STK24_ENST00000539966.1_Frame_Shift_Del_p.G300fs|STK24_ENST00000397517.2_Frame_Shift_Del_p.G319fs	NM_003576.3	NP_003567.2	Q9Y6E0	STK24_HUMAN	serine/threonine kinase 24	331					apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|execution phase of apoptosis (GO:0097194)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|negative regulation of cell migration (GO:0030336)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of axon regeneration (GO:0048679)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(7)|ovary(1)|skin(1)	17	all_neural(89;0.0982)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.233)			AGAATCACTGCCCCCCGAGGC	0.532																																					p.G331fs		Atlas-INDEL	.											.,1	STK24	40	.	0			c.993delC						.						108.0	105.0	106.0					13																	99114125		2203	4300	6503	SO:0001589	frameshift_variant	8428	exon8			.	AF024636	CCDS9488.1, CCDS32001.1, CCDS66573.1	13q31.2-q32.3	2010-06-25	2010-06-25		ENSG00000102572	ENSG00000102572			11403	protein-coding gene	gene with protein product	"""STE20-like kinase 3"", ""sterile 20-like kinase 3"""	604984	"""serine/threonine kinase 24 (Ste20, yeast homolog)"""			9353338, 10644707	Standard	NM_003576		Approved	MST-3, MST3, MST3B, STK3, STE20	uc001vnn.1	Q9Y6E0	OTTHUMG00000017250	ENST00000376547.3:c.992delG	chr13.hg19:g.99114125delC	ENSP00000365730:p.Gly331fs	289.0	0.0		178.0	11.0	NM_003576	O14840|Q5JV92	Frame_Shift_Del	DEL	ENST00000376547.3	hg19	CCDS9488.1																																																																																			.	.		0.532	STK24-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045549.2	NM_003576	
PHF21A	51317	hgsc.bcm.edu	37	11	45992680	45992680	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:45992680delT	ENST00000418153.2	-	7	798	c.599delA	c.(598-600)aacfs	p.N200fs	PHF21A_ENST00000257821.4_Frame_Shift_Del_p.N200fs|PHF21A_ENST00000323180.6_Frame_Shift_Del_p.N200fs			Q96BD5	PF21A_HUMAN	PHD finger protein 21A	200					blood coagulation (GO:0007596)|chromatin modification (GO:0016568)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription, DNA-templated (GO:0006355)|suckling behavior (GO:0001967)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(10)|lung(9)|skin(2)|upper_aerodigestive_tract(2)	29						AGTGACTGTGTTTTTTGCCAC	0.507																																					p.N200fs		Atlas-INDEL	.											.	PHF21A	107	.	0			c.600delC						.						104.0	84.0	91.0					11																	45992680		2202	4299	6501	SO:0001589	frameshift_variant	51317	exon7			.	AL359593	CCDS31474.1, CCDS44578.1	11p11.2	2013-01-28			ENSG00000135365	ENSG00000135365		"""Zinc fingers, PHD-type"""	24156	protein-coding gene	gene with protein product		608325				11214970, 12032298	Standard	NM_001101802		Approved	BHC80, KIAA1696, BM-006	uc001ncc.4	Q96BD5	OTTHUMG00000167038	ENST00000418153.2:c.599delA	chr11.hg19:g.45992680delT	ENSP00000398824:p.Asn200fs	392.0	0.0		264.0	17.0	NM_016621	D3DQP5|Q6AWA2|Q9C0G7|Q9H8V9|Q9HAK6|Q9NZE9	Frame_Shift_Del	DEL	ENST00000418153.2	hg19	CCDS44578.1																																																																																			.	.		0.507	PHF21A-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000392583.1	NM_016621	
USP6	9098	hgsc.bcm.edu	37	17	5073793	5073793	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:5073793delA	ENST00000574788.1	+	36	5767	c.3537delA	c.(3535-3537)agafs	p.R1179fs	USP6_ENST00000332776.4_3'UTR|USP6_ENST00000304328.5_Frame_Shift_Del_p.R862fs|USP6_ENST00000250066.6_Frame_Shift_Del_p.R1179fs			P35125	UBP6_HUMAN	ubiquitin specific peptidase 6	1179	USP.				cellular protein modification process (GO:0006464)|protein deubiquitination (GO:0016579)|regulation of vesicle-mediated transport (GO:0060627)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	calmodulin binding (GO:0005516)|cysteine-type endopeptidase activity (GO:0004197)|nucleic acid binding (GO:0003676)|Rab GTPase activator activity (GO:0005097)|ubiquitin-specific protease activity (GO:0004843)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	34						CTTCATCAAGAAAAAGTGGAA	0.507			T	"""COL1A1, CDH11, ZNF9, OMD"""	aneurysmal bone cysts																																p.R1179fs		Atlas-INDEL	.		Dom	yes		17	17p13	9098	ubiquitin specific peptidase 6 (Tre-2 oncogene)		M	.	USP6	213	.	0			c.3536delG						.						16.0	18.0	17.0					17																	5073793		2044	4157	6201	SO:0001589	frameshift_variant	9098	exon28			.	X63547	CCDS11069.2	17p13	2014-06-12	2014-06-12		ENSG00000129204	ENSG00000129204	3.4.19.12	"""Ubiquitin-specific peptidases"""	12629	protein-coding gene	gene with protein product	"""ubiquitin carboxyl-terminal hydrolase 6"", ""TBC1D3 and USP32 fusion"", ""Tre-2 oncogene"""	604334	"""ubiquitin specific protease 6 (Tre-2 oncogene)"", ""TRE oncogene, Smith Magenis syndrome chromosome region"", ""ubiquitin specific peptidase 6 (Tre-2 oncogene)"""	HRP1, TRESMCR		12838346, 1349106	Standard	NM_004505		Approved	Tre-2, TRE17, Tre2	uc002gav.1	P35125	OTTHUMG00000099449	ENST00000574788.1:c.3537delA	chr17.hg19:g.5073793delA	ENSP00000460380:p.Arg1179fs	155.0	0.0		160.0	10.0	NM_004505	Q15634|Q86WP6|Q8IWT4	Frame_Shift_Del	DEL	ENST00000574788.1	hg19	CCDS11069.2																																																																																			.	.		0.507	USP6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438990.1	NM_004505	
LCA5	167691	hgsc.bcm.edu	37	6	80223315	80223315	+	Frame_Shift_Del	DEL	T	T	-	rs576105476	byFrequency	TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:80223315delT	ENST00000392959.1	-	4	945	c.334delA	c.(334-336)atcfs	p.I112fs	LCA5_ENST00000467898.3_Frame_Shift_Del_p.I112fs|LCA5_ENST00000369846.4_Frame_Shift_Del_p.I112fs	NM_181714.3	NP_859065.2	Q86VQ0	LCA5_HUMAN	Leber congenital amaurosis 5	112					intraciliary transport (GO:0042073)|photoreceptor cell maintenance (GO:0045494)|protein transport (GO:0015031)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	protein complex binding (GO:0032403)			haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(11)|lung(15)|prostate(2)|skin(1)	32		all_cancers(76;3.32e-05)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.0176)		BRCA - Breast invasive adenocarcinoma(397;0.0657)		AACTCATTGATTTTTAGCAGT	0.418																																					p.I112fs		Atlas-INDEL	.											.	LCA5	71	.	0			c.335delT						.						98.0	105.0	103.0					6																	80223315		2203	4298	6501	SO:0001589	frameshift_variant	167691	exon3			.		CCDS4990.1	6q14	2014-01-28			ENSG00000135338	ENSG00000135338			31923	protein-coding gene	gene with protein product	"""lebercilin"""	611408	"""chromosome 6 open reading frame 152"""	C6orf152		10631161, 17546029	Standard	NM_181714		Approved		uc003pix.3	Q86VQ0	OTTHUMG00000015080	ENST00000392959.1:c.334delA	chr6.hg19:g.80223315delT	ENSP00000376686:p.Ile112fs	216.0	0.0		148.0	10.0	NM_001122769	E1P542|Q9BWX7	Frame_Shift_Del	DEL	ENST00000392959.1	hg19	CCDS4990.1																																																																																			.	.		0.418	LCA5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259269.1	NM_181714	
ITPR2	3709	hgsc.bcm.edu	37	12	26839461	26839461	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:26839461delA	ENST00000381340.3	-	11	1517	c.1101delT	c.(1099-1101)tttfs	p.F367fs		NM_002223.2	NP_002214.2	Q14571	ITPR2_HUMAN	inositol 1,4,5-trisphosphate receptor, type 2	367	MIR 4. {ECO:0000255|PROSITE- ProRule:PRU00131}.				activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cellular response to cAMP (GO:0071320)|cellular response to ethanol (GO:0071361)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|regulation of insulin secretion (GO:0050796)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	cell cortex (GO:0005938)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|phosphatidylinositol binding (GO:0035091)		ETV6/ITPR2(2)	biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(20)|liver(1)|lung(51)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	125	Colorectal(261;0.0847)				Caffeine(DB00201)	CATCTAGTTCAAAAAGGGATG	0.408																																					p.E368fs		Atlas-INDEL	.											ITPR2,NS,carcinoma,0,1	ITPR2	270	.	0			c.1102delG						.						140.0	132.0	134.0					12																	26839461		1894	4119	6013	SO:0001589	frameshift_variant	3709	exon11			.	D26350	CCDS41764.1	12p11.23	2014-07-18	2011-04-28		ENSG00000123104	ENSG00000123104		"""Ion channels / Inositol triphosphate receptors"""	6181	protein-coding gene	gene with protein product	"""cilia and flagella associated protein 48"""	600144	"""inositol 1,4,5-triphosphate receptor, type 2"""			8081734	Standard	XM_006719064		Approved	IP3R2, CFAP48	uc001rhg.3	Q14571	OTTHUMG00000169181	ENST00000381340.3:c.1101delT	chr12.hg19:g.26839461delA	ENSP00000370744:p.Phe367fs	200.0	0.0		142.0	14.0	NM_002223	O94773	Frame_Shift_Del	DEL	ENST00000381340.3	hg19	CCDS41764.1																																																																																			.	.		0.408	ITPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402732.1	NM_002223	
QRFPR	84109	hgsc.bcm.edu	37	4	122253996	122253996	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:122253996delT	ENST00000394427.2	-	4	1188	c.777delA	c.(775-777)aaafs	p.K259fs	QRFPR_ENST00000334383.5_Intron	NM_198179.2	NP_937822.2	Q96P65	QRFPR_HUMAN	pyroglutamylated RFamide peptide receptor	259				VILFLLPLMVMLILYSKIGYELWIKKRVGDGSVLRTIHGKE MSKIAR -> SSSSSCLLW (in Ref. 1; AAL26488). {ECO:0000305}.	G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|neuropeptide Y receptor activity (GO:0004983)			endometrium(1)|kidney(2)|large_intestine(9)|lung(10)|prostate(2)|skin(3)|stomach(1)	28						TGGACATTTCTTTTCCATGAA	0.358																																					p.E260fs		Atlas-INDEL	.											QRFPR,NS,carcinoma,0,1	QRFPR	65	.	0			c.778delG						.						72.0	70.0	71.0					4																	122253996		2203	4300	6503	SO:0001589	frameshift_variant	84109	exon4			.	AF411117	CCDS3719.1	4q27	2012-08-10	2008-12-18	2008-12-18	ENSG00000186867	ENSG00000186867		"""GPCR / Class A : RF amide peptide receptors"""	15565	protein-coding gene	gene with protein product		606925	"""G protein-coupled receptor 103"""	GPR103		11574155	Standard	NM_198179		Approved		uc010inj.1	Q96P65	OTTHUMG00000133036	ENST00000394427.2:c.777delA	chr4.hg19:g.122253996delT	ENSP00000377948:p.Lys259fs	300.0	0.0		221.0	15.0	NM_198179		Frame_Shift_Del	DEL	ENST00000394427.2	hg19	CCDS3719.1																																																																																			.	.		0.358	QRFPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256641.2	NM_198179	
ADAMTSL4	54507	hgsc.bcm.edu	37	1	150531054	150531054	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:150531054delC	ENST00000369038.2	+	13	2689	c.2488delC	c.(2488-2490)cccfs	p.P831fs	ADAMTSL4_ENST00000369039.5_Frame_Shift_Del_p.P854fs|RP11-54A4.2_ENST00000442435.2_RNA|ADAMTSL4_ENST00000271643.4_Frame_Shift_Del_p.P831fs|ADAMTSL4_ENST00000369041.5_Frame_Shift_Del_p.P831fs			Q6UY14	ATL4_HUMAN	ADAMTS-like 4	831	TSP type-1 3. {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)			CCCCCCGCAGCCCCCCAGCAG	0.657																																					p.Q829fs		Atlas-INDEL	.											.	ADAMTSL4	101	.	0			c.2487delG						.						56.0	62.0	60.0					1																	150531054		2203	4300	6503	SO:0001589	frameshift_variant	54507	exon15			.	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.2488delC	chr1.hg19:g.150531054delC	ENSP00000358034:p.Pro831fs	201.0	0.0		219.0	14.0	NM_019032	B2RTT0|F8WAD0|Q5T5F7|Q6IPM6|Q8N643|Q9HBS6	Frame_Shift_Del	DEL	ENST00000369038.2	hg19	CCDS955.1																																																																																			.	.		0.657	ADAMTSL4-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084395.4	NM_019032	
AHI1	54806	hgsc.bcm.edu	37	6	135768254	135768254	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:135768254delT	ENST00000367800.4	-	11	1887	c.1671delA	c.(1669-1671)aaafs	p.K557fs	AHI1_ENST00000327035.6_Frame_Shift_Del_p.K557fs|AHI1_ENST00000457866.2_Frame_Shift_Del_p.K557fs	NM_001134830.1	NP_001128302.1	Q8N157	AHI1_HUMAN	Abelson helper integration site 1	557					cellular protein localization (GO:0034613)|central nervous system development (GO:0007417)|cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|cloaca development (GO:0035844)|heart looping (GO:0001947)|hindbrain development (GO:0030902)|Kupffer's vesicle development (GO:0070121)|left/right axis specification (GO:0070986)|morphogenesis of a polarized epithelium (GO:0001738)|negative regulation of apoptotic process (GO:0043066)|otic vesicle development (GO:0071599)|photoreceptor cell outer segment organization (GO:0035845)|positive regulation of polarized epithelial cell differentiation (GO:0030862)|positive regulation of receptor internalization (GO:0002092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|pronephric duct morphogenesis (GO:0039023)|pronephric nephron tubule morphogenesis (GO:0039008)|protein localization to organelle (GO:0033365)|regulation of behavior (GO:0050795)|retina layer formation (GO:0010842)|specification of axis polarity (GO:0065001)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vesicle targeting (GO:0006903)|vesicle-mediated transport (GO:0016192)	adherens junction (GO:0005912)|cell-cell junction (GO:0005911)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|nonmotile primary cilium (GO:0031513)|photoreceptor outer segment (GO:0001750)|primary cilium (GO:0072372)|TCTN-B9D complex (GO:0036038)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(18)|ovary(1)	37	Breast(56;0.239)|Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00904)|OV - Ovarian serous cystadenocarcinoma(155;0.00991)		CTGGTTTACCTTTTTCCTCCT	0.373																																					p.G558fs		Atlas-INDEL	.											.	AHI1	81	.	0			c.1672delG						.						169.0	161.0	164.0					6																	135768254		1878	4118	5996	SO:0001589	frameshift_variant	54806	exon12			.	AJ459824	CCDS47483.1, CCDS47484.1	6q23.2	2013-01-10	2005-11-29		ENSG00000135541	ENSG00000135541		"""WD repeat domain containing"""	21575	protein-coding gene	gene with protein product	"""Jouberin"""	608894	"""Abelson helper integration site"""			15060101, 16240161	Standard	NM_017651		Approved	FLJ20069, ORF1, JBTS3	uc003qgj.3	Q8N157	OTTHUMG00000015631	ENST00000367800.4:c.1671delA	chr6.hg19:g.135768254delT	ENSP00000356774:p.Lys557fs	208.0	0.0		161.0	10.0	NM_001134832	E1P584|Q4FD35|Q504T3|Q5TCP9|Q6P098|Q6PIT6|Q8NDX0|Q9H0H2	Frame_Shift_Del	DEL	ENST00000367800.4	hg19	CCDS47483.1																																																																																			.	.		0.373	AHI1-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391948.1	NM_017651	
TRPV1	7442	hgsc.bcm.edu	37	17	3495572	3495572	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:3495572delG	ENST00000571088.1	-	2	286	c.73delC	c.(73-75)ctgfs	p.L25fs	TRPV1_ENST00000576351.1_Frame_Shift_Del_p.L25fs|TRPV1_ENST00000310522.5_Frame_Shift_Del_p.L25fs|SHPK_ENST00000572705.1_Frame_Shift_Del_p.L25fs|TRPV1_ENST00000399759.3_Frame_Shift_Del_p.L25fs|TRPV1_ENST00000399756.4_Frame_Shift_Del_p.L25fs|TRPV1_ENST00000425167.2_Frame_Shift_Del_p.L25fs|TRPV1_ENST00000174621.6_5'UTR	NM_018727.5	NP_061197.4	Q8NER1	TRPV1_HUMAN	transient receptor potential cation channel, subfamily V, member 1	25					calcium ion transmembrane transport (GO:0070588)|cell surface receptor signaling pathway (GO:0007166)|cellular response to alkaloid (GO:0071312)|cellular response to ATP (GO:0071318)|chemosensory behavior (GO:0007635)|ion transmembrane transport (GO:0034220)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|calcium-release channel activity (GO:0015278)|excitatory extracellular ligand-gated ion channel activity (GO:0005231)|phosphoprotein binding (GO:0051219)|transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|urinary_tract(1)	17				Lung(1;0.055)|COAD - Colon adenocarcinoma(5;0.0896)|LUAD - Lung adenocarcinoma(1115;0.131)	Alpha-Linolenic Acid(DB00132)|Aspartame(DB00168)|Icosapent(DB00159)	TCTCCATCCAGGGGGTCTGGG	0.632																																					p.L25fs	Melanoma(38;962 1762 15789)	Atlas-INDEL	.											.	TRPV1	99	.	0			c.74delT						.						44.0	49.0	48.0					17																	3495572		2027	4179	6206	SO:0001589	frameshift_variant	7442	exon2			.	AJ272063	CCDS45576.1	17p13.2	2014-08-12	2002-01-29	2002-02-01	ENSG00000196689	ENSG00000262304		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	12716	protein-coding gene	gene with protein product		602076	"""vanilloid receptor subtype 1"""	VR1		9349813, 11549313, 16382100	Standard	NM_018727		Approved		uc010vrt.2	Q8NER1	OTTHUMG00000177649	ENST00000571088.1:c.73delC	chr17.hg19:g.3495572delG	ENSP00000461007:p.Leu25fs	159.0	0.0		132.0	11.0	NM_018727	A2RUA9|Q3LU47|Q9H0G9|Q9H303|Q9H304|Q9NQ74|Q9NY22	Frame_Shift_Del	DEL	ENST00000571088.1	hg19	CCDS45576.1																																																																																			.	.		0.632	TRPV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438254.1	NM_018727	
F2R	2149	hgsc.bcm.edu	37	5	76029269	76029269	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:76029269delA	ENST00000319211.4	+	2	1484	c.1219delA	c.(1219-1221)aaafs	p.K407fs		NM_001992.3	NP_001983.2	P25116	PAR1_HUMAN	coagulation factor II (thrombin) receptor	407					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of MAPKK activity (GO:0000186)|anatomical structure morphogenesis (GO:0009653)|blood coagulation (GO:0007596)|connective tissue replacement involved in inflammatory response wound healing (GO:0002248)|establishment of synaptic specificity at neuromuscular junction (GO:0007529)|G-protein coupled receptor signaling pathway (GO:0007186)|homeostasis of number of cells within a tissue (GO:0048873)|inflammatory response (GO:0006954)|negative regulation of cell proliferation (GO:0008285)|negative regulation of glomerular filtration (GO:0003105)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of renin secretion into blood stream (GO:1900134)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|platelet activation (GO:0030168)|platelet dense granule organization (GO:0060155)|positive regulation of blood coagulation (GO:0030194)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-6 secretion (GO:2000778)|positive regulation of interleukin-8 secretion (GO:2000484)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of Rho protein signal transduction (GO:0035025)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of vasoconstriction (GO:0045907)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of blood coagulation (GO:0030193)|regulation of interleukin-1 beta production (GO:0032651)|regulation of sensory perception of pain (GO:0051930)|release of sequestered calcium ion into cytosol (GO:0051209)|response to lipopolysaccharide (GO:0032496)|response to wounding (GO:0009611)|STAT protein import into nucleus (GO:0007262)|tyrosine phosphorylation of STAT protein (GO:0007260)	caveola (GO:0005901)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|platelet dense tubular network (GO:0031094)|postsynaptic membrane (GO:0045211)	G-protein alpha-subunit binding (GO:0001965)|G-protein beta-subunit binding (GO:0031681)|G-protein coupled receptor activity (GO:0004930)|receptor binding (GO:0005102)|thrombin receptor activity (GO:0015057)			NS(1)|breast(1)|endometrium(3)|kidney(1)|lung(7)|ovary(3)	16		all_lung(232;0.000414)|Lung NSC(167;0.0011)|Prostate(461;0.00955)|Ovarian(174;0.0129)		all cancers(79;4.43e-43)	Streptokinase(DB00086)	GATGGCAAGTAAAATGGATAC	0.413																																					p.S406fs		Atlas-INDEL	.											.	F2R	58	.	0			c.1218delT						.						81.0	86.0	85.0					5																	76029269		2203	4300	6503	SO:0001589	frameshift_variant	2149	exon2			.	M62424	CCDS4032.1	5q13	2012-08-08			ENSG00000181104	ENSG00000181104		"""GPCR / Class A : Protease activated receptors"""	3537	protein-coding gene	gene with protein product		187930				8395910	Standard	NM_001992		Approved	TR, CF2R, PAR1, PAR-1	uc003ken.4	P25116	OTTHUMG00000131299	ENST00000319211.4:c.1219delA	chr5.hg19:g.76029269delA	ENSP00000321326:p.Lys407fs	325.0	0.0		202.0	13.0	NM_001992	Q53XV0|Q96RF7|Q9BUN4	Frame_Shift_Del	DEL	ENST00000319211.4	hg19	CCDS4032.1																																																																																			.	.		0.413	F2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254068.2		
SI	6476	hgsc.bcm.edu	37	3	164700065	164700065	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:164700065delT	ENST00000264382.3	-	47	5443	c.5381delA	c.(5380-5382)aatfs	p.N1794fs		NM_001041.3	NP_001032.2	P14410	SUIS_HUMAN	sucrase-isomaltase (alpha-glucosidase)	1794	Sucrase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	brush border (GO:0005903)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|carbohydrate binding (GO:0030246)|oligo-1,6-glucosidase activity (GO:0004574)|sucrose alpha-glucosidase activity (GO:0004575)			NS(4)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(6)|kidney(10)|large_intestine(18)|lung(124)|ovary(9)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(16)|urinary_tract(1)	218		Prostate(884;0.00314)|Melanoma(1037;0.0153)|all_neural(597;0.0199)			Acarbose(DB00284)|Scopolamine(DB00747)	AGGAAGCGAATTTTTATTTCC	0.343										HNSCC(35;0.089)																											p.N1794fs		Atlas-INDEL	.											.	SI	500	.	0			c.5382delT						.						117.0	112.0	114.0					3																	164700065		2202	4299	6501	SO:0001589	frameshift_variant	6476	exon47			.	X63597	CCDS3196.1	3q25.2-q26.2	2004-04-06	2004-04-06		ENSG00000090402	ENSG00000090402	3.2.1.10		10856	protein-coding gene	gene with protein product	"""Oligosaccharide alpha-1,6-glucosidase"""	609845	"""sucrase-isomaltase"""			2962903, 1353958	Standard	NM_001041		Approved		uc003fei.3	P14410	OTTHUMG00000158065	ENST00000264382.3:c.5381delA	chr3.hg19:g.164700065delT	ENSP00000264382:p.Asn1794fs	194.0	0.0		147.0	10.0	NM_001041	A2RUC3|Q1JQ80|Q1RMC2	Frame_Shift_Del	DEL	ENST00000264382.3	hg19	CCDS3196.1																																																																																			.	.		0.343	SI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350116.1	NM_001041	
MICALCL	84953	hgsc.bcm.edu	37	11	12315123	12315123	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:12315123delC	ENST00000256186.2	+	3	436	c.145delC	c.(145-147)cccfs	p.P49fs		NM_032867.2	NP_116256.2	Q6ZW33	MICLK_HUMAN	MICAL C-terminal like	49	Ser-rich.				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)		AGCTTCTGAGCCCCTCTCGCA	0.458																																					p.E48fs		Atlas-INDEL	.											.	MICALCL	59	.	0			c.144delG						.						111.0	112.0	111.0					11																	12315123		1869	4102	5971	SO:0001589	frameshift_variant	84953	exon3			.	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.145delC	chr11.hg19:g.12315123delC	ENSP00000256186:p.Pro49fs	137.0	0.0		142.0	10.0	NM_032867	Q7RTP7|Q96JU6	Frame_Shift_Del	DEL	ENST00000256186.2	hg19	CCDS41620.1																																																																																			.	.		0.458	MICALCL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386164.1	NM_032867	
OXR1	55074	hgsc.bcm.edu	37	8	107726147	107726147	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:107726147delA	ENST00000442977.2	+	10	1992	c.1893delA	c.(1891-1893)gtafs	p.V631fs	OXR1_ENST00000312046.6_Frame_Shift_Del_p.V623fs|OXR1_ENST00000452423.2_Frame_Shift_Del_p.V120fs|OXR1_ENST00000531443.1_Frame_Shift_Del_p.V630fs|OXR1_ENST00000445937.1_Frame_Shift_Del_p.V630fs|OXR1_ENST00000517566.2_Frame_Shift_Del_p.V630fs	NM_001198532.1	NP_001185461.1	Q8N573	OXR1_HUMAN	oxidation resistance 1	631					adult walking behavior (GO:0007628)|cellular response to hydroperoxide (GO:0071447)|negative regulation of neuron apoptotic process (GO:0043524)|response to oxidative stress (GO:0006979)	mitochondrion (GO:0005739)|nucleolus (GO:0005730)	oxidoreductase activity (GO:0016491)			NS(2)|breast(2)|endometrium(2)|large_intestine(9)|lung(10)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	31			OV - Ovarian serous cystadenocarcinoma(57;1.81e-09)			TTATAGTAGTAAAAAAGATTG	0.378																																					p.V631fs		Atlas-INDEL	.											.	OXR1	190	.	0			c.1892delT						.						83.0	89.0	87.0					8																	107726147		2203	4300	6503	SO:0001589	frameshift_variant	55074	exon10			.	AF309387	CCDS6304.2, CCDS47909.1, CCDS56547.1, CCDS56548.1, CCDS56549.1, CCDS56550.1	8q23	2013-03-14			ENSG00000164830	ENSG00000164830			15822	protein-coding gene	gene with protein product	"""TBC/LysM-associated domain containing 3"""	605609				11114193	Standard	NM_181354		Approved	TLDC3	uc011lht.2	Q8N573	OTTHUMG00000167682	ENST00000442977.2:c.1893delA	chr8.hg19:g.107726147delA	ENSP00000405424:p.Val631fs	245.0	0.0		223.0	14.0	NM_001198532	A6NK11|A8KA34|B3KXL1|B7Z402|B7Z8N5|D3HIS6|Q3LIB5|Q6ZVK9|Q8N8V0|Q9H266|Q9NWC7	Frame_Shift_Del	DEL	ENST00000442977.2	hg19	CCDS56548.1																																																																																			.	.		0.378	OXR1-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_181354	
RALGPS2	55103	hgsc.bcm.edu	37	1	178780494	178780494	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:178780494delA	ENST00000367635.3	+	6	680	c.342delA	c.(340-342)ttafs	p.L114fs	RALGPS2_ENST00000367634.2_Frame_Shift_Del_p.L114fs	NM_152663.3	NP_689876.2	Q86X27	RGPS2_HUMAN	Ral GEF with PH domain and SH3 binding motif 2	114	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(11)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	29						CTCAAACATTAAAAATTAGAG	0.249																																					p.L114X		Atlas-INDEL	.											.	RALGPS2	69	.	0			c.341delT						.						60.0	71.0	67.0					1																	178780494		2202	4280	6482	SO:0001589	frameshift_variant	55103	exon6			.	AK098470	CCDS1325.1, CCDS65733.1	1q24	2013-01-11			ENSG00000116191	ENSG00000116191		"""Pleckstrin homology (PH) domain containing"""	30279	protein-coding gene	gene with protein product						10747847, 12102558	Standard	NM_152663		Approved	KIAA0351, FLJ10244, FLJ25604	uc001glz.3	Q86X27	OTTHUMG00000035076	ENST00000367635.3:c.342delA	chr1.hg19:g.178780494delA	ENSP00000356607:p.Leu114fs	200.0	0.0		309.0	19.0	NM_152663	B7Z7B1|Q5T5Z1|Q5VZ67|Q9NW78	Frame_Shift_Del	DEL	ENST00000367635.3	hg19	CCDS1325.1																																																																																			.	.		0.249	RALGPS2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084926.2	NM_152663	
ZFY	7544	hgsc.bcm.edu	37	Y	2847675	2847675	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrY:2847675delA	ENST00000155093.3	+	8	2368	c.2047delA	c.(2047-2049)aaafs	p.K684fs	ZFY_ENST00000383052.1_Frame_Shift_Del_p.K684fs|ZFY-AS1_ENST00000417305.1_RNA|ZFY_ENST00000431102.1_Frame_Shift_Del_p.K493fs|ZFY_ENST00000449237.1_Frame_Shift_Del_p.K607fs	NM_003411.3	NP_003402.2	P08048	ZFY_HUMAN	zinc finger protein, Y-linked	684					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			biliary_tract(1)|kidney(3)|large_intestine(1)|lung(3)	8						CCACAAAGGTAAAAAAATGCA	0.398																																					p.G682fs		Atlas-INDEL	.											.	ZFY	20	.	0			c.2046delT						.						85.0	75.0	78.0					Y																	2847675		610	1971	2581	SO:0001589	frameshift_variant	7544	exon8			.	L10393	CCDS14774.1, CCDS48200.1, CCDS48201.1	Yp11.3	2013-01-08			ENSG00000067646	ENSG00000067646		"""Zinc fingers, C2H2-type"""	12870	protein-coding gene	gene with protein product		490000				2497060	Standard	NM_001145275		Approved	ZNF911	uc004fqj.3	P08048	OTTHUMG00000036159	ENST00000155093.3:c.2047delA	chrY.hg19:g.2847675delA	ENSP00000155093:p.Lys684fs	264.0	0.0		186.0	13.0	NM_003411	B4DVF7|Q14021|Q15558|Q1RME9|Q24JR0|Q96TF3	Frame_Shift_Del	DEL	ENST00000155093.3	hg19	CCDS14774.1																																																																																			.	.		0.398	ZFY-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088063.1	NM_003411	
SPAG1	6674	hgsc.bcm.edu	37	8	101252868	101252868	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:101252868delT	ENST00000388798.2	+	18	2709	c.2518delT	c.(2518-2520)tttfs	p.F840fs	SPAG1_ENST00000251809.3_Frame_Shift_Del_p.F840fs	NM_003114.4	NP_003105.2	Q07617	SPAG1_HUMAN	sperm associated antigen 1	840					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)		TTTGCCGATGTTTTTAAGTAA	0.373																																					p.M839fs		Atlas-INDEL	.											.	SPAG1	80	.	0			c.2517delG						.						78.0	74.0	75.0					8																	101252868		2203	4300	6503	SO:0001589	frameshift_variant	6674	exon18			.	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.2518delT	chr8.hg19:g.101252868delT	ENSP00000373450:p.Phe840fs	216.0	0.0		236.0	18.0	NM_172218	A6NP70|B3KQ58|G3XAM3|Q7Z5G1	Frame_Shift_Del	DEL	ENST00000388798.2	hg19	CCDS34930.1																																																																																			.	.		0.373	SPAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379853.2	NM_172218	
IBTK	25998	hgsc.bcm.edu	37	6	82949918	82949918	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:82949918delA	ENST00000306270.7	-	2	835	c.286delT	c.(286-288)tatfs	p.Y96fs	IBTK_ENST00000510291.1_Frame_Shift_Del_p.Y96fs|IBTK_ENST00000503631.1_Frame_Shift_Del_p.Y96fs	NM_015525.2	NP_056340.2	Q9P2D0	IBTK_HUMAN	inhibitor of Bruton agammaglobulinemia tyrosine kinase	96					negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein tyrosine kinase activity (GO:0061099)|release of sequestered calcium ion into cytosol (GO:0051209)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|protein tyrosine kinase inhibitor activity (GO:0030292)			central_nervous_system(2)|endometrium(9)|kidney(3)|large_intestine(10)|lung(19)|ovary(3)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	54		all_cancers(76;3.38e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.0037)		BRCA - Breast invasive adenocarcinoma(397;0.0901)		ATATGTCCATAAAAAATGCTT	0.333																																					p.Y96fs		Atlas-INDEL	.											.	IBTK	128	.	0			c.287delA						.						130.0	118.0	122.0					6																	82949918		2203	4300	6503	SO:0001589	frameshift_variant	25998	exon2			.	AF235049	CCDS34490.1, CCDS75486.1	6q14.3	2013-01-10	2003-10-06	2003-10-08	ENSG00000005700	ENSG00000005700		"""BTB/POZ domain containing"", ""Ankyrin repeat domain containing"""	17853	protein-coding gene	gene with protein product		606457	"""Bruton agammaglobulinemia tyrosine kinase inhibitor"""	BTKI		11577348	Standard	XM_006715453		Approved	DKFZP564B116, BTBD26	uc003pjl.1	Q9P2D0	OTTHUMG00000015102	ENST00000306270.7:c.286delT	chr6.hg19:g.82949918delA	ENSP00000305721:p.Tyr96fs	222.0	0.0		171.0	11.0	NM_015525	Q2QKU2|Q2QKU3|Q2QKU4|Q5TFD7|Q5TFD9|Q8IUQ9|Q8IUY7|Q8TAI4|Q9HBI8|Q9Y3T8	Frame_Shift_Del	DEL	ENST00000306270.7	hg19	CCDS34490.1																																																																																			.	.		0.333	IBTK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041337.2	NM_015525	
FAM117B	150864	hgsc.bcm.edu	37	2	203630172	203630172	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:203630172delA	ENST00000392238.2	+	8	1455	c.1455delA	c.(1453-1455)ccafs	p.P485fs	FAM117B_ENST00000303116.6_Frame_Shift_Del_p.P241fs			Q6P1L5	F117B_HUMAN	family with sequence similarity 117, member B	485										breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(4)|lung(5)|ovary(1)	17						TGTCTAGGCCAAAACAGCTTC	0.343																																					p.P485fs		Atlas-INDEL	.											.	FAM117B	73	.	0			c.1454delC						.						90.0	94.0	93.0					2																	203630172		2203	4300	6503	SO:0001589	frameshift_variant	150864	exon8			.	AB053315	CCDS33362.1, CCDS33362.2	2q33	2008-08-18	2008-08-18	2008-08-18	ENSG00000138439	ENSG00000138439			14440	protein-coding gene	gene with protein product			"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 13"""	ALS2CR13		11586298	Standard	NM_173511		Approved	FLJ38771	uc010zhx.2	Q6P1L5	OTTHUMG00000154550	ENST00000392238.2:c.1455delA	chr2.hg19:g.203630172delA	ENSP00000376071:p.Pro485fs	163.0	0.0		140.0	10.0	NM_173511	Q53QZ5|Q585T9|Q8N8W1|Q96Q34	Frame_Shift_Del	DEL	ENST00000392238.2	hg19	CCDS33362.2																																																																																			.	.		0.343	FAM117B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000335888.3	NM_173511	
FAHD2A	51011	hgsc.bcm.edu	37	2	96078466	96078466	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:96078466delC	ENST00000233379.4	+	7	989	c.836delC	c.(835-837)accfs	p.T279fs	FAHD2A_ENST00000447036.1_Frame_Shift_Del_p.T279fs	NM_016044.2	NP_057128.2	Q96GK7	FAH2A_HUMAN	fumarylacetoacetate hydrolase domain containing 2A	279							hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|lung(3)|ovary(1)	8						CTAACTGGGACCCCCCCAGGT	0.562																																					p.T279fs		Atlas-INDEL	.											.,1	FAHD2A	25	.	0			c.835delA						.						43.0	43.0	43.0					2																	96078466		2203	4298	6501	SO:0001589	frameshift_variant	51011	exon7			.	AF151863	CCDS2014.1	2q11.2	2008-02-05			ENSG00000115042	ENSG00000115042			24252	protein-coding gene	gene with protein product							Standard	NM_016044		Approved	CGI-105	uc002sur.3	Q96GK7	OTTHUMG00000130397	ENST00000233379.4:c.836delC	chr2.hg19:g.96078466delC	ENSP00000233379:p.Thr279fs	293.0	0.0		214.0	14.0	NM_016044	Q9Y3B0	Frame_Shift_Del	DEL	ENST00000233379.4	hg19	CCDS2014.1																																																																																			.	.		0.562	FAHD2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252778.1	NM_016044	
GMPPA	29926	hgsc.bcm.edu	37	2	220364899	220364899	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:220364899delG	ENST00000358215.3	+	3	466	c.97delG	c.(97-99)gggfs	p.G33fs	GMPPA_ENST00000313597.5_Frame_Shift_Del_p.G33fs|GMPPA_ENST00000373908.1_Frame_Shift_Del_p.G33fs|RP11-316O14.1_ENST00000601508.1_RNA|AC053503.11_ENST00000429882.1_RNA|GMPPA_ENST00000373917.3_Frame_Shift_Del_p.G33fs|GMPPA_ENST00000341142.3_Frame_Shift_Del_p.G33fs	NM_205847.2	NP_995319.1	Q96IJ6	GMPPA_HUMAN	GDP-mannose pyrophosphorylase A	33					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)	nucleotidyltransferase activity (GO:0016779)			breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(7)|lung(6)|prostate(1)|skin(1)	20		Renal(207;0.0183)		Epithelial(149;3.82e-10)|all cancers(144;6.25e-08)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00807)|READ - Rectum adenocarcinoma(5;0.148)		TCCTGTGGCAGGGGTCCCTAT	0.537																																					p.A32fs		Atlas-INDEL	.											.	GMPPA	50	.	0			c.96delA						.						76.0	61.0	66.0					2																	220364899		2203	4299	6502	SO:0001589	frameshift_variant	29926	exon3			.	AF135422	CCDS2441.1	2q36.1	2008-02-05			ENSG00000144591	ENSG00000144591			22923	protein-coding gene	gene with protein product		615495					Standard	NM_205847		Approved		uc002vlr.3	Q96IJ6	OTTHUMG00000058922	ENST00000358215.3:c.97delG	chr2.hg19:g.220364899delG	ENSP00000350949:p.Gly33fs	239.0	0.0		152.0	11.0	NM_205847	A6NJ74|A8K3Q6|B3KMT4|Q53GI0|Q9NWC3|Q9Y5P5	Frame_Shift_Del	DEL	ENST00000358215.3	hg19	CCDS2441.1																																																																																			.	.		0.537	GMPPA-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130230.1	NM_013335	
NCF1	653361	hgsc.bcm.edu	37	7	74202414	74202414	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:74202414delG	ENST00000289473.4	+	9	957	c.887delG	c.(886-888)cggfs	p.R296fs		NM_000265.4	NP_000256.4	P14598	NCF1_HUMAN	neutrophil cytosolic factor 1	296	Arg/Lys-rich (highly basic).				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)|cell proliferation (GO:0008283)|cellular defense response (GO:0006968)|hydrogen peroxide biosynthetic process (GO:0050665)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interaction with host (GO:0051701)|leukotriene metabolic process (GO:0006691)|negative regulation of smooth muscle contraction (GO:0045986)|neutrophil mediated killing of fungus (GO:0070947)|neutrophil mediated killing of gram-positive bacterium (GO:0070946)|oxidation-reduction process (GO:0055114)|phagosome maturation (GO:0090382)|protein targeting to membrane (GO:0006612)|respiratory burst (GO:0045730)|respiratory burst involved in defense response (GO:0002679)|response to yeast (GO:0001878)|superoxide anion generation (GO:0042554)|superoxide metabolic process (GO:0006801)	cytosol (GO:0005829)|dendrite (GO:0030425)|extrinsic component of membrane (GO:0019898)|Golgi apparatus (GO:0005794)|NADPH oxidase complex (GO:0043020)|neuronal cell body (GO:0043025)|phagolysosome (GO:0032010)|rough endoplasmic reticulum (GO:0005791)	electron carrier activity (GO:0009055)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|SH3 domain binding (GO:0017124)|superoxide-generating NADPH oxidase activity (GO:0016175)			breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|skin(3)	10					Dextromethorphan(DB00514)	CAGATCAAGCGGGGGGCGCCG	0.667																																					p.R296fs		Atlas-INDEL	.											.,1	NCF1	26	.	0			c.886delC						.						1.0	1.0	1.0					7																	74202414		219	155	374	SO:0001589	frameshift_variant	653361	exon9			.	M25665	CCDS34657.1	7q11.23	2014-09-17	2008-07-31		ENSG00000158517	ENSG00000158517			7660	protein-coding gene	gene with protein product	"""NADPH oxidase organizer 2"", ""chronic granulomatous disease, autosomal 1"""	608512	"""neutrophil cytosolic factor 1 (47kD, chronic granulomatous disease, autosomal 1)"""				Standard	NM_000265		Approved	p47phox, NOXO2, NCF1A, SH3PXD1A	uc022aft.1	P14598	OTTHUMG00000149965	ENST00000289473.4:c.887delG	chr7.hg19:g.74202414delG	ENSP00000289473:p.Arg296fs	221.0	0.0		158.0	11.0	NM_000265	A6NEH2|A8K7S9|O43842|Q2PP07|Q53FR5|Q9BU90|Q9BXI7|Q9BXI8|Q9UDV9|Q9UMU2	Frame_Shift_Del	DEL	ENST00000289473.4	hg19	CCDS34657.1																																																																																			.	.		0.667	NCF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314560.1	NM_000265	
TNS1	7145	hgsc.bcm.edu	37	2	218674974	218674974	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:218674974delC	ENST00000171887.4	-	29	5241	c.4789delG	c.(4789-4791)gcafs	p.A1598fs	TNS1_ENST00000419504.1_Frame_Shift_Del_p.A1584fs|TNS1_ENST00000430930.1_Frame_Shift_Del_p.A1577fs	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	1598					cell-substrate junction assembly (GO:0007044)|fibroblast migration (GO:0010761)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)	poly(A) RNA binding (GO:0044822)			breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(23)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	79		Renal(207;0.0483)|Lung NSC(271;0.213)		Epithelial(149;4.43e-06)|all cancers(144;0.000653)|LUSC - Lung squamous cell carcinoma(224;0.0091)|Lung(261;0.013)		CACTCACCTGCCCCTTGTTTC	0.547																																					p.A1597fs		Atlas-INDEL	.											.	TNS1	251	.	0			c.4790delC						.						105.0	100.0	102.0					2																	218674974		2203	4300	6503	SO:0001589	frameshift_variant	7145	exon29			.	AB209238	CCDS2407.1	2q35-q36	2014-06-13	2005-05-13	2005-05-13	ENSG00000079308	ENSG00000079308		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"", ""SH2 domain containing"""	11973	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 155"""	600076	"""tensin"", ""matrix-remodelling associated 6"""	TNS, MXRA6			Standard	NM_022648		Approved	DKFZp586K0617, PPP1R155	uc002vgt.2	Q9HBL0	OTTHUMG00000133056	ENST00000171887.4:c.4789delG	chr2.hg19:g.218674974delC	ENSP00000171887:p.Ala1598fs	224.0	0.0		158.0	13.0	NM_022648	Q4ZG71|Q6IPI5	Frame_Shift_Del	DEL	ENST00000171887.4	hg19	CCDS2407.1																																																																																			.	.		0.547	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648	
YTHDC1	91746	hgsc.bcm.edu	37	4	69195927	69195927	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:69195927delT	ENST00000344157.4	-	8	1559	c.1224delA	c.(1222-1224)aaafs	p.K408fs	YTHDC1_ENST00000579690.1_Frame_Shift_Del_p.K408fs|YTHDC1_ENST00000355665.3_Frame_Shift_Del_p.K390fs	NM_001031732.2	NP_001026902.1	Q96MU7	YTDC1_HUMAN	YTH domain containing 1	408	YTH. {ECO:0000255|PROSITE- ProRule:PRU00225}.				mRNA splice site selection (GO:0006376)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	30						TACCTTGAAATTTTCCACTCT	0.294																																					p.F409fs		Atlas-INDEL	.											.	YTHDC1	81	.	0			c.1225delT						.						23.0	24.0	23.0					4																	69195927		2186	4275	6461	SO:0001589	frameshift_variant	91746	exon8			.	AK098515	CCDS3522.2, CCDS33992.1	4q13.3	2009-01-14			ENSG00000083896	ENSG00000083896			30626	protein-coding gene	gene with protein product						12368078, 10564280	Standard	XM_005265706		Approved	YT521, KIAA1966, YT521-B	uc003hdx.3	Q96MU7	OTTHUMG00000129306	ENST00000344157.4:c.1224delA	chr4.hg19:g.69195927delT	ENSP00000339245:p.Lys408fs	149.0	0.0		185.0	12.0	NM_001031732	Q4W5Q3|Q7Z622|Q8TF35	Frame_Shift_Del	DEL	ENST00000344157.4	hg19	CCDS33992.1																																																																																			.	.		0.294	YTHDC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251437.1	NM_133370	
ZNF33A	7581	hgsc.bcm.edu	37	10	38344315	38344315	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:38344315delT	ENST00000458705.2	+	5	1418	c.1260delT	c.(1258-1260)actfs	p.T420fs	ZNF33A_ENST00000307441.9_Frame_Shift_Del_p.T420fs|ZNF33A_ENST00000374618.3_Frame_Shift_Del_p.T421fs|ZNF33A_ENST00000469037.2_Intron|ZNF33A_ENST00000432900.2_Frame_Shift_Del_p.T427fs			Q06730	ZN33A_HUMAN	zinc finger protein 33A	420					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)			cervix(2)|endometrium(2)|large_intestine(8)|liver(2)|lung(27)|ovary(2)|prostate(1)|skin(2)	46						GTGGGAAAACTTTTTGCCAGA	0.438																																					p.T421fs		Atlas-INDEL	.											.	ZNF33A	103	.	0			c.1262delC						.		,	0,4264		0,0,2132	100.0	102.0	101.0		,	1.4	1.0	10		102	1,8253		0,1,4126	no	frameshift,frameshift	ZNF33A	NM_006974.2,NM_006954.1	,	0,1,6258	A1A1,A1R,RR		0.0121,0.0,0.0080	,	,	38344315	1,12517	2203	4300	6503	SO:0001589	frameshift_variant	7581	exon5			.	D31763	CCDS31182.1, CCDS60514.1, CCDS73088.1, CCDS73089.1	10p11.2	2013-01-08	2005-03-18		ENSG00000189180	ENSG00000189180		"""Zinc fingers, C2H2-type"", ""-"""	13096	protein-coding gene	gene with protein product	"""zinc finger and ZAK associated protein with KRAB domain"""	194521	"""zinc finger protein 33a (KOX 31)"", ""zinc finger protein 11A"""	ZNF33, ZNF11A		2014798, 8464732	Standard	NM_006974		Approved	KOX5, KOX31, KIAA0065, FLJ23404, ZZAPK	uc031pui.1	Q06730	OTTHUMG00000017983	ENST00000458705.2:c.1260delT	chr10.hg19:g.38344315delT	ENSP00000387713:p.Thr420fs	164.0	0.0		152.0	10.0	NM_006954	A8K9X9|B4E0M8|F6TH33|F8WAJ5|P17013|Q5VZ86	Frame_Shift_Del	DEL	ENST00000458705.2	hg19	CCDS31182.1																																																																																			.	.		0.438	ZNF33A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000047614.1	NM_006974	
HYDIN	54768	hgsc.bcm.edu	37	16	70843883	70843883	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:70843883delG	ENST00000393567.2	-	85	14836	c.14686delC	c.(14686-14688)ctgfs	p.L4896fs		NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	4896					cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)		p.L4895M(1)|p.L4847M(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				CCAGCTTTCAGGGGCTGAAAT	0.483																																					p.L4896fs		Atlas-INDEL	.											.	HYDIN	788	.	2	Substitution - Missense(2)	lung(2)	c.14687delT						.						220.0	227.0	225.0					16																	70843883		1940	4133	6073	SO:0001589	frameshift_variant	54768	exon85			.	AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	19368	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 31"""	610812	"""hydrocephalus inducing"", ""hydrocephalus inducing homolog (mouse)"""			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.14686delC	chr16.hg19:g.70843883delG	ENSP00000377197:p.Leu4896fs	241.0	0.0		145.0	10.0	NM_001270974	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Frame_Shift_Del	DEL	ENST00000393567.2	hg19	CCDS59269.1																																																																																			.	.		0.483	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3		
TSPAN14	81619	hgsc.bcm.edu	37	10	82271995	82271995	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:82271995delC	ENST00000429989.3	+	6	769	c.546delC	c.(544-546)gtcfs	p.V182fs	TSPAN14_ENST00000372164.3_Frame_Shift_Del_p.V165fs|TSPAN14_ENST00000372158.1_Frame_Shift_Del_p.V182fs|TSPAN14_ENST00000481124.1_Frame_Shift_Del_p.V59fs|TSPAN14_ENST00000372156.1_Frame_Shift_Del_p.V182fs|TSPAN14_ENST00000341863.6_Frame_Shift_Del_p.V125fs	NM_030927.2	NP_112189.2	Q8NG11	TSN14_HUMAN	tetraspanin 14	182					establishment of protein localization to plasma membrane (GO:0090002)|positive regulation of Notch signaling pathway (GO:0045747)|protein maturation (GO:0051604)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tetraspanin-enriched microdomain (GO:0097197)	enzyme binding (GO:0019899)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(1)|ovary(1)|skin(1)	7			Colorectal(32;0.229)			AGTGCGGGGTCCCCTTCTCCT	0.612																																					p.V182fs		Atlas-INDEL	.											.	TSPAN14	29	.	0			c.545delT						.						77.0	74.0	75.0					10																	82271995		2203	4300	6503	SO:0001589	frameshift_variant	81619	exon6			.	AF311903	CCDS7369.1, CCDS44448.1	10q23.1	2013-02-14	2005-03-21	2005-03-21	ENSG00000108219	ENSG00000108219		"""Tetraspanins"""	23303	protein-coding gene	gene with protein product			"""transmembrane 4 superfamily member 14"""	TM4SF14		11230166	Standard	NM_030927		Approved	DC-TM4F2, MGC11352	uc001kcj.4	Q8NG11	OTTHUMG00000018615	ENST00000429989.3:c.546delC	chr10.hg19:g.82271995delC	ENSP00000396270:p.Val182fs	233.0	0.0		166.0	10.0	NM_030927	A6NHE1|B4DHY6|D3DWD7|D3DWD8|Q567U7|Q9BU34|Q9H0U1	Frame_Shift_Del	DEL	ENST00000429989.3	hg19	CCDS7369.1																																																																																			.	.		0.612	TSPAN14-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049081.2	NM_030927	
ADAM8	101	hgsc.bcm.edu	37	10	135089017	135089017	+	Frame_Shift_Del	DEL	G	G	-	rs201802022	byFrequency	TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:135089017delG	ENST00000445355.3	-	2	171	c.121delC	c.(121-123)cgafs	p.R41fs	ADAM8_ENST00000485491.2_Intron|ADAM8_ENST00000559180.1_5'UTR|ADAM8_ENST00000415217.3_Frame_Shift_Del_p.R41fs	NM_001109.4	NP_001100.3	P78325	ADAM8_HUMAN	ADAM metallopeptidase domain 8	41					activation of MAPK activity involved in innate immune response (GO:0035419)|angiogenesis (GO:0001525)|cell morphogenesis (GO:0000902)|cellular response to hypoxia (GO:0071456)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inflammatory response (GO:0006954)|leukocyte migration involved in inflammatory response (GO:0002523)|lymphocyte chemotaxis (GO:0048247)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of bone resorption (GO:0045780)|positive regulation of cell adhesion (GO:0045785)|positive regulation of eosinophil migration (GO:2000418)|positive regulation of fibronectin-dependent thymocyte migration (GO:2000415)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of neutrophil extravasation (GO:2000391)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein processing (GO:0010954)|positive regulation of protein secretion (GO:0050714)|positive regulation of T cell differentiation in thymus (GO:0033089)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of tumor necrosis factor (ligand) superfamily member 11 production (GO:2000309)|regulation of cell-cell adhesion (GO:0022407)|single organismal cell-cell adhesion (GO:0016337)	alpha9-beta1 integrin-ADAM8 complex (GO:0071133)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|dense core granule membrane (GO:0032127)|integral component of plasma membrane (GO:0005887)|phagolysosome (GO:0032010)|plasma membrane (GO:0005886)|podosome (GO:0002102)|specific granule (GO:0042581)|tertiary granule (GO:0070820)	calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|protein self-association (GO:0043621)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(4)|large_intestine(3)|lung(6)|ovary(1)|prostate(2)	17		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		all cancers(32;7.72e-06)|OV - Ovarian serous cystadenocarcinoma(35;8.23e-06)|Epithelial(32;1.02e-05)		CGGCGGACTCGGGGGCCTGGC	0.652																																					p.R41fs		Atlas-INDEL	.											.	ADAM8	41	.	0			c.122delG						.						11.0	13.0	13.0					10																	135089017		2093	4162	6255	SO:0001589	frameshift_variant	101	exon2			.	D26579	CCDS31319.2, CCDS58102.1, CCDS58103.1	10q26.3	2014-03-20	2005-08-18		ENSG00000151651	ENSG00000151651		"""ADAM metallopeptidase domain containing"", ""CD molecules"""	215	protein-coding gene	gene with protein product		602267	"""a disintegrin and metalloproteinase domain 8"""			9126482	Standard	NM_001109		Approved	CD156, MS2, CD156a	uc021qbe.1	P78325	OTTHUMG00000019309	ENST00000445355.3:c.121delC	chr10.hg19:g.135089017delG	ENSP00000453302:p.Arg41fs	299.0	0.0		247.0	16.0	NM_001164489	B4DVM6|H0YL36|H0YLR0|H0YN39	Frame_Shift_Del	DEL	ENST00000445355.3	hg19	CCDS31319.2																																																																																			.	.		0.652	ADAM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051118.4	NM_001109	
HLA-A	3105	hgsc.bcm.edu	37	6	29910372	29910372	+	Frame_Shift_Del	DEL	G	G	-	rs200905772|rs41548119	byFrequency	TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:29910372delG	ENST00000396634.1	+	3	383	c.42delG	c.(40-42)tcgfs	p.S14fs	HLA-A_ENST00000376802.2_Frame_Shift_Del_p.S14fs|HLA-A_ENST00000376809.5_Frame_Shift_Del_p.S14fs|HLA-A_ENST00000376806.5_Frame_Shift_Del_p.S14fs			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	14					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						TGCTACTCTCGGGGGCCCTGG	0.706									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)																											p.S14fs		Atlas-INDEL	.											.	HLA-A	89	.	0			c.41delC						.																																			SO:0001589	frameshift_variant	3105	exon1	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	.	D32129	CCDS34373.1	6p21.3	2013-01-11			ENSG00000206503	ENSG00000206503		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4931	protein-coding gene	gene with protein product		142800				8838351	Standard	NM_001242758		Approved		uc003nol.3	P01891	OTTHUMG00000130501	ENST00000396634.1:c.42delG	chr6.hg19:g.29910372delG	ENSP00000379873:p.Ser14fs	292.0	0.0		200.0	16.0	NM_002116	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Frame_Shift_Del	DEL	ENST00000396634.1	hg19	CCDS34373.1																																																																																			.	.		0.706	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
GRIN2D	2906	hgsc.bcm.edu	37	19	48918135	48918135	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:48918135delC	ENST00000263269.3	+	6	1515	c.1427delC	c.(1426-1428)gccfs	p.A476fs		NM_000836.2	NP_000827.2	O15399	NMDE4_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2D	476					adult locomotory behavior (GO:0008344)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|regulation of sensory perception of pain (GO:0051930)|signal transduction (GO:0007165)|startle response (GO:0001964)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)			autonomic_ganglia(1)|breast(6)|endometrium(2)|large_intestine(9)|lung(12)|ovary(5)|pancreas(1)|prostate(1)	37		all_epithelial(76;1.11e-06)|all_lung(116;5.79e-06)|Lung NSC(112;1.18e-05)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		all cancers(93;0.00014)|OV - Ovarian serous cystadenocarcinoma(262;0.000233)|Epithelial(262;0.0112)|GBM - Glioblastoma multiforme(486;0.0161)	Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Gabapentin(DB00996)|Ketobemidone(DB06738)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	CCACCGGATGCCCCCCGCCCG	0.607																																					p.A476fs		Atlas-INDEL	.											.	GRIN2D	76	.	0			c.1426delG						.						43.0	49.0	47.0					19																	48918135		2203	4300	6503	SO:0001589	frameshift_variant	2906	exon6			.	U77783	CCDS12719.1	19q13.33	2012-08-29			ENSG00000105464	ENSG00000105464		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4588	protein-coding gene	gene with protein product	"""N-methyl-d-aspartate receptor subunit 2D"""	602717		NMDAR2D		9480759, 9418891	Standard	NM_000836		Approved	GluN2D, EB11, NR2D	uc002pjc.4	O15399		ENST00000263269.3:c.1427delC	chr19.hg19:g.48918135delC	ENSP00000263269:p.Ala476fs	244.0	0.0		162.0	11.0	NM_000836		Frame_Shift_Del	DEL	ENST00000263269.3	hg19	CCDS12719.1																																																																																			.	.		0.607	GRIN2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466121.1		
SCLT1	132320	hgsc.bcm.edu	37	4	129873978	129873978	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:129873978delT	ENST00000281142.5	-	14	1667	c.1164delA	c.(1162-1164)aaafs	p.K388fs	SCLT1_ENST00000503215.1_Intron|SCLT1_ENST00000434680.1_Intron|SCLT1_ENST00000502495.1_5'UTR|SCLT1_ENST00000439369.2_Intron	NM_144643.2	NP_653244.2	Q96NL6	SCLT1_HUMAN	sodium channel and clathrin linker 1	388					cilium assembly (GO:0042384)|clustering of voltage-gated sodium channels (GO:0045162)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary transition fiber (GO:0097539)|clathrin complex (GO:0071439)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule cytoskeleton (GO:0015630)	sodium channel regulator activity (GO:0017080)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(10)|ovary(3)|prostate(1)|skin(1)|stomach(1)	29						TATTACATTGTTTTTTGGTGT	0.254																																					p.Q389fs		Atlas-INDEL	.											.	SCLT1	136	.	0			c.1165delC						.						118.0	121.0	120.0					4																	129873978		2200	4296	6496	SO:0001589	frameshift_variant	132320	exon14			.	AK055217	CCDS3740.1	4q28.2	2008-05-02			ENSG00000151466	ENSG00000151466			26406	protein-coding gene	gene with protein product		611399				15797711	Standard	XM_005262732		Approved	hCAP-1A, FLJ30655	uc003igp.2	Q96NL6	OTTHUMG00000133346	ENST00000281142.5:c.1164delA	chr4.hg19:g.129873978delT	ENSP00000281142:p.Lys388fs	227.0	0.0		175.0	17.0	NM_144643	A4QN04|Q0VAH2|Q6P2M4	Frame_Shift_Del	DEL	ENST00000281142.5	hg19	CCDS3740.1																																																																																			.	.		0.254	SCLT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257176.2	NM_144643	
DCTN2	10540	hgsc.bcm.edu	37	12	57928844	57928844	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:57928844delT	ENST00000548249.1	-	5	625	c.358delA	c.(358-360)atcfs	p.I120fs	DCTN2_ENST00000551400.1_5'UTR|DCTN2_ENST00000543672.1_Frame_Shift_Del_p.I125fs|DCTN2_ENST00000537439.1_Frame_Shift_Del_p.I97fs|DCTN2_ENST00000434715.3_Frame_Shift_Del_p.I125fs	NM_001261412.1|NM_001261413.1	NP_001248341.1|NP_001248342.1	Q13561	DCTN2_HUMAN	dynactin 2 (p50)	120					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						GTTACCTTGATTTTTTCAACT	0.493																																					p.I122fs		Atlas-INDEL	.											.	DCTN2	51	.	0			c.365delT						.						149.0	143.0	145.0					12																	57928844		1942	4133	6075	SO:0001589	frameshift_variant	10540	exon5			.	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.358delA	chr12.hg19:g.57928844delT	ENSP00000447824:p.Ile120fs	289.0	0.0		209.0	13.0	NM_001261412	B2RBK5|Q86YN2|Q9BW17	Frame_Shift_Del	DEL	ENST00000548249.1	hg19	CCDS58245.1																																																																																			.	.		0.493	DCTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407393.2	NM_006400	
STAB1	23166	hgsc.bcm.edu	37	3	52543930	52543930	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:52543930delG	ENST00000321725.6	+	23	2468	c.2392delG	c.(2392-2394)gggfs	p.G799fs		NM_015136.2	NP_055951.2	Q9NY15	STAB1_HUMAN	stabilin 1	799					cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|defense response to bacterium (GO:0042742)|inflammatory response (GO:0006954)|negative regulation of angiogenesis (GO:0016525)|oxidation-reduction process (GO:0055114)|receptor-mediated endocytosis (GO:0006898)	endocytic vesicle membrane (GO:0030666)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	hyaluronic acid binding (GO:0005540)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein receptor activity (GO:0005041)|protein disulfide oxidoreductase activity (GO:0015035)|scavenger receptor activity (GO:0005044)			breast(4)|central_nervous_system(3)|endometrium(7)|kidney(2)|large_intestine(13)|liver(1)|lung(27)|ovary(1)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	76				BRCA - Breast invasive adenocarcinoma(193;1.73e-05)|Kidney(197;0.00182)|KIRC - Kidney renal clear cell carcinoma(197;0.00205)|OV - Ovarian serous cystadenocarcinoma(275;0.0482)		CCCAGGCAGTGGGGGGGTGTG	0.652																																					p.S797fs		Atlas-INDEL	.											.	STAB1	178	.	0			c.2391delT						.						36.0	39.0	38.0					3																	52543930		2203	4296	6499	SO:0001589	frameshift_variant	23166	exon23			.	AJ275213	CCDS33768.1	3p21.31	2008-07-18			ENSG00000010327	ENSG00000010327			18628	protein-coding gene	gene with protein product	"""MS-1 antigen"", ""fasciclin egf-like, laminin-type egf-like, and link domain-containing scavenger receptor-1"", ""common lymphatic endothelial and vascular endothelial receptor-1"""	608560				11829752, 12077138	Standard	XM_005264973		Approved	KIAA0246, STAB-1, FEEL-1, CLEVER-1, FELE-1, FEX1	uc003dej.3	Q9NY15	OTTHUMG00000158574	ENST00000321725.6:c.2392delG	chr3.hg19:g.52543930delG	ENSP00000312946:p.Gly799fs	278.0	0.0		219.0	16.0	NM_015136	A7E297|Q8IUH0|Q8IUH1|Q93072	Frame_Shift_Del	DEL	ENST00000321725.6	hg19	CCDS33768.1																																																																																			.	.		0.652	STAB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351380.2	NM_015136	
CAB39	51719	hgsc.bcm.edu	37	2	231657931	231657931	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:231657931delA	ENST00000258418.5	+	4	712	c.283delA	c.(283-285)aaafs	p.K96fs	CAB39_ENST00000409788.3_Frame_Shift_Del_p.K96fs|CAB39_ENST00000410084.3_Frame_Shift_Del_p.K96fs	NM_016289.3	NP_057373.1	Q9Y376	CAB39_HUMAN	calcium binding protein 39	96					activation of protein kinase activity (GO:0032147)|cell cycle arrest (GO:0007050)|cellular hypotonic response (GO:0071476)|insulin receptor signaling pathway (GO:0008286)|intracellular signal transduction (GO:0035556)|negative regulation of potassium ion transmembrane transport (GO:1901380)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of rubidium ion transmembrane transporter activity (GO:2000687)|negative regulation of rubidium ion transport (GO:2000681)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|protein heterooligomerization (GO:0051291)|signal transduction by phosphorylation (GO:0023014)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	kinase binding (GO:0019900)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activator activity (GO:0043539)			central_nervous_system(1)|large_intestine(1)|skin(1)	3		all_lung(227;4.63e-07)|all_hematologic(139;1.83e-06)|Lung NSC(271;2.11e-05)|Acute lymphoblastic leukemia(138;5.51e-05)|Hepatocellular(293;0.0207)|Lung SC(224;0.187)		all cancers(144;1.64e-12)|Epithelial(121;5.29e-11)|LUSC - Lung squamous cell carcinoma(224;0.0154)|Lung(119;0.0177)|COAD - Colon adenocarcinoma(134;0.226)		CTAATAGGGCAAAAAAGACGT	0.358																																					p.G94fs		Atlas-INDEL	.											.	CAB39	30	.	0			c.282delC						.						119.0	117.0	118.0					2																	231657931		2203	4300	6503	SO:0001589	frameshift_variant	51719	exon4			.	AF113536	CCDS2478.1	2q37.1	2008-02-05			ENSG00000135932	ENSG00000135932			20292	protein-coding gene	gene with protein product		612174					Standard	NM_016289		Approved	CGI-66, MO25	uc002vqx.3	Q9Y376	OTTHUMG00000133220	ENST00000258418.5:c.283delA	chr2.hg19:g.231657931delA	ENSP00000258418:p.Lys96fs	271.0	0.0		177.0	15.0	NM_001130850	A8K8L7	Frame_Shift_Del	DEL	ENST00000258418.5	hg19	CCDS2478.1																																																																																			.	.		0.358	CAB39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256955.2	NM_016289	
SUPT5H	6829	hgsc.bcm.edu	37	19	39959402	39959402	+	Frame_Shift_Del	DEL	G	G	-	rs140361350	byFrequency	TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:39959402delG	ENST00000599117.1	+	15	1411	c.1044delG	c.(1042-1044)ctgfs	p.L348fs	SUPT5H_ENST00000432763.2_Frame_Shift_Del_p.L348fs|SUPT5H_ENST00000402194.2_Frame_Shift_Del_p.L344fs|SUPT5H_ENST00000359191.6_Frame_Shift_Del_p.L344fs|SUPT5H_ENST00000598725.1_Frame_Shift_Del_p.L348fs			O00267	SPT5H_HUMAN	suppressor of Ty 5 homolog (S. cerevisiae)	348	Interaction with RNA polymerase II.				7-methylguanosine mRNA capping (GO:0006370)|cell cycle (GO:0007049)|chromatin remodeling (GO:0006338)|DNA-templated transcription, elongation (GO:0006354)|gene expression (GO:0010467)|negative regulation of DNA-templated transcription, elongation (GO:0032785)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of macroautophagy (GO:0016239)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|response to organic substance (GO:0010033)|single stranded viral RNA replication via double stranded DNA intermediate (GO:0039692)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	DSIF complex (GO:0032044)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|protein heterodimerization activity (GO:0046982)			breast(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(13)|lung(12)|ovary(3)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)	51	all_cancers(60;6.69e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;1.57e-06)|Ovarian(47;0.159)		Epithelial(26;3.9e-26)|all cancers(26;1.35e-23)|LUSC - Lung squamous cell carcinoma(53;0.000657)			CCAGGTCCCTGGGGGGTGATG	0.517																																					p.L348fs		Atlas-INDEL	.											.	SUPT5H	119	.	0			c.1043delT						.						61.0	60.0	60.0					19																	39959402		2203	4300	6503	SO:0001589	frameshift_variant	6829	exon13			.	U56402	CCDS12536.1, CCDS46072.1	19q13	2008-07-22	2001-11-28			ENSG00000196235			11469	protein-coding gene	gene with protein product		602102	"""suppressor of Ty (S.cerevisiae) 5 homolog"""			8975720	Standard	NM_003169		Approved	SPT5H, SPT5, FLJ34157	uc002olp.4	O00267		ENST00000599117.1:c.1044delG	chr19.hg19:g.39959402delG	ENSP00000470252:p.Leu348fs	167.0	0.0		121.0	10.0	NM_003169	O43279|Q59G52|Q99639	Frame_Shift_Del	DEL	ENST00000599117.1	hg19	CCDS12536.1																																																																																			.	.		0.517	SUPT5H-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464918.1	NM_003169	
DST	667	hgsc.bcm.edu	37	6	56340988	56340988	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:56340988delG	ENST00000361203.3	-	87	20870	c.20863delC	c.(20863-20865)cagfs	p.Q6955fs	DST_ENST00000244364.6_Frame_Shift_Del_p.Q4652fs|DST_ENST00000446842.2_Frame_Shift_Del_p.Q6740fs|DST_ENST00000370788.2_Frame_Shift_Del_p.Q4869fs|DST_ENST00000370769.4_Frame_Shift_Del_p.Q7066fs|DST_ENST00000421834.2_Frame_Shift_Del_p.Q4978fs|DST_ENST00000370754.5_Frame_Shift_Del_p.Q7244fs|DST_ENST00000312431.6_3'UTR			Q03001	DYST_HUMAN	dystonin	6953					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)			NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			TCGATCTCCTGGGGGATGACT	0.408																																					p.Q4652fs		Atlas-INDEL	.											.	DST	1427	.	0			c.13955delA						.						90.0	86.0	87.0					6																	56340988		1898	4112	6010	SO:0001589	frameshift_variant	667	exon73			.	M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"""EF-hand domain containing"""	1090	protein-coding gene	gene with protein product		113810	"""bullous pemphigoid antigen 1, 230/240kDa"""	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000361203.3:c.20863delC	chr6.hg19:g.56340988delG	ENSP00000354508:p.Gln6955fs	198.0	0.0		153.0	11.0	NM_015548	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Frame_Shift_Del	DEL	ENST00000361203.3	hg19																																																																																				.	.		0.408	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723	
HIRA	7290	hgsc.bcm.edu	37	22	19346949	19346949	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr22:19346949delC	ENST00000263208.5	-	18	2400	c.2144delG	c.(2143-2145)ggcfs	p.G715fs	HIRA_ENST00000541063.1_Frame_Shift_Del_p.G671fs|HIRA_ENST00000340170.4_Intron|HIRA_ENST00000546308.1_Frame_Shift_Del_p.G671fs	NM_003325.3	NP_003316.3	P54198	HIRA_HUMAN	histone cell cycle regulator	715	Interaction with CCNA1.|Interaction with PAX3. {ECO:0000250}.|Interaction with histone H2B.				anatomical structure morphogenesis (GO:0009653)|chromatin modification (GO:0016568)|DNA replication-independent nucleosome assembly (GO:0006336)|gastrulation (GO:0007369)|muscle cell differentiation (GO:0042692)|osteoblast differentiation (GO:0001649)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(14)|ovary(2)|prostate(1)|skin(1)	37	Colorectal(54;0.0993)					CAGCTTCACGCCCCCCACCAC	0.597																																					p.G715fs		Atlas-INDEL	.											.	HIRA	100	.	0			c.2145delC						.						146.0	121.0	129.0					22																	19346949		2203	4300	6503	SO:0001589	frameshift_variant	7290	exon18			.	X75296	CCDS13759.1	22q11.2	2013-05-03	2013-05-03		ENSG00000100084	ENSG00000100084		"""WD repeat domain containing"""	4916	protein-coding gene	gene with protein product	"""DiGeorge critical region gene 1"""	600237	"""HIR (histone cell cycle regulation defective) homolog A (S. cerevisiae)"", ""HIR histone cell cycle regulation defective homolog A (S. cerevisiae)"""	TUPLE1		8111380, 7633437, 9731536	Standard	NM_003325		Approved	DGCR1, TUP1	uc002zpf.1	P54198	OTTHUMG00000150134	ENST00000263208.5:c.2144delG	chr22.hg19:g.19346949delC	ENSP00000263208:p.Gly715fs	182.0	0.0		147.0	10.0	NM_003325	Q05BU9|Q8IXN2	Frame_Shift_Del	DEL	ENST00000263208.5	hg19	CCDS13759.1																																																																																			.	.		0.597	HIRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316488.2	NM_003325	
SAMM50	25813	hgsc.bcm.edu	37	22	44368791	44368791	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr22:44368791delA	ENST00000350028.4	+	6	627	c.470delA	c.(469-471)gaafs	p.E157fs	SAMM50_ENST00000493161.1_3'UTR|SAMM50_ENST00000396202.3_Intron	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	208.0	0.0		142.0	11.0	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	
ENGASE	64772	hgsc.bcm.edu	37	17	77075666	77075666	+	Frame_Shift_Del	DEL	T	T	-	rs113488517		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:77075666delT	ENST00000579016.1	+	4	512	c.512delT	c.(511-513)attfs	p.I171fs	ENGASE_ENST00000539857.2_Intron	NM_001042573.2	NP_001036038.1	Q8NFI3	ENASE_HUMAN	endo-beta-N-acetylglucosaminidase	171						cytoplasm (GO:0005737)	mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity (GO:0033925)			breast(2)|endometrium(4)|large_intestine(1)|lung(15)|prostate(2)|skin(1)	25						ACCGTCACCATTCCCCCAGTG	0.587																																					p.I171fs		Atlas-INDEL	.											.	ENGASE	55	.	0			c.511delA						.						105.0	129.0	121.0					17																	77075666		2116	4222	6338	SO:0001589	frameshift_variant	64772	exon4			.	AF512564	CCDS42394.1	17q25.3	2009-03-03			ENSG00000167280	ENSG00000167280	3.2.1.96		24622	protein-coding gene	gene with protein product	"""Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase"", ""Di-N-acetylchitobiosyl beta-N-acetylglucosaminidase"""	611898				12114544, 18586680	Standard	NM_001042573		Approved	FLJ21865	uc002jwv.4	Q8NFI3	OTTHUMG00000167714	ENST00000579016.1:c.512delT	chr17.hg19:g.77075666delT	ENSP00000462333:p.Ile171fs	156.0	0.0		156.0	10.0	NM_001042573	Q659F0|Q8TB86|Q9H6U4	Frame_Shift_Del	DEL	ENST00000579016.1	hg19	CCDS42394.1																																																																																			.	.		0.587	ENGASE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395807.1	NM_022759	
ERF	2077	hgsc.bcm.edu	37	19	42753385	42753385	+	Frame_Shift_Del	DEL	C	C	-	rs201956380		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:42753385delC	ENST00000222329.4	-	4	1036	c.879delG	c.(877-879)gggfs	p.G293fs	ERF_ENST00000595941.1_5'Flank|AC006486.9_ENST00000594664.1_Intron|ERF_ENST00000440177.2_Frame_Shift_Del_p.G218fs	NM_006494.2	NP_006485.2	P50548	ERF_HUMAN	Ets2 repressor factor	293	Poly-Gly.				cell cycle (GO:0007049)|cell differentiation (GO:0030154)|chorio-allantoic fusion (GO:0060710)|ectodermal cell differentiation (GO:0010668)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)|trophoblast giant cell differentiation (GO:0060707)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(7)|skin(1)	17		Prostate(69;0.00682)				AGCCGCTGGGCCCCCCGCCAC	0.667																																					p.P294fs		Atlas-INDEL	.											.	ERF	47	.	0			c.880delC						.						26.0	30.0	29.0					19																	42753385		2197	4288	6485	SO:0001589	frameshift_variant	2077	exon4			.	U58535	CCDS12600.1	19q13	2008-07-16				ENSG00000105722			3444	protein-coding gene	gene with protein product	"""Ets2 repressor factor"""	611888				7588608, 9192842	Standard	XM_005258644		Approved	PE-2, PE2	uc002ote.4	P50548		ENST00000222329.4:c.879delG	chr19.hg19:g.42753385delC	ENSP00000222329:p.Gly293fs	187.0	0.0		163.0	11.0	NM_006494	B2RAP1|B7Z4R0|Q59G38|Q9UPI7	Frame_Shift_Del	DEL	ENST00000222329.4	hg19	CCDS12600.1																																																																																			.	.		0.667	ERF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463684.1	NM_006494	
CCT8	10694	hgsc.bcm.edu	37	21	30439316	30439316	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr21:30439316delT	ENST00000286788.4	-	5	664	c.458delA	c.(457-459)aacfs	p.N153fs	CCT8_ENST00000540844.1_Frame_Shift_Del_p.N80fs|CCT8_ENST00000470450.1_5'UTR|CCT8_ENST00000542732.1_Frame_Shift_Del_p.N134fs	NM_006585.2	NP_006576.2	P50990	TCPQ_HUMAN	chaperonin containing TCP1, subunit 8 (theta)	153					'de novo' posttranslational protein folding (GO:0051084)|ATP catabolic process (GO:0006200)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)	aggresome (GO:0016235)|cell body (GO:0044297)|centrosome (GO:0005813)|chaperonin-containing T-complex (GO:0005832)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intermediate filament cytoskeleton (GO:0045111)|microtubule (GO:0005874)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)			breast(3)|endometrium(1)|kidney(1)|large_intestine(4)|liver(1)|lung(1)|prostate(3)	14						ATCTCGAAGGTTTTTTGCAGA	0.358																																					p.N153fs		Atlas-INDEL	.											CCT8,NS,carcinoma,0,1	CCT8	38	.	0			c.459delC						.						88.0	83.0	84.0					21																	30439316		2203	4300	6503	SO:0001589	frameshift_variant	10694	exon5			.	Z37163	CCDS33528.1, CCDS68180.1	21q21.3	2011-09-02			ENSG00000156261	ENSG00000156261		"""Heat Shock Proteins / Chaperonins"""	1623	protein-coding gene	gene with protein product			"""chromosome 21 open reading frame 112"""	C21orf112		7890169	Standard	NM_006585		Approved	Cctq, PRED71	uc002ynb.3	P50990	OTTHUMG00000044595	ENST00000286788.4:c.458delA	chr21.hg19:g.30439316delT	ENSP00000286788:p.Asn153fs	317.0	0.0		257.0	16.0	NM_006585	A6NN54|B4DEM7|B4DQH4|Q4VBP8	Frame_Shift_Del	DEL	ENST00000286788.4	hg19	CCDS33528.1																																																																																			.	.		0.358	CCT8-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171822.1		
SRRM1	10250	hgsc.bcm.edu	37	1	24996012	24996012	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:24996012delC	ENST00000323848.9	+	14	2453	c.2138delC	c.(2137-2139)tccfs	p.S713fs	SRRM1_ENST00000447431.2_Frame_Shift_Del_p.S725fs|SRRM1_ENST00000374389.4_Frame_Shift_Del_p.S722fs|SRRM1_ENST00000479034.1_3'UTR|snoU13_ENST00000459464.1_RNA	NM_005839.3	NP_005830.2	Q8IYB3	SRRM1_HUMAN	serine/arginine repetitive matrix 1	713	Arg-rich.|Pro-rich.|Ser-rich.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|lung(9)|ovary(2)|prostate(1)|urinary_tract(2)	36		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000946)|all_lung(284;0.00125)|Ovarian(437;0.00764)|Breast(348;0.0148)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.19)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0422)|OV - Ovarian serous cystadenocarcinoma(117;1.01e-24)|Colorectal(126;5.95e-08)|COAD - Colon adenocarcinoma(152;3.24e-06)|GBM - Glioblastoma multiforme(114;0.000148)|BRCA - Breast invasive adenocarcinoma(304;0.00177)|KIRC - Kidney renal clear cell carcinoma(1967;0.00348)|STAD - Stomach adenocarcinoma(196;0.00483)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.138)		AGAAGGCAGTCCCCGTCTCCA	0.498																																					p.S713fs	Ovarian(68;897 1494 3282 17478)	Atlas-INDEL	.											.	SRRM1	81	.	0			c.2137delT						.						40.0	39.0	39.0					1																	24996012		2203	4297	6500	SO:0001589	frameshift_variant	10250	exon14			.	AF048977	CCDS255.1	1p36	2010-04-22			ENSG00000133226	ENSG00000133226			16638	protein-coding gene	gene with protein product	"""Ser/Arg-related nuclear matrix protein"", ""plenty of prolines 101-like"""	605975				9531537	Standard	NM_005839		Approved	SRM160, POP101, MGC39488	uc001bjm.3	Q8IYB3	OTTHUMG00000003320	ENST00000323848.9:c.2138delC	chr1.hg19:g.24996012delC	ENSP00000326261:p.Ser713fs	198.0	0.0		126.0	10.0	NM_005839	O60585|Q5VVN4	Frame_Shift_Del	DEL	ENST00000323848.9	hg19	CCDS255.1																																																																																			.	.		0.498	SRRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009292.2	NM_005839	
COL6A3	1293	hgsc.bcm.edu	37	2	238285701	238285701	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:238285701delA	ENST00000295550.4	-	7	3236	c.2784delT	c.(2782-2784)tttfs	p.F928fs	COL6A3_ENST00000347401.3_Frame_Shift_Del_p.F727fs|COL6A3_ENST00000409809.1_Frame_Shift_Del_p.F722fs|COL6A3_ENST00000346358.4_Frame_Shift_Del_p.F728fs|COL6A3_ENST00000392004.3_Frame_Shift_Del_p.F722fs|COL6A3_ENST00000392003.2_Frame_Shift_Del_p.F521fs|COL6A3_ENST00000353578.4_Frame_Shift_Del_p.F722fs|COL6A3_ENST00000472056.1_Frame_Shift_Del_p.F321fs	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	928	Nonhelical region.|VWFA 5. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		CAGACTTCACAAAAATGTACC	0.537																																					p.V929X		Atlas-INDEL	.											.	COL6A3	608	.	0			c.2785delG						.						85.0	73.0	77.0					2																	238285701		2203	4300	6503	SO:0001589	frameshift_variant	1293	exon7			.	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.2784delT	chr2.hg19:g.238285701delA	ENSP00000295550:p.Phe928fs	233.0	0.0		154.0	11.0	NM_004369	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Frame_Shift_Del	DEL	ENST00000295550.4	hg19	CCDS33412.1																																																																																			.	.		0.537	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369	
UGT1A5	54579	hgsc.bcm.edu	37	2	234622350	234622350	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:234622350delT	ENST00000373414.3	+	1	713	c.713delT	c.(712-714)cttfs	p.L238fs	UGT1A9_ENST00000354728.4_Intron|UGT1A7_ENST00000373426.3_Intron|UGT1A1_ENST00000609637.1_Intron|UGT1A6_ENST00000373424.1_Intron|UGT1A6_ENST00000406651.1_Intron|UGT1A10_ENST00000373445.1_Intron|UGT1A6_ENST00000305139.6_Intron|UGT1A1_ENST00000373450.4_Intron|UGT1A10_ENST00000344644.5_Intron|UGT1A6_ENST00000480628.1_Intron|UGT1A1_ENST00000608381.1_Frame_Shift_Del_p.L238fs			P35504	UD15_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A5	238						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)			cervix(1)|endometrium(3)|large_intestine(4)|lung(9)|ovary(1)|skin(3)|urinary_tract(1)	22		Breast(86;0.000765)|all_lung(227;0.00267)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0328)|Lung NSC(271;0.0457)|Lung SC(224;0.128)		Epithelial(121;4.51e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000523)|Lung(119;0.00271)|LUSC - Lung squamous cell carcinoma(224;0.00645)		GCCTCTGAGCTTTTTCAGAGA	0.527																																					p.L238fs		Atlas-INDEL	.											.	UGT1A5	66	.	0			c.712delC						.						225.0	217.0	220.0					2																	234622350		2203	4300	6503	SO:0001589	frameshift_variant	54579	exon1			.	M84129	CCDS33404.1	2q37	2010-03-05	2005-07-20		ENSG00000240224	ENSG00000240224		"""UDP glucuronosyltransferases"""	12537	other	complex locus constituent		606430	"""UDP glycosyltransferase 1 family, polypeptide A5"""			9295054, 1339448	Standard	NM_019078		Approved	UGT1E		P35504	OTTHUMG00000059120	ENST00000373414.3:c.713delT	chr2.hg19:g.234622350delT	ENSP00000362513:p.Leu238fs	328.0	0.0		198.0	13.0	NM_019078	B8K294	Frame_Shift_Del	DEL	ENST00000373414.3	hg19	CCDS33404.1																																																																																			.	.		0.527	UGT1A5-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000130985.1	NM_019078	
WBP11	51729	hgsc.bcm.edu	37	12	14941929	14941929	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:14941929delG	ENST00000261167.2	-	11	1681	c.1448delC	c.(1447-1449)cctfs	p.P484fs		NM_016312.2	NP_057396.1	Q9Y2W2	WBP11_HUMAN	WW domain binding protein 11	484	Pro-rich.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|protein phosphatase type 1 regulator activity (GO:0008599)|single-stranded DNA binding (GO:0003697)|WW domain binding (GO:0050699)			endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(16)|ovary(1)|prostate(1)	30						TCCACGAGGAGGGGGACCAGG	0.582																																					p.P483fs		Atlas-INDEL	.											.	WBP11	66	.	0			c.1449delT						.						17.0	20.0	19.0					12																	14941929		2203	4299	6502	SO:0001589	frameshift_variant	51729	exon11			.	AB029309	CCDS8666.1	12p12.3	2014-06-13			ENSG00000084463	ENSG00000084463			16461	protein-coding gene	gene with protein product	"""splicing factor, PQBP1 and PP1 interacting"", ""protein phosphatase 1, regulatory subunit 165"""					10593949	Standard	NM_016312		Approved	NPWBP, SIPP1, PPP1R165	uc001rci.3	Q9Y2W2	OTTHUMG00000168737	ENST00000261167.2:c.1448delC	chr12.hg19:g.14941929delG	ENSP00000261167:p.Pro484fs	181.0	0.0		151.0	10.0	NM_016312	Q96AY8	Frame_Shift_Del	DEL	ENST00000261167.2	hg19	CCDS8666.1																																																																																			.	.		0.582	WBP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400850.1	NM_016312	
RPS27A	6233	hgsc.bcm.edu	37	2	55461316	55461316	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:55461316delT	ENST00000272317.6	+	4	489	c.165delT	c.(163-165)actfs	p.T55fs	CLHC1_ENST00000406076.1_5'Flank|CLHC1_ENST00000401408.1_5'Flank|RPS27A_ENST00000402285.3_Frame_Shift_Del_p.T55fs|RPS27A_ENST00000404735.1_Frame_Shift_Del_p.T55fs|CLHC1_ENST00000407122.1_5'Flank|CLHC1_ENST00000494539.1_5'Flank|CLHC1_ENST00000406437.2_5'Flank	NM_002954.5	NP_002945.1	P62979	RS27A_HUMAN	ribosomal protein S27a	55	Ubiquitin-like. {ECO:0000255|PROSITE- ProRule:PRU00214}.				activation of MAPK activity (GO:0000187)|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)|apoptotic signaling pathway (GO:0097190)|carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|cellular response to hypoxia (GO:0071456)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|endosomal transport (GO:0016197)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|gene expression (GO:0010467)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|intracellular transport of virus (GO:0075733)|ion transmembrane transport (GO:0034220)|JNK cascade (GO:0007254)|membrane organization (GO:0061024)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|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 epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of type I interferon production (GO:0032480)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|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 I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|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 transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of type I interferon production (GO:0032479)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|stress-activated MAPK cascade (GO:0051403)|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)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|transmembrane transport (GO:0055085)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|viral transcription (GO:0019083)|virion assembly (GO:0019068)	cytosol (GO:0005829)|cytosolic small ribosomal subunit (GO:0022627)|endocytic vesicle membrane (GO:0030666)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|small ribosomal subunit (GO:0015935)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			cervix(1)|ovary(1)|urinary_tract(1)	3						ATGGACGTACTTTGTCTGACT	0.353																																					p.T55fs		Atlas-INDEL	.											.	RPS27A	12	.	0			c.164delC						.						84.0	87.0	86.0					2																	55461316		2203	4300	6503	SO:0001589	frameshift_variant	6233	exon4			.	AB007163	CCDS33202.1	2p16	2011-04-06			ENSG00000143947	ENSG00000143947		"""S ribosomal proteins"""	10417	protein-coding gene	gene with protein product	"""ubiquitin carboxyl extension protein 80"""	191343				9582194	Standard	NM_001135592		Approved	UBCEP80, Uba80, S27A	uc010yow.2	P62979	OTTHUMG00000151919	ENST00000272317.6:c.165delT	chr2.hg19:g.55461316delT	ENSP00000272317:p.Thr55fs	329.0	0.0		249.0	16.0	NM_001135592	P02248|P02249|P02250|P14798|P62988|Q29120|Q6LBL4|Q6LDU5|Q8WYN8|Q91887|Q91888|Q9BQ77|Q9BWD6|Q9BX98|Q9UEF2|Q9UEG1|Q9UEK8|Q9UPK7	Frame_Shift_Del	DEL	ENST00000272317.6	hg19	CCDS33202.1																																																																																			.	.		0.353	RPS27A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324423.15		
SECISBP2L	9728	hgsc.bcm.edu	37	15	49304846	49304846	+	Splice_Site	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:49304846delT	ENST00000559471.1	-	12	1993	c.1730delA	c.(1729-1731)aag>ag	p.K577fs	SECISBP2L_ENST00000261847.3_Splice_Site_p.K532fs	NM_001193489.1	NP_001180418.1	Q93073	SBP2L_HUMAN	SECIS binding protein 2-like	577							poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(5)|kidney(8)|large_intestine(12)|lung(11)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|urinary_tract(1)	46						TTGGTTTACCTTTTTAAGTGC	0.328																																					p.K577fs		Atlas-INDEL	.											.	SECISBP2L	118	.	0			c.1731delG						.						94.0	97.0	96.0					15																	49304846		2197	4295	6492	SO:0001630	splice_region_variant	9728	exon12			.	BC033001	CCDS32234.1, CCDS53942.1	15q21.1	2014-02-12				ENSG00000138593			28997	protein-coding gene	gene with protein product		615756					Standard	NM_001193489		Approved	KIAA0256	uc001zxe.2	Q93073		ENST00000559471.1:c.1731+1A>-	chr15.hg19:g.49304846delT		165.0	0.0		141.0	10.0	NM_001193489	Q8N767	Frame_Shift_Del	DEL	ENST00000559471.1	hg19	CCDS53942.1																																																																																			.	.		0.328	SECISBP2L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417277.1	NM_014701	Frame_Shift_Del
PHF3	23469	hgsc.bcm.edu	37	6	64404551	64404551	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:64404551delG	ENST00000262043.3	+	6	2917	c.2577delG	c.(2575-2577)atgfs	p.M859fs	PHF3_ENST00000393387.1_Frame_Shift_Del_p.M859fs			Q92576	PHF3_HUMAN	PHD finger protein 3	859					multicellular organismal development (GO:0007275)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(7)|cervix(2)|endometrium(8)|kidney(7)|large_intestine(18)|lung(21)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(6)	75	all_cancers(3;0.0241)|all_epithelial(2;0.00306)|Lung NSC(77;0.121)		LUSC - Lung squamous cell carcinoma(74;0.0644)|Lung(124;0.148)			TTCGTAAGATGGGACAACCAG	0.383																																					p.M859fs	GBM(135;136 1820 29512 34071 46235)	Atlas-INDEL	.											.	PHF3	191	.	0			c.2576delT						.						100.0	113.0	108.0					6																	64404551		2202	4300	6502	SO:0001589	frameshift_variant	23469	exon5			.	AF091622	CCDS4966.1	6q12	2013-09-24			ENSG00000118482	ENSG00000118482		"""Zinc fingers, PHD-type"""	8921	protein-coding gene	gene with protein product		607789				11856869	Standard	XM_005248701		Approved		uc003pep.1	Q92576	OTTHUMG00000014952	ENST00000262043.3:c.2577delG	chr6.hg19:g.64404551delG	ENSP00000262043:p.Met859fs	215.0	0.0		164.0	11.0	NM_015153	A3KFI8|Q14CR5|Q5CZI1|Q5T1T6|Q9NQ16|Q9UI45	Frame_Shift_Del	DEL	ENST00000262043.3	hg19	CCDS4966.1																																																																																			.	.		0.383	PHF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041086.2		
SCEL	8796	hgsc.bcm.edu	37	13	78188077	78188077	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr13:78188077delA	ENST00000349847.3	+	24	1522	c.1438delA	c.(1438-1440)aaafs	p.K480fs	SCEL_ENST00000377246.3_Frame_Shift_Del_p.K460fs|SCEL_ENST00000469982.1_3'UTR|SCEL_ENST00000535157.1_Frame_Shift_Del_p.K438fs	NM_144777.2	NP_659001.2	O95171	SCEL_HUMAN	sciellin	480	16 X approximate tandem repeats.		K -> R (in dbSNP:rs8002725).		embryo development (GO:0009790)|epidermis development (GO:0008544)|keratinocyte differentiation (GO:0030216)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(18)|ovary(5)|prostate(1)|stomach(1)|urinary_tract(1)	40		Acute lymphoblastic leukemia(28;0.0282)|Breast(118;0.037)		GBM - Glioblastoma multiforme(99;0.0233)		CAAAGCTGTCAAAAACACTGA	0.328																																					p.V479fs		Atlas-INDEL	.											.	SCEL	85	.	0			c.1437delC						.						181.0	173.0	176.0					13																	78188077		2203	4300	6503	SO:0001589	frameshift_variant	8796	exon24			.	AF045941	CCDS9458.1, CCDS9459.1, CCDS53877.1	13q22	2008-07-18			ENSG00000136155	ENSG00000136155			10573	protein-coding gene	gene with protein product		604112				9813070	Standard	NM_003843		Approved	FLJ21667, MGC22531	uc001vki.3	O95171	OTTHUMG00000017107	ENST00000349847.3:c.1438delA	chr13.hg19:g.78188077delA	ENSP00000302579:p.Lys480fs	300.0	0.0		204.0	15.0	NM_144777	B7Z797|F5H651|Q53H61|Q5W0S8|Q5W0S9|Q86X00	Frame_Shift_Del	DEL	ENST00000349847.3	hg19	CCDS9459.1																																																																																			.	.		0.328	SCEL-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045339.2	NM_144777	
PTCH2	8643	hgsc.bcm.edu	37	1	45293130	45293130	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:45293130delG	ENST00000372192.3	-	15	2445	c.2315delC	c.(2314-2316)ccafs	p.P773fs	PTCH2_ENST00000447098.2_Frame_Shift_Del_p.P773fs	NM_003738.4	NP_003729.3	Q9Y6C5	PTC2_HUMAN	patched 2	773					epidermis development (GO:0008544)|hair cycle (GO:0042633)|negative regulation of smoothened signaling pathway (GO:0045879)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	hedgehog family protein binding (GO:0097108)|hedgehog receptor activity (GO:0008158)|smoothened binding (GO:0005119)			NS(2)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(19)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	50	Acute lymphoblastic leukemia(166;0.155)					GGTGGCCGGTGGGGGCAGCAC	0.662									Basal Cell Nevus syndrome																												p.P772fs		Atlas-INDEL	.											.	PTCH2	96	.	0			c.2316delA						.						46.0	56.0	53.0					1																	45293130		2203	4300	6503	SO:0001589	frameshift_variant	8643	exon15	Familial Cancer Database	Gorlin syndrome, Gorlin-Golz syndrome, Naevoid Basal Cell Carcinoma syndrome, NBCCS	.	AF091501	CCDS516.1, CCDS53312.1	1p34.1	2010-06-24	2010-06-24		ENSG00000117425	ENSG00000117425			9586	protein-coding gene	gene with protein product		603673	"""patched (Drosophila) homolog 2"", ""patched homolog 2 (Drosophila)"""			9811851, 9931336	Standard	NM_003738		Approved		uc010olf.2	Q9Y6C5	OTTHUMG00000008490	ENST00000372192.3:c.2315delC	chr1.hg19:g.45293130delG	ENSP00000361266:p.Pro773fs	241.0	0.0		189.0	13.0	NM_003738	O95341|O95856|Q53Z57|Q5QP87|Q6UX14	Frame_Shift_Del	DEL	ENST00000372192.3	hg19	CCDS516.1																																																																																			.	.		0.662	PTCH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000023428.4	NM_003738	
TRIM27	5987	hgsc.bcm.edu	37	6	28887983	28887983	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:28887983delC	ENST00000377199.3	-	3	909	c.553delG	c.(553-555)gagfs	p.E185fs	TRIM27_ENST00000377194.3_Frame_Shift_Del_p.E185fs|TRIM27_ENST00000498117.1_5'UTR	NM_006510.4	NP_006501.1	P14373	TRI27_HUMAN	tripartite motif containing 27	185					Arp2/3 complex-mediated actin nucleation (GO:0034314)|cell proliferation (GO:0008283)|innate immune response (GO:0045087)|interferon-gamma secretion (GO:0072643)|negative regulation of adaptive immune response (GO:0002820)|negative regulation of calcium ion import (GO:0090281)|negative regulation of gene expression, epigenetic (GO:0045814)|negative regulation of interleukin-2 secretion (GO:1900041)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of tumor necrosis factor production (GO:0032720)|negative regulation of viral release from host cell (GO:1902187)|negative regulation of viral transcription (GO:0032897)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein K63-linked ubiquitination (GO:0070534)|protein trimerization (GO:0070206)|retrograde transport, endosome to Golgi (GO:0042147)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(2)|lung(6)|ovary(1)	10						TGCTCAAACTCCCAAACAATC	0.493			T	RET	papillary thyroid																																p.E185fs		Atlas-INDEL	.		Dom	yes		6	6p22	5987	tripartite motif-containing 27		E	.	TRIM27	26	.	0			c.554delA						.						172.0	162.0	166.0					6																	28887983		2203	4300	6503	SO:0001589	frameshift_variant	5987	exon3			.	Z58939	CCDS4654.1	6p22	2013-01-09	2011-01-25	2006-09-26	ENSG00000204713	ENSG00000204713		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	9975	protein-coding gene	gene with protein product		602165	"""ret finger protein"", ""tripartite motif-containing 27"""	RFP		8114113	Standard	NM_006510		Approved	RNF76	uc003nlr.3	P14373	OTTHUMG00000031215	ENST00000377199.3:c.553delG	chr6.hg19:g.28887983delC	ENSP00000366404:p.Glu185fs	249.0	0.0		181.0	11.0	NM_006510	A2BE15|Q5RJA8|Q5ST26|Q6LA73|Q6NXR9|Q9BZY6|Q9UJL3	Frame_Shift_Del	DEL	ENST00000377199.3	hg19	CCDS4654.1																																																																																			.	.		0.493	TRIM27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076442.2	NM_030950	
SPHK2	56848	hgsc.bcm.edu	37	19	49132347	49132347	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:49132347delC	ENST00000245222.4	+	7	1648	c.1282delC	c.(1282-1284)cccfs	p.P428fs	SPHK2_ENST00000340932.3_Frame_Shift_Del_p.P390fs|SPHK2_ENST00000600537.1_Frame_Shift_Del_p.P369fs|SPHK2_ENST00000599029.1_Frame_Shift_Del_p.P392fs|SPHK2_ENST00000598088.1_Frame_Shift_Del_p.P428fs|SPHK2_ENST00000443164.1_Frame_Shift_Del_p.P490fs|SPHK2_ENST00000599748.1_Frame_Shift_Del_p.P392fs	NM_001204158.2|NM_001243876.1|NM_020126.4	NP_001191087.1|NP_001230805.1|NP_064511.2	Q9NRA0	SPHK2_HUMAN	sphingosine kinase 2	428					blood vessel development (GO:0001568)|brain development (GO:0007420)|cell proliferation (GO:0008283)|lipid phosphorylation (GO:0046834)|negative regulation of apoptotic process (GO:0043066)|positive regulation of cell proliferation (GO:0008284)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|small molecule metabolic process (GO:0044281)|sphinganine-1-phosphate biosynthetic process (GO:0006669)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingosine metabolic process (GO:0006670)	cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	ATP binding (GO:0005524)|D-erythro-sphingosine kinase activity (GO:0017050)|diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951)|Ras GTPase binding (GO:0017016)|sphinganine kinase activity (GO:0008481)			NS(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(4)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	19		all_lung(116;0.000125)|Lung NSC(112;0.000202)|all_epithelial(76;0.000283)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000102)|all cancers(93;0.000117)|GBM - Glioblastoma multiforme(486;0.00627)|Epithelial(262;0.0158)		tcttcccctgccccagcctgc	0.697																																					p.L427fs		Atlas-INDEL	.											.	SPHK2	62	.	0			c.1281delG						.						22.0	24.0	23.0					19																	49132347		2201	4293	6494	SO:0001589	frameshift_variant	56848	exon7			.	AF245447	CCDS12727.1, CCDS59404.1, CCDS59405.1, CCDS74414.1	19q13.33	2013-09-20			ENSG00000063176	ENSG00000063176			18859	protein-coding gene	gene with protein product		607092				10751414, 17895250	Standard	NM_020126		Approved		uc002pjs.3	Q9NRA0	OTTHUMG00000183318	ENST00000245222.4:c.1282delC	chr19.hg19:g.49132347delC	ENSP00000245222:p.Pro428fs	235.0	0.0		177.0	11.0	NM_020126	A0T4C8|B4DU87|Q9BRN1|Q9H0Q2|Q9NWU7	Frame_Shift_Del	DEL	ENST00000245222.4	hg19	CCDS12727.1																																																																																			.	.		0.697	SPHK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466153.1		
CCDC126	90693	hgsc.bcm.edu	37	7	23650955	23650955	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:23650955delA	ENST00000307471.3	+	3	478	c.21delA	c.(19-21)agafs	p.R7fs	CCDC126_ENST00000486109.1_3'UTR|CCDC126_ENST00000410069.1_Frame_Shift_Del_p.R7fs|CCDC126_ENST00000409765.1_Frame_Shift_Del_p.R7fs	NM_138771.3	NP_620126.2	Q96EE4	CC126_HUMAN	coiled-coil domain containing 126	7					protein N-linked glycosylation (GO:0006487)	extracellular region (GO:0005576)|membrane (GO:0016020)	alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase activity (GO:0030144)			endometrium(3)|kidney(1)|large_intestine(1)|ovary(1)|skin(1)	7						CAATCTCAAGAAAAAATATGT	0.323																																					p.R7fs		Atlas-INDEL	.											.	CCDC126	16	.	0			c.20delG						.						76.0	78.0	77.0					7																	23650955		2203	4300	6503	SO:0001589	frameshift_variant	90693	exon3			.	BC012427	CCDS5384.1	7p15.3	2006-08-15			ENSG00000169193	ENSG00000169193			22398	protein-coding gene	gene with protein product						12477932	Standard	NM_138771		Approved	FLJ23031	uc003swl.3	Q96EE4	OTTHUMG00000128461	ENST00000307471.3:c.21delA	chr7.hg19:g.23650955delA	ENSP00000304355:p.Arg7fs	164.0	0.0		229.0	15.0	NM_138771	A8K1J6|Q6UWP1|Q75MQ6	Frame_Shift_Del	DEL	ENST00000307471.3	hg19	CCDS5384.1																																																																																			.	.		0.323	CCDC126-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250259.1	NM_138771	
NCKAP5L	57701	hgsc.bcm.edu	37	12	50186232	50186232	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:50186232delG	ENST00000335999.6	-	12	3990	c.3789delC	c.(3787-3789)cccfs	p.P1263fs		NM_001037806.3	NP_001032895.2	Q9HCH0	NCK5L_HUMAN	NCK-associated protein 5-like	1259	Pro-rich.									central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(8)|prostate(2)	18						TTCTCACCATGGGGGTCCTGG	0.612																																					p.M1264fs		Atlas-INDEL	.											.	NCKAP5L	142	.	0			c.3790delA						.						27.0	31.0	29.0					12																	50186232		1950	4137	6087	SO:0001589	frameshift_variant	57701	exon12			.	AB046822	CCDS41781.2	12q13.12	2009-08-14	2009-08-14	2009-08-14	ENSG00000167566	ENSG00000167566			29321	protein-coding gene	gene with protein product		615104	"""KIAA1602"""	KIAA1602			Standard	NM_001037806		Approved		uc009zlk.2	Q9HCH0	OTTHUMG00000156969	ENST00000335999.6:c.3789delC	chr12.hg19:g.50186232delG	ENSP00000337998:p.Pro1263fs	165.0	0.0		149.0	13.0	NM_001037806	Q2TB26|Q71RH1|Q8N4W1|Q96HX2	Frame_Shift_Del	DEL	ENST00000335999.6	hg19	CCDS41781.2																																																																																			.	.		0.612	NCKAP5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346884.2	XM_035497	
IFI27L1	122509	hgsc.bcm.edu	37	14	94568273	94568273	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr14:94568273delG	ENST00000555523.1	+	4	394	c.175delG	c.(175-177)gggfs	p.G61fs	IFI27L1_ENST00000554562.1_Frame_Shift_Del_p.G61fs|IFI27L1_ENST00000554544.1_Intron|IFI27L1_ENST00000557066.1_Intron|IFI27L1_ENST00000556381.1_Frame_Shift_Del_p.G60fs|IFI27L1_ENST00000553664.1_Frame_Shift_Del_p.R81fs|IFI27L1_ENST00000557218.1_Intron|IFI27L1_ENST00000553350.1_Intron|IFI27L1_ENST00000393115.3_Frame_Shift_Del_p.G61fs	NM_206949.2	NP_996832.1	Q96BM0	I27L1_HUMAN	interferon, alpha-inducible protein 27-like 1	61						integral component of membrane (GO:0016021)				lung(2)	2						CATTGCCAACGGGGGCGGAGT	0.592																																					p.N58fs		Atlas-INDEL	.											.	IFI27L1	11	.	0			c.174delC						.						114.0	95.0	101.0					14																	94568273		2203	4300	6503	SO:0001589	frameshift_variant	122509	exon4			.	BC015423	CCDS9919.1	14q32.13	2008-10-08	2008-10-08	2008-10-08		ENSG00000165948			19754	protein-coding gene	gene with protein product		611320	"""family with sequence similarity 14, member B"""	FAM14B			Standard	NM_145249		Approved		uc001yck.3	Q96BM0		ENST00000555523.1:c.175delG	chr14.hg19:g.94568273delG	ENSP00000451851:p.Gly61fs	319.0	0.0		265.0	16.0	NM_145249		Frame_Shift_Del	DEL	ENST00000555523.1	hg19	CCDS9919.1																																																																																			.	.		0.592	IFI27L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412868.1	NM_206949	
PLB1	151056	hgsc.bcm.edu	37	2	28820879	28820879	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:28820879delG	ENST00000327757.5	+	34	2373	c.2329delG	c.(2329-2331)gggfs	p.G777fs	PLB1_ENST00000422425.2_Frame_Shift_Del_p.G766fs	NM_153021.4	NP_694566.4	Q6P1J6	PLB1_HUMAN	phospholipase B1	777	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)					CAGTGCAGGAGGGGACGGCTC	0.527																																					p.G776fs		Atlas-INDEL	.											.	PLB1	255	.	0			c.2328delA						.						118.0	100.0	106.0					2																	28820879		2203	4300	6503	SO:0001589	frameshift_variant	151056	exon34			.		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.2329delG	chr2.hg19:g.28820879delG	ENSP00000330442:p.Gly777fs	225.0	0.0		177.0	11.0	NM_153021	A8KAX2|Q53S03|Q8IUP7|Q96DP9	Frame_Shift_Del	DEL	ENST00000327757.5	hg19	CCDS33168.1																																																																																			.	.		0.527	PLB1-012	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353348.2		
ARHGAP39	80728	hgsc.bcm.edu	37	8	145759584	145759584	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:145759584delC	ENST00000276826.5	-	6	2725	c.2524delG	c.(2524-2526)gtgfs	p.V842fs	ARHGAP39_ENST00000540274.1_Frame_Shift_Del_p.V842fs|ARHGAP39_ENST00000377307.2_Frame_Shift_Del_p.V873fs			Q9C0H5	RHG39_HUMAN	Rho GTPase activating protein 39	842	MyTH4. {ECO:0000255|PROSITE- ProRule:PRU00359}.				axon guidance (GO:0007411)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nucleus (GO:0005634)				NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(11)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	22						CTTATCGCCACCCCTGGAAAG	0.647																																					p.V873fs		Atlas-INDEL	.											.	ARHGAP39	80	.	0			c.2618delT						.						95.0	90.0	91.0					8																	145759584		2203	4300	6503	SO:0001589	frameshift_variant	80728	exon9			.		CCDS34971.1	8q24.3	2011-06-29			ENSG00000147799	ENSG00000147799		"""Rho GTPase activating proteins"""	29351	protein-coding gene	gene with protein product	"""RhoGAP93B homolog (Drosophila)"", ""crossGAP homolog (Drosophila)"""	615880				15755809	Standard	XM_005272344		Approved	KIAA1688, Vilse, CrGAP	uc003zds.1	Q9C0H5	OTTHUMG00000165182	ENST00000276826.5:c.2524delG	chr8.hg19:g.145759584delC	ENSP00000276826:p.Val842fs	233.0	0.0		235.0	15.0	NM_025251	B4E1I1	Frame_Shift_Del	DEL	ENST00000276826.5	hg19																																																																																				.	.		0.647	ARHGAP39-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382509.1		
MID2	11043	hgsc.bcm.edu	37	X	107084012	107084012	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:107084012delC	ENST00000262843.6	+	2	665	c.117delC	c.(115-117)gacfs	p.D39fs	MID2_ENST00000443968.2_Frame_Shift_Del_p.D39fs	NM_012216.3|NM_052817.2	NP_036348.2|NP_438112.2	Q9UJV3	TRIM1_HUMAN	midline 2	39					innate immune response (GO:0045087)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral release from host cell (GO:1902187)|negative regulation of viral transcription (GO:0032897)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein localization to microtubule (GO:0035372)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	ligase activity (GO:0016874)|microtubule binding (GO:0008017)|phosphoprotein binding (GO:0051219)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(7)|ovary(1)|prostate(2)	19						TGTTTGAAGACCCCCTTCTGC	0.488																																					p.D39fs		Atlas-INDEL	.											.	MID2	122	.	0			c.116delA						.						188.0	178.0	182.0					X																	107084012		2203	4300	6503	SO:0001589	frameshift_variant	11043	exon2			.		CCDS14532.2, CCDS14533.2	Xq22.1-q22.2	2013-02-11			ENSG00000080561	ENSG00000080561		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"", ""Fibronectin type III domain containing"""	7096	protein-coding gene	gene with protein product		300204				10400986	Standard	NM_012216		Approved	FXY2, TRIM1, RNF60	uc004enl.3	Q9UJV3	OTTHUMG00000022171	ENST00000262843.6:c.117delC	chrX.hg19:g.107084012delC	ENSP00000262843:p.Asp39fs	246.0	0.0		158.0	10.0	NM_012216	A6NEL8|A6PVI5|Q5JYF5|Q8WWK1|Q9UJR9	Frame_Shift_Del	DEL	ENST00000262843.6	hg19	CCDS14532.2																																																																																			.	.		0.488	MID2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057852.2	NM_012216	
TEFM	79736	hgsc.bcm.edu	37	17	29231265	29231265	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:29231265delT	ENST00000581216.1	-	2	935	c.314delA	c.(313-315)aacfs	p.N105fs	TEFM_ENST00000580840.1_Frame_Shift_Del_p.N105fs	NM_024683.3	NP_078959.3	Q96QE5	TEFM_HUMAN	transcription elongation factor, mitochondrial	105					DNA metabolic process (GO:0006259)|oxidative phosphorylation (GO:0006119)|regulation of transcription, DNA-templated (GO:0006355)|transcription from mitochondrial promoter (GO:0006390)	mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|ribonucleoprotein complex (GO:0030529)	DNA polymerase processivity factor activity (GO:0030337)|poly(A) RNA binding (GO:0044822)										TGGCCCAAAGTTTTCTCTGTG	0.373																																					p.N105fs		Atlas-INDEL	.											.	.	.	.	0			c.315delC						.						100.0	92.0	94.0					17																	29231265		1842	4080	5922	SO:0001589	frameshift_variant	79736	exon2			.		CCDS42291.1	17q11.2	2011-12-12	2011-12-12	2011-12-12	ENSG00000172171	ENSG00000172171			26223	protein-coding gene	gene with protein product			"""chromosome 17 open reading frame 42"""	C17orf42		11468690, 10843809, 21278163	Standard	NM_024683		Approved	FLJ22729	uc002hfu.2	Q96QE5		ENST00000581216.1:c.314delA	chr17.hg19:g.29231265delT	ENSP00000462963:p.Asn105fs	246.0	0.0		164.0	10.0	NM_024683	E1P655|Q6GPG5|Q6PJ19|Q96H04|Q9H5Z9	Frame_Shift_Del	DEL	ENST00000581216.1	hg19	CCDS42291.1																																																																																			.	.		0.373	TEFM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444498.1	NM_024683	
PIWIL3	440822	hgsc.bcm.edu	37	22	25153878	25153878	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr22:25153878delT	ENST00000332271.5	-	4	768	c.352delA	c.(352-354)acafs	p.T118fs	PIWIL3_ENST00000532537.2_5'UTR|PIWIL3_ENST00000533313.1_Frame_Shift_Del_p.T9fs|PIWIL3_ENST00000527701.1_Frame_Shift_Del_p.T9fs	NM_001008496.3|NM_001255975.1	NP_001008496.2|NP_001242904.1	Q7Z3Z3	PIWL3_HUMAN	piwi-like RNA-mediated gene silencing 3	118					cell differentiation (GO:0030154)|gene silencing by RNA (GO:0031047)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)	RNA binding (GO:0003723)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(14)|lung(15)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	50						AACATACCTGTTTTTGAGTCT	0.418																																					p.T118fs		Atlas-INDEL	.											.	PIWIL3	115	.	0			c.353delC						.			4,4260		1,2,2129	163.0	162.0	162.0			-0.9	0.0	22		161	11,8243		2,7,4118	no	frameshift	PIWIL3	NM_001008496.2		3,9,6247	A1A1,A1R,RR		0.1333,0.0938,0.1198			25153878	15,12503	2203	4300	6503	SO:0001589	frameshift_variant	440822	exon4			.	AB079368	CCDS33623.1	22q11.23	2013-02-15	2013-02-15		ENSG00000184571	ENSG00000184571		"""Argonaute/PIWI family"""	18443	protein-coding gene	gene with protein product		610314	"""piwi-like 3 (Drosophila)"""			12906857	Standard	NM_001008496		Approved	HIWI3	uc003abd.2	Q7Z3Z3	OTTHUMG00000150788	ENST00000332271.5:c.352delA	chr22.hg19:g.25153878delT	ENSP00000330031:p.Thr118fs	176.0	0.0		137.0	12.0	NM_001008496		Frame_Shift_Del	DEL	ENST00000332271.5	hg19	CCDS33623.1																																																																																			.	.		0.418	PIWIL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320084.2	NM_001008496	
LCE2D	353141	hgsc.bcm.edu	37	1	152636615	152636615	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:152636615delC	ENST00000368784.1	+	2	89	c.34delC	c.(34-36)cccfs	p.P14fs		NM_178430.2	NP_848517.1	Q5TA82	LCE2D_HUMAN	late cornified envelope 2D	14	Cys-rich.				keratinization (GO:0031424)					large_intestine(1)|lung(7)|prostate(2)	10	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			GCAGTGCCAGCCCCCTCCCAA	0.493																																					p.Q11fs		Atlas-INDEL	.											.	LCE2D	26	.	0			c.33delG						.						106.0	112.0	110.0					1																	152636615		2203	4300	6503	SO:0001589	frameshift_variant	353141	exon2			.	BI670513	CCDS1018.1	1q21.3	2008-02-05	2004-10-11	2004-10-15	ENSG00000187223	ENSG00000187223		"""Late cornified envelopes"""	16518	protein-coding gene	gene with protein product		612612	"""small proline rich-like (epidermal differentiation complex) 1A"""	SPRL1A		11698679	Standard	NM_178430		Approved	LEP12	uc001fag.4	Q5TA82	OTTHUMG00000014400	ENST00000368784.1:c.34delC	chr1.hg19:g.152636615delC	ENSP00000357773:p.Pro14fs	181.0	0.0		266.0	16.0	NM_178430	A1L4M8	Frame_Shift_Del	DEL	ENST00000368784.1	hg19	CCDS1018.1																																																																																			.	.		0.493	LCE2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040058.1	NM_178430	
CDH10	1008	hgsc.bcm.edu	37	5	24509876	24509876	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:24509876delT	ENST00000264463.4	-	7	1562	c.1055delA	c.(1054-1056)aacfs	p.N352fs		NM_006727.3	NP_006718.2	Q9Y6N8	CAD10_HUMAN	cadherin 10, type 2 (T2-cadherin)	352	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(29)|lung(111)|ovary(6)|pancreas(6)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)	185				STAD - Stomach adenocarcinoma(35;0.0556)		TACATGGGTGTTTTCTGCTTC	0.363										HNSCC(23;0.051)																											p.N352fs		Atlas-INDEL	.											.	CDH10	391	.	0			c.1056delC						.						70.0	72.0	72.0					5																	24509876		2203	4300	6503	SO:0001589	frameshift_variant	1008	exon7			.	AF039747	CCDS3892.1	5p14.2	2010-01-26			ENSG00000040731	ENSG00000040731		"""Cadherins / Major cadherins"""	1749	protein-coding gene	gene with protein product		604555				2059658	Standard	NM_006727		Approved		uc003jgr.2	Q9Y6N8	OTTHUMG00000090667	ENST00000264463.4:c.1055delA	chr5.hg19:g.24509876delT	ENSP00000264463:p.Asn352fs	147.0	0.0		117.0	10.0	NM_006727	Q9ULB3	Frame_Shift_Del	DEL	ENST00000264463.4	hg19	CCDS3892.1																																																																																			.	.		0.363	CDH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207345.2	NM_006727	
BST2	684	hgsc.bcm.edu	37	19	17516225	17516225	+	Frame_Shift_Del	DEL	G	G	-	rs200950817	byFrequency	TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:17516225delG	ENST00000252593.6	-	1	232	c.160delC	c.(160-162)cggfs	p.R54fs	CTD-2521M24.9_ENST00000500836.2_lincRNA|BST2_ENST00000527220.1_5'UTR	NM_004335.2	NP_004326.1	Q10589	BST2_HUMAN	bone marrow stromal cell antigen 2	54					B cell activation (GO:0042113)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|multicellular organismal development (GO:0007275)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of intracellular transport of viral material (GO:1901253)|negative regulation of plasmacytoid dendritic cell cytokine production (GO:0002737)|negative regulation of viral genome replication (GO:0045071)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of actin cytoskeleton organization (GO:0032956)|response to interferon-alpha (GO:0035455)|response to interferon-beta (GO:0035456)|response to interferon-gamma (GO:0034341)|response to virus (GO:0009615)|signal transduction (GO:0007165)	anchored component of membrane (GO:0031225)|apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	metalloendopeptidase inhibitor activity (GO:0008191)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|signal transducer activity (GO:0004871)			endometrium(1)|large_intestine(2)|lung(1)|ovary(3)|prostate(2)	9						AGGCCGTCCCGGCAGGCCTCG	0.572																																					p.R54fs		Atlas-INDEL	.											.	BST2	28	.	0			c.161delG						.						92.0	77.0	82.0					19																	17516225		2203	4300	6503	SO:0001589	frameshift_variant	684	exon1			.		CCDS12358.1	19p13.2	2009-10-30				ENSG00000130303		"""CD molecules"""	1119	protein-coding gene	gene with protein product		600534				7607676	Standard	NM_004335		Approved	CD317, tetherin	uc002ngl.3	Q10589		ENST00000252593.6:c.160delC	chr19.hg19:g.17516225delG	ENSP00000252593:p.Arg54fs	203.0	0.0		173.0	11.0	NM_004335	A8K4Y4|Q53G07	Frame_Shift_Del	DEL	ENST00000252593.6	hg19	CCDS12358.1																																																																																			.	.		0.572	BST2-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387346.1	NM_004335	
AFF1	4299	hgsc.bcm.edu	37	4	88053466	88053466	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:88053466delA	ENST00000307808.6	+	18	3616	c.3196delA	c.(3196-3198)aaafs	p.K1067fs	AFF1_ENST00000395146.4_Frame_Shift_Del_p.K1074fs|AFF1_ENST00000544085.1_Frame_Shift_Del_p.K705fs	NM_005935.2	NP_005926.1	P51825	AFF1_HUMAN	AF4/FMR2 family, member 1	1067					positive regulation of transcription, DNA-templated (GO:0045893)	transcription elongation factor complex (GO:0008023)	sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|large_intestine(2)	3		Acute lymphoblastic leukemia(40;0.0935)|all_hematologic(202;0.111)|Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000233)		GTTTCGTTGTAAAAAAGACAT	0.413																																					p.C1072X		Atlas-INDEL	.											.	AFF1	102	.	0			c.3216delT						.						115.0	107.0	110.0					4																	88053466		2203	4300	6503	SO:0001589	frameshift_variant	4299	exon19			.	L22179	CCDS3616.1, CCDS54775.1	4q21.3	2009-08-04	2005-06-27	2005-06-27	ENSG00000172493	ENSG00000172493			7135	protein-coding gene	gene with protein product		159557	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 2"", ""pre-B-cell monocytic leukemia partner 1"""	PBM1, MLLT2		7689231, 1423625, 8353274	Standard	NM_005935		Approved	AF-4, AF4	uc011ccz.2	P51825	OTTHUMG00000130603	ENST00000307808.6:c.3196delA	chr4.hg19:g.88053466delA	ENSP00000305689:p.Lys1067fs	330.0	0.0		220.0	14.0	NM_001166693	B4DTU1|E9PBM3	Frame_Shift_Del	DEL	ENST00000307808.6	hg19	CCDS3616.1																																																																																			.	.		0.413	AFF1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253053.3	NM_005935	
TMEM200B	399474	hgsc.bcm.edu	37	1	29447542	29447542	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:29447542delC	ENST00000420504.2	-	2	956	c.799delG	c.(799-801)gagfs	p.E267fs	TMEM200B_ENST00000521452.1_Frame_Shift_Del_p.E267fs	NM_001171868.1	NP_001165339.1	Q69YZ2	T200B_HUMAN	transmembrane protein 200B	267						integral component of membrane (GO:0016021)				ovary(1)	1		Colorectal(325;3.46e-05)|Breast(348;0.00765)|Lung NSC(340;0.0153)|all_lung(284;0.0173)|all_neural(195;0.0199)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)|Medulloblastoma(700;0.123)		Colorectal(126;7.32e-08)|COAD - Colon adenocarcinoma(152;4.92e-06)|STAD - Stomach adenocarcinoma(196;0.00618)|BRCA - Breast invasive adenocarcinoma(304;0.0501)|READ - Rectum adenocarcinoma(331;0.0649)|KIRC - Kidney renal clear cell carcinoma(1967;0.126)		AGGAGGAGCTCCCCAAGGCCC	0.632																																					p.E267fs		Atlas-INDEL	.											.	TMEM200B	9	.	0			c.800delA						.						25.0	27.0	26.0					1																	29447542		2202	4300	6502	SO:0001589	frameshift_variant	399474	exon2			.		CCDS30658.1	1p35	2007-12-18			ENSG00000253304	ENSG00000253304			33785	protein-coding gene	gene with protein product						15722956	Standard	NM_001003682		Approved	TTMB	uc001brn.2	Q69YZ2	OTTHUMG00000003658	ENST00000420504.2:c.799delG	chr1.hg19:g.29447542delC	ENSP00000428544:p.Glu267fs	240.0	0.0		195.0	12.0	NM_001171868	Q6P2G8|Q6P2Q5	Frame_Shift_Del	DEL	ENST00000420504.2	hg19	CCDS30658.1																																																																																			.	.		0.632	TMEM200B-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010377.2	NM_001003682	
IPPK	64768	hgsc.bcm.edu	37	9	95432235	95432235	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:95432235delC	ENST00000287996.3	-	1	312	c.36delG	c.(34-36)gggfs	p.G12fs		NM_022755.5	NP_073592.1	Q9H8X2	IPPK_HUMAN	inositol 1,3,4,5,6-pentakisphosphate 2-kinase	12					inositol phosphate metabolic process (GO:0043647)|inositol phosphorylation (GO:0052746)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|intracellular (GO:0005622)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|inositol pentakisphosphate 2-kinase activity (GO:0035299)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|skin(2)|urinary_tract(1)	15						CTCCGTGGTACCCCCATTCAT	0.697																																					p.Y13fs		Atlas-INDEL	.											.	IPPK	34	.	0			c.37delT						.						134.0	104.0	114.0					9																	95432235		2203	4300	6503	SO:0001589	frameshift_variant	64768	exon1			.	AK023225	CCDS6699.1	9q22.31	2010-12-02	2005-10-20	2005-10-20	ENSG00000127080	ENSG00000127080			14645	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 12"""	C9orf12		12084730	Standard	NM_022755		Approved	INSP5K2, FLJ13163, IP5K, IPK1	uc004asl.1	Q9H8X2	OTTHUMG00000020231	ENST00000287996.3:c.36delG	chr9.hg19:g.95432235delC	ENSP00000287996:p.Gly12fs	167.0	0.0		105.0	10.0	NM_022755	Q5T9F7|Q9H7V8	Frame_Shift_Del	DEL	ENST00000287996.3	hg19	CCDS6699.1																																																																																			.	.		0.697	IPPK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053101.1	NM_022755	
WNK1	65125	hgsc.bcm.edu	37	12	989892	989892	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:989892delC	ENST00000315939.6	+	12	3481	c.2838delC	c.(2836-2838)ttcfs	p.F946fs	WNK1_ENST00000537687.1_Frame_Shift_Del_p.F1206fs|WNK1_ENST00000535572.1_Intron|WNK1_ENST00000530271.2_Frame_Shift_Del_p.F1444fs|WNK1_ENST00000340908.4_Frame_Shift_Del_p.F539fs	NM_018979.3	NP_061852.3	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1	946					intracellular signal transduction (GO:0035556)|ion transport (GO:0006811)|negative regulation of pancreatic juice secretion (GO:0090188)|negative regulation of phosphatase activity (GO:0010923)|neuron development (GO:0048666)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of systemic arterial blood pressure (GO:0003084)|protein phosphorylation (GO:0006468)|regulation of cellular process (GO:0050794)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|phosphatase binding (GO:0019902)|protein kinase inhibitor activity (GO:0004860)|protein serine/threonine kinase activity (GO:0004674)			breast(7)|central_nervous_system(1)|endometrium(3)|kidney(6)|large_intestine(15)|lung(43)|ovary(6)|prostate(3)|skin(7)|stomach(8)|upper_aerodigestive_tract(3)|urinary_tract(2)	104	all_cancers(10;0.00611)|all_epithelial(11;0.00825)|all_lung(10;0.0331)|Ovarian(42;0.0512)|Lung NSC(10;0.0632)		Epithelial(1;1.74e-08)|all cancers(1;7.04e-08)|OV - Ovarian serous cystadenocarcinoma(31;0.000423)|BRCA - Breast invasive adenocarcinoma(9;0.0149)|Colorectal(1;0.0197)			CACAGGGCTTCCCACCTCGAC	0.463																																					p.F1206fs	Colon(19;451 567 6672 12618 28860)	Atlas-INDEL	.											.	WNK1	403	.	0			c.3617delT						.						297.0	317.0	310.0					12																	989892		2203	4300	6503	SO:0001589	frameshift_variant	65125	exon12			.	AJ296290	CCDS8506.1, CCDS53731.1, CCDS73419.1	12p13.3	2014-09-17	2005-01-19	2005-01-21	ENSG00000060237	ENSG00000060237			14540	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 167"""	605232	"""protein kinase, lysine deficient 1"", ""hereditary sensory neuropathy, type II"""	PRKWNK1, HSN2			Standard	NM_001184985		Approved	HSAN2, PPP1R167	uc031qfk.1	Q9H4A3	OTTHUMG00000090321	ENST00000315939.6:c.2838delC	chr12.hg19:g.989892delC	ENSP00000313059:p.Phe946fs	317.0	0.0		220.0	14.0	NM_001184985	A1L4B0|C5HTZ5|C5HTZ6|C5HTZ7|H6WZW3|O15052|P54963|Q4VBX9|Q6IFS5|Q86WL5|Q8N673|Q96CZ6|Q9P1S9	Frame_Shift_Del	DEL	ENST00000315939.6	hg19	CCDS8506.1																																																																																			.	.		0.463	WNK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206683.1	NM_018979	
GDF5	8200	hgsc.bcm.edu	37	20	34022065	34022065	+	Frame_Shift_Del	DEL	G	G	-	rs149633982	byFrequency	TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr20:34022065delG	ENST00000374372.1	-	4	1651	c.1148delC	c.(1147-1149)ccafs	p.P383fs	GDF5OS_ENST00000374375.1_Frame_Shift_Del_p.G37fs|GDF5_ENST00000374369.3_Frame_Shift_Del_p.P383fs			P43026	GDF5_HUMAN	growth differentiation factor 5	383					cell-cell signaling (GO:0007267)|chondrocyte differentiation (GO:0002062)|embryonic limb morphogenesis (GO:0030326)|extracellular matrix organization (GO:0030198)|forelimb morphogenesis (GO:0035136)|growth (GO:0040007)|hindlimb morphogenesis (GO:0035137)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mesenchymal cell apoptotic process (GO:2001054)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of neuron differentiation (GO:0045666)|regulation of multicellular organism growth (GO:0040014)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	growth factor activity (GO:0008083)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(3)|lung(9)|skin(3)	26	Lung NSC(9;0.00642)|all_lung(11;0.0094)		BRCA - Breast invasive adenocarcinoma(18;0.00663)			AGTGGCCAGTGGGGCCCGCCG	0.582																																					p.P383fs		Atlas-INDEL	.											.	GDF5	66	.	0			c.1149delA						.						75.0	79.0	78.0					20																	34022065		2203	4300	6503	SO:0001589	frameshift_variant	8200	exon2			.	X80915	CCDS13254.1	20q11.2	2008-05-22	2007-04-12		ENSG00000125965	ENSG00000125965			4220	protein-coding gene	gene with protein product	"""cartilage-derived morphogenetic protein-1"""	601146				9288091, 9288098	Standard	NM_000557		Approved	CDMP1, BMP14	uc002xck.1	P43026	OTTHUMG00000032341	ENST00000374372.1:c.1148delC	chr20.hg19:g.34022065delG	ENSP00000363492:p.Pro383fs	195.0	0.0		154.0	11.0	NM_000557	E1P5Q2|Q96SB1	Frame_Shift_Del	DEL	ENST00000374372.1	hg19	CCDS13254.1																																																																																			.	.		0.582	GDF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078875.2		
CDK12	51755	hgsc.bcm.edu	37	17	37681026	37681026	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:37681026delT	ENST00000447079.4	+	12	3228	c.3195delT	c.(3193-3195)actfs	p.T1065fs	CDK12_ENST00000430627.2_Frame_Shift_Del_p.T1065fs	NM_015083.1|NM_016507.2	NP_055898.1|NP_057591.2	Q9NYV4	CDK12_HUMAN	cyclin-dependent kinase 12	1065					mRNA processing (GO:0006397)|phosphorylation of RNA polymerase II C-terminal domain (GO:0070816)|protein autophosphorylation (GO:0046777)|regulation of MAP kinase activity (GO:0043405)|RNA splicing (GO:0008380)	cyclin K-CDK12 complex (GO:0002944)|nuclear cyclin-dependent protein kinase holoenzyme complex (GO:0019908)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin binding (GO:0030332)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)			NS(4)|breast(3)|endometrium(5)|kidney(4)|large_intestine(11)|lung(23)|ovary(11)|prostate(4)|skin(2)|urinary_tract(3)	70						CATCCAAAACTTCTCGAAAAG	0.557			"""Mis, N, F"""		serous ovarian					TCGA Ovarian(9;0.13)																											p.T1065fs		Atlas-INDEL	.		Rec	yes		17	17q12	51755	cyclin-dependent kinase 12		E	.	CDK12	161	.	0			c.3194delC						.						118.0	118.0	118.0					17																	37681026		2203	4300	6503	SO:0001589	frameshift_variant	51755	exon12			.	AF227198	CCDS11337.1, CCDS45666.1	17q12	2011-10-25	2009-12-16	2009-12-16	ENSG00000167258	ENSG00000167258		"""Cyclin-dependent kinases"""	24224	protein-coding gene	gene with protein product	"""CDC2 related protein kinase 7"""	615514	"""Cdc2-related kinase, arginine/serine-rich"""	CRKRS		10048485, 11683387, 19884882	Standard	XM_005257456		Approved	CRK7, CRKR, KIAA0904	uc010cvv.3	Q9NYV4	OTTHUMG00000133214	ENST00000447079.4:c.3195delT	chr17.hg19:g.37681026delT	ENSP00000398880:p.Thr1065fs	226.0	0.0		156.0	10.0	NM_016507	A7E2B2|B4DYX4|B9EIQ6|O94978	Frame_Shift_Del	DEL	ENST00000447079.4	hg19	CCDS11337.1																																																																																			.	.		0.557	CDK12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256941.4	NM_016507	
HEATR9	256957	hgsc.bcm.edu	37	17	34195732	34195732	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:34195732delT	ENST00000311880.2	-	1	163	c.15delA	c.(13-15)aaafs	p.K5fs	C17orf66_ENST00000592980.1_Frame_Shift_Del_p.K5fs|AC015849.2_ENST00000413928.1_RNA|C17orf66_ENST00000587585.1_5'UTR	NM_152781.2	NP_689994.2	A2RTY3	HEAT9_HUMAN		5					hematopoietic progenitor cell differentiation (GO:0002244)					breast(3)|central_nervous_system(1)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(6)|lung(11)|skin(2)|stomach(4)	38		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0184)		TATCAGTTGATTTTTCATAGG	0.527																																					p.S6fs		Atlas-INDEL	.											.	C17orf66	57	.	0			c.16delT						.						120.0	98.0	106.0					17																	34195732		2203	4300	6503	SO:0001589	frameshift_variant	256957	exon1			.																												ENST00000311880.2:c.15delA	chr17.hg19:g.34195732delT	ENSP00000309560:p.Lys5fs	157.0	0.0		112.0	10.0	NM_152781	B4DX21|B4DXA4|B4DXF0|Q8N4R4|Q96M46	Frame_Shift_Del	DEL	ENST00000311880.2	hg19	CCDS11299.1																																																																																			.	.		0.527	C17orf66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256487.1		
ATF6	22926	hgsc.bcm.edu	37	1	161816357	161816357	+	Frame_Shift_Del	DEL	A	A	-	rs368810553		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:161816357delA	ENST00000367942.3	+	10	1373	c.1306delA	c.(1306-1308)aaafs	p.K436fs	ATF6_ENST00000476437.1_3'UTR	NM_007348.3	NP_031374.2	P18850	ATF6A_HUMAN	activating transcription factor 6	436					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|positive regulation of transcription from RNA polymerase II promoter involved in unfolded protein response (GO:0006990)|protein folding (GO:0006457)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to stress (GO:0006950)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			breast(2)|endometrium(3)|kidney(2)|large_intestine(8)|lung(14)|ovary(3)|skin(1)|stomach(1)	34	all_hematologic(112;0.156)		BRCA - Breast invasive adenocarcinoma(70;0.00953)		Pseudoephedrine(DB00852)	TATTATCCAGAAAAACAGCTA	0.403																																					p.Q435fs		Atlas-INDEL	.											ATF6,NS,carcinoma,0,1	ATF6	84	.	0			c.1305delG						.						117.0	110.0	112.0					1																	161816357		2203	4300	6503	SO:0001589	frameshift_variant	22926	exon10			.	AB015856	CCDS1235.1	1q22-q23	2013-01-10			ENSG00000118217	ENSG00000118217		"""basic leucine zipper proteins"""	791	protein-coding gene	gene with protein product	"""activating transcription factor 6 alpha"""	605537				9837962, 9271374, 11256944	Standard	NM_007348		Approved	ATF6A	uc001gbs.3	P18850	OTTHUMG00000023961	ENST00000367942.3:c.1306delA	chr1.hg19:g.161816357delA	ENSP00000356919:p.Lys436fs	144.0	0.0		181.0	11.0	NM_007348	O15139|Q5VW62|Q6IPB5|Q9UEC9	Frame_Shift_Del	DEL	ENST00000367942.3	hg19	CCDS1235.1																																																																																			.	.		0.403	ATF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060304.2	NM_007348	
FKBP4	2288	hgsc.bcm.edu	37	12	2907011	2907011	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:2907011delC	ENST00000001008.4	+	3	554	c.367delC	c.(367-369)cccfs	p.P124fs	RP4-816N1.7_ENST00000547042.1_RNA|RP4-816N1.6_ENST00000547834.1_RNA	NM_002014.3	NP_002005.1	Q02790	FKBP4_HUMAN	FK506 binding protein 4, 59kDa	124	PPIase FKBP-type 1. {ECO:0000255|PROSITE- ProRule:PRU00277}.				androgen receptor signaling pathway (GO:0030521)|chaperone-mediated protein folding (GO:0061077)|copper ion transport (GO:0006825)|embryo implantation (GO:0007566)|male sex differentiation (GO:0046661)|negative regulation of microtubule polymerization (GO:0031115)|negative regulation of microtubule polymerization or depolymerization (GO:0031111)|negative regulation of neuron projection development (GO:0010977)|prostate gland development (GO:0030850)|protein complex localization (GO:0031503)|protein folding (GO:0006457)|protein peptidyl-prolyl isomerization (GO:0000413)|steroid hormone receptor complex assembly (GO:0006463)	axonal growth cone (GO:0044295)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ATP binding (GO:0005524)|FK506 binding (GO:0005528)|GTP binding (GO:0005525)|heat shock protein binding (GO:0031072)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(3)|prostate(2)|skin(1)	14			OV - Ovarian serous cystadenocarcinoma(31;0.00105)			TCCAAAGATTCCCCCCAATGC	0.552																																					p.I122fs		Atlas-INDEL	.											.	FKBP4	29	.	0			c.366delT						.						161.0	136.0	145.0					12																	2907011		2203	4300	6503	SO:0001589	frameshift_variant	2288	exon3			.	M88279	CCDS8512.1	12p13.33	2013-01-10	2002-08-29		ENSG00000004478	ENSG00000004478		"""Tetratricopeptide (TTC) repeat domain containing"""	3720	protein-coding gene	gene with protein product		600611	"""FK506-binding protein 4 (59kD)"""			1279700	Standard	NM_002014		Approved	FKBP59, FKBP52	uc001qkz.3	Q02790	OTTHUMG00000090429	ENST00000001008.4:c.367delC	chr12.hg19:g.2907011delC	ENSP00000001008:p.Pro124fs	213.0	0.0		187.0	13.0	NM_002014	D3DUQ1|Q9UCP1|Q9UCV7	Frame_Shift_Del	DEL	ENST00000001008.4	hg19	CCDS8512.1																																																																																			.	.		0.552	FKBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206861.1		
CCDC79	283847	hgsc.bcm.edu	37	16	66824575	66824575	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:66824575delT	ENST00000558713.2	-	4	266	c.194delA	c.(193-195)aatfs	p.N65fs	CCDC79_ENST00000415744.1_Frame_Shift_Del_p.N65fs|CCDC79_ENST00000433154.1_Frame_Shift_Del_p.N65fs|CCDC79_ENST00000432602.1_Frame_Shift_Del_p.N65fs|CCDC79_ENST00000433574.1_Frame_Shift_Del_p.N65fs|CCDC79_ENST00000561333.1_5'UTR			Q8NA31	TERB1_HUMAN	coiled-coil domain containing 79	65					meiotic telomere clustering (GO:0045141)|synapsis (GO:0007129)	chromosome, telomeric region (GO:0000781)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(1)|endometrium(2)|kidney(1)|large_intestine(1)|skin(2)	7						CTTTGCAAGATTTTTTACAAA	0.294																																					p.N65fs		Atlas-Indel,Pindel	.											.,1	CCDC79	32	.	0			c.195delT						.						107.0	87.0	93.0					16																	66824575		692	1587	2279	SO:0001589	frameshift_variant	283847	exon5			.	AK093213		16q22.1	2012-10-03			ENSG00000249961	ENSG00000249961			26675	protein-coding gene	gene with protein product							Standard	NM_001136505		Approved	FLJ35894	uc010viv.2	Q8NA31	OTTHUMG00000133562	ENST00000558713.2:c.194delA	chr16.hg19:g.66824575delT	ENSP00000462883:p.Asn65fs	284.0	0.0		236.0	16.0	NM_001136505	A0AUW1	Frame_Shift_Del	DEL	ENST00000558713.2	hg19																																																																																				.	.		0.294	CCDC79-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000418864.2		
TOP2A	7153	hgsc.bcm.edu	37	17	38552661	38552661	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:38552661delC	ENST00000423485.1	-	28	3752	c.3594delG	c.(3592-3594)gggfs	p.G1198fs		NM_001067.3	NP_001058.2	P11388	TOP2A_HUMAN	topoisomerase (DNA) II alpha 170kDa	1198					apoptotic chromosome condensation (GO:0030263)|ATP catabolic process (GO:0006200)|cellular response to DNA damage stimulus (GO:0006974)|chromosome segregation (GO:0007059)|DNA ligation (GO:0006266)|DNA topological change (GO:0006265)|DNA unwinding involved in DNA replication (GO:0006268)|embryonic cleavage (GO:0040016)|hematopoietic progenitor cell differentiation (GO:0002244)|mitotic cell cycle (GO:0000278)|mitotic DNA integrity checkpoint (GO:0044774)|mitotic recombination (GO:0006312)|positive regulation of apoptotic process (GO:0043065)|positive regulation of single stranded viral RNA replication via double stranded DNA intermediate (GO:0045870)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral genome replication (GO:0045070)|resolution of meiotic recombination intermediates (GO:0000712)|sister chromatid segregation (GO:0000819)	condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|DNA topoisomerase complex (ATP-hydrolyzing) (GO:0009330)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|DNA topoisomerase type II (ATP-hydrolyzing) activity (GO:0003918)|DNA-dependent ATPase activity (GO:0008094)|drug binding (GO:0008144)|enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|magnesium ion binding (GO:0000287)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)|ubiquitin binding (GO:0043130)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(9)|ovary(5)|pancreas(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	39		Breast(137;0.00328)	STAD - Stomach adenocarcinoma(5;0.00183)		Amsacrine(DB00276)|Ciprofloxacin(DB00537)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Dexrazoxane(DB00380)|Doxorubicin(DB00997)|Enoxacin(DB00467)|Epirubicin(DB00445)|Etoposide(DB00773)|Fleroxacin(DB04576)|Idarubicin(DB01177)|Levofloxacin(DB01137)|Lomefloxacin(DB00978)|Lucanthone(DB04967)|Mitoxantrone(DB01204)|Moxifloxacin(DB00218)|Norfloxacin(DB01059)|Ofloxacin(DB01165)|Pefloxacin(DB00487)|Podofilox(DB01179)|Sparfloxacin(DB01208)|Teniposide(DB00444)|Trovafloxacin(DB00685)|Valrubicin(DB00385)	CCTTGGCCTTCCCCCCTTTCC	0.428																																					p.K1199fs		Atlas-INDEL	.											.	TOP2A	124	.	0			c.3595delA						.						118.0	110.0	112.0					17																	38552661		1841	4091	5932	SO:0001589	frameshift_variant	7153	exon28			.		CCDS45672.1	17q21-q22	2008-08-06	2002-08-29		ENSG00000131747	ENSG00000131747	5.99.1.2		11989	protein-coding gene	gene with protein product		126430	"""topoisomerase (DNA) II alpha (170kD)"""	TOP2			Standard	NM_001067		Approved		uc002huq.3	P11388	OTTHUMG00000155008	ENST00000423485.1:c.3594delG	chr17.hg19:g.38552661delC	ENSP00000411532:p.Gly1198fs	205.0	0.0		120.0	10.0	NM_001067	B2RTS1|Q71UN1|Q71UQ5|Q9HB24|Q9HB25|Q9HB26|Q9UP44|Q9UQP9	Frame_Shift_Del	DEL	ENST00000423485.1	hg19	CCDS45672.1																																																																																			.	.		0.428	TOP2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338035.1		
DOCK4	9732	hgsc.bcm.edu	37	7	111448882	111448882	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:111448882delT	ENST00000437633.1	-	30	3417	c.3161delA	c.(3160-3162)aacfs	p.N1054fs	DOCK4_ENST00000428084.1_Frame_Shift_Del_p.N1054fs|DOCK4-AS1_ENST00000452714.1_RNA	NM_014705.3	NP_055520.3	Q8N1I0	DOCK4_HUMAN	dedicator of cytokinesis 4	1054					cell chemotaxis (GO:0060326)|positive regulation of Rac GTPase activity (GO:0032855)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)|stereocilium (GO:0032420)|stereocilium bundle (GO:0032421)	guanyl-nucleotide exchange factor activity (GO:0005085)|PDZ domain binding (GO:0030165)|Rac GTPase activator activity (GO:0030675)|Rac GTPase binding (GO:0048365)|receptor tyrosine kinase binding (GO:0030971)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(13)|lung(31)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(4)	72		Acute lymphoblastic leukemia(1;0.0441)				CTTACCTAGGTTTTGCCACAT	0.413																																					p.N1054fs		Atlas-INDEL	.											.	DOCK4	365	.	0			c.3162delC						.						116.0	104.0	108.0					7																	111448882		1898	4124	6022	SO:0001589	frameshift_variant	9732	exon30			.		CCDS47688.1	7q31.1	2007-08-07			ENSG00000128512	ENSG00000128512			19192	protein-coding gene	gene with protein product		607679				12432077, 12628187	Standard	XM_006716188		Approved	FLJ34238, KIAA0716	uc003vfx.3	Q8N1I0	OTTHUMG00000155077	ENST00000437633.1:c.3161delA	chr7.hg19:g.111448882delT	ENSP00000404179:p.Asn1054fs	288.0	0.0		253.0	16.0	NM_014705	O14584|O94824|Q8NB45	Frame_Shift_Del	DEL	ENST00000437633.1	hg19	CCDS47688.1																																																																																			.	.		0.413	DOCK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338369.4	NM_014705	
SPTBN4	57731	hgsc.bcm.edu	37	19	41009859	41009859	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:41009859delG	ENST00000352632.3	+	12	1571	c.1485delG	c.(1483-1485)ttgfs	p.L495fs	SPTBN4_ENST00000595535.1_Frame_Shift_Del_p.L495fs|SPTBN4_ENST00000344104.3_Frame_Shift_Del_p.L495fs|SPTBN4_ENST00000338932.3_Frame_Shift_Del_p.L495fs|SPTBN4_ENST00000598249.1_Frame_Shift_Del_p.L495fs			Q9H254	SPTN4_HUMAN	spectrin, beta, non-erythrocytic 4	495					actin filament capping (GO:0051693)|adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cardiac conduction (GO:0061337)|central nervous system projection neuron axonogenesis (GO:0021952)|clustering of voltage-gated sodium channels (GO:0045162)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization to plasma membrane (GO:0090002)|fertilization (GO:0009566)|negative regulation of heart rate (GO:0010459)|positive regulation of multicellular organism growth (GO:0040018)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of sodium ion transport (GO:0002028)|sensory perception of sound (GO:0007605)|transmission of nerve impulse (GO:0019226)|vesicle-mediated transport (GO:0016192)	adherens junction (GO:0005912)|axon hillock (GO:0043203)|axon initial segment (GO:0043194)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|nuclear matrix (GO:0016363)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|PML body (GO:0016605)|spectrin (GO:0008091)	actin binding (GO:0003779)|ankyrin binding (GO:0030506)|phosphatase binding (GO:0019902)|phospholipid binding (GO:0005543)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			breast(4)|central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(9)|lung(32)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	73			Lung(22;0.000114)|LUSC - Lung squamous cell carcinoma(20;0.000384)			CCCAGGCATTGGCAGCCGAAG	0.667																																					p.L495fs		Atlas-INDEL	.											.	SPTBN4	213	.	0			c.1484delT						.						36.0	38.0	37.0					19																	41009859		2203	4300	6503	SO:0001589	frameshift_variant	57731	exon12			.	AF082075	CCDS12559.1, CCDS42569.1	19q13.13	2013-01-10				ENSG00000160460		"""Pleckstrin homology (PH) domain containing"""	14896	protein-coding gene	gene with protein product		606214				11086001	Standard	NM_020971		Approved	SPTBN3, KIAA1642	uc002onz.3	Q9H254		ENST00000352632.3:c.1485delG	chr19.hg19:g.41009859delG	ENSP00000263373:p.Leu495fs	213.0	0.0		148.0	10.0	NM_020971	E9PGQ5|Q9H1K7|Q9H1K8|Q9H1K9|Q9H253|Q9H3G8|Q9HCD0	Frame_Shift_Del	DEL	ENST00000352632.3	hg19	CCDS12559.1																																																																																			.	.		0.667	SPTBN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462559.2		
EMC10	284361	hgsc.bcm.edu	37	19	50983927	50983927	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:50983927delC	ENST00000334976.6	+	5	538	c.492delC	c.(490-492)cacfs	p.H164fs	EMC10_ENST00000598585.1_Frame_Shift_Del_p.H164fs|EMC10_ENST00000376918.3_Frame_Shift_Del_p.H164fs|CTD-2545M3.2_ENST00000598194.1_RNA	NM_206538.2	NP_996261.1	Q5UCC4	EMC10_HUMAN	ER membrane protein complex subunit 10	164						ER membrane protein complex (GO:0072546)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)											TGGTGACGCACCCCGGGGGCT	0.697																																					p.H164fs		Atlas-INDEL	.											.	.	.	.	0			c.491delA						.						24.0	25.0	25.0					19																	50983927		2189	4291	6480	SO:0001589	frameshift_variant	284361	exon5			.	BC062607	CCDS12796.1, CCDS42594.1	19q13.33	2012-05-30	2012-05-30	2012-05-30	ENSG00000161671	ENSG00000161671			27609	protein-coding gene	gene with protein product	"""hematopoietic signal peptide-containing secreted 1"", ""hematopoietic signal peptide-containing membrane domain-containing 1"""	614545	"""chromosome 19 open reading frame 63"""	C19orf63		12975309, 22119785	Standard	NM_175063		Approved	INM02, HSS1, HSM1	uc002psl.3	Q5UCC4		ENST00000334976.6:c.492delC	chr19.hg19:g.50983927delC	ENSP00000334037:p.His164fs	94.0	0.0		77.0	10.0	NM_175063	Q5UCC6|Q69YT5|Q6UWP3|Q86YL4|Q8N541	Frame_Shift_Del	DEL	ENST00000334976.6	hg19	CCDS12796.1																																																																																			.	.		0.697	EMC10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464760.2	NM_175063	
ARHGAP5	394	hgsc.bcm.edu	37	14	32560705	32560705	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr14:32560705delA	ENST00000345122.3	+	2	1145	c.830delA	c.(829-831)gaafs	p.E277fs	ARHGAP5_ENST00000396582.2_Intron|ARHGAP5_ENST00000432921.1_Frame_Shift_Del_p.E277fs|ARHGAP5_ENST00000433497.1_Intron|ARHGAP5_ENST00000539826.2_Frame_Shift_Del_p.E277fs|ARHGAP5_ENST00000556611.1_Frame_Shift_Del_p.E277fs	NM_001030055.1	NP_001025226.1	Q13017	RHG05_HUMAN	Rho GTPase activating protein 5	277	FF 1.				cell adhesion (GO:0007155)|GTP catabolic process (GO:0006184)|mammary gland development (GO:0030879)|positive regulation of cell migration (GO:0030335)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell size (GO:0008361)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|Rho GTPase activator activity (GO:0005100)|SH2 domain binding (GO:0042169)			NS(2)|breast(10)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(12)|ovary(4)|skin(1)|stomach(1)|urinary_tract(4)	55	Hepatocellular(127;0.0604)|Prostate(35;0.15)|Breast(36;0.186)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.00714)|BRCA - Breast invasive adenocarcinoma(188;0.0952)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00566)		GATAAGTTTGAAAAACTTGTG	0.323																																					p.E277fs	NSCLC(9;77 350 3443 29227 41353)	Atlas-INDEL	.											.	ARHGAP5	166	.	0			c.829delG						.						114.0	131.0	125.0					14																	32560705		2202	4298	6500	SO:0001589	frameshift_variant	394	exon2			.	U17032	CCDS32062.1, CCDS45095.1	14q12	2010-02-05						"""Rho GTPase activating proteins"""	675	protein-coding gene	gene with protein product		602680	"""growth factor independent 2"""	GFI2		8537347	Standard	XM_005267635		Approved	RhoGAP5, p190-B, p190BRhoGAP	uc001wrn.3	Q13017		ENST00000345122.3:c.830delA	chr14.hg19:g.32560705delA	ENSP00000371897:p.Glu277fs	215.0	0.0		169.0	13.0	NM_001173	A1L375|A1L376|A8KAA1|D3DS89|D3DS90|Q05BE8|Q05BU8|Q59ER0|Q6DHZ3	Frame_Shift_Del	DEL	ENST00000345122.3	hg19	CCDS32062.1																																																																																			.	.		0.323	ARHGAP5-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409735.1	NM_001030055	
SLC22A4	6583	hgsc.bcm.edu	37	5	131660257	131660257	+	Intron	DEL	C	C	-	rs528013729	byFrequency	TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:131660257delC	ENST00000200652.3	+	4	998				AC034220.3_ENST00000417795.1_RNA	NM_003059.2	NP_003050.2	Q9H015	S22A4_HUMAN	solute carrier family 22 (organic cation/zwitterion transporter), member 4						body fluid secretion (GO:0007589)|carnitine metabolic process (GO:0009437)|carnitine transmembrane transport (GO:1902603)|carnitine transport (GO:0015879)|cation transmembrane transport (GO:0098655)|organic cation transport (GO:0015695)|quaternary ammonium group transport (GO:0015697)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|triglyceride metabolic process (GO:0006641)	apical plasma membrane (GO:0016324)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|carnitine transmembrane transporter activity (GO:0015226)|cation:cation antiporter activity (GO:0015491)|nucleotide binding (GO:0000166)|PDZ domain binding (GO:0030165)|quaternary ammonium group transmembrane transporter activity (GO:0015651)|secondary active organic cation transmembrane transporter activity (GO:0008513)|symporter activity (GO:0015293)			endometrium(1)|kidney(3)|large_intestine(2)|lung(8)|ovary(1)|urinary_tract(1)	16		all_cancers(142;0.0752)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)		Amiloride(DB00594)|Aminohippurate(DB00345)|Benzylpenicillin(DB01053)|Choline(DB00122)|Cimetidine(DB00501)|Clonidine(DB00575)|Desipramine(DB01151)|Guanidine(DB00536)|Imipramine(DB00458)|Ipratropium bromide(DB00332)|L-Arginine(DB00125)|L-Carnitine(DB00583)|L-Lysine(DB00123)|Levofloxacin(DB01137)|Mepyramine(DB06691)|Nicotine(DB00184)|Ofloxacin(DB01165)|Procainamide(DB01035)|Quinidine(DB00908)|Quinine(DB00468)|Spermine(DB00127)|Testosterone(DB00624)|Tiotropium(DB01409)|Verapamil(DB00661)	GCTGAGTGCTCCCCCTGAACA	0.522													CCCCC|CCCCC|CCCC|deletion	3	0.000599042	0.0	0.0	5008	,	,		20111	0.0		0.0	False		,,,				2504	0.0031				.		Atlas-INDEL	.											.	.	.	.	0			.						.																																			SO:0001627	intron_variant	0	.			.	AB007448	CCDS4153.1	5q23.3	2013-07-18	2013-07-18		ENSG00000197208	ENSG00000197208		"""Solute carriers"""	10968	protein-coding gene	gene with protein product		604190	"""solute carrier family 22 (organic cation/ergothioneine transporter), member 4"""			9426230, 15795384	Standard	NM_003059		Approved	OCTN1, MGC34546	uc003kwq.3	Q9H015	OTTHUMG00000059648	ENST00000200652.3:c.824+2209C>-	chr5.hg19:g.131660257delC		230.0	0.0		189.0	12.0	.	O14546	RNA	DEL	ENST00000200652.3	hg19	CCDS4153.1																																																																																			.	.		0.522	SLC22A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132661.1	NM_003059	
PCNXL4	64430	hgsc.bcm.edu	37	14	60587948	60587948	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr14:60587948delT	ENST00000406854.1	+	8	2531	c.1977delT	c.(1975-1977)cgtfs	p.R659fs	PCNXL4_ENST00000535349.1_5'UTR|PCNXL4_ENST00000406949.1_Frame_Shift_Del_p.R425fs|PCNXL4_ENST00000404681.2_Frame_Shift_Del_p.R659fs|PCNXL4_ENST00000317623.4_Frame_Shift_Del_p.R425fs			Q63HM2	PCX4_HUMAN	pecanex-like 4 (Drosophila)	659						integral component of membrane (GO:0016021)											ACTTGGGCCGTTTTCAGGATC	0.318																																					p.R425fs		Atlas-INDEL	.											.	.	.	.	0			c.1274delG						.						183.0	169.0	174.0					14																	60587948		2203	4300	6503	SO:0001589	frameshift_variant	64430	exon7			.	AK022861		14q23.1	2012-07-18	2012-07-18	2012-07-18	ENSG00000126773	ENSG00000126773			20349	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 135"""	C14orf135			Standard	NM_022495		Approved		uc001xer.4	Q63HM2	OTTHUMG00000150361	ENST00000406854.1:c.1977delT	chr14.hg19:g.60587948delT	ENSP00000384801:p.Arg659fs	233.0	0.0		180.0	12.0	NM_022495	A8MXM2|Q9BQG8|Q9H9F2	Frame_Shift_Del	DEL	ENST00000406854.1	hg19																																																																																				.	.		0.318	PCNXL4-005	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000317847.1	NM_022495	
PLCH1	23007	hgsc.bcm.edu	37	3	155199916	155199916	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:155199916delG	ENST00000340059.7	-	23	3922	c.3923delC	c.(3922-3924)cctfs	p.P1308fs	PLCH1_ENST00000460012.1_Frame_Shift_Del_p.P1270fs|PLCH1_ENST00000494598.1_Intron|PLCH1_ENST00000414191.1_Frame_Shift_Del_p.P1270fs|PLCH1_ENST00000447496.2_3'UTR|PLCH1_ENST00000334686.6_Frame_Shift_Del_p.P1270fs	NM_001130960.1	NP_001124432.1	Q4KWH8	PLCH1_HUMAN	phospholipase C, eta 1	1308					inositol phosphate metabolic process (GO:0043647)|lipid catabolic process (GO:0016042)|phosphatidylinositol-mediated signaling (GO:0048015)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase C activity (GO:0050429)|phosphatidylinositol phospholipase C activity (GO:0004435)|signal transducer activity (GO:0004871)			NS(3)|breast(3)|endometrium(9)|kidney(4)|large_intestine(20)|lung(45)|ovary(2)|prostate(5)|skin(8)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	107			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)			AGAAGTATTAGGGGATCCAGG	0.498																																					p.P1308fs		Atlas-INDEL	.											.	PLCH1	406	.	0			c.3924delT						.						122.0	124.0	123.0					3																	155199916		2203	4300	6503	SO:0001589	frameshift_variant	23007	exon23			.	AB028992	CCDS33881.1, CCDS46939.1, CCDS46940.1	3q25	2013-01-10	2006-03-16	2006-03-16	ENSG00000114805	ENSG00000114805	3.1.4.11	"""EF-hand domain containing"""	29185	protein-coding gene	gene with protein product		612835	"""phospholipase C-like 3"""	PLCL3		15702972	Standard	NM_014996		Approved	KIAA1069, MGC117152, DKFZp434C1372, PLCeta1	uc021xge.1	Q4KWH8	OTTHUMG00000158477	ENST00000340059.7:c.3923delC	chr3.hg19:g.155199916delG	ENSP00000345988:p.Pro1308fs	243.0	0.0		198.0	13.0	NM_001130960	Q29RV9|Q4KWH9|Q68CN0|Q86XK4|Q9H9U2|Q9UPT3	Frame_Shift_Del	DEL	ENST00000340059.7	hg19	CCDS46939.1																																																																																			.	.		0.498	PLCH1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000351125.1	NM_014996	
IFNA16	3449	hgsc.bcm.edu	37	9	21216773	21216773	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:21216773delA	ENST00000380216.1	-	1	537	c.532delT	c.(532-534)tcafs	p.S178fs		NM_002173.2	NP_002164.1	P05015	IFN16_HUMAN	interferon, alpha 16	178					adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|natural killer cell activation involved in immune response (GO:0002323)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to exogenous dsRNA (GO:0043330)|T cell activation involved in immune response (GO:0002286)|type I interferon signaling pathway (GO:0060337)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|type I interferon receptor binding (GO:0005132)			central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|skin(1)	13				Lung(24;2.12e-22)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.116)		AAGTTTGTTGAAAAAGAGAAG	0.368																																					p.S178X		Atlas-INDEL	.											.	IFNA16	27	.	0			c.533delC						.						211.0	203.0	205.0					9																	21216773		2203	4300	6503	SO:0001589	frameshift_variant	3449	exon1			.		CCDS34996.1	9p22	2010-12-10			ENSG00000147885	ENSG00000147885		"""Interferons"""	5421	protein-coding gene	gene with protein product		147580				1385305	Standard	NM_002173		Approved	IFN-alphaO	uc003zor.1	P05015	OTTHUMG00000019663	ENST00000380216.1:c.532delT	chr9.hg19:g.21216773delA	ENSP00000369564:p.Ser178fs	448.0	0.0		312.0	22.0	NM_002173	Q5VV12	Frame_Shift_Del	DEL	ENST00000380216.1	hg19	CCDS34996.1																																																																																			.	.		0.368	IFNA16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051892.1	NM_002173	
APEH	327	hgsc.bcm.edu	37	3	49714427	49714427	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:49714427delC	ENST00000296456.5	+	10	1369	c.969delC	c.(967-969)atcfs	p.I323fs	APEH_ENST00000438011.1_Frame_Shift_Del_p.I323fs	NM_001640.3	NP_001631.3	P13798	ACPH_HUMAN	acylaminoacyl-peptide hydrolase	323					beta-amyloid metabolic process (GO:0050435)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear membrane (GO:0031965)	omega peptidase activity (GO:0008242)|poly(A) RNA binding (GO:0044822)|serine-type endopeptidase activity (GO:0004252)			endometrium(3)|large_intestine(1)|lung(6)|ovary(1)|skin(1)|stomach(2)|urinary_tract(1)	15				BRCA - Breast invasive adenocarcinoma(193;4.53e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		CATCTCTGATCCCCCATCACC	0.602																																					p.I323fs		Atlas-INDEL	.											.	APEH	45	.	0			c.968delT						.						83.0	72.0	76.0					3																	49714427		2203	4300	6503	SO:0001589	frameshift_variant	327	exon10			.	D38441	CCDS2801.1	3p21	2013-05-29	2013-05-29		ENSG00000164062	ENSG00000164062	3.4.19.1		586	protein-coding gene	gene with protein product	"""acylaminoacyl-peptidase"""	102645	"""N-acylaminoacyl-peptide hydrolase"""	D3F15S2, DNF15S2, D3S48E		2392324	Standard	NM_001640		Approved		uc003cxf.3	P13798	OTTHUMG00000156882	ENST00000296456.5:c.969delC	chr3.hg19:g.49714427delC	ENSP00000296456:p.Ile323fs	279.0	0.0		194.0	13.0	NM_001640	Q9BQ33|Q9P0Y2	Frame_Shift_Del	DEL	ENST00000296456.5	hg19	CCDS2801.1																																																																																			.	.		0.602	APEH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346415.2		
MAPT	4137	hgsc.bcm.edu	37	17	44039763	44039763	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:44039763delG	ENST00000571987.1	+	1	60	c.60delG	c.(58-60)ttgfs	p.L20fs	MAPT_ENST00000446361.3_Frame_Shift_Del_p.L20fs|MAPT_ENST00000334239.8_Frame_Shift_Del_p.L20fs|MAPT_ENST00000262410.5_Frame_Shift_Del_p.L20fs|MAPT_ENST00000347967.5_5'UTR|MAPT_ENST00000351559.5_Frame_Shift_Del_p.L20fs|MAPT_ENST00000535772.1_Frame_Shift_Del_p.L20fs|MAPT_ENST00000431008.3_Frame_Shift_Del_p.L20fs|MAPT_ENST00000420682.2_Frame_Shift_Del_p.L20fs|MAPT_ENST00000340799.5_Frame_Shift_Del_p.L20fs|MAPT_ENST00000574436.1_Frame_Shift_Del_p.L20fs|MAPT_ENST00000415613.2_Frame_Shift_Del_p.L20fs|MAPT_ENST00000344290.5_Frame_Shift_Del_p.L20fs|MAPT_ENST00000570299.1_3'UTR			P10636	TAU_HUMAN	microtubule-associated protein tau	20					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)	CGTACGGGTTGGGGGACAGGA	0.577																																					p.L20fs		Atlas-INDEL	.											.	MAPT	135	.	0			c.59delT						.						54.0	43.0	47.0					17																	44039763		2203	4300	6503	SO:0001589	frameshift_variant	4137	exon2			.	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.60delG	chr17.hg19:g.44039763delG	ENSP00000458742:p.Leu20fs	151.0	0.0		151.0	10.0	NM_005910	P18518|Q14799|Q15549|Q15550|Q15551|Q1RMF6|Q53YB1|Q5CZI7|Q5XWF0|Q6QT54|Q9UDJ3|Q9UMH0|Q9UQ96	Frame_Shift_Del	DEL	ENST00000571987.1	hg19	CCDS11501.1																																																																																			.	.		0.577	MAPT-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000440133.1	NM_016835	
CNOT2	4848	hgsc.bcm.edu	37	12	70747643	70747643	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:70747643delG	ENST00000418359.3	+	17	2022	c.1571delG	c.(1570-1572)cggfs	p.R524fs	CNOT2_ENST00000229195.3_Frame_Shift_Del_p.R524fs|CNOT2_ENST00000551483.1_Frame_Shift_Del_p.R175fs	NM_001199302.1	NP_001186231.1	Q9NZN8	CNOT2_HUMAN	CCR4-NOT transcription complex, subunit 2	524	Repressor domain.				gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of cytoplasmic mRNA processing body assembly (GO:0010606)|regulation of stem cell maintenance (GO:2000036)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|transcription from RNA polymerase II promoter (GO:0006366)|trophectodermal cell differentiation (GO:0001829)	CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	RNA polymerase II transcription cofactor activity (GO:0001104)|RNA polymerase II transcription corepressor binding (GO:0001226)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(10)|pancreas(2)|urinary_tract(1)	20	Renal(347;0.236)		GBM - Glioblastoma multiforme(1;4.77e-09)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00243)|STAD - Stomach adenocarcinoma(21;0.0118)			TTAGAAGAACGGCCTCACCTG	0.343																																					p.R524fs		Atlas-INDEL	.											CNOT2,NS,carcinoma,0,1	CNOT2	53	.	0			c.1570delC						.						79.0	87.0	84.0					12																	70747643		2203	4300	6503	SO:0001589	frameshift_variant	4848	exon17			.	AF180473	CCDS31857.1	12q15	2008-05-14				ENSG00000111596			7878	protein-coding gene	gene with protein product		604909		NOT2		10637334	Standard	NM_014515		Approved	CDC36, NOT2H	uc001svv.3	Q9NZN8		ENST00000418359.3:c.1571delG	chr12.hg19:g.70747643delG	ENSP00000412091:p.Arg524fs	261.0	0.0		175.0	11.0	NM_001199302	Q9H3E0|Q9NSX5|Q9NWR6|Q9P028	Frame_Shift_Del	DEL	ENST00000418359.3	hg19	CCDS31857.1																																																																																			.	.		0.343	CNOT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404260.1		
ASIC5	51802	hgsc.bcm.edu	37	4	156763391	156763391	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:156763391delT	ENST00000537611.2	-	6	1023	c.977delA	c.(976-978)aagfs	p.K326fs		NM_017419.2	NP_059115.1	Q9NY37	ASIC5_HUMAN	acid-sensing (proton-gated) ion channel family member 5	326					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hydrogen ion channel activity (GO:0015252)|ligand-gated sodium channel activity (GO:0015280)										TCCACATTGCTTTTTTATGTG	0.418																																					p.K326fs		Atlas-INDEL	.											.	.	.	.	0			c.978delG						.						142.0	136.0	138.0					4																	156763391		2203	4300	6503	SO:0001589	frameshift_variant	51802	exon6			.	AJ252011	CCDS3793.1	4q32.1	2012-10-03	2012-03-02	2012-03-02	ENSG00000256394	ENSG00000256394			17537	protein-coding gene	gene with protein product			"""amiloride-sensitive cation channel 5, intestinal"""	ACCN5		10767424	Standard	NM_017419		Approved	INAC, HINAC	uc003ipe.1	Q9NY37	OTTHUMG00000161941	ENST00000537611.2:c.977delA	chr4.hg19:g.156763391delT	ENSP00000442477:p.Lys326fs	214.0	0.0		182.0	11.0	NM_017419		Frame_Shift_Del	DEL	ENST00000537611.2	hg19	CCDS3793.1																																																																																			.	.		0.418	ASIC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366464.1		
PLD2	5338	hgsc.bcm.edu	37	17	4719139	4719139	+	Frame_Shift_Del	DEL	G	G	-	rs368018438		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:4719139delG	ENST00000263088.6	+	14	1496	c.1365delG	c.(1363-1365)ctgfs	p.L455fs	PLD2_ENST00000572940.1_Frame_Shift_Del_p.L455fs	NM_001243108.1|NM_002663.4	NP_001230037.1|NP_002654.3	O14939	PLD2_HUMAN	phospholipase D2	455	Catalytic.|PLD phosphodiesterase 1. {ECO:0000255|PROSITE-ProRule:PRU00153}.				cytoskeleton organization (GO:0007010)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|G-protein coupled receptor internalization (GO:0002031)|glycerophospholipid biosynthetic process (GO:0046474)|innate immune response (GO:0045087)|lipid catabolic process (GO:0016042)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	brush border membrane (GO:0031526)|endoplasmic reticulum membrane (GO:0005789)|plasma membrane (GO:0005886)	N-acylphosphatidylethanolamine-specific phospholipase D activity (GO:0070290)|phosphatidylinositol binding (GO:0035091)|phospholipase D activity (GO:0004630)			autonomic_ganglia(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(3)|lung(10)|ovary(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)	31					Choline(DB00122)	TAGCATTCCTGGGGGGACTGG	0.597											OREG0024105	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L455fs		Atlas-INDEL	.											.	PLD2	138	.	0			c.1364delT						.						168.0	134.0	146.0					17																	4719139		2203	4300	6503	SO:0001589	frameshift_variant	5338	exon14			.	AF035483	CCDS11057.1, CCDS58507.1	17p13.3	2008-04-14			ENSG00000129219	ENSG00000129219	3.1.4.4		9068	protein-coding gene	gene with protein product	"""choline phosphatase 2"""	602384				9858823, 9582313	Standard	NM_002663		Approved		uc002fzc.3	O14939	OTTHUMG00000090779	ENST00000263088.6:c.1365delG	chr17.hg19:g.4719139delG	ENSP00000263088:p.Leu455fs	376.0	0.0	621	228.0	14.0	NM_001243108	I3L2C9|O43540|O43579|O43580|Q6PGR0|Q96BY3	Frame_Shift_Del	DEL	ENST00000263088.6	hg19	CCDS11057.1																																																																																			.	.		0.597	PLD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207561.3	NM_002663	
UNG	7374	hgsc.bcm.edu	37	12	109541376	109541376	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:109541376delG	ENST00000242576.2	+	6	867	c.761delG	c.(760-762)tggfs	p.W254fs	UNG_ENST00000336865.2_Frame_Shift_Del_p.W245fs	NM_080911.2	NP_550433.1			uracil-DNA glycosylase											central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(4)|ovary(1)	9						TTCTTGCTCTGGGGCTCTTAT	0.403								Base excision repair (BER), DNA glycosylases	Immune Deficiency with Hyper-IgM																												p.W254fs		Atlas-INDEL	.											.	UNG	30	.	0			c.760delT						.						79.0	62.0	68.0					12																	109541376		2203	4300	6503	SO:0001589	frameshift_variant	7374	exon6	Familial Cancer Database	Hypogammaglobulinemia with Hyper-IgM, HIGM type I-V, XLHIGM	.	A64377	CCDS9124.1, CCDS9125.1	12q23-q24.1	2014-09-17			ENSG00000076248	ENSG00000076248	3.2.2.27		12572	protein-coding gene	gene with protein product	"""uracil-DNA glycosylase 1, uracil-DNA glycosylase 2"""	191525		DGU		1923798, 17101234	Standard	NM_080911		Approved	UDG, UNG1, UNG2, HIGM4	uc001tnz.2	P13051	OTTHUMG00000169247	ENST00000242576.2:c.761delG	chr12.hg19:g.109541376delG	ENSP00000242576:p.Trp254fs	227.0	0.0		147.0	11.0	NM_080911		Frame_Shift_Del	DEL	ENST00000242576.2	hg19	CCDS9124.1																																																																																			.	.		0.403	UNG-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000403067.1	NM_080911	
PDLIM7	9260	hgsc.bcm.edu	37	5	176918124	176918124	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:176918124delG	ENST00000355841.2	-	6	488	c.422delC	c.(421-423)ccafs	p.P141fs	PDLIM7_ENST00000356618.4_Frame_Shift_Del_p.P141fs|PDLIM7_ENST00000359895.2_Frame_Shift_Del_p.P107fs|PDLIM7_ENST00000355572.2_Frame_Shift_Del_p.P141fs|PDLIM7_ENST00000393551.1_Frame_Shift_Del_p.P141fs	NM_005451.3	NP_005442.2	Q9NR12	PDLI7_HUMAN	PDZ and LIM domain 7 (enigma)	141					actin cytoskeleton organization (GO:0030036)|cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|positive regulation of osteoblast differentiation (GO:0045669)|receptor-mediated endocytosis (GO:0006898)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|ruffle (GO:0001726)|stress fiber (GO:0001725)	zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|ovary(1)|urinary_tract(1)	10	all_cancers(89;0.00033)|Renal(175;0.000269)|Lung NSC(126;0.00161)|all_lung(126;0.00286)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GCTGGCATCTGGGACCAGCGG	0.682																																					p.P141fs		Atlas-INDEL	.											.	PDLIM7	32	.	0			c.423delA						.						14.0	18.0	17.0					5																	176918124		2202	4298	6500	SO:0001589	frameshift_variant	9260	exon6			.	BC001093	CCDS4422.1, CCDS4423.1, CCDS4424.1	5q35.3	2008-02-05			ENSG00000196923	ENSG00000196923			22958	protein-coding gene	gene with protein product		605903				11874232	Standard	NM_005451		Approved	ENIGMA	uc003mhc.1	Q9NR12	OTTHUMG00000130853	ENST00000355841.2:c.422delC	chr5.hg19:g.176918124delG	ENSP00000348099:p.Pro141fs	221.0	0.0		153.0	10.0	NM_213636	Q14250|Q5XG82|Q6NVZ5|Q96C91|Q9BXB8|Q9BXB9	Frame_Shift_Del	DEL	ENST00000355841.2	hg19	CCDS4422.1																																																																																			.	.		0.682	PDLIM7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253423.1	NM_005451	
SYNC	81493	hgsc.bcm.edu	37	1	33147421	33147421	+	3'UTR	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:33147421delT	ENST00000409190.3	-	0	1937				SYNC_ENST00000373484.3_Frame_Shift_Del_p.T467fs|RBBP4_ENST00000373493.5_3'UTR	NM_030786.2	NP_110413	Q9H7C4	SYNCI_HUMAN	syncoilin, intermediate filament protein						intermediate filament-based process (GO:0045103)	cytosol (GO:0005829)|intermediate filament (GO:0005882)|neuromuscular junction (GO:0031594)|sarcolemma (GO:0042383)|Z disc (GO:0030018)	structural molecule activity (GO:0005198)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	12						TTTTTTGCTGTTTCCGGGTTA	0.403																																					p.T467fs		Atlas-INDEL	.											.	SYNC	36	.	0			c.1400delC						.						131.0	116.0	121.0					1																	33147421		2203	4299	6502	SO:0001624	3_prime_UTR_variant	81493	exon4			.	AK024707	CCDS367.2, CCDS53294.1	1p35.1	2013-01-16	2008-09-19	2008-09-19	ENSG00000162520	ENSG00000162520		"""Intermediate filaments type III"""	28897	protein-coding gene	gene with protein product		611750	"""syncoilin, intermediate filament 1"""	SYNC1		11053421	Standard	NM_030786		Approved	SYNCOILIN	uc001bvt.2	Q9H7C4	OTTHUMG00000008087	ENST00000409190.3:c.*30A>-	chr1.hg19:g.33147421delT		292.0	0.0		238.0	15.0	NM_001161708	B4DNK8|B4DY58|C9IY41	Frame_Shift_Del	DEL	ENST00000409190.3	hg19	CCDS367.2																																																																																			.	.		0.403	SYNC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022129.3	NM_030786	
CC2D1A	54862	hgsc.bcm.edu	37	19	14031457	14031457	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:14031457delC	ENST00000318003.7	+	13	1685	c.1444delC	c.(1444-1446)cccfs	p.P483fs	CC2D1A_ENST00000589606.1_Frame_Shift_Del_p.P483fs	NM_017721.4	NP_060191.3	Q6P1N0	C2D1A_HUMAN	coiled-coil and C2 domain containing 1A	483					positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(12)|prostate(2)|skin(2)	27			OV - Ovarian serous cystadenocarcinoma(19;3.49e-23)			AGCCAAAGCGCCCCCCAAAGC	0.647																																					p.A481fs		Atlas-INDEL	.											CC2D1A,colon,carcinoma,0,1	CC2D1A	67	.	0			c.1443delG						.						41.0	55.0	50.0					19																	14031457		1912	4119	6031	SO:0001589	frameshift_variant	54862	exon13			.	AF536205	CCDS42512.1	19p13.12	2007-01-08				ENSG00000132024			30237	protein-coding gene	gene with protein product	"""mental retardation, nonsyndromic, autosomal recessive, 3"""	610055				12761501, 16033914	Standard	NM_017721		Approved	FLJ20241, MRT3	uc002mxo.2	Q6P1N0		ENST00000318003.7:c.1444delC	chr19.hg19:g.14031457delC	ENSP00000313601:p.Pro483fs	209.0	0.0		182.0	11.0	NM_017721	Q7Z435|Q86XV0|Q8NF89|Q9H603|Q9NXI1	Frame_Shift_Del	DEL	ENST00000318003.7	hg19	CCDS42512.1																																																																																			.	.		0.647	CC2D1A-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457954.1	NM_017721	
SNTN	132203	hgsc.bcm.edu	37	3	63645488	63645488	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:63645488delA	ENST00000343837.3	+	3	253	c.233delA	c.(232-234)gaafs	p.E78fs	SNTN_ENST00000496807.1_Frame_Shift_Del_p.E74fs	NM_001080537.1	NP_001074006.1	A6NMZ2	SNTAN_HUMAN	sentan, cilia apical structure protein	78						cilium (GO:0005929)	calcium ion binding (GO:0005509)			endometrium(2)|ovary(1)	3						GGTAAACTTGAAAAAGCTATT	0.413																																					p.E78fs		Atlas-INDEL	.											.	SNTN	17	.	0			c.232delG						.						126.0	125.0	125.0					3																	63645488		2203	4300	6503	SO:0001589	frameshift_variant	132203	exon3			.	AK126350	CCDS33779.1	3p14.2	2009-03-10	2009-03-10		ENSG00000188817	ENSG00000188817			33706	protein-coding gene	gene with protein product	"""S100A-like protein"""					18829862	Standard	NM_001080537		Approved	FLJ44379, S100AL	uc003dlr.3	A6NMZ2	OTTHUMG00000158766	ENST00000343837.3:c.233delA	chr3.hg19:g.63645488delA	ENSP00000341442:p.Glu78fs	206.0	0.0		161.0	10.0	NM_001080537	B7FF65	Frame_Shift_Del	DEL	ENST00000343837.3	hg19	CCDS33779.1																																																																																			.	.		0.413	SNTN-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352094.1	NM_001080537	
SEC23IP	11196	hgsc.bcm.edu	37	10	121675303	121675303	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:121675303delT	ENST00000369075.3	+	8	1518	c.1446delT	c.(1444-1446)catfs	p.H482fs	SEC23IP_ENST00000543134.1_Frame_Shift_Del_p.H271fs	NM_007190.3	NP_009121.1	Q9Y6Y8	S23IP_HUMAN	SEC23 interacting protein	482					acrosome assembly (GO:0001675)|Golgi organization (GO:0007030)|intracellular protein transport (GO:0006886)|single fertilization (GO:0007338)	cis-Golgi network (GO:0005801)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum exit site (GO:0070971)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|perinuclear endoplasmic reticulum (GO:0097038)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(12)|ovary(3)|prostate(1)|stomach(3)|urinary_tract(1)	36		Lung NSC(174;0.109)|all_lung(145;0.142)|all_neural(114;0.234)		all cancers(201;0.00515)		TGCGGACACATTTCAAGAAAT	0.398																																					p.H482fs		Atlas-INDEL	.											.	SEC23IP	100	.	0			c.1445delA						.						114.0	115.0	115.0					10																	121675303		2203	4300	6503	SO:0001589	frameshift_variant	11196	exon8			.	AB019435	CCDS7618.1	10q26.11-q26.12	2013-01-10			ENSG00000107651	ENSG00000107651		"""Sterile alpha motif (SAM) domain containing"""	17018	protein-coding gene	gene with protein product						10400679	Standard	NM_007190		Approved	p125	uc001leu.2	Q9Y6Y8	OTTHUMG00000019161	ENST00000369075.3:c.1446delT	chr10.hg19:g.121675303delT	ENSP00000358071:p.His482fs	107.0	0.0		99.0	10.0	NM_007190	D3DRD2|Q8IXH5|Q9BUK5	Frame_Shift_Del	DEL	ENST00000369075.3	hg19	CCDS7618.1																																																																																			.	.		0.398	SEC23IP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050688.1		
LRBA	987	hgsc.bcm.edu	37	4	151789357	151789357	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:151789357delA	ENST00000357115.3	-	21	2793	c.2550delT	c.(2548-2550)tttfs	p.F850fs	LRBA_ENST00000507224.1_Frame_Shift_Del_p.F850fs|LRBA_ENST00000510413.1_Frame_Shift_Del_p.F850fs|LRBA_ENST00000535741.1_Frame_Shift_Del_p.F850fs	NM_006726.4	NP_006717.2	P50851	LRBA_HUMAN	LPS-responsive vesicle trafficking, beach and anchor containing	850						cytoplasmic membrane-bounded vesicle (GO:0016023)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(20)|lung(32)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	91	all_hematologic(180;0.151)					TACTGTTATTAAAAAGTTTAA	0.358																																					p.N851fs		Atlas-INDEL	.											.	LRBA	253	.	0			c.2551delA						.						73.0	78.0	76.0					4																	151789357		2203	4300	6503	SO:0001589	frameshift_variant	987	exon21			.	AF216648	CCDS3773.1, CCDS58928.1	4q13	2013-01-10		2001-10-05	ENSG00000198589	ENSG00000198589		"""WD repeat domain containing"""	1742	protein-coding gene	gene with protein product		606453		CDC4L		1505956, 11254716	Standard	NM_006726		Approved	BGL, LAB300, LBA	uc010ipj.3	P50851	OTTHUMG00000161443	ENST00000357115.3:c.2550delT	chr4.hg19:g.151789357delA	ENSP00000349629:p.Phe850fs	215.0	0.0		161.0	10.0	NM_006726	Q4W5J4|Q4W5L6|Q8NFQ0|Q9H2U3|Q9H2U4	Frame_Shift_Del	DEL	ENST00000357115.3	hg19	CCDS3773.1																																																																																			.	.		0.358	LRBA-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364939.1		
PARD3B	117583	hgsc.bcm.edu	37	2	206305272	206305272	+	Frame_Shift_Del	DEL	C	C	-	rs201407485		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:206305272delC	ENST00000406610.2	+	20	3127	c.2920delC	c.(2920-2922)cccfs	p.P975fs	PARD3B_ENST00000349953.3_Intron|PARD3B_ENST00000358768.2_Frame_Shift_Del_p.P913fs|PARD3B_ENST00000351153.1_Frame_Shift_Del_p.P906fs	NM_057177.6|NM_152526.5|NM_205863.3	NP_476518.4|NP_689739.4|NP_995585.2	Q8TEW8	PAR3L_HUMAN	par-3 family cell polarity regulator beta	975					cell cycle (GO:0007049)|cell division (GO:0051301)	membrane (GO:0016020)|tight junction (GO:0005923)				breast(1)|endometrium(9)|kidney(2)|large_intestine(6)|liver(4)|lung(33)|ovary(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)	65		all_cancers(1;2.88e-06)|all_epithelial(1;3.23e-06)		Epithelial(149;0.0739)		ATCTCCATCTCCCCCTCGAGC	0.483																																					p.S911fs		Atlas-INDEL	.											.	PARD3B	314	.	0			c.2733delT						.						137.0	140.0	139.0					2																	206305272		2007	4146	6153	SO:0001589	frameshift_variant	117583	exon19			.	AB053321	CCDS42804.1, CCDS42805.1, CCDS42806.1	2q33.3	2013-08-28	2013-08-28	2006-09-28	ENSG00000116117	ENSG00000116117			14446	protein-coding gene	gene with protein product			"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 19"", ""par-3 partitioning defective 3 homolog B (C. elegans)"""	ALS2CR19		11586298, 12459187	Standard	NM_057177		Approved	Par3L, PAR3beta	uc002vap.2	Q8TEW8	OTTHUMG00000154562	ENST00000406610.2:c.2920delC	chr2.hg19:g.206305272delC	ENSP00000385848:p.Pro975fs	293.0	0.0		210.0	14.0	NM_152526	E9PE87|Q8IUC7|Q8IUC9|Q96DK9|Q96N09|Q96NX6|Q96NX7|Q96Q29	Frame_Shift_Del	DEL	ENST00000406610.2	hg19																																																																																				.	.		0.483	PARD3B-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000335992.1	NM_057177	
KIF20A	10112	hgsc.bcm.edu	37	5	137522908	137522908	+	Frame_Shift_Del	DEL	A	A	-	rs17234961	byFrequency	TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:137522908delA	ENST00000394894.3	+	19	2705	c.2479delA	c.(2479-2481)aaafs	p.K828fs	KIF20A_ENST00000508792.1_Frame_Shift_Del_p.K810fs	NM_005733.2	NP_005724.1	O95235	KI20A_HUMAN	kinesin family member 20A	828	Globular. {ECO:0000255}.				ATP catabolic process (GO:0006200)|cytokinesis (GO:0000910)|metabolic process (GO:0008152)|microtubule bundle formation (GO:0001578)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|protein kinase binding (GO:0019901)|transporter activity (GO:0005215)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(3)|liver(2)|lung(9)|prostate(2)|upper_aerodigestive_tract(1)	27			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			GGTTTCTGCCAAAAAGCGCCT	0.473																																					p.A826fs		Atlas-INDEL	.											.	KIF20A	53	.	0			c.2478delC						.						91.0	88.0	89.0					5																	137522908		2203	4300	6503	SO:0001589	frameshift_variant	10112	exon19			.	AF070672	CCDS4199.1	5q31	2008-02-05	2003-01-13	2003-01-17	ENSG00000112984	ENSG00000112984		"""Kinesins"""	9787	protein-coding gene	gene with protein product		605664	"""RAB6 interacting, kinesin-like (rabkinesin6)"""	RAB6KIFL		11416179, 10806357	Standard	NM_005733		Approved		uc003lcj.3	O95235	OTTHUMG00000129195	ENST00000394894.3:c.2479delA	chr5.hg19:g.137522908delA	ENSP00000378356:p.Lys828fs	175.0	0.0		139.0	10.0	NM_005733	B4DL79|D3DQB6	Frame_Shift_Del	DEL	ENST00000394894.3	hg19	CCDS4199.1																																																																																			.	.		0.473	KIF20A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251272.1	NM_005733	
CCT7	10574	hgsc.bcm.edu	37	2	73471802	73471802	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:73471802delA	ENST00000258091.5	+	6	718	c.577delA	c.(577-579)aaafs	p.K193fs	CCT7_ENST00000538797.1_Frame_Shift_Del_p.K65fs|CCT7_ENST00000539919.1_Frame_Shift_Del_p.K149fs|CCT7_ENST00000473786.1_3'UTR|CCT7_ENST00000537131.1_Frame_Shift_Del_p.K93fs|CCT7_ENST00000540468.1_Frame_Shift_Del_p.K106fs|CCT7_ENST00000398422.2_Intron	NM_006429.3	NP_006420.1	Q99832	TCPH_HUMAN	chaperonin containing TCP1, subunit 7 (eta)	193					'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)	cell body (GO:0044297)|chaperonin-containing T-complex (GO:0005832)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|unfolded protein binding (GO:0051082)			breast(1)|cervix(1)|endometrium(1)|lung(3)|stomach(1)	7						GCTGCAGCTTAAAATGATTGG	0.498																																					p.L192fs		Atlas-INDEL	.											.	CCT7	60	.	0			c.576delT						.						62.0	61.0	62.0					2																	73471802		2031	4189	6220	SO:0001589	frameshift_variant	10574	exon6			.	AF026292	CCDS42696.1, CCDS46336.1, CCDS54366.1, CCDS54367.1	2p13.2	2011-09-02			ENSG00000135624	ENSG00000135624		"""Heat Shock Proteins / Chaperonins"""	1622	protein-coding gene	gene with protein product		605140				9819444	Standard	NM_006429		Approved	Ccth, Nip7-1	uc002siz.3	Q99832	OTTHUMG00000152765	ENST00000258091.5:c.577delA	chr2.hg19:g.73471802delA	ENSP00000258091:p.Lys193fs	241.0	0.0		169.0	11.0	NM_006429	A8K7E6|A8MWI8|B7WNW9|B7Z4T9|B7Z4Z7|O14871|Q6FI26	Frame_Shift_Del	DEL	ENST00000258091.5	hg19	CCDS46336.1																																																																																			.	.		0.498	CCT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327714.2		
EVPL	2125	hgsc.bcm.edu	37	17	74018287	74018287	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:74018287delG	ENST00000301607.3	-	6	881	c.628delC	c.(628-630)caafs	p.Q210fs	EVPL_ENST00000586740.1_Frame_Shift_Del_p.Q210fs	NM_001988.2	NP_001979.2	Q92817	EVPL_HUMAN	envoplakin	210	Globular 1.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)	cell junction (GO:0030054)|cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(4)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(14)|ovary(2)|pancreas(2)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)	54						TCTCGGTATTGGCTCCGGATG	0.687																																					p.Q210fs		Atlas-INDEL	.											.	EVPL	155	.	0			c.629delA						.						27.0	31.0	29.0					17																	74018287		2203	4299	6502	SO:0001589	frameshift_variant	2125	exon6			.	U53786	CCDS11737.1	17q25	2008-07-18				ENSG00000167880			3503	protein-coding gene	gene with protein product		601590				8938451, 10409435	Standard	NM_001988		Approved	EVPK	uc002jqi.2	Q92817		ENST00000301607.3:c.628delC	chr17.hg19:g.74018287delG	ENSP00000301607:p.Gln210fs	130.0	0.0		164.0	10.0	NM_001988	A0AUV5	Frame_Shift_Del	DEL	ENST00000301607.3	hg19	CCDS11737.1																																																																																			.	.		0.687	EVPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449483.1	NM_001988	
PRR22	163154	hgsc.bcm.edu	37	19	5783634	5783634	+	Frame_Shift_Del	DEL	T	T	-	rs2446210	byFrequency	TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:5783634delT	ENST00000419421.2	-	3	728	c.624delA	c.(622-624)ccafs	p.P208fs		NM_001134316.1	NP_001127788.1	Q8IZ63	PRR22_HUMAN	proline rich 22	208	Pro-rich.									endometrium(2)|large_intestine(1)|prostate(1)|urinary_tract(1)	5						TGTAGGCGTCTGGGGGCAGTG	0.706																																					p.D209fs		Atlas-INDEL	.											.	PRR22	25	.	0			c.625delG						.						13.0	16.0	15.0					19																	5783634		2189	4293	6482	SO:0001589	frameshift_variant	163154	exon3			.	BC023278	CCDS45933.1	19p13.3	2012-12-20			ENSG00000212123	ENSG00000212123			28354	protein-coding gene	gene with protein product						12477932	Standard	NM_001134316		Approved	MGC24975	uc010xiv.1	Q8IZ63	OTTHUMG00000180553	ENST00000419421.2:c.624delA	chr19.hg19:g.5783634delT	ENSP00000407653:p.Pro208fs	263.0	0.0		182.0	11.0	NM_001134316	E9PB31	Frame_Shift_Del	DEL	ENST00000419421.2	hg19	CCDS45933.1																																																																																			.	.		0.706	PRR22-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368523.1	NM_153359	
ATG2A	23130	hgsc.bcm.edu	37	11	64673130	64673130	+	Intron	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:64673130delG	ENST00000377264.3	-	24	3484				ATG2A_ENST00000421419.2_Intron	NM_015104.2	NP_055919.2	Q2TAZ0	ATG2A_HUMAN	autophagy related 2A						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						AGAGTGGCCTGGGGGTGATAC	0.622																																					.		Atlas-INDEL	.											.	ATG2A	133	.	0			c.3372-2C>-						.						107.0	92.0	97.0					11																	64673130		2199	4297	6496	SO:0001627	intron_variant	23130	exon25			.		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.3372-3C>-	chr11.hg19:g.64673130delG		215.0	0.0		176.0	11.0	NM_015104	O43154|Q14DM2|Q6ZTV2|Q7Z6K8|Q8IVY5|Q8TAI8|Q96HH7	Splice_Site	DEL	ENST00000377264.3	hg19	CCDS31602.1																																																																																			.	.		0.622	ATG2A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000143224.1	NM_015104	
SOX2	6657	hgsc.bcm.edu	37	3	181431356	181431356	+	3'UTR	DEL	G	G	-	rs563991531		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:181431356delG	ENST00000325404.1	+	0	1635					NM_003106.3	NP_003097.1	P48431	SOX2_HUMAN	SRY (sex determining region Y)-box 2						adenohypophysis development (GO:0021984)|cell cycle arrest (GO:0007050)|cerebral cortex development (GO:0021987)|chromatin organization (GO:0006325)|detection of mechanical stimulus involved in equilibrioception (GO:0050973)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|diencephalon morphogenesis (GO:0048852)|endodermal cell fate specification (GO:0001714)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|eye development (GO:0001654)|forebrain development (GO:0030900)|forebrain neuron differentiation (GO:0021879)|glial cell fate commitment (GO:0021781)|inner ear development (GO:0048839)|inner ear morphogenesis (GO:0042472)|lens induction in camera-type eye (GO:0060235)|lung alveolus development (GO:0048286)|male genitalia development (GO:0030539)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron fate commitment (GO:0048663)|neuronal stem cell maintenance (GO:0097150)|olfactory placode formation (GO:0030910)|osteoblast differentiation (GO:0001649)|pigment biosynthetic process (GO:0046148)|pituitary gland development (GO:0021983)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of gene expression (GO:0010468)|regulation of transcription, DNA-templated (GO:0006355)|response to growth factor (GO:0070848)|response to retinoic acid (GO:0032526)|response to wounding (GO:0009611)|retina morphogenesis in camera-type eye (GO:0060042)|somatic stem cell maintenance (GO:0035019)|tongue development (GO:0043586)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear transcription factor complex (GO:0044798)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|miRNA binding (GO:0035198)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(1)|skin(1)	10	all_cancers(143;1.22e-16)|Ovarian(172;0.0283)		all cancers(12;1.82e-48)|Epithelial(37;9.85e-40)|OV - Ovarian serous cystadenocarcinoma(80;7.37e-23)|Lung(8;2.01e-21)|GBM - Glioblastoma multiforme(1;2.13e-08)			ACTTCTTTTTGGGGGACTATT	0.463			A		"""NSCLC, oesophageal squamous carcinoma"""		MICROPHTHALMIA AND ESOPHAGEAL ATRESIA SYNDROME																														.		Atlas-INDEL	.		Dom	yes		3	3q26.3-q27	6657	SRY (sex determining region Y)-box 2	yes	E	.	SOX2	28	.	0			.						.																																			SO:0001624	3_prime_UTR_variant	6657	.			.	BC013923	CCDS3239.1	3q26.3-q27	2014-09-17						"""SRY (sex determining region Y)-boxes"""	11195	protein-coding gene	gene with protein product		184429				7849401	Standard	NM_003106		Approved		uc003fkx.3	P48431		ENST00000325404.1:c.*254G>-	chr3.hg19:g.181431356delG		135.0	0.0		123.0	11.0	.	Q14537	RNA	DEL	ENST00000325404.1	hg19	CCDS3239.1																																																																																			.	.		0.463	SOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350419.1	NM_003106	
BRAP	8315	hgsc.bcm.edu	37	12	112082345	112082345	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:112082345delT	ENST00000327551.6	-	12	1487	c.1347delA	c.(1345-1347)aaafs	p.K449fs	BRAP_ENST00000539060.1_Frame_Shift_Del_p.K300fs|BRAP_ENST00000419234.4_Frame_Shift_Del_p.K479fs			Q6UWU4	CF089_HUMAN	BRCA1 associated protein	0					epithelial cell proliferation (GO:0050673)|positive regulation of cell cycle (GO:0045787)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				cervix(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(5)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	20						GTTTGGCCACTTTTGTGTTTA	0.448																																					p.V480fs	Pancreas(146;846 1904 7830 25130 26065)	Atlas-INDEL	.											.	BRAP	42	.	0			c.1438delG						.						103.0	97.0	99.0					12																	112082345		2203	4300	6503	SO:0001589	frameshift_variant	8315	exon12			.	AF035620	CCDS9154.1	12q24.12	2014-09-11			ENSG00000089234	ENSG00000089234		"""RING-type (C3HC4) zinc fingers"""	1099	protein-coding gene	gene with protein product	"""impedes mitogenic signal propagation"", ""galectin-2-binding protein"""	604986				9497340, 19198608	Standard	XM_005253944		Approved	BRAP2, RNF52, IMP	uc001tsn.4	Q7Z569	OTTHUMG00000169600	ENST00000327551.6:c.1347delA	chr12.hg19:g.112082345delT	ENSP00000330813:p.Lys449fs	236.0	0.0		186.0	13.0	NM_006768	B4DTT1|F4NAR0|F4NAR1|Q6ZMG5|Q7Z356|Q8IZ35	Frame_Shift_Del	DEL	ENST00000327551.6	hg19																																																																																				.	.		0.448	BRAP-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000404994.2		
CCDC38	120935	hgsc.bcm.edu	37	12	96275288	96275288	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:96275288delA	ENST00000344280.3	-	11	1522	c.965delT	c.(964-966)ttafs	p.L322fs	SNRPF_ENST00000552085.1_Intron	NM_182496.2	NP_872302.2	Q502W7	CCD38_HUMAN	coiled-coil domain containing 38	322										breast(1)|endometrium(2)|large_intestine(3)|lung(9)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						TTCATCATCTAAAAGGAATTC	0.318																																					p.L322fs		Atlas-INDEL	.											.	CCDC38	45	.	0			c.966delA						.						80.0	76.0	77.0					12																	96275288		2203	4300	6503	SO:0001589	frameshift_variant	120935	exon11			.	AK097408	CCDS9056.1	12q23.1	2005-11-02				ENSG00000165972			26843	protein-coding gene	gene with protein product							Standard	NM_182496		Approved	FLJ40089	uc001tek.2	Q502W7	OTTHUMG00000170352	ENST00000344280.3:c.965delT	chr12.hg19:g.96275288delA	ENSP00000345470:p.Leu322fs	244.0	0.0		194.0	12.0	NM_182496	Q8N835	Frame_Shift_Del	DEL	ENST00000344280.3	hg19	CCDS9056.1																																																																																			.	.		0.318	CCDC38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408634.1	NM_182496	
NEXN	91624	hgsc.bcm.edu	37	1	78401592	78401592	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:78401592delA	ENST00000334785.7	+	11	1520	c.1336delA	c.(1336-1338)aaafs	p.K446fs	NEXN_ENST00000330010.8_Frame_Shift_Del_p.K382fs|NEXN_ENST00000480732.2_3'UTR|NEXN_ENST00000457030.1_Frame_Shift_Del_p.K432fs	NM_144573.3	NP_653174.3			nexilin (F actin binding protein)											breast(2)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(5)|lung(7)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	30				Colorectal(170;0.114)		TATTCAAGCTAAAAACCTAAA	0.323																																					p.A445fs		Atlas-INDEL	.											.	NEXN	77	.	0			c.1335delT						.						56.0	56.0	56.0					1																	78401592		1790	4059	5849	SO:0001589	frameshift_variant	91624	exon11			.	AK057954	CCDS41351.1, CCDS53335.1	1p31.1	2014-09-17			ENSG00000162614	ENSG00000162614		"""Immunoglobulin superfamily / I-set domain containing"""	29557	protein-coding gene	gene with protein product		613121				12053183, 8227983	Standard	NM_144573		Approved	nexilin, NELIN	uc001dic.4	Q0ZGT2	OTTHUMG00000040533	ENST00000334785.7:c.1336delA	chr1.hg19:g.78401592delA	ENSP00000333938:p.Lys446fs	265.0	0.0		193.0	12.0	NM_144573		Frame_Shift_Del	DEL	ENST00000334785.7	hg19	CCDS41351.1																																																																																			.	.		0.323	NEXN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097549.1	NM_144573	
ARID4A	5926	hgsc.bcm.edu	37	14	58796746	58796746	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr14:58796746delA	ENST00000355431.3	+	11	1138	c.765delA	c.(763-765)ttafs	p.L255fs	ARID4A_ENST00000348476.3_Frame_Shift_Del_p.L255fs|ARID4A_ENST00000395168.3_Frame_Shift_Del_p.L255fs|ARID4A_ENST00000431317.2_Frame_Shift_Del_p.L255fs	NM_002892.3	NP_002883.3	P29374	ARI4A_HUMAN	AT rich interactive domain 4A (RBP1-like)	255					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						GCATCTTCTTAAAAACTAGAG	0.388																																					p.L255X		Atlas-INDEL	.											.	ARID4A	222	.	0			c.764delT						.						94.0	101.0	98.0					14																	58796746		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.765delA	chr14.hg19:g.58796746delA	ENSP00000347602:p.Leu255fs	195.0	0.0		167.0	11.0	NM_002892	Q15991|Q15992|Q15993	Frame_Shift_Del	DEL	ENST00000355431.3	hg19	CCDS9732.1																																																																																			.	.		0.388	ARID4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276927.2	NM_023001	
PDIA5	10954	hgsc.bcm.edu	37	3	122869147	122869147	+	Frame_Shift_Del	DEL	G	G	-	rs114278681	byFrequency	TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:122869147delG	ENST00000316218.7	+	14	1304	c.1209delG	c.(1207-1209)gtgfs	p.V403fs	PDIA5_ENST00000467157.1_3'UTR	NM_006810.3	NP_006801.1	Q14554	PDIA5_HUMAN	protein disulfide isomerase family A, member 5	403	Thioredoxin 3. {ECO:0000255|PROSITE- ProRule:PRU00691}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cell redox homeostasis (GO:0045454)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|oxidation-reduction process (GO:0055114)|protein folding (GO:0006457)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)	oxidoreductase activity (GO:0016491)|protein disulfide isomerase activity (GO:0003756)			breast(1)|endometrium(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	21				GBM - Glioblastoma multiforme(114;0.0427)		TGCACCTGGTGGGGGACAACT	0.602																																					p.V403fs		Atlas-INDEL	.											.	PDIA5	66	.	0			c.1208delT						.						89.0	84.0	85.0					3																	122869147		2203	4300	6503	SO:0001589	frameshift_variant	10954	exon14			.	AK054963	CCDS3020.1	3q21.1	2009-11-20	2005-06-29		ENSG00000065485	ENSG00000065485	5.3.4.1	"""Protein disulfide isomerases"""	24811	protein-coding gene	gene with protein product			"""protein disulfide isomerase-associated 5"""			7556671	Standard	NM_006810		Approved	PDIR, FLJ30401	uc003egc.2	Q14554	OTTHUMG00000159558	ENST00000316218.7:c.1209delG	chr3.hg19:g.122869147delG	ENSP00000323313:p.Val403fs	141.0	0.0		144.0	10.0	NM_006810	D3DN95|Q9BV43	Frame_Shift_Del	DEL	ENST00000316218.7	hg19	CCDS3020.1																																																																																			.	.		0.602	PDIA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356192.1	NM_006810	
NUDCD3	23386	hgsc.bcm.edu	37	7	44425624	44425624	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:44425624delC	ENST00000355451.7	-	6	1351	c.1072delG	c.(1072-1074)gctfs	p.A358fs	NUDCD3_ENST00000460110.1_5'UTR	NM_015332.3	NP_056147.2	Q8IVD9	NUDC3_HUMAN	NudC domain containing 3	358										endometrium(2)|large_intestine(1)|lung(3)|skin(1)	7						AACTGCACAGCCCCCGGGGAG	0.577																																					p.A358fs		Atlas-INDEL	.											.	NUDCD3	20	.	0			c.1073delC						.						68.0	63.0	64.0					7																	44425624		2203	4300	6503	SO:0001589	frameshift_variant	23386	exon6			.	BC003691	CCDS5490.2	7p13-p12	2005-03-18			ENSG00000015676	ENSG00000015676			22208	protein-coding gene	gene with protein product		610296					Standard	NM_015332		Approved	KIAA1068	uc003tkz.3	Q8IVD9	OTTHUMG00000129174	ENST00000355451.7:c.1072delG	chr7.hg19:g.44425624delC	ENSP00000347626:p.Ala358fs	124.0	0.0		183.0	11.0	NM_015332	Q9BTI3|Q9H7W9|Q9UPT4	Frame_Shift_Del	DEL	ENST00000355451.7	hg19	CCDS5490.2																																																																																			.	.		0.577	NUDCD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251248.3	NM_015332	
NAGS	162417	hgsc.bcm.edu	37	17	42084998	42084998	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:42084998delG	ENST00000293404.3	+	6	1426	c.1308delG	c.(1306-1308)ctgfs	p.L436fs		NM_153006.2	NP_694551.1	Q8N159	NAGS_HUMAN	N-acetylglutamate synthase	436	N-acetyltransferase. {ECO:0000255|PROSITE-ProRule:PRU00532}.				arginine biosynthetic process (GO:0006526)|cellular nitrogen compound metabolic process (GO:0034641)|glutamate metabolic process (GO:0006536)|small molecule metabolic process (GO:0044281)|urea cycle (GO:0000050)	mitochondrial matrix (GO:0005759)	acetyl-CoA:L-glutamate N-acetyltransferase activity (GO:0004042)			endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	8		Breast(137;0.00536)|Prostate(33;0.0724)		BRCA - Breast invasive adenocarcinoma(366;0.113)		AGCCCGTCCTGGGGGGCACCC	0.682											OREG0024449	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L436fs		Atlas-INDEL	.											.	NAGS	25	.	0			c.1307delT						.						15.0	18.0	17.0					17																	42084998		2197	4293	6490	SO:0001589	frameshift_variant	162417	exon6			.	AY116537	CCDS11473.1	17q21.31	2008-02-05				ENSG00000161653			17996	protein-coding gene	gene with protein product		608300				15050968, 12459178	Standard	NM_153006		Approved	AGAS, ARGA, NAT7	uc002ies.3	Q8N159		ENST00000293404.3:c.1308delG	chr17.hg19:g.42084998delG	ENSP00000293404:p.Leu436fs	254.0	0.0	906	153.0	11.0	NM_153006	B2RAZ9|Q8IWR4	Frame_Shift_Del	DEL	ENST00000293404.3	hg19	CCDS11473.1																																																																																			.	.		0.682	NAGS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457660.1	NM_153006	
TRMT11	60487	hgsc.bcm.edu	37	6	126332450	126332450	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:126332450delG	ENST00000334379.5	+	9	933	c.812delG	c.(811-813)aggfs	p.R271fs	TRMT11_ENST00000368332.3_Frame_Shift_Del_p.R271fs	NM_001031712.2	NP_001026882.2	Q7Z4G4	TRM11_HUMAN	tRNA methyltransferase 11 homolog (S. cerevisiae)	271					tRNA processing (GO:0008033)		methyltransferase activity (GO:0008168)|tRNA binding (GO:0000049)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18				GBM - Glioblastoma multiforme(226;0.0356)		GAAAACATTAGGGCCAATCTT	0.398																																					p.R271fs		Atlas-INDEL	.											.	TRMT11	43	.	0			c.811delA						.						104.0	84.0	91.0					6																	126332450		2203	4300	6503	SO:0001589	frameshift_variant	60487	exon9			.	AF182423	CCDS35496.1	6q11.1-q22.33	2009-06-15	2006-11-28	2006-11-28	ENSG00000066651	ENSG00000066651			21080	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 75"""	C6orf75			Standard	XM_006715546		Approved	MDS024, dJ187J11.2, TRM11, TRMT11-1	uc003qam.3	Q7Z4G4	OTTHUMG00000015515	ENST00000334379.5:c.812delG	chr6.hg19:g.126332450delG	ENSP00000333934:p.Arg271fs	165.0	0.0		140.0	10.0	NM_001031712	E1P570|Q5JY11|Q6PGQ5|Q9HC13	Frame_Shift_Del	DEL	ENST00000334379.5	hg19	CCDS35496.1																																																																																			.	.		0.398	TRMT11-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_021820	
CIB3	117286	hgsc.bcm.edu	37	19	16275654	16275654	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	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	243.0	0.0		226.0	16.0	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	
CORO2A	7464	hgsc.bcm.edu	37	9	100890927	100890927	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:100890927delT	ENST00000343933.5	-	9	1299	c.1042delA	c.(1042-1044)agcfs	p.S348fs	CORO2A_ENST00000375077.4_Frame_Shift_Del_p.S348fs	NM_003389.3	NP_003380.3	Q92828	COR2A_HUMAN	coronin, actin binding protein, 2A	348					actin cytoskeleton organization (GO:0030036)|intracellular signal transduction (GO:0035556)	actin cytoskeleton (GO:0015629)|transcriptional repressor complex (GO:0017053)	actin filament binding (GO:0051015)			endometrium(2)|kidney(2)|large_intestine(8)|lung(7)|ovary(1)|pancreas(1)|skin(4)|urinary_tract(1)	26		Acute lymphoblastic leukemia(62;0.0559)				TCGATGAGGCTTTTGGTTGTG	0.592																																					p.S348fs		Atlas-INDEL	.											.	CORO2A	54	.	0			c.1043delG						.						119.0	106.0	110.0					9																	100890927		2203	4300	6503	SO:0001589	frameshift_variant	7464	exon9			.	U57057	CCDS6735.1	9q22.3	2013-01-10	2001-11-28		ENSG00000106789	ENSG00000106789		"""Coronins"", ""WD repeat domain containing"""	2255	protein-coding gene	gene with protein product	"""coronin 2A"", ""coronin-like protein B"", ""WD protein IR10"", ""WD-repeat protein 2"""	602159	"""coronin, actin-binding protein, 2A"""			8985118	Standard	NM_052820		Approved	IR10, WDR2	uc004aym.3	Q92828	OTTHUMG00000020340	ENST00000343933.5:c.1042delA	chr9.hg19:g.100890927delT	ENSP00000343746:p.Ser348fs	203.0	0.0		178.0	12.0	NM_003389	Q5TBR5|Q92829|Q9BWS5	Frame_Shift_Del	DEL	ENST00000343933.5	hg19	CCDS6735.1																																																																																			.	.		0.592	CORO2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053357.1	NM_003389	
WDR93	56964	hgsc.bcm.edu	37	15	90278766	90278766	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:90278766delC	ENST00000268130.7	+	14	1691	c.1590delC	c.(1588-1590)gtcfs	p.V530fs	WDR93_ENST00000444934.2_Frame_Shift_Del_p.V247fs|WDR93_ENST00000560294.1_Frame_Shift_Del_p.V502fs	NM_020212.1	NP_064597.1	Q6P2C0	WDR93_HUMAN	WD repeat domain 93	530					electron transport chain (GO:0022900)		oxidoreductase activity, acting on NAD(P)H (GO:0016651)			NS(1)|breast(3)|endometrium(2)|kidney(4)|large_intestine(5)|liver(2)|lung(8)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	33	Lung NSC(78;0.0237)|all_lung(78;0.0478)		KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|BRCA - Breast invasive adenocarcinoma(143;0.128)			TGGCCCCAGTCCCAGCCTTAC	0.443																																					p.V530fs		Atlas-INDEL	.											.	WDR93	63	.	0			c.1589delT						.						125.0	117.0	120.0					15																	90278766		2200	4299	6499	SO:0001589	frameshift_variant	56964	exon14			.		CCDS32326.1, CCDS66862.1, CCDS73779.1	15q26.1	2012-11-02						"""WD repeat domain containing"""	26924	protein-coding gene	gene with protein product							Standard	NM_020212		Approved		uc002boj.3	Q6P2C0		ENST00000268130.7:c.1590delC	chr15.hg19:g.90278766delC	ENSP00000268130:p.Val530fs	156.0	0.0		137.0	10.0	NM_020212	Q8N7Y8|Q9NP89	Frame_Shift_Del	DEL	ENST00000268130.7	hg19	CCDS32326.1																																																																																			.	.		0.443	WDR93-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000416369.1	NM_020212	
IDI1	3422	hgsc.bcm.edu	37	10	1087256	1087256	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:1087256delT	ENST00000381344.3	-	5	892	c.726delA	c.(724-726)aaafs	p.K242fs	IDI2-AS1_ENST00000428780.2_RNA|IDI2-AS1_ENST00000420381.1_RNA|IDI2-AS1_ENST00000536039.1_RNA|RNU7-163P_ENST00000459467.1_RNA|IDI1_ENST00000491735.1_5'UTR|IDI2-AS1_ENST00000437374.1_RNA	NM_004508.2	NP_004499.2	Q13907	IDI1_HUMAN	isopentenyl-diphosphate delta isomerase 1	185					cholesterol biosynthetic process (GO:0006695)|dimethylallyl diphosphate biosynthetic process (GO:0050992)|isoprenoid biosynthetic process (GO:0008299)|response to stilbenoid (GO:0035634)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|peroxisome (GO:0005777)	hydrolase activity (GO:0016787)|isopentenyl-diphosphate delta-isomerase activity (GO:0004452)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|metal ion binding (GO:0046872)			large_intestine(3)|lung(2)|prostate(1)	6		all_epithelial(10;0.107)|Colorectal(49;0.14)	OV - Ovarian serous cystadenocarcinoma(33;0.221)	Epithelial(11;0.0972)		CACTGGCTGCTTTTTTCAGAA	0.333																																					p.A243fs		Atlas-INDEL	.											.,1	IDI1	22	.	0			c.727delG						.						82.0	82.0	82.0					10																	1087256		2202	4297	6499	SO:0001589	frameshift_variant	3422	exon5			.	BC006999	CCDS7056.1	10p15.3	2003-11-12	2005-07-25		ENSG00000067064	ENSG00000067064	5.3.3.2		5387	protein-coding gene	gene with protein product	"""IPP isomerase"""	604055	"""isopentenyl-diphosphate delta isomerase"""			8020941	Standard	NM_004508		Approved		uc001iga.3	Q13907	OTTHUMG00000017536	ENST00000381344.3:c.726delA	chr10.hg19:g.1087256delT	ENSP00000370748:p.Lys242fs	255.0	0.0		219.0	14.0	NM_004508	B4E155|Q32Q13|Q53GQ6|Q86U81|Q8WUX8|Q96IZ4|Q9BQ74	Frame_Shift_Del	DEL	ENST00000381344.3	hg19	CCDS7056.1																																																																																			.	.		0.333	IDI1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046409.2	NM_004508	
NUMBL	9253	hgsc.bcm.edu	37	19	41174028	41174028	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:41174028delC	ENST00000252891.4	-	10	1342	c.1175delG	c.(1174-1176)ggtfs	p.G392fs	NUMBL_ENST00000598779.1_Frame_Shift_Del_p.G351fs|NUMBL_ENST00000540131.1_Frame_Shift_Del_p.G351fs	NM_004756.3	NP_004747.1	Q9Y6R0	NUMBL_HUMAN	numb homolog (Drosophila)-like	392					adherens junction organization (GO:0034332)|axonogenesis (GO:0007409)|cytokine-mediated signaling pathway (GO:0019221)|lateral ventricle development (GO:0021670)|nervous system development (GO:0007399)|neuroblast division in subventricular zone (GO:0021849)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of neurogenesis (GO:0050769)|protein metabolic process (GO:0019538)	cytoplasm (GO:0005737)				NS(1)|breast(1)|endometrium(1)|large_intestine(5)|lung(6)|ovary(2)	16			Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105)			GGAGGGCTCACCCCAGGCAGA	0.652																																					p.G392fs		Atlas-INDEL	.											.	NUMBL	49	.	0			c.1176delT						.						10.0	12.0	11.0					19																	41174028		2192	4279	6471	SO:0001589	frameshift_variant	9253	exon10			.	AF015401	CCDS12561.1	19q13.13-q13.2	2008-07-17	2001-11-28			ENSG00000105245			8061	protein-coding gene	gene with protein product		604018	"""numb (Drosophila) homolog-like"""			9225980, 9303539	Standard	XM_006723471		Approved	NUMB-R, CTG3a, CAG3A, TNRC23, NUMBR, NUMBLIKE	uc002oon.3	Q9Y6R0		ENST00000252891.4:c.1175delG	chr19.hg19:g.41174028delC	ENSP00000252891:p.Gly392fs	148.0	0.0		142.0	11.0	NM_004756	Q7Z4J9	Frame_Shift_Del	DEL	ENST00000252891.4	hg19	CCDS12561.1																																																																																			.	.		0.652	NUMBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462749.2	NM_004756	
OR2T35	403244	hgsc.bcm.edu	37	1	248801642	248801642	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:248801642delC	ENST00000317450.3	-	1	917	c.918delG	c.(916-918)gggfs	p.G306fs		NM_001001827.1	NP_001001827.1	Q8NGX2	O2T35_HUMAN	olfactory receptor, family 2, subfamily T, member 35	306						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(1)|lung(1)|ovary(1)|prostate(1)|skin(1)	6	all_cancers(71;2.04e-05)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)	all_cancers(173;0.237)	OV - Ovarian serous cystadenocarcinoma(106;0.0265)			AACCACATCTCCCTAGTACTT	0.537																																					p.R307fs		Atlas-INDEL	.											.	OR2T35	19	.	0			c.919delA						.						12.0	4.0	7.0					1																	248801642		1964	2979	4943	SO:0001589	frameshift_variant	403244	exon1			.	BK004475	CCDS31123.1	1q44	2012-08-09			ENSG00000177151	ENSG00000177151		"""GPCR / Class A : Olfactory receptors"""	31257	protein-coding gene	gene with protein product							Standard	NM_001001827		Approved		uc001ies.1	Q8NGX2	OTTHUMG00000040380	ENST00000317450.3:c.918delG	chr1.hg19:g.248801642delC	ENSP00000324369:p.Gly306fs	116.0	0.0		160.0	10.0	NM_001001827	Q6IEY7	Frame_Shift_Del	DEL	ENST00000317450.3	hg19	CCDS31123.1																																																																																			.	.		0.537	OR2T35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097130.1	NM_001001827	
STRAP	11171	hgsc.bcm.edu	37	12	16047053	16047053	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:16047053delT	ENST00000419869.2	+	5	789	c.476delT	c.(475-477)cttfs	p.L159fs	STRAP_ENST00000538352.1_Frame_Shift_Del_p.L65fs|STRAP_ENST00000025399.6_Frame_Shift_Del_p.L172fs	NM_007178.3	NP_009109.3	Q9Y3F4	STRAP_HUMAN	serine/threonine kinase receptor associated protein	159					maintenance of gastrointestinal epithelium (GO:0030277)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of pathway-restricted SMAD protein phosphorylation (GO:0060394)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|spliceosomal snRNP assembly (GO:0000387)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)	poly(A) RNA binding (GO:0044822)			cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(6)|skin(1)	15		Hepatocellular(102;0.121)				AAACAGATTCTTTCTGCTGAT	0.358																																					p.L159fs		Atlas-INDEL	.											.	STRAP	33	.	0			c.475delC						.						107.0	118.0	115.0					12																	16047053		2203	4300	6503	SO:0001589	frameshift_variant	11171	exon5			.	AB024327	CCDS8676.1	12p13.1	2013-01-10			ENSG00000023734	ENSG00000023734		"""WD repeat domain containing"""	30796	protein-coding gene	gene with protein product	"""Unr-interacting protein"""	605986					Standard	NM_007178		Approved	UNRIP, pt-wd, MAWD	uc001rdc.4	Q9Y3F4	OTTHUMG00000168791	ENST00000419869.2:c.476delT	chr12.hg19:g.16047053delT	ENSP00000392270:p.Leu159fs	256.0	0.0		171.0	14.0	NM_007178	B2R5S5|B4DNJ6|Q5TZT4|Q9NTK0|Q9UQC8	Frame_Shift_Del	DEL	ENST00000419869.2	hg19	CCDS8676.1																																																																																			.	.		0.358	STRAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401114.1	NM_007178	
OPA1	4976	hgsc.bcm.edu	37	3	193332740	193332740	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:193332740delT	ENST00000392438.3	+	2	495	c.261delT	c.(259-261)aatfs	p.N87fs	OPA1_ENST00000487986.1_3'UTR|OPA1_ENST00000361510.2_Frame_Shift_Del_p.N87fs|OPA1_ENST00000361715.2_Frame_Shift_Del_p.N87fs|OPA1_ENST00000361908.3_Frame_Shift_Del_p.N87fs|OPA1_ENST00000361828.2_Frame_Shift_Del_p.N87fs|OPA1_ENST00000361150.2_Frame_Shift_Del_p.N87fs	NM_015560.2	NP_056375.2	O60313	OPA1_HUMAN	optic atrophy 1 (autosomal dominant)	87					apoptotic process (GO:0006915)|axon transport of mitochondrion (GO:0019896)|cellular senescence (GO:0090398)|GTP catabolic process (GO:0006184)|inner mitochondrial membrane organization (GO:0007007)|mitochondrial fission (GO:0000266)|mitochondrial fusion (GO:0008053)|mitochondrion organization (GO:0007005)|negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway (GO:1902236)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|neural tube closure (GO:0001843)|visual perception (GO:0007601)	dendrite (GO:0030425)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial crista (GO:0030061)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|magnesium ion binding (GO:0000287)			breast(1)|cervix(2)|endometrium(3)|kidney(3)|large_intestine(4)|lung(15)|upper_aerodigestive_tract(1)|urinary_tract(2)	31	all_cancers(143;9.56e-09)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;9.19e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;0.000162)		CTCGCAGGAATTTTTGGCCAG	0.428																																					p.N87fs		Atlas-INDEL	.											.	OPA1	79	.	0			c.260delA						.						49.0	48.0	48.0					3																	193332740		2203	4300	6503	SO:0001589	frameshift_variant	4976	exon2			.	AB011139	CCDS33917.1, CCDS43186.1	3q29	2014-09-17			ENSG00000198836	ENSG00000198836			8140	protein-coding gene	gene with protein product	"""mitochondrial dynamin-like GTPase"", ""dynamin-like guanosine triphosphatase"", ""Dynamin-like 120 kDa protein, mitochondrial"""	605290				9490303	Standard	NM_015560		Approved	NTG, KIAA0567, FLJ12460, NPG, MGM1	uc003ftg.3	O60313	OTTHUMG00000149897	ENST00000392438.3:c.261delT	chr3.hg19:g.193332740delT	ENSP00000376233:p.Asn87fs	240.0	0.0		175.0	11.0	NM_130832	D3DNW4	Frame_Shift_Del	DEL	ENST00000392438.3	hg19	CCDS43186.1																																																																																			.	.		0.428	OPA1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313812.2	NM_130837	
SEC31B	25956	hgsc.bcm.edu	37	10	102249484	102249484	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:102249484delG	ENST00000370345.3	-	22	3097	c.3000delC	c.(2998-3000)cccfs	p.P1000fs		NM_015490.3	NP_056305.1	Q9NQW1	SC31B_HUMAN	SEC31 homolog B (S. cerevisiae)	1000	Pro-rich.				protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|vesicle coat (GO:0030120)				NS(1)|breast(2)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(3)|lung(17)|ovary(1)|urinary_tract(1)	36		Colorectal(252;0.117)		Epithelial(162;2.36e-10)|all cancers(201;2.09e-08)		GGTTTCCCCTGGGGGCTGGGG	0.458																																					p.R1001fs		Atlas-INDEL	.											.	SEC31B	84	.	0			c.3001delA						.						80.0	84.0	83.0					10																	102249484		2203	4300	6503	SO:0001589	frameshift_variant	25956	exon22			.	AF274863	CCDS7495.1	10q24.32	2013-01-10	2006-10-05	2006-09-07	ENSG00000075826	ENSG00000075826		"""WD repeat domain containing"""	23197	protein-coding gene	gene with protein product		610258	"""SEC31-like 2 (S. cerevisiae)"""	SEC31L2		16495487	Standard	NM_015490		Approved	SEC31B-1, DKFZP434M183	uc001krc.1	Q9NQW1	OTTHUMG00000019342	ENST00000370345.3:c.3000delC	chr10.hg19:g.102249484delG	ENSP00000359370:p.Pro1000fs	178.0	0.0		142.0	10.0	NM_015490	B7ZM75|Q6MZS3|Q86UF0|Q9Y4Q8	Frame_Shift_Del	DEL	ENST00000370345.3	hg19	CCDS7495.1																																																																																			.	.		0.458	SEC31B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051198.1	NM_015490	
MATR3	9782	hgsc.bcm.edu	37	5	138657644	138657644	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:138657644delA	ENST00000394805.3	+	10	1995	c.1660delA	c.(1660-1662)aaafs	p.K555fs	MATR3_ENST00000394800.2_Frame_Shift_Del_p.K555fs|MATR3_ENST00000510056.1_Frame_Shift_Del_p.K555fs|MATR3_ENST00000502929.1_Frame_Shift_Del_p.K555fs|MATR3_ENST00000504203.1_Frame_Shift_Del_p.K217fs|MATR3_ENST00000502499.1_Frame_Shift_Del_p.K217fs|MATR3_ENST00000361059.2_Frame_Shift_Del_p.K555fs|MATR3_ENST00000503811.1_Frame_Shift_Del_p.K267fs|MATR3_ENST00000509990.1_Frame_Shift_Del_p.K555fs	NM_001194955.1|NM_018834.5	NP_001181884.1|NP_061322.2	P43243	MATR3_HUMAN	matrin 3	555	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				cell death (GO:0008219)	membrane (GO:0016020)|nuclear inner membrane (GO:0005637)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)|zinc ion binding (GO:0008270)			breast(2)|endometrium(3)|kidney(4)|large_intestine(6)|lung(9)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	29			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			CCATTGTTTGAAAAAAGCCCT	0.353																																					p.L553fs		Atlas-INDEL	.											.	MATR3	85	.	0			c.1659delG						.						133.0	133.0	133.0					5																	138657644		2203	4300	6503	SO:0001589	frameshift_variant	9782	exon10			.	M63483	CCDS4210.1, CCDS54908.1, CCDS75316.1	5q31.3	2010-08-12			ENSG00000015479	ENSG00000015479			6912	protein-coding gene	gene with protein product		164015	"""myopathy, distal 2"""	MPD2		2033075, 19344878	Standard	NM_018834		Approved	KIAA0723, MGC9105, VCPDM	uc003ldx.3	P43243	OTTHUMG00000129229	ENST00000394805.3:c.1660delA	chr5.hg19:g.138657644delA	ENSP00000378284:p.Lys555fs	152.0	0.0		135.0	10.0	NM_018834	B7ZAV5|D3DQC3|Q9UHW0|Q9UQ27	Frame_Shift_Del	DEL	ENST00000394805.3	hg19	CCDS4210.1																																																																																			.	.		0.353	MATR3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251324.2	NM_018834	
SLC12A7	10723	hgsc.bcm.edu	37	5	1078065	1078065	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:1078065delG	ENST00000264930.5	-	12	1555	c.1512delC	c.(1510-1512)cccfs	p.P504fs		NM_006598.2	NP_006589.2	Q9Y666	S12A7_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 7	504					cell volume homeostasis (GO:0006884)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|potassium ion transport (GO:0006813)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)			breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	32	Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;5.44e-09)		Epithelial(17;0.000497)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00241)|Lung(60;0.165)		Potassium Chloride(DB00761)	CGATGACCCAGGGGGAGGGCC	0.701																																					p.W505fs		Atlas-INDEL	.											.	SLC12A7	97	.	0			c.1513delT						.						20.0	23.0	22.0					5																	1078065		2179	4286	6465	SO:0001589	frameshift_variant	10723	exon12			.	AF105365	CCDS34129.1	5p15	2013-07-18	2013-07-18		ENSG00000113504	ENSG00000113504		"""Solute carriers"""	10915	protein-coding gene	gene with protein product		604879				10347194	Standard	NM_006598		Approved	KCC4, DKFZP434F076	uc003jbu.3	Q9Y666	OTTHUMG00000161931	ENST00000264930.5:c.1512delC	chr5.hg19:g.1078065delG	ENSP00000264930:p.Pro504fs	173.0	0.0		189.0	13.0	NM_006598	A6NDS8|Q4G0F3|Q96I81|Q9H7I3|Q9H7I7|Q9UFW2	Frame_Shift_Del	DEL	ENST00000264930.5	hg19	CCDS34129.1																																																																																			.	.		0.701	SLC12A7-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366446.2	NM_006598	
TDRD7	23424	hgsc.bcm.edu	37	9	100203999	100203999	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:100203999delA	ENST00000355295.4	+	6	992	c.697delA	c.(697-699)aaafs	p.K233fs	TDRD7_ENST00000422139.2_Frame_Shift_Del_p.K159fs	NM_014290.2	NP_055105.2	Q8NHU6	TDRD7_HUMAN	tudor domain containing 7	233	HTH OST-type 2. {ECO:0000255|PROSITE- ProRule:PRU00975}.				germ cell development (GO:0007281)|lens fiber cell differentiation (GO:0070306)|lens morphogenesis in camera-type eye (GO:0002089)|posttranscriptional regulation of gene expression (GO:0010608)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)|P granule (GO:0043186)|ribonucleoprotein granule (GO:0035770)	mRNA binding (GO:0003729)			endometrium(3)|kidney(4)|large_intestine(6)|lung(8)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29		Acute lymphoblastic leukemia(62;0.158)				TTACACTTATAAAATGGATGA	0.284																																					p.Y232X		Atlas-INDEL	.											.	TDRD7	78	.	0			c.696delT						.						63.0	64.0	64.0					9																	100203999		2203	4300	6503	SO:0001589	frameshift_variant	23424	exon6			.	AB025254	CCDS6725.1	9q22.33	2013-01-23			ENSG00000196116	ENSG00000196116		"""Tudor domain containing"""	30831	protein-coding gene	gene with protein product		611258				21436445	Standard	NM_014290		Approved	PCTAIRE2BP	uc004axj.3	Q8NHU6	OTTHUMG00000020326	ENST00000355295.4:c.697delA	chr9.hg19:g.100203999delA	ENSP00000347444:p.Lys233fs	238.0	0.0		191.0	12.0	NM_014290	A6NCI6|B2RBX3|B4DG99|B4DXF7|E7EQD4|Q5VV27|Q96JT1|Q9UFF0|Q9Y2M3	Frame_Shift_Del	DEL	ENST00000355295.4	hg19	CCDS6725.1																																																																																			.	.		0.284	TDRD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053322.1	NM_014290	
SLC12A1	6557	hgsc.bcm.edu	37	15	48527143	48527143	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:48527143delT	ENST00000558405.1	+	8	1171	c.1157delT	c.(1156-1158)attfs	p.I386fs	SLC12A1_ENST00000330289.6_Frame_Shift_Del_p.I386fs|SLC12A1_ENST00000380993.3_Frame_Shift_Del_p.I386fs|SLC12A1_ENST00000396577.3_Frame_Shift_Del_p.I386fs			Q13621	S12A1_HUMAN	solute carrier family 12 (sodium/potassium/chloride transporter), member 1	386					cell death (GO:0008219)|chemical homeostasis (GO:0048878)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|kidney development (GO:0001822)|potassium ion transport (GO:0006813)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium:potassium:chloride symporter activity (GO:0008511)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(30)|ovary(1)|prostate(2)|skin(1)	59		all_lung(180;0.00219)		all cancers(107;1.76e-09)|GBM - Glioblastoma multiforme(94;1.48e-06)	Bumetanide(DB00887)|Chlormerodrin(DB00534)|Chlorthalidone(DB00310)|Ethacrynic acid(DB00903)|Furosemide(DB00695)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Potassium Chloride(DB00761)|Quinethazone(DB01325)|Torasemide(DB00214)|Trichlormethiazide(DB01021)	GTCTTTGCCATTTTTTTCCCA	0.433																																					p.I386fs		Atlas-INDEL	.											.,2	SLC12A1	243	.	0			c.1156delA						.						121.0	123.0	122.0					15																	48527143		2198	4297	6495	SO:0001589	frameshift_variant	6557	exon9			.		CCDS10129.2, CCDS53940.1	15q15-q21	2013-07-18	2013-07-18		ENSG00000074803	ENSG00000074803		"""Solute carriers"""	10910	protein-coding gene	gene with protein product		600839				8640224	Standard	NM_000338		Approved	NKCC2	uc010bem.3	Q13621	OTTHUMG00000131495	ENST00000558405.1:c.1157delT	chr15.hg19:g.48527143delT	ENSP00000453409:p.Ile386fs	258.0	0.0		219.0	15.0	NM_001184832	A8JYA2|E9PDW4	Frame_Shift_Del	DEL	ENST00000558405.1	hg19	CCDS10129.2																																																																																			.	.		0.433	SLC12A1-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417131.1		
MMP16	4325	hgsc.bcm.edu	37	8	89179946	89179946	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:89179946delG	ENST00000286614.6	-	4	942	c.661delC	c.(661-663)catfs	p.H221fs	MMP16_ENST00000544227.1_5'UTR	NM_005941.4	NP_005932.2	P51512	MMP16_HUMAN	matrix metallopeptidase 16 (membrane-inserted)	221					chondrocyte proliferation (GO:0035988)|collagen catabolic process (GO:0030574)|craniofacial suture morphogenesis (GO:0097094)|embryonic cranial skeleton morphogenesis (GO:0048701)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of catalytic activity (GO:0043085)	Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|enzyme activator activity (GO:0008047)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(5)|liver(1)|lung(51)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	81					Marimastat(DB00786)	GAGTCAAAATGGGTATCTCCT	0.408																																					p.H221fs		Atlas-INDEL	.											.	MMP16	176	.	0			c.662delA						.						94.0	81.0	86.0					8																	89179946		2203	4300	6503	SO:0001589	frameshift_variant	4325	exon4			.	D85511	CCDS6246.1	8q21	2009-01-09	2005-08-08		ENSG00000156103	ENSG00000156103			7162	protein-coding gene	gene with protein product		602262	"""matrix metalloproteinase 16 (membrane-inserted)"", ""chromosome 8 open reading frame 57"""	C8orf57		7559440	Standard	NM_005941		Approved	MT3-MMP, DKFZp761D112	uc003yeb.4	P51512	OTTHUMG00000163769	ENST00000286614.6:c.661delC	chr8.hg19:g.89179946delG	ENSP00000286614:p.His221fs	166.0	0.0		194.0	14.0	NM_005941	B2RAN7|Q14824|Q52H48	Frame_Shift_Del	DEL	ENST00000286614.6	hg19	CCDS6246.1																																																																																			.	.		0.408	MMP16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375304.2	NM_005941	
PROX1	5629	hgsc.bcm.edu	37	1	214209037	214209037	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:214209037delT	ENST00000366958.4	+	5	2682	c.2074delT	c.(2074-2076)tttfs	p.F693fs	PROX1_ENST00000498508.2_Frame_Shift_Del_p.F693fs|PROX1_ENST00000261454.4_Frame_Shift_Del_p.F693fs|PROX1_ENST00000435016.1_Frame_Shift_Del_p.F693fs	NM_001270616.1	NP_001257545.1	Q92786	PROX1_HUMAN	prospero homeobox 1	693	Prospero-like.				aorta smooth muscle tissue morphogenesis (GO:0060414)|atrial cardiac muscle tissue morphogenesis (GO:0055009)|brain development (GO:0007420)|cell fate determination (GO:0001709)|cerebellar granule cell differentiation (GO:0021707)|dentate gyrus development (GO:0021542)|dorsal spinal cord development (GO:0021516)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|endocardium formation (GO:0060214)|hepatocyte cell migration (GO:0002194)|hepatocyte differentiation (GO:0070365)|hepatocyte proliferation (GO:0072574)|kidney development (GO:0001822)|lens development in camera-type eye (GO:0002088)|lens fiber cell morphogenesis (GO:0070309)|liver development (GO:0001889)|lung development (GO:0030324)|lymphangiogenesis (GO:0001946)|lymphatic endothelial cell differentiation (GO:0060836)|negative regulation of bile acid biosynthetic process (GO:0070858)|negative regulation of cell proliferation (GO:0008285)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of viral genome replication (GO:0045071)|neural tube development (GO:0021915)|neuronal stem cell maintenance (GO:0097150)|olfactory placode formation (GO:0030910)|optic placode formation involved in camera-type eye formation (GO:0046619)|otic placode formation (GO:0043049)|pancreas development (GO:0031016)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell cycle checkpoint (GO:1901978)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045737)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of forebrain neuron differentiation (GO:2000979)|positive regulation of heart growth (GO:0060421)|positive regulation of neural precursor cell proliferation (GO:2000179)|positive regulation of sarcomere organization (GO:0060298)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of circadian rhythm (GO:0042752)|regulation of gene expression (GO:0010468)|regulation of transcription involved in lymphatic endothelial cell fate commitment (GO:0060849)|response to nutrient levels (GO:0031667)|retina morphogenesis in camera-type eye (GO:0060042)|skeletal muscle thin filament assembly (GO:0030240)|venous blood vessel morphogenesis (GO:0048845)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|ventricular cardiac myofibril assembly (GO:0055005)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|DBD domain binding (GO:0050692)|DNA binding (GO:0003677)|LBD domain binding (GO:0050693)|ligand-dependent nuclear receptor binding (GO:0016922)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(6)|lung(15)|ovary(3)|prostate(2)|skin(4)	47				OV - Ovarian serous cystadenocarcinoma(81;0.0179)|all cancers(67;0.0488)|GBM - Glioblastoma multiforme(131;0.188)|Epithelial(68;0.219)		ATTACGGGAGTTTTTCAATGC	0.423																																					p.E691fs		Atlas-INDEL	.											.	PROX1	124	.	0			c.2073delG						.						87.0	81.0	83.0					1																	214209037		2203	4300	6503	SO:0001589	frameshift_variant	5629	exon5			.	U44060	CCDS31021.1	1q41	2011-06-20	2007-06-01		ENSG00000117707	ENSG00000117707		"""Homeoboxes / PROS class"""	9459	protein-coding gene	gene with protein product		601546	"""prospero-related homeobox 1"""			8812486	Standard	NM_002763		Approved		uc001hkg.2	Q92786	OTTHUMG00000036946	ENST00000366958.4:c.2074delT	chr1.hg19:g.214209037delT	ENSP00000355925:p.Phe693fs	249.0	0.0		267.0	17.0	NM_001270616	A6NK29|A8K2B1|Q5SW76|Q8TB91	Frame_Shift_Del	DEL	ENST00000366958.4	hg19	CCDS31021.1																																																																																			.	.		0.423	PROX1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089727.6	NM_002763	
EPHA5	2044	hgsc.bcm.edu	37	4	66467573	66467573	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:66467573delT	ENST00000273854.3	-	3	1296	c.696delA	c.(694-696)aaafs	p.K232fs	EPHA5_ENST00000432638.2_Frame_Shift_Del_p.K232fs|EPHA5_ENST00000511294.1_Frame_Shift_Del_p.K232fs|EPHA5_ENST00000354839.4_Frame_Shift_Del_p.K232fs	NM_001281765.1|NM_004439.5	NP_001268694.1|NP_004430.4	P54756	EPHA5_HUMAN	EPH receptor A5	232	Cys-rich.|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						CAGAAGGGCATTTTTTATAGT	0.448										TSP Lung(17;0.13)																											p.C233fs		Atlas-INDEL	.											.	EPHA5	315	.	0			c.697delT						.						68.0	66.0	67.0					4																	66467573		2203	4300	6503	SO:0001589	frameshift_variant	2044	exon3			.	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.696delA	chr4.hg19:g.66467573delT	ENSP00000273854:p.Lys232fs	175.0	0.0		128.0	10.0	NM_182472	Q7Z3F2	Frame_Shift_Del	DEL	ENST00000273854.3	hg19	CCDS3513.1																																																																																			.	.		0.448	EPHA5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251388.2	NM_004439	
SORBS2	8470	hgsc.bcm.edu	37	4	186598269	186598273	+	Intron	DEL	TCCTG	TCCTG	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	TCCTG	TCCTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:186598269_186598273delTCCTG	ENST00000284776.7	-	4	465				SORBS2_ENST00000448662.2_Intron|SORBS2_ENST00000319471.9_Intron|SORBS2_ENST00000437304.2_Frame_Shift_Del_p.QD124fs|SORBS2_ENST00000355634.5_Intron|SORBS2_ENST00000431808.1_Intron|SORBS2_ENST00000393528.3_Intron|SORBS2_ENST00000449407.2_Intron|RP11-626E13.1_ENST00000447277.1_RNA	NM_021069.4	NP_066547.1	O94875	SRBS2_HUMAN	sorbin and SH3 domain containing 2						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)		GCTTTCAAGATCCTGTCCTGAAAGG	0.498																																					p.124_125del	Esophageal Squamous(153;41 2433 9491 36028)	Atlas-Indel,Pindel	.											.	SORBS2	300	.	0			c.371_375del						.																																			SO:0001627	intron_variant	8470	exon5			.		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.44+1303CAGGA>-	chr4.hg19:g.186598274_186598278delTCCTG		167.0	0.0		126.0	41.0	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																																																																																			.	.		0.498	SORBS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347944.3	NM_003603	
VPS13D	55187	hgsc.bcm.edu	37	1	12414184	12414184	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:12414184delT	ENST00000358136.3	+	47	9715	c.9585delT	c.(9583-9585)gatfs	p.D3195fs	VPS13D_ENST00000356315.4_Frame_Shift_Del_p.D3170fs	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)		GTGAACTTGATTTTTATGTTA	0.438																																					p.D3195fs		Atlas-INDEL	.											.	VPS13D	316	.	0			c.9584delA						.						113.0	110.0	111.0					1																	12414184		2203	4300	6503	SO:0001589	frameshift_variant	55187	exon47			.	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.9585delT	chr1.hg19:g.12414184delT	ENSP00000350854:p.Asp3195fs	271.0	0.0		195.0	14.0	NM_015378		Frame_Shift_Del	DEL	ENST00000358136.3	hg19	CCDS30588.1																																																																																			.	.		0.438	VPS13D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000036897.2	NM_015378	
PTPRT	11122	hgsc.bcm.edu	37	20	40944372	40944372	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr20:40944372delT	ENST00000373187.1	-	12	2129	c.2130delA	c.(2128-2130)aaafs	p.K710fs	PTPRT_ENST00000373184.1_Frame_Shift_Del_p.K710fs|PTPRT_ENST00000356100.2_Frame_Shift_Del_p.K710fs|PTPRT_ENST00000373190.1_Frame_Shift_Del_p.K710fs|PTPRT_ENST00000373198.4_Frame_Shift_Del_p.K710fs|PTPRT_ENST00000373201.1_Frame_Shift_Del_p.K710fs|PTPRT_ENST00000373193.3_Frame_Shift_Del_p.K710fs			O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T	710	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|delta-catenin binding (GO:0070097)|gamma-catenin binding (GO:0045295)|protein tyrosine phosphatase activity (GO:0004725)			NS(2)|breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(12)|large_intestine(26)|liver(1)|lung(63)|ovary(8)|pancreas(2)|prostate(5)|skin(35)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	176		Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783)				CTCCATTGGCTTTGCTGAGTG	0.468																																					p.A711fs		Atlas-INDEL	.											.	PTPRT	372	.	0			c.2131delG						.						74.0	71.0	72.0					20																	40944372		1948	4140	6088	SO:0001589	frameshift_variant	11122	exon12			.	AF043644	CCDS42874.1, CCDS68127.1	20q12-q13	2013-02-11			ENSG00000196090	ENSG00000196090		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	9682	protein-coding gene	gene with protein product		608712				9486824, 9602027	Standard	NM_133170		Approved	RPTPrho, KIAA0283	uc010ggj.3	O14522	OTTHUMG00000033040	ENST00000373187.1:c.2130delA	chr20.hg19:g.40944372delT	ENSP00000362283:p.Lys710fs	245.0	0.0		198.0	12.0	NM_007050	A8E4R6|O43655|O75664|Q5W0X9|Q5W0Y1|Q9BR24|Q9BR28|Q9H0Y8|Q9NTL1|Q9NU72|Q9UBD2|Q9UJL7	Frame_Shift_Del	DEL	ENST00000373187.1	hg19	CCDS42874.1																																																																																			.	.		0.468	PTPRT-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000080315.1		
GIGYF2	26058	hgsc.bcm.edu	37	2	233659657	233659657	+	Intron	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:233659657delA	ENST00000409547.1	+	15	1790				GIGYF2_ENST00000452341.2_Intron|GIGYF2_ENST00000373566.3_Intron|GIGYF2_ENST00000373563.4_Intron|GIGYF2_ENST00000409196.3_Intron|GIGYF2_ENST00000409480.1_Intron|GIGYF2_ENST00000409451.3_Intron	NM_015575.3	NP_056390.2	Q6Y7W6	PERQ2_HUMAN	GRB10 interacting GYF protein 2						adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|feeding behavior (GO:0007631)|homeostasis of number of cells within a tissue (GO:0048873)|insulin-like growth factor receptor signaling pathway (GO:0048009)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|musculoskeletal movement (GO:0050881)|negative regulation of translation (GO:0017148)|neuromuscular process controlling balance (GO:0050885)|post-embryonic development (GO:0009791)|spinal cord motor neuron differentiation (GO:0021522)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(17)|lung(11)|ovary(5)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	63		Breast(86;0.00279)|all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;7.37e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000472)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(119;0.0118)|GBM - Glioblastoma multiforme(43;0.0145)		TGGAGCAGGTAAAAATCCTGT	0.398																																					.		Atlas-INDEL	.											.	GIGYF2	288	.	0			c.1461+2A>-						.						126.0	135.0	132.0					2																	233659657		2203	4300	6503	SO:0001627	intron_variant	26058	exon12			.	U80751	CCDS33401.1, CCDS46542.1, CCDS46543.1	2q37.1	2011-07-06	2008-02-11	2008-02-11	ENSG00000204120	ENSG00000204120		"""Trinucleotide (CAG) repeat containing"""	11960	protein-coding gene	gene with protein product	"""GYF domain containing 2"""	612003	"""PERQ amino acid rich, with GYF domain 2"", ""PERQ amino acid rich, with GYF domain 3"", ""trinucleotide repeat containing 15"", ""Parkinson disease (autosomal recessive, early onset) 11"""	PERQ2, PERQ3, TNRC15, PARK11		9225980, 9734811, 12771153, 18358451, 19279319	Standard	NM_015575		Approved	KIAA0642, GYF2	uc002vtk.4	Q6Y7W6	OTTHUMG00000153237	ENST00000409547.1:c.1479+3A>-	chr2.hg19:g.233659657delA		200.0	0.0		139.0	10.0	NM_001103148	A6H8W4|B9EG55|E9PBB0|O75137|Q7Z2Z8|Q7Z3I2|Q96HU4|Q9NV82	Splice_Site	DEL	ENST00000409547.1	hg19	CCDS33401.1																																																																																			.	.		0.398	GIGYF2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000330316.2	NM_001103146	
MYH14	79784	hgsc.bcm.edu	37	19	50771494	50771494	+	Frame_Shift_Del	DEL	G	G	-	rs561594120		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:50771494delG	ENST00000596571.1	+	21	2780	c.2780delG	c.(2779-2781)cggfs	p.R927fs	MYH14_ENST00000262269.8_Frame_Shift_Del_p.R968fs|MYH14_ENST00000440075.2_Frame_Shift_Del_p.R968fs|MYH14_ENST00000598205.1_Frame_Shift_Del_p.R935fs|MYH14_ENST00000425460.1_Frame_Shift_Del_p.R935fs|MYH14_ENST00000376970.2_Frame_Shift_Del_p.R960fs|MYH14_ENST00000601313.1_Frame_Shift_Del_p.R968fs			Q7Z406	MYH14_HUMAN	myosin, heavy chain 14, non-muscle	927					actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|mitochondrion morphogenesis (GO:0070584)|neuronal action potential (GO:0019228)|regulation of cell shape (GO:0008360)|sensory perception of sound (GO:0007605)|skeletal muscle atrophy (GO:0014732)|skeletal muscle contraction (GO:0003009)|skeletal muscle tissue development (GO:0007519)|vocalization behavior (GO:0071625)	actomyosin (GO:0042641)|axon (GO:0030424)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|membrane (GO:0016020)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|stress fiber (GO:0001725)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(10)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	46		all_neural(266;0.0571)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00389)|GBM - Glioblastoma multiforme(134;0.0195)		GAGGAGACGCGGGGGAGGCTG	0.657																																					p.R968fs		Atlas-INDEL	.											.	MYH14	261	.	0			c.2902delC						.																																			SO:0001589	frameshift_variant	79784	exon24			.	AY165122	CCDS46151.1, CCDS54295.1, CCDS59411.1	19q13.33	2011-09-27	2009-11-19			ENSG00000105357		"""Myosins / Myosin superfamily : Class II"""	23212	protein-coding gene	gene with protein product		608568	"""myosin, heavy polypeptide 14"", ""myosin, heavy chain 14"""	DFNA4		12909352, 15015131, 17940200	Standard	NM_024729		Approved	FLJ13881, KIAA2034, MHC16, MYH17	uc010enu.1	Q7Z406		ENST00000596571.1:c.2780delG	chr19.hg19:g.50771494delG	ENSP00000472819:p.Arg927fs	219.0	0.0		161.0	10.0	NM_001145809	B0I1S2|C3TTN4|Q5CZ75|Q6XYE4|Q76B62|Q8WV23|Q96I22|Q9BT27|Q9BW35|Q9H882	Frame_Shift_Del	DEL	ENST00000596571.1	hg19	CCDS59411.1																																																																																			.	.		0.657	MYH14-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464710.2	NM_024729	
ZNF658B	401509	hgsc.bcm.edu	37	9	39445798	39445798	+	RNA	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:39445798delC	ENST00000602828.1	-	0	1390					NR_027861.1																						TAAGGTTTCTCCCCCGTGTGA	0.418																																					.		Atlas-INDEL	.											.	.	.	.	0			.						.																																					0	.			.																													chr9.hg19:g.39445798delC		277.0	0.0		234.0	15.0	.		RNA	DEL	ENST00000602828.1	hg19																																																																																				.	.		0.418	CTD-2173L22.4-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000467935.2		
COL11A1	1301	hgsc.bcm.edu	37	1	103364549	103364549	+	Splice_Site	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:103364549delC	ENST00000370096.3	-	55	4400	c.4088delG	c.(4087-4089)ggt>gt	p.G1363fs	COL11A1_ENST00000353414.4_Splice_Site_p.G1324fs|COL11A1_ENST00000512756.1_Splice_Site_p.G1247fs|COL11A1_ENST00000358392.2_Splice_Site_p.G1375fs	NM_001854.3	NP_001845.3	P12107	COBA1_HUMAN	collagen, type XI, alpha 1	1363	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)		TCCAGGAGGACCCTATAGACA	0.279																																					p.G1375fs		Atlas-INDEL	.											.	COL11A1	972	.	0			c.4125delT						.						41.0	42.0	42.0					1																	103364549		2201	4297	6498	SO:0001630	splice_region_variant	1301	exon55			.	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.4087-1G>-	chr1.hg19:g.103364549delC		174.0	0.0		171.0	13.0	NM_080629	B1ASK7|D3DT73|E9PCU0|Q14034|Q149N0|Q9UIT4|Q9UIT5|Q9UIT6	Frame_Shift_Del	DEL	ENST00000370096.3	hg19	CCDS778.1																																																																																			.	.		0.279	COL11A1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029997.1	NM_080630	Frame_Shift_Del
OR10H1	26539	hgsc.bcm.edu	37	19	15917904	15917904	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:15917904delT	ENST00000334920.2	-	1	1032	c.944delA	c.(943-945)aatfs	p.N315fs		NM_013940.2	NP_039228.1	Q9Y4A9	O10H1_HUMAN	olfactory receptor, family 10, subfamily H, member 1	315						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(8)|ovary(4)|skin(2)|urinary_tract(1)	29						CATCATTACATTTTTTTCTGG	0.438																																					p.N315fs		Atlas-INDEL	.											.	OR10H1	59	.	0			c.945delT						.						87.0	86.0	86.0					19																	15917904		2203	4300	6503	SO:0001589	frameshift_variant	26539	exon1			.	AC004510	CCDS12335.1	19p13.1	2012-08-09				ENSG00000186723		"""GPCR / Class A : Olfactory receptors"""	8172	protein-coding gene	gene with protein product							Standard	NM_013940		Approved		uc002nbq.2	Q9Y4A9		ENST00000334920.2:c.944delA	chr19.hg19:g.15917904delT	ENSP00000335596:p.Asn315fs	250.0	0.0		178.0	11.0	NM_013940	Q6IFQ2|Q96R59	Frame_Shift_Del	DEL	ENST00000334920.2	hg19	CCDS12335.1																																																																																			.	.		0.438	OR10H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460364.1		
MTBP	27085	hgsc.bcm.edu	37	8	121528183	121528183	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:121528183delA	ENST00000305949.1	+	18	2043	c.1998delA	c.(1996-1998)cgafs	p.R666fs		NM_022045.4	NP_071328.2	Q96DY7	MTBP_HUMAN	MDM2 binding protein	666	Interaction with MDM2. {ECO:0000250}.				cell cycle arrest (GO:0007050)|mitotic spindle checkpoint (GO:0071174)|negative regulation of cell proliferation (GO:0008285)|protein localization to kinetochore (GO:0034501)|traversing start control point of mitotic cell cycle (GO:0007089)	chromatin (GO:0000785)|kinetochore (GO:0000776)				NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	30	Lung NSC(37;5.68e-08)|Ovarian(258;0.00769)|all_neural(195;0.0804)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00503)			TGGATGACCGAAAAGCTTTGG	0.388																																					p.R666fs		Atlas-INDEL	.											MTBP,colon,carcinoma,0,1	MTBP	77	.	0			c.1997delG						.						85.0	84.0	84.0					8																	121528183		2203	4299	6502	SO:0001589	frameshift_variant	27085	exon18			.		CCDS6333.1	8q24.1-q24.2	2014-03-03	2014-03-03		ENSG00000172167	ENSG00000172167			7417	protein-coding gene	gene with protein product		605927	"""MDM2 (mouse double minute 2)-binding protein, 104kD"", ""Mdm2, transformed 3T3 cell double minute 2, p53 binding protein (mouse) binding protein, 104kDa"""			10906133, 11060448	Standard	NM_022045		Approved		uc003ypc.2	Q96DY7	OTTHUMG00000165040	ENST00000305949.1:c.1998delA	chr8.hg19:g.121528183delA	ENSP00000303398:p.Arg666fs	167.0	0.0		177.0	11.0	NM_022045	B4DUR5|Q9HA89	Frame_Shift_Del	DEL	ENST00000305949.1	hg19	CCDS6333.1																																																																																			.	.		0.388	MTBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381530.1	NM_022045	
GALNTL5	168391	hgsc.bcm.edu	37	7	151704993	151704993	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:151704993delT	ENST00000392800.2	+	7	1244	c.990delT	c.(988-990)gatfs	p.D330fs	GALNTL5_ENST00000431418.2_Frame_Shift_Del_p.D330fs|GALNTL5_ENST00000483959.1_3'UTR	NM_145292.3	NP_660335.2	Q7Z4T8	GLTL5_HUMAN	polypeptide N-acetylgalactosaminyltransferase-like 5	330	Catalytic subdomain B.				spermatid development (GO:0007286)	endosome (GO:0005768)|integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)			NS(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(11)|ovary(2)|prostate(2)|skin(3)	32	all_neural(206;0.187)	all_hematologic(28;0.0749)	OV - Ovarian serous cystadenocarcinoma(82;0.00427)	UCEC - Uterine corpus endometrioid carcinoma (81;0.18)|BRCA - Breast invasive adenocarcinoma(188;0.166)		AGGATATGGATTTTTGGGGAA	0.343																																					p.D330fs		Atlas-INDEL	.											.	GALNTL5	87	.	0			c.989delA						.						106.0	109.0	108.0					7																	151704993		2203	4300	6503	SO:0001589	frameshift_variant	168391	exon7			.	AF440400	CCDS5929.1	7q36.2	2014-03-13	2014-03-13	2004-07-28	ENSG00000106648	ENSG00000106648		"""Glycosyltransferase family 2 domain containing"""	21725	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase-like 5"""	615133	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 15"", ""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 5"""	GALNT15			Standard	NM_145292		Approved	GalNAc-T5L	uc003wkp.3	Q7Z4T8	OTTHUMG00000157306	ENST00000392800.2:c.990delT	chr7.hg19:g.151704993delT	ENSP00000376548:p.Asp330fs	173.0	0.0		155.0	10.0	NM_145292	Q75KN2|Q75MD3|Q8NCV4|Q8WW05|Q9UDR9	Frame_Shift_Del	DEL	ENST00000392800.2	hg19	CCDS5929.1																																																																																			.	.		0.343	GALNTL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348395.1	NM_145292	
GATA1	2623	hgsc.bcm.edu	37	X	48652397	48652397	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:48652397delC	ENST00000376670.3	+	6	1179	c.1068delC	c.(1066-1068)ggcfs	p.G356fs	GATA1_ENST00000376665.3_Intron	NM_002049.3	NP_002040.1	P15976	GATA1_HUMAN	GATA binding protein 1 (globin transcription factor 1)	356					basophil differentiation (GO:0030221)|blood coagulation (GO:0007596)|cell-cell signaling (GO:0007267)|cellular response to thyroid hormone stimulus (GO:0097067)|dendritic cell differentiation (GO:0097028)|embryonic hemopoiesis (GO:0035162)|eosinophil differentiation (GO:0030222)|eosinophil fate commitment (GO:0035854)|erythrocyte development (GO:0048821)|erythrocyte differentiation (GO:0030218)|in utero embryonic development (GO:0001701)|male gonad development (GO:0008584)|megakaryocyte differentiation (GO:0030219)|negative regulation of apoptotic process (GO:0043066)|negative regulation of bone mineralization (GO:0030502)|negative regulation of cell proliferation (GO:0008285)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|platelet aggregation (GO:0070527)|platelet formation (GO:0030220)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of definitive erythrocyte differentiation (GO:0010724)|regulation of glycoprotein biosynthetic process (GO:0010559)|transcription from RNA polymerase II promoter (GO:0006366)|transcriptional activation by promoter-enhancer looping (GO:0071733)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	C2H2 zinc finger domain binding (GO:0070742)|chromatin DNA binding (GO:0031490)|DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|enhancer sequence-specific DNA binding (GO:0001158)|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 regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(259)|large_intestine(8)|lung(9)|prostate(1)	283						TGACACTGGGCCCCCCAGGTA	0.647			"""Mis, F"""		megakaryoblastic leukemia of Downs Syndrome																																p.G356fs	Pancreas(9;429 505 11287 29617)	Atlas-INDEL	.		Dom	yes		X	Xp11.23	2623	GATA binding protein 1 (globin transcription factor 1)		L	.	GATA1	342	.	0			c.1067delG						.						36.0	33.0	34.0					X																	48652397		2203	4299	6502	SO:0001589	frameshift_variant	2623	exon6			.	X17254	CCDS14305.1	Xp11.23	2014-09-17	2001-11-28		ENSG00000102145	ENSG00000102145		"""GATA zinc finger domain containing"""	4170	protein-coding gene	gene with protein product	"""nuclear factor, erythroid 1"""	305371	"""GATA-binding protein 1 (globin transcription factor 1)"""	GF1		1999341	Standard	NM_002049		Approved	ERYF1, NFE1, GATA-1, NF-E1	uc004dkq.4	P15976	OTTHUMG00000021504	ENST00000376670.3:c.1068delC	chrX.hg19:g.48652397delC	ENSP00000365858:p.Gly356fs	179.0	0.0		159.0	10.0	NM_002049	Q96GB8	Frame_Shift_Del	DEL	ENST00000376670.3	hg19	CCDS14305.1																																																																																			.	.		0.647	GATA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056517.1	NM_002049	
UBR2	23304	hgsc.bcm.edu	37	6	42620286	42620286	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:42620286delT	ENST00000372899.1	+	25	2930	c.2672delT	c.(2671-2673)attfs	p.I891fs	UBR2_ENST00000372901.1_Frame_Shift_Del_p.I891fs|UBR2_ENST00000372883.3_Frame_Shift_Del_p.I395fs	NM_015255.2	NP_056070.1	Q8IWV8	UBR2_HUMAN	ubiquitin protein ligase E3 component n-recognin 2	891					cellular response to leucine (GO:0071233)|chromatin silencing (GO:0006342)|histone H2A ubiquitination (GO:0033522)|male meiosis I (GO:0007141)|negative regulation of TOR signaling (GO:0032007)|spermatogenesis (GO:0007283)|ubiquitin-dependent protein catabolic process (GO:0006511)	chromatin (GO:0000785)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	leucine binding (GO:0070728)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(10)|kidney(7)|large_intestine(14)|lung(22)|ovary(3)|pancreas(1)|skin(5)	64	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.004)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.196)			CTGGTTAACATTTTGCAGTCA	0.448																																					p.I891fs		Atlas-INDEL	.											.	UBR2	134	.	0			c.2671delA						.						237.0	206.0	217.0					6																	42620286		2203	4300	6503	SO:0001589	frameshift_variant	23304	exon25			.	BC024217	CCDS4870.1, CCDS55001.1	6p21.1	2008-06-23	2005-01-10	2005-01-12	ENSG00000024048	ENSG00000024048		"""Ubiquitin protein ligase E3 component n-recognins"""	21289	protein-coding gene	gene with protein product		609134	"""chromosome 6 open reading frame 133"""	C6orf133			Standard	NM_015255		Approved	bA49A4.1, dJ392M17.3, KIAA0349	uc011dur.2	Q8IWV8	OTTHUMG00000014703	ENST00000372899.1:c.2672delT	chr6.hg19:g.42620286delT	ENSP00000361990:p.Ile891fs	240.0	0.0		183.0	13.0	NM_015255	O15057|Q4VXK2|Q5TFH6|Q6P2I2|Q6ZUD0	Frame_Shift_Del	DEL	ENST00000372899.1	hg19	CCDS4870.1																																																																																			.	.		0.448	UBR2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040558.2	NM_015255	
ZHX1	11244	hgsc.bcm.edu	37	8	124266657	124266657	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:124266657delT	ENST00000522655.1	-	3	2070	c.1530delA	c.(1528-1530)aaafs	p.K510fs	ZHX1_ENST00000297857.2_Frame_Shift_Del_p.K510fs|ZHX1_ENST00000522595.1_5'Flank|ZHX1-C8ORF76_ENST00000357082.4_Intron|ZHX1_ENST00000395571.3_Frame_Shift_Del_p.K510fs			Q9UKY1	ZHX1_HUMAN	zinc fingers and homeoboxes 1	510	Required for interaction with NFYA.				cell differentiation (GO:0030154)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|liver(1)|lung(5)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	29	Lung NSC(37;1.25e-09)|Ovarian(258;0.0154)		STAD - Stomach adenocarcinoma(47;0.00527)			CACTAAACCATTTTTTAATCT	0.348																																					p.W511fs		Atlas-INDEL	.											.	ZHX1	89	.	0			c.1531delT						.						122.0	124.0	124.0					8																	124266657		2203	4300	6503	SO:0001589	frameshift_variant	11244	exon3			.	AF106862	CCDS6342.1	8q24.13	2012-03-09	2004-01-23		ENSG00000165156	ENSG00000165156		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	12871	protein-coding gene	gene with protein product		604764	"""zinc-fingers and homeoboxes 1"""			10441475	Standard	NM_001017926		Approved		uc003yqe.3	Q9UKY1	OTTHUMG00000165088	ENST00000522655.1:c.1530delA	chr8.hg19:g.124266657delT	ENSP00000428821:p.Lys510fs	192.0	0.0		210.0	14.0	NM_001017926	Q8IWD8	Frame_Shift_Del	DEL	ENST00000522655.1	hg19	CCDS6342.1																																																																																			.	.		0.348	ZHX1-003	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000381759.1		
TFPI	7035	hgsc.bcm.edu	37	2	188349646	188349646	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:188349646delA	ENST00000233156.3	-	5	721	c.427delT	c.(427-429)tatfs	p.Y143fs	AC007319.1_ENST00000453517.1_RNA|TFPI_ENST00000339091.4_Frame_Shift_Del_p.Y143fs|AC007319.1_ENST00000412276.1_RNA|TFPI_ENST00000409676.1_Frame_Shift_Del_p.Y143fs|TFPI_ENST00000392365.1_Frame_Shift_Del_p.Y143fs	NM_006287.4	NP_006278.1	P10646	TFPI1_HUMAN	tissue factor pathway inhibitor (lipoprotein-associated coagulation inhibitor)	143	BPTI/Kunitz inhibitor 2. {ECO:0000255|PROSITE-ProRule:PRU00031}.				blood coagulation (GO:0007596)|blood coagulation, extrinsic pathway (GO:0007598)|negative regulation of endopeptidase activity (GO:0010951)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|skin(1)	9			OV - Ovarian serous cystadenocarcinoma(117;0.0554)		Coagulation factor VIIa(DB00036)|Dalteparin(DB06779)	TGATTGTTATAAAAATACCTG	0.343																																					p.Y143fs		Atlas-INDEL	.											.	TFPI	66	.	0			c.428delA						.						93.0	92.0	92.0					2																	188349646		2202	4296	6498	SO:0001589	frameshift_variant	7035	exon5			.		CCDS2294.1, CCDS33349.1	2q32	2008-06-02			ENSG00000003436	ENSG00000003436			11760	protein-coding gene	gene with protein product	"""extrinsic pathway inhibitor"""	152310		LACI		1993173	Standard	XM_005246818		Approved	EPI, TFI, TFPI1	uc002upy.3	P10646	OTTHUMG00000132634	ENST00000233156.3:c.427delT	chr2.hg19:g.188349646delA	ENSP00000233156:p.Tyr143fs	246.0	0.0		165.0	10.0	NM_001032281	O95103|Q53TS4	Frame_Shift_Del	DEL	ENST00000233156.3	hg19	CCDS2294.1																																																																																			.	.		0.343	TFPI-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255881.1	NM_006287	
UGT2B28	54490	hgsc.bcm.edu	37	4	70156317	70156317	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:70156317delA	ENST00000335568.5	+	5	1100	c.1098delA	c.(1096-1098)ccafs	p.P366fs	UGT2B28_ENST00000511240.1_Intron	NM_053039.1	NP_444267.1	Q9BY64	UDB28_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B28	366					metabolic process (GO:0008152)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(16)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	31						TAGGTCTTCCAAAAACCAGAG	0.383																																					p.P366fs		Atlas-INDEL	.											.	UGT2B28	101	.	0			c.1097delC						.						53.0	55.0	54.0					4																	70156317		1999	4190	6189	SO:0001589	frameshift_variant	54490	exon5			.	AF177272	CCDS3528.1, CCDS56330.1	4q13.3	2011-02-09	2005-07-20		ENSG00000135226	ENSG00000135226		"""UDP glucuronosyltransferases"""	13479	protein-coding gene	gene with protein product		606497	"""UDP glycosyltransferase 2 family, polypeptide B28"""			11300766	Standard	NM_053039		Approved		uc003hej.3	Q9BY64	OTTHUMG00000129401	ENST00000335568.5:c.1098delA	chr4.hg19:g.70156317delA	ENSP00000334276:p.Pro366fs	210.0	0.0		185.0	12.0	NM_053039	B5BUM0|Q9BY62|Q9BY63	Frame_Shift_Del	DEL	ENST00000335568.5	hg19	CCDS3528.1																																																																																			.	.		0.383	UGT2B28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251557.2	NM_053039	
TSPAN12	23554	hgsc.bcm.edu	37	7	120450526	120450526	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:120450526delA	ENST00000222747.3	-	6	1066	c.459delT	c.(457-459)tttfs	p.F153fs	TSPAN12_ENST00000415871.1_Frame_Shift_Del_p.F153fs	NM_012338.3	NP_036470.1	O95859	TSN12_HUMAN	tetraspanin 12	153					angiogenesis (GO:0001525)|cell surface receptor signaling pathway (GO:0007166)|regulation of angiogenesis (GO:0045765)|retina layer formation (GO:0010842)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)				endometrium(3)|kidney(1)|lung(4)|ovary(1)|skin(1)	10	all_neural(327;0.117)					CCTCTCTCTGAAAAAAATTCC	0.398																																					p.Q154fs		Atlas-INDEL	.											.	TSPAN12	25	.	0			c.460delC						.						118.0	113.0	115.0					7																	120450526		2203	4300	6503	SO:0001589	frameshift_variant	23554	exon6			.	AF124522	CCDS5777.1	7q31.31	2013-02-14	2005-03-21	2005-03-21	ENSG00000106025	ENSG00000106025		"""Tetraspanins"""	21641	protein-coding gene	gene with protein product		613138	"""transmembrane 4 superfamily member 12"""	TM4SF12			Standard	NM_012338		Approved	NET-2	uc003vjk.3	O95859	OTTHUMG00000156980	ENST00000222747.3:c.459delT	chr7.hg19:g.120450526delA	ENSP00000222747:p.Phe153fs	164.0	0.0		154.0	11.0	NM_012338	A4D0V8|B4DRG6|Q549U9|Q8N5Y0	Frame_Shift_Del	DEL	ENST00000222747.3	hg19	CCDS5777.1																																																																																			.	.		0.398	TSPAN12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346951.1	NM_012338	
MICU3	286097	hgsc.bcm.edu	37	8	16939226	16939226	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:16939226delT	ENST00000318063.5	+	5	713	c.671delT	c.(670-672)cttfs	p.L224fs		NM_181723.2	NP_859074.1	Q86XE3	MICU3_HUMAN	mitochondrial calcium uptake family, member 3	224						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)										ACAGAATATCTTTTTCTTTTA	0.259																																					p.L224fs		Atlas-INDEL	.											.	EFHA2	60	.	0			c.670delC						.						34.0	32.0	33.0					8																	16939226		1995	3915	5910	SO:0001589	frameshift_variant	286097	exon5			.	BC032868	CCDS5999.1	8p22	2013-03-26	2013-03-26	2013-03-14	ENSG00000155970	ENSG00000155970		"""EF-hand domain containing"""	27820	protein-coding gene	gene with protein product		610633	"""EF hand domain family A2"", ""EF-hand domain family, member A2"""	EFHA2		23409044	Standard	NM_181723		Approved	DKFZp313A0139	uc003wxd.2	Q86XE3	OTTHUMG00000096965	ENST00000318063.5:c.671delT	chr8.hg19:g.16939226delT	ENSP00000321455:p.Leu224fs	171.0	0.0		110.0	13.0	NM_181723	Q8IYZ3	Frame_Shift_Del	DEL	ENST00000318063.5	hg19	CCDS5999.1																																																																																			.	.		0.259	MICU3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214031.1	NM_181723	
SCN1A	6323	hgsc.bcm.edu	37	2	166903299	166903299	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:166903299delT	ENST00000303395.4	-	9	1357	c.1358delA	c.(1357-1359)aagfs	p.K453fs	SCN1A_ENST00000423058.2_Frame_Shift_Del_p.K453fs|SCN1A_ENST00000375405.3_Frame_Shift_Del_p.K453fs|SCN1A_ENST00000409050.1_Frame_Shift_Del_p.K453fs|AC010127.3_ENST00000595647.1_RNA|AC010127.3_ENST00000595268.1_RNA|AC010127.3_ENST00000599041.1_RNA			P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha subunit	453					adult walking behavior (GO:0007628)|membrane depolarization during action potential (GO:0086010)|neuromuscular process controlling posture (GO:0050884)|neuronal action potential (GO:0019228)|neuronal action potential propagation (GO:0019227)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon initial segment (GO:0043194)|intercalated disc (GO:0014704)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	voltage-gated sodium channel activity (GO:0005248)			NS(4)|breast(5)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(33)|lung(87)|ovary(7)|pancreas(1)|prostate(9)|skin(23)|upper_aerodigestive_tract(2)|urinary_tract(1)	200					Dronedarone(DB04855)|Nitrazepam(DB01595)|Permethrin(DB04930)|Phenacemide(DB01121)|Phenazopyridine(DB01438)|Phenytoin(DB00252)|Topiramate(DB00273)|Valproic Acid(DB00313)|Zonisamide(DB00909)	CTCCTGTTGCTTTTTAAGCTG	0.468																																					p.K453fs		Atlas-INDEL	.											.	SCN1A	641	.	0			c.1359delG						.						104.0	92.0	96.0					2																	166903299		2203	4300	6503	SO:0001589	frameshift_variant	6323	exon9			.	AB093548	CCDS33316.1, CCDS54413.1, CCDS54414.1	2q24.3	2014-09-17	2007-01-23		ENSG00000144285	ENSG00000144285		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10585	protein-coding gene	gene with protein product		182389	"""febrile convulsions 3"""	SCN1, FEB3		8062593, 16382098, 11823106	Standard	NM_006920		Approved	Nav1.1, GEFSP2, HBSCI, NAC1, SMEI	uc021vsb.1	P35498	OTTHUMG00000044173	ENST00000303395.4:c.1358delA	chr2.hg19:g.166903299delT	ENSP00000303540:p.Lys453fs	244.0	0.0		172.0	12.0	NM_001165964	E9PG49|Q16172|Q585T7|Q8IUJ6|Q96LA3|Q9C008	Frame_Shift_Del	DEL	ENST00000303395.4	hg19	CCDS54413.1																																																																																			.	.		0.468	SCN1A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102661.1	NM_006920	
CLIP3	25999	hgsc.bcm.edu	37	19	36523228	36523228	+	Frame_Shift_Del	DEL	G	G	-	rs200629687		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:36523228delG	ENST00000360535.4	-	2	259	c.32delC	c.(31-33)ccgfs	p.P13fs	CLIP3_ENST00000593074.1_Frame_Shift_Del_p.P13fs|AC002116.7_ENST00000586962.1_RNA	NM_015526.2	NP_056341.1	Q96DZ5	CLIP3_HUMAN	CAP-GLY domain containing linker protein 3	13					chaperone-mediated protein transport (GO:0072321)|fat cell differentiation (GO:0045444)|membrane biogenesis (GO:0044091)|negative regulation of microtubule polymerization (GO:0031115)|peptidyl-L-cysteine S-palmitoylation (GO:0018230)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endocytosis (GO:0045807)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of glucose transport (GO:0010828)|positive regulation of protein phosphorylation (GO:0001934)	early endosome membrane (GO:0031901)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)|trans-Golgi network (GO:0005802)|trans-Golgi network membrane (GO:0032588)	ganglioside binding (GO:0035594)|microtubule binding (GO:0008017)			cervix(1)|endometrium(6)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	23	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			tcGGGGTGGCGGGGCCATCGG	0.677																																					p.P11fs		Atlas-INDEL	.											.	CLIP3	53	.	0			c.33delG						.						3.0	4.0	4.0					19																	36523228		1968	3910	5878	SO:0001589	frameshift_variant	25999	exon1			.	AJ427922	CCDS12486.1	19q13.12	2014-08-12			ENSG00000105270	ENSG00000105270		"""Ankyrin repeat domain containing"""	24314	protein-coding gene	gene with protein product	"""CLIP-170-related"", ""restin-like 1"""	607382				11854307	Standard	NM_015526		Approved	CLIPR-59, RSNL1	uc002ocz.2	Q96DZ5	OTTHUMG00000181747	ENST00000360535.4:c.32delC	chr19.hg19:g.36523228delG	ENSP00000353732:p.Pro13fs	153.0	0.0		149.0	11.0	NM_001199570	A8K0E4|Q8WWL1|Q96C99|Q9UFT7	Frame_Shift_Del	DEL	ENST00000360535.4	hg19	CCDS12486.1																																																																																			.	.		0.677	CLIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457426.1	NM_015526	
FANCG	2189	hgsc.bcm.edu	37	9	35078176	35078176	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:35078176delC	ENST00000378643.3	-	4	963	c.472delG	c.(472-474)gacfs	p.D158fs	FANCG_ENST00000476212.1_5'Flank	NM_004629.1	NP_004620.1	O15287	FANCG_HUMAN	Fanconi anemia, complementation group G	158					cell cycle checkpoint (GO:0000075)|DNA repair (GO:0006281)|mitochondrion organization (GO:0007005)|ovarian follicle development (GO:0001541)|response to radiation (GO:0009314)|spermatid development (GO:0007286)	cytoplasm (GO:0005737)|Fanconi anaemia nuclear complex (GO:0043240)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	damaged DNA binding (GO:0003684)			NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(7)|ovary(2)|prostate(3)|stomach(1)	28			LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)			AAGGCCAGGTCCCCAAGACGG	0.592			"""Mis, N, F, S"""			"""AML, leukemia"""		Involved in tolerance or repair of DNA crosslinks																													p.D158fs		Atlas-INDEL	.	yes	Rec		Fanconi anaemia G	9	9p13	2189	"""Fanconi anemia, complementation group G"""		L	.	FANCG	56	.	0			c.473delA						.						74.0	78.0	77.0					9																	35078176		2203	4300	6503	SO:0001589	frameshift_variant	2189	exon4			.	AJ007669	CCDS6574.1	9p13	2014-09-17			ENSG00000221829	ENSG00000221829		"""Fanconi anemia, complementation groups"""	3588	protein-coding gene	gene with protein product	"""DNA repair protein XRCC9"", ""X-ray repair, complementing defective, in Chinese hamster, 9"", ""X-ray repair complementing defective repair in Chinese hamster cells 9"""	602956		XRCC9		9256465, 9382107	Standard	NM_004629		Approved	FAG	uc003zwb.1	O15287	OTTHUMG00000019850	ENST00000378643.3:c.472delG	chr9.hg19:g.35078176delC	ENSP00000367910:p.Asp158fs	272.0	0.0		172.0	11.0	NM_004629		Frame_Shift_Del	DEL	ENST00000378643.3	hg19	CCDS6574.1																																																																																			.	.		0.592	FANCG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052269.1	NM_004629	
PRCP	5547	hgsc.bcm.edu	37	11	82536121	82536121	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:82536121delC	ENST00000313010.3	-	9	1512	c.1318delG	c.(1318-1320)gatfs	p.D440fs	PRCP_ENST00000393399.2_Frame_Shift_Del_p.D461fs|PRCP_ENST00000535099.1_Frame_Shift_Del_p.D335fs|PRCP_ENST00000525772.1_5'UTR	NM_005040.2	NP_005031.1	P42785	PCP_HUMAN	prolylcarboxypeptidase (angiotensinase C)	440					angiogenesis involved in wound healing (GO:0060055)|blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|energy homeostasis (GO:0097009)|glucose homeostasis (GO:0042593)|negative regulation of systemic arterial blood pressure (GO:0003085)|plasma kallikrein-kinin cascade (GO:0002353)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of reactive oxygen species metabolic process (GO:2000377)|regulation of thyroid hormone mediated signaling pathway (GO:0002155)	basal part of cell (GO:0045178)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	serine-type carboxypeptidase activity (GO:0004185)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(7)|prostate(1)|skin(2)|urinary_tract(1)	17						TCTGTGATATCCTTAGTTACT	0.448																																					p.D461fs		Atlas-INDEL	.											.	PRCP	69	.	0			c.1382delA						.						87.0	80.0	83.0					11																	82536121		2203	4300	6503	SO:0001589	frameshift_variant	5547	exon10			.	BC001500, BI827978, L13977	CCDS8262.1, CCDS41695.1	11q14	2005-10-04				ENSG00000137509			9344	protein-coding gene	gene with protein product		176785				8344943	Standard	NM_199418		Approved	PCP, HUMPCP	uc001ozr.3	P42785		ENST00000313010.3:c.1318delG	chr11.hg19:g.82536121delC	ENSP00000317362:p.Asp440fs	244.0	0.0		171.0	11.0	NM_199418	A8MU24|B2R7B7|B3KRK5|B5BU34	Frame_Shift_Del	DEL	ENST00000313010.3	hg19	CCDS8262.1																																																																																			.	.		0.448	PRCP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391792.1	NM_005040	
DLG2	1740	hgsc.bcm.edu	37	11	83183770	83183770	+	Splice_Site	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:83183770delT	ENST00000532653.1	-	18	2277	c.1975delA	c.(1975-1977)ata>ta	p.I659fs	DLG2_ENST00000376106.3_Splice_Site_p.I141fs|DLG2_ENST00000280241.8_Splice_Site_p.I716fs|DLG2_ENST00000543673.1_Splice_Site_p.I782fs|DLG2_ENST00000418306.2_Splice_Site_p.I556fs|DLG2_ENST00000398309.2_Splice_Site_p.I677fs|DLG2_ENST00000537455.1_Splice_Site_p.I427fs|DLG2_ENST00000404783.3_Splice_Site_p.I155fs|DLG2_ENST00000531015.1_Splice_Site_p.I644fs|DLG2_ENST00000330014.6_Splice_Site_p.I598fs|DLG2_ENST00000426717.2_Splice_Site_p.I141fs|DLG2_ENST00000376104.2_Splice_Site_p.I782fs|DLG2_ENST00000524982.1_Splice_Site_p.I673fs			Q14168	MPP2_HUMAN	discs, large homolog 2 (Drosophila)	371					nucleotide phosphorylation (GO:0046939)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	guanylate kinase activity (GO:0004385)			breast(1)|central_nervous_system(1)|endometrium(8)|kidney(3)|large_intestine(11)|lung(35)|ovary(3)|pancreas(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	71		all_cancers(6;0.00791)|Acute lymphoblastic leukemia(157;4.44e-05)|all_hematologic(158;0.0036)				GGAAACTTACTTTCCTGCCTT	0.428																																					.		Atlas-INDEL	.											.	DLG2	448	.	0			c.2029+1A>-						.						113.0	111.0	111.0					11																	83183770		1908	4100	6008	SO:0001630	splice_region_variant	1740	exon19			.	U32376	CCDS41696.1, CCDS44690.1, CCDS44691.1, CCDS44692.1, CCDS55782.1, CCDS73357.1	11q21	2012-04-17	2008-12-15		ENSG00000150672	ENSG00000150672		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	2901	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 58"""	603583	"""discs, large homolog 2, chapsyn-110 (Drosophila)"""			8755482, 9806853	Standard	NM_001142702		Approved	PSD-93, PSD93, chapsyn-110, PPP1R58	uc001pak.2	Q15700	OTTHUMG00000134309	ENST00000532653.1:c.1975+1A>-	chr11.hg19:g.83183770delT		219.0	0.0		161.0	10.0	NM_001364	B4DGE9|B4DRJ0|B7Z3G8|E7EV80|E7EV91|E7EX01|Q53ES9|Q5CZB9|Q9BQJ2	Splice_Site	DEL	ENST00000532653.1	hg19																																																																																				.	.		0.428	DLG2-009	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000259253.2	NM_001364	Frame_Shift_Del
SIKE1	80143	hgsc.bcm.edu	37	1	115321811	115321811	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:115321811delT	ENST00000060969.5	-	3	429	c.360delA	c.(358-360)aaafs	p.K120fs	SIKE1_ENST00000506320.1_5'UTR|SIKE1_ENST00000369528.5_Frame_Shift_Del_p.K124fs			Q9BRV8	SIKE1_HUMAN	suppressor of IKBKE 1	120					innate immune response (GO:0045087)	cytosol (GO:0005829)				endometrium(1)|kidney(2)|large_intestine(1)|lung(2)	6						CATCCACCGCTTTTTTAGCAA	0.398																																					p.A125fs		Atlas-INDEL	.											.	SIKE1	12	.	0			c.373delG						.						172.0	172.0	172.0					1																	115321811		2203	4300	6503	SO:0001589	frameshift_variant	80143	exon3			.	AK024821	CCDS878.1, CCDS41371.1	1p13.1	2009-08-13			ENSG00000052723	ENSG00000052723			26119	protein-coding gene	gene with protein product	"""suppressor of IKK epsilon"""	611656				16281057	Standard	NM_025073		Approved	FLJ21168, SIKE	uc001efp.4	Q9BRV8	OTTHUMG00000012061	ENST00000060969.5:c.360delA	chr1.hg19:g.115321811delT	ENSP00000060969:p.Lys120fs	195.0	0.0		150.0	11.0	NM_001102396	Q5TEZ7|Q5TEZ9|Q68DZ4|Q9H778	Frame_Shift_Del	DEL	ENST00000060969.5	hg19	CCDS878.1																																																																																			.	.		0.398	SIKE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033401.1	NM_025073	
PLBD1	79887	hgsc.bcm.edu	37	12	14693810	14693810	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:14693810delT	ENST00000240617.5	-	4	1098	c.446delA	c.(445-447)aatfs	p.N149fs		NM_024829.5	NP_079105.4	Q6P4A8	PLBL1_HUMAN	phospholipase B domain containing 1	149					glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|lysosome (GO:0005764)	hydrolase activity (GO:0016787)			central_nervous_system(1)|cervix(2)|endometrium(3)|kidney(3)|large_intestine(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	16						TTCTTTGATATTTTTCCGGGT	0.393																																					p.N149fs		Atlas-INDEL	.											.	PLBD1	36	.	0			c.447delT						.						166.0	162.0	163.0					12																	14693810		2203	4300	6503	SO:0001589	frameshift_variant	79887	exon4			.	BC000909	CCDS31751.1	12p13.1	2013-10-11			ENSG00000121316	ENSG00000121316			26215	protein-coding gene	gene with protein product	"""PLB homolog 1 (Dictyostelium)"""					15193148, 19019078	Standard	NM_024829		Approved	FLJ22662	uc001rcc.1	Q6P4A8	OTTHUMG00000168821	ENST00000240617.5:c.446delA	chr12.hg19:g.14693810delT	ENSP00000240617:p.Asn149fs	209.0	0.0		165.0	12.0	NM_024829	A8K4E9|Q9BVV3|Q9H625	Frame_Shift_Del	DEL	ENST00000240617.5	hg19	CCDS31751.1																																																																																			.	.		0.393	PLBD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401203.1	NM_024829	
APOF	319	hgsc.bcm.edu	37	12	56755066	56755066	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:56755066delC	ENST00000398189.3	-	2	1001	c.924delG	c.(922-924)gggfs	p.G308fs	APOF_ENST00000541105.1_Frame_Shift_Del_p.G290fs|STAT2_ENST00000418572.2_5'Flank|STAT2_ENST00000314128.4_5'Flank|STAT2_ENST00000557235.1_5'Flank	NM_001638.2	NP_001629.1	Q13790	APOF_HUMAN	apolipoprotein F	308					cholesterol efflux (GO:0033344)|cholesterol metabolic process (GO:0008203)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|triglyceride metabolic process (GO:0006641)	extracellular region (GO:0005576)|high-density lipoprotein particle (GO:0034364)|low-density lipoprotein particle (GO:0034362)	cholesterol binding (GO:0015485)|lipid transporter activity (GO:0005319)|receptor binding (GO:0005102)			breast(1)|lung(3)|prostate(1)|stomach(1)	6						TTATGGCCCACCCCCAGTAGG	0.448																																					p.W309fs		Atlas-INDEL	.											.	APOF	13	.	0			c.925delT						.						63.0	63.0	63.0					12																	56755066		1869	4084	5953	SO:0001589	frameshift_variant	319	exon2			.	L27050	CCDS44923.1	12q13	2013-01-24				ENSG00000175336		"""Apolipoproteins"""	615	protein-coding gene	gene with protein product		107760				8093033	Standard	NM_001638		Approved		uc001sle.1	Q13790		ENST00000398189.3:c.924delG	chr12.hg19:g.56755066delC	ENSP00000381250:p.Gly308fs	251.0	0.0		192.0	12.0	NM_001638	Q8TC13	Frame_Shift_Del	DEL	ENST00000398189.3	hg19	CCDS44923.1																																																																																			.	.		0.448	APOF-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410076.1		
FAT1	2195	hgsc.bcm.edu	37	4	187510197	187510197	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:187510197delG	ENST00000441802.2	-	27	13525	c.13316delC	c.(13315-13317)ccafs	p.P4439fs		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	4439					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						GAAGTCTTCTGGGGGTGGAGG	0.537										HNSCC(5;0.00058)																											p.P4439fs	Colon(197;1040 2055 4143 4984 49344)	Atlas-INDEL	.											.	FAT1	500	.	0			c.13317delA						.						217.0	223.0	221.0					4																	187510197		1989	4144	6133	SO:0001589	frameshift_variant	2195	exon27			.	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.13316delC	chr4.hg19:g.187510197delG	ENSP00000406229:p.Pro4439fs	224.0	0.0		229.0	15.0	NM_005245		Frame_Shift_Del	DEL	ENST00000441802.2	hg19	CCDS47177.1																																																																																			.	.		0.537	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245	
RSPH1	89765	hgsc.bcm.edu	37	21	43905780	43905780	+	Splice_Site	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr21:43905780delT	ENST00000291536.3	-	5	667	c.500delA	c.(499-501)aat>at	p.N167fs	RSPH1_ENST00000398352.3_Splice_Site_p.N129fs	NM_080860.2	NP_543136.1	Q8WYR4	RSPH1_HUMAN	radial spoke head 1 homolog (Chlamydomonas)	167					axoneme assembly (GO:0035082)|meiotic nuclear division (GO:0007126)	cytosol (GO:0005829)|motile cilium (GO:0031514)|nucleus (GO:0005634)				large_intestine(7)|lung(2)|ovary(1)|prostate(1)|stomach(1)	12						TGGACTTACATTTTTGTTCAA	0.493																																					p.N167fs	Esophageal Squamous(23;63 706 6286 10288 12913)	Atlas-INDEL	.											.	RSPH1	36	.	0			c.501delT						.						130.0	115.0	120.0					21																	43905780		2203	4300	6503	SO:0001630	splice_region_variant	89765	exon5			.	AB006536	CCDS13688.1, CCDS68210.1	21q22.3	2014-02-03	2007-06-25	2007-06-25	ENSG00000160188	ENSG00000160188			12371	protein-coding gene	gene with protein product	"""meichroacidin"""	609314	"""testis specific A2 homolog (mouse)"""	TSGA2		9403069, 9578619, 17451891	Standard	XM_005261208		Approved	FLJ32753, RSP44, RSPH10A, CILD24	uc002zbg.3	Q8WYR4	OTTHUMG00000086804	ENST00000291536.3:c.501+1A>-	chr21.hg19:g.43905780delT		267.0	0.0		199.0	12.0	NM_080860	A8MWV0|B2RBN9|Q3MJA1	Frame_Shift_Del	DEL	ENST00000291536.3	hg19	CCDS13688.1																																																																																			.	.		0.493	RSPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195379.1		Frame_Shift_Del
FKBP11	51303	hgsc.bcm.edu	37	12	49318434	49318434	+	Intron	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:49318434delG	ENST00000550765.1	-	3	594				FKBP11_ENST00000552878.1_Intron|CCDC65_ENST00000266984.5_Intron|FKBP11_ENST00000444214.2_Intron|FKBP11_ENST00000453172.2_Intron|AC073610.5_ENST00000537495.1_Intron|RP11-302B13.5_ENST00000398092.4_Intron	NM_016594.2	NP_057678.1	Q9NYL4	FKB11_HUMAN	FK506 binding protein 11, 19 kDa						chaperone-mediated protein folding (GO:0061077)|protein peptidyl-prolyl isomerization (GO:0000413)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	FK506 binding (GO:0005528)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			kidney(1)|large_intestine(3)|lung(1)	5						AAGCTTCCCTGGGGGGAGAGA	0.577											OREG0021773	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									.		Atlas-INDEL	.											.	FKBP11	12	.	0			c.196-2C>-						.																																			SO:0001627	intron_variant	51303	exon4			.	AF238079	CCDS8773.1, CCDS44870.1, CCDS44871.1	12q13.12	2008-08-04	2002-08-29			ENSG00000134285			18624	protein-coding gene	gene with protein product		610571	"""FK506 binding protein 11 (19 kDa)"""			12036304, 16596453	Standard	NM_016594		Approved	FKBP19	uc001rsp.3	Q9NYL4		ENST00000550765.1:c.196-3C>-	chr12.hg19:g.49318434delG		149.0	0.0	961	111.0	10.0	NM_016594	B4DWB7	Splice_Site	DEL	ENST00000550765.1	hg19	CCDS8773.1																																																																																			.	.		0.577	FKBP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408927.1	NM_016594	
ARHGAP30	257106	hgsc.bcm.edu	37	1	161017601	161017601	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:161017601delG	ENST00000368013.3	-	12	3530	c.3210delC	c.(3208-3210)cccfs	p.P1070fs	ARHGAP30_ENST00000368015.1_Frame_Shift_Del_p.P893fs|USF1_ENST00000435396.1_5'Flank|ARHGAP30_ENST00000368016.3_Frame_Shift_Del_p.P859fs|USF1_ENST00000368020.1_5'Flank|USF1_ENST00000368021.3_5'Flank	NM_001025598.1|NM_181720.2	NP_001020769.1|NP_859071.2	Q7Z6I6	RHG30_HUMAN	Rho GTPase activating protein 30	1070					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)	GTPase activator activity (GO:0005096)			breast(2)|cervix(3)|endometrium(4)|kidney(2)|large_intestine(4)|lung(6)|ovary(4)|pancreas(1)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	37	all_cancers(52;8.05e-20)|Breast(13;0.00188)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00122)			GGGGTTCTCTGGGGGGCAGAC	0.567																																					p.R1071fs		Atlas-INDEL	.											.	ARHGAP30	105	.	0			c.3211delA						.						68.0	75.0	72.0					1																	161017601		2203	4300	6503	SO:0001589	frameshift_variant	257106	exon12			.	AL832852	CCDS1215.1, CCDS30918.1, CCDS72958.1	1q23.3	2011-06-29			ENSG00000186517	ENSG00000186517		"""Rho GTPase activating proteins"""	27414	protein-coding gene	gene with protein product		614264					Standard	NM_001287602		Approved	FLJ00267	uc001fxl.3	Q7Z6I6	OTTHUMG00000031477	ENST00000368013.3:c.3210delC	chr1.hg19:g.161017601delG	ENSP00000356992:p.Pro1070fs	116.0	0.0		203.0	13.0	NM_001025598	Q5SY52|Q5SY53|Q5SY54|Q6ZML6|Q7Z3J8|Q86XI7	Frame_Shift_Del	DEL	ENST00000368013.3	hg19	CCDS30918.1																																																																																			.	.		0.567	ARHGAP30-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077090.2	NM_181720	
ADAMTS19	171019	hgsc.bcm.edu	37	5	128864241	128864241	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:128864241delA	ENST00000274487.4	+	6	1326	c.1181delA	c.(1180-1182)gaafs	p.E394fs	CTC-575N7.1_ENST00000503616.1_RNA	NM_133638.3	NP_598377.3	Q8TE59	ATS19_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 19	394	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.					proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|endometrium(10)|kidney(9)|large_intestine(14)|lung(34)|ovary(6)|pancreas(1)|prostate(6)|skin(6)	91		all_cancers(142;0.0148)|Prostate(80;0.0494)|Breast(839;0.238)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.222)		CATCATGGAGAAAAAATGCTA	0.353																																					p.E394fs		Atlas-INDEL	.											.	ADAMTS19	216	.	0			c.1180delG						.						67.0	71.0	70.0					5																	128864241		2203	4300	6503	SO:0001589	frameshift_variant	171019	exon6			.	AJ311904	CCDS4146.1	5q23.3	2009-04-27	2005-08-19		ENSG00000145808	ENSG00000145808		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	17111	protein-coding gene	gene with protein product		607513	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 19"""			11867212	Standard	NM_133638		Approved		uc003kvb.1	Q8TE59	OTTHUMG00000128990	ENST00000274487.4:c.1181delA	chr5.hg19:g.128864241delA	ENSP00000274487:p.Glu394fs	234.0	0.0		179.0	11.0	NM_133638		Frame_Shift_Del	DEL	ENST00000274487.4	hg19	CCDS4146.1																																																																																			.	.		0.353	ADAMTS19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250979.2	NM_133638	
PVRL3	25945	hgsc.bcm.edu	37	3	110852954	110852954	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:110852954delA	ENST00000485303.1	+	6	1817	c.1542delA	c.(1540-1542)ctafs	p.L514fs	PVRL3_ENST00000493615.1_Intron	NM_001243286.1|NM_015480.2	NP_001230215.1|NP_056295.1	Q9NQS3	PVRL3_HUMAN	poliovirus receptor-related 3	514					adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|fertilization (GO:0009566)|homophilic cell adhesion (GO:0007156)|lens morphogenesis in camera-type eye (GO:0002089)|retina morphogenesis in camera-type eye (GO:0060042)|single organismal cell-cell adhesion (GO:0016337)	apical junction complex (GO:0043296)|cell-cell adherens junction (GO:0005913)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	cell adhesion molecule binding (GO:0050839)|protein homodimerization activity (GO:0042803)			breast(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(7)|upper_aerodigestive_tract(3)	19						ATGAAGATCTAAAAATGGGAA	0.343																																					p.L514fs		Atlas-INDEL	.											.	PVRL3	78	.	0			c.1541delT						.						58.0	60.0	59.0					3																	110852954		2203	4294	6497	SO:0001589	frameshift_variant	25945	exon6			.	AF282874	CCDS2957.1, CCDS58842.1, CCDS58843.1	3q13	2013-01-29			ENSG00000177707	ENSG00000177707		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	17664	protein-coding gene	gene with protein product		607147				11024295	Standard	NM_015480		Approved	nectin-3, PPR3, PVRR3, DKFZP566B0846, CDw113, CD113	uc003dxt.2	Q9NQS3	OTTHUMG00000159239	ENST00000485303.1:c.1542delA	chr3.hg19:g.110852954delA	ENSP00000418070:p.Leu514fs	234.0	0.0		171.0	11.0	NM_015480	E9PFR0|Q6NVZ3|Q8NC05|Q8WVU4|Q9BVA9|Q9Y412	Frame_Shift_Del	DEL	ENST00000485303.1	hg19	CCDS2957.1																																																																																			.	.		0.343	PVRL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354045.1	NM_015480	
EPPK1	83481	hgsc.bcm.edu	37	8	144946981	144946981	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:144946981delC	ENST00000525985.1	-	2	512	c.441delG	c.(439-441)gggfs	p.G147fs				P58107	EPIPL_HUMAN	epiplakin 1	147						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(2)|lung(30)|ovary(2)|pancreas(1)|prostate(10)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(97;1.42e-10)|all_epithelial(106;1.99e-09)|Lung NSC(106;0.000126)|all_lung(105;0.000354)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;2.88e-40)|all cancers(56;1.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			GCCAGCTCTGCCCCAGGGCCC	0.697																																					p.Q148fs		Atlas-INDEL	.											.	EPPK1	199	.	0			c.442delC						.						15.0	18.0	17.0					8																	144946981		1905	4054	5959	SO:0001589	frameshift_variant	83481	exon1			.	AB051895	CCDS75800.1	8q24.3	2014-09-17				ENSG00000261150			15577	protein-coding gene	gene with protein product	"""epidermal autoantigen 450K"""	607553				11278896, 15671067	Standard	NM_031308		Approved	EPIPL1	uc003zaa.1	P58107		ENST00000525985.1:c.441delG	chr8.hg19:g.144946981delC	ENSP00000436337:p.Gly147fs	191.0	0.0		172.0	11.0	NM_031308	Q76E58|Q9NSU9	Frame_Shift_Del	DEL	ENST00000525985.1	hg19																																																																																				.	.		0.697	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308	
BCL9	607	hgsc.bcm.edu	37	1	147091647	147091647	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:147091647delC	ENST00000234739.3	+	8	2426	c.1686delC	c.(1684-1686)ctcfs	p.L562fs		NM_004326.2	NP_004317.2	O00512	BCL9_HUMAN	B-cell CLL/lymphoma 9	562	Pro-rich.				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)		p.L562L(1)		breast(1)|large_intestine(2)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	7	all_hematologic(923;0.115)					AGATGCGCCTCCCTGGATTTG	0.557			T	"""IGH@, IGL@"""	B-ALL																																p.L562fs		Atlas-INDEL	.		Dom	yes		1	1q21	607	B-cell CLL/lymphoma 9		L	.	BCL9	150	.	1	Substitution - coding silent(1)	kidney(1)	c.1685delT						.						67.0	73.0	71.0					1																	147091647		2203	4300	6503	SO:0001589	frameshift_variant	607	exon8			.	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.1686delC	chr1.hg19:g.147091647delC	ENSP00000234739:p.Leu562fs	121.0	0.0		163.0	10.0	NM_004326	Q5T489	Frame_Shift_Del	DEL	ENST00000234739.3	hg19	CCDS30833.1																																																																																			.	.		0.557	BCL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039468.1	NM_004326	
PRDM6	93166	hgsc.bcm.edu	37	5	122425749	122425749	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:122425749delA	ENST00000407847.4	+	2	454	c.40delA	c.(40-42)aaafs	p.K14fs	AC106786.1_ENST00000458103.2_RNA|AC106786.1_ENST00000442777.2_RNA	NM_001136239.1	NP_001129711.1	Q9NQX0	PRDM6_HUMAN	PR domain containing 6	14					negative regulation of smooth muscle cell differentiation (GO:0051151)|negative regulation of transcription, DNA-templated (GO:0045892)|neurogenesis (GO:0022008)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)|metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	7						GGCCTTCCTCAAAGTGGACCC	0.706																																					p.L13fs		Atlas-INDEL	.											.	PRDM6	26	.	0			c.39delC						.						3.0	4.0	4.0					5																	122425749		559	1401	1960	SO:0001589	frameshift_variant	93166	exon2			.	AF272898	CCDS47259.1	5q21-q23	2013-01-08			ENSG00000061455	ENSG00000061455		"""Zinc fingers, C2H2-type"""	9350	protein-coding gene	gene with protein product							Standard	NM_001136239		Approved		uc003kti.3	Q9NQX0	OTTHUMG00000150469	ENST00000407847.4:c.40delA	chr5.hg19:g.122425749delA	ENSP00000384725:p.Lys14fs	253.0	0.0		170.0	12.0	NM_001136239	B5MCJ4|Q9NQW9	Frame_Shift_Del	DEL	ENST00000407847.4	hg19	CCDS47259.1																																																																																			.	.		0.706	PRDM6-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318226.2	XM_049619	
PUM1	9698	hgsc.bcm.edu	37	1	31418315	31418315	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:31418315delC	ENST00000257075.5	-	18	2959	c.2866delG	c.(2866-2868)gaafs	p.E956fs	PUM1_ENST00000423018.2_Frame_Shift_Del_p.E814fs|PUM1_ENST00000373741.4_Frame_Shift_Del_p.E994fs|PUM1_ENST00000426105.2_Frame_Shift_Del_p.E958fs|PUM1_ENST00000424085.2_Frame_Shift_Del_p.E714fs|PUM1_ENST00000373742.2_Frame_Shift_Del_p.E897fs|PUM1_ENST00000373747.3_Frame_Shift_Del_p.E959fs|PUM1_ENST00000440538.2_Frame_Shift_Del_p.E932fs	NM_014676.2	NP_055491.1	Q14671	PUM1_HUMAN	pumilio RNA-binding family member 1	956	PUM-HD. {ECO:0000255|PROSITE- ProRule:PRU00318}.				membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of translation (GO:0006417)	cytosol (GO:0005829)	poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(2)|endometrium(8)|kidney(4)|large_intestine(8)|lung(17)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	48		Colorectal(325;0.0211)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|all_neural(195;0.0381)|Breast(348;0.0848)|Medulloblastoma(700;0.123)		STAD - Stomach adenocarcinoma(196;0.0232)|READ - Rectum adenocarcinoma(331;0.0681)		CCATCTAGTTCCCGAACCATC	0.403																																					p.E958fs		Atlas-INDEL	.											.	PUM1	107	.	0			c.2873delA						.						93.0	84.0	87.0					1																	31418315		2203	4300	6503	SO:0001589	frameshift_variant	9698	exon18			.	AF315592	CCDS338.1, CCDS44099.1	1p35.2	2013-09-02	2013-09-02		ENSG00000134644	ENSG00000134644			14957	protein-coding gene	gene with protein product		607204	"""pumilio (Drosophila) homolog 1"", ""pumilio homolog 1 (Drosophila)"""				Standard	NM_001020658		Approved	PUMH1, KIAA0099	uc001bsh.1	Q14671	OTTHUMG00000003795	ENST00000257075.5:c.2866delG	chr1.hg19:g.31418315delC	ENSP00000257075:p.Glu956fs	199.0	0.0		136.0	10.0	NM_001020658	A8K6W4|B4DG92|D3DPN3|E9PCJ0|Q53HH5|Q5VXY7|Q9HAN1	Frame_Shift_Del	DEL	ENST00000257075.5	hg19	CCDS338.1																																																																																			.	.		0.403	PUM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000010671.1		
IFT172	26160	hgsc.bcm.edu	37	2	27707958	27707958	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:27707958delA	ENST00000260570.3	-	3	326	c.223delT	c.(223-225)tctfs	p.S75fs	IFT172_ENST00000416524.2_Frame_Shift_Del_p.S54fs|IFT172_ENST00000359466.6_Frame_Shift_Del_p.S75fs	NM_015662.1	NP_056477.1	Q9UG01	IF172_HUMAN	intraflagellar transport 172	75					bone development (GO:0060348)|brain development (GO:0007420)|cilium assembly (GO:0042384)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|epidermis development (GO:0008544)|heart looping (GO:0001947)|hindgut development (GO:0061525)|left/right axis specification (GO:0070986)|limb development (GO:0060173)|negative regulation of epithelial cell proliferation (GO:0050680)|neural tube closure (GO:0001843)|Notch signaling pathway (GO:0007219)|palate development (GO:0060021)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|smoothened signaling pathway (GO:0007224)|spinal cord motor neuron differentiation (GO:0021522)	axoneme (GO:0005930)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|intraciliary transport particle B (GO:0030992)|sperm midpiece (GO:0097225)|sperm principal piece (GO:0097228)|vesicle (GO:0031982)				central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(17)|lung(17)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	43	Acute lymphoblastic leukemia(172;0.155)					GAATCAGGAGAAAAAGCCATG	0.373																																					p.S75fs		Atlas-INDEL	.											.	IFT172	119	.	0			c.224delC						.						157.0	157.0	157.0					2																	27707958		2203	4300	6503	SO:0001589	frameshift_variant	26160	exon3			.	AB033005	CCDS1755.1	2p23.3	2014-07-03	2014-07-03		ENSG00000138002	ENSG00000138002		"""Intraflagellar transport homologs"", ""WD repeat domain containing"""	30391	protein-coding gene	gene with protein product	"""wimple homolog"""	607386	"""intraflagellar transport 172 homolog (Chlamydomonas)"""			10788441, 10574461, 24140113	Standard	XM_005264254		Approved	SLB, wim, osm-1, NPHP17	uc002rku.3	Q9UG01	OTTHUMG00000128425	ENST00000260570.3:c.223delT	chr2.hg19:g.27707958delA	ENSP00000260570:p.Ser75fs	254.0	0.0		213.0	13.0	NM_015662	A5PKZ0|B2RNU5|Q86X44|Q96HW4|Q9UFJ9|Q9ULP1	Frame_Shift_Del	DEL	ENST00000260570.3	hg19	CCDS1755.1																																																																																			.	.		0.373	IFT172-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250213.2	NM_015662	
BHLHA15	168620	hgsc.bcm.edu	37	7	97841927	97841927	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:97841927delC	ENST00000609256.1	+	2	432	c.306delC	c.(304-306)atcfs	p.I102fs	BHLHA15_ENST00000314018.2_Frame_Shift_Del_p.I102fs			Q7RTS1	BHA15_HUMAN	basic helix-loop-helix family, member a15	102	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				calcium-mediated signaling (GO:0019722)|cell maturation (GO:0048469)|cell-cell signaling (GO:0007267)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|Golgi organization (GO:0007030)|intracellular distribution of mitochondria (GO:0048312)|mitochondrial calcium ion transport (GO:0006851)	nucleus (GO:0005634)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)										GTGAAGTCATCCCCCACGTGC	0.602																																					p.I102fs		Atlas-INDEL	.											.	BHLHA15	11	.	0			c.305delT						.						64.0	48.0	53.0					7																	97841927		2200	4297	6497	SO:0001589	frameshift_variant	168620	exon1			.	BK000276	CCDS5655.1	7q21.3	2009-01-12	2009-01-12	2009-01-12	ENSG00000180535	ENSG00000180535		"""Basic helix-loop-helix proteins"""	22265	protein-coding gene	gene with protein product		608606	"""basic helix-loop-helix domain containing, class B, 8"""	BHLHB8		14516699, 18557763	Standard	NM_177455		Approved	MIST1, bHLHa15	uc003upf.1	Q7RTS1	OTTHUMG00000154289	ENST00000609256.1:c.306delC	chr7.hg19:g.97841927delC	ENSP00000476312:p.Ile102fs	218.0	0.0		209.0	13.0	NM_177455	A4D271|Q14DE4	Frame_Shift_Del	DEL	ENST00000609256.1	hg19	CCDS5655.1																																																																																			.	.		0.602	BHLHA15-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000472733.1	NM_177455	
ADAMTS3	9508	hgsc.bcm.edu	37	4	73205236	73205236	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:73205236delT	ENST00000286657.4	-	5	872	c.836delA	c.(835-837)aacfs	p.N279fs		NM_014243.2	NP_055058.2	O15072	ATS3_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 3	279	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix organization (GO:0030198)|positive regulation of vascular endothelial growth factor signaling pathway (GO:1900748)|protein processing (GO:0016485)|vascular endothelial growth factor production (GO:0010573)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	endopeptidase activity (GO:0004175)|heparin binding (GO:0008201)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(21)|lung(33)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	76			Epithelial(6;4.97e-05)|OV - Ovarian serous cystadenocarcinoma(6;5.66e-05)|all cancers(17;0.000486)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			CAGGAGGTAGTTTTGGACGTG	0.443																																					p.N279fs	NSCLC(168;1941 2048 2918 13048 43078)	Atlas-INDEL	.											.	ADAMTS3	164	.	0			c.837delC						.						310.0	318.0	315.0					4																	73205236		2203	4300	6503	SO:0001589	frameshift_variant	9508	exon5			.	AB002364	CCDS3553.1	4q21	2008-07-29	2005-08-19		ENSG00000156140	ENSG00000156140	3.4.24.-	"""ADAM metallopeptidases with thrombospondin type 1 motif"""	219	protein-coding gene	gene with protein product		605011	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 3"""			10094461	Standard	NM_014243		Approved	KIAA0366, ADAMTS-4	uc003hgk.2	O15072	OTTHUMG00000129912	ENST00000286657.4:c.836delA	chr4.hg19:g.73205236delT	ENSP00000286657:p.Asn279fs	236.0	0.0		181.0	11.0	NM_014243	A1L3U9|Q9BXZ8	Frame_Shift_Del	DEL	ENST00000286657.4	hg19	CCDS3553.1																																																																																			.	.		0.443	ADAMTS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252164.2		
PAN2	9924	hgsc.bcm.edu	37	12	56716892	56716892	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:56716892delT	ENST00000425394.2	-	17	2835	c.2459delA	c.(2458-2460)aacfs	p.N820fs	PAN2_ENST00000548043.1_Frame_Shift_Del_p.N820fs|PAN2_ENST00000257931.5_Frame_Shift_Del_p.N819fs|PAN2_ENST00000440411.3_Frame_Shift_Del_p.N816fs	NM_001127460.2	NP_001120932	Q9HBH5	RDH14_HUMAN	PAN2 poly(A) specific ribonuclease subunit	142					osteoblast differentiation (GO:0001649)	endoplasmic reticulum (GO:0005783)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	oxidoreductase activity (GO:0016491)			NS(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|liver(1)|lung(18)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	41					Vitamin A(DB00162)	CAGCCCTTTGTTTTTGGTCAT	0.498																																					p.N820fs		Atlas-INDEL	.											.	PAN2	107	.	0			c.2460delC						.						162.0	160.0	161.0					12																	56716892		2203	4300	6503	SO:0001589	frameshift_variant	9924	exon17			.	AB014610	CCDS8915.1, CCDS44922.1, CCDS53802.1	12q13.2	2014-03-27	2014-03-27	2008-01-08		ENSG00000135473		"""Ubiquitin-specific peptidases"""	20074	protein-coding gene	gene with protein product	"""PAN2 homolog, PABP1 dependent poly A specific ribonuclease subunit (S. cerevisiae)"""		"""ubiquitin specific protease 52"", ""ubiquitin specific peptidase 52"", ""PAN2 poly(A) specific ribonuclease subunit homolog (S. cerevisiae)"""	USP52		12838346, 14583602	Standard	NM_014871		Approved	KIAA0710, hPAN2	uc001skx.3	Q504Q3	OTTHUMG00000170412	ENST00000425394.2:c.2459delA	chr12.hg19:g.56716892delT	ENSP00000401721:p.Asn820fs	188.0	0.0		150.0	10.0	NM_001127460		Frame_Shift_Del	DEL	ENST00000425394.2	hg19	CCDS44922.1																																																																																			.	.		0.498	PAN2-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409024.1	NM_014871	
CTSF	8722	hgsc.bcm.edu	37	11	66330266	66330266	+	IGR	DEL	G	G	-	rs374534956		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:66330266delG	ENST00000310325.5	-	0	2035				ACTN3_ENST00000502692.1_RNA|CTD-3074O7.2_ENST00000504911.1_lincRNA|ACTN3_ENST00000513398.1_RNA	NM_003793.3	NP_003784.2	Q9UBX1	CATF_HUMAN	cathepsin F						antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|proteolysis (GO:0006508)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|vesicle (GO:0031982)	cysteine-type endopeptidase activity (GO:0004197)			endometrium(1)|large_intestine(7)|lung(8)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	19						TATCCCTGCAGGGGGAAGTGG	0.602																																					.		Atlas-INDEL	.											.	ACTN3	27	.	0			c.2518-2G>-						.						139.0	153.0	149.0					11																	66330266		2194	4292	6486	SO:0001628	intergenic_variant	89	exon20			.	AF071749	CCDS8144.1	11q13.2	2012-02-29			ENSG00000174080	ENSG00000174080		"""Cathepsins"""	2531	protein-coding gene	gene with protein product		603539				9822672, 10318784	Standard	NM_003793		Approved	CATSF, CLN13	uc001oip.3	Q9UBX1	OTTHUMG00000167090		chr11.hg19:g.66330266delG		316.0	0.0		227.0	15.0	NM_001258371	B2R964|O95240|Q9NSU4|Q9UKQ5	Splice_Site	DEL	ENST00000310325.5	hg19	CCDS8144.1																																																																																			.	.		0.602	CTSF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393047.1	NM_003793	
CLEC4A	50856	hgsc.bcm.edu	37	12	8289428	8289428	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:8289428delG	ENST00000229332.5	+	5	742	c.495delG	c.(493-495)gtgfs	p.V165fs	CLEC4A_ENST00000345999.3_Frame_Shift_Del_p.V93fs|CLEC4A_ENST00000360500.3_Frame_Shift_Del_p.V126fs|CLEC4A_ENST00000352620.3_Frame_Shift_Del_p.V132fs	NM_016184.3|NM_194447.2|NM_194450.2	NP_057268.1|NP_919429.2|NP_919432.1	Q9UMR7	CLC4A_HUMAN	C-type lectin domain family 4, member A	165	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|innate immune response (GO:0045087)	integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)|transmembrane signaling receptor activity (GO:0004888)			cervix(1)|endometrium(3)|large_intestine(2)|lung(4)|prostate(1)	11				Kidney(36;0.0915)		CTTATTTTGTGGGGCTCTCAG	0.413																																					p.V165fs		Atlas-INDEL	.											.	CLEC4A	28	.	0			c.494delT						.						97.0	102.0	100.0					12																	8289428		2203	4300	6503	SO:0001589	frameshift_variant	50856	exon5			.	AJ133532	CCDS8590.1, CCDS8591.1, CCDS8592.1, CCDS41745.1	12p13	2005-02-09	2005-02-09	2005-02-09	ENSG00000111729	ENSG00000111729		"""C-type lectin domain containing"""	13257	protein-coding gene	gene with protein product		605306	"""C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 6"""	CLECSF6		10438934	Standard	NM_016184		Approved	DCIR, DDB27	uc001qtz.1	Q9UMR7	OTTHUMG00000168571	ENST00000229332.5:c.495delG	chr12.hg19:g.8289428delG	ENSP00000229332:p.Val165fs	274.0	0.0		176.0	11.0	NM_016184	Q17R69|Q8WXW9|Q9H2Z9|Q9NS33|Q9UI34	Frame_Shift_Del	DEL	ENST00000229332.5	hg19	CCDS8590.1																																																																																			.	.		0.413	CLEC4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400257.1	NM_194450	
PRRC2A	7916	hgsc.bcm.edu	37	6	31602310	31602310	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:31602310delT	ENST00000376033.2	+	20	5145	c.4911delT	c.(4909-4911)cctfs	p.P1637fs	PRRC2A_ENST00000376007.4_Frame_Shift_Del_p.P1637fs	NM_004638.3	NP_004629.3	P48634	PRC2A_HUMAN	proline-rich coiled-coil 2A	1637	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						CCCTGAGTCCTTTTGAGGATG	0.572																																					p.P1637fs		Atlas-INDEL	.											.	PRRC2A	152	.	0			c.4910delC						.						35.0	32.0	33.0					6																	31602310		1511	2708	4219	SO:0001589	frameshift_variant	7916	exon20			.	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.4911delT	chr6.hg19:g.31602310delT	ENSP00000365201:p.Pro1637fs	125.0	0.0		110.0	10.0	NM_004638	B0UX77|B0UZE9|B0UZL3|O95875|Q05BK4|Q4LE37|Q5SQ29|Q5SQ30|Q5ST84|Q5STX6|Q5STX7|Q68DW9|Q6P9P7|Q6PIN1|Q8MGQ9|Q96QC6	Frame_Shift_Del	DEL	ENST00000376033.2	hg19	CCDS4708.1																																																																																			.	.		0.572	PRRC2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259319.1	NM_080686	
SPAG17	200162	hgsc.bcm.edu	37	1	118583387	118583387	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:118583387delC	ENST00000336338.5	-	22	3197	c.3132delG	c.(3130-3132)gggfs	p.G1044fs		NM_206996.2	NP_996879.1	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	1044						cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)|sperm flagellum (GO:0036126)				NS(1)|biliary_tract(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(30)|liver(2)|lung(56)|ovary(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1)	123	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)		CTTCAATCTGCCCCCCATCAG	0.368																																					p.Q1045fs		Atlas-INDEL	.											SPAG17,mouth,carcinoma,0,1	SPAG17	263	.	0			c.3133delC						.						131.0	112.0	118.0					1																	118583387		2203	4300	6503	SO:0001589	frameshift_variant	200162	exon22			.		CCDS899.1	1p12	2014-01-21			ENSG00000155761	ENSG00000155761			26620	protein-coding gene	gene with protein product							Standard	NM_206996		Approved	FLJ34497, PF6, RP4-776P7.2, CT143	uc001ehk.2	Q6Q759	OTTHUMG00000012198	ENST00000336338.5:c.3132delG	chr1.hg19:g.118583387delC	ENSP00000337804:p.Gly1044fs	284.0	0.0		200.0	13.0	NM_206996	Q8NAZ1|Q9NT21	Frame_Shift_Del	DEL	ENST00000336338.5	hg19	CCDS899.1																																																																																			.	.		0.368	SPAG17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033723.1	NM_206996	
ASCC3	10973	hgsc.bcm.edu	37	6	101086535	101086535	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:101086535delT	ENST00000369162.2	-	25	4408	c.4064delA	c.(4063-4065)aagfs	p.K1355fs		NM_006828.2	NP_006819.2	Q8N3C0	ASCC3_HUMAN	activating signal cointegrator 1 complex subunit 3	1355	Helicase ATP-binding 2. {ECO:0000255|PROSITE-ProRule:PRU00541}.				cell proliferation (GO:0008283)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA duplex unwinding (GO:0032508)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|poly(A) RNA binding (GO:0044822)			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)		TGCAACAGTCTTTCCCGATCC	0.373																																					p.K1355fs		Atlas-INDEL	.											.	ASCC3	205	.	0			c.4065delG						.						136.0	124.0	128.0					6																	101086535		2203	4300	6503	SO:0001589	frameshift_variant	10973	exon25			.	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.4064delA	chr6.hg19:g.101086535delT	ENSP00000358159:p.Lys1355fs	233.0	0.0		165.0	11.0	NM_006828	E7EW23|O43738|Q4G1A0|Q5VTN2|Q9H1I9|Q9H5A2|Q9NTR0	Frame_Shift_Del	DEL	ENST00000369162.2	hg19	CCDS5046.1																																																																																			.	.		0.373	ASCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041632.2	NM_006828	
SLC39A12	221074	hgsc.bcm.edu	37	10	18331679	18331679	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:18331679delT	ENST00000377369.2	+	13	2266	c.1993delT	c.(1993-1995)tttfs	p.F665fs	SLC39A12_ENST00000377371.3_Frame_Shift_Del_p.F664fs|SLC39A12_ENST00000539911.1_Frame_Shift_Del_p.F531fs|SLC39A12_ENST00000377374.4_Frame_Shift_Del_p.F628fs	NM_001145195.1|NM_001282733.1|NM_001282734.1	NP_001138667.1|NP_001269662.1|NP_001269663.1	Q504Y0	S39AC_HUMAN	solute carrier family 39 (zinc transporter), member 12	665					regulation of microtubule polymerization (GO:0031113)|regulation of neuron projection development (GO:0010975)|signal transduction (GO:0007165)|zinc ion transmembrane import (GO:0071578)	integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	zinc ion transmembrane transporter activity (GO:0005385)			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|kidney(3)|large_intestine(5)|lung(38)|ovary(3)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	60						CTGGATGATGTTTCTCCTGCA	0.358																																					p.M664fs		Atlas-INDEL	.											.	SLC39A12	181	.	0			c.1992delG						.						117.0	112.0	114.0					10																	18331679		2203	4300	6503	SO:0001589	frameshift_variant	221074	exon13			.		CCDS7124.1, CCDS44362.1, CCDS60493.1, CCDS60494.1	10p12.33	2013-05-22			ENSG00000148482	ENSG00000148482		"""Solute carriers"""	20860	protein-coding gene	gene with protein product		608734	"""solute carrier family 39 (metal ion transporter), member 12"""			12659941	Standard	NM_152725		Approved	FLJ30499	uc001ipo.2	Q504Y0	OTTHUMG00000017759	ENST00000377369.2:c.1993delT	chr10.hg19:g.18331679delT	ENSP00000366586:p.Phe665fs	151.0	0.0		146.0	10.0	NM_001145195	B7ZL35|C9JJL4|Q49AN8|Q4G0L3|Q5VWV8|Q5VWV9|Q6NZY5|Q96NN4	Frame_Shift_Del	DEL	ENST00000377369.2	hg19	CCDS44362.1																																																																																			.	.		0.358	SLC39A12-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_152725	
LMBRD1	55788	hgsc.bcm.edu	37	6	70500277	70500277	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:70500277delA	ENST00000370577.3	-	2	386	c.157delT	c.(157-159)tctfs	p.S53fs	LMBRD1_ENST00000370570.1_5'UTR	NM_018368.3	NP_060838.3	Q9NUN5	LMBD1_HUMAN	LMBR1 domain containing 1	53					cobalamin metabolic process (GO:0009235)|insulin receptor internalization (GO:0038016)|negative regulation of glucose import (GO:0046325)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of protein kinase B signaling (GO:0051898)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	clathrin-coated endocytic vesicle (GO:0045334)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cobalamin binding (GO:0031419)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(7)|lung(11)|ovary(2)|upper_aerodigestive_tract(1)	31						ATTGCTAGAGAAAAAATTGCT	0.343																																					p.S53fs		Atlas-INDEL	.											LMBRD1,NS,carcinoma,0,1	LMBRD1	61	.	0			c.158delC						.						121.0	128.0	126.0					6																	70500277		2203	4300	6503	SO:0001589	frameshift_variant	55788	exon2			.	AF113224	CCDS4969.1	6q13	2011-05-12	2005-07-25	2005-07-25	ENSG00000168216	ENSG00000168216			23038	protein-coding gene	gene with protein product		612625	"""chromosome 6 open reading frame 209"""	C6orf209		19136951	Standard	NM_018368		Approved	FLJ11240, bA810I22.1, cblF	uc003pfa.3	Q9NUN5	OTTHUMG00000014985	ENST00000370577.3:c.157delT	chr6.hg19:g.70500277delA	ENSP00000359609:p.Ser53fs	186.0	0.0		123.0	10.0	NM_018368	A8K204|E1P531|Q5VUN6|Q86Y70|Q96FW4|Q9BY56|Q9NZD6	Frame_Shift_Del	DEL	ENST00000370577.3	hg19	CCDS4969.1																																																																																			.	.		0.343	LMBRD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041124.1	NM_018368	
CEP128	145508	hgsc.bcm.edu	37	14	81307070	81307070	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr14:81307070delC	ENST00000555265.1	-	10	1180	c.805delG	c.(805-807)gcafs	p.A269fs	CEP128_ENST00000281129.3_Frame_Shift_Del_p.A269fs|CEP128_ENST00000216517.6_Frame_Shift_Del_p.A269fs			Q6ZU80	CE128_HUMAN	centrosomal protein 128kDa	269						centriole (GO:0005814)|cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|spindle pole (GO:0000922)				NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(22)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	51						TTTTTTATTGCCCCCTCATGC	0.338																																					p.A269fs		Atlas-INDEL	.											.	CEP128	146	.	0			c.806delC						.						233.0	222.0	226.0					14																	81307070		2202	4299	6501	SO:0001589	frameshift_variant	145508	exon9			.	AK056756	CCDS32130.1	14q31.1	2014-02-20	2011-05-06	2011-05-06	ENSG00000100629	ENSG00000100629			20359	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 61"", ""chromosome 14 open reading frame 145"""	C14orf61, C14orf145		21399614	Standard	NM_152446		Approved		uc001xux.2	Q6ZU80		ENST00000555265.1:c.805delG	chr14.hg19:g.81307070delC	ENSP00000451162:p.Ala269fs	209.0	0.0		180.0	11.0	NM_152446	B9EK52|Q86X97|Q96ML4	Frame_Shift_Del	DEL	ENST00000555265.1	hg19	CCDS32130.1																																																																																			.	.		0.338	CEP128-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413415.1	NM_152446	
EDEM3	80267	hgsc.bcm.edu	37	1	184680896	184680896	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:184680896delT	ENST00000318130.8	-	15	1918	c.1652delA	c.(1651-1653)aatfs	p.N551fs	EDEM3_ENST00000367512.3_Frame_Shift_Del_p.N508fs|EDEM3_ENST00000466392.1_5'Flank	NM_025191.3	NP_079467.3	Q9BZQ6	EDEM3_HUMAN	ER degradation enhancer, mannosidase alpha-like 3	551					cellular protein metabolic process (GO:0044267)|glycoprotein catabolic process (GO:0006516)|post-translational protein modification (GO:0043687)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|response to unfolded protein (GO:0006986)	endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)	calcium ion binding (GO:0005509)|glycoprotein endo-alpha-1,2-mannosidase activity (GO:0004569)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)			breast(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(14)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						ATCCACCACATTTTTCAAGGG	0.363																																					p.N551fs		Atlas-INDEL	.											.	EDEM3	63	.	0			c.1653delT						.						116.0	108.0	110.0					1																	184680896		2203	4300	6503	SO:0001589	frameshift_variant	80267	exon15			.	AF288393	CCDS1363.2	1q25	2008-02-05	2006-03-31	2006-03-31	ENSG00000116406	ENSG00000116406			16787	protein-coding gene	gene with protein product		610214	"""chromosome 1 open reading frame 22"""	C1orf22		15537790, 15579471	Standard	NM_025191		Approved		uc010pok.2	Q9BZQ6	OTTHUMG00000035387	ENST00000318130.8:c.1652delA	chr1.hg19:g.184680896delT	ENSP00000318147:p.Asn551fs	130.0	0.0		163.0	11.0	NM_025191	B2RCH6|B7ZLZ2|Q0VGM5|Q5TEZ0|Q9HCW1|Q9UFV7	Frame_Shift_Del	DEL	ENST00000318130.8	hg19	CCDS1363.2																																																																																			.	.		0.363	EDEM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085785.3	NM_025191	
MAP3K4	4216	hgsc.bcm.edu	37	6	161532936	161532936	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:161532936delA	ENST00000392142.4	+	24	4613	c.4465delA	c.(4465-4467)aaafs	p.K1489fs	MAP3K4_ENST00000366919.2_Frame_Shift_Del_p.K1439fs|MAP3K4_ENST00000348824.7_Frame_Shift_Del_p.K1435fs|MAP3K4_ENST00000366920.2_Frame_Shift_Del_p.K1485fs	NM_005922.2	NP_005913	Q9Y6R4	M3K4_HUMAN	mitogen-activated protein kinase kinase kinase 4	1489	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPKK activity (GO:0000186)|chorionic trophoblast cell differentiation (GO:0060718)|intracellular signal transduction (GO:0035556)|male germ-line sex determination (GO:0019100)|MAPK cascade (GO:0000165)|placenta development (GO:0001890)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of p38MAPK cascade (GO:1900745)|regulation of gene expression (GO:0010468)|response to UV-C (GO:0010225)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|metal ion binding (GO:0046872)			breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|lung(28)|ovary(3)|skin(2)|stomach(1)	77		Breast(66;0.000776)|Ovarian(120;0.0367)|Prostate(117;0.0771)		OV - Ovarian serous cystadenocarcinoma(65;1.85e-18)|BRCA - Breast invasive adenocarcinoma(81;3.04e-05)		AGTAAAGCTCAAAAACAATGC	0.468																																					p.L1488fs		Atlas-INDEL	.											.	MAP3K4	364	.	0			c.4464delC						.						202.0	187.0	192.0					6																	161532936		2203	4300	6503	SO:0001589	frameshift_variant	4216	exon24			.	AF002715	CCDS34565.1, CCDS34566.1, CCDS75544.1	6q26	2012-10-02			ENSG00000085511	ENSG00000085511		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6856	protein-coding gene	gene with protein product		602425		MEKK4		9305639	Standard	XM_005266988		Approved	MTK1, MAPKKK4, KIAA0213	uc003qtn.3	Q9Y6R4	OTTHUMG00000015968	ENST00000392142.4:c.4465delA	chr6.hg19:g.161532936delA	ENSP00000375986:p.Lys1489fs	392.0	0.0		298.0	18.0	NM_005922	A6H8W0|B7ZLD3|B9EG75|Q5VTT8|Q5VTT9|Q92612|Q9H408	Frame_Shift_Del	DEL	ENST00000392142.4	hg19	CCDS34565.1																																																																																			.	.		0.468	MAP3K4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042988.3		
FPGT-TNNI3K	100526835	hgsc.bcm.edu	37	1	74901809	74901809	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:74901809delT	ENST00000370899.3	+	20	2158	c.2121delT	c.(2119-2121)gatfs	p.D707fs	FPGT-TNNI3K_ENST00000557284.2_Frame_Shift_Del_p.D720fs|TNNI3K_ENST00000370891.2_Frame_Shift_Del_p.D707fs|TNNI3K_ENST00000326637.3_Frame_Shift_Del_p.D606fs	NM_001199327.1	NP_001186256			FPGT-TNNI3K readthrough																		TGGTGGCAGATTTTGGAGGTG	0.373																																					p.D707fs		Atlas-INDEL	.											.	.	.	.	0			c.2120delA						.						139.0	127.0	131.0					1																	74901809		2203	4300	6503	SO:0001589	frameshift_variant	100526835	exon20			.			1p31.3	2014-03-14			ENSG00000259030	ENSG00000259030			42952	other	readthrough							Standard	NM_001112808		Approved		uc001dge.2		OTTHUMG00000166281	ENST00000370899.3:c.2121delT	chr1.hg19:g.74901809delT	ENSP00000359936:p.Asp707fs	272.0	0.0		235.0	16.0	NM_001199327		Frame_Shift_Del	DEL	ENST00000370899.3	hg19																																																																																				.	.		0.373	FPGT-TNNI3K-003	NOVEL	basic|appris_candidate|readthrough_transcript|exp_conf	protein_coding	protein_coding	OTTHUMT00000026438.3		
OR5T2	219464	hgsc.bcm.edu	37	11	55999651	55999651	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:55999651delT	ENST00000313264.4	-	1	1086	c.1011delA	c.(1009-1011)aaafs	p.K337fs		NM_001004746.1	NP_001004746.1	Q8NGG2	OR5T2_HUMAN	olfactory receptor, family 5, subfamily T, member 2	337						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(6)|kidney(1)|large_intestine(5)|lung(22)|ovary(2)|prostate(1)|skin(1)|stomach(3)	41	Esophageal squamous(21;0.00448)					TCATTGAGTCTTTTACATCTT	0.338																																					p.D338fs		Atlas-INDEL	.											.	OR5T2	107	.	0			c.1012delG						.						71.0	68.0	69.0					11																	55999651		2201	4296	6497	SO:0001589	frameshift_variant	219464	exon1			.	AB065838	CCDS31523.1	11q11	2012-08-09			ENSG00000181718	ENSG00000181718		"""GPCR / Class A : Olfactory receptors"""	15296	protein-coding gene	gene with protein product							Standard	NM_001004746		Approved		uc010rjc.2	Q8NGG2	OTTHUMG00000166851	ENST00000313264.4:c.1011delA	chr11.hg19:g.55999651delT	ENSP00000323688:p.Lys337fs	160.0	0.0		155.0	10.0	NM_001004746	B9EGX5|Q6IFC8	Frame_Shift_Del	DEL	ENST00000313264.4	hg19	CCDS31523.1																																																																																			.	.		0.338	OR5T2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391598.1	NM_001004746	
RBM33	155435	hgsc.bcm.edu	37	7	155537920	155537920	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:155537920delA	ENST00000401878.3	+	14	2801	c.2603delA	c.(2602-2604)caafs	p.Q868fs	RBM33_ENST00000341148.3_5'Flank	NM_053043.2	NP_444271.2	Q96EV2	RBM33_HUMAN	RNA binding motif protein 33	868							nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(3)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(4)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	27	all_neural(206;0.101)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.011)	UCEC - Uterine corpus endometrioid carcinoma (81;0.2)		CAGGTCAGACAAAATGTGAAG	0.498																																					p.Q868fs		Atlas-INDEL	.											.	RBM33	157	.	0			c.2602delC						.						54.0	45.0	48.0					7																	155537920		2203	4300	6503	SO:0001589	frameshift_variant	155435	exon14			.	AL832196	CCDS5941.2	7q36.3	2013-02-12			ENSG00000184863	ENSG00000184863		"""RNA binding motif (RRM) containing"""	27223	protein-coding gene	gene with protein product			"""proline rich 8"""	PRR8			Standard	NM_053043		Approved	DKFZp686F102, MGC20460, DKFZp434D1319	uc010lqk.1	Q96EV2	OTTHUMG00000150260	ENST00000401878.3:c.2603delA	chr7.hg19:g.155537920delA	ENSP00000384160:p.Gln868fs	258.0	0.0		225.0	15.0	NM_053043	A4D244|B5MC24|Q52LF5|Q75LN9|Q75ML5|Q9NSV0	Frame_Shift_Del	DEL	ENST00000401878.3	hg19	CCDS5941.2																																																																																			.	.		0.498	RBM33-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317225.3	NM_001008408	
TLK1	9874	hgsc.bcm.edu	37	2	171923383	171923383	+	Intron	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:171923383delA	ENST00000431350.2	-	4	735				TLK1_ENST00000521943.1_Intron|TLK1_ENST00000360843.3_Intron|TLK1_ENST00000486857.1_Intron|TLK1_ENST00000434911.2_Frame_Shift_Del_p.L4fs|TLK1_ENST00000442919.2_Intron			Q9UKI8	TLK1_HUMAN	tousled-like kinase 1						cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|chromatin modification (GO:0016568)|intracellular protein transport (GO:0006886)|intracellular signal transduction (GO:0035556)|protein phosphorylation (GO:0006468)|regulation of chromatin assembly or disassembly (GO:0001672)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(8)|liver(3)|lung(10)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	33						ATACAAGAATAAAACAGCCAT	0.323																																					p.L4fs		Atlas-INDEL	.											.	TLK1	134	.	0			c.12delA						.						27.0	25.0	26.0					2																	171923383		1520	3492	5012	SO:0001627	intron_variant	9874	exon1			.	AB004885	CCDS2241.1, CCDS46447.1, CCDS46448.1	2q31.1	2010-04-19			ENSG00000198586	ENSG00000198586			11841	protein-coding gene	gene with protein product		608438				9427565, 12660173	Standard	NM_012290		Approved	KIAA0137, PKU-BETA	uc002ugp.2	Q9UKI8	OTTHUMG00000132243	ENST00000431350.2:c.331-5717T>-	chr2.hg19:g.171923383delA		229.0	0.0		167.0	11.0	NM_001136555	B3KR15|B4DX87|Q14150|Q8N591|Q9NYH2|Q9Y4F6	Frame_Shift_Del	DEL	ENST00000431350.2	hg19	CCDS2241.1																																																																																			.	.		0.323	TLK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255314.1	NM_012290	
TULP4	56995	hgsc.bcm.edu	37	6	158923160	158923160	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:158923160delC	ENST00000367097.3	+	13	3822	c.2465delC	c.(2464-2466)gccfs	p.A822fs	TULP4_ENST00000367094.2_Intron	NM_020245.4	NP_064630.2	Q9NRJ4	TULP4_HUMAN	tubby like protein 4	822					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)|regulation of transcription, DNA-templated (GO:0006355)|response to nutrient (GO:0007584)	cytoplasm (GO:0005737)	sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(7)|kidney(2)|large_intestine(15)|lung(17)|ovary(1)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	49		Breast(66;0.000781)|Ovarian(120;0.0308)|Lung SC(201;0.164)|Prostate(117;0.171)		OV - Ovarian serous cystadenocarcinoma(65;1.64e-18)|BRCA - Breast invasive adenocarcinoma(81;2.67e-05)		GTCTTTAGTGCCCCCCAGGAG	0.672																																					p.A822fs		Atlas-INDEL	.											.,1	TULP4	137	.	0			c.2464delG						.																																			SO:0001589	frameshift_variant	56995	exon13			.		CCDS34561.1, CCDS34562.1	6q25-q26	2013-01-10			ENSG00000130338	ENSG00000130338		"""WD repeat domain containing"""	15530	protein-coding gene	gene with protein product						11595174	Standard	NM_020245		Approved	TUSP, KIAA1397	uc003qrf.3	Q9NRJ4	OTTHUMG00000015910	ENST00000367097.3:c.2465delC	chr6.hg19:g.158923160delC	ENSP00000356064:p.Ala822fs	176.0	0.0		147.0	11.0	NM_020245	Q5T3M2|Q5T3M3|Q9HD22|Q9P2F0	Frame_Shift_Del	DEL	ENST00000367097.3	hg19	CCDS34561.1																																																																																			.	.		0.672	TULP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042869.1	NM_020245	
RBM46	166863	hgsc.bcm.edu	37	4	155720297	155720297	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:155720297delA	ENST00000281722.3	+	4	1218	c.983delA	c.(982-984)gaafs	p.E328fs	RBM46_ENST00000510397.1_Frame_Shift_Del_p.E328fs|RBM46_ENST00000514866.1_Frame_Shift_Del_p.E328fs	NM_144979.3	NP_659416.1	Q8TBY0	RBM46_HUMAN	RNA binding motif protein 46	328							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)				CCAAATTCTGAAAATCTGATT	0.413																																					p.E328fs		Atlas-INDEL	.											.	RBM46	76	.	0			c.982delG						.						64.0	68.0	67.0					4																	155720297		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.983delA	chr4.hg19:g.155720297delA	ENSP00000281722:p.Glu328fs	226.0	0.0		198.0	12.0	NM_144979	B3KWU8|B4DZ27	Frame_Shift_Del	DEL	ENST00000281722.3	hg19	CCDS3790.1																																																																																			.	.		0.413	RBM46-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365259.1	NM_144979	
ABHD5	51099	hgsc.bcm.edu	37	3	43753215	43753215	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:43753215delT	ENST00000458276.2	+	4	644	c.521delT	c.(520-522)attfs	p.I174fs		NM_016006.4	NP_057090.2	Q8WTS1	ABHD5_HUMAN	abhydrolase domain containing 5	174					cell differentiation (GO:0030154)|fatty acid metabolic process (GO:0006631)|negative regulation of sequestering of triglyceride (GO:0010891)|phosphatidic acid biosynthetic process (GO:0006654)|positive regulation of lipoprotein lipase activity (GO:0051006)|positive regulation of triglyceride catabolic process (GO:0010898)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|lipid particle (GO:0005811)|nucleus (GO:0005634)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)|lysophosphatidic acid acyltransferase activity (GO:0042171)			kidney(3)|large_intestine(2)|liver(2)|lung(5)|ovary(1)|skin(1)	14		Renal(3;0.0134)		KIRC - Kidney renal clear cell carcinoma(197;0.0546)|Kidney(197;0.0687)		AATCATCTCATTTTAGTGGAG	0.408																																					p.I174fs		Atlas-INDEL	.											.	ABHD5	33	.	0			c.520delA						.						102.0	96.0	98.0					3																	43753215		2203	4300	6503	SO:0001589	frameshift_variant	51099	exon4			.	AF007132	CCDS2711.1	3p21.33	2012-05-16			ENSG00000011198	ENSG00000011198		"""Abhydrolase domain containing"""	21396	protein-coding gene	gene with protein product		604780				11590543, 18606822	Standard	NM_016006		Approved	CGI-58, NCIE2	uc003cmx.3	Q8WTS1	OTTHUMG00000133039	ENST00000458276.2:c.521delT	chr3.hg19:g.43753215delT	ENSP00000390849:p.Ile174fs	211.0	0.0		151.0	11.0	NM_016006	B2R9K0|Q9Y369	Frame_Shift_Del	DEL	ENST00000458276.2	hg19	CCDS2711.1																																																																																			.	.		0.408	ABHD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256644.2	NM_016006	
ABCF2	10061	hgsc.bcm.edu	37	7	150923507	150923507	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:150923507delT	ENST00000287844.2	-	2	147	c.38delA	c.(37-39)aagfs	p.K14fs	ABCF2_ENST00000222388.2_Frame_Shift_Del_p.K14fs	NM_007189.1	NP_009120.1	Q9UG63	ABCF2_HUMAN	ATP-binding cassette, sub-family F (GCN20), member 2	14					transport (GO:0006810)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|membrane (GO:0016020)|mitochondrial envelope (GO:0005740)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|transporter activity (GO:0005215)			breast(1)|central_nervous_system(1)|large_intestine(4)|lung(15)|ovary(1)|skin(2)	24			OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		AGCCTCCTTCTTTTTGGCTGC	0.512																																					p.K13fs		Atlas-INDEL	.											.	ABCF2	54	.	0			c.39delG						.						119.0	115.0	116.0					7																	150923507		2203	4300	6503	SO:0001589	frameshift_variant	10061	exon2			.	AJ005016	CCDS5922.1, CCDS5923.1	7q36.1	2012-03-14			ENSG00000033050	ENSG00000033050		"""ATP binding cassette transporters / subfamily F"""	71	protein-coding gene	gene with protein product		612510				8894702	Standard	NM_007189		Approved	EST133090, ABC28, M-ABC1, HUSSY-18	uc003wjo.1	Q9UG63	OTTHUMG00000154570	ENST00000287844.2:c.38delA	chr7.hg19:g.150923507delT	ENSP00000287844:p.Lys14fs	202.0	0.0		202.0	13.0	NM_005692	O60864|Q75MJ0|Q75MJ1|Q96TE8	Frame_Shift_Del	DEL	ENST00000287844.2	hg19	CCDS5923.1																																																																																			.	.		0.512	ABCF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336086.1	NM_005692	
SUPT6H	6830	hgsc.bcm.edu	37	17	27030897	27030897	+	IGR	DEL	T	T	-	rs151135532		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:27030897delT	ENST00000314616.6	+	0	6518				PROCA1_ENST00000579650.1_5'Flank|PROCA1_ENST00000301039.2_Frame_Shift_Del_p.K230fs|PROCA1_ENST00000581289.1_3'UTR|PROCA1_ENST00000439862.3_Frame_Shift_Del_p.K232fs	NM_003170.3	NP_003161.2	Q7KZ85	SPT6H_HUMAN	suppressor of Ty 6 homolog (S. cerevisiae)						chromatin remodeling (GO:0006338)|mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|negative regulation of histone H3-K27 methylation (GO:0061086)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|regulation of isotype switching (GO:0045191)|regulation of mRNA export from nucleus (GO:0010793)|regulation of mRNA processing (GO:0050684)|regulation of muscle cell differentiation (GO:0051147)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|hydrolase activity, acting on ester bonds (GO:0016788)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(4)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(15)|lung(21)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64	Lung NSC(42;0.00431)					CTTTCTTGGcttttttcttca	0.483																																					p.A231fs		Atlas-INDEL	.											.	PROCA1	28	.	0			c.691delG						.						91.0	95.0	94.0					17																	27030897		2202	4300	6502	SO:0001628	intergenic_variant	147011	exon4			.	U38658	CCDS32596.1	17q11.2	2013-02-14	2001-11-28			ENSG00000109111		"""SH2 domain containing"""	11470	protein-coding gene	gene with protein product		601333	"""suppressor of Ty (S.cerevisiae) 6 homolog"""			8786132	Standard	XM_005258026		Approved	KIAA0162, SPT6H	uc002hby.3	Q7KZ85			chr17.hg19:g.27030897delT		311.0	0.0		237.0	15.0	NM_152465	A7E2B4|Q15737|Q6GMQ4|Q7KYW9|Q7LDK4|Q8N526|Q92775|Q96AH3|Q9BTH9|Q9BTI2	Frame_Shift_Del	DEL	ENST00000314616.6	hg19	CCDS32596.1																																																																																			.	.		0.483	SUPT6H-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446422.2	NM_003170	
MFAP1	4236	hgsc.bcm.edu	37	15	44109627	44109627	+	Frame_Shift_Del	DEL	T	T	-	rs373137037		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:44109627delT	ENST00000267812.3	-	2	331	c.99delA	c.(97-99)aaafs	p.K33fs		NM_005926.2	NP_005917.2	P55081	MFAP1_HUMAN	microfibrillar-associated protein 1	33					extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|microfibril (GO:0001527)	poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(1)|kidney(1)|lung(6)|skin(2)|upper_aerodigestive_tract(3)	15		all_cancers(109;7.57e-15)|all_epithelial(112;3.51e-12)|Lung NSC(122;4.72e-08)|all_lung(180;4.9e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;4.33e-07)		TTACCTTCACTTTTTCCATTG	0.443																																					p.V34X		Atlas-INDEL	.											.	MFAP1	36	.	0			c.100delG						.						92.0	87.0	89.0					15																	44109627		2198	4298	6496	SO:0001589	frameshift_variant	4236	exon2			.		CCDS10105.1	15q15-q21	2014-05-20			ENSG00000140259	ENSG00000140259			7032	protein-coding gene	gene with protein product		600215				7835894	Standard	NM_005926		Approved		uc001zth.1	P55081	OTTHUMG00000060145	ENST00000267812.3:c.99delA	chr15.hg19:g.44109627delT	ENSP00000267812:p.Lys33fs	482.0	0.0		378.0	23.0	NM_005926	Q86TG6	Frame_Shift_Del	DEL	ENST00000267812.3	hg19	CCDS10105.1																																																																																			.	.		0.443	MFAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133491.2	NM_005926	
FASTK	10922	hgsc.bcm.edu	37	7	150775131	150775131	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:150775131delG	ENST00000297532.6	-	5	951	c.874delC	c.(874-876)ctgfs	p.L292fs	FASTK_ENST00000482571.1_Frame_Shift_Del_p.L265fs|FASTK_ENST00000540185.1_Frame_Shift_Del_p.P151fs|FASTK_ENST00000353841.2_Frame_Shift_Del_p.L151fs|RP11-148K1.12_ENST00000485974.1_RNA|FASTK_ENST00000489884.1_5'UTR	NM_006712.4	NP_006703.1	Q14296	FASTK_HUMAN	Fas-activated serine/threonine kinase	292					apoptotic signaling pathway (GO:0097190)|protein phosphorylation (GO:0006468)|regulation of RNA splicing (GO:0043484)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|Fas-activated serine/threonine kinase activity (GO:0033867)|protein serine/threonine kinase activity (GO:0004674)			lung(4)|stomach(2)	6			OV - Ovarian serous cystadenocarcinoma(82;0.00989)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)|LUSC - Lung squamous cell carcinoma(290;0.0718)|Lung(243;0.138)		TGCTGTTCCAGGGGCAGGTAG	0.542																																					p.L292fs		Atlas-INDEL	.											.	FASTK	29	.	0			c.875delT						.						94.0	97.0	96.0					7																	150775131		2203	4300	6503	SO:0001589	frameshift_variant	10922	exon5			.		CCDS5918.1, CCDS5919.1, CCDS59088.1	7q35	2006-07-06			ENSG00000164896	ENSG00000164896			24676	protein-coding gene	gene with protein product		606965				7544399, 15572676	Standard	NM_006712		Approved	FAST	uc003wix.2	Q14296	OTTHUMG00000158694	ENST00000297532.6:c.874delC	chr7.hg19:g.150775131delG	ENSP00000297532:p.Leu292fs	196.0	0.0		187.0	12.0	NM_006712	A8K867|F8VTW9|Q59EM8|Q8IVA0	Frame_Shift_Del	DEL	ENST00000297532.6	hg19	CCDS5918.1																																																																																			.	.		0.542	FASTK-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351832.2	NM_006712	
ATP1A3	478	hgsc.bcm.edu	37	19	42479905	42479905	+	Frame_Shift_Del	DEL	G	G	-	rs141362710		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:42479905delG	ENST00000302102.5	-	16	2289	c.2139delC	c.(2137-2139)cccfs	p.P713fs	ATP1A3_ENST00000543770.1_Frame_Shift_Del_p.P724fs|ATP1A3_ENST00000545399.1_Frame_Shift_Del_p.P726fs|ATP1A3_ENST00000602133.1_Frame_Shift_Del_p.P683fs	NM_152296.4	NP_689509.1	P13637	AT1A3_HUMAN	ATPase, Na+/K+ transporting, alpha 3 polypeptide	713					adult locomotory behavior (GO:0008344)|ATP biosynthetic process (GO:0006754)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular potassium ion homeostasis (GO:0030007)|cellular response to steroid hormone stimulus (GO:0071383)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|memory (GO:0007613)|potassium ion import (GO:0010107)|response to drug (GO:0042493)|sodium ion export from cell (GO:0036376)|transmembrane transport (GO:0055085)|visual learning (GO:0008542)	axon (GO:0030424)|dendritic spine head (GO:0044327)|dendritic spine neck (GO:0044326)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|myelin sheath (GO:0043209)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sodium:potassium-exchanging ATPase complex (GO:0005890)|synapse (GO:0045202)|vesicle (GO:0031982)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|metal ion binding (GO:0046872)|sodium:potassium-exchanging ATPase activity (GO:0005391)|steroid hormone binding (GO:1990239)			NS(1)|breast(2)|endometrium(7)|kidney(2)|large_intestine(11)|liver(1)|lung(19)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	52						TCTTCAGAGCGGGGGAGTCGT	0.612																																					p.A727fs		Atlas-INDEL	.											.	ATP1A3	117	.	0			c.2179delG						.						131.0	112.0	118.0					19																	42479905		2203	4300	6503	SO:0001589	frameshift_variant	478	exon16			.		CCDS12594.1, CCDS58663.1, CCDS58664.1	19q13.2	2012-10-22			ENSG00000105409	ENSG00000105409	3.6.3.9	"""ATPases / P-type"""	801	protein-coding gene	gene with protein product	"""sodium/potassium-transporting ATPase subunit alpha-3"", ""sodium pump subunit alpha-3"", ""sodium-potassium ATPase catalytic subunit alpha-3"""	182350	"""dystonia 12"""	DYT12		17282997	Standard	NM_152296		Approved		uc002osh.4	P13637	OTTHUMG00000137384	ENST00000302102.5:c.2139delC	chr19.hg19:g.42479905delG	ENSP00000302397:p.Pro713fs	215.0	0.0		165.0	12.0	NM_001256214	B7Z2T0|B7Z401|F5H6J6|Q16732|Q16735|Q969K5	Frame_Shift_Del	DEL	ENST00000302102.5	hg19	CCDS12594.1																																																																																			.	.		0.612	ATP1A3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268107.1	NM_152296	
UPF1	5976	hgsc.bcm.edu	37	19	18971165	18971165	+	Frame_Shift_Del	DEL	C	C	-	rs1062846		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:18971165delC	ENST00000599848.1	+	16	2460	c.2251delC	c.(2251-2253)cccfs	p.P751fs	UPF1_ENST00000262803.5_Frame_Shift_Del_p.P740fs			Q92900	RENT1_HUMAN	UPF1 regulator of nonsense transcripts homolog (yeast)	751					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|dosage compensation by inactivation of X chromosome (GO:0009048)|gene expression (GO:0010467)|histone mRNA catabolic process (GO:0071044)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process (GO:0000956)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of translational termination (GO:0006449)|RNA metabolic process (GO:0016070)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|exon-exon junction complex (GO:0035145)|nucleus (GO:0005634)|supraspliceosomal complex (GO:0044530)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(11)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	40						CTTCCAGTGGCCCCAACCCGA	0.557																																					p.W739fs		Atlas-INDEL	.											.	UPF1	88	.	0			c.2217delG						.						171.0	153.0	159.0					19																	18971165		2203	4300	6503	SO:0001589	frameshift_variant	5976	exon16			.	AF074016	CCDS12386.1, CCDS74315.1	19p13.2-p13.11	2012-02-29	2006-02-07	2006-02-07	ENSG00000005007	ENSG00000005007			9962	protein-coding gene	gene with protein product	"""UP Frameshift 1"", ""smg-2 homolog, nonsense mediated mRNA decay factor (C. elegans)"""	601430	"""regulator of nonsense transcripts 1"""	RENT1		8855285, 9064659	Standard	XM_005260015		Approved	HUPF1, KIAA0221, NORF1, pNORF1, smg-2	uc002nkf.3	Q92900		ENST00000599848.1:c.2251delC	chr19.hg19:g.18971165delC	ENSP00000470142:p.Pro751fs	269.0	0.0		175.0	11.0	NM_002911	O00239|O43343|Q86Z25|Q92842	Frame_Shift_Del	DEL	ENST00000599848.1	hg19																																																																																				.	.		0.557	UPF1-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000464684.1	NM_002911	
ITGA11	22801	hgsc.bcm.edu	37	15	68624271	68624271	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:68624271delG	ENST00000315757.7	-	14	1782	c.1696delC	c.(1696-1698)ctgfs	p.L566fs	ITGA11_ENST00000423218.2_Frame_Shift_Del_p.L566fs	NM_001004439.1	NP_001004439.1	Q9UKX5	ITA11_HUMAN	integrin, alpha 11	566					cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell-matrix adhesion (GO:0007160)|collagen-activated signaling pathway (GO:0038065)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|muscle organ development (GO:0007517)|osteoblast differentiation (GO:0001649)|substrate-dependent cell migration (GO:0006929)	focal adhesion (GO:0005925)|integrin alpha11-beta1 complex (GO:0034681)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|collagen receptor activity (GO:0038064)|metal ion binding (GO:0046872)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(6)|large_intestine(6)|lung(22)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	52						TTGTCCTCCAGGGGGGCTCCC	0.572																																					p.L566fs		Atlas-INDEL	.											.	ITGA11	110	.	0			c.1697delT						.						57.0	56.0	56.0					15																	68624271		1979	4149	6128	SO:0001589	frameshift_variant	22801	exon14			.	AF109681	CCDS45291.1	15q22.3-q23	2010-03-23				ENSG00000137809		"""Integrins"""	6136	protein-coding gene	gene with protein product		604789				10486209	Standard	NM_001004439		Approved	HsT18964	uc002ari.3	Q9UKX5		ENST00000315757.7:c.1696delC	chr15.hg19:g.68624271delG	ENSP00000327290:p.Leu566fs	249.0	0.0		164.0	10.0	NM_001004439	J3KQM2|Q8WYI8|Q9UKQ1	Frame_Shift_Del	DEL	ENST00000315757.7	hg19	CCDS45291.1																																																																																			.	.		0.572	ITGA11-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_012211	
PHLPP2	23035	hgsc.bcm.edu	37	16	71724608	71724608	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:71724608delT	ENST00000568954.1	-	4	801	c.423delA	c.(421-423)aaafs	p.K141fs	PHLPP2_ENST00000393524.2_Frame_Shift_Del_p.K141fs|PHLPP2_ENST00000360429.3_Frame_Shift_Del_p.K141fs|PHLPP2_ENST00000356272.3_Frame_Shift_Del_p.K141fs|PHLPP2_ENST00000567016.1_Frame_Shift_Del_p.K176fs			Q6ZVD8	PHLP2_HUMAN	PH domain and leucine rich repeat protein phosphatase 2	141					epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment membrane (GO:0042622)	metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)			central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(7)|lung(15)|ovary(1)|prostate(1)|skin(1)|stomach(1)	37						TGTGGCATGGTTTTTCTGAAA	0.403																																					p.P142fs		Atlas-INDEL	.											.	PHLPP2	96	.	0			c.424delC						.						66.0	58.0	60.0					16																	71724608		2198	4300	6498	SO:0001589	frameshift_variant	23035	exon3			.	BX647823	CCDS32479.1, CCDS73910.1	16q22.2	2013-01-11	2009-05-26	2009-05-26	ENSG00000040199	ENSG00000040199		"""Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"", ""Pleckstrin homology (PH) domain containing"""	29149	protein-coding gene	gene with protein product		611066	"""PH domain and leucine rich repeat protein phosphatase-like"""	PHLPPL		17386267	Standard	NM_001289003		Approved	KIAA0931	uc002fax.3	Q6ZVD8		ENST00000568954.1:c.423delA	chr16.hg19:g.71724608delT	ENSP00000457991:p.Lys141fs	181.0	0.0		144.0	10.0	NM_015020	A1L374|Q9NV17|Q9Y2E3	Frame_Shift_Del	DEL	ENST00000568954.1	hg19	CCDS32479.1																																																																																			.	.		0.403	PHLPP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000434139.1	NM_015020	
DERL1	79139	hgsc.bcm.edu	37	8	124031435	124031435	+	Splice_Site	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:124031435delA	ENST00000259512.4	-	7	917	c.617delT	c.(616-618)ttg>tg	p.L206fs	DERL1_ENST00000519018.1_Splice_Site_p.L106fs|DERL1_ENST00000523036.1_Splice_Site_p.L106fs|RP11-557C18.3_ENST00000521258.1_RNA|DERL1_ENST00000405944.3_Splice_Site_p.L186fs|DERL1_ENST00000419562.2_Splice_Site_p.L106fs	NM_001134671.2|NM_024295.5	NP_001128143.1|NP_077271.1	Q9BUN8	DERL1_HUMAN	derlin 1	206					endoplasmic reticulum unfolded protein response (GO:0030968)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|establishment of protein localization (GO:0045184)|intracellular transport of viral protein in host cell (GO:0019060)|response to unfolded protein (GO:0006986)|retrograde protein transport, ER to cytosol (GO:0030970)	early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|Hrd1p ubiquitin ligase complex (GO:0000836)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)	MHC class I protein binding (GO:0042288)|receptor activity (GO:0004872)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(3)	8	Lung NSC(37;1.06e-09)|Ovarian(258;0.0205)		STAD - Stomach adenocarcinoma(47;0.00527)			AAACACTTACAAAAACTGAGG	0.398																																					.		Atlas-INDEL	.											.	DERL1	27	.	0			c.557+1T>-						.						92.0	87.0	89.0					8																	124031435		2203	4300	6503	SO:0001630	splice_region_variant	79139	exon8			.	BC002457	CCDS6337.1, CCDS47915.1	8q24.13	2012-02-01	2012-02-01		ENSG00000136986	ENSG00000136986			28454	protein-coding gene	gene with protein product		608813	"""Der1-like domain family, member 1"""			12975309, 15215855	Standard	NM_024295		Approved	MGC3067, PRO2577, FLJ13784, DER1, DER-1, derlin-1	uc003ypl.3	Q9BUN8	OTTHUMG00000165080	ENST00000259512.4:c.617+1T>-	chr8.hg19:g.124031435delA		216.0	0.0		182.0	11.0	NM_001134671	B3KW41|E9PH19	Splice_Site	DEL	ENST00000259512.4	hg19	CCDS6337.1																																																																																			.	.		0.398	DERL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381714.2	NM_024295	Frame_Shift_Del
CCDC169	728591	hgsc.bcm.edu	37	13	36805370	36805370	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr13:36805370delT	ENST00000239859.7	-	8	636	c.605delA	c.(604-606)aagfs	p.K202fs	CCDC169_ENST00000379862.2_Frame_Shift_Del_p.K100fs|SOHLH2_ENST00000554962.1_Intron|CCDC169_ENST00000239860.6_Intron|CCDC169_ENST00000503173.1_Intron|CCDC169_ENST00000491049.2_Intron|CCDC169_ENST00000379864.2_Intron|CCDC169_ENST00000510088.1_Frame_Shift_Del_p.K100fs|CCDC169-SOHLH2_ENST00000511166.1_Intron			A6NNP5	CC169_HUMAN	coiled-coil domain containing 169	202										breast(1)|endometrium(1)	2						TCTTGTAATCTTTTTTACTGG	0.338																																					p.K202fs		Atlas-INDEL	.											.	CCDC169	20	.	0			c.606delG						.						464.0	392.0	414.0					13																	36805370		692	1591	2283	SO:0001589	frameshift_variant	728591	exon8			.		CCDS45027.1, CCDS45028.1, CCDS45029.1, CCDS53863.1, CCDS55897.1	13q13.3	2011-08-09	2011-08-09	2011-08-09	ENSG00000242715	ENSG00000242715			34361	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 38"""	C13orf38			Standard	NM_001144981		Approved	RP11-251J8.1, LOC728591		A6NNP5	OTTHUMG00000016731	ENST00000239859.7:c.605delA	chr13.hg19:g.36805370delT	ENSP00000239859:p.Lys202fs	332.0	0.0		219.0	14.0	NM_001144981	A6NC13|A6NCT2|B7ZW45|B7ZW49|B9EJF2|Q9H1T4|Q9H1T5	Frame_Shift_Del	DEL	ENST00000239859.7	hg19	CCDS45028.1																																																																																			.	.		0.338	CCDC169-014	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368255.1	NM_001144981	
ABCB8	11194	hgsc.bcm.edu	37	7	150742395	150742395	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:150742395delA	ENST00000297504.6	+	17	2233	c.2167delA	c.(2167-2169)aaafs	p.K724fs	ABCB8_ENST00000356058.4_3'UTR|ABCB8_ENST00000542328.1_Frame_Shift_Del_p.K619fs|ASIC3_ENST00000357922.4_5'Flank|ABCB8_ENST00000498578.1_Frame_Shift_Del_p.K682fs|ABCB8_ENST00000358849.4_Frame_Shift_Del_p.K707fs			Q9NUT2	ABCB8_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 8	724					transmembrane transport (GO:0055085)|transport (GO:0006810)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial envelope (GO:0005740)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	26			OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)	Doxorubicin(DB00997)	CCCACCGCCCAAAAAGCCAGA	0.652																																					p.P705fs		Atlas-INDEL	.											.	ABCB8	65	.	0			c.2115delC						.						43.0	42.0	42.0					7																	150742395		2203	4300	6503	SO:0001589	frameshift_variant	11194	exon16			.	AF047690	CCDS5913.1, CCDS64798.1, CCDS64799.1, CCDS64800.1	7q36.1	2012-05-16			ENSG00000197150	ENSG00000197150		"""ATP binding cassette transporters / subfamily B"""	49	protein-coding gene	gene with protein product	"""mitochondrial ABC protein"""	605464				8894702	Standard	NM_001282291		Approved	EST328128, M-ABC1, MABC1	uc003wik.4	Q9NUT2	OTTHUMG00000158686	ENST00000297504.6:c.2167delA	chr7.hg19:g.150742395delA	ENSP00000297504:p.Lys724fs	132.0	0.0		159.0	10.0	NM_007188	A5D8W3|B2RBL8|B3KND2|B4DG02|G3XAP3|O95787|Q53GM0	Frame_Shift_Del	DEL	ENST00000297504.6	hg19																																																																																				.	.		0.652	ABCB8-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351733.2	NM_007188	
NEBL	10529	hgsc.bcm.edu	37	10	21178796	21178796	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:21178796delT	ENST00000377122.4	-	3	632	c.236delA	c.(235-237)aatfs	p.N79fs	NEBL_ENST00000417816.2_Intron|NEBL_ENST00000377159.4_Intron|NEBL_ENST00000377119.1_Frame_Shift_Del_p.N79fs	NM_006393.2	NP_006384.1	O76041	NEBL_HUMAN	nebulette	79					cardiac muscle thin filament assembly (GO:0071691)	extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|cytoskeletal protein binding (GO:0008092)|filamin binding (GO:0031005)|structural constituent of muscle (GO:0008307)|tropomyosin binding (GO:0005523)			NS(2)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(14)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(8)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	70						AGCACCGATATTTTTTACATG	0.313																																					p.N79fs		Atlas-INDEL	.											.	NEBL	199	.	0			c.237delT						.						92.0	95.0	94.0					10																	21178796		2202	4300	6502	SO:0001589	frameshift_variant	10529	exon3			.	Y16241	CCDS7133.1, CCDS7134.1	10p12	2014-09-17			ENSG00000078114	ENSG00000078114			16932	protein-coding gene	gene with protein product		605491				9733644, 10470015	Standard	NM_213569		Approved		uc001iqi.3	O76041	OTTHUMG00000017788	ENST00000377122.4:c.236delA	chr10.hg19:g.21178796delT	ENSP00000366326:p.Asn79fs	217.0	0.0		159.0	11.0	NM_006393	B0YJ45|Q2TBD0|Q70I54|Q9UIC4	Frame_Shift_Del	DEL	ENST00000377122.4	hg19	CCDS7134.1																																																																																			.	.		0.313	NEBL-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000047113.1	NM_006393	
BAZ2A	11176	hgsc.bcm.edu	37	12	56994135	56994135	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:56994135delA	ENST00000551812.1	-	24	4941	c.4748delT	c.(4747-4749)ttgfs	p.L1583fs	BAZ2A_ENST00000179765.5_Frame_Shift_Del_p.L1551fs|BAZ2A_ENST00000549884.1_Frame_Shift_Del_p.L1581fs|BAZ2A_ENST00000553222.1_5'Flank|BAZ2A_ENST00000379441.3_Frame_Shift_Del_p.L1553fs	NM_013449.3	NP_038477.2	Q9UIF9	BAZ2A_HUMAN	bromodomain adjacent to zinc finger domain, 2A	1583					chromatin remodeling (GO:0006338)|chromatin silencing at rDNA (GO:0000183)|DNA methylation (GO:0006306)|heterochromatin assembly involved in chromatin silencing (GO:0070869)|histone deacetylation (GO:0016575)|histone H3-K9 methylation (GO:0051567)|histone H4 deacetylation (GO:0070933)|histone H4-K20 methylation (GO:0034770)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromatin silencing complex (GO:0005677)|nucleolus (GO:0005730)|rDNA heterochromatin (GO:0033553)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|lysine-acetylated histone binding (GO:0070577)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(1)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(15)|urinary_tract(1)	31						AGCCAGGTCCAAAGGGTTGGT	0.607																																					p.L1583fs		Atlas-INDEL	.											.	BAZ2A	263	.	0			c.4749delG						.						50.0	57.0	55.0					12																	56994135		2082	4201	6283	SO:0001589	frameshift_variant	11176	exon24			.	AB032254	CCDS44924.1, CCDS73483.1	12q13.3	2013-01-28				ENSG00000076108		"""Zinc fingers, PHD-type"""	962	protein-coding gene	gene with protein product	"""TTF-I interacting peptide 5"""	605682				10662543, 11532953	Standard	XM_005268596		Approved	KIAA0314, TIP5, WALp3	uc001slq.1	Q9UIF9	OTTHUMG00000170332	ENST00000551812.1:c.4748delT	chr12.hg19:g.56994135delA	ENSP00000446880:p.Leu1583fs	169.0	0.0		129.0	10.0	NM_013449	B3KN66|O00536|O15030|Q68DI8|Q96H26	Frame_Shift_Del	DEL	ENST00000551812.1	hg19	CCDS44924.1																																																																																			.	.		0.607	BAZ2A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408561.1	NM_013449	
PDILT	204474	hgsc.bcm.edu	37	16	20387460	20387460	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:20387460delA	ENST00000302451.4	-	4	721	c.473delT	c.(472-474)ttgfs	p.L158fs		NM_174924.1	NP_777584.1	Q8N807	PDILT_HUMAN	protein disulfide isomerase-like, testis expressed	158					cell migration (GO:0016477)|cell redox homeostasis (GO:0045454)|multicellular organismal development (GO:0007275)|protein folding (GO:0006457)|spermatid development (GO:0007286)	endoplasmic reticulum (GO:0005783)	protein disulfide isomerase activity (GO:0003756)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(13)|liver(1)|lung(33)|prostate(3)|skin(1)|urinary_tract(1)	61						GCTGTTGAACAAAAATGCTTT	0.488																																					p.L158fs		Atlas-INDEL	.											.	PDILT	120	.	0			c.474delG						.						132.0	101.0	111.0					16																	20387460		2203	4300	6503	SO:0001589	frameshift_variant	204474	exon4			.		CCDS10584.1	16p12.3	2011-11-10	2009-02-23		ENSG00000169340	ENSG00000169340		"""Protein disulfide isomerases"""	27338	protein-coding gene	gene with protein product	"""protein disulfide isomerase family A, member 7"", ""protein disulfide isomerase-like protein of the testis"""					15475357	Standard	NM_174924		Approved	PDIA7	uc002dhc.1	Q8N807	OTTHUMG00000131487	ENST00000302451.4:c.473delT	chr16.hg19:g.20387460delA	ENSP00000305465:p.Leu158fs	221.0	0.0		132.0	10.0	NM_174924	Q8IVQ5	Frame_Shift_Del	DEL	ENST00000302451.4	hg19	CCDS10584.1																																																																																			.	.		0.488	PDILT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254332.1	NM_174924	
IGF1R	3480	hgsc.bcm.edu	37	15	99459962	99459962	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:99459962delC	ENST00000268035.6	+	10	2669	c.2058delC	c.(2056-2058)aacfs	p.N686fs	IGF1R_ENST00000558762.1_Frame_Shift_Del_p.N686fs	NM_000875.3	NP_000866.1	P08069	IGF1R_HUMAN	insulin-like growth factor 1 receptor	686	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axonogenesis (GO:0007409)|brain development (GO:0007420)|epidermis development (GO:0008544)|establishment of cell polarity (GO:0030010)|exocrine pancreas development (GO:0031017)|immune response (GO:0006955)|inactivation of MAPKK activity (GO:0051389)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|male sex determination (GO:0030238)|mammary gland development (GO:0030879)|negative regulation of apoptotic process (GO:0043066)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|peptidyl-tyrosine autophosphorylation (GO:0038083)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokinesis (GO:0032467)|positive regulation of DNA replication (GO:0045740)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mitosis (GO:0045840)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of steroid hormone biosynthetic process (GO:0090031)|prostate gland epithelium morphogenesis (GO:0060740)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein tetramerization (GO:0051262)|regulation of JNK cascade (GO:0046328)|response to vitamin E (GO:0033197)|signal transduction (GO:0007165)	caveola (GO:0005901)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor binding (GO:0005520)|insulin-like growth factor I binding (GO:0031994)|insulin-like growth factor-activated receptor activity (GO:0005010)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)			NS(2)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(13)|lung(20)|ovary(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63	all_cancers(4;4.17e-14)|all_epithelial(3;4.34e-15)|Lung NSC(78;0.00175)|all_lung(78;0.00351)|Melanoma(26;0.00505)|Medulloblastoma(229;0.163)		Epithelial(2;1.94e-12)|all cancers(5;6.83e-11)|BRCA - Breast invasive adenocarcinoma(2;2.88e-09)|OV - Ovarian serous cystadenocarcinoma(32;0.00261)		"""""""Insulin(DB00071)|Insulin Glargine(DB00047)|Insulin Lispro(DB00046)|Insulin Regular(DB00030)|Mecasermin(DB01277)"""	TCACAGAGAACCCCAAGACTG	0.542																																					p.N686fs		Atlas-INDEL	.											.	IGF1R	147	.	0			c.2057delA						.						79.0	80.0	80.0					15																	99459962		2197	4297	6494	SO:0001589	frameshift_variant	3480	exon10			.	M69229	CCDS10378.1, CCDS73785.1	15q26.3	2013-02-11			ENSG00000140443	ENSG00000140443		"""CD molecules"", ""Fibronectin type III domain containing"""	5465	protein-coding gene	gene with protein product		147370				1316909	Standard	XM_006720486		Approved	JTK13, CD221, IGFIR, MGC18216, IGFR	uc002bul.3	P08069	OTTHUMG00000149851	ENST00000268035.6:c.2058delC	chr15.hg19:g.99459962delC	ENSP00000268035:p.Asn686fs	220.0	0.0		165.0	10.0	NM_000875	B1B5Y2|Q14CV2|Q9UCC0	Frame_Shift_Del	DEL	ENST00000268035.6	hg19	CCDS10378.1																																																																																			.	.		0.542	IGF1R-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313537.2	NM_000875	
TSPYL6	388951	hgsc.bcm.edu	37	2	54482889	54482889	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:54482889delC	ENST00000317802.7	-	1	520	c.400delG	c.(400-402)gcafs	p.A134fs	ACYP2_ENST00000394666.3_Intron|ACYP2_ENST00000607452.1_Intron|ACYP2_ENST00000303536.4_Intron|ACYP2_ENST00000606865.1_Intron	NM_001003937.2	NP_001003937.2	Q8N831	TSYL6_HUMAN	TSPY-like 6	134					nucleosome assembly (GO:0006334)	nucleus (GO:0005634)				NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(1)|ovary(1)|skin(1)|stomach(2)	20						GACCTCCCTGCCCCACAGGTT	0.602																																					p.A134fs		Atlas-INDEL	.											.	TSPYL6	54	.	0			c.401delC						.						61.0	65.0	64.0					2																	54482889		2093	4231	6324	SO:0001589	frameshift_variant	388951	exon1			.	AK097417	CCDS42682.1	2p16.3	2007-10-22			ENSG00000178021	ENSG00000178021			14521	protein-coding gene	gene with protein product							Standard	NM_001003937		Approved		uc002rxr.2	Q8N831	OTTHUMG00000151823	ENST00000317802.7:c.400delG	chr2.hg19:g.54482889delC	ENSP00000417919:p.Ala134fs	116.0	0.0		104.0	10.0	NM_001003937	Q6NUJ3	Frame_Shift_Del	DEL	ENST00000317802.7	hg19	CCDS42682.1																																																																																			.	.		0.602	TSPYL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324069.3	XM_371494	
TFEB	7942	hgsc.bcm.edu	37	6	41655721	41655721	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:41655721delG	ENST00000230323.4	-	6	896	c.595delC	c.(595-597)cagfs	p.Q199fs	TFEB_ENST00000403298.4_Frame_Shift_Del_p.Q199fs|TFEB_ENST00000394283.1_Frame_Shift_Del_p.Q199fs|TFEB_ENST00000358871.2_Frame_Shift_Del_p.Q213fs|TFEB_ENST00000373033.1_Frame_Shift_Del_p.Q199fs|TFEB_ENST00000420312.1_Frame_Shift_Del_p.Q114fs	NM_001271945.1|NM_007162.2	NP_001258874.1|NP_009093.1	P19484	TFEB_HUMAN	transcription factor EB	199					autophagy (GO:0006914)|embryonic placenta development (GO:0001892)|humoral immune response (GO:0006959)|lysosome organization (GO:0007040)|positive regulation of autophagy (GO:0010508)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)	11	Ovarian(28;0.0355)|Colorectal(47;0.121)		Epithelial(12;7.61e-05)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00507)			GCTGTGACCTGGGGGTCGCTG	0.657			T	ALPHA	renal (childhood epithelioid)																																p.Q213fs		Atlas-INDEL	.		Dom	yes		6	6p21	7942	transcription factor EB		"""E,M"""	.	TFEB	37	.	0			c.638delA						.						65.0	65.0	65.0					6																	41655721		2203	4300	6503	SO:0001589	frameshift_variant	7942	exon5			.	M33782	CCDS4858.1, CCDS64424.1, CCDS64425.1	6p21	2013-05-21			ENSG00000112561	ENSG00000112561		"""Basic helix-loop-helix proteins"""	11753	protein-coding gene	gene with protein product		600744				2115126	Standard	NM_007162		Approved	TCFEB, bHLHe35	uc003oqu.2	P19484	OTTHUMG00000014684	ENST00000230323.4:c.595delC	chr6.hg19:g.41655721delG	ENSP00000230323:p.Gln199fs	253.0	0.0		205.0	14.0	NM_001167827	Q709B3|Q7Z6P9|Q9BRJ5|Q9UJD8	Frame_Shift_Del	DEL	ENST00000230323.4	hg19	CCDS4858.1																																																																																			.	.		0.657	TFEB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040522.3		
FAM8A1	51439	hgsc.bcm.edu	37	6	17608468	17608468	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:17608468delT	ENST00000259963.3	+	5	1195	c.1140delT	c.(1138-1140)tctfs	p.S380fs		NM_016255.2	NP_057339.1	Q9UBU6	FA8A1_HUMAN	family with sequence similarity 8, member A1	380	RDD.					integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(2)|lung(3)	6	Breast(50;0.0259)|Ovarian(93;0.0584)	all_hematologic(90;0.143)	all cancers(50;0.176)|Epithelial(50;0.204)			CAATTGCTTCTTTTTTCCCTG	0.343																																					p.S380fs		Atlas-INDEL	.											.	FAM8A1	26	.	0			c.1139delC						.						148.0	148.0	148.0					6																	17608468		2203	4300	6503	SO:0001589	frameshift_variant	51439	exon5			.	AF097027	CCDS4540.1	6p23	2010-11-22			ENSG00000137414	ENSG00000137414			16372	protein-coding gene	gene with protein product						11707071	Standard	NM_016255		Approved	AHCP	uc003ncc.3	Q9UBU6	OTTHUMG00000014309	ENST00000259963.3:c.1140delT	chr6.hg19:g.17608468delT	ENSP00000259963:p.Ser380fs	211.0	0.0		172.0	11.0	NM_016255	B2R725	Frame_Shift_Del	DEL	ENST00000259963.3	hg19	CCDS4540.1																																																																																			.	.		0.343	FAM8A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039950.1		
PRG4	10216	hgsc.bcm.edu	37	1	186282017	186282017	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:186282017delT	ENST00000445192.2	+	12	4153	c.4108delT	c.(4108-4110)tttfs	p.F1370fs	PRG4_ENST00000367486.3_Frame_Shift_Del_p.F1327fs|PRG4_ENST00000367484.3_Frame_Shift_Del_p.F899fs|PRG4_ENST00000367485.4_Frame_Shift_Del_p.F1277fs|PRG4_ENST00000367483.4_Frame_Shift_Del_p.F1329fs|RNU6-1240P_ENST00000365155.1_RNA|TPR_ENST00000367478.4_3'UTR	NM_005807.3	NP_005798.2	Q92954	PRG4_HUMAN	proteoglycan 4	1370					cell proliferation (GO:0008283)|hematopoietic stem cell proliferation (GO:0071425)|immune response (GO:0006955)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|regulation of cell proliferation (GO:0042127)	extracellular space (GO:0005615)	polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(33)|prostate(7)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1)	102						TTACTATGCCTTTTCTAAAGG	0.383																																					p.A1369fs		Atlas-INDEL	.											.	PRG4	259	.	0			c.4107delC						.						100.0	94.0	96.0					1																	186282017		2203	4300	6503	SO:0001589	frameshift_variant	10216	exon12			.	U70136	CCDS1369.1, CCDS44287.1, CCDS44288.1	1q25-q31	2008-07-18	2004-11-15		ENSG00000116690	ENSG00000116690			9364	protein-coding gene	gene with protein product	"""lubricin"", ""megakaryocyte stimulating factor"", ""articular superficial zone protein"", ""Jacobs camptodactyly-arthropathy-pericarditis syndrome"", ""camptodactyly, arthropathy, coxa vara, pericarditis syndrome"", ""bG174L6.2 (MSF: megakaryocyte stimulating factor )"""	604283	"""proteoglycan 4, (megakaryocyte stimulating factor, articular superficial zone protein, camptodactyly, arthropathy, coxa vara, pericarditis syndrome)"""	CACP		10545950, 9920774	Standard	NM_005807		Approved	JCAP, SZP, MSF, HAPO, bG174L6.2, FLJ32635	uc001gru.4	Q92954	OTTHUMG00000035574	ENST00000445192.2:c.4108delT	chr1.hg19:g.186282017delT	ENSP00000399679:p.Phe1370fs	147.0	0.0		193.0	13.0	NM_005807	Q6DNC4|Q6DNC5|Q6ZMZ5|Q9BX49	Frame_Shift_Del	DEL	ENST00000445192.2	hg19	CCDS1369.1																																																																																			.	.		0.383	PRG4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086346.1	NM_005807	
RBFOX2	23543	hgsc.bcm.edu	37	22	36161472	36161472	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr22:36161472delT	ENST00000438146.2	-	7	814	c.815delA	c.(814-816)aatfs	p.N272fs	RBFOX2_ENST00000449924.2_Frame_Shift_Del_p.N201fs|RBFOX2_ENST00000414461.2_Frame_Shift_Del_p.N201fs|RBFOX2_ENST00000416721.2_Frame_Shift_Del_p.N201fs|RBFOX2_ENST00000397303.2_Frame_Shift_Del_p.N182fs|RBFOX2_ENST00000359369.4_Frame_Shift_Del_p.N181fs|RBFOX2_ENST00000405409.2_Frame_Shift_Del_p.N202fs|RBFOX2_ENST00000262829.7_Frame_Shift_Del_p.N183fs	NM_001082578.1|NM_001082579.1	NP_001076047|NP_001076048.1	O43251	RFOX2_HUMAN	RNA binding protein, fox-1 homolog (C. elegans) 2	211					dendrite morphogenesis (GO:0048813)|intracellular estrogen receptor signaling pathway (GO:0030520)|mRNA processing (GO:0006397)|negative regulation of transcription, DNA-templated (GO:0045892)|neuromuscular process controlling balance (GO:0050885)|radial glia guided migration of Purkinje cell (GO:0021942)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of cell proliferation (GO:0042127)|regulation of definitive erythrocyte differentiation (GO:0010724)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			endometrium(4)|large_intestine(7)|lung(7)	18						TTTCTTACCATTTGCATATGG	0.328																																					p.N272fs		Atlas-INDEL	.											.	RBFOX2	62	.	0			c.816delT						.						79.0	70.0	73.0					22																	36161472		2203	4298	6501	SO:0001589	frameshift_variant	23543	exon7			.	AL009266	CCDS13921.1, CCDS43013.1, CCDS46699.1, CCDS46700.1, CCDS46701.1	22q12-q13	2013-02-12	2010-09-10	2010-09-10	ENSG00000100320	ENSG00000100320		"""RNA binding motif (RRM) containing"""	9906	protein-coding gene	gene with protein product	"""hexaribonucleotide binding protein 2"""	612149	"""RNA binding motif protein 9"""	RBM9			Standard	NM_014309		Approved	HNRBP2, FOX-2, HRNBP2	uc003aon.4	O43251	OTTHUMG00000150585	ENST00000438146.2:c.815delA	chr22.hg19:g.36161472delT	ENSP00000413035:p.Asn272fs	243.0	0.0		183.0	11.0	NM_001082578	A4F5G8|A8K5Z5|B0QYY8|B0QYY9|Q0PRL5|Q0VH35|Q5TF71|Q6IC09|Q8TD00|Q8WYB1|Q96DZ6|Q96NL7|Q9UGW4|Q9UH33	Frame_Shift_Del	DEL	ENST00000438146.2	hg19	CCDS43013.1																																																																																			.	.		0.328	RBFOX2-005	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319299.3		
TRPC1	7220	hgsc.bcm.edu	37	3	142443550	142443550	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:142443550delT	ENST00000476941.1	+	1	635	c.149delT	c.(148-150)cttfs	p.L50fs	TRPC1_ENST00000273482.6_Frame_Shift_Del_p.L50fs	NM_001251845.1	NP_001238774.1	P48995	TRPC1_HUMAN	transient receptor potential cation channel, subfamily C, member 1	50					axon guidance (GO:0007411)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|response to calcium ion (GO:0051592)|saliva secretion (GO:0046541)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|sarcomere (GO:0030017)	calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)|inositol 1,4,5 trisphosphate binding (GO:0070679)|ion channel binding (GO:0044325)|store-operated calcium channel activity (GO:0015279)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(18)|ovary(2)|skin(2)|stomach(3)|urinary_tract(1)	37						AATGAGAAGCTTTTCTTGCTG	0.572																																					p.L50fs		Atlas-INDEL	.											.	TRPC1	82	.	0			c.148delC						.						154.0	132.0	139.0					3																	142443550		2203	4300	6503	SO:0001589	frameshift_variant	7220	exon1			.	X89066	CCDS3126.1, CCDS58856.1	3q23	2011-12-14			ENSG00000144935	ENSG00000144935		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	12333	protein-coding gene	gene with protein product		602343				7568191, 16382100	Standard	NM_001251845		Approved	HTRP-1	uc003evc.3	P48995	OTTHUMG00000159301	ENST00000476941.1:c.149delT	chr3.hg19:g.142443550delT	ENSP00000419313:p.Leu50fs	168.0	0.0		121.0	10.0	NM_001251845	Q14CE4	Frame_Shift_Del	DEL	ENST00000476941.1	hg19	CCDS58856.1																																																																																			.	.		0.572	TRPC1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354520.1	NM_003304	
CASC5	57082	hgsc.bcm.edu	37	15	40920324	40920324	+	Frame_Shift_Del	DEL	A	A	-	rs200029926	byFrequency	TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:40920324delA	ENST00000346991.5	+	12	5901	c.5511delA	c.(5509-5511)atafs	p.I1837fs	CASC5_ENST00000399668.2_Frame_Shift_Del_p.I1811fs			Q8NG31	CASC5_HUMAN	cancer susceptibility candidate 5	1837	Necessary for kinetochore localization and for interaction with NSL1 and DSN1.				acrosome assembly (GO:0001675)|attachment of spindle microtubules to kinetochore (GO:0008608)|CENP-A containing nucleosome assembly (GO:0034080)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of phosphatase activity (GO:0010923)|nucleosome assembly (GO:0006334)|protein localization to kinetochore (GO:0034501)|spindle assembly checkpoint (GO:0071173)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				NS(1)|breast(7)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(13)|lung(16)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	57		all_cancers(109;2.03e-18)|all_epithelial(112;4.26e-15)|Lung NSC(122;1.12e-10)|all_lung(180;2.59e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;4.99e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0861)|COAD - Colon adenocarcinoma(120;0.211)		GTGTATTGATAAAAAACCTGA	0.388																																					p.I1837fs		Atlas-INDEL	.											.	CASC5	269	.	0			c.5510delT						.						88.0	90.0	90.0					15																	40920324		1833	4084	5917	SO:0001589	frameshift_variant	57082	exon12			.	AF173994	CCDS42023.1, CCDS42024.1	15q14	2013-07-03			ENSG00000137812	ENSG00000137812		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	24054	protein-coding gene	gene with protein product	"""cancer/testis antigen 29"", ""kinetochore null 1 homolog (C. elegans)"", ""blinkin, bub-linking kinetochore protein"", ""protein phosphatase 1, regulatory subunit 55"""	609173				10980622, 10780384, 18045986	Standard	NM_170589		Approved	D40, AF15Q14, CT29, hKNL-1, KNL1, hSpc105, PPP1R55, Spc7	uc010bbt.1	Q8NG31	OTTHUMG00000166532	ENST00000346991.5:c.5511delA	chr15.hg19:g.40920324delA	ENSP00000335463:p.Ile1837fs	272.0	0.0		172.0	11.0	NM_170589	Q8NHE1|Q8WXA6|Q9HCK2|Q9NR92	Frame_Shift_Del	DEL	ENST00000346991.5	hg19	CCDS42023.1																																																																																			.	.		0.388	CASC5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390224.2	NM_144508	
SSR2	6746	hgsc.bcm.edu	37	1	155979390	155979390	+	Frame_Shift_Del	DEL	G	G	-	rs531493503		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:155979390delG	ENST00000295702.4	-	6	564	c.493delC	c.(493-495)ctgfs	p.L167fs	SSR2_ENST00000529008.1_3'UTR|SSR2_ENST00000496742.1_3'UTR|SSR2_ENST00000480567.1_Frame_Shift_Del_p.L167fs	NM_003145.3	NP_003136.1	P43308	SSRB_HUMAN	signal sequence receptor, beta (translocon-associated protein beta)	167					cellular protein metabolic process (GO:0044267)|cotranslational protein targeting to membrane (GO:0006613)|gene expression (GO:0010467)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(4)|stomach(1)	10	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)					CACAATAGCAGGGGGATGCCG	0.517																																					p.L165fs		Atlas-INDEL	.											.	SSR2	20	.	0			c.494delT						.						125.0	115.0	118.0					1																	155979390		2203	4300	6503	SO:0001589	frameshift_variant	6746	exon6			.	BC000341	CCDS1126.1	1q21-q23	2008-02-05			ENSG00000163479	ENSG00000163479			11324	protein-coding gene	gene with protein product		600867				7789174	Standard	NM_003145		Approved	TLAP, TRAPB	uc001fmx.3	P43308	OTTHUMG00000017456	ENST00000295702.4:c.493delC	chr1.hg19:g.155979390delG	ENSP00000295702:p.Leu167fs	246.0	0.0		287.0	18.0	NM_003145	B2R9K9|D3DVA7|Q53HI0|Q5VY95|Q5VY96|Q6IB31|Q9BWE4	Frame_Shift_Del	DEL	ENST00000295702.4	hg19	CCDS1126.1																																																																																			.	.		0.517	SSR2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046172.2	NM_003145	
APOL2	23780	hgsc.bcm.edu	37	22	36623560	36623560	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr22:36623560delC	ENST00000249066.6	-	6	1380	c.904delG	c.(904-906)gcafs	p.A302fs	APOL2_ENST00000358502.5_Frame_Shift_Del_p.A302fs|APOL2_ENST00000451256.2_Frame_Shift_Del_p.A414fs	NM_145637.1	NP_663612.1	Q9BQE5	APOL2_HUMAN	apolipoprotein L, 2	302					acute-phase response (GO:0006953)|cholesterol metabolic process (GO:0008203)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)|maternal process involved in female pregnancy (GO:0060135)|multicellular organismal development (GO:0007275)	endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|membrane (GO:0016020)	high-density lipoprotein particle binding (GO:0008035)|lipid binding (GO:0008289)|receptor binding (GO:0005102)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(1)|skin(1)|urinary_tract(2)	9						TCTGACTTTGCCCCCTCAAGC	0.557																																					p.A302fs		Atlas-INDEL	.											.	APOL2	20	.	0			c.905delC						.						98.0	104.0	102.0					22																	36623560		2203	4300	6503	SO:0001589	frameshift_variant	23780	exon5			.	AF324224	CCDS43014.1	22q12.3	2013-09-20			ENSG00000128335	ENSG00000128335		"""Apolipoproteins"""	619	protein-coding gene	gene with protein product	"""apolipoprotein L-II"""	607252				10591208, 11374903	Standard	NM_145637		Approved	APOL-II	uc003apa.3	Q9BQE5	OTTHUMG00000150634	ENST00000249066.6:c.904delG	chr22.hg19:g.36623560delC	ENSP00000249066:p.Ala302fs	266.0	0.0		166.0	10.0	NM_030882	B0QYK7|O95915|Q59GW9|Q5TH96|Q969T6|Q9BT28|Q9UGT1|Q9UH10	Frame_Shift_Del	DEL	ENST00000249066.6	hg19	CCDS43014.1																																																																																			.	.		0.557	APOL2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000319279.1	NM_145637	
TMEM39B	55116	hgsc.bcm.edu	37	1	32542775	32542775	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:32542775delG	ENST00000336294.5	+	5	592	c.446delG	c.(445-447)aggfs	p.R149fs	TMEM39B_ENST00000373634.4_Intron|TMEM39B_ENST00000487305.1_3'UTR|TMEM39B_ENST00000427288.1_Frame_Shift_Del_p.R34fs|TMEM39B_ENST00000456834.2_Intron	NM_018056.2	NP_060526.2	Q9GZU3	TM39B_HUMAN	transmembrane protein 39B	149						integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|lung(5)|ovary(1)|prostate(2)	11		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.101)|Breast(348;0.174)				GCCTCTCAGAGGGGGAAGGTC	0.622																																					p.R149fs		Atlas-INDEL	.											.	TMEM39B	66	.	0			c.445delA						.						128.0	116.0	120.0					1																	32542775		2203	4300	6503	SO:0001589	frameshift_variant	55116	exon5			.	AL136695	CCDS351.2	1p35.1	2008-02-05			ENSG00000121775	ENSG00000121775			25510	protein-coding gene	gene with protein product						12477932	Standard	NM_018056		Approved	FLJ10315	uc010ogv.2	Q9GZU3	OTTHUMG00000004020	ENST00000336294.5:c.446delG	chr1.hg19:g.32542775delG	ENSP00000338165:p.Arg149fs	225.0	0.0		152.0	11.0	NM_018056	B4DKN8|B4DQE6|B4DTN8|D3DPP4|Q6IA44	Frame_Shift_Del	DEL	ENST00000336294.5	hg19	CCDS351.2																																																																																			.	.		0.622	TMEM39B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011489.2	NM_018056	
DUOX1	53905	hgsc.bcm.edu	37	15	45446158	45446158	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:45446158delC	ENST00000321429.4	+	28	3941	c.3534delC	c.(3532-3534)ctcfs	p.L1178fs	DUOX1_ENST00000389037.3_Frame_Shift_Del_p.L1178fs|CTD-2651B20.1_ENST00000558039.1_lincRNA|DUOX1_ENST00000561166.1_Frame_Shift_Del_p.L824fs|DUOX1_ENST00000559221.1_3'UTR	NM_017434.3	NP_059130.2	Q9NRD9	DUOX1_HUMAN	dual oxidase 1	1178	Ferric oxidoreductase.|Interaction with TXNDC11. {ECO:0000250}.		L -> F (in dbSNP:rs2458236). {ECO:0000269|PubMed:11514595}.		cuticle development (GO:0042335)|cytokine-mediated signaling pathway (GO:0019221)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide biosynthetic process (GO:0050665)|hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)|response to cAMP (GO:0051591)|superoxide anion generation (GO:0042554)|thyroid hormone generation (GO:0006590)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|NAD(P)H oxidase activity (GO:0016174)|NADP binding (GO:0050661)|peroxidase activity (GO:0004601)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(13)|lung(16)|ovary(6)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)	57		all_cancers(109;5.7e-11)|all_epithelial(112;4.65e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;5.77e-18)|GBM - Glioblastoma multiforme(94;5.11e-07)|COAD - Colon adenocarcinoma(120;0.071)|Colorectal(133;0.0717)		GGTCTGAGCTCCCCCAGAAGT	0.493																																					p.L1178fs		Atlas-INDEL	.											.	DUOX1	125	.	0			c.3533delT						.						97.0	88.0	91.0					15																	45446158		2198	4298	6496	SO:0001589	frameshift_variant	53905	exon28			.	AF213465	CCDS32221.1	15q21	2013-01-10				ENSG00000137857		"""EF-hand domain containing"""	3062	protein-coding gene	gene with protein product	"""NADPH thyroid oxidase 1"", ""flavoprotein NADPH oxidase"", ""nicotinamide adenine dinucleotide phosphate oxidase"""	606758				10806195	Standard	XM_005254463		Approved	NOXEF1, THOX1, LNOX1	uc001zut.1	Q9NRD9		ENST00000321429.4:c.3534delC	chr15.hg19:g.45446158delC	ENSP00000317997:p.Leu1178fs	182.0	0.0		152.0	11.0	NM_017434	A6NH28|Q14C94|Q6ZMB3|Q6ZR09|Q9NZC1	Frame_Shift_Del	DEL	ENST00000321429.4	hg19	CCDS32221.1																																																																																			.	.		0.493	DUOX1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416251.1	NM_017434	
PIK3CB	5291	hgsc.bcm.edu	37	3	138461437	138461437	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	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	216.0	0.0		151.0	12.0	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		
ZNF689	115509	hgsc.bcm.edu	37	16	30616564	30616564	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:30616564delT	ENST00000287461.3	-	3	861	c.524delA	c.(523-525)aagfs	p.K175fs	ZNF689_ENST00000566673.1_5'UTR|RP11-146F11.5_ENST00000563540.1_RNA	NM_138447.1	NP_612456.1	Q96CS4	ZN689_HUMAN	zinc finger protein 689	175					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)			AGGGTAAGGCTTTTTTAGATT	0.617																																					p.K175fs		Atlas-INDEL	.											.	ZNF689	48	.	0			c.525delG						.						73.0	79.0	77.0					16																	30616564		2197	4300	6497	SO:0001589	frameshift_variant	115509	exon3			.	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.524delA	chr16.hg19:g.30616564delT	ENSP00000287461:p.Lys175fs	235.0	0.0		166.0	11.0	NM_138447	Q658J5	Frame_Shift_Del	DEL	ENST00000287461.3	hg19	CCDS10686.1																																																																																			.	.		0.617	ZNF689-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255552.1	NM_138447	
ENG	2022	hgsc.bcm.edu	37	9	130592021	130592021	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:130592021delT	ENST00000373203.4	-	3	705	c.305delA	c.(304-306)aacfs	p.N102fs	Y_RNA_ENST00000410489.1_RNA|ENG_ENST00000344849.3_Frame_Shift_Del_p.N102fs	NM_000118.2|NM_001114753.1|NM_001278138.1	NP_000109.1|NP_001108225.1|NP_001265067.1	P17813	EGLN_HUMAN	endoglin	102	Required for interaction with EGL.				artery morphogenesis (GO:0048844)|BMP signaling pathway (GO:0030509)|bone development (GO:0060348)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell migration (GO:0016477)|cell migration involved in endocardial cushion formation (GO:0003273)|cell motility (GO:0048870)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|chronological cell aging (GO:0001300)|detection of hypoxia (GO:0070483)|extracellular matrix constituent secretion (GO:0070278)|extracellular matrix disassembly (GO:0022617)|heart looping (GO:0001947)|intracellular signal transduction (GO:0035556)|negative regulation of cell migration (GO:0030336)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of nitric-oxide synthase activity (GO:0051001)|negative regulation of pathway-restricted SMAD protein phosphorylation (GO:0060394)|negative regulation of protein autophosphorylation (GO:0031953)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|patterning of blood vessels (GO:0001569)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of gene expression (GO:0010628)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of systemic arterial blood pressure (GO:0003084)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell adhesion (GO:0030155)|regulation of cell proliferation (GO:0042127)|regulation of phosphorylation (GO:0042325)|regulation of transcription, DNA-templated (GO:0006355)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|response to corticosteroid (GO:0031960)|response to hypoxia (GO:0001666)|response to statin (GO:0036273)|response to transforming growth factor beta (GO:0071559)|smooth muscle tissue development (GO:0048745)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vasculogenesis (GO:0001570)|venous blood vessel morphogenesis (GO:0048845)|wound healing (GO:0042060)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|endothelial microparticle (GO:0072563)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|transforming growth factor beta receptor homodimeric complex (GO:0070022)	activin binding (GO:0048185)|galactose binding (GO:0005534)|glycosaminoglycan binding (GO:0005539)|protein homodimerization activity (GO:0042803)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta receptor, cytoplasmic mediator activity (GO:0005072)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane signaling receptor activity (GO:0004888)|type I transforming growth factor beta receptor binding (GO:0034713)|type II transforming growth factor beta receptor binding (GO:0005114)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)	17						GACACTGCTGTTTACACTGAG	0.612									Juvenile Polyposis;Hereditary Hemorrhagic Telangiectasia																												p.N102fs		Atlas-INDEL	.											.	ENG	44	.	0			c.306delC						.						125.0	103.0	111.0					9																	130592021		2203	4300	6503	SO:0001589	frameshift_variant	2022	exon3	Familial Cancer Database	incl.: Juvenile Polyposis of the Stomach;HHT, Rendu-Osler-Weber disease, incl.: Pulmonary arteriovenous malformations, hypertrophic osteoarthropathy and juvenile polyposis,	.	AF035753	CCDS6880.1, CCDS48029.1, CCDS75906.1	9q34.11	2014-09-17	2008-09-04		ENSG00000106991	ENSG00000106991		"""CD molecules"""	3349	protein-coding gene	gene with protein product		131195	"""Osler-Rendu-Weber syndrome 1"""	ORW1, ORW		8404038, 10548503	Standard	NM_001278138		Approved	END, HHT1, CD105	uc031tfe.1	P17813	OTTHUMG00000020723	ENST00000373203.4:c.305delA	chr9.hg19:g.130592021delT	ENSP00000362299:p.Asn102fs	204.0	0.0		157.0	10.0	NM_001114753	Q14248|Q14926|Q5T9C0	Frame_Shift_Del	DEL	ENST00000373203.4	hg19	CCDS48029.1																																																																																			.	.		0.612	ENG-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054313.1		
VPS39	23339	hgsc.bcm.edu	37	15	42480005	42480005	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:42480005delT	ENST00000348544.4	-	7	424	c.425delA	c.(424-426)aagfs	p.K143fs	VPS39_ENST00000318006.5_Frame_Shift_Del_p.K132fs			Q96JC1	VPS39_HUMAN	vacuolar protein sorting 39 homolog (S. cerevisiae)	143	CNH. {ECO:0000255|PROSITE- ProRule:PRU00795}.				intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	endosome (GO:0005768)|HOPS complex (GO:0030897)|lysosomal membrane (GO:0005765)	small GTPase regulator activity (GO:0005083)			breast(2)|kidney(5)|large_intestine(4)|lung(8)|ovary(1)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	28		all_cancers(109;6.78e-16)|all_epithelial(112;1.81e-14)|Lung NSC(122;5.01e-09)|all_lung(180;2.24e-08)|Melanoma(134;0.0574)|Colorectal(260;0.152)		GBM - Glioblastoma multiforme(94;3.05e-06)		CTGCAGCTTCTTTTTTACTGC	0.493																																					p.K131fs		Atlas-INDEL	.											.	VPS39	53	.	0			c.393delG						.						214.0	213.0	213.0					15																	42480005		2203	4299	6502	SO:0001589	frameshift_variant	23339	exon6			.	AF280814	CCDS10083.1, CCDS73710.1	15q14	2008-02-05	2006-12-19		ENSG00000166887	ENSG00000166887			20593	protein-coding gene	gene with protein product		612188	"""vacuolar protein sorting 39 (yeast)"""			11448994	Standard	XM_005254259		Approved	KIAA0770, VAM6	uc001zpc.3	Q96JC1	OTTHUMG00000130467	ENST00000348544.4:c.425delA	chr15.hg19:g.42480005delT	ENSP00000335193:p.Lys143fs	239.0	0.0		162.0	11.0	NM_015289	O94869|Q71SQ6|Q7Z3V3|Q96B93|Q96RM0	Frame_Shift_Del	DEL	ENST00000348544.4	hg19	CCDS10083.1																																																																																			.	.		0.493	VPS39-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000420472.1	NM_015289	
MLXIP	22877	hgsc.bcm.edu	37	12	122614541	122614541	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:122614541delC	ENST00000319080.7	+	6	924	c.792delC	c.(790-792)gtcfs	p.V264fs	MLXIP_ENST00000538698.1_5'Flank					MLX interacting protein											NS(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(7)|ovary(3)	20	all_neural(191;0.0837)|Medulloblastoma(191;0.163)	Lung NSC(355;0.0659)		OV - Ovarian serous cystadenocarcinoma(86;0.000599)|Epithelial(86;0.00102)|BRCA - Breast invasive adenocarcinoma(302;0.233)		AGACCCCCGTCCCCATGGAGG	0.557																																					p.V264fs	Esophageal Squamous(105;787 1493 16200 18566 52466)	Atlas-INDEL	.											.	MLXIP	46	.	0			c.791delT						.						65.0	69.0	67.0					12																	122614541		2082	4219	6301	SO:0001589	frameshift_variant	22877	exon6			.	AB020674	CCDS73540.1	12q21.31	2013-05-21				ENSG00000175727		"""Basic helix-loop-helix proteins"""	17055	protein-coding gene	gene with protein product		608090				10048485, 11073985	Standard	XM_006719290		Approved	MONDOA, KIAA0867, MIR, bHLHe36	uc001ubq.3	Q9HAP2		ENST00000319080.7:c.792delC	chr12.hg19:g.122614541delC	ENSP00000312834:p.Val264fs	216.0	0.0		157.0	10.0	NM_014938		Frame_Shift_Del	DEL	ENST00000319080.7	hg19																																																																																				.	.		0.557	MLXIP-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000401718.2	NM_014938	
SGCA	6442	hgsc.bcm.edu	37	17	48245832	48245832	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:48245832delG	ENST00000262018.3	+	5	519	c.483delG	c.(481-483)ttgfs	p.L161fs	SGCA_ENST00000451235.2_Frame_Shift_Del_p.L59fs|SGCA_ENST00000543315.1_Frame_Shift_Del_p.L161fs|HILS1_ENST00000504307.1_RNA|SGCA_ENST00000513942.1_3'UTR|SGCA_ENST00000344627.6_Frame_Shift_Del_p.L161fs	NM_000023.2	NP_000014.1	Q16586	SGCA_HUMAN	sarcoglycan, alpha (50kDa dystrophin-associated glycoprotein)	161					muscle contraction (GO:0006936)|muscle organ development (GO:0007517)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|sarcoglycan complex (GO:0016012)|sarcolemma (GO:0042383)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|lung(7)|ovary(2)|skin(1)	14						TCTCAGCCTTGGGGGGACTCT	0.657																																					p.L161fs		Atlas-INDEL	.											.	SGCA	35	.	0			c.482delT						.						18.0	19.0	19.0					17																	48245832		2200	4297	6497	SO:0001589	frameshift_variant	6442	exon5			.	L34355	CCDS32679.1, CCDS45729.1	17q21	2014-09-17	2002-08-29		ENSG00000108823	ENSG00000108823			10805	protein-coding gene	gene with protein product	"""50kD DAG"", ""Sarcoglycan, alpha (50kD dystrophin-associated glycoprotein; adhalin)"", ""adhalin (limb girdle muscular dystrophy 2D)"""	600119	"""sarcoglycan, alpha (50kD dystrophin-associated glycoprotein)"""	ADL		7937874	Standard	NM_000023		Approved	SCARMD1, LGMD2D, adhalin, DMDA2, A2	uc002iqi.3	Q16586	OTTHUMG00000162024	ENST00000262018.3:c.483delG	chr17.hg19:g.48245832delG	ENSP00000262018:p.Leu161fs	232.0	0.0		163.0	12.0	NM_001135697	A6NEB8|A8K3K7|Q13710|Q13712	Frame_Shift_Del	DEL	ENST00000262018.3	hg19	CCDS32679.1																																																																																			.	.		0.657	SGCA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366841.1	NM_000023	
THG1L	54974	hgsc.bcm.edu	37	5	157160024	157160024	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:157160024delA	ENST00000231198.7	+	2	584	c.340delA	c.(340-342)aaafs	p.K114fs	AC026407.1_ENST00000599823.1_Frame_Shift_Del_p.F57fs	NM_017872.3	NP_060342.2	Q9NWX6	THG1_HUMAN	tRNA-histidine guanylyltransferase 1-like (S. cerevisiae)	114					protein homotetramerization (GO:0051289)|tRNA modification (GO:0006400)|tRNA processing (GO:0008033)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|identical protein binding (GO:0042802)|magnesium ion binding (GO:0000287)|tRNA binding (GO:0000049)|tRNA guanylyltransferase activity (GO:0008193)			NS(1)|central_nervous_system(2)|kidney(1)|large_intestine(1)|lung(5)|prostate(2)|skin(1)	13	Renal(175;0.00488)	Medulloblastoma(196;0.0523)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			GTTCAAGCGGAAAACCAATTG	0.423																																					p.R113fs		Atlas-INDEL	.											.	THG1L	31	.	0			c.339delG						.						157.0	141.0	147.0					5																	157160024		2203	4300	6503	SO:0001589	frameshift_variant	54974	exon2			.	AK223119	CCDS4341.1	5q33.3	2008-02-05			ENSG00000113272	ENSG00000113272			26053	protein-coding gene	gene with protein product	"""interphase cytoplasmic foci protein 45"""					11230166	Standard	XM_005265939		Approved	ICF45, FLJ11601, FLJ20546	uc003lxd.3	Q9NWX6	OTTHUMG00000130254	ENST00000231198.7:c.340delA	chr5.hg19:g.157160024delA	ENSP00000231198:p.Lys114fs	247.0	0.0		171.0	11.0	NM_017872	D3DQJ5|Q53G12|Q7L5R3|Q9H0S2	Frame_Shift_Del	DEL	ENST00000231198.7	hg19	CCDS4341.1																																																																																			.	.		0.423	THG1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252579.2	NM_017872	
ZYG11B	79699	hgsc.bcm.edu	37	1	53287272	53287272	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:53287272delA	ENST00000294353.6	+	14	2351	c.2206delA	c.(2206-2208)aaafs	p.K737fs	ZYG11B_ENST00000443756.2_Frame_Shift_Del_p.K667fs	NM_024646.2	NP_078922.1	Q9C0D3	ZY11B_HUMAN	zyg-11 family member B, cell cycle regulator	737										breast(1)|endometrium(1)|kidney(6)|large_intestine(5)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	30						ACCTCCCTGTAAAAAACAGCC	0.433																																					p.C735X		Atlas-INDEL	.											.	ZYG11B	61	.	0			c.2205delT						.						67.0	66.0	66.0					1																	53287272		2203	4300	6503	SO:0001589	frameshift_variant	79699	exon14			.	AB051517	CCDS30717.1	1p32.3	2013-01-17	2012-12-10	2005-07-11	ENSG00000162378	ENSG00000162378		"""ZYG11 cell cycle regulator family"""	25820	protein-coding gene	gene with protein product			"""zyg-11 homolog (C. elegans)"", ""zyg-11 homolog B (C. elegans)"""	ZYG11		11214970	Standard	NM_024646		Approved	FLJ13456	uc001cuj.3	Q9C0D3	OTTHUMG00000008938	ENST00000294353.6:c.2206delA	chr1.hg19:g.53287272delA	ENSP00000294353:p.Lys737fs	276.0	0.0		222.0	15.0	NM_024646	Q8N2X3|Q9H8L8	Frame_Shift_Del	DEL	ENST00000294353.6	hg19	CCDS30717.1																																																																																			.	.		0.433	ZYG11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024749.1	NM_024646	
COL11A2	1302	hgsc.bcm.edu	37	6	33136315	33136315	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:33136315delG	ENST00000374708.4	-	52	3941	c.3683delC	c.(3682-3684)ccafs	p.P1228fs	COL11A2_ENST00000374713.1_Frame_Shift_Del_p.P1267fs|COL11A2_ENST00000477772.1_Intron|COL11A2_ENST00000395197.1_Frame_Shift_Del_p.P1254fs|COL11A2_ENST00000361917.1_Frame_Shift_Del_p.P1207fs|COL11A2_ENST00000374714.1_Frame_Shift_Del_p.P1288fs|COL11A2_ENST00000357486.1_Frame_Shift_Del_p.P1293fs|COL11A2_ENST00000374712.1_Frame_Shift_Del_p.P1233fs|COL11A2_ENST00000341947.2_Frame_Shift_Del_p.P1314fs	NM_080681.2	NP_542412.2	P13942	COBA2_HUMAN	collagen, type XI, alpha 2	1314	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						AAGTGGCCCTGGGGGTCCATT	0.632																																					p.P1314fs	Melanoma(1;90 116 3946 5341 17093)	Atlas-INDEL	.											.	COL11A2	124	.	0			c.3942delA						.						52.0	48.0	49.0					6																	33136315		1511	2709	4220	SO:0001589	frameshift_variant	1302	exon54			.	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.3683delC	chr6.hg19:g.33136315delG	ENSP00000363840:p.Pro1228fs	142.0	0.0		119.0	10.0	NM_080680	A6NLX2|E7ER90|Q07751|Q13271|Q13272|Q13273|Q5JP94|Q5SUI8|Q7Z6C3|Q99866|Q9UIP9	Frame_Shift_Del	DEL	ENST00000374708.4	hg19	CCDS43452.1																																																																																			.	.		0.632	COL11A2-001	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076032.2		
SLC13A2	9058	hgsc.bcm.edu	37	17	26817514	26817514	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:26817514delG	ENST00000314669.5	+	3	694	c.274delG	c.(274-276)gggfs	p.G93fs	SLC13A2_ENST00000545060.1_Frame_Shift_Del_p.G50fs|SLC13A2_ENST00000537681.1_Frame_Shift_Del_p.G22fs|SLC13A2_ENST00000444914.3_Frame_Shift_Del_p.G142fs	NM_003984.3	NP_003975.1	Q13183	S13A2_HUMAN	solute carrier family 13 (sodium-dependent dicarboxylate transporter), member 2	93					dicarboxylic acid transport (GO:0006835)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	low-affinity sodium:dicarboxylate symporter activity (GO:0015361)			breast(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26	all_lung(13;0.000871)|Lung NSC(42;0.0027)			UCEC - Uterine corpus endometrioid carcinoma (53;0.154)	Succinic acid(DB00139)	CCTGTTCTTCGGGGGGCTGCT	0.637																																					p.F140fs		Atlas-INDEL	.											.	SLC13A2	125	.	0			c.420delC						.						124.0	110.0	115.0					17																	26817514		2203	4300	6503	SO:0001589	frameshift_variant	9058	exon3			.	U26209	CCDS11231.1, CCDS54098.1	17p13.2	2013-05-22			ENSG00000007216	ENSG00000007216		"""Solute carriers"""	10917	protein-coding gene	gene with protein product		604148				8967342, 10343111	Standard	NM_001145975		Approved	NaDC-1	uc010wan.2	Q13183	OTTHUMG00000132523	ENST00000314669.5:c.274delG	chr17.hg19:g.26817514delG	ENSP00000316202:p.Gly93fs	223.0	0.0		148.0	11.0	NM_001145975	B2RBI9|B4DPL1|E7ETH5|Q4VAR7	Frame_Shift_Del	DEL	ENST00000314669.5	hg19	CCDS11231.1																																																																																			.	.		0.637	SLC13A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255722.1	NM_003984	
STXBP5	134957	hgsc.bcm.edu	37	6	147648266	147648266	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:147648266delT	ENST00000321680.6	+	18	1934	c.1934delT	c.(1933-1935)gttfs	p.V645fs	STXBP5_ENST00000179882.6_Frame_Shift_Del_p.V316fs|STXBP5_ENST00000367481.3_Frame_Shift_Del_p.V645fs|STXBP5_ENST00000367480.3_Frame_Shift_Del_p.V645fs	NM_001127715.2	NP_001121187.1	Q5T5C0	STXB5_HUMAN	syntaxin binding protein 5 (tomosyn)	645					exocytosis (GO:0006887)|negative regulation of exocytosis (GO:0045920)|positive regulation of exocytosis (GO:0045921)|protein transport (GO:0015031)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|synapse (GO:0045202)	syntaxin-1 binding (GO:0017075)			breast(2)|endometrium(4)|kidney(3)|large_intestine(6)|lung(21)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	42		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;1.77e-09)|GBM - Glioblastoma multiforme(68;0.0694)		CCCAGGGTGGTTTTTGGCAAT	0.388																																					p.V645fs		Atlas-INDEL	.											.	STXBP5	163	.	0			c.1933delG						.						155.0	145.0	149.0					6																	147648266		2203	4300	6503	SO:0001589	frameshift_variant	134957	exon18			.	AK055484	CCDS5211.1, CCDS47499.1	6q24.3	2013-01-10			ENSG00000164506	ENSG00000164506		"""WD repeat domain containing"""	19665	protein-coding gene	gene with protein product		604586				9620695, 14767561	Standard	NM_139244		Approved	tomosyn, LLGL3	uc010khz.2	Q5T5C0	OTTHUMG00000015766	ENST00000321680.6:c.1934delT	chr6.hg19:g.147648266delT	ENSP00000321826:p.Val645fs	198.0	0.0		140.0	12.0	NM_139244	Q14DF3|Q5T5C1|Q5T5C2|Q8NBG8|Q96NG9	Frame_Shift_Del	DEL	ENST00000321680.6	hg19	CCDS47499.1																																																																																			.	.		0.388	STXBP5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042606.1		
PMS1	5378	hgsc.bcm.edu	37	2	190719401	190719401	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:190719401delA	ENST00000441310.2	+	9	1636	c.1403delA	c.(1402-1404)gaafs	p.E468fs	PMS1_ENST00000447232.2_Frame_Shift_Del_p.E468fs|PMS1_ENST00000409823.3_Frame_Shift_Del_p.E429fs|PMS1_ENST00000421722.1_3'UTR|PMS1_ENST00000432292.3_Frame_Shift_Del_p.E292fs|PMS1_ENST00000418224.3_Frame_Shift_Del_p.E292fs	NM_000534.4	NP_000525.1	P54277	PMS1_HUMAN	PMS1 postmeiotic segregation increased 1 (S. cerevisiae)	468					ATP catabolic process (GO:0006200)|mismatch repair (GO:0006298)|response to drug (GO:0042493)	MutLalpha complex (GO:0032389)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|mismatched DNA binding (GO:0030983)|single-stranded DNA binding (GO:0003697)	p.N469fs*7(1)		breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(5)|lung(16)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36			OV - Ovarian serous cystadenocarcinoma(117;0.0013)|Epithelial(96;0.0263)|all cancers(119;0.0751)			ACCCAGTCAGAAAATGGCAAT	0.403			"""Mis, N"""			"""colorectal, endometrial, ovarian"""		Direct reversal of damage;Mismatch excision repair (MMR)																													p.E468fs		Atlas-INDEL	.	yes	Rec		Hereditary non-polyposis colorectal cancer	2	2q31-q33	5378	PMS1 postmeiotic segregation increased 1 (S. cerevisiae)		E	.	PMS1	78	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1402delG						.						54.0	58.0	56.0					2																	190719401		2202	4297	6499	SO:0001589	frameshift_variant	5378	exon9			.		CCDS2302.1, CCDS46473.1, CCDS46474.1, CCDS74615.1	2q31-q33	2014-09-17	2001-11-28		ENSG00000064933	ENSG00000064933			9121	protein-coding gene	gene with protein product		600258	"""postmeiotic segregation increased (S. cerevisiae) 1"""	PMSL1		8072530	Standard	NM_000534		Approved		uc002urh.4	P54277	OTTHUMG00000132664	ENST00000441310.2:c.1403delA	chr2.hg19:g.190719401delA	ENSP00000406490:p.Glu468fs	169.0	0.0		121.0	10.0	NM_001128144	D3DPI1|Q4VAL4|Q5FBZ3|Q5FBZ6|Q5FBZ8	Frame_Shift_Del	DEL	ENST00000441310.2	hg19	CCDS2302.1																																																																																			.	.		0.403	PMS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255918.2		
NOM1	64434	hgsc.bcm.edu	37	7	156755794	156755794	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:156755794delG	ENST00000275820.3	+	6	1851	c.1836delG	c.(1834-1836)gtgfs	p.V612fs		NM_138400.1	NP_612409.1	Q5C9Z4	NOM1_HUMAN	nucleolar protein with MIF4G domain 1	612						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)		GGTGGATTGTGGGGTCCGCCT	0.622																																					p.V612fs		Atlas-INDEL	.											.	NOM1	73	.	0			c.1835delT						.						53.0	46.0	48.0					7																	156755794		2203	4300	6503	SO:0001589	frameshift_variant	64434	exon6			.	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.1836delG	chr7.hg19:g.156755794delG	ENSP00000275820:p.Val612fs	129.0	0.0		155.0	12.0	NM_138400	Q96I08	Frame_Shift_Del	DEL	ENST00000275820.3	hg19	CCDS34787.1																																																																																			.	.		0.622	NOM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327098.1	NM_138400	
CRYBB3	1417	hgsc.bcm.edu	37	22	25603032	25603032	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr22:25603032delC	ENST00000215855.2	+	6	569	c.489delC	c.(487-489)ttcfs	p.F163fs	CRYBB3_ENST00000404334.1_3'UTR	NM_004076.3	NP_004067.1	P26998	CRBB3_HUMAN	crystallin, beta B3	163	Beta/gamma crystallin 'Greek key' 4. {ECO:0000255|PROSITE-ProRule:PRU00028}.				visual perception (GO:0007601)		structural constituent of eye lens (GO:0005212)			large_intestine(2)|lung(2)|prostate(1)	5						GCTATGAGTTCCCCGGCTACC	0.642																																					p.L163fs		Atlas-INDEL	.											.	CRYBB3	13	.	0			c.488delT						.						69.0	60.0	63.0					22																	25603032		2203	4298	6501	SO:0001589	frameshift_variant	1417	exon6			.		CCDS13830.1	22q11.23	2008-06-10			ENSG00000100053	ENSG00000100053			2400	protein-coding gene	gene with protein product		123630		CRYB3		8999933	Standard	NM_004076		Approved		uc003abo.2	P26998	OTTHUMG00000150869	ENST00000215855.2:c.489delC	chr22.hg19:g.25603032delC	ENSP00000215855:p.Phe163fs	212.0	0.0		139.0	10.0	NM_004076	Q3B7S9|Q3T1B7|Q6ISK6|Q92965|Q9UH09	Frame_Shift_Del	DEL	ENST00000215855.2	hg19	CCDS13830.1																																																																																			.	.		0.642	CRYBB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320352.1	NM_004076	
MGA	23269	hgsc.bcm.edu	37	15	42054541	42054541	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:42054541delA	ENST00000570161.1	+	21	7725	c.7725delA	c.(7723-7725)agafs	p.R2575fs	MGA_ENST00000219905.7_Frame_Shift_Del_p.R2575fs|MGA_ENST00000389936.4_Frame_Shift_Del_p.R2536fs|MGA_ENST00000545763.1_Frame_Shift_Del_p.R2366fs|MGA_ENST00000566586.1_Frame_Shift_Del_p.R2366fs			O43451	MGA_HUMAN	MGA, MAX dimerization protein	0					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)			NS(1)|breast(4)|central_nervous_system(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(33)|ovary(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)	Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	TTCTTTCCAGAAAAAAAGACC	0.423																																					p.R2575fs		Atlas-INDEL	.											.,1	MGA	264	.	0			c.7724delG						.						72.0	73.0	73.0					15																	42054541		1839	4074	5913	SO:0001589	frameshift_variant	23269	exon22			.	AB011090	CCDS55959.1, CCDS55960.1	15q15	2012-11-15	2012-11-15		ENSG00000174197	ENSG00000174197		"""MAX dimerization proteins"", ""T-boxes"""	14010	protein-coding gene	gene with protein product			"""MAX gene associated"""				Standard	NM_001080541		Approved	KIAA0518, MAD5, MXD5, FLJ12634	uc010ucy.2	Q8IWI9		ENST00000570161.1:c.7725delA	chr15.hg19:g.42054541delA	ENSP00000457035:p.Arg2575fs	248.0	0.0		155.0	10.0	NM_001164273	Q0VAX6|Q75ME7|Q86UM5	Frame_Shift_Del	DEL	ENST00000570161.1	hg19	CCDS55959.1																																																																																			.	.		0.423	MGA-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420229.1	NM_001164273.1	
FAM83B	222584	hgsc.bcm.edu	37	6	54806060	54806060	+	Frame_Shift_Del	DEL	C	C	-	rs200345393	byFrequency	TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:54806060delC	ENST00000306858.7	+	5	2407	c.2291delC	c.(2290-2292)tccfs	p.S764fs	RP3-523K23.2_ENST00000562834.1_RNA	NM_001010872.1	NP_001010872.1	Q5T0W9	FA83B_HUMAN	family with sequence similarity 83, member B	764										autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(28)|ovary(6)|prostate(6)|skin(6)|upper_aerodigestive_tract(1)	71	Lung NSC(77;0.0178)|Renal(3;0.122)					GTTAAGGGTTCCCCAAGTTTT	0.373																																					p.S764fs		Atlas-INDEL	.											.	FAM83B	186	.	0			c.2290delT						.						56.0	59.0	58.0					6																	54806060		2203	4300	6503	SO:0001589	frameshift_variant	222584	exon5			.	AK055204	CCDS34479.1	6p12.1	2014-03-13	2006-03-23	2006-03-23	ENSG00000168143	ENSG00000168143			21357	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 143"""	C6orf143		22886302	Standard	NM_001010872		Approved	FLJ30642	uc003pck.4	Q5T0W9	OTTHUMG00000014899	ENST00000306858.7:c.2291delC	chr6.hg19:g.54806060delC	ENSP00000304078:p.Ser764fs	126.0	0.0		77.0	10.0	NM_001010872	Q2M1P3|Q96DQ2	Frame_Shift_Del	DEL	ENST00000306858.7	hg19	CCDS34479.1																																																																																			.	.		0.373	FAM83B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040994.1	XM_294139	
CYP4B1	1580	hgsc.bcm.edu	37	1	47284400	47284400	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:47284400delC	ENST00000271153.4	+	12	1486	c.1450delC	c.(1450-1452)cccfs	p.P484fs	CYP4B1_ENST00000452782.2_Frame_Shift_Del_p.P322fs|CYP4B1_ENST00000371923.4_Frame_Shift_Del_p.P485fs|CYP4B1_ENST00000371919.4_Frame_Shift_Del_p.P470fs			P13584	CP4B1_HUMAN	cytochrome P450, family 4, subfamily B, polypeptide 1	484					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)	CTCACGGCTGCCCATCAAGAT	0.567																																					p.L484fs		Atlas-INDEL	.											.	CYP4B1	81	.	0			c.1452delG						.						144.0	127.0	132.0					1																	47284400		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.1450delC	chr1.hg19:g.47284400delC	ENSP00000271153:p.Pro484fs	245.0	0.0		166.0	10.0	NM_001099772	Q1HBI2|Q8TD85|Q8WWF2|Q8WWU9|Q8WWV0	Frame_Shift_Del	DEL	ENST00000271153.4	hg19	CCDS542.1																																																																																			.	.		0.567	CYP4B1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000021911.1	NM_000779	
EYS	346007	hgsc.bcm.edu	37	6	65301367	65301367	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:65301367delC	ENST00000370621.3	-	26	4919	c.4393delG	c.(4393-4395)gctfs	p.A1465fs	EYS_ENST00000503581.1_Frame_Shift_Del_p.A1465fs|EYS_ENST00000370616.2_Frame_Shift_Del_p.A1465fs			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	1465					detection of light stimulus involved in visual perception (GO:0050908)|skeletal muscle tissue regeneration (GO:0043403)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	69						TCCTCTTGAGCCCCCCTAGAG	0.463																																					p.A1465fs		Atlas-INDEL	.											EYS_ENST00000370621,NS,carcinoma,0,1	EYS	527	.	0			c.4394delC						.						53.0	54.0	54.0					6																	65301367		692	1591	2283	SO:0001589	frameshift_variant	346007	exon26			.		CCDS4967.1, CCDS47445.1, CCDS47446.1	6q12	2014-01-28	2008-10-20	2008-10-20	ENSG00000188107	ENSG00000188107			21555	protein-coding gene	gene with protein product		612424	"""chromosome 6 open reading frame 180"", ""EGF-like-domain, multiple 11"", ""retinitis pigmentosa 25 (autosomal recessive)"", ""EGF-like-domain, multiple 10"", ""chromosome 6 open reading frame 178"", ""chromosome 6 open reading frame 179"""	C6orf180, EGFL11, RP25, EGFL10, C6orf178, C6orf179		18836446, 18976725	Standard	NM_001142800		Approved	dJ1018A4.2, bA166P24.2, SPAM, bA307F22.3, dJ303F19.1, bA74E24.1	uc011dxu.1	Q5T1H1	OTTHUMG00000014971	ENST00000370621.3:c.4393delG	chr6.hg19:g.65301367delC	ENSP00000359655:p.Ala1465fs	266.0	0.0		157.0	10.0	NM_001142800	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Frame_Shift_Del	DEL	ENST00000370621.3	hg19																																																																																				.	.		0.463	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050	
RAPGEF4	11069	hgsc.bcm.edu	37	2	173866030	173866030	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:173866030delT	ENST00000397081.3	+	17	1759	c.1616delT	c.(1615-1617)gttfs	p.V539fs	RAPGEF4_ENST00000539331.1_Frame_Shift_Del_p.V386fs|RAPGEF4_ENST00000538974.1_Frame_Shift_Del_p.V368fs|RAPGEF4_ENST00000397087.3_Frame_Shift_Del_p.V395fs|RAPGEF4_ENST00000540783.1_Frame_Shift_Del_p.V386fs|RAPGEF4_ENST00000264111.6_Frame_Shift_Del_p.V538fs|RAPGEF4_ENST00000409036.1_Frame_Shift_Del_p.V539fs|RAPGEF4_ENST00000535187.1_Frame_Shift_Del_p.V319fs	NM_007023.3	NP_008954.2	Q8WZA2	RPGF4_HUMAN	Rap guanine nucleotide exchange factor (GEF) 4	539	N-terminal Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00135}.				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)			ATGCACTGTGTTTTTATGCCA	0.408																																					p.V539fs		Atlas-INDEL	.											.	RAPGEF4	103	.	0			c.1615delG						.						189.0	166.0	173.0					2																	173866030		1826	4086	5912	SO:0001589	frameshift_variant	11069	exon17			.	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.1616delT	chr2.hg19:g.173866030delT	ENSP00000380271:p.Val539fs	215.0	0.0		118.0	10.0	NM_007023	B2R7R3|B7Z283|B7Z3T6|B7Z912|O95636|Q8IXK6|Q8TAA4	Frame_Shift_Del	DEL	ENST00000397081.3	hg19	CCDS42775.1																																																																																			.	.		0.408	RAPGEF4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257864.2	NM_007023	
BTBD8	284697	hgsc.bcm.edu	37	1	92568057	92568057	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:92568057delA	ENST00000342818.3	+	3	611	c.375delA	c.(373-375)atafs	p.I125fs	BTBD8_ENST00000540648.1_Frame_Shift_Del_p.I125fs|BTBD8_ENST00000370382.3_Frame_Shift_Del_p.I125fs	NM_183242.3	NP_899065.2	Q5XKL5	BTBD8_HUMAN	BTB (POZ) domain containing 8	125	BTB 1. {ECO:0000255|PROSITE- ProRule:PRU00037}.					nucleus (GO:0005634)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(8)|ovary(1)	16		all_lung(203;0.0484)|Lung NSC(277;0.126)|Glioma(108;0.222)		all cancers(265;0.0153)|Epithelial(280;0.0982)		ACAGAAACATAAAAAACTATG	0.269																																					p.I125fs		Atlas-INDEL	.											.	BTBD8	32	.	0			c.374delT						.						37.0	37.0	37.0					1																	92568057		2201	4297	6498	SO:0001589	frameshift_variant	284697	exon3			.	AY346333	CCDS737.1	1p22.1	2013-01-08			ENSG00000189195	ENSG00000189195		"""BTB/POZ domain containing"""	21019	protein-coding gene	gene with protein product						14654994	Standard	NM_183242		Approved		uc001doo.3	Q5XKL5	OTTHUMG00000010289	ENST00000342818.3:c.375delA	chr1.hg19:g.92568057delA	ENSP00000343686:p.Ile125fs	180.0	0.0		150.0	12.0	NM_183242	Q6V9S5	Frame_Shift_Del	DEL	ENST00000342818.3	hg19	CCDS737.1																																																																																			.	.		0.269	BTBD8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028372.1	NM_183242	
NPC1	4864	hgsc.bcm.edu	37	18	21141327	21141327	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr18:21141327delA	ENST00000269228.5	-	5	1182	c.628delT	c.(628-630)tcafs	p.S210fs	NPC1_ENST00000412552.2_5'Flank|NPC1_ENST00000540608.1_5'UTR	NM_000271.4	NP_000262.2	O15118	NPC1_HUMAN	Niemann-Pick disease, type C1	210					adult walking behavior (GO:0007628)|autophagy (GO:0006914)|bile acid metabolic process (GO:0008206)|cellular response to low-density lipoprotein particle stimulus (GO:0071404)|cellular response to steroid hormone stimulus (GO:0071383)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|endocytosis (GO:0006897)|establishment of protein localization to membrane (GO:0090150)|lysosomal transport (GO:0007041)|membrane raft organization (GO:0031579)|negative regulation of cell death (GO:0060548)|negative regulation of macroautophagy (GO:0016242)|protein glycosylation (GO:0006486)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|signal transduction (GO:0007165)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|membrane raft (GO:0045121)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)	cholesterol binding (GO:0015485)|hedgehog receptor activity (GO:0008158)|receptor activity (GO:0004872)|sterol transporter activity (GO:0015248)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(10)|lung(13)|ovary(2)|stomach(1)	38	all_cancers(21;0.000106)|all_epithelial(16;6.57e-07)|Lung NSC(20;0.00166)|all_lung(20;0.00536)|Colorectal(14;0.0202)|Ovarian(20;0.127)					TACCTACCTGAAAACACAGGA	0.463																																					p.S210X		Atlas-INDEL	.											.	NPC1	114	.	0			c.629delC						.						169.0	153.0	158.0					18																	21141327		2203	4300	6503	SO:0001589	frameshift_variant	4864	exon5			.	AF002020	CCDS11878.1	18q11.2	2014-06-17			ENSG00000141458	ENSG00000141458			7897	protein-coding gene	gene with protein product		607623				8446622	Standard	NM_000271		Approved		uc002kum.4	O15118	OTTHUMG00000131873	ENST00000269228.5:c.628delT	chr18.hg19:g.21141327delA	ENSP00000269228:p.Ser210fs	180.0	0.0		127.0	10.0	NM_000271	B4DET3|Q9P130	Frame_Shift_Del	DEL	ENST00000269228.5	hg19	CCDS11878.1																																																																																			.	.		0.463	NPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254823.2	NM_000271	
SLIT1	6585	hgsc.bcm.edu	37	10	98766401	98766401	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:98766401delC	ENST00000266058.4	-	32	3663	c.3418delG	c.(3418-3420)gccfs	p.A1140fs	ARHGAP19-SLIT1_ENST00000453547.2_3'UTR|SLIT1_ENST00000371070.4_Frame_Shift_Del_p.A1140fs	NM_003061.2	NP_003052.2	O75093	SLIT1_HUMAN	slit homolog 1 (Drosophila)	1140	EGF-like 6. {ECO:0000255|PROSITE- ProRule:PRU00076}.				axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|dorsal/ventral axon guidance (GO:0033563)|establishment of nucleus localization (GO:0040023)|forebrain morphogenesis (GO:0048853)|motor neuron axon guidance (GO:0008045)|negative chemotaxis (GO:0050919)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of synapse assembly (GO:0051964)|retinal ganglion cell axon guidance (GO:0031290)|spinal cord development (GO:0021510)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)	extracellular space (GO:0005615)	calcium ion binding (GO:0005509)|Roundabout binding (GO:0048495)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(37)|ovary(5)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	78		Colorectal(252;0.162)		Epithelial(162;2.02e-08)|all cancers(201;1.5e-06)		ACACAGTTGGCCCCATTCTGG	0.592																																					p.A1140fs		Atlas-INDEL	.											.	SLIT1	154	.	0			c.3419delC						.						49.0	41.0	44.0					10																	98766401		2203	4300	6503	SO:0001589	frameshift_variant	6585	exon32			.	AB011537	CCDS7453.1	10q23.3-q24	2008-08-01	2001-11-28		ENSG00000187122	ENSG00000187122			11085	protein-coding gene	gene with protein product		603742	"""slit (Drosophila) homolog 1"""	SLIL1		9693030, 9813312	Standard	NM_003061		Approved	slit1, MEGF4, Slit-1, SLIT3	uc001kmw.2	O75093	OTTHUMG00000018843	ENST00000266058.4:c.3418delG	chr10.hg19:g.98766401delC	ENSP00000266058:p.Ala1140fs	190.0	0.0		137.0	10.0	NM_003061	Q5T0V1|Q8WWZ2|Q9UIL7	Frame_Shift_Del	DEL	ENST00000266058.4	hg19	CCDS7453.1																																																																																			.	.		0.592	SLIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049636.1	NM_003061	
ABCA5	23461	hgsc.bcm.edu	37	17	67285378	67285378	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:67285378delT	ENST00000392676.3	-	14	1906	c.1842delA	c.(1840-1842)aaafs	p.K614fs	ABCA5_ENST00000588877.1_Frame_Shift_Del_p.K614fs|ABCA5_ENST00000392677.2_Frame_Shift_Del_p.K614fs			Q8WWZ7	ABCA5_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 5	614	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				cholesterol efflux (GO:0033344)|high-density lipoprotein particle remodeling (GO:0034375)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|reverse cholesterol transport (GO:0043691)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosome (GO:0005764)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(18)|lung(19)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	54	Breast(10;3.72e-11)				Tacrolimus(DB00864)	CACCACTTAATTTTTTAGCTT	0.303																																					p.L615X		Atlas-INDEL	.											ABCA5,NS,carcinoma,0,1	ABCA5	162	.	0			c.1843delT						.						93.0	91.0	92.0					17																	67285378		2203	4297	6500	SO:0001589	frameshift_variant	23461	exon13			.	U66672	CCDS11685.1	17q24.3	2012-03-14			ENSG00000154265	ENSG00000154265		"""ATP binding cassette transporters / subfamily A"""	35	protein-coding gene	gene with protein product		612503				8894702	Standard	NM_172232		Approved	EST90625	uc002jig.2	Q8WWZ7		ENST00000392676.3:c.1842delA	chr17.hg19:g.67285378delT	ENSP00000376443:p.Lys614fs	217.0	0.0		199.0	12.0	NM_018672	Q8IVJ2|Q96LJ1|Q96MS4|Q96PZ9|Q9NY14	Frame_Shift_Del	DEL	ENST00000392676.3	hg19	CCDS11685.1																																																																																			.	.		0.303	ABCA5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450654.1	NM_018672	
MPV17L2	84769	hgsc.bcm.edu	37	19	18305819	18305819	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:18305819delC	ENST00000599612.2	+	4	587	c.487delC	c.(487-489)cccfs	p.P164fs		NM_032683.2	NP_116072.2	Q567V2	M17L2_HUMAN	MPV17 mitochondrial membrane protein-like 2	164						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				large_intestine(1)|lung(2)|urinary_tract(1)	4						CCTCTTCGTGCCCCCCCAATT	0.652																																					p.V162fs		Atlas-INDEL	.											.	MPV17L2	12	.	0			c.486delG						.						114.0	114.0	114.0					19																	18305819		2081	4206	6287	SO:0001589	frameshift_variant	84769	exon4			.	AK094091	CCDS42522.1	19p13.11	2011-05-26			ENSG00000254858	ENSG00000254858			28177	protein-coding gene	gene with protein product						12477932	Standard	NM_032683		Approved	FKSG24, MGC12972	uc002nid.3	Q567V2	OTTHUMG00000165628	ENST00000599612.2:c.487delC	chr19.hg19:g.18305819delC	ENSP00000469836:p.Pro164fs	190.0	0.0		137.0	10.0	NM_032683	Q96P34|Q96QA0|Q9BSG4	Frame_Shift_Del	DEL	ENST00000599612.2	hg19	CCDS42522.1																																																																																			.	.		0.652	MPV17L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466294.2	NM_032683	
NAV3	89795	hgsc.bcm.edu	37	12	78443808	78443808	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:78443808delA	ENST00000397909.2	+	10	2232	c.2059delA	c.(2059-2061)aaafs	p.K687fs	NAV3_ENST00000266692.7_Frame_Shift_Del_p.K687fs|NAV3_ENST00000228327.6_Frame_Shift_Del_p.K687fs|RP11-136F16.1_ENST00000549103.1_RNA|NAV3_ENST00000536525.2_Frame_Shift_Del_p.K687fs			Q8IVL0	NAV3_HUMAN	neuron navigator 3	687						membrane (GO:0016020)|nuclear envelope (GO:0005635)				NS(2)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(13)|kidney(16)|large_intestine(39)|liver(2)|lung(126)|ovary(5)|pancreas(3)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(1)	236						GAGAACAGTTAAAAACATAGC	0.343										HNSCC(70;0.22)																											p.V686fs		Atlas-INDEL	.											.	NAV3	506	.	0			c.2058delT						.						85.0	84.0	85.0					12																	78443808		1843	4084	5927	SO:0001589	frameshift_variant	89795	exon10			.	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.2059delA	chr12.hg19:g.78443808delA	ENSP00000381007:p.Lys687fs	177.0	0.0		153.0	13.0	NM_014903	Q8NFW7|Q9Y2E7	Frame_Shift_Del	DEL	ENST00000397909.2	hg19																																																																																				.	.		0.343	NAV3-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000406812.1	NM_001024383	
SUV420H1	51111	hgsc.bcm.edu	37	11	67934514	67934514	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:67934514delT	ENST00000304363.4	-	10	1462	c.1109delA	c.(1108-1110)aatfs	p.N370fs	SUV420H1_ENST00000405515.1_Frame_Shift_Del_p.N370fs|SUV420H1_ENST00000402789.1_Frame_Shift_Del_p.N370fs|SUV420H1_ENST00000401547.2_Frame_Shift_Del_p.N370fs|SUV420H1_ENST00000402185.2_Frame_Shift_Del_p.N347fs	NM_017635.3	NP_060105	Q4FZB7	SV421_HUMAN	suppressor of variegation 4-20 homolog 1 (Drosophila)	370					histone H4-K20 trimethylation (GO:0034773)|muscle organ development (GO:0007517)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	condensed nuclear chromosome, centromeric region (GO:0000780)	histone methyltransferase activity (H4-K20 specific) (GO:0042799)|histone-lysine N-methyltransferase activity (GO:0018024)			NS(1)|breast(3)|endometrium(4)|kidney(3)|large_intestine(9)|lung(15)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	46						ACTGTCTGAATTTTTGCTGCT	0.383																																					p.N370fs		Atlas-INDEL	.											.	SUV420H1	125	.	0			c.1110delT						.						161.0	149.0	153.0					11																	67934514		2200	4294	6494	SO:0001589	frameshift_variant	51111	exon10			.	AL512763	CCDS31623.1, CCDS44660.1	11q13.2	2011-07-01			ENSG00000110066	ENSG00000110066		"""Chromatin-modifying enzymes / K-methyltransferases"""	24283	protein-coding gene	gene with protein product		610881				10810093, 11401438	Standard	NM_016028		Approved	CGI-85, KMT5B	uc001onm.1	Q4FZB7	OTTHUMG00000150484	ENST00000304363.4:c.1109delA	chr11.hg19:g.67934514delT	ENSP00000305899:p.Asn370fs	254.0	0.0		206.0	15.0	NM_017635	B7WNX7|Q3SX56|Q4V775|Q6P150|Q96E44|Q9BUL0|Q9H022|Q9H2K3|Q9NXV3|Q9Y393	Frame_Shift_Del	DEL	ENST00000304363.4	hg19	CCDS31623.1																																																																																			.	.		0.383	SUV420H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318319.1	NM_017635	
STH	246744	hgsc.bcm.edu	37	17	44076686	44076686	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:44076686delC	ENST00000537309.1	+	1	71	c.41delC	c.(40-42)gccfs	p.A14fs	MAPT_ENST00000446361.3_Intron|MAPT_ENST00000576518.1_Intron|MAPT_ENST00000262410.5_Intron|MAPT_ENST00000347967.5_Intron|MAPT_ENST00000351559.5_Intron|MAPT_ENST00000535772.1_Intron|MAPT_ENST00000431008.3_Intron|MAPT_ENST00000571987.1_Intron|MAPT_ENST00000420682.2_Intron|MAPT_ENST00000340799.5_Intron|MAPT_ENST00000334239.8_Intron|MAPT_ENST00000574436.1_Intron|MAPT_ENST00000415613.2_Intron|MAPT_ENST00000344290.5_Intron|MAPT_ENST00000570299.1_Intron	NM_001007532.2	NP_001007533.1	Q8IWL8	STH_HUMAN	saitohin	14						cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	7						atttttgcagcccccacaaga	0.537																																					p.A14fs		Atlas-INDEL	.											.	STH	14	.	0			c.40delG						.						55.0	54.0	54.0					17																	44076686		1962	4160	6122	SO:0001589	frameshift_variant	246744	exon1			.	AA325304	CCDS54136.1	17q21.1	2008-01-22				ENSG00000256762			18839	protein-coding gene	gene with protein product	"""microtubule-associated protein tau (MAPT) intronic transcript"""	607067				12032355, 16186110	Standard	NM_001007532		Approved	MAPTIT	uc002ijy.2	Q8IWL8		ENST00000537309.1:c.41delC	chr17.hg19:g.44076686delC	ENSP00000443168:p.Ala14fs	288.0	0.0		205.0	13.0	NM_001007532	A1L3X7	Frame_Shift_Del	DEL	ENST00000537309.1	hg19	CCDS54136.1																																																																																			.	.		0.537	STH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400444.1		
RARB	5915	hgsc.bcm.edu	37	3	25470337	25470337	+	Intron	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:25470337delG	ENST00000404969.1	+	2	178				RARB_ENST00000330688.4_Frame_Shift_Del_p.G39fs|RARB_ENST00000462272.1_3'UTR|RARB_ENST00000437042.2_Intron			P10826	RARB_HUMAN	retinoic acid receptor, beta						embryonic digestive tract development (GO:0048566)|embryonic eye morphogenesis (GO:0048048)|embryonic hindlimb morphogenesis (GO:0035116)|gene expression (GO:0010467)|glandular epithelial cell development (GO:0002068)|growth plate cartilage development (GO:0003417)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cartilage development (GO:0061037)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|outflow tract septum morphogenesis (GO:0003148)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell proliferation (GO:0008284)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of myelination (GO:0031641)|retinal pigment epithelium development (GO:0003406)|signal transduction (GO:0007165)|striatum development (GO:0021756)|transcription initiation from RNA polymerase II promoter (GO:0006367)|ureteric bud development (GO:0001657)|ventricular cardiac muscle cell differentiation (GO:0055012)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|drug binding (GO:0008144)|retinoic acid receptor activity (GO:0003708)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			breast(3)|kidney(1)|large_intestine(10)|lung(11)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	28					Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Tamibarotene(DB04942)|Tazarotene(DB00799)	ATGCTTCAGTGGATTGACCCA	0.458																																					p.S38fs		Atlas-INDEL	.											.	RARB	123	.	0			c.114delT						.						149.0	126.0	134.0					3																	25470337		2203	4300	6503	SO:0001627	intron_variant	5915	exon1			.	Y00291	CCDS2642.1, CCDS46775.1	3p24	2013-01-16			ENSG00000077092	ENSG00000077092		"""Nuclear hormone receptors"""	9865	protein-coding gene	gene with protein product		180220					Standard	NM_016152		Approved	HAP, NR1B2, RRB2	uc003cdh.3	P10826	OTTHUMG00000130480	ENST00000404969.1:c.179-32347G>-	chr3.hg19:g.25470337delG		213.0	0.0		142.0	10.0	NM_000965	P12891|Q00989|Q15298|Q9UN48	Frame_Shift_Del	DEL	ENST00000404969.1	hg19																																																																																				.	.		0.458	RARB-201	KNOWN	basic	protein_coding	protein_coding		NM_000965, NM_016152	
ZNF142	7701	hgsc.bcm.edu	37	2	219509322	219509322	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:219509322delC	ENST00000449707.1	-	8	2338	c.1917delG	c.(1915-1917)gggfs	p.G639fs	ZNF142_ENST00000411696.2_Frame_Shift_Del_p.G639fs	NM_001105537.1	NP_001099007.1	P52746	ZN142_HUMAN	zinc finger protein 142	639					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(7)|endometrium(7)|large_intestine(5)|lung(12)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	38		Renal(207;0.0474)		Epithelial(149;5.21e-07)|all cancers(144;0.000106)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)		CGTGACCTGGCCCCTCAGGTC	0.632																																					p.P640fs	Colon(170;867 1942 8995 15834 18053)	Atlas-INDEL	.											.	ZNF142	190	.	0			c.1918delC						.						35.0	38.0	37.0					2																	219509322		1989	4145	6134	SO:0001589	frameshift_variant	7701	exon8			.	U09849	CCDS42817.1	2q35	2013-01-08	2006-06-13		ENSG00000115568	ENSG00000115568		"""Zinc fingers, C2H2-type"""	12927	protein-coding gene	gene with protein product		604083	"""zinc finger protein 142 (clone pHZ-49)"""				Standard	NM_001105537		Approved	KIAA0236, pHZ-49	uc002vin.4	P52746	OTTHUMG00000154736	ENST00000449707.1:c.1917delG	chr2.hg19:g.219509322delC	ENSP00000408643:p.Gly639fs	179.0	0.0		158.0	11.0	NM_001105537	Q92510	Frame_Shift_Del	DEL	ENST00000449707.1	hg19	CCDS42817.1																																																																																			.	.		0.632	ZNF142-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336833.1	NM_005081	
PTCD2	79810	hgsc.bcm.edu	37	5	71648518	71648518	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:71648518delA	ENST00000380639.5	+	9	895	c.879delA	c.(877-879)ctafs	p.L293fs	PTCD2_ENST00000536805.1_Frame_Shift_Del_p.L121fs|PTCD2_ENST00000543322.1_3'UTR|PTCD2_ENST00000503868.1_Frame_Shift_Del_p.L184fs|PTCD2_ENST00000460837.2_3'UTR	NM_024754.3	NP_079030.3	Q8WV60	PTCD2_HUMAN	pentatricopeptide repeat domain 2	293					kidney development (GO:0001822)|liver development (GO:0001889)|mitochondrion organization (GO:0007005)|mRNA processing (GO:0006397)|muscle fiber development (GO:0048747)|regulation of mRNA processing (GO:0050684)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(6)|lung(1)|skin(1)	11		Lung NSC(167;0.00237)|Ovarian(174;0.0175)|Prostate(461;0.141)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;1.73e-53)		TAAAGACTCTAAAAAATGCTG	0.348																																					p.L293fs		Atlas-INDEL	.											.	PTCD2	31	.	0			c.878delT						.						74.0	76.0	75.0					5																	71648518		2203	4300	6503	SO:0001589	frameshift_variant	79810	exon9			.	BC018720	CCDS4014.2, CCDS68891.1, CCDS68892.1, CCDS75258.1	5q13.2	2008-02-05			ENSG00000049883	ENSG00000049883			25734	protein-coding gene	gene with protein product		615484				12477932	Standard	XM_005248601		Approved	FLJ12598	uc003kcb.3	Q8WV60	OTTHUMG00000100953	ENST00000380639.5:c.879delA	chr5.hg19:g.71648518delA	ENSP00000370013:p.Leu293fs	301.0	0.0		199.0	12.0	NM_024754	B7Z5D0|B7Z8L7|E9PFV7|Q6IA65|Q9H9R0	Frame_Shift_Del	DEL	ENST00000380639.5	hg19	CCDS4014.2																																																																																			.	.		0.348	PTCD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218562.6	NM_024754	
PDZD4	57595	hgsc.bcm.edu	37	X	153073936	153073936	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:153073936delC	ENST00000164640.4	-	2	366	c.175delG	c.(175-177)gacfs	p.D59fs	PDZD4_ENST00000393758.2_5'UTR|PDZD4_ENST00000475140.1_5'UTR|PDZD4_ENST00000544474.1_Intron	NM_032512.2	NP_115901.2	Q76G19	PDZD4_HUMAN	PDZ domain containing 4	59						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)					CAGGAGCTGTCCCCCCGGAGG	0.657																																					p.D59fs		Atlas-INDEL	.											.	PDZD4	67	.	0			c.176delA						.						44.0	34.0	38.0					X																	153073936		2202	4296	6498	SO:0001589	frameshift_variant	57595	exon2			.	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.175delG	chrX.hg19:g.153073936delC	ENSP00000164640:p.Asp59fs	241.0	0.0		162.0	10.0	NM_032512	B3KXB1|B7ZKY3|Q8NB75|Q9BUH9|Q9P284	Frame_Shift_Del	DEL	ENST00000164640.4	hg19	CCDS14732.1																																																																																			.	.		0.657	PDZD4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061013.3	NM_032512	
LAMA5	3911	hgsc.bcm.edu	37	20	60894843	60894843	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr20:60894843delC	ENST00000252999.3	-	51	6834	c.6768delG	c.(6766-6768)gggfs	p.G2256fs		NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	2256	Domain II and I.				angiogenesis (GO:0001525)|branching involved in salivary gland morphogenesis (GO:0060445)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|embryo development (GO:0009790)|endothelial cell differentiation (GO:0045446)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|hair follicle development (GO:0001942)|integrin-mediated signaling pathway (GO:0007229)|lung development (GO:0030324)|morphogenesis of a polarized epithelium (GO:0001738)|morphogenesis of embryonic epithelium (GO:0016331)|muscle organ development (GO:0007517)|neural crest cell migration (GO:0001755)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of embryonic development (GO:0045995)|substrate adhesion-dependent cell spreading (GO:0034446)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)|laminin-5 complex (GO:0005610)|nucleus (GO:0005634)	integrin binding (GO:0005178)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|lung(40)|ovary(1)|pancreas(1)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	81	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			GGTCTCGGGTCCCCACGGCCT	0.711																																					p.T2257fs		Atlas-INDEL	.											.	LAMA5	268	.	0			c.6769delA						.						11.0	11.0	11.0					20																	60894843		2063	4088	6151	SO:0001589	frameshift_variant	3911	exon51			.	AF443072	CCDS33502.1	20q13.2-q13.3	2013-03-01			ENSG00000130702	ENSG00000130702		"""Laminins"""	6485	protein-coding gene	gene with protein product		601033				9271224	Standard	NM_005560		Approved		uc002ycq.3	O15230	OTTHUMG00000032908	ENST00000252999.3:c.6768delG	chr20.hg19:g.60894843delC	ENSP00000252999:p.Gly2256fs	124.0	0.0		104.0	10.0	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Frame_Shift_Del	DEL	ENST00000252999.3	hg19	CCDS33502.1																																																																																			.	.		0.711	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560	
EME1	146956	hgsc.bcm.edu	37	17	48452975	48452975	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:48452975delA	ENST00000338165.4	+	2	488	c.406delA	c.(406-408)aaafs	p.K137fs	MRPL27_ENST00000225969.4_5'Flank|MRPL27_ENST00000503633.1_5'Flank|MRPL27_ENST00000507088.1_5'Flank|EME1_ENST00000393271.2_Frame_Shift_Del_p.K137fs|MRPL27_ENST00000442592.3_5'Flank|EME1_ENST00000511648.2_Frame_Shift_Del_p.K137fs	NM_152463.2	NP_689676.2	Q96AY2	EME1_HUMAN	essential meiotic structure-specific endonuclease 1	137					DNA recombination (GO:0006310)|DNA repair (GO:0006281)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	cytoplasm (GO:0005737)|nuclear heterochromatin (GO:0005720)|nucleus (GO:0005634)	DNA binding (GO:0003677)|endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)			endometrium(4)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|stomach(2)|upper_aerodigestive_tract(1)	19	Breast(11;5.62e-19)		BRCA - Breast invasive adenocarcinoma(22;2.43e-08)			ATGTGACTGGAAAAAGCCCTT	0.463								Direct reversal of damage;Homologous recombination																													p.W135X		Atlas-INDEL	.											.	EME1	39	.	0			c.405delG						.						77.0	81.0	79.0					17																	48452975		2203	4300	6503	SO:0001589	frameshift_variant	146956	exon2			.	BC016470	CCDS11565.1, CCDS54141.1	17q21.33	2013-07-03	2013-07-03			ENSG00000154920			24965	protein-coding gene	gene with protein product	"""SLX2 structure-specific endonuclease subunit homolog A (S. cerevisiae)"""	610885	"""essential meiotic endonuclease 1 homolog 1 (S. pombe)"""			12721304	Standard	NM_001166131		Approved	FLJ31364, MMS4L, SLX2A	uc010dbp.2	Q96AY2		ENST00000338165.4:c.406delA	chr17.hg19:g.48452975delA	ENSP00000339897:p.Lys137fs	257.0	0.0		173.0	11.0	NM_152463	Q96N62	Frame_Shift_Del	DEL	ENST00000338165.4	hg19	CCDS11565.1																																																																																			.	.		0.463	EME1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367118.3	NM_152463	
RIPK3	11035	hgsc.bcm.edu	37	14	24808407	24808407	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr14:24808407delT	ENST00000216274.5	-	3	503	c.285delA	c.(283-285)aaafs	p.K95fs	RP11-934B9.3_ENST00000555591.1_5'Flank|RIPK3_ENST00000554338.1_5'UTR	NM_006871.3	NP_006862.2	Q9Y572	RIPK3_HUMAN	receptor-interacting serine-threonine kinase 3	95	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of protein kinase activity (GO:0032147)|amyloid fibril formation (GO:1990000)|apoptotic signaling pathway (GO:0097190)|cellular protein modification process (GO:0006464)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|lymph node development (GO:0048535)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|necroptotic process (GO:0070266)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of ligase activity (GO:0051351)|positive regulation of necroptotic process (GO:0060545)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of phosphatase activity (GO:0010922)|positive regulation of protein deacetylation (GO:0090312)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of type I interferon production (GO:0032481)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of activated T cell proliferation (GO:0046006)|regulation of activation-induced cell death of T cells (GO:0070235)|regulation of adaptive immune response (GO:0002819)|regulation of CD8-positive, alpha-beta cytotoxic T cell extravasation (GO:2000452)|regulation of interferon-gamma production (GO:0032649)|regulation of T cell mediated cytotoxicity (GO:0001914)|signal transduction (GO:0007165)|spleen development (GO:0048536)|T cell differentiation in thymus (GO:0033077)|T cell homeostasis (GO:0043029)|thymus development (GO:0048538)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|ripoptosome (GO:0097342)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|NF-kappaB-inducing kinase activity (GO:0004704)|protein complex binding (GO:0032403)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|transcription coactivator activity (GO:0003713)			NS(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(4)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23				GBM - Glioblastoma multiforme(265;0.0181)		TCTCCATGAATTTAGTCACCA	0.582																																					p.F96fs	Pancreas(58;918 1191 4668 13304 15331)	Atlas-INDEL	.											.	RIPK3	43	.	0			c.286delT						.						83.0	75.0	78.0					14																	24808407		2203	4300	6503	SO:0001589	frameshift_variant	11035	exon3			.	AF156884	CCDS9628.1	14q12	2006-05-15			ENSG00000129465	ENSG00000129465			10021	protein-coding gene	gene with protein product		605817				10339433, 10358032	Standard	NM_006871		Approved	RIP3	uc001wpb.3	Q9Y572	OTTHUMG00000029349	ENST00000216274.5:c.285delA	chr14.hg19:g.24808407delT	ENSP00000216274:p.Lys95fs	195.0	0.0		162.0	10.0	NM_006871	B4DJL9|C4AM87|Q5J795|Q5J796|Q6P5Y1	Frame_Shift_Del	DEL	ENST00000216274.5	hg19	CCDS9628.1																																																																																			.	.		0.582	RIPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073203.4	NM_006871	
FAM71A	149647	hgsc.bcm.edu	37	1	212799568	212799568	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:212799568delG	ENST00000294829.3	+	1	1780	c.1349delG	c.(1348-1350)aggfs	p.R450fs	RP11-338C15.5_ENST00000427949.1_RNA	NM_153606.3	NP_705834.2	Q8IYT1	FA71A_HUMAN	family with sequence similarity 71, member A	450						nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(7)|liver(1)|lung(12)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				OV - Ovarian serous cystadenocarcinoma(81;0.00631)|all cancers(67;0.00981)|GBM - Glioblastoma multiforme(131;0.0715)|Epithelial(68;0.094)		CACAAAACAAGGGGAGACAAG	0.562																																					p.R450fs		Atlas-INDEL	.											.	FAM71A	87	.	0			c.1348delA						.						62.0	77.0	72.0					1																	212799568		2203	4300	6503	SO:0001589	frameshift_variant	149647	exon1			.		CCDS1507.1	1q32.3	2008-02-05			ENSG00000162771	ENSG00000162771			26541	protein-coding gene	gene with protein product						12477932	Standard	NM_153606		Approved	FLJ32796	uc010pth.1	Q8IYT1	OTTHUMG00000041084	ENST00000294829.3:c.1349delG	chr1.hg19:g.212799568delG	ENSP00000294829:p.Arg450fs	107.0	0.0		141.0	12.0	NM_153606	Q5VTZ1	Frame_Shift_Del	DEL	ENST00000294829.3	hg19	CCDS1507.1																																																																																			.	.		0.562	FAM71A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098529.1	NM_153606	
PELP1	27043	hgsc.bcm.edu	37	17	4576386	4576386	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:4576386delG	ENST00000574876.1	-	16	1917	c.1900delC	c.(1900-1902)cggfs	p.R634fs	PELP1_ENST00000269230.7_Frame_Shift_Del_p.R546fs|PELP1_ENST00000572293.1_Frame_Shift_Del_p.R684fs|PELP1_ENST00000436683.2_Frame_Shift_Del_p.R487fs|AC091153.4_ENST00000441700.2_RNA|PELP1_ENST00000301396.4_Frame_Shift_Del_p.R778fs			Q8IZL8	PELP1_HUMAN	proline, glutamate and leucine rich protein 1	634	Pro-rich.				cellular response to estrogen stimulus (GO:0071391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|MLL1 complex (GO:0071339)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcriptionally active chromatin (GO:0035327)	chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(2)|endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	15						GGAGGAACCCGGGGGTGGGTC	0.627																																					p.R634fs		Atlas-INDEL	.											.	PELP1	102	.	0			c.1901delG						.						19.0	22.0	21.0					17																	4576386		1945	4080	6025	SO:0001589	frameshift_variant	27043	exon16			.		CCDS58503.1, CCDS58503.2, CCDS62038.1	17p13.2	2012-05-02	2008-02-21			ENSG00000141456			30134	protein-coding gene	gene with protein product		609455	"""proline, glutamic acid and leucine rich protein 1"""			11481323, 12682072	Standard	NM_014389		Approved	MNAR	uc002fyi.4	Q8IZL8		ENST00000574876.1:c.1900delC	chr17.hg19:g.4576386delG	ENSP00000461625:p.Arg634fs	178.0	0.0		166.0	11.0	NM_014389	O15450|Q5EGN3|Q6NTE6|Q96FT1|Q9BU60	Frame_Shift_Del	DEL	ENST00000574876.1	hg19	CCDS58503.1																																																																																			.	.		0.627	PELP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000439140.2	NM_014389	
SLCO3A1	28232	hgsc.bcm.edu	37	15	92706012	92706012	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:92706012delG	ENST00000318445.6	+	10	1994	c.1780delG	c.(1780-1782)gggfs	p.G594fs	RP11-152L20.3_ENST00000561674.1_RNA|SLCO3A1_ENST00000424469.2_Frame_Shift_Del_p.G594fs|SLCO3A1_ENST00000555549.1_3'UTR|RP11-24J19.1_ENST00000557683.1_RNA	NM_013272.3	NP_037404.2	Q9UIG8	SO3A1_HUMAN	solute carrier organic anion transporter family, member 3A1	594					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)			breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(6)|pancreas(1)|prostate(1)|skin(2)	25	Lung NSC(78;0.0158)|all_lung(78;0.0255)		BRCA - Breast invasive adenocarcinoma(143;0.0841)		Alprostadil(DB00770)|Aminohippurate(DB00345)|Benzylpenicillin(DB01053)|Conjugated Estrogens(DB00286)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Iloprost(DB01088)|Methotrexate(DB00563)	CCTCATCTTCGGGGCTGGCAT	0.567																																					p.F593fs		Atlas-INDEL	.											.	SLCO3A1	84	.	0			c.1779delC						.						54.0	49.0	51.0					15																	92706012		2198	4298	6496	SO:0001589	frameshift_variant	28232	exon10			.	AB031050	CCDS10371.1, CCDS45354.1	15q26	2013-05-22	2003-11-25	2003-11-26	ENSG00000176463	ENSG00000176463		"""Solute carriers"""	10952	protein-coding gene	gene with protein product		612435	"""solute carrier family 21 (organic anion transporter), member 11"""	SLC21A11			Standard	NM_001145044		Approved	OATP-D, OATP3A1	uc002bqx.2	Q9UIG8	OTTHUMG00000149846	ENST00000318445.6:c.1780delG	chr15.hg19:g.92706012delG	ENSP00000320634:p.Gly594fs	329.0	0.0		211.0	13.0	NM_013272	A8K4A7|B3KPY5|B3KUR7|C6G486|Q9BW73|Q9GZV2	Frame_Shift_Del	DEL	ENST00000318445.6	hg19	CCDS10371.1																																																																																			.	.		0.567	SLCO3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313529.1	NM_013272	
FILIP1L	11259	hgsc.bcm.edu	37	3	99568351	99568351	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:99568351delT	ENST00000354552.3	-	5	2639	c.2169delA	c.(2167-2169)aaafs	p.K723fs	CMSS1_ENST00000421999.2_Intron|FILIP1L_ENST00000383694.2_Frame_Shift_Del_p.K483fs|FILIP1L_ENST00000476723.1_Intron|CMSS1_ENST00000496116.1_Intron|FILIP1L_ENST00000471562.1_Frame_Shift_Del_p.K483fs|FILIP1L_ENST00000331335.5_Frame_Shift_Del_p.K723fs|FILIP1L_ENST00000487087.1_Frame_Shift_Del_p.K299fs	NM_182909.2	NP_878913.2	Q4L180	FIL1L_HUMAN	filamin A interacting protein 1-like	723						cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	35						GAATTTTCTCTTTTAATGCAT	0.403																																					p.E724fs		Atlas-INDEL	.											.	FILIP1L	154	.	0			c.2170delG						.						167.0	147.0	153.0					3																	99568351		1858	4092	5950	SO:0001589	frameshift_variant	11259	exon5			.		CCDS43117.1, CCDS43118.1, CCDS43119.1, CCDS63700.1, CCDS74969.1	3q12.1	2011-10-21			ENSG00000168386	ENSG00000168386			24589	protein-coding gene	gene with protein product	"""downregulated in ovarian cancer 1"", ""GPBP-interacting protein of 130 kDa"""	612993				8314147, 15935955, 21832087	Standard	NM_001282793		Approved	DOC-1, GIP130	uc003dtm.3	Q4L180	OTTHUMG00000159055	ENST00000354552.3:c.2169delA	chr3.hg19:g.99568351delT	ENSP00000346560:p.Lys723fs	355.0	0.0		199.0	12.0	NM_001042459	B2CNV7|B2CNV8|Q13597|Q2YDY5|Q6KFX5|Q6KFX6|Q6KFX7|Q8IUM3|Q8N6Z0	Frame_Shift_Del	DEL	ENST00000354552.3	hg19	CCDS43117.1																																																																																			.	.		0.403	FILIP1L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000353069.1	NM_014890	
PROL1	58503	hgsc.bcm.edu	37	4	71275514	71275514	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:71275514delC	ENST00000399575.2	+	3	643	c.469delC	c.(469-471)cccfs	p.P158fs	PROL1_ENST00000514338.1_3'UTR	NM_021225.4	NP_067048.4	Q99935	PROL1_HUMAN	proline rich, lacrimal 1	158	Thr-rich.				negative regulation of endopeptidase activity (GO:0010951)|regulation of sensory perception of pain (GO:0051930)|retina homeostasis (GO:0001895)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	endopeptidase inhibitor activity (GO:0004866)|peptidase inhibitor activity (GO:0030414)			endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|prostate(1)|skin(3)	15		all_hematologic(202;0.196)				CACCACAAATCCCCCCACCAC	0.468																																					p.N156fs		Atlas-INDEL	.											.	PROL1	46	.	0			c.468delT						.						162.0	197.0	185.0					4																	71275514		2030	4195	6225	SO:0001589	frameshift_variant	58503	exon3			.	S83198	CCDS43235.1	4q13.3	2011-10-28	2005-02-07		ENSG00000171199	ENSG00000171199			17279	protein-coding gene	gene with protein product		608936	"""proline rich 1"""			8670737	Standard	NM_021225		Approved	BPLP, PRL1, opiorphin	uc003hfi.3	Q99935	OTTHUMG00000160845	ENST00000399575.2:c.469delC	chr4.hg19:g.71275514delC	ENSP00000382485:p.Pro158fs	456.0	0.0		291.0	24.0	NM_021225	A8MZ07|P85047	Frame_Shift_Del	DEL	ENST00000399575.2	hg19	CCDS43235.1																																																																																			.	.		0.468	PROL1-001	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000362639.1	NM_021225	
RHOXF2B	727940	hgsc.bcm.edu	37	X	119210952	119210952	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:119210952delC	ENST00000371402.2	-	2	570	c.381delG	c.(379-381)gggfs	p.G127fs	RP4-755D9.1_ENST00000553843.1_RNA	NM_001099685.1	NP_001093155.1	P0C7M4	RHF2B_HUMAN	Rhox homeobox family, member 2B	127					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			kidney(1)|large_intestine(2)|skin(3)|upper_aerodigestive_tract(1)	7						CAGGCTCCAGCCCCCCGACGG	0.657																																					p.L128fs		Atlas-INDEL	.											.	RHOXF2	19	.	0			c.382delC						.						5.0	6.0	6.0					X																	119210952		1460	3040	4500	SO:0001589	frameshift_variant	84528	exon2			.		CCDS43985.1	Xq24	2011-06-20			ENSG00000203989	ENSG00000203989		"""Homeoboxes / PRD class"""	33519	protein-coding gene	gene with protein product							Standard	NM_001099685		Approved		uc004esj.4	P0C7M4	OTTHUMG00000022288	ENST00000371402.2:c.381delG	chrX.hg19:g.119210952delC	ENSP00000360455:p.Gly127fs	214.0	0.0		174.0	11.0	NM_032498		Frame_Shift_Del	DEL	ENST00000371402.2	hg19	CCDS43985.1																																																																																			.	.		0.657	RHOXF2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058081.2	NM_001099685	
ACO1	48	hgsc.bcm.edu	37	9	32418340	32418340	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:32418340delT	ENST00000309951.6	+	6	627	c.489delT	c.(487-489)gctfs	p.A163fs	ACO1_ENST00000541043.1_Frame_Shift_Del_p.A64fs|ACO1_ENST00000379923.1_Frame_Shift_Del_p.A163fs	NM_002197.2	NP_002188.1	P21399	ACOC_HUMAN	aconitase 1, soluble	163					cellular iron ion homeostasis (GO:0006879)|citrate metabolic process (GO:0006101)|intestinal absorption (GO:0050892)|post-embryonic development (GO:0009791)|regulation of translation (GO:0006417)|response to iron(II) ion (GO:0010040)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)	4 iron, 4 sulfur cluster binding (GO:0051539)|aconitate hydratase activity (GO:0003994)|iron-responsive element binding (GO:0030350)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)			breast(1)|endometrium(7)|kidney(5)|large_intestine(6)|lung(6)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	30			LUSC - Lung squamous cell carcinoma(29;0.00813)	GBM - Glioblastoma multiforme(74;3.94e-06)		GTTCCCAGGCTTTTCACAACA	0.463																																					p.A163fs		Atlas-INDEL	.											.	ACO1	149	.	0			c.488delC						.						67.0	70.0	69.0					9																	32418340		2203	4300	6503	SO:0001589	frameshift_variant	48	exon6			.	M58510	CCDS6525.1	9p21.1	2013-05-21			ENSG00000122729	ENSG00000122729	4.2.1.3		117	protein-coding gene	gene with protein product	"""aconitate hydratase, cytoplasmic"""	100880		IREB1		2172968, 2771641	Standard	NM_002197		Approved	IRP1, IREBP	uc003zqw.4	P21399	OTTHUMG00000019740	ENST00000309951.6:c.489delT	chr9.hg19:g.32418340delT	ENSP00000309477:p.Ala163fs	252.0	0.0		193.0	12.0	NM_002197	D3DRK7|Q14652|Q5VZA7	Frame_Shift_Del	DEL	ENST00000309951.6	hg19	CCDS6525.1																																																																																			.	.		0.463	ACO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051998.3	NM_002197	
KIFC2	90990	hgsc.bcm.edu	37	8	145692926	145692926	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:145692926delG	ENST00000301332.2	+	5	905	c.528delG	c.(526-528)ctgfs	p.L176fs	CYHR1_ENST00000438911.2_5'Flank|KIFC2_ENST00000301331.5_5'Flank|CYHR1_ENST00000306145.5_5'Flank|CTD-2517M22.16_ENST00000525461.1_RNA|CYHR1_ENST00000424149.2_5'Flank|CYHR1_ENST00000403000.2_5'Flank	NM_145754.2	NP_665697.1	Q96AC6	KIFC2_HUMAN	kinesin family member C2	176					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)			GCGAGCCACTGGGGGATGAGA	0.627											OREG0019057	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L176fs		Atlas-INDEL	.											.	KIFC2	53	.	0			c.527delT						.						63.0	67.0	66.0					8																	145692926		2202	4300	6502	SO:0001589	frameshift_variant	90990	exon5			.	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.528delG	chr8.hg19:g.145692926delG	ENSP00000301332:p.Leu176fs	146.0	0.0	1696	161.0	10.0	NM_145754	E9PHB2|Q96NN6	Frame_Shift_Del	DEL	ENST00000301332.2	hg19	CCDS6427.1																																																																																			.	.		0.627	KIFC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382052.2	NM_145754	
CCDC174	51244	hgsc.bcm.edu	37	3	14708332	14708332	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:14708332delA	ENST00000383794.3	+	7	675	c.602delA	c.(601-603)gaafs	p.E201fs	CCDC174_ENST00000303688.7_Frame_Shift_Del_p.E201fs	NM_016474.4	NP_057558.3	Q6PII3	CC174_HUMAN	coiled-coil domain containing 174	201						cytoplasm (GO:0005737)|nucleus (GO:0005634)											CCTGCTAATGAAAAAACCCTA	0.418																																					p.E201fs		Atlas-INDEL	.											.	.	.	.	0			c.601delG						.						133.0	155.0	147.0					3																	14708332		2203	4300	6503	SO:0001589	frameshift_variant	51244	exon7			.	AF151046	CCDS2620.2	3p25.1	2012-09-20	2012-09-20	2012-09-20	ENSG00000154781	ENSG00000154781			28033	protein-coding gene	gene with protein product			"""chromosome 3 open reading frame 19"""	C3orf19		11042152	Standard	NM_016474		Approved	FLJ33839	uc003byw.3	Q6PII3	OTTHUMG00000129837	ENST00000383794.3:c.602delA	chr3.hg19:g.14708332delA	ENSP00000373304:p.Glu201fs	228.0	0.0		153.0	10.0	NM_016474	Q96CS5	Frame_Shift_Del	DEL	ENST00000383794.3	hg19	CCDS2620.2																																																																																			.	.		0.418	CCDC174-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252077.2	NM_016474	
SNRPB2	6629	hgsc.bcm.edu	37	20	16721542	16721542	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr20:16721542delT	ENST00000246071.6	+	7	786	c.570delT	c.(568-570)gctfs	p.A190fs	SNRPB2_ENST00000377943.5_Frame_Shift_Del_p.A190fs	NM_003092.4	NP_003083.1	P08579	RU2B_HUMAN	small nuclear ribonucleoprotein polypeptide B	190	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U2 snRNP (GO:0005686)	nucleotide binding (GO:0000166)|snRNA binding (GO:0017069)			large_intestine(2)|lung(2)|urinary_tract(1)	5						ATGACATTGCTTTTGTTGAAT	0.428																																					p.A190fs		Atlas-INDEL	.											.	SNRPB2	12	.	0			c.569delC						.						108.0	98.0	101.0					20																	16721542		2203	4300	6503	SO:0001589	frameshift_variant	6629	exon7			.		CCDS13123.1	20p12.1	2013-02-12	2010-07-07		ENSG00000125870	ENSG00000125870		"""RNA binding motif (RRM) containing"""	11155	protein-coding gene	gene with protein product		603520	"""small nuclear ribonucleoprotein polypeptide B2"", ""small nuclear ribonucleoprotein polypeptide B''"""			2951739	Standard	NM_198220		Approved	Msl1	uc002wpi.2	P08579	OTTHUMG00000031933	ENST00000246071.6:c.570delT	chr20.hg19:g.16721542delT	ENSP00000246071:p.Ala190fs	193.0	0.0		152.0	10.0	NM_003092	B2R7J3|D3DW21|Q9UJD4	Frame_Shift_Del	DEL	ENST00000246071.6	hg19	CCDS13123.1																																																																																			.	.		0.428	SNRPB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078110.1	NM_003092	
HMGB4	127540	hgsc.bcm.edu	37	1	34329847	34329847	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:34329847delT	ENST00000522796.1	+	4	1960	c.55delT	c.(55-57)tttfs	p.F19fs	HMGB4_ENST00000519684.1_Frame_Shift_Del_p.F19fs|HMGB4_ENST00000425537.1_Intron|CSMD2_ENST00000373381.4_Intron			Q8WW32	HMGB4_HUMAN	high mobility group box 4	19						chromosome (GO:0005694)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|breast(1)|large_intestine(1)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	12		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)				TTACGTTCACTTTTTGCTGAA	0.393																																					p.H18fs		Atlas-INDEL	.											.	HMGB4	27	.	0			c.54delC						.						83.0	87.0	85.0					1																	34329847		2203	4300	6503	SO:0001589	frameshift_variant	127540	exon2			.		CCDS30668.1	1p35.1	2011-07-01	2011-04-05		ENSG00000176256	ENSG00000176256		"""High-mobility group / Canonical"""	24954	protein-coding gene	gene with protein product			"""high-mobility group box 4"""				Standard	NR_033264		Approved	FLJ40388	uc001bxp.3	Q8WW32	OTTHUMG00000013143	ENST00000522796.1:c.55delT	chr1.hg19:g.34329847delT	ENSP00000430919:p.Phe19fs	263.0	0.0		159.0	10.0	NM_145205	B2R4X7|Q0QWA4	Frame_Shift_Del	DEL	ENST00000522796.1	hg19	CCDS30668.1																																																																																			.	.		0.393	HMGB4-004	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375773.1	NM_145205	
DZIP1L	199221	hgsc.bcm.edu	37	3	137787113	137787113	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:137787113delG	ENST00000327532.2	-	13	2074	c.1712delC	c.(1711-1713)ccafs	p.P572fs	DZIP1L_ENST00000488595.1_5'Flank	NM_173543.2	NP_775814.2	Q8IYY4	DZI1L_HUMAN	DAZ interacting zinc finger protein 1-like	572					cilium assembly (GO:0042384)	ciliary basal body (GO:0036064)	metal ion binding (GO:0046872)			breast(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(6)|lung(15)|ovary(1)|pancreas(2)|prostate(1)|skin(1)	35						ACGAGTTGGTGGGGGTGGCTC	0.667																																					p.P571fs		Atlas-INDEL	.											.	DZIP1L	88	.	0			c.1713delA						.						56.0	66.0	62.0					3																	137787113		2203	4300	6503	SO:0001589	frameshift_variant	199221	exon13			.	AK057406	CCDS3096.1, CCDS54645.1	3q22.3	2013-05-22	2013-05-22		ENSG00000158163	ENSG00000158163			26551	protein-coding gene	gene with protein product			"""DAZ interacting protein 1-like"""			12477932	Standard	NM_173543		Approved	FLJ32844, DZIP2	uc003erq.3	Q8IYY4	OTTHUMG00000159819	ENST00000327532.2:c.1712delC	chr3.hg19:g.137787113delG	ENSP00000332148:p.Pro572fs	258.0	0.0		191.0	13.0	NM_173543	C9JUG5|Q96M38	Frame_Shift_Del	DEL	ENST00000327532.2	hg19	CCDS3096.1																																																																																			.	.		0.667	DZIP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357548.1	NM_173543	
TP53I13	90313	hgsc.bcm.edu	37	17	27899664	27899664	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:27899664delG	ENST00000301057.7	+	6	1133	c.1018delG	c.(1018-1020)gggfs	p.G340fs	RP11-68I3.4_ENST00000579050.1_RNA|RP11-68I3.2_ENST00000581474.1_RNA	NM_138349.2	NP_612358.3	Q8NBR0	P5I13_HUMAN	tumor protein p53 inducible protein 13	340						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|kidney(1)|lung(1)|urinary_tract(1)	4				READ - Rectum adenocarcinoma(3;0.236)		CTTCCGACGCGGGGAGAGCAT	0.682																																					p.R339fs		Atlas-INDEL	.											.	TP53I13	17	.	0			c.1017delC						.						7.0	8.0	7.0					17																	27899664		2092	4184	6276	SO:0001589	frameshift_variant	90313	exon6			.	AK075341	CCDS42289.1	17q11.2	2006-01-16				ENSG00000167543			25102	protein-coding gene	gene with protein product						14767535	Standard	NM_138349		Approved	DSCP1	uc002hee.3	Q8NBR0		ENST00000301057.7:c.1018delG	chr17.hg19:g.27899664delG	ENSP00000301057:p.Gly340fs	204.0	0.0		155.0	11.0	NM_138349	Q7L5U3	Frame_Shift_Del	DEL	ENST00000301057.7	hg19	CCDS42289.1																																																																																			.	.		0.682	TP53I13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447804.2	NM_138349	
COL24A1	255631	hgsc.bcm.edu	37	1	86313395	86313395	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:86313395delT	ENST00000370571.2	-	39	3781	c.3415delA	c.(3415-3417)attfs	p.I1139fs	COL24A1_ENST00000436319.1_Frame_Shift_Del_p.I1139fs	NM_152890.5	NP_690850.2	Q17RW2	COOA1_HUMAN	collagen, type XXIV, alpha 1	1139	Collagen-like 11.				extracellular matrix organization (GO:0030198)|hematopoietic progenitor cell differentiation (GO:0002244)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)			NS(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(9)|liver(1)|lung(56)|ovary(4)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	101				all cancers(265;0.0627)|Epithelial(280;0.0689)		CTTTTCCCAATTTTTCCAGGA	0.443																																					p.I1139fs		Atlas-INDEL	.											.	COL24A1	202	.	0			c.3416delT						.						148.0	139.0	142.0					1																	86313395		1872	4092	5964	SO:0001589	frameshift_variant	255631	exon39			.	AF410793	CCDS41353.1	1p22.3-p22.2	2013-01-16			ENSG00000171502	ENSG00000171502		"""Collagens"""	20821	protein-coding gene	gene with protein product		610025					Standard	NM_152890		Approved		uc001dlj.3	Q17RW2	OTTHUMG00000010629	ENST00000370571.2:c.3415delA	chr1.hg19:g.86313395delT	ENSP00000359603:p.Ile1139fs	209.0	0.0		178.0	11.0	NM_152890	C9J1X6|Q14BD7|Q59EX5|Q5VY50|Q7Z5L5	Frame_Shift_Del	DEL	ENST00000370571.2	hg19	CCDS41353.1																																																																																			.	.		0.443	COL24A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029335.4	NM_152890	
TACC2	10579	hgsc.bcm.edu	37	10	123970853	123970853	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:123970853delA	ENST00000369005.1	+	9	7253	c.6913delA	c.(6913-6915)aaafs	p.K2306fs	TACC2_ENST00000369000.1_Frame_Shift_Del_p.K10fs|TACC2_ENST00000368999.1_Frame_Shift_Del_p.K384fs|TACC2_ENST00000358010.1_Frame_Shift_Del_p.K452fs|TACC2_ENST00000360561.3_Frame_Shift_Del_p.K384fs|TACC2_ENST00000515603.1_Frame_Shift_Del_p.K2261fs|TACC2_ENST00000369001.1_Frame_Shift_Del_p.K10fs|TACC2_ENST00000334433.3_Frame_Shift_Del_p.K2306fs|TACC2_ENST00000369004.3_Frame_Shift_Del_p.K384fs|TACC2_ENST00000513429.1_Frame_Shift_Del_p.K452fs|TACC2_ENST00000453444.2_Frame_Shift_Del_p.K2310fs|TACC2_ENST00000515273.1_Frame_Shift_Del_p.K2310fs|TACC2_ENST00000260733.3_Frame_Shift_Del_p.K384fs	NM_206862.2	NP_996744.2	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing protein 2	2306					astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of microtubule-based process (GO:0032886)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	nuclear hormone receptor binding (GO:0035257)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(15)|lung(27)|ovary(6)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	83		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)				GCCAAAGATGAAAAAGACACC	0.498																																					p.M2304fs		Atlas-INDEL	.											.	TACC2	271	.	0			c.6912delG						.						95.0	98.0	97.0					10																	123970853		2203	4300	6503	SO:0001589	frameshift_variant	10579	exon9			.	AF095791	CCDS7625.1, CCDS7626.1, CCDS7627.1, CCDS7628.1	10q26	2008-07-29			ENSG00000138162	ENSG00000138162			11523	protein-coding gene	gene with protein product		605302				14767476	Standard	XM_005269388		Approved	AZU-1	uc001lfv.3	O95359	OTTHUMG00000019181	ENST00000369005.1:c.6913delA	chr10.hg19:g.123970853delA	ENSP00000358001:p.Lys2306fs	243.0	0.0		244.0	15.0	NM_206862	Q4VXL0|Q4VXL3|Q4VXL6|Q4VXL7|Q5U5T7|Q86WG6|Q86WG7|Q8TCK9|Q9BVQ1|Q9NZ41|Q9NZR5	Frame_Shift_Del	DEL	ENST00000369005.1	hg19	CCDS7626.1																																																																																			.	.		0.498	TACC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090004.1		
SLCO1B3	28234	hgsc.bcm.edu	37	12	21054325	21054325	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:21054325delA	ENST00000381545.3	+	15	2008	c.1789delA	c.(1789-1791)aaafs	p.K597fs	SLCO1B3_ENST00000261196.2_Frame_Shift_Del_p.K597fs|SLCO1B7_ENST00000554957.1_Intron|SLCO1B3_ENST00000553473.1_Frame_Shift_Del_p.K597fs|LST3_ENST00000540229.1_Frame_Shift_Del_p.K597fs|LST3_ENST00000381541.3_Intron	NM_019844.3	NP_062818.1	Q9NPD5	SO1B3_HUMAN	solute carrier organic anion transporter family, member 1B3	597					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)	TCTGATTGATAAAACATGTAT	0.383																																					p.D596fs		Atlas-INDEL	.											.	SLCO1B3	151	.	0			c.1788delT						.						185.0	178.0	180.0					12																	21054325		2203	4300	6503	SO:0001589	frameshift_variant	28234	exon15			.		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.1789delA	chr12.hg19:g.21054325delA	ENSP00000370956:p.Lys597fs	244.0	0.0		200.0	14.0	NM_019844	E7EMT8|Q5JAR4	Frame_Shift_Del	DEL	ENST00000381545.3	hg19	CCDS8684.1																																																																																			.	.		0.383	SLCO1B3-001	KNOWN	upstream_ATG|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000401936.1	NM_019844	
DDB2	1643	hgsc.bcm.edu	37	11	47259439	47259439	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:47259439delC	ENST00000256996.4	+	8	1270	c.1075delC	c.(1075-1077)cctfs	p.P359fs	DDB2_ENST00000378600.3_Frame_Shift_Del_p.P170fs|DDB2_ENST00000378603.3_Frame_Shift_Del_p.P295fs|DDB2_ENST00000378601.3_3'UTR|ACP2_ENST00000525230.1_5'Flank	NM_000107.2	NP_000098.1	Q92466	DDB2_HUMAN	damage-specific DNA binding protein 2, 48kDa	359					DNA repair (GO:0006281)|histone H2A monoubiquitination (GO:0035518)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|protein autoubiquitination (GO:0051865)|protein polyubiquitination (GO:0000209)|pyrimidine dimer repair (GO:0006290)|response to UV (GO:0009411)|UV-damage excision repair (GO:0070914)	Cul4B-RING E3 ubiquitin ligase complex (GO:0031465)|nucleoplasm (GO:0005654)|protein complex (GO:0043234)	damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)			breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|skin(1)	17						ATACCCAGATCCTAATTTCAA	0.488			"""Mis, N"""			"""skin basal cell, skin squamous cell, melanoma"""		Direct reversal of damage;Nucleotide excision repair (NER)	Xeroderma Pigmentosum																												p.D358fs		Atlas-INDEL	.	yes	Rec		Xeroderma pigmentosum (E)	11	11p12	1643	damage-specific DNA binding protein 2		E	.	DDB2	31	.	0			c.1074delT						.						115.0	110.0	112.0					11																	47259439		2201	4298	6499	SO:0001589	frameshift_variant	1643	exon8	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	.		CCDS7927.1, CCDS73284.1	11p12-p11	2014-09-17	2002-08-29			ENSG00000134574		"""WD repeat domain containing"""	2718	protein-coding gene	gene with protein product	"""xeroderma pigmentosum group E protein"", ""UV-damaged DNA-binding protein 2"", ""DDB p48 subunit"""	600811	"""damage-specific DNA binding protein 2 (48kD)"""			8407967, 8530102	Standard	NM_000107		Approved	DDBB, UV-DDB2, FLJ34321	uc001neb.2	Q92466		ENST00000256996.4:c.1075delC	chr11.hg19:g.47259439delC	ENSP00000256996:p.Pro359fs	232.0	0.0		122.0	10.0	NM_000107	B2R875|Q76E54|Q76E55|Q76E56|Q76E57	Frame_Shift_Del	DEL	ENST00000256996.4	hg19	CCDS7927.1																																																																																			.	.		0.488	DDB2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_000107	
RNF123	63891	hgsc.bcm.edu	37	3	49740083	49740083	+	Frame_Shift_Del	DEL	C	C	-	rs188127966		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:49740083delC	ENST00000327697.6	+	20	1791	c.1647delC	c.(1645-1647)tgcfs	p.C549fs	RNF123_ENST00000432042.1_Frame_Shift_Del_p.C403fs	NM_022064.3	NP_071347.2	Q5XPI4	RN123_HUMAN	ring finger protein 123	549					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)		CCATGCTCTGCCCCCCTGAGT	0.552																																					p.C549fs		Atlas-INDEL	.											.	RNF123	100	.	0			c.1646delG						.						245.0	199.0	214.0					3																	49740083		2203	4300	6503	SO:0001589	frameshift_variant	63891	exon20			.	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.1647delC	chr3.hg19:g.49740083delC	ENSP00000328287:p.Cys549fs	250.0	0.0		180.0	11.0	NM_022064	A1L4Q3|A6NLS5|Q5I022|Q6PFW4|Q71RH0|Q8IW18|Q9H0M8|Q9H5L8|Q9H9T2	Frame_Shift_Del	DEL	ENST00000327697.6	hg19	CCDS33758.1																																																																																			.	.		0.552	RNF123-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346475.2	NM_022064	
MTCL1	23255	hgsc.bcm.edu	37	18	8783591	8783591	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr18:8783591delA	ENST00000306329.11	+	5	1561	c.1561delA	c.(1561-1563)aaafs	p.K522fs	SOGA2_ENST00000517570.1_Frame_Shift_Del_p.K162fs|SOGA2_ENST00000359865.3_Frame_Shift_Del_p.K162fs|SOGA2_ENST00000306285.7_5'UTR|SOGA2_ENST00000400050.3_Frame_Shift_Del_p.K162fs																							CCTGATGCGCAAAAAGATGGC	0.567																																					p.R160fs		Atlas-INDEL	.											.	.	.	.	0			c.480delC						.						39.0	41.0	40.0					18																	8783591		2203	4300	6503	SO:0001589	frameshift_variant	23255	exon6			.																												ENST00000306329.11:c.1561delA	chr18.hg19:g.8783591delA	ENSP00000305027:p.Lys522fs	253.0	0.0		187.0	13.0	NM_015210		Frame_Shift_Del	DEL	ENST00000306329.11	hg19																																																																																				.	.		0.567	SOGA2-015	PUTATIVE	basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000444141.1		
MARCH5	54708	hgsc.bcm.edu	37	10	94110929	94110929	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:94110929delA	ENST00000358935.2	+	6	1134	c.802delA	c.(802-804)aaafs	p.K268fs		NM_017824.4	NP_060294.1	Q9NX47	MARH5_HUMAN	membrane-associated ring finger (C3HC4) 5	268					negative regulation of cell aging (GO:0090344)|positive regulation of mitochondrial fission (GO:0090141)|protein autoubiquitination (GO:0051865)|protein localization to mitochondrion (GO:0070585)|protein polyubiquitination (GO:0000209)|regulation of mitochondrial fission (GO:0090140)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)	GTPase binding (GO:0051020)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(1)|lung(3)|skin(1)|urinary_tract(1)	9						GGCACACCGCAAAATTCTGAA	0.358																																					p.R267fs		Atlas-INDEL	.											.	MARCH5	28	.	0			c.801delC						.						81.0	78.0	79.0					10																	94110929		2203	4300	6503	SO:0001589	frameshift_variant	54708	exon6			.	BC015480	CCDS7420.1	10q23.32-q23.33	2013-01-09	2005-01-26	2005-01-27	ENSG00000198060	ENSG00000198060		"""MARCH membrane-associated ring fingers"", ""RING-type (C3HC4) zinc fingers"""	26025	protein-coding gene	gene with protein product		610637	"""ring finger protein 153"""	RNF153		14722266	Standard	XM_005269923		Approved	FLJ20445, MARCH-V	uc001khx.1	Q9NX47	OTTHUMG00000018757	ENST00000358935.2:c.802delA	chr10.hg19:g.94110929delA	ENSP00000351813:p.Lys268fs	206.0	0.0		166.0	10.0	NM_017824		Frame_Shift_Del	DEL	ENST00000358935.2	hg19	CCDS7420.1																																																																																			.	.		0.358	MARCH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049388.1	NM_017824	
CTAG2	30848	hgsc.bcm.edu	37	X	153880814	153880814	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:153880814delC	ENST00000247306.4	-	2	424	c.361delG	c.(361-363)gcgfs	p.A121fs	CTAG2_ENST00000369585.3_Frame_Shift_Del_p.A121fs	NM_020994.3	NP_066274.2	O75638	CTAG2_HUMAN	cancer/testis antigen 2	121						centrosome (GO:0005813)				central_nervous_system(1)|endometrium(1)|lung(6)|ovary(1)|pancreas(1)	10	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					TTCAGAACCGCCCCTGGTCGG	0.647																																					p.A121fs		Atlas-INDEL	.											.	CTAG2	88	.	0			c.362delC						.						51.0	50.0	50.0					X																	153880814		2203	4297	6500	SO:0001589	frameshift_variant	30848	exon2			.	AJ012833	CCDS14759.1, CCDS35455.1	Xq28	2009-08-18			ENSG00000126890	ENSG00000126890			2492	protein-coding gene	gene with protein product	"""CTL-recognized antigen on melanoma"", ""LAGE-1a protein"", ""cancer/testis antigen family 6, member 2a"", ""cancer/testis antigen family 6, member 2b"""	300396				9626360, 10399963	Standard	NM_020994		Approved	LAGE-1, CAMEL, LAGE1, ESO2, MGC3803, MGC138724, CT6.2a, CT6.2b, LAGE-1a, LAGE-1b	uc004fmi.2	O75638	OTTHUMG00000024239	ENST00000247306.4:c.361delG	chrX.hg19:g.153880814delC	ENSP00000247306:p.Ala121fs	139.0	0.0		110.0	10.0	NM_020994	O75637|Q0VIL6|Q14CD6|Q2Z1N4|Q9BU80|Q9UJ89|Q9Y479	Frame_Shift_Del	DEL	ENST00000247306.4	hg19	CCDS14759.1																																																																																			.	.		0.647	CTAG2-001	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000061176.1	NM_020994	
SEMA3F	6405	hgsc.bcm.edu	37	3	50225339	50225339	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:50225339delC	ENST00000002829.3	+	19	2633	c.2149delC	c.(2149-2151)cccfs	p.P718fs	SEMA3F_ENST00000413852.1_Frame_Shift_Del_p.P619fs|SEMA3F_ENST00000434342.1_Frame_Shift_Del_p.P687fs	NM_004186.3	NP_004177.3	Q13275	SEM3F_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3F	718					axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|branchiomotor neuron axon guidance (GO:0021785)|facial nerve structural organization (GO:0021612)|negative regulation of axon extension involved in axon guidance (GO:0048843)|nerve development (GO:0021675)|neural crest cell migration (GO:0001755)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|semaphorin-plexin signaling pathway involved in neuron projection guidance (GO:1902285)|sympathetic ganglion development (GO:0061549)|sympathetic neuron projection extension (GO:0097490)|sympathetic neuron projection guidance (GO:0097491)|trigeminal nerve structural organization (GO:0021637)	extracellular space (GO:0005615)|membrane (GO:0016020)	chemorepellent activity (GO:0045499)|receptor activity (GO:0004872)			central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(1)|skin(2)	17				BRCA - Breast invasive adenocarcinoma(193;0.00013)|KIRC - Kidney renal clear cell carcinoma(197;0.00599)|Kidney(197;0.00688)		CGCCCCGCCACCCCCAGGCGC	0.647																																					p.P716fs		Atlas-INDEL	.											.	SEMA3F	62	.	0			c.2148delA						.						18.0	18.0	18.0					3																	50225339		2201	4296	6497	SO:0001589	frameshift_variant	6405	exon19			.	U33920	CCDS2811.1	3p21.3	2013-01-11			ENSG00000001617	ENSG00000001617		"""Semaphorins"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10728	protein-coding gene	gene with protein product	"""sema IV"""	601124				8786119, 8649831	Standard	NM_004186		Approved	SEMAK, Sema4	uc003cyj.3	Q13275	OTTHUMG00000156806	ENST00000002829.3:c.2149delC	chr3.hg19:g.50225339delC	ENSP00000002829:p.Pro718fs	315.0	0.0		261.0	16.0	NM_004186	C9JQ85|Q13274|Q13372|Q15704|Q6GTR4	Frame_Shift_Del	DEL	ENST00000002829.3	hg19	CCDS2811.1																																																																																			.	.		0.647	SEMA3F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345929.1	NM_004186	
MDGA1	266727	hgsc.bcm.edu	37	6	37605207	37605207	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:37605207delG	ENST00000434837.3	-	17	3983	c.2805delC	c.(2803-2805)cccfs	p.P935fs	MDGA1_ENST00000297153.7_Frame_Shift_Del_p.P939fs	NM_153487.3	NP_705691.1	Q8NFP4	MDGA1_HUMAN	MAM domain containing glycosylphosphatidylinositol anchor 1	935					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						TGGACTGGCAGGGGGCTCCAC	0.657																																					p.C936fs		Atlas-INDEL	.											.	MDGA1	104	.	0			c.2806delT						.						36.0	41.0	39.0					6																	37605207		2028	4189	6217	SO:0001589	frameshift_variant	266727	exon17			.	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.2805delC	chr6.hg19:g.37605207delG	ENSP00000402584:p.Pro935fs	284.0	0.0		210.0	13.0	NM_153487	A6NHG0|Q8NBE3	Frame_Shift_Del	DEL	ENST00000434837.3	hg19	CCDS47417.1																																																																																			.	.		0.657	MDGA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040419.3		
SLCO4C1	353189	hgsc.bcm.edu	37	5	101595975	101595975	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:101595975delT	ENST00000310954.6	-	6	1356	c.1070delA	c.(1069-1071)aatfs	p.N357fs		NM_180991.4	NP_851322.3			solute carrier organic anion transporter family, member 4C1											breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(16)|ovary(1)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(5)	50		all_cancers(142;1.86e-08)|all_epithelial(76;5.24e-12)|Prostate(80;0.00124)|Colorectal(57;0.00332)|Ovarian(225;0.024)|Lung NSC(167;0.0402)|all_lung(232;0.0486)		Epithelial(69;4.07e-14)|COAD - Colon adenocarcinoma(37;0.00986)		TGCATTACTATTACTCTGATG	0.274																																					p.N357fs		Atlas-INDEL	.											.	SLCO4C1	113	.	0			c.1071delT						.						45.0	45.0	45.0					5																	101595975		2200	4296	6496	SO:0001589	frameshift_variant	353189	exon6			.	AY273896	CCDS34205.1	5q21	2013-05-22	2003-11-25		ENSG00000173930	ENSG00000173930		"""Solute carriers"""	23612	protein-coding gene	gene with protein product		609013					Standard	NM_180991		Approved	SLC21A20, OATP4C1, OATPX, OATP-H	uc003knm.3	Q6ZQN7	OTTHUMG00000162757	ENST00000310954.6:c.1070delA	chr5.hg19:g.101595975delT	ENSP00000309741:p.Asn357fs	242.0	0.0		180.0	11.0	NM_180991		Frame_Shift_Del	DEL	ENST00000310954.6	hg19	CCDS34205.1																																																																																			.	.		0.274	SLCO4C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370332.1	NM_180991	
GUCY2C	2984	hgsc.bcm.edu	37	12	14825857	14825857	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:14825857delC	ENST00000261170.3	-	9	1256	c.1120delG	c.(1120-1122)gatfs	p.D374fs	RP11-174G6.1_ENST00000501178.2_RNA	NM_004963.3	NP_004954.2	P25092	GUC2C_HUMAN	guanylate cyclase 2C (heat stable enterotoxin receptor)	374					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)	CTGTCAACATCCCCCCAGTCA	0.473																																					p.D374fs		Atlas-INDEL	.											.	GUCY2C	126	.	0			c.1121delA						.						195.0	163.0	174.0					12																	14825857		2203	4300	6503	SO:0001589	frameshift_variant	2984	exon9			.		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.1120delG	chr12.hg19:g.14825857delC	ENSP00000261170:p.Asp374fs	246.0	0.0		177.0	11.0	NM_004963	B2RMY6	Frame_Shift_Del	DEL	ENST00000261170.3	hg19	CCDS8664.1																																																																																			.	.		0.473	GUCY2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400835.1		
DHX29	54505	hgsc.bcm.edu	37	5	54565369	54565369	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:54565369delT	ENST00000251636.5	-	21	3314	c.3166delA	c.(3166-3168)attfs	p.I1056fs	RP11-506H20.1_ENST00000506435.1_RNA	NM_019030.2	NP_061903.2	Q7Z478	DHX29_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 29	1056						eukaryotic 43S preinitiation complex (GO:0016282)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)|ribosomal small subunit binding (GO:0043024)|translation initiation factor activity (GO:0003743)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(5)|large_intestine(11)|lung(6)|ovary(4)|prostate(1)|skin(3)|urinary_tract(2)	46		Lung NSC(810;4.08e-05)|Breast(144;0.0544)|Prostate(74;0.183)				CAAGCTCCAATTTTTCGGAGC	0.428																																					p.I1056fs		Atlas-INDEL	.											.	DHX29	116	.	0			c.3167delT						.						95.0	86.0	89.0					5																	54565369		2203	4300	6503	SO:0001589	frameshift_variant	54505	exon21			.	AY036974	CCDS34158.1	5q11.2	2008-02-05	2003-06-13	2003-06-20	ENSG00000067248	ENSG00000067248		"""DEAH-boxes"""	15815	protein-coding gene	gene with protein product		612720	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 29"""	DDX29			Standard	XM_005248544		Approved		uc003jpx.3	Q7Z478	OTTHUMG00000162313	ENST00000251636.5:c.3166delA	chr5.hg19:g.54565369delT	ENSP00000251636:p.Ile1056fs	242.0	0.0		181.0	11.0	NM_019030	O75549|Q63HN0|Q63HN3|Q8IWW2|Q8N3A1|Q9UMH2	Frame_Shift_Del	DEL	ENST00000251636.5	hg19	CCDS34158.1																																																																																			.	.		0.428	DHX29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368532.1	NM_019030	
IL18R1	8809	hgsc.bcm.edu	37	2	103013192	103013192	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:103013192delT	ENST00000409599.1	+	12	1828	c.1472delT	c.(1471-1473)cttfs	p.L492fs	IL18R1_ENST00000233957.1_Frame_Shift_Del_p.L492fs			Q13478	IL18R_HUMAN	interleukin 18 receptor 1	492	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				immune response (GO:0006955)|natural killer cell activation (GO:0030101)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|signal transduction (GO:0007165)|T-helper 1 cell differentiation (GO:0045063)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-1 receptor activity (GO:0004908)|interleukin-18 receptor activity (GO:0042008)|receptor activity (GO:0004872)			breast(1)|endometrium(3)|large_intestine(11)|lung(12)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	34						TCACTAAAGCTTTTGAAATCT	0.358																																					p.L491fs		Atlas-INDEL	.											.	IL18R1	72	.	0			c.1471delC						.						90.0	96.0	94.0					2																	103013192		2203	4300	6503	SO:0001589	frameshift_variant	8809	exon10			.	U43672	CCDS2060.1	2q12	2013-01-29			ENSG00000115604	ENSG00000115604		"""Interleukins and interleukin receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5988	protein-coding gene	gene with protein product		604494				8626725, 10191101	Standard	NM_003855		Approved	IL1RRP, IL-1Rrp, CD218a	uc010fiy.3	Q13478	OTTHUMG00000130780	ENST00000409599.1:c.1472delT	chr2.hg19:g.103013192delT	ENSP00000387211:p.Leu492fs	449.0	0.0		307.0	21.0	NM_003855	B2R9Y5|Q52LC9	Frame_Shift_Del	DEL	ENST00000409599.1	hg19	CCDS2060.1																																																																																			.	.		0.358	IL18R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253294.2	NM_003855	
KIAA1468	57614	hgsc.bcm.edu	37	18	59895676	59895676	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr18:59895676delA	ENST00000398130.2	+	8	1525	c.1293delA	c.(1291-1293)ggafs	p.G431fs	KIAA1468_ENST00000256858.6_Frame_Shift_Del_p.G431fs|KIAA1468_ENST00000592479.1_3'UTR	NM_020854.3	NP_065905.2	Q9P260	K1468_HUMAN	KIAA1468	431										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)				CAGACAAGGGAAAAAACACAG	0.433																																					p.G431fs		Atlas-INDEL	.											.	KIAA1468	93	.	0			c.1292delG						.						111.0	99.0	103.0					18																	59895676		2203	4300	6503	SO:0001589	frameshift_variant	57614	exon8			.	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.1293delA	chr18.hg19:g.59895676delA	ENSP00000381198:p.Gly431fs	215.0	0.0		137.0	14.0	NM_020854		Frame_Shift_Del	DEL	ENST00000398130.2	hg19	CCDS11979.2																																																																																			.	.		0.433	KIAA1468-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256187.1	NM_020854	
SLCO1B1	10599	hgsc.bcm.edu	37	12	21375253	21375253	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:21375253delA	ENST00000256958.2	+	13	1798	c.1702delA	c.(1702-1704)aaafs	p.K568fs		NM_006446.4	NP_006437.3	Q9Y6L6	SO1B1_HUMAN	solute carrier organic anion transporter family, member 1B1	568					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)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium-independent organic anion transmembrane transporter activity (GO:0015347)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(33)|ovary(3)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)	70					Acetylcysteine(DB06151)|Aminohippurate(DB00345)|Atorvastatin(DB01076)|Axitinib(DB06626)|Benzylpenicillin(DB01053)|Bezafibrate(DB01393)|Cabazitaxel(DB06772)|Caspofungin(DB00520)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dabrafenib(DB08912)|Dextrothyroxine(DB00509)|Digoxin(DB00390)|Dinoprostone(DB00917)|Eltrombopag(DB06210)|Estradiol(DB00783)|Estrone(DB00655)|Ezetimibe(DB00973)|Fexofenadine(DB00950)|Fluvastatin(DB01095)|Gadoxetate(DB08884)|Gemfibrozil(DB01241)|Indinavir(DB00224)|Irinotecan(DB00762)|L-Carnitine(DB00583)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)|Lovastatin(DB00227)|Methotrexate(DB00563)|Mycophenolate mofetil(DB00688)|Nelfinavir(DB00220)|Olmesartan(DB00275)|Ouabain(DB01092)|Pantoprazole(DB00213)|Pazopanib(DB06589)|Penicillamine(DB00859)|Pioglitazone(DB01132)|Pitavastatin(DB08860)|Pravastatin(DB00175)|Quinidine(DB00908)|Repaglinide(DB00912)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Ritonavir(DB00503)|Rosiglitazone(DB00412)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|SIMEPREVIR(DB06290)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sumatriptan(DB00669)|Valsartan(DB00177)|Verapamil(DB00661)	ACCTGAATTGAAATCACTTGC	0.264																																					p.L567fs		Atlas-INDEL	.											.	SLCO1B1	151	.	0			c.1701delG						.						110.0	106.0	107.0					12																	21375253		2203	4300	6503	SO:0001589	frameshift_variant	10599	exon13			.		CCDS8685.1	12p12	2013-05-22	2003-11-25	2003-11-26	ENSG00000134538	ENSG00000134538		"""Solute carriers"""	10959	protein-coding gene	gene with protein product		604843	"""solute carrier family 21 (organic anion transporter), member 6"""	SLC21A6		10358072	Standard	NM_006446		Approved	OATP-C, LST-1, OATP1B1	uc001req.4	Q9Y6L6	OTTHUMG00000169047	ENST00000256958.2:c.1702delA	chr12.hg19:g.21375253delA	ENSP00000256958:p.Lys568fs	252.0	0.0		182.0	13.0	NM_006446	B2R7G2|Q29R64|Q9NQ37|Q9UBF3|Q9UH89	Frame_Shift_Del	DEL	ENST00000256958.2	hg19	CCDS8685.1																																																																																			.	.		0.264	SLCO1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402070.1	NM_006446	
EXOSC9	5393	hgsc.bcm.edu	37	4	122737569	122737569	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:122737569delT	ENST00000243498.5	+	11	1310	c.1202delT	c.(1201-1203)attfs	p.I401fs	EXOSC9_ENST00000379663.3_Frame_Shift_Del_p.I418fs|EXOSC9_ENST00000512454.1_Frame_Shift_Del_p.I385fs	NM_005033.2	NP_005024.2	Q06265	EXOS9_HUMAN	exosome component 9	401					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|immune response (GO:0006955)|mRNA metabolic process (GO:0016071)|nuclear mRNA surveillance (GO:0071028)|nuclear polyadenylation-dependent rRNA catabolic process (GO:0071035)|nuclear-transcribed mRNA catabolic process (GO:0000956)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|positive regulation of cell growth (GO:0030307)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|exosome (RNase complex) (GO:0000178)|intermediate filament cytoskeleton (GO:0045111)|nuclear exosome (RNase complex) (GO:0000176)|nucleolus (GO:0005730)|nucleus (GO:0005634)	3'-5'-exoribonuclease activity (GO:0000175)|AU-rich element binding (GO:0017091)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(4)|urinary_tract(1)	16						GAAATGATCATTTTGGAACCA	0.284																																					p.I418fs		Atlas-INDEL	.											.	EXOSC9	51	.	0			c.1252delA						.						71.0	80.0	77.0					4																	122737569		2199	4294	6493	SO:0001589	frameshift_variant	5393	exon12			.	M58460	CCDS3722.2, CCDS34057.1	4q27	2010-05-07	2004-06-16	2004-06-18	ENSG00000123737	ENSG00000123737	3.1.13.-		9137	protein-coding gene	gene with protein product	"""polymyositis/scleroderma autoantigen 1 (75kD)"""	606180	"""polymyositis/scleroderma autoantigen 1, 75kDa"""	PMSCL1			Standard	XR_427545		Approved	PM/Scl-75, Rrp45p, RRP45, p5, p6	uc003idz.3	Q06265	OTTHUMG00000128783	ENST00000243498.5:c.1202delT	chr4.hg19:g.122737569delT	ENSP00000243498:p.Ile401fs	274.0	0.0		261.0	20.0	NM_001034194	Q12883|Q4W5P5|Q86Y41|Q86Y48	Frame_Shift_Del	DEL	ENST00000243498.5	hg19	CCDS3722.2																																																																																			.	.		0.284	EXOSC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250708.2	NM_005033	
GDA	9615	hgsc.bcm.edu	37	9	74860174	74860174	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:74860174delT	ENST00000358399.3	+	12	1339	c.1246delT	c.(1246-1248)tttfs	p.F417fs	GDA_ENST00000545168.1_Frame_Shift_Del_p.F343fs|GDA_ENST00000376986.1_Frame_Shift_Del_p.F339fs|GDA_ENST00000238018.4_Frame_Shift_Del_p.F417fs|GDA_ENST00000376989.3_Frame_Shift_Del_p.F356fs	NM_001242505.2|NM_001242506.2|NM_004293.4	NP_001229434.1|NP_001229435.1|NP_004284.1	Q9Y2T3	GUAD_HUMAN	guanine deaminase	417					guanine catabolic process (GO:0006147)|nervous system development (GO:0007399)|nucleobase-containing compound metabolic process (GO:0006139)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide catabolic process (GO:0006195)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)	guanine deaminase activity (GO:0008892)|zinc ion binding (GO:0008270)			central_nervous_system(4)|endometrium(1)|kidney(1)|large_intestine(1)|lung(20)|ovary(2)|skin(2)|urinary_tract(1)	32		Myeloproliferative disorder(762;0.0122)		Lung(182;0.0583)		TTATGGGGACTTTTTTGGTGA	0.378																																					p.D415fs		Atlas-INDEL	.											.	GDA	113	.	0			c.1245delC						.						148.0	146.0	146.0					9																	74860174		2203	4300	6503	SO:0001589	frameshift_variant	9615	exon12			.	AF095286	CCDS6641.1, CCDS56576.1, CCDS56577.1	9q21.13	2008-05-14			ENSG00000119125	ENSG00000119125			4212	protein-coding gene	gene with protein product		139260				10075721, 3966794	Standard	NM_001242507		Approved		uc004air.3	Q9Y2T3	OTTHUMG00000020005	ENST00000358399.3:c.1246delT	chr9.hg19:g.74860174delT	ENSP00000351170:p.Phe417fs	147.0	0.0		131.0	13.0	NM_001242505	B4DTY5|Q5SZC7|Q9H335|Q9ULG2	Frame_Shift_Del	DEL	ENST00000358399.3	hg19	CCDS6641.1																																																																																			.	.		0.378	GDA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052633.1		
RFT1	91869	hgsc.bcm.edu	37	3	53126003	53126003	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:53126003delC	ENST00000296292.3	-	13	1603	c.1542delG	c.(1540-1542)gggfs	p.G514fs	RFT1_ENST00000394738.3_Frame_Shift_Del_p.G475fs|RP11-894J14.5_ENST00000607203.1_Intron	NM_052859.3	NP_443091.1	Q96AA3	RFT1_HUMAN	RFT1 homolog (S. cerevisiae)	514					carbohydrate transport (GO:0008643)|cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	integral component of membrane (GO:0016021)	lipid transporter activity (GO:0005319)			NS(1)|breast(1)|kidney(1)|lung(5)|skin(2)|urinary_tract(2)	12				BRCA - Breast invasive adenocarcinoma(193;6.98e-05)|Kidney(197;0.0017)|KIRC - Kidney renal clear cell carcinoma(197;0.00192)|OV - Ovarian serous cystadenocarcinoma(275;0.104)		GGAATGCTGTCCCGAGAGTTG	0.552																																					p.T515fs		Atlas-INDEL	.											.	RFT1	34	.	0			c.1543delA						.						114.0	98.0	103.0					3																	53126003		2203	4300	6503	SO:0001589	frameshift_variant	91869	exon13			.	AJ318099	CCDS2869.1	3p21.1	2014-02-06	2005-01-26		ENSG00000163933	ENSG00000163933			30220	protein-coding gene	gene with protein product	"""congenital disorder of glycosylation 1N"""	611908	"""RFT1, requiring fifty three 1 homolog (S. cerevisiae)"""			12477932	Standard	NM_052859		Approved	CDG1N	uc003dgj.3	Q96AA3	OTTHUMG00000074035	ENST00000296292.3:c.1542delG	chr3.hg19:g.53126003delC	ENSP00000296292:p.Gly514fs	300.0	0.0		209.0	13.0	NM_052859	Q96J03	Frame_Shift_Del	DEL	ENST00000296292.3	hg19	CCDS2869.1																																																																																			.	.		0.552	RFT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157136.2	NM_052859	
TBC1D12	23232	hgsc.bcm.edu	37	10	96269902	96269902	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:96269902delC	ENST00000225235.4	+	8	1765	c.1655delC	c.(1654-1656)tccfs	p.S552fs	TBC1D12_ENST00000485048.1_3'UTR	NM_015188.1	NP_056003.1	O60347	TBC12_HUMAN	TBC1 domain family, member 12	552	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.						Rab GTPase activator activity (GO:0005097)			breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(5)|upper_aerodigestive_tract(2)	20		Colorectal(252;0.0429)				TTGGACATATCCCGTACATTT	0.373																																					p.S552fs		Atlas-INDEL	.											.	TBC1D12	51	.	0			c.1654delT						.						178.0	165.0	169.0					10																	96269902		1847	4099	5946	SO:0001589	frameshift_variant	23232	exon8			.	AB011180	CCDS41553.1	10q23.33	2013-09-20			ENSG00000108239	ENSG00000108239			29082	protein-coding gene	gene with protein product						9628581	Standard	NM_015188		Approved	KIAA0608	uc001kjr.2	O60347	OTTHUMG00000018794	ENST00000225235.4:c.1655delC	chr10.hg19:g.96269902delC	ENSP00000225235:p.Ser552fs	184.0	0.0		148.0	11.0	NM_015188	Q5VYA6|Q8WX26|Q8WX59|Q9UG83	Frame_Shift_Del	DEL	ENST00000225235.4	hg19	CCDS41553.1																																																																																			.	.		0.373	TBC1D12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049482.2		
WBP11	51729	hgsc.bcm.edu	37	12	14943574	14943574	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:14943574delT	ENST00000261167.2	-	10	1358	c.1125delA	c.(1123-1125)aaafs	p.K375fs		NM_016312.2	NP_057396.1	Q9Y2W2	WBP11_HUMAN	WW domain binding protein 11	375					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|protein phosphatase type 1 regulator activity (GO:0008599)|single-stranded DNA binding (GO:0003697)|WW domain binding (GO:0050699)			endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(16)|ovary(1)|prostate(1)	30						GGGATTCCTCTTTATGCTGCT	0.498																																					p.E376fs		Atlas-INDEL	.											.	WBP11	66	.	0			c.1126delG						.						172.0	156.0	161.0					12																	14943574		2203	4300	6503	SO:0001589	frameshift_variant	51729	exon10			.	AB029309	CCDS8666.1	12p12.3	2014-06-13			ENSG00000084463	ENSG00000084463			16461	protein-coding gene	gene with protein product	"""splicing factor, PQBP1 and PP1 interacting"", ""protein phosphatase 1, regulatory subunit 165"""					10593949	Standard	NM_016312		Approved	NPWBP, SIPP1, PPP1R165	uc001rci.3	Q9Y2W2	OTTHUMG00000168737	ENST00000261167.2:c.1125delA	chr12.hg19:g.14943574delT	ENSP00000261167:p.Lys375fs	246.0	0.0		163.0	10.0	NM_016312	Q96AY8	Frame_Shift_Del	DEL	ENST00000261167.2	hg19	CCDS8666.1																																																																																			.	.		0.498	WBP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400850.1	NM_016312	
ENAM	10117	hgsc.bcm.edu	37	4	71501578	71501578	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:71501578delC	ENST00000396073.3	+	7	782	c.501delC	c.(499-501)ttcfs	p.F167fs		NM_031889.2	NP_114095.2	Q9NRM1	ENAM_HUMAN	enamelin	167					amelogenesis (GO:0097186)|biomineral tissue development (GO:0031214)	proteinaceous extracellular matrix (GO:0005578)				haematopoietic_and_lymphoid_tissue(1)|ovary(3)|upper_aerodigestive_tract(2)	6			Lung(101;0.235)			ATGGGCTATTCCCCTATCAAC	0.308																																					p.F167fs		Atlas-INDEL	.											.	ENAM	140	.	0			c.500delT						.						129.0	141.0	137.0					4																	71501578		2203	4296	6499	SO:0001589	frameshift_variant	10117	exon7			.	AF125373	CCDS3544.2	4q13.3	2008-02-05			ENSG00000132464	ENSG00000132464			3344	protein-coding gene	gene with protein product		606585	"""amelogenesis imperfecta 2, hypocalcification (autosomal dominant)"""	AIH2		11978766	Standard	NM_031889		Approved		uc011caw.1	Q9NRM1	OTTHUMG00000129914	ENST00000396073.3:c.501delC	chr4.hg19:g.71501578delC	ENSP00000379383:p.Phe167fs	210.0	0.0		142.0	11.0	NM_031889	Q17RI5|Q9H3D1	Frame_Shift_Del	DEL	ENST00000396073.3	hg19	CCDS3544.2																																																																																			.	.		0.308	ENAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252166.3	NM_031889	
TYW3	127253	hgsc.bcm.edu	37	1	75229675	75229675	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:75229675delA	ENST00000370867.3	+	6	747	c.658delA	c.(658-660)aaafs	p.K221fs	TYW3_ENST00000479111.1_Frame_Shift_Del_p.K101fs|TYW3_ENST00000457880.2_Frame_Shift_Del_p.K188fs|TYW3_ENST00000421739.2_Frame_Shift_Del_p.K137fs|TYW3_ENST00000467646.1_3'UTR	NM_138467.2	NP_612476.1	Q6IPR3	TYW3_HUMAN	tRNA-yW synthesizing protein 3 homolog (S. cerevisiae)	221					tRNA processing (GO:0008033)		methyltransferase activity (GO:0008168)			central_nervous_system(1)|endometrium(2)|kidney(1)|lung(7)|ovary(2)|prostate(1)|skin(1)	15						TATTCATAAGAAAAAAAGAAA	0.343																																					p.K219fs		Atlas-INDEL	.											.	TYW3	36	.	0			c.657delG						.						81.0	87.0	85.0					1																	75229675		2203	4300	6503	SO:0001589	frameshift_variant	127253	exon6			.	BX647591	CCDS666.1, CCDS53334.1	1p31.1	2008-02-05	2006-05-25	2006-05-25	ENSG00000162623	ENSG00000162623			24757	protein-coding gene	gene with protein product		611245	"""chromosome 1 open reading frame 171"""	C1orf171		17150819	Standard	NM_138467		Approved	FLJ40918	uc001dgn.3	Q6IPR3	OTTHUMG00000009641	ENST00000370867.3:c.658delA	chr1.hg19:g.75229675delA	ENSP00000359904:p.Lys221fs	288.0	0.0		243.0	17.0	NM_138467	B4DSP9|E9PGR7|Q5HYJ0|Q8N7L1	Frame_Shift_Del	DEL	ENST00000370867.3	hg19	CCDS666.1																																																																																			.	.		0.343	TYW3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026573.1	NM_138467	
TBX3	6926	hgsc.bcm.edu	37	12	115118903	115118903	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:115118903delT	ENST00000257566.3	-	2	827	c.438delA	c.(436-438)aaafs	p.K146fs	TBX3_ENST00000349155.2_Frame_Shift_Del_p.K146fs	NM_016569.3	NP_057653.3	O15119	TBX3_HUMAN	T-box 3	146					anterior/posterior axis specification, embryo (GO:0008595)|atrioventricular bundle cell differentiation (GO:0003167)|blood vessel development (GO:0001568)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cardiac muscle cell fate commitment (GO:0060923)|cell aging (GO:0007569)|cellular senescence (GO:0090398)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|female genitalia development (GO:0030540)|follicle-stimulating hormone secretion (GO:0046884)|forelimb morphogenesis (GO:0035136)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|limbic system development (GO:0021761)|luteinizing hormone secretion (GO:0032275)|male genitalia development (GO:0030539)|mammary gland development (GO:0030879)|mammary placode formation (GO:0060596)|mesoderm morphogenesis (GO:0048332)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epithelial cell differentiation (GO:0030857)|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)|organ morphogenesis (GO:0009887)|outflow tract morphogenesis (GO:0003151)|palate development (GO:0060021)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|sinoatrial node cell development (GO:0060931)|skeletal system development (GO:0001501)|specification of organ position (GO:0010159)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|ventricular septum morphogenesis (GO:0060412)	nucleus (GO:0005634)	RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(5)|endometrium(1)|kidney(1)|large_intestine(6)|lung(21)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	47	Medulloblastoma(191;0.163)|all_neural(191;0.178)			BRCA - Breast invasive adenocarcinoma(302;0.0574)		TGTATTTGGCTTTTTTATCCA	0.383																																					p.A147fs		Atlas-INDEL	.											.,2	TBX3	106	.	0			c.439delG						.						131.0	139.0	136.0					12																	115118903		2203	4300	6503	SO:0001589	frameshift_variant	6926	exon2			.	BC025258	CCDS9175.1, CCDS9176.1	12q24.21	2013-09-05	2008-07-31		ENSG00000135111	ENSG00000135111		"""T-boxes"""	11602	protein-coding gene	gene with protein product		601621	"""ulnar mammary syndrome"""	UMS		8988164	Standard	NM_005996		Approved	TBX3-ISO, XHL	uc001tvt.1	O15119	OTTHUMG00000169586	ENST00000257566.3:c.438delA	chr12.hg19:g.115118903delT	ENSP00000257566:p.Lys146fs	244.0	0.0		182.0	11.0	NM_005996	Q8TB20|Q9UKF8	Frame_Shift_Del	DEL	ENST00000257566.3	hg19	CCDS9176.1																																																																																			.	.		0.383	TBX3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000404947.2	NM_016569, NM_005996	
CUX2	23316	hgsc.bcm.edu	37	12	111785948	111785948	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:111785948delC	ENST00000261726.6	+	22	4434	c.4280delC	c.(4279-4281)gccfs	p.A1427fs		NM_015267.3	NP_056082.2	O14529	CUX2_HUMAN	cut-like homeobox 2	1427	Pro-rich.				cellular response to organic substance (GO:0071310)|cognition (GO:0050890)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of gene expression (GO:0010628)|positive regulation of synapse assembly (GO:0051965)|short-term memory (GO:0007614)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding (GO:0043565)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(24)|ovary(5)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	55						CCACCTGGCGCCCCCCCTGCC	0.657																																					p.A1427fs		Atlas-INDEL	.											CUX2,NS,carcinoma,0,1	CUX2	145	.	0			c.4279delG						.						45.0	53.0	50.0					12																	111785948		2032	4169	6201	SO:0001589	frameshift_variant	23316	exon22			.	AB006631	CCDS41837.1	12q24.12	2011-06-20	2007-11-07	2007-11-07	ENSG00000111249	ENSG00000111249		"""Homeoboxes / CUT class"""	19347	protein-coding gene	gene with protein product		610648	"""cut-like 2 (Drosophila)"""	CUTL2			Standard	NM_015267		Approved	KIAA0293, CDP2	uc001tsa.2	O14529	OTTHUMG00000169546	ENST00000261726.6:c.4280delC	chr12.hg19:g.111785948delC	ENSP00000261726:p.Ala1427fs	223.0	0.0		166.0	10.0	NM_015267	A7E2Y4	Frame_Shift_Del	DEL	ENST00000261726.6	hg19	CCDS41837.1																																																																																			.	.		0.657	CUX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404765.1	NM_015267	
HAGH	3029	hgsc.bcm.edu	37	16	1866951	1866951	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:1866951delA	ENST00000397356.3	-	7	1096	c.690delT	c.(688-690)tttfs	p.F230fs	HAGH_ENST00000566709.1_Frame_Shift_Del_p.F182fs|HAGH_ENST00000397353.2_Frame_Shift_Del_p.F182fs|HAGH_ENST00000455446.2_Frame_Shift_Del_p.L194fs	NM_005326.4	NP_005317.2	Q16775	GLO2_HUMAN	hydroxyacylglutathione hydrolase	230					glutathione biosynthetic process (GO:0006750)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	hydroxyacylglutathione hydrolase activity (GO:0004416)|zinc ion binding (GO:0008270)			kidney(2)|lung(1)|ovary(1)|skin(1)	5		Hepatocellular(780;0.00335)			Glutathione(DB00143)	CGTGGCGTGCAAACTTGAGGT	0.607																																					p.A231fs	Pancreas(55;1048 1176 25227 40124 41333)	Atlas-INDEL	.											.	HAGH	20	.	0			c.691delG						.						122.0	100.0	108.0					16																	1866951		2199	4300	6499	SO:0001589	frameshift_variant	3029	exon7			.	X90999	CCDS32366.1, CCDS10447.2, CCDS66900.1	16p13.3	2012-10-02	2003-11-04		ENSG00000063854	ENSG00000063854	3.1.2.6		4805	protein-coding gene	gene with protein product		138760	"""hydroxyacyl glutathione hydrolase"""			3025077, 7327557	Standard	NM_001286249		Approved	GLO2, GLXII, HAGH1	uc002cna.3	Q16775	OTTHUMG00000128662	ENST00000397356.3:c.690delT	chr16.hg19:g.1866951delA	ENSP00000380514:p.Phe230fs	188.0	0.0		165.0	10.0	NM_005326	A8K290|B4DP33|B4DRA7|E7EN93	Frame_Shift_Del	DEL	ENST00000397356.3	hg19	CCDS10447.2																																																																																			.	.		0.607	HAGH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250548.2	NM_005326	
CHPF	79586	hgsc.bcm.edu	37	2	220405010	220405010	+	Frame_Shift_Del	DEL	G	G	-	rs538123825		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:220405010delG	ENST00000243776.6	-	4	1671	c.1423delC	c.(1423-1425)cagfs	p.Q475fs	CHPF_ENST00000535926.1_Frame_Shift_Del_p.Q313fs	NM_024536.5	NP_078812	Q8IZ52	CHSS2_HUMAN	chondroitin polymerizing factor	475					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)|mitochondrion (GO:0005739)	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047238)|metal ion binding (GO:0046872)|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity (GO:0050510)			central_nervous_system(1)|cervix(1)|endometrium(4)|large_intestine(3)|lung(10)|ovary(1)|prostate(1)	21		Renal(207;0.0183)		Epithelial(149;3.02e-08)|all cancers(144;3.41e-06)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00802)		CGGCCTCCCTGGGGGGTCAGT	0.662																																					p.Q475fs		Atlas-INDEL	.											.	CHPF	56	.	0			c.1424delA						.						26.0	29.0	28.0					2																	220405010		2203	4296	6499	SO:0001589	frameshift_variant	79586	exon4			.	BC008878	CCDS2443.1, CCDS56169.1	2q35	2014-02-12			ENSG00000123989	ENSG00000123989	2.4.1.175, 2.4.1.226	"""Beta 3-glycosyltransferases"", ""Beta 4-glycosyltransferases"""	24291	protein-coding gene	gene with protein product	"""chondroitin sulfate synthase 2"""	610405				11230166, 12716890	Standard	NM_024536		Approved	CSS2, CHSY2	uc002vmc.4	Q8IZ52	OTTHUMG00000058929	ENST00000243776.6:c.1423delC	chr2.hg19:g.220405010delG	ENSP00000243776:p.Gln475fs	317.0	0.0		214.0	15.0	NM_024536	B4DXU0|Q6UXD6|Q7L4G1|Q9H0F8|Q9H618	Frame_Shift_Del	DEL	ENST00000243776.6	hg19	CCDS2443.1																																																																																			.	.		0.662	CHPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130268.1	NM_024536	
COL16A1	1307	hgsc.bcm.edu	37	1	32134408	32134408	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:32134408delC	ENST00000373672.3	-	50	3760	c.3244delG	c.(3244-3246)gagfs	p.E1082fs	COL16A1_ENST00000271069.6_Frame_Shift_Del_p.E1082fs	NM_001856.3	NP_001847.3	Q07092	COGA1_HUMAN	collagen, type XVI, alpha 1	1082	Triple-helical region 2 (COL2) with 2 imperfections.				cell adhesion (GO:0007155)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|female pregnancy (GO:0007565)|integrin-mediated signaling pathway (GO:0007229)	collagen type XVI trimer (GO:0005597)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	integrin binding (GO:0005178)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(7)|lung(15)|ovary(8)|prostate(4)	48		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0423)|all_neural(195;0.0837)|Breast(348;0.116)		STAD - Stomach adenocarcinoma(196;0.059)		CTTACCGGCTCCCCCTTGTCT	0.607																																					p.E1082fs	Colon(143;498 1786 21362 25193 36625)	Atlas-INDEL	.											.	COL16A1	137	.	0			c.3245delA						.						68.0	72.0	71.0					1																	32134408		1909	4112	6021	SO:0001589	frameshift_variant	1307	exon50			.	M92642	CCDS41297.1	1p35-p34	2013-01-16			ENSG00000084636	ENSG00000084636		"""Collagens"""	2193	protein-coding gene	gene with protein product		120326				1631157	Standard	NM_001856		Approved		uc001btk.1	Q07092	OTTHUMG00000003883	ENST00000373672.3:c.3244delG	chr1.hg19:g.32134408delC	ENSP00000362776:p.Glu1082fs	192.0	0.0		132.0	10.0	NM_001856	Q16593|Q59F89|Q71RG9	Frame_Shift_Del	DEL	ENST00000373672.3	hg19	CCDS41297.1																																																																																			.	.		0.607	COL16A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011057.2	NM_001856	
PTPRC	5788	hgsc.bcm.edu	37	1	198717290	198717290	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:198717290delA	ENST00000367376.2	+	27	3065	c.2894delA	c.(2893-2895)gaafs	p.E965fs	PTPRC_ENST00000348564.6_Frame_Shift_Del_p.E806fs|PTPRC_ENST00000442510.2_Frame_Shift_Del_p.E967fs|PTPRC_ENST00000352140.3_Frame_Shift_Del_p.E917fs|PTPRC_ENST00000594404.1_Frame_Shift_Del_p.E804fs	NM_002838.4	NP_002829.3	P08575	PTPRC_HUMAN	protein tyrosine phosphatase, receptor type, C	965	Tyrosine-protein phosphatase 2. {ECO:0000255|PROSITE-ProRule:PRU00160}.				axon guidance (GO:0007411)|B cell proliferation (GO:0042100)|B cell receptor signaling pathway (GO:0050853)|bone marrow development (GO:0048539)|cell cycle phase transition (GO:0044770)|cell surface receptor signaling pathway (GO:0007166)|defense response to virus (GO:0051607)|dephosphorylation (GO:0016311)|hematopoietic progenitor cell differentiation (GO:0002244)|immunoglobulin biosynthetic process (GO:0002378)|negative regulation of cell adhesion involved in substrate-bound cell migration (GO:0006933)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of antigen receptor-mediated signaling pathway (GO:0050857)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of hematopoietic stem cell migration (GO:2000473)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of T cell proliferation (GO:0042102)|protein dephosphorylation (GO:0006470)|regulation of cell cycle (GO:0051726)|release of sequestered calcium ion into cytosol (GO:0051209)|stem cell development (GO:0048864)|T cell differentiation (GO:0030217)|T cell receptor signaling pathway (GO:0050852)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(7)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(22)|lung(41)|ovary(4)|pancreas(2)|prostate(1)|skin(13)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	111						AATCAAGAAGAAAATAAAAGT	0.269																																					p.E967fs		Atlas-INDEL	.											.	PTPRC	229	.	0			c.2899delG						.						21.0	21.0	21.0					1																	198717290		2050	4177	6227	SO:0001589	frameshift_variant	5788	exon27			.	Y00062	CCDS1397.1, CCDS1398.1, CCDS44291.1, CCDS1397.2, CCDS1398.2, CCDS44291.2	1q31-q32	2014-09-17			ENSG00000081237	ENSG00000081237		"""CD molecules"", ""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9666	protein-coding gene	gene with protein product		151460		CD45		2169617	Standard	NM_001267798		Approved	LCA, T200, GP180	uc001gur.2	P08575	OTTHUMG00000035702	ENST00000367376.2:c.2894delA	chr1.hg19:g.198717290delA	ENSP00000356346:p.Glu965fs	95.0	0.0		134.0	11.0	NM_002838	A8K7W6|Q16614|Q9H0Y6	Frame_Shift_Del	DEL	ENST00000367376.2	hg19																																																																																				.	.		0.269	PTPRC-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding			
FABP12	646486	hgsc.bcm.edu	37	8	82441805	82441805	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:82441805delT	ENST00000360464.4	-	2	176	c.114delA	c.(112-114)aaafs	p.K38fs	RP11-257P3.3_ENST00000523380.1_RNA	NM_001105281.1	NP_001098751.1	A6NFH5	FBP12_HUMAN	fatty acid binding protein 12	38							lipid binding (GO:0008289)|transporter activity (GO:0005215)			large_intestine(1)|lung(3)	4						TCACAGTGGGTTTTGCCAAAC	0.373																																					p.P39fs		Atlas-INDEL	.											.	FABP12	20	.	0			c.115delC						.						97.0	91.0	93.0					8																	82441805		1845	4092	5937	SO:0001589	frameshift_variant	646486	exon2			.		CCDS47882.1	8q21.13	2013-03-01			ENSG00000197416	ENSG00000197416		"""Fatty acid binding protein family"""	34524	protein-coding gene	gene with protein product						18786628	Standard	NM_001105281		Approved		uc011lfp.2	A6NFH5	OTTHUMG00000164679	ENST00000360464.4:c.114delA	chr8.hg19:g.82441805delT	ENSP00000353650:p.Lys38fs	173.0	0.0		175.0	11.0	NM_001105281	B7SUN0	Frame_Shift_Del	DEL	ENST00000360464.4	hg19	CCDS47882.1																																																																																			.	.		0.373	FABP12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379720.1	NM_001105281	
UGP2	7360	hgsc.bcm.edu	37	2	64084969	64084969	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:64084969delA	ENST00000337130.5	+	3	630	c.154delA	c.(154-156)aaafs	p.K53fs	UGP2_ENST00000394417.2_Frame_Shift_Del_p.K42fs|UGP2_ENST00000445915.2_Frame_Shift_Del_p.K62fs|UGP2_ENST00000467648.2_Frame_Shift_Del_p.K42fs|UGP2_ENST00000487469.1_Intron	NM_006759.3	NP_006750.3	Q16851	UGPA_HUMAN	UDP-glucose pyrophosphorylase 2	53					carbohydrate metabolic process (GO:0005975)|cellular glucuronidation (GO:0052695)|glucose 1-phosphate metabolic process (GO:0019255)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|small molecule metabolic process (GO:0044281)|UDP-glucose metabolic process (GO:0006011)|UDP-glucuronate biosynthetic process (GO:0006065)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	glucose binding (GO:0005536)|metal ion binding (GO:0046872)|pyrimidine ribonucleotide binding (GO:0032557)|UTP:glucose-1-phosphate uridylyltransferase activity (GO:0003983)			endometrium(2)|kidney(1)|large_intestine(8)|lung(6)|prostate(1)	18						ACAGCACACCAAAAAAGACCT	0.358																																					p.T51fs		Atlas-INDEL	.											.	UGP2	38	.	0			c.153delC						.						161.0	191.0	181.0					2																	64084969		2203	4300	6503	SO:0001589	frameshift_variant	7360	exon3			.		CCDS1875.1, CCDS42690.1	2p14-p13	2012-10-02			ENSG00000169764	ENSG00000169764	2.7.7.9		12527	protein-coding gene	gene with protein product		191760	"""UDP-glucose pyrophosphorylase 1"""	UGP1			Standard	NM_006759		Approved	UGPP1	uc002scm.3	Q16851	OTTHUMG00000129513	ENST00000337130.5:c.154delA	chr2.hg19:g.64084969delA	ENSP00000338703:p.Lys53fs	134.0	0.0		106.0	10.0	NM_006759	Q07131|Q0P6K2|Q86Y81|Q9BU15	Frame_Shift_Del	DEL	ENST00000337130.5	hg19	CCDS1875.1																																																																																			.	.		0.358	UGP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251688.1	NM_006759	
PARP9	83666	hgsc.bcm.edu	37	3	122274440	122274440	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:122274440delT	ENST00000360356.2	-	4	910	c.683delA	c.(682-684)aatfs	p.N228fs	PARP9_ENST00000492382.1_Intron|PARP9_ENST00000471785.1_Frame_Shift_Del_p.N193fs|PARP9_ENST00000477522.2_Frame_Shift_Del_p.N193fs|PARP9_ENST00000462315.1_Frame_Shift_Del_p.N193fs	NM_001146102.1|NM_031458.2	NP_001139574.1|NP_113646.2	Q8IXQ6	PARP9_HUMAN	poly (ADP-ribose) polymerase family, member 9	228	Macro 1. {ECO:0000255|PROSITE- ProRule:PRU00490}.				cell migration (GO:0016477)|double-strand break repair (GO:0006302)|regulation of response to interferon-gamma (GO:0060330)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	NAD+ ADP-ribosyltransferase activity (GO:0003950)			endometrium(3)|kidney(2)|large_intestine(9)|liver(1)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(3)	34				GBM - Glioblastoma multiforme(114;0.0519)		AATGTGAGTATTTTTATAGAT	0.423																																					p.N228fs		Atlas-INDEL	.											.	PARP9	72	.	0			c.684delT						.						67.0	68.0	68.0					3																	122274440		2203	4300	6503	SO:0001589	frameshift_variant	83666	exon4			.	AF307339	CCDS3014.1, CCDS54633.1, CCDS54634.1	3q13-q21	2010-02-16			ENSG00000138496	ENSG00000138496		"""Poly (ADP-ribose) polymerases"""	24118	protein-coding gene	gene with protein product		612065				11110709	Standard	NM_031458		Approved	BAL, BAL1	uc003efi.3	Q8IXQ6	OTTHUMG00000159522	ENST00000360356.2:c.683delA	chr3.hg19:g.122274440delT	ENSP00000353512:p.Asn228fs	179.0	0.0		162.0	10.0	NM_001146102	A8KA94|B2R8S9|E9PFM7|Q8TCP3|Q9BZL8|Q9BZL9	Frame_Shift_Del	DEL	ENST00000360356.2	hg19	CCDS3014.1																																																																																			.	.		0.423	PARP9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355957.1	NM_031458	
REPS2	9185	hgsc.bcm.edu	37	X	17024379	17024379	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:17024379delT	ENST00000357277.3	+	2	480	c.309delT	c.(307-309)tatfs	p.Y103fs	REPS2_ENST00000303843.7_Frame_Shift_Del_p.Y103fs|REPS2_ENST00000380064.4_5'UTR	NM_001080975.1|NM_004726.2	NP_001074444.1|NP_004717.2	Q8NFH8	REPS2_HUMAN	RALBP1 associated Eps domain containing 2	103	EH 1. {ECO:0000255|PROSITE- ProRule:PRU00077}.				epidermal growth factor receptor signaling pathway (GO:0007173)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(6)|ovary(2)|skin(3)|urinary_tract(1)	17	Hepatocellular(33;0.183)					GGGTTGGTTATTTTGGTCCAA	0.423																																					p.Y103fs		Atlas-INDEL	.											.	REPS2	76	.	0			c.308delA						.						242.0	206.0	217.0					X																	17024379		1902	4115	6017	SO:0001589	frameshift_variant	9185	exon2			.	AF010233	CCDS14180.2, CCDS43919.1	Xp22.2	2013-01-10			ENSG00000169891	ENSG00000169891		"""EF-hand domain containing"""	9963	protein-coding gene	gene with protein product		300317				9422736, 9928989	Standard	NM_001080975		Approved	POB1	uc004cxv.1	Q8NFH8	OTTHUMG00000021199	ENST00000357277.3:c.309delT	chrX.hg19:g.17024379delT	ENSP00000349824:p.Tyr103fs	167.0	0.0		153.0	10.0	NM_001080975	A6PWZ6|O43428|Q5JNZ8|Q8NFI5	Frame_Shift_Del	DEL	ENST00000357277.3	hg19	CCDS14180.2																																																																																			.	.		0.423	REPS2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000316778.1	NM_004726	
KBTBD12	166348	hgsc.bcm.edu	37	3	127642893	127642893	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:127642893delA	ENST00000405109.1	+	2	1456	c.989delA	c.(988-990)gaafs	p.E330fs	KBTBD12_ENST00000343941.4_Intron|KBTBD12_ENST00000407609.3_Intron|KBTBD12_ENST00000405256.1_Frame_Shift_Del_p.E330fs			Q3ZCT8	KBTBC_HUMAN	kelch repeat and BTB (POZ) domain containing 12	330										endometrium(1)|large_intestine(6)|lung(5)|ovary(1)	13						GTTGTCATGGAAAATAATACT	0.383																																					p.E330fs		Atlas-INDEL	.											.	KBTBD12	41	.	0			c.988delG						.						126.0	123.0	124.0					3																	127642893		1889	4097	5986	SO:0001589	frameshift_variant	166348	exon1			.		CCDS33848.2	3q21.3	2013-01-08	2009-10-01	2009-10-01	ENSG00000187715	ENSG00000187715		"""BTB/POZ domain containing"""	25731	protein-coding gene	gene with protein product			"""kelch domain containing 6"""	KLHDC6			Standard	NM_207335		Approved	FLJ46299	uc010hsr.3	Q3ZCT8	OTTHUMG00000150508	ENST00000405109.1:c.989delA	chr3.hg19:g.127642893delA	ENSP00000385957:p.Glu330fs	177.0	0.0		108.0	11.0	NM_207335	B5MCC6|Q6ZRK1	Frame_Shift_Del	DEL	ENST00000405109.1	hg19	CCDS33848.2																																																																																			.	.		0.383	KBTBD12-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318682.1	NM_207335	
PTCH2	8643	hgsc.bcm.edu	37	1	45296538	45296538	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:45296538delG	ENST00000372192.3	-	6	925	c.795delC	c.(793-795)cccfs	p.P265fs	PTCH2_ENST00000447098.2_Frame_Shift_Del_p.P265fs	NM_003738.4	NP_003729.3	Q9Y6C5	PTC2_HUMAN	patched 2	265					epidermis development (GO:0008544)|hair cycle (GO:0042633)|negative regulation of smoothened signaling pathway (GO:0045879)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	hedgehog family protein binding (GO:0097108)|hedgehog receptor activity (GO:0008158)|smoothened binding (GO:0005119)			NS(2)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(19)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	50	Acute lymphoblastic leukemia(166;0.155)					TGTGATGGTTGGGGGCACTAG	0.622									Basal Cell Nevus syndrome																												p.N266fs		Atlas-INDEL	.											.	PTCH2	96	.	0			c.796delA						.						49.0	51.0	50.0					1																	45296538		2203	4300	6503	SO:0001589	frameshift_variant	8643	exon6	Familial Cancer Database	Gorlin syndrome, Gorlin-Golz syndrome, Naevoid Basal Cell Carcinoma syndrome, NBCCS	.	AF091501	CCDS516.1, CCDS53312.1	1p34.1	2010-06-24	2010-06-24		ENSG00000117425	ENSG00000117425			9586	protein-coding gene	gene with protein product		603673	"""patched (Drosophila) homolog 2"", ""patched homolog 2 (Drosophila)"""			9811851, 9931336	Standard	NM_003738		Approved		uc010olf.2	Q9Y6C5	OTTHUMG00000008490	ENST00000372192.3:c.795delC	chr1.hg19:g.45296538delG	ENSP00000361266:p.Pro265fs	241.0	0.0		163.0	11.0	NM_003738	O95341|O95856|Q53Z57|Q5QP87|Q6UX14	Frame_Shift_Del	DEL	ENST00000372192.3	hg19	CCDS516.1																																																																																			.	.		0.622	PTCH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000023428.4	NM_003738	
MYO5A	4644	hgsc.bcm.edu	37	15	52688534	52688534	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:52688534delT	ENST00000399231.3	-	11	1623	c.1380delA	c.(1378-1380)aaafs	p.K460fs	MYO5A_ENST00000399233.2_Frame_Shift_Del_p.K460fs|MYO5A_ENST00000358212.6_Frame_Shift_Del_p.K460fs|MYO5A_ENST00000553916.1_Frame_Shift_Del_p.K460fs|MYO5A_ENST00000356338.6_Frame_Shift_Del_p.K460fs	NM_000259.3	NP_000250	Q9Y4I1	MYO5A_HUMAN	myosin VA (heavy chain 12, myoxin)	460	Myosin motor.				actin filament-based movement (GO:0030048)|anagen (GO:0042640)|cellular protein metabolic process (GO:0044267)|cellular response to insulin stimulus (GO:0032869)|endoplasmic reticulum localization (GO:0051643)|exocytosis (GO:0006887)|insulin secretion (GO:0030073)|locomotion involved in locomotory behavior (GO:0031987)|long-chain fatty acid biosynthetic process (GO:0042759)|melanin biosynthetic process (GO:0042438)|melanocyte differentiation (GO:0030318)|melanosome transport (GO:0032402)|membrane organization (GO:0061024)|myelination (GO:0042552)|odontogenesis (GO:0042476)|post-Golgi vesicle-mediated transport (GO:0006892)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)|regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031585)|secretory granule localization (GO:0032252)|synapse organization (GO:0050808)|synaptic transmission (GO:0007268)|transport (GO:0006810)|vesicle transport along actin filament (GO:0030050)|vesicle-mediated transport (GO:0016192)|visual perception (GO:0007601)	actomyosin (GO:0042641)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium tip (GO:0032433)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|insulin-responsive compartment (GO:0032593)|intermediate filament (GO:0005882)|melanosome (GO:0042470)|membrane (GO:0016020)|microtubule plus-end (GO:0035371)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|photoreceptor outer segment (GO:0001750)|ruffle (GO:0001726)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|microfilament motor activity (GO:0000146)|poly(A) RNA binding (GO:0044822)|Rab GTPase binding (GO:0017137)			breast(4)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(7)|large_intestine(12)|lung(19)|ovary(3)|skin(3)|stomach(1)	57				all cancers(107;0.0085)|Colorectal(133;0.077)|READ - Rectum adenocarcinoma(133;0.196)		GTTGCTGTAGTTTTTCATTTG	0.279																																					p.L461fs		Atlas-INDEL	.											.	MYO5A	145	.	0			c.1381delC						.						63.0	59.0	60.0					15																	52688534		1767	4049	5816	SO:0001589	frameshift_variant	4644	exon11			.		CCDS42037.1, CCDS45262.1	15q21	2014-09-17	2006-09-29		ENSG00000197535	ENSG00000197535		"""Myosins / Myosin superfamily : Class V"""	7602	protein-coding gene	gene with protein product	"""myosin, heavy polypeptide kinase"", ""myosin heavy chain 12"", ""myoxin"", ""myosin V"""	160777	"""myosin VA (heavy polypeptide 12, myoxin)"""	MYH12		8188282, 8022818	Standard	NM_000259		Approved	MYO5, GS1, MYR12	uc002aby.2	Q9Y4I1	OTTHUMG00000137383	ENST00000399231.3:c.1380delA	chr15.hg19:g.52688534delT	ENSP00000382177:p.Lys460fs	260.0	0.0		179.0	12.0	NM_000259	A8MZC5|O60653|Q07902|Q16249|Q9UE30|Q9UE31	Frame_Shift_Del	DEL	ENST00000399231.3	hg19	CCDS42037.1																																																																																			.	.		0.279	MYO5A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268102.1	NM_000259	
FAM122A	116224	hgsc.bcm.edu	37	9	71395729	71395729	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:71395729delT	ENST00000394264.3	+	1	766	c.649delT	c.(649-651)tttfs	p.F218fs	PIP5K1B_ENST00000265382.3_Intron|PIP5K1B_ENST00000541509.1_Intron	NM_138333.3	NP_612206.3	Q96E09	F122A_HUMAN	family with sequence similarity 122A	218										endometrium(1)|lung(2)	3						GCCAAAGAGATTTTTCCAGGG	0.458																																					p.R216fs		Atlas-INDEL	.											.	FAM122A	14	.	0			c.648delA						.						113.0	110.0	111.0					9																	71395729		2203	4300	6503	SO:0001589	frameshift_variant	116224	exon1			.	AK126379	CCDS6623.1	9q21.13	2011-02-10	2006-07-11	2006-07-11	ENSG00000187866	ENSG00000187866			23490	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 42"""	C9orf42		12477932	Standard	NM_138333		Approved	MGC17347	uc004agw.1	Q96E09	OTTHUMG00000019971	ENST00000394264.3:c.649delT	chr9.hg19:g.71395729delT	ENSP00000377807:p.Phe218fs	227.0	0.0		165.0	11.0	NM_138333		Frame_Shift_Del	DEL	ENST00000394264.3	hg19	CCDS6623.1																																																																																			.	.		0.458	FAM122A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052556.1	NM_138333	
UBE2O	63893	hgsc.bcm.edu	37	17	74388089	74388089	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:74388089delG	ENST00000319380.7	-	16	3116	c.3052delC	c.(3052-3054)cacfs	p.H1018fs		NM_022066.3	NP_071349.3	Q9C0C9	UBE2O_HUMAN	ubiquitin-conjugating enzyme E2O	1018					positive regulation of BMP signaling pathway (GO:0030513)|protein K63-linked ubiquitination (GO:0070534)|protein monoubiquitination (GO:0006513)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|ovary(2)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	36						TAGCAGAAGTGGGGGGGCACG	0.582																																					p.H1018fs		Atlas-INDEL	.											.	UBE2O	207	.	0			c.3053delA						.						29.0	29.0	29.0					17																	74388089		2203	4300	6503	SO:0001589	frameshift_variant	63893	exon16			.	AB051521	CCDS32742.1	17q25.1	2013-10-09			ENSG00000175931	ENSG00000175931			29554	protein-coding gene	gene with protein product						11311559, 11214970	Standard	NM_022066		Approved	E2-230K	uc002jrm.4	Q9C0C9	OTTHUMG00000180178	ENST00000319380.7:c.3052delC	chr17.hg19:g.74388089delG	ENSP00000323687:p.His1018fs	126.0	0.0		178.0	13.0	NM_022066	A6NDU5|Q69YP4|Q6PIZ2|Q86UA4|Q8N425|Q8TBN1|Q9BSW1|Q9H6E6|Q9H7E4|Q9H9B2	Frame_Shift_Del	DEL	ENST00000319380.7	hg19	CCDS32742.1																																																																																			.	.		0.582	UBE2O-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450123.1	NM_022066	
FAM171A1	221061	hgsc.bcm.edu	37	10	15255681	15255681	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:15255681delG	ENST00000378116.4	-	8	1912	c.1906delC	c.(1906-1908)cagfs	p.Q636fs	FAM171A1_ENST00000477161.1_5'Flank	NM_001010924.1	NP_001010924.1	Q5VUB5	F1711_HUMAN	family with sequence similarity 171, member A1	636						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(6)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(20)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	52						GACAGGGGCTGGGGCTGGATC	0.612																																					p.Q636fs		Atlas-INDEL	.											.	FAM171A1	252	.	0			c.1907delA						.						50.0	59.0	56.0					10																	15255681		2203	4300	6503	SO:0001589	frameshift_variant	221061	exon8			.	AK022946	CCDS31154.1	10p13	2008-06-16	2008-06-16	2008-06-16	ENSG00000148468	ENSG00000148468			23522	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 38"""	C10orf38			Standard	NM_001010924		Approved	FLJ12884	uc001iob.3	Q5VUB5	OTTHUMG00000017732	ENST00000378116.4:c.1906delC	chr10.hg19:g.15255681delG	ENSP00000367356:p.Gln636fs	205.0	0.0		165.0	10.0	NM_001010924	D3DRT9|Q32M49|Q8N4I0	Frame_Shift_Del	DEL	ENST00000378116.4	hg19	CCDS31154.1																																																																																			.	.		0.612	FAM171A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046984.1	XM_167709	
DSG3	1830	hgsc.bcm.edu	37	18	29037066	29037066	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	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	157.0	0.0		126.0	11.0	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	
PLPPR2	64748	hgsc.bcm.edu	37	19	11470601	11470601	+	Frame_Shift_Del	DEL	C	C	-	rs201978882		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:11470601delC	ENST00000251473.5	+	5	736	c.360delC	c.(358-360)agcfs	p.S120fs	DKFZP761J1410_ENST00000591608.1_Frame_Shift_Del_p.S95fs	NM_001170635.1|NM_022737.2	NP_001164106.1|NP_073574.2																					GCCGCTTCAGCCCCCCAGTGC	0.627																																					p.S120fs		Atlas-INDEL	.											.	LPPR2	21	.	0			c.359delG						.						34.0	35.0	35.0					19																	11470601		2203	4300	6503	SO:0001589	frameshift_variant	0	exon5			.																												ENST00000251473.5:c.360delC	chr19.hg19:g.11470601delC	ENSP00000251473:p.Ser120fs	173.0	0.0		123.0	10.0	NM_022737		Frame_Shift_Del	DEL	ENST00000251473.5	hg19	CCDS12258.1																																																																																			.	.		0.627	DKFZP761J1410-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458779.1		
SEPT2	4735	hgsc.bcm.edu	37	2	242275390	242275390	+	Splice_Site	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:242275390delA	ENST00000391973.2	+	5	746	c.218delA	c.(217-219)gaa>ga	p.E73fs	SEPT2_ENST00000401990.1_Splice_Site_p.E83fs|SEPT2_ENST00000407971.1_Splice_Site_p.E33fs|SEPT2_ENST00000402092.2_Splice_Site_p.E73fs|SEPT2_ENST00000391971.2_Splice_Site_p.E73fs|SEPT2_ENST00000360051.3_Splice_Site_p.E73fs	NM_006155.1	NP_006146.1	Q15019	SEPT2_HUMAN	septin 2	73	Septin-type G.				cilium assembly (GO:0042384)|mitotic nuclear division (GO:0007067)|neuron projection development (GO:0031175)|regulation of L-glutamate transport (GO:0002036)|regulation of protein localization (GO:0032880)|smoothened signaling pathway (GO:0007224)	actin cytoskeleton (GO:0015629)|cell surface (GO:0009986)|ciliary membrane (GO:0060170)|ciliary transition zone (GO:0035869)|cytoplasm (GO:0005737)|exocyst (GO:0000145)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|septin complex (GO:0031105)|synapse (GO:0045202)	enzyme regulator activity (GO:0030234)|GTP binding (GO:0005525)			central_nervous_system(2)|endometrium(1)|large_intestine(4)|lung(3)|skin(2)	12		all_cancers(19;7.62e-41)|all_epithelial(40;1.71e-18)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00338)|Ovarian(221;0.00556)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;1.24e-34)|all cancers(36;7.15e-32)|OV - Ovarian serous cystadenocarcinoma(60;1.21e-15)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;3.16e-06)|Lung(119;7.81e-05)|LUSC - Lung squamous cell carcinoma(224;0.000742)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0889)		TCTTTTCTAGAAAAAATTGAA	0.433																																					.		Atlas-INDEL	.											.	SEPT2	33	.	0			c.218-1A>-						.						66.0	69.0	68.0					2																	242275390		2203	4300	6503	SO:0001630	splice_region_variant	4735	exon5			.	D28540	CCDS2548.1, CCDS63195.1, CCDS74682.1	2q37.3	2013-01-21	2005-01-11	2005-01-12	ENSG00000168385	ENSG00000168385		"""Septins"""	7729	protein-coding gene	gene with protein product		601506	"""neural precursor cell expressed, developmentally down-regulated 5"""	DIFF6, NEDD5		8697812	Standard	XM_005247011		Approved	KIAA0158, hNedd5, Pnutl3	uc002wbd.3	Q15019	OTTHUMG00000133394	ENST00000391973.2:c.218-1A>-	chr2.hg19:g.242275390delA		207.0	0.0		143.0	13.0	NM_006155	B4DGE8|Q14132|Q53QU3|Q8IUK9|Q96CB0	Splice_Site	DEL	ENST00000391973.2	hg19	CCDS2548.1																																																																																			.	.		0.433	SEPT2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323177.3	NM_006155	Frame_Shift_Del
CACNG3	10368	hgsc.bcm.edu	37	16	24358078	24358078	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:24358078delA	ENST00000005284.3	+	2	1437	c.235delA	c.(235-237)aaafs	p.K79fs		NM_006539.3	NP_006530.1	O60359	CCG3_HUMAN	calcium channel, voltage-dependent, gamma subunit 3	79					calcium ion transport (GO:0006816)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|synaptic transmission (GO:0007268)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(1)|endometrium(4)|kidney(2)|large_intestine(10)|lung(13)|ovary(2)|prostate(4)|skin(2)	40				GBM - Glioblastoma multiforme(48;0.0809)		CGTGTGCAAGAAAATCGATCA	0.577																																					p.K78fs		Atlas-INDEL	.											CACNG3,NS,carcinoma,0,1	CACNG3	112	.	0			c.234delG						.						81.0	76.0	78.0					16																	24358078		2197	4300	6497	SO:0001589	frameshift_variant	10368	exon2			.	AF131911	CCDS10620.1	16p12.1	2008-05-14			ENSG00000006116	ENSG00000006116		"""Calcium channel subunits"""	1407	protein-coding gene	gene with protein product		606403				10221464, 10493829	Standard	NM_006539		Approved		uc002dmf.3	O60359	OTTHUMG00000131651	ENST00000005284.3:c.235delA	chr16.hg19:g.24358078delA	ENSP00000005284:p.Lys79fs	174.0	0.0		112.0	11.0	NM_006539		Frame_Shift_Del	DEL	ENST00000005284.3	hg19	CCDS10620.1																																																																																			.	.		0.577	CACNG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254548.1	NM_006539	
PCDHB14	56122	hgsc.bcm.edu	37	5	140603423	140603423	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:140603423delT	ENST00000239449.4	+	1	346	c.346delT	c.(346-348)tttfs	p.F117fs	PCDHB14_ENST00000515856.2_Intron	NM_018934.2	NP_061757.1	Q9Y5E9	PCDBE_HUMAN	protocadherin beta 14	117	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(21)|ovary(2)|prostate(3)|skin(6)|urinary_tract(1)	49			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CCCTTTACAGTTTTTTCGGTT	0.423																																					p.Q115fs	Ovarian(141;50 1831 27899 33809 37648)	Atlas-INDEL	.											.	PCDHB14	132	.	0			c.345delG						.						92.0	103.0	99.0					5																	140603423		2203	4299	6502	SO:0001589	frameshift_variant	56122	exon1			.	AF152493	CCDS4256.1	5q31	2010-01-26			ENSG00000120327	ENSG00000120327		"""Cadherins / Protocadherins : Clustered"""	8685	other	protocadherin		606340				10380929	Standard	NM_018934		Approved	PCDH-BETA14	uc003ljb.3	Q9Y5E9	OTTHUMG00000129619	ENST00000239449.4:c.346delT	chr5.hg19:g.140603423delT	ENSP00000239449:p.Phe117fs	225.0	0.0		192.0	12.0	NM_018934	B4DPE2|Q4FZA4|Q4KN11	Frame_Shift_Del	DEL	ENST00000239449.4	hg19	CCDS4256.1																																																																																			.	.		0.423	PCDHB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251814.2	NM_018934	
PLIN4	729359	hgsc.bcm.edu	37	19	4512723	4512723	+	Frame_Shift_Del	DEL	C	C	-	rs560523069	byFrequency	TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:4512723delC	ENST00000301286.3	-	3	1206	c.1207delG	c.(1207-1209)gccfs	p.A403fs		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	403	27 X 33 AA approximate tandem repeat.					cytoplasm (GO:0005737)|lipid particle (GO:0005811)|plasma membrane (GO:0005886)				NS(2)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|skin(2)|soft_tissue(1)|stomach(2)	41						GTTTGCATGGCCCCCTTGGCC	0.567																																					p.A403fs		Atlas-INDEL	.											.	PLIN4	191	.	0			c.1208delC						.						74.0	104.0	95.0					19																	4512723		1570	4153	5723	SO:0001589	frameshift_variant	729359	exon3			.	AB067468	CCDS45927.1	19p13.3	2009-10-06	2009-08-12	2009-08-12	ENSG00000167676	ENSG00000167676		"""Perilipins"""	29393	protein-coding gene	gene with protein product		613247	"""KIAA1881"""	KIAA1881		11572484, 19638644	Standard	NM_001080400		Approved	S3-12	uc002mar.1	Q96Q06	OTTHUMG00000167571	ENST00000301286.3:c.1207delG	chr19.hg19:g.4512723delC	ENSP00000301286:p.Ala403fs	334.0	0.0		228.0	14.0	NM_001080400	A6NEI2	Frame_Shift_Del	DEL	ENST00000301286.3	hg19	CCDS45927.1																																																																																			.	.		0.567	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395095.1	XM_170901	
MUC5B	727897	hgsc.bcm.edu	37	11	1276641	1276641	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:1276641delC	ENST00000529681.1	+	37	15977	c.15919delC	c.(15919-15921)cccfs	p.P5308fs	MUC5B_ENST00000447027.1_Frame_Shift_Del_p.P5311fs	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	5308					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)		CAACCTTGTGCCCCCGGGCCC	0.687																																					p.V5306fs		Atlas-INDEL	.											.	MUC5B	473	.	0			c.15918delG						.						24.0	26.0	26.0					11																	1276641		1993	4153	6146	SO:0001589	frameshift_variant	727897	exon37			.	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.15919delC	chr11.hg19:g.1276641delC	ENSP00000436812:p.Pro5308fs	249.0	0.0		142.0	10.0	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Frame_Shift_Del	DEL	ENST00000529681.1	hg19	CCDS44515.2																																																																																			.	.		0.687	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
BTG3	10950	hgsc.bcm.edu	37	21	18981340	18981340	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr21:18981340delT	ENST00000348354.6	-	2	379	c.123delA	c.(121-123)aaafs	p.K41fs	BTG3_ENST00000464058.1_5'UTR|BTG3_ENST00000339775.6_Frame_Shift_Del_p.K41fs	NM_006806.4	NP_006797.3	Q14201	BTG3_HUMAN	BTG family, member 3	41					negative regulation of cell proliferation (GO:0008285)|negative regulation of mitotic cell cycle (GO:0045930)	cytoplasm (GO:0005737)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)	8				Epithelial(23;0.000283)|all cancers(11;0.0012)|Lung(58;0.0191)|OV - Ovarian serous cystadenocarcinoma(11;0.0206)|COAD - Colon adenocarcinoma(22;0.0315)|LUSC - Lung squamous cell carcinoma(23;0.0703)|Colorectal(24;0.0971)		GATTTTTATATTTTTCTTGAA	0.393																																					p.Y42fs		Atlas-INDEL	.											.	BTG3	27	.	0			c.124delT						.						140.0	134.0	136.0					21																	18981340		2203	4300	6503	SO:0001589	frameshift_variant	10950	exon2			.	D64110	CCDS13569.1, CCDS46636.1	21q21.1	2006-12-16			ENSG00000154640	ENSG00000154640			1132	protein-coding gene	gene with protein product		605674				9632145	Standard	NM_006806		Approved	ANA, tob55	uc002ykk.3	Q14201	OTTHUMG00000074501	ENST00000348354.6:c.123delA	chr21.hg19:g.18981340delT	ENSP00000284879:p.Lys41fs	153.0	0.0		166.0	11.0	NM_006806	D3DSC4|Q53XV1|Q96ET7	Frame_Shift_Del	DEL	ENST00000348354.6	hg19	CCDS13569.1																																																																																			.	.		0.393	BTG3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000158196.1	NM_006806	
RANBP6	26953	hgsc.bcm.edu	37	9	6015153	6015153	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:6015153delT	ENST00000259569.5	-	1	465	c.455delA	c.(454-456)aatfs	p.N152fs	RANBP6_ENST00000485372.1_Intron	NM_001243202.1|NM_001243203.1|NM_012416.3	NP_001230131.1|NP_001230132.1|NP_036548.1	O60518	RNBP6_HUMAN	RAN binding protein 6	152					protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|breast(4)|central_nervous_system(1)|endometrium(8)|kidney(5)|large_intestine(8)|lung(9)|ovary(7)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	51		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00522)|Lung(218;0.101)		TAGAACCACATTTTTGGAGTA	0.438																																					p.N152fs		Atlas-INDEL	.											.	RANBP6	127	.	0			c.456delT						.						52.0	53.0	53.0					9																	6015153		2203	4300	6503	SO:0001589	frameshift_variant	26953	exon1			.	AF039023	CCDS6467.1	9p24.1	2008-03-26			ENSG00000137040	ENSG00000137040			9851	protein-coding gene	gene with protein product							Standard	NM_001243202		Approved		uc003zjr.3	O60518	OTTHUMG00000019512	ENST00000259569.5:c.455delA	chr9.hg19:g.6015153delT	ENSP00000259569:p.Asn152fs	181.0	0.0		159.0	10.0	NM_012416	Q5T7X4|Q7Z3V2|Q96E78	Frame_Shift_Del	DEL	ENST00000259569.5	hg19	CCDS6467.1																																																																																			.	.		0.438	RANBP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051650.1	NM_012416	
RYR2	6262	hgsc.bcm.edu	37	1	237778080	237778080	+	Frame_Shift_Del	DEL	G	G	-	rs202117250		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:237778080delG	ENST00000366574.2	+	37	5969	c.5652delG	c.(5650-5652)aagfs	p.K1884fs	RYR2_ENST00000542537.1_Frame_Shift_Del_p.K1868fs|RYR2_ENST00000360064.6_Frame_Shift_Del_p.K1882fs	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	1884	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)	p.K1882N(1)		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)			AAGAAGCCAAGGGGGGCAAGC	0.512																																					p.K1884fs		Atlas-INDEL	.											.	RYR2	1273	.	1	Substitution - Missense(1)	lung(1)	c.5651delA						.						45.0	48.0	47.0					1																	237778080		2000	4162	6162	SO:0001589	frameshift_variant	6262	exon37			.	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.5652delG	chr1.hg19:g.237778080delG	ENSP00000355533:p.Lys1884fs	154.0	0.0		182.0	13.0	NM_001035	Q15411|Q546N8|Q5T3P2	Frame_Shift_Del	DEL	ENST00000366574.2	hg19	CCDS55691.1																																																																																			.	.		0.512	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035	
FRY	10129	hgsc.bcm.edu	37	13	32722055	32722055	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr13:32722055delT	ENST00000380250.3	+	13	1859	c.1363delT	c.(1363-1365)tttfs	p.F455fs		NM_023037.2	NP_075463.2	Q5TBA9	FRY_HUMAN	furry homolog (Drosophila)	455						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				NS(3)|breast(4)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(31)|lung(50)|ovary(5)|pancreas(1)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	132		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)		TCTGAACATCTTTGTGAAAAT	0.473																																					p.I454fs		Atlas-INDEL	.											.	FRY	312	.	0			c.1362delC						.						124.0	119.0	121.0					13																	32722055		1853	4096	5949	SO:0001589	frameshift_variant	10129	exon13			.	AL049784	CCDS41875.1	13q13.1	2008-02-05	2005-11-24	2005-11-24	ENSG00000073910	ENSG00000073910			20367	protein-coding gene	gene with protein product		614818	"""chromosome 13 open reading frame 14"""	C13orf14		14702039, 8812419	Standard	NM_023037		Approved	bA37E23.1, 13CDNA73, CG003	uc001utx.3	Q5TBA9	OTTHUMG00000016696	ENST00000380250.3:c.1363delT	chr13.hg19:g.32722055delT	ENSP00000369600:p.Phe455fs	225.0	0.0		174.0	12.0	NM_023037	Q9Y3N6	Frame_Shift_Del	DEL	ENST00000380250.3	hg19	CCDS41875.1																																																																																			.	.		0.473	FRY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044405.1	NM_023037	
DNAJC10	54431	hgsc.bcm.edu	37	2	183582853	183582865	+	Frame_Shift_Del	DEL	TTGAAAAGGATCA	TTGAAAAGGATCA	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	TTGAAAAGGATCA	TTGAAAAGGATCA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:183582853_183582865delTTGAAAAGGATCA	ENST00000264065.7	+	3	455_467	c.40_52delTTGAAAAGGATCA	c.(40-54)ttgaaaaggatcattfs	p.LKRII14fs	DNAJC10_ENST00000469118.1_Intron|DNAJC10_ENST00000537515.1_Frame_Shift_Del_p.LKRII14fs	NM_018981.1	NP_061854.1	Q8IXB1	DJC10_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 10	14					cell redox homeostasis (GO:0045454)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of protein phosphorylation (GO:0001933)|positive regulation of ATPase activity (GO:0032781)|protein folding in endoplasmic reticulum (GO:0034975)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum chaperone complex (GO:0034663)|endoplasmic reticulum lumen (GO:0005788)|membrane (GO:0016020)	ATPase activator activity (GO:0001671)|ATPase binding (GO:0051117)|chaperone binding (GO:0051087)|disulfide oxidoreductase activity (GO:0015036)|Hsp70 protein binding (GO:0030544)|misfolded protein binding (GO:0051787)|oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor (GO:0016671)|protein disulfide oxidoreductase activity (GO:0015035)			breast(3)|endometrium(1)|kidney(4)|large_intestine(7)|lung(15)|ovary(1)|skin(1)	32			OV - Ovarian serous cystadenocarcinoma(117;0.0942)|Epithelial(96;0.209)			TATCAGAGACTTGAAAAGGATCATTCTCTGTTT	0.366																																					p.13_17del	Pancreas(56;860 1183 25669 35822 48585)	Atlas-INDEL	.											.	DNAJC10	76	.	0			c.39_51del						.																																			SO:0001589	frameshift_variant	54431	exon3			.		CCDS33345.1, CCDS74613.1	2q32.1	2011-11-23			ENSG00000077232	ENSG00000077232		"""Heat shock proteins / DNAJ (HSP40)"", ""Protein disulfide isomerases"""	24637	protein-coding gene	gene with protein product	"""protein disulfide isomerase family A, member 19"""	607987				12411443, 12446677	Standard	NM_018981		Approved	ERdj5, PDIA19	uc002uow.2	Q8IXB1	OTTHUMG00000154209	ENST00000264065.7:c.40_52delTTGAAAAGGATCA	chr2.hg19:g.183582853_183582865delTTGAAAAGGATCA	ENSP00000264065:p.Leu14fs	156.0	0.0		79.0	13.0	NM_001271581	Q17RJ6|Q3B7W8|Q4ZG06|Q53QT7|Q6UWZ6|Q86T61|Q8NC82|Q8TD87|Q96K38|Q96K44|Q96K54|Q9NSY6	Frame_Shift_Del	DEL	ENST00000264065.7	hg19	CCDS33345.1																																																																																			.	.		0.366	DNAJC10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334418.2	NM_018981	
KDM2B	84678	hgsc.bcm.edu	37	12	121880092	121880092	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:121880092delG	ENST00000377071.4	-	19	3224	c.3152delC	c.(3151-3153)ccgfs	p.P1052fs	KDM2B_ENST00000536437.1_Intron|KDM2B_ENST00000542973.1_Frame_Shift_Del_p.P420fs|KDM2B_ENST00000377069.4_Frame_Shift_Del_p.P983fs	NM_032590.4	NP_115979.3	Q8NHM5	KDM2B_HUMAN	lysine (K)-specific demethylase 2B	1052	Pro-rich.				embryonic camera-type eye morphogenesis (GO:0048596)|forebrain development (GO:0030900)|fourth ventricle development (GO:0021592)|hindbrain development (GO:0030902)|histone demethylation (GO:0016577)|histone H2A monoubiquitination (GO:0035518)|initiation of neural tube closure (GO:0021993)|lateral ventricle development (GO:0021670)|midbrain development (GO:0030901)|midbrain-hindbrain boundary morphogenesis (GO:0021555)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|spermatogenesis (GO:0007283)|third ventricle development (GO:0021678)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (GO:0032452)|histone demethylase activity (H3-K36 specific) (GO:0051864)|rRNA binding (GO:0019843)|zinc ion binding (GO:0008270)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	19						CGAGTCAGGCGGGGGGCTGAT	0.672																																					p.P1051fs		Atlas-INDEL	.											.	KDM2B	218	.	0			c.3153delG						.						14.0	16.0	16.0					12																	121880092		1912	4085	5997	SO:0001589	frameshift_variant	84678	exon19			.	AJ459424	CCDS41849.1, CCDS41850.1	12q24.31	2014-02-18	2009-04-06	2009-04-06	ENSG00000089094	ENSG00000089094		"""F-boxes / Leucine-rich repeats"", ""Chromatin-modifying enzymes / K-demethylases"""	13610	protein-coding gene	gene with protein product	"""jumonji C domain-containing histone demethylase 1B"""	609078	"""F-box and leucine-rich repeat protein 10"""	FBXL10		10799292	Standard	NM_032590		Approved	PCCX2, CXXC2, Fbl10, JHDM1B	uc001uat.3	Q8NHM5	OTTHUMG00000169071	ENST00000377071.4:c.3152delC	chr12.hg19:g.121880092delG	ENSP00000366271:p.Pro1052fs	171.0	0.0		178.0	13.0	NM_032590	A8MRS1|Q8NCI2|Q96HC7|Q96SL0|Q96T03|Q9NS96|Q9UF75	Frame_Shift_Del	DEL	ENST00000377071.4	hg19	CCDS41850.1																																																																																			.	.		0.672	KDM2B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402132.2	NM_032590	
FAM63A	55793	hgsc.bcm.edu	37	1	150974245	150974245	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:150974245delG	ENST00000361936.5	-	4	1421	c.467delC	c.(466-468)ccgfs	p.P156fs	FAM63A_ENST00000470877.1_5'UTR|FAM63A_ENST00000493834.2_Frame_Shift_Del_p.P61fs|FAM63A_ENST00000361738.6_Frame_Shift_Del_p.P204fs|FAM63A_ENST00000312210.5_Frame_Shift_Del_p.P14fs	NM_018379.4	NP_060849	Q8N5J2	FA63A_HUMAN	family with sequence similarity 63, member A	156						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(3)|large_intestine(4)|lung(11)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	23	all_lung(15;1.09e-34)|Lung NSC(24;1.1e-30)|Lung SC(34;0.00202)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			TTCCTTCTGCGGGGGGAGCTT	0.562																																					p.P204fs		Atlas-INDEL	.											.	FAM63A	42	.	0			c.612delG						.						60.0	54.0	56.0					1																	150974245		2203	4300	6503	SO:0001589	frameshift_variant	55793	exon4			.	BC032321	CCDS976.1, CCDS30854.1, CCDS53361.1, CCDS55635.1	1q21.2	2008-02-05			ENSG00000143409	ENSG00000143409			25648	protein-coding gene	gene with protein product						10718198	Standard	NM_001040217		Approved	FLJ11280	uc010pcn.2	Q8N5J2	OTTHUMG00000035061	ENST00000361936.5:c.467delC	chr1.hg19:g.150974245delG	ENSP00000354814:p.Pro156fs	179.0	0.0		192.0	15.0	NM_001163258	B3KWP4|B3KWV8|B4DXF2|B4E1S4|D3DV09|J3KP53|Q5SZF0|Q9NUL9|Q9P2F7	Frame_Shift_Del	DEL	ENST00000361936.5	hg19	CCDS976.1																																																																																			.	.		0.562	FAM63A-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411753.1	NM_018379	
ANO1	55107	hgsc.bcm.edu	37	11	70033894	70033894	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:70033894delC	ENST00000355303.5	+	26	3050	c.2745delC	c.(2743-2745)atcfs	p.I915fs	ANO1_ENST00000398543.2_Frame_Shift_Del_p.I769fs|ANO1_ENST00000525494.1_3'UTR|ANO1_ENST00000530676.1_Frame_Shift_Del_p.I769fs|ANO1-AS1_ENST00000524987.1_RNA|ANO1_ENST00000538023.1_Frame_Shift_Del_p.I915fs|ANO1_ENST00000531349.1_Frame_Shift_Del_p.I624fs	NM_018043.5	NP_060513.5	Q5XXA6	ANO1_HUMAN	anoctamin 1, calcium activated chloride channel	915					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|regulation of membrane potential (GO:0042391)|trachea development (GO:0060438)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|chloride channel complex (GO:0034707)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|intracellular calcium activated chloride channel activity (GO:0005229)	p.I915I(2)		central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(12)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(1)	29					Crofelemer(DB04941)	TCCCGGACATCCCCAAGGACA	0.582																																					p.I915fs		Atlas-INDEL	.											.	ANO1	156	.	2	Substitution - coding silent(2)	lung(2)	c.2744delT						.						42.0	48.0	46.0					11																	70033894		2117	4239	6356	SO:0001589	frameshift_variant	55107	exon26			.	BC033036	CCDS44663.1	11q13.2	2014-04-09	2008-08-28	2008-08-28	ENSG00000131620	ENSG00000131620		"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	21625	protein-coding gene	gene with protein product		610108	"""oral cancer overexpressed 2"", ""transmembrane protein 16A"""	ORAOV2, TMEM16A		15067359, 18724360, 24692353	Standard	NM_018043		Approved	TAOS2, FLJ10261, DOG1	uc001opj.3	Q5XXA6	OTTHUMG00000167204	ENST00000355303.5:c.2745delC	chr11.hg19:g.70033894delC	ENSP00000347454:p.Ile915fs	231.0	0.0		180.0	11.0	NM_018043	A8KAM3|Q8IYY8|Q8N7V3	Frame_Shift_Del	DEL	ENST00000355303.5	hg19	CCDS44663.1																																																																																			.	.		0.582	ANO1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000393685.1	NM_018043	
WNK1	65125	hgsc.bcm.edu	37	12	987482	987482	+	Frame_Shift_Del	DEL	G	G	-	rs1012729	byFrequency	TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:987482delG	ENST00000315939.6	+	10	2971	c.2328delG	c.(2326-2328)cagfs	p.Q776fs	WNK1_ENST00000537687.1_Frame_Shift_Del_p.Q1189fs|WNK1_ENST00000535572.1_Frame_Shift_Del_p.Q775fs|WNK1_ENST00000530271.2_Frame_Shift_Del_p.Q1274fs|WNK1_ENST00000340908.4_Frame_Shift_Del_p.Q369fs	NM_018979.3	NP_061852.3	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1	776					intracellular signal transduction (GO:0035556)|ion transport (GO:0006811)|negative regulation of pancreatic juice secretion (GO:0090188)|negative regulation of phosphatase activity (GO:0010923)|neuron development (GO:0048666)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of systemic arterial blood pressure (GO:0003084)|protein phosphorylation (GO:0006468)|regulation of cellular process (GO:0050794)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|phosphatase binding (GO:0019902)|protein kinase inhibitor activity (GO:0004860)|protein serine/threonine kinase activity (GO:0004674)			breast(7)|central_nervous_system(1)|endometrium(3)|kidney(6)|large_intestine(15)|lung(43)|ovary(6)|prostate(3)|skin(7)|stomach(8)|upper_aerodigestive_tract(3)|urinary_tract(2)	104	all_cancers(10;0.00611)|all_epithelial(11;0.00825)|all_lung(10;0.0331)|Ovarian(42;0.0512)|Lung NSC(10;0.0632)		Epithelial(1;1.74e-08)|all cancers(1;7.04e-08)|OV - Ovarian serous cystadenocarcinoma(31;0.000423)|BRCA - Breast invasive adenocarcinoma(9;0.0149)|Colorectal(1;0.0197)			CAGTGAGTCAGCCTCAAGCTC	0.443																																					p.Q1274fs	Colon(19;451 567 6672 12618 28860)	Atlas-INDEL	.											.	WNK1	403	.	0			c.3821delA						.						95.0	86.0	89.0					12																	987482		2203	4300	6503	SO:0001589	frameshift_variant	65125	exon12			.	AJ296290	CCDS8506.1, CCDS53731.1, CCDS73419.1	12p13.3	2014-09-17	2005-01-19	2005-01-21	ENSG00000060237	ENSG00000060237			14540	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 167"""	605232	"""protein kinase, lysine deficient 1"", ""hereditary sensory neuropathy, type II"""	PRKWNK1, HSN2			Standard	NM_001184985		Approved	HSAN2, PPP1R167	uc031qfk.1	Q9H4A3	OTTHUMG00000090321	ENST00000315939.6:c.2328delG	chr12.hg19:g.987482delG	ENSP00000313059:p.Gln776fs	256.0	0.0		216.0	13.0	NM_213655	A1L4B0|C5HTZ5|C5HTZ6|C5HTZ7|H6WZW3|O15052|P54963|Q4VBX9|Q6IFS5|Q86WL5|Q8N673|Q96CZ6|Q9P1S9	Frame_Shift_Del	DEL	ENST00000315939.6	hg19	CCDS8506.1																																																																																			.	.		0.443	WNK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206683.1	NM_018979	
FAM71B	153745	hgsc.bcm.edu	37	5	156592606	156592606	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	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	354.0	0.0		212.0	14.0	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	
CHD6	84181	hgsc.bcm.edu	37	20	40084446	40084446	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr20:40084446delA	ENST00000373233.3	-	19	3180	c.3003delT	c.(3001-3003)tttfs	p.F1001fs	CHD6_ENST00000309279.7_Intron	NM_032221.3	NP_115597.3	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6	1001					ATP catabolic process (GO:0006200)|chromatin modification (GO:0016568)|positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0036091)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|transcription cofactor binding (GO:0001221)			breast(8)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(24)|lung(53)|ovary(8)|prostate(5)|skin(8)|stomach(1)|urinary_tract(9)	129		Myeloproliferative disorder(115;0.00425)				GTACCTTGGCAAAAGTGGACC	0.483																																					p.A1002fs		Atlas-INDEL	.											.	CHD6	312	.	0			c.3004delG						.						221.0	209.0	213.0					20																	40084446		2203	4300	6503	SO:0001589	frameshift_variant	84181	exon19			.	AF525085	CCDS13317.1	20q12	2003-03-07			ENSG00000124177	ENSG00000124177			19057	protein-coding gene	gene with protein product						11889561	Standard	NM_032221		Approved	KIAA1335, FLJ22369, dJ620E11.1, CHD5, RIGB	uc002xka.1	Q8TD26	OTTHUMG00000032487	ENST00000373233.3:c.3003delT	chr20.hg19:g.40084446delA	ENSP00000362330:p.Phe1001fs	274.0	0.0		202.0	13.0	NM_032221	Q5JYQ0|Q5TGZ9|Q5TH00|Q5TH01|Q8IZR2|Q8WTY0|Q9H4H6|Q9H6D4|Q9NTT7|Q9P2L1	Frame_Shift_Del	DEL	ENST00000373233.3	hg19	CCDS13317.1																																																																																			.	.		0.483	CHD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079270.1		
ZSCAN4	201516	hgsc.bcm.edu	37	19	58189897	58189897	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:58189897delA	ENST00000318203.5	+	5	1623	c.926delA	c.(925-927)caafs	p.Q309fs		NM_152677.2	NP_689890.1	Q8NAM6	ZSCA4_HUMAN	zinc finger and SCAN domain containing 4	309					telomere maintenance via telomere lengthening (GO:0010833)|transcription, DNA-templated (GO:0006351)	nuclear chromosome, telomeric region (GO:0000784)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|large_intestine(5)|liver(2)|lung(17)|ovary(1)|skin(1)|stomach(1)	30		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		CATGGAGTCCAAAAATCATAC	0.458																																					p.Q309fs		Atlas-INDEL	.											.	ZSCAN4	72	.	0			c.925delC						.						106.0	98.0	101.0					19																	58189897		2203	4300	6503	SO:0001589	frameshift_variant	201516	exon5			.	AK092424	CCDS12958.1	19q13.43	2013-01-08	2004-11-01	2004-11-02		ENSG00000180532		"""-"", ""Zinc fingers, C2H2-type"""	23709	protein-coding gene	gene with protein product		613419	"""zinc finger protein 494"""	ZNF494			Standard	NM_152677		Approved	FLJ35105	uc002qpu.3	Q8NAM6		ENST00000318203.5:c.926delA	chr19.hg19:g.58189897delA	ENSP00000321963:p.Gln309fs	213.0	0.0		143.0	11.0	NM_152677	Q3MIQ2	Frame_Shift_Del	DEL	ENST00000318203.5	hg19	CCDS12958.1																																																																																			.	.		0.458	ZSCAN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466812.1	NM_152677	
FLT3	2322	hgsc.bcm.edu	37	13	28626770	28626770	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr13:28626770delT	ENST00000241453.7	-	5	607	c.526delA	c.(526-528)atgfs	p.M176fs	FLT3_ENST00000380982.4_Frame_Shift_Del_p.M176fs|FLT3_ENST00000537084.1_Frame_Shift_Del_p.M176fs	NM_004119.2	NP_004110.2	P36888	FLT3_HUMAN	fms-related tyrosine kinase 3	176					B cell differentiation (GO:0030183)|cellular response to cytokine stimulus (GO:0071345)|common myeloid progenitor cell proliferation (GO:0035726)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell differentiation (GO:0097028)|hemopoiesis (GO:0030097)|leukocyte homeostasis (GO:0001776)|lymphocyte proliferation (GO:0046651)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of B cell differentiation (GO:0045578)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of tyrosine phosphorylation of STAT protein (GO:0042531)|pro-B cell differentiation (GO:0002328)|pro-T cell differentiation (GO:0002572)|protein autophosphorylation (GO:0046777)|regulation of apoptotic process (GO:0042981)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor signaling pathway (GO:0038084)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|cytokine receptor activity (GO:0004896)|protein homodimerization activity (GO:0042803)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)	p.M176V(1)		NS(1)|breast(3)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(12329)|kidney(2)|large_intestine(8)|lung(30)|ovary(4)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	12390	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0156)|Ovarian(182;0.0392)	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	OV - Ovarian serous cystadenocarcinoma(117;0.00154)|all cancers(112;0.00459)|GBM - Glioblastoma multiforme(144;0.00562)|Epithelial(112;0.0959)|Lung(94;0.212)	Ponatinib(DB08901)|Sorafenib(DB00398)|Sunitinib(DB01268)	TGGTTTTCCATTTTTCTAAAG	0.408			"""Mis, O"""		"""AML, ALL"""																																p.M176fs		Atlas-INDEL	.		Dom	yes		13	13q12	2322	fms-related tyrosine kinase 3		L	.	FLT3	15525	.	1	Substitution - Missense(1)	lung(1)	c.527delT						.						109.0	107.0	108.0					13																	28626770		2203	4300	6503	SO:0001589	frameshift_variant	2322	exon5			.	U02687	CCDS31953.1	13q12	2014-09-17			ENSG00000122025	ENSG00000122025	2.7.10.1	"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	3765	protein-coding gene	gene with protein product		136351				8394751	Standard	NM_004119		Approved	STK1, FLK2, CD135	uc001urw.3	P36888	OTTHUMG00000016646	ENST00000241453.7:c.526delA	chr13.hg19:g.28626770delT	ENSP00000241453:p.Met176fs	174.0	0.0		152.0	10.0	NM_004119	A0AVG9|B7ZLT7|B7ZLT8|F5H0A0|Q13414	Frame_Shift_Del	DEL	ENST00000241453.7	hg19	CCDS31953.1																																																																																			.	.		0.408	FLT3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000044319.2		
USH2A	7399	hgsc.bcm.edu	37	1	216019331	216019331	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:216019331delA	ENST00000307340.3	-	45	9276	c.8890delT	c.(8890-8892)tggfs	p.W2964fs	USH2A_ENST00000366943.2_Frame_Shift_Del_p.W2964fs	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	2964	Fibronectin type-III 16. {ECO:0000255|PROSITE-ProRule:PRU00316}.				hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		GCAGAACTCCAAAAAAGTGTG	0.398										HNSCC(13;0.011)																											p.W2964X		Atlas-INDEL	.											.	USH2A	1168	.	0			c.8891delG						.						85.0	84.0	84.0					1																	216019331		2203	4300	6503	SO:0001589	frameshift_variant	7399	exon45			.	AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"""Fibronectin type III domain containing"""	12601	protein-coding gene	gene with protein product	"""usherin"""	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.8890delT	chr1.hg19:g.216019331delA	ENSP00000305941:p.Trp2964fs	189.0	0.0		215.0	14.0	NM_206933	Q5VVM9|Q6S362|Q9NS27	Frame_Shift_Del	DEL	ENST00000307340.3	hg19	CCDS31025.1																																																																																			.	.		0.398	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123	
DSP	1832	hgsc.bcm.edu	37	6	7574928	7574928	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:7574928delA	ENST00000379802.3	+	17	2677	c.2336delA	c.(2335-2337)caafs	p.Q779fs	DSP_ENST00000418664.2_Frame_Shift_Del_p.Q779fs	NM_004415.2	NP_004406.2	P15924	DESP_HUMAN	desmoplakin	779	Globular 1.				adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|desmosome organization (GO:0002934)|epidermis development (GO:0008544)|intermediate filament organization (GO:0045109)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|protein localization to adherens junction (GO:0071896)|regulation of heart rate by cardiac conduction (GO:0086091)|single organismal cell-cell adhesion (GO:0016337)|ventricular cardiac muscle cell action potential (GO:0086005)|ventricular compact myocardium morphogenesis (GO:0003223)|wound healing (GO:0042060)	basolateral plasma membrane (GO:0016323)|cornified envelope (GO:0001533)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)|protein kinase C binding (GO:0005080)|scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			biliary_tract(1)|breast(6)|central_nervous_system(7)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|liver(2)|lung(27)|ovary(4)|prostate(1)|skin(8)|stomach(3)|upper_aerodigestive_tract(7)|urinary_tract(5)	101	Ovarian(93;0.0584)	all_hematologic(90;0.236)		OV - Ovarian serous cystadenocarcinoma(45;0.000508)		GCTATTCTCCAAACAGAAGAC	0.453																																					p.Q779fs		Atlas-INDEL	.											.	DSP	306	.	0			c.2335delC						.						128.0	120.0	123.0					6																	7574928		2203	4300	6503	SO:0001589	frameshift_variant	1832	exon17			.	J05211	CCDS4501.1, CCDS47368.1	6p24.3	2014-09-17	2003-05-20		ENSG00000096696	ENSG00000096696			3052	protein-coding gene	gene with protein product		125647	"""desmoplakin (DPI, DPII)"""			1889810	Standard	NM_004415		Approved	KPPS2, PPKS2, DPI, DPII	uc003mxp.1	P15924	OTTHUMG00000014212	ENST00000379802.3:c.2336delA	chr6.hg19:g.7574928delA	ENSP00000369129:p.Gln779fs	216.0	0.0		134.0	10.0	NM_004415	B2RTT2|D7RX09|O75993|Q14189|Q9UHN4	Frame_Shift_Del	DEL	ENST00000379802.3	hg19	CCDS4501.1																																																																																			.	.		0.453	DSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039786.2	NM_004415	
COL28A1	340267	hgsc.bcm.edu	37	7	7559697	7559697	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:7559697delT	ENST00000399429.3	-	6	949	c.809delA	c.(808-810)aacfs	p.N270fs		NM_001037763.2	NP_001032852.2	Q2UY09	COSA1_HUMAN	collagen, type XXVIII, alpha 1	270	Collagen-like 1.				cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(23)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	42		Ovarian(82;0.0789)		UCEC - Uterine corpus endometrioid carcinoma (126;0.228)		ATTTACCGGGTTTCCTTTTGG	0.318																																					p.N270fs		Atlas-INDEL	.											.	COL28A1	113	.	0			c.810delC						.						80.0	74.0	76.0					7																	7559697		1801	4073	5874	SO:0001589	frameshift_variant	340267	exon6			.	AJ890451	CCDS43553.1	7p21.3	2013-01-16			ENSG00000215018	ENSG00000215018		"""Collagens"""	22442	protein-coding gene	gene with protein product		609996				16330543	Standard	NM_001037763		Approved		uc003src.1	Q2UY09	OTTHUMG00000150034	ENST00000399429.3:c.809delA	chr7.hg19:g.7559697delT	ENSP00000382356:p.Asn270fs	140.0	0.0		231.0	15.0	NM_001037763	A4D101|A4D106|A4D107|A8MVR2|B9EGX9|Q2UY07|Q2UY08	Frame_Shift_Del	DEL	ENST00000399429.3	hg19	CCDS43553.1																																																																																			.	.		0.318	COL28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315899.1	NM_001037763	
TMEM130	222865	hgsc.bcm.edu	37	7	98460876	98460876	+	Frame_Shift_Del	DEL	G	G	-	rs369651719		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:98460876delG	ENST00000416379.2	-	2	237	c.233delC	c.(232-234)ccgfs	p.P78fs	TMEM130_ENST00000450876.1_5'UTR|TMEM130_ENST00000546258.1_Frame_Shift_Del_p.P59fs|TMEM130_ENST00000345589.4_Intron|TMEM130_ENST00000339375.4_Frame_Shift_Del_p.P78fs			Q8N3G9	TM130_HUMAN	transmembrane protein 130	78						Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(7)|lung(6)|ovary(2)|prostate(2)|skin(3)|urinary_tract(1)	25	all_cancers(62;4.05e-09)|all_epithelial(64;2.62e-09)|Lung NSC(181;0.01)|all_lung(186;0.0115)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)			AAGCACCAGCGGGGTGTGGAT	0.662																																					p.P78fs		Atlas-INDEL	.											.	TMEM130	54	.	0			c.234delG						.						59.0	58.0	58.0					7																	98460876		2203	4300	6503	SO:0001589	frameshift_variant	222865	exon2			.		CCDS5658.1, CCDS47649.1, CCDS47650.1	7q22.1	2006-03-09			ENSG00000166448	ENSG00000166448			25429	protein-coding gene	gene with protein product						12975309	Standard	NM_152913		Approved	DKFZp761L1417, FLJ42643	uc003upo.3	Q8N3G9	OTTHUMG00000154419	ENST00000416379.2:c.233delC	chr7.hg19:g.98460876delG	ENSP00000413163:p.Pro78fs	180.0	0.0		174.0	12.0	NM_152913	A4D266|B7Z364|Q8IY46|Q8N0W9|Q8N3R2	Frame_Shift_Del	DEL	ENST00000416379.2	hg19	CCDS47650.1																																																																																			.	.		0.662	TMEM130-008	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000380713.1	NM_152913	
ATG16L1	55054	hgsc.bcm.edu	37	2	234178690	234178690	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:234178690delA	ENST00000392017.4	+	6	941	c.684delA	c.(682-684)gcafs	p.A228fs	ATG16L1_ENST00000347464.5_Frame_Shift_Del_p.A84fs|ATG16L1_ENST00000373525.5_Frame_Shift_Del_p.A84fs|ATG16L1_ENST00000498620.1_3'UTR|ATG16L1_ENST00000392018.1_Frame_Shift_Del_p.A228fs|ATG16L1_ENST00000392020.4_Frame_Shift_Del_p.A228fs	NM_001190266.1|NM_001190267.1|NM_030803.6	NP_001177195.1|NP_001177196.1|NP_110430.5	Q676U5	A16L1_HUMAN	autophagy related 16-like 1 (S. cerevisiae)	228	WIPI2-binding. {ECO:0000269|PubMed:24954904}.				autophagic vacuole assembly (GO:0000045)|negative stranded viral RNA replication (GO:0039689)|protein homooligomerization (GO:0051260)|protein transport (GO:0015031)	autophagic vacuole (GO:0005776)|autophagic vacuole membrane (GO:0000421)|axoneme (GO:0005930)	identical protein binding (GO:0042802)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(5)|lung(7)|prostate(3)|skin(1)	25		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0327)|Lung NSC(271;0.0539)		Epithelial(121;1.53e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000379)|LUSC - Lung squamous cell carcinoma(224;0.00619)|Lung(119;0.00732)|GBM - Glioblastoma multiforme(43;0.11)		CAGAAGCAGCAAAGGAACCTC	0.388																																					p.A228fs		Atlas-INDEL	.											.	ATG16L1	83	.	0			c.683delC						.						77.0	92.0	87.0					2																	234178690		2203	4300	6503	SO:0001589	frameshift_variant	55054	exon6			.	AK000897	CCDS2502.2, CCDS2503.2, CCDS54438.1	2q37.1	2014-02-12	2012-06-06	2005-09-13	ENSG00000085978	ENSG00000085978		"""WD repeat domain containing"""	21498	protein-coding gene	gene with protein product		610767	"""APG16 autophagy 16-like (S. cerevisiae)"", ""ATG16 autophagy related 16-like (S. cerevisiae)"", ""ATG16 autophagy related 16-like 1 (S. cerevisiae)"""	APG16L, ATG16L			Standard	NM_017974		Approved	WDR30, FLJ10035, ATG16A	uc002vty.3	Q676U5	OTTHUMG00000133619	ENST00000392017.4:c.684delA	chr2.hg19:g.234178690delA	ENSP00000375872:p.Ala228fs	287.0	0.0		249.0	15.0	NM_017974	A3EXK9|A3EXL0|B6ZDH0|Q6IPN1|Q6UXW4|Q6ZVZ5|Q8NCY2|Q96JV5|Q9H619	Frame_Shift_Del	DEL	ENST00000392017.4	hg19	CCDS2503.2																																																																																			.	.		0.388	ATG16L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257069.2	NM_017974	
ARCN1	372	hgsc.bcm.edu	37	11	118452086	118452086	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:118452086delA	ENST00000264028.4	+	2	224	c.129delA	c.(127-129)ggafs	p.G43fs	ARCN1_ENST00000392859.3_Intron|ARCN1_ENST00000359415.4_Frame_Shift_Del_p.G84fs|ARCN1_ENST00000534182.2_Frame_Shift_Del_p.G43fs	NM_001655.4	NP_001646.2	P48444	COPD_HUMAN	archain 1	43					adult locomotory behavior (GO:0008344)|cerebellar Purkinje cell layer maturation (GO:0021691)|COPI coating of Golgi vesicle (GO:0048205)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|pigmentation (GO:0043473)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	clathrin adaptor complex (GO:0030131)|COPI vesicle coat (GO:0030126)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(2)|large_intestine(3)|lung(4)|ovary(2)|urinary_tract(1)	13	all_hematologic(175;0.0349)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.0564)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.28e-05)		TGAACACTGGAAAACAACATA	0.403																																					p.G43fs		Atlas-INDEL	.											.	ARCN1	33	.	0			c.128delG						.						110.0	103.0	106.0					11																	118452086		2200	4295	6495	SO:0001589	frameshift_variant	372	exon2			.	X81197	CCDS8400.1, CCDS44749.1	11q23.3	2010-04-21	2003-01-29		ENSG00000095139	ENSG00000095139			649	protein-coding gene	gene with protein product		600820	"""coatomer protein complex, subunit delta"""	COPD		7782067, 8854871	Standard	NM_001655		Approved		uc001ptq.3	P48444	OTTHUMG00000166340	ENST00000264028.4:c.129delA	chr11.hg19:g.118452086delA	ENSP00000264028:p.Gly43fs	260.0	0.0		151.0	10.0	NM_001655	B4E1X2|E9PEU4|Q52M80	Frame_Shift_Del	DEL	ENST00000264028.4	hg19	CCDS8400.1																																																																																			.	.		0.403	ARCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389278.1		
LGI1	9211	hgsc.bcm.edu	37	10	95552602	95552602	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:95552602delC	ENST00000371418.4	+	6	866	c.606delC	c.(604-606)ggcfs	p.G202fs	LGI1_ENST00000542308.1_Frame_Shift_Del_p.G154fs|LGI1_ENST00000371413.3_Frame_Shift_Del_p.G202fs	NM_005097.2	NP_005088.1	O95970	LGI1_HUMAN	leucine-rich, glioma inactivated 1	202	LRRCT.				axon guidance (GO:0007411)|cell proliferation (GO:0008283)|nervous system development (GO:0007399)|neuron projection development (GO:0031175)|positive regulation of cell growth (GO:0030307)|positive regulation of synaptic transmission (GO:0050806)|protein homooligomerization (GO:0051260)	cell junction (GO:0030054)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|synapse (GO:0045202)	receptor binding (GO:0005102)	p.E205fs*9(1)		central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(18)|ovary(2)|skin(1)	29		Colorectal(252;0.124)				ACTGCGAAGGCCCCCCAGAAT	0.418																																					p.G202fs		Atlas-INDEL	.											.,1	LGI1	69	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.605delG						.						133.0	135.0	134.0					10																	95552602		2203	4300	6503	SO:0001589	frameshift_variant	9211	exon6			.	AF055636	CCDS7431.1	10q24	2008-08-01	2002-06-05		ENSG00000108231	ENSG00000108231			6572	protein-coding gene	gene with protein product		604619	"""epilepsy, partial"""	EPT		9879993, 11978770, 15079011	Standard	NM_005097		Approved	IB1099, ETL1, EPITEMPIN	uc001kjc.4	O95970	OTTHUMG00000018777	ENST00000371418.4:c.606delC	chr10.hg19:g.95552602delC	ENSP00000360472:p.Gly202fs	231.0	0.0		177.0	12.0	NM_005097	A8K0Z1|B4E1S0|Q5W001|Q5W002|Q8NI23|Q96LF5	Frame_Shift_Del	DEL	ENST00000371418.4	hg19	CCDS7431.1																																																																																			.	.		0.418	LGI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049445.1	NM_005097	
RREB1	6239	hgsc.bcm.edu	37	6	7232097	7232097	+	Frame_Shift_Del	DEL	C	C	-	rs552152051		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:7232097delC	ENST00000349384.6	+	10	4079	c.3765delC	c.(3763-3765)ttcfs	p.F1255fs	RREB1_ENST00000379938.2_Frame_Shift_Del_p.F1255fs|RREB1_ENST00000334984.6_Frame_Shift_Del_p.F1255fs|RREB1_ENST00000379933.3_Frame_Shift_Del_p.F1255fs	NM_001003698.3	NP_001003698.1	Q92766	RREB1_HUMAN	ras responsive element binding protein 1	1255					multicellular organismal development (GO:0007275)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|Ras protein signal transduction (GO:0007265)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear body (GO:0016604)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(18)|ovary(5)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58	Ovarian(93;0.0398)	all_hematologic(90;0.0384)|Prostate(151;0.191)				CCCGGGTTTTCCCTTGGGCCA	0.617																																					p.F1255fs		Atlas-INDEL	.											.	RREB1	242	.	0			c.3764delT						.						54.0	40.0	45.0					6																	7232097		2203	4300	6503	SO:0001589	frameshift_variant	6239	exon10			.	U26914	CCDS34335.1, CCDS34336.1, CCDS54963.1	6p25	2013-01-08			ENSG00000124782	ENSG00000124782		"""Zinc fingers, C2H2-type"""	10449	protein-coding gene	gene with protein product	"""hindsight homolog (drosophila)"""	602209				9367691, 18394891	Standard	NM_001003698		Approved	HNT	uc003mxb.3	Q92766	OTTHUMG00000014201	ENST00000349384.6:c.3765delC	chr6.hg19:g.7232097delC	ENSP00000305560:p.Phe1255fs	246.0	0.0		180.0	11.0	NM_001003700	A2RRF5|E2GM80|E2GM81|O75567|O75568|Q5VYB2|Q6BEP5|Q6BEP6|Q6BEP8|Q86SU2|Q9Y474	Frame_Shift_Del	DEL	ENST00000349384.6	hg19	CCDS34336.1																																																																																			.	.		0.617	RREB1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352985.1		
TTLL6	284076	hgsc.bcm.edu	37	17	46846369	46846369	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:46846369delT	ENST00000393382.3	-	15	2799	c.2658delA	c.(2656-2658)aaafs	p.K886fs	TTLL6_ENST00000433608.2_Frame_Shift_Del_p.K579fs	NM_001130918.1	NP_001124390.1			tubulin tyrosine ligase-like family, member 6											endometrium(1)|large_intestine(5)|lung(9)|prostate(1)|skin(2)	18						TCTCACATCCTTTTTGGCCAG	0.493																																					p.G887fs		Atlas-INDEL	.											.	TTLL6	113	.	0			c.2659delG						.						175.0	146.0	156.0					17																	46846369		2203	4300	6503	SO:0001589	frameshift_variant	284076	exon15			.	AK093127	CCDS11537.2, CCDS45724.1	17q21.32	2013-02-14			ENSG00000170703	ENSG00000170703		"""Tubulin tyrosine ligase-like family"""	26664	protein-coding gene	gene with protein product		610849				15890843	Standard	NM_173623		Approved	FLJ35808	uc021tzm.1	Q8N841	OTTHUMG00000156978	ENST00000393382.3:c.2658delA	chr17.hg19:g.46846369delT	ENSP00000377043:p.Lys886fs	246.0	0.0		204.0	13.0	NM_001130918		Frame_Shift_Del	DEL	ENST00000393382.3	hg19	CCDS45724.1																																																																																			.	.		0.493	TTLL6-003	KNOWN	downstream_ATG|non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346939.3	NM_173623	
CDC27	996	hgsc.bcm.edu	37	17	45209674	45209674	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:45209674delT	ENST00000066544.3	-	15	2073	c.1980delA	c.(1978-1980)aaafs	p.K660fs	CDC27_ENST00000446365.2_Frame_Shift_Del_p.K599fs|CDC27_ENST00000527547.1_Frame_Shift_Del_p.K659fs|CDC27_ENST00000531206.1_Frame_Shift_Del_p.K666fs	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	660					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|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 K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	protein phosphatase binding (GO:0019903)			NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						TATCAAGCGCTTTTTGGAAAT	0.299																																					p.A667fs		Atlas-INDEL	.											.	CDC27	337	.	0			c.1999delG						.						84.0	85.0	84.0					17																	45209674		2203	4300	6503	SO:0001589	frameshift_variant	996	exon15			.	U00001	CCDS11509.1, CCDS45720.1, CCDS74090.1	17q21.32	2013-01-17	2013-01-17		ENSG00000004897	ENSG00000004897		"""Anaphase promoting complex subunits"", ""Tetratricopeptide (TTC) repeat domain containing"""	1728	protein-coding gene	gene with protein product	"""anaphase promoting complex subunit 3"""	116946	"""cell division cycle 27"", ""cell division cycle 27 homolog (S. cerevisiae)"""	D0S1430E, D17S978E		8234252	Standard	XM_005257892		Approved	APC3, ANAPC3, NUC2	uc002ile.4	P30260	OTTHUMG00000166429	ENST00000066544.3:c.1980delA	chr17.hg19:g.45209674delT	ENSP00000066544:p.Lys660fs	118.0	0.0		115.0	10.0	NM_001114091	G3V1C4|Q16349|Q96F35	Frame_Shift_Del	DEL	ENST00000066544.3	hg19	CCDS11509.1																																																																																			.	.		0.299	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389742.2		
ERAP1	51752	hgsc.bcm.edu	37	5	96139154	96139154	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:96139154delA	ENST00000443439.2	-	2	542	c.476delT	c.(475-477)ttcfs	p.F159fs	CTD-2260A17.3_ENST00000606346.1_RNA|CTD-2260A17.3_ENST00000606656.1_RNA|ERAP1_ENST00000296754.3_Frame_Shift_Del_p.F159fs	NM_001040458.1|NM_001198541.1	NP_001035548.1|NP_001185470.1	Q9NZ08	ERAP1_HUMAN	endoplasmic reticulum aminopeptidase 1	159					angiogenesis (GO:0001525)|antigen processing and presentation of endogenous peptide antigen via MHC class I (GO:0019885)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|fat cell differentiation (GO:0045444)|membrane protein ectodomain proteolysis (GO:0006509)|positive regulation of angiogenesis (GO:0045766)|regulation of blood pressure (GO:0008217)|regulation of innate immune response (GO:0045088)|response to bacterium (GO:0009617)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	aminopeptidase activity (GO:0004177)|interleukin-1, Type II receptor binding (GO:0005151)|interleukin-6 receptor binding (GO:0005138)|metalloexopeptidase activity (GO:0008235)|zinc ion binding (GO:0008270)			endometrium(7)|large_intestine(5)|lung(3)|ovary(1)|pancreas(1)|stomach(2)	19		all_cancers(142;1.75e-06)|all_epithelial(76;3.08e-09)|all_lung(232;0.000435)|Lung NSC(167;0.000601)|Ovarian(225;0.024)|Colorectal(57;0.0432)|Breast(839;0.244)		all cancers(79;7.26e-15)|COAD - Colon adenocarcinoma(37;0.071)		AAATCCGTGGAAAGTCTCCGA	0.483																																					p.F159fs		Atlas-INDEL	.											.	ERAP1	59	.	0			c.477delC						.						76.0	81.0	79.0					5																	96139154		2203	4300	6503	SO:0001589	frameshift_variant	51752	exon2			.	AB011097	CCDS4085.1, CCDS47250.1	5q15	2014-04-07			ENSG00000164307	ENSG00000164307			18173	protein-coding gene	gene with protein product	"""aminopeptidase regulator of TNFR1 shedding"", ""adipocyte-derived leucine aminopeptidase"", ""puromycin-insensitive leucyl-specific aminopeptidase"""	606832				10220586, 12189246, 16286653	Standard	NM_001198541		Approved	ARTS-1, A-LAP, PILS-AP, KIAA0525, ERAAP1	uc003kml.3	Q9NZ08	OTTHUMG00000128721	ENST00000443439.2:c.476delT	chr5.hg19:g.96139154delA	ENSP00000406304:p.Phe159fs	227.0	0.0		173.0	11.0	NM_001198541	O60278|Q6UWY6|Q8NEL4|Q8TAD0|Q9UHF8|Q9UKY2	Frame_Shift_Del	DEL	ENST00000443439.2	hg19	CCDS47250.1																																																																																			.	.		0.483	ERAP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370699.1	NM_016442	
CCDC89	220388	hgsc.bcm.edu	37	11	85397087	85397087	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:85397087delT	ENST00000316398.3	-	1	233	c.87delA	c.(85-87)aaafs	p.K29fs		NM_152723.1	NP_689936.1	Q8N998	CCD89_HUMAN	coiled-coil domain containing 89	29						cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(6)|skin(1)	15		Acute lymphoblastic leukemia(157;4.88e-06)|all_hematologic(158;0.00572)				GGTTGTTCAGTTTTTCATTTT	0.552																																					p.L30X		Atlas-INDEL	.											.	CCDC89	45	.	0			c.88delC						.						79.0	76.0	77.0					11																	85397087		2203	4299	6502	SO:0001589	frameshift_variant	220388	exon1			.	AK095478	CCDS8270.1	11q14.1	2006-03-16			ENSG00000179071	ENSG00000179071			26762	protein-coding gene	gene with protein product						12477932	Standard	NM_152723		Approved	FLJ38159	uc001pau.1	Q8N998	OTTHUMG00000166976	ENST00000316398.3:c.87delA	chr11.hg19:g.85397087delT	ENSP00000320649:p.Lys29fs	237.0	0.0		176.0	11.0	NM_152723		Frame_Shift_Del	DEL	ENST00000316398.3	hg19	CCDS8270.1																																																																																			.	.		0.552	CCDC89-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392182.1	NM_152723	
CDK8	1024	hgsc.bcm.edu	37	13	26923240	26923240	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr13:26923240delT	ENST00000381527.3	+	3	739	c.236delT	c.(235-237)attfs	p.I79fs	CDK8_ENST00000536792.1_Frame_Shift_Del_p.I79fs	NM_001260.1	NP_001251.1	P49336	CDK8_HUMAN	cyclin-dependent kinase 8	79	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				gene expression (GO:0010467)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	mediator complex (GO:0016592)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)			breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(11)|ovary(1)|skin(1)|urinary_tract(1)	25	Colorectal(5;0.000442)	Lung SC(185;0.0156)|Breast(139;0.147)		all cancers(112;0.0384)|Epithelial(112;0.142)|OV - Ovarian serous cystadenocarcinoma(117;0.188)		CCAAACGTCATTTCTCTTCAA	0.403																																					p.I79fs		Atlas-INDEL	.											.	CDK8	61	.	0			c.235delA						.						236.0	215.0	222.0					13																	26923240		2203	4300	6503	SO:0001589	frameshift_variant	1024	exon3			.	X85753	CCDS9317.1	13q12	2011-11-08			ENSG00000132964	ENSG00000132964		"""Cyclin-dependent kinases"""	1779	protein-coding gene	gene with protein product		603184				7568034	Standard	NM_001260		Approved	K35	uc001uqr.1	P49336	OTTHUMG00000016617	ENST00000381527.3:c.236delT	chr13.hg19:g.26923240delT	ENSP00000370938:p.Ile79fs	251.0	0.0		182.0	11.0	NM_001260	Q5VUF3|Q6ISB5	Frame_Shift_Del	DEL	ENST00000381527.3	hg19	CCDS9317.1																																																																																			.	.		0.403	CDK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044250.1		
FAT1	2195	hgsc.bcm.edu	37	4	187541324	187541324	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:187541324delT	ENST00000441802.2	-	10	6625	c.6416delA	c.(6415-6417)aagfs	p.K2139fs		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	2139	Cadherin 19. {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						CTCAAATTGCTTTTTCAGTGA	0.428										HNSCC(5;0.00058)																											p.K2139fs	Colon(197;1040 2055 4143 4984 49344)	Atlas-INDEL	.											.	FAT1	500	.	0			c.6417delG						.						79.0	75.0	76.0					4																	187541324		1857	4112	5969	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.6416delA	chr4.hg19:g.187541324delT	ENSP00000406229:p.Lys2139fs	177.0	0.0		168.0	11.0	NM_005245		Frame_Shift_Del	DEL	ENST00000441802.2	hg19	CCDS47177.1																																																																																			.	.		0.428	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245	
MMP8	4317	hgsc.bcm.edu	37	11	102587087	102587087	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:102587087delA	ENST00000236826.3	-	6	946	c.848delT	c.(847-849)ttgfs	p.L283fs		NM_002424.2	NP_002415.1	P22894	MMP8_HUMAN	matrix metallopeptidase 8 (neutrophil collagenase)	283					collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|serine-type endopeptidase activity (GO:0004252)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(3)|kidney(1)|large_intestine(4)|lung(11)|ovary(4)|skin(6)|stomach(1)|urinary_tract(1)	32	all_cancers(8;0.00092)|all_epithelial(12;0.00389)|Lung NSC(15;0.227)	all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	Epithelial(9;0.0555)|Lung(13;0.0828)|LUSC - Lung squamous cell carcinoma(19;0.151)|all cancers(10;0.189)	BRCA - Breast invasive adenocarcinoma(274;0.0141)	Marimastat(DB00786)	ATCAAATGTCAAACTGGGGTC	0.363																																					p.L283fs		Atlas-INDEL	.											.	MMP8	68	.	0			c.849delG						.						128.0	133.0	131.0					11																	102587087		2203	4299	6502	SO:0001589	frameshift_variant	4317	exon6			.	J05556	CCDS8320.1	11q21-q22	2008-02-05	2005-08-08		ENSG00000118113	ENSG00000118113	3.4.24.34		7175	protein-coding gene	gene with protein product		120355	"""matrix metalloproteinase 8 (neutrophil collagenase)"""	CLG1			Standard	NM_002424		Approved		uc001phe.2	P22894	OTTHUMG00000167587	ENST00000236826.3:c.848delT	chr11.hg19:g.102587087delA	ENSP00000236826:p.Leu283fs	120.0	0.0		144.0	10.0	NM_002424	Q45F99	Frame_Shift_Del	DEL	ENST00000236826.3	hg19	CCDS8320.1																																																																																			.	.		0.363	MMP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395223.1	NM_002424	
TMEM229B	161145	hgsc.bcm.edu	37	14	67940172	67940172	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr14:67940172delG	ENST00000557006.1	-	4	751	c.469delC	c.(469-471)ctafs	p.L157fs	TMEM229B_ENST00000357461.2_Frame_Shift_Del_p.L157fs			Q8NBD8	T229B_HUMAN	transmembrane protein 229B	157						integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)	5						GCCAGGGCTAGGGCGCCGCTG	0.637																																					p.L157fs		Atlas-INDEL	.											.	TMEM229B	20	.	0			c.470delT						.						45.0	50.0	48.0					14																	67940172		2203	4300	6503	SO:0001589	frameshift_variant	161145	exon3			.	AK090706	CCDS9783.1	14q23.3-q24.1	2009-09-22	2009-09-22	2009-09-22	ENSG00000198133	ENSG00000198133			20130	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 83"""	C14orf83			Standard	NM_182526		Approved	FLJ33387	uc001xjk.3	Q8NBD8		ENST00000557006.1:c.469delC	chr14.hg19:g.67940172delG	ENSP00000451774:p.Leu157fs	209.0	0.0		153.0	10.0	NM_182526		Frame_Shift_Del	DEL	ENST00000557006.1	hg19	CCDS9783.1																																																																																			.	.		0.637	TMEM229B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412718.2	NM_182526	
TLDC1	57707	hgsc.bcm.edu	37	16	84520325	84520325	+	Frame_Shift_Del	DEL	T	T	-	rs431389	byFrequency	TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:84520325delT	ENST00000343629.6	-	5	1052	c.870delA	c.(868-870)ggafs	p.G290fs	TLDC1_ENST00000535580.1_Frame_Shift_Del_p.G263fs|TLDC1_ENST00000561807.1_5'Flank	NM_020947.3	NP_065998.3	Q6P9B6	TLDC1_HUMAN	TBC/LysM-associated domain containing 1	290	TLD.					lysosomal membrane (GO:0005765)											CCACACAGGGTCCCCGGTGAG	0.587																																					p.P291fs		Atlas-INDEL	.											.	KIAA1609	39	.	0			c.871delC						.						77.0	69.0	72.0					16																	84520325		2200	4300	6500	SO:0001589	frameshift_variant	57707	exon5			.	AB046829	CCDS32498.1	16q24.1	2013-03-14	2013-03-14	2013-03-14	ENSG00000140950	ENSG00000140950			29325	protein-coding gene	gene with protein product	"""TLD domain containing 1"""		"""KIAA1609"""	KIAA1609		10997877	Standard	NM_020947		Approved		uc002fib.3	Q6P9B6	OTTHUMG00000176739	ENST00000343629.6:c.870delA	chr16.hg19:g.84520325delT	ENSP00000343635:p.Gly290fs	244.0	0.0		138.0	10.0	NM_020947	Q8IZ64|Q9HCG3|Q9NTE8	Frame_Shift_Del	DEL	ENST00000343629.6	hg19	CCDS32498.1																																																																																			.	.		0.587	TLDC1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433421.1	NM_020947	
PRKACB	5567	hgsc.bcm.edu	37	1	84679946	84679946	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:84679946delA	ENST00000370689.2	+	9	1140	c.876delA	c.(874-876)atafs	p.I292fs	PRKACB_ENST00000370685.3_Frame_Shift_Del_p.I339fs|PRKACB_ENST00000370682.3_Frame_Shift_Del_p.I296fs|PRKACB_ENST00000394839.2_Frame_Shift_Del_p.I262fs|PRKACB_ENST00000394838.2_Frame_Shift_Del_p.I299fs	NM_001242862.1|NM_002731.2	NP_001229791.1|NP_002722.1	P22694	KAPCB_HUMAN	protein kinase, cAMP-dependent, catalytic, beta	292	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|blood coagulation (GO:0007596)|carbohydrate metabolic process (GO:0005975)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|negative regulation of meiotic cell cycle (GO:0051447)|negative regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:1901621)|neural tube closure (GO:0001843)|neurotrophin TRK receptor signaling pathway (GO:0048011)|protein phosphorylation (GO:0006468)|regulation of insulin secretion (GO:0050796)|regulation of protein processing (GO:0070613)|response to clozapine (GO:0097338)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|triglyceride catabolic process (GO:0019433)|water transport (GO:0006833)	cAMP-dependent protein kinase complex (GO:0005952)|centrosome (GO:0005813)|ciliary base (GO:0097546)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cAMP-dependent protein kinase activity (GO:0004691)|magnesium ion binding (GO:0000287)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(2)|kidney(1)|lung(11)|ovary(1)	16				all cancers(265;0.00536)|Epithelial(280;0.0161)|OV - Ovarian serous cystadenocarcinoma(397;0.141)		TCAGTGATATAAAAACTCACA	0.388																																					p.I339fs		Atlas-INDEL	.											.	PRKACB	174	.	0			c.1016delT						.						85.0	85.0	85.0					1																	84679946		2203	4300	6503	SO:0001589	frameshift_variant	5567	exon9			.	BC035058	CCDS691.1, CCDS692.1, CCDS693.1, CCDS55610.1, CCDS55611.1, CCDS72812.1, CCDS72813.1, CCDS72814.1, CCDS72815.1, CCDS72816.1	1p36.1	2012-10-02			ENSG00000142875	ENSG00000142875	2.7.11.1		9381	protein-coding gene	gene with protein product		176892					Standard	XM_005271016		Approved	PKACb	uc001djl.3	P22694	OTTHUMG00000009975	ENST00000370689.2:c.876delA	chr1.hg19:g.84679946delA	ENSP00000359723:p.Ile292fs	165.0	0.0		131.0	13.0	NM_182948	B1APG4|B4DKB0|B4E2Q1|Q14VH1|Q59GC0|Q5BNE9|Q5BNF0|Q5BNF1|Q5BNF2|Q5BNF3|Q5CZ92|Q5T1K3|Q7Z3M1|Q8IYR5|Q8IZQ0|Q96B09	Frame_Shift_Del	DEL	ENST00000370689.2	hg19	CCDS691.1																																																																																			.	.		0.388	PRKACB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000027641.1	NM_182948	
ZNF77	58492	hgsc.bcm.edu	37	19	2934192	2934192	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:2934192delA	ENST00000314531.4	-	4	1025	c.933delT	c.(931-933)tttfs	p.F311fs		NM_021217.2	NP_067040.1	Q15935	ZNF77_HUMAN	zinc finger protein 77	311					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(3)|kidney(3)|large_intestine(3)|lung(5)|ovary(1)	17				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)|GBM - Glioblastoma multiforme(1328;2.11e-07)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|Lung(535;0.174)|STAD - Stomach adenocarcinoma(1328;0.18)		CGTGATCTCTAAAGGAGGAGT	0.453																																					p.R312fs		Atlas-INDEL	.											.	ZNF77	47	.	0			c.934delA						.						177.0	159.0	166.0					19																	2934192		2203	4300	6503	SO:0001589	frameshift_variant	58492	exon4			.	X65230	CCDS12099.1	19p13.3	2013-01-08	2006-05-12					"""Zinc fingers, C2H2-type"", ""-"""	13150	protein-coding gene	gene with protein product		194551	"""zinc finger protein 77 (pT1)"""			8478004	Standard	NM_021217		Approved	pT1	uc002lws.4	Q15935		ENST00000314531.4:c.933delT	chr19.hg19:g.2934192delA	ENSP00000319053:p.Phe311fs	258.0	0.0		180.0	12.0	NM_021217	Q86XJ3|Q9NPP0	Frame_Shift_Del	DEL	ENST00000314531.4	hg19	CCDS12099.1																																																																																			.	.		0.453	ZNF77-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451924.1	NM_021217	
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32548050	32548050	+	Intron	DEL	G	G	-	rs28732250	byFrequency	TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:32548050delG	ENST00000360004.5	-	5	869					NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1						antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)				large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(2)|stomach(1)	10						AGAGTGTCCTGGGAAAAAGAG	0.438										Multiple Myeloma(14;0.17)																											.		Atlas-INDEL	.											.	HLA-DRB1	41	.	0			c.764-2C>-						.						29.0	32.0	31.0					6																	32548050		2097	4053	6150	SO:0001627	intron_variant	3123	exon6			.	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.764-3C>-	chr6.hg19:g.32548050delG		215.0	0.0		130.0	10.0	NM_002124	P01914|Q9MYF5	Splice_Site	DEL	ENST00000360004.5	hg19	CCDS47409.1																																																																																			.	.		0.438	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124	
EYS	346007	hgsc.bcm.edu	37	6	66054028	66054028	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:66054028delA	ENST00000370621.3	-	10	2028	c.1502delT	c.(1501-1503)ttcfs	p.F502fs	EYS_ENST00000370618.3_Frame_Shift_Del_p.F502fs|EYS_ENST00000342421.5_Frame_Shift_Del_p.F502fs|EYS_ENST00000503581.1_Frame_Shift_Del_p.F502fs|EYS_ENST00000370616.2_Frame_Shift_Del_p.F502fs|EYS_ENST00000393380.2_Frame_Shift_Del_p.F502fs			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	502					detection of light stimulus involved in visual perception (GO:0050908)|skeletal muscle tissue regeneration (GO:0043403)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	69						AGCCAGAAAGAAATAGGCATC	0.358																																					p.F501fs		Atlas-INDEL	.											EYS_ENST00000370621,NS,carcinoma,0,2	EYS	527	.	0			c.1503delC						.						100.0	100.0	100.0					6																	66054028		2203	4300	6503	SO:0001589	frameshift_variant	346007	exon10			.		CCDS4967.1, CCDS47445.1, CCDS47446.1	6q12	2014-01-28	2008-10-20	2008-10-20	ENSG00000188107	ENSG00000188107			21555	protein-coding gene	gene with protein product		612424	"""chromosome 6 open reading frame 180"", ""EGF-like-domain, multiple 11"", ""retinitis pigmentosa 25 (autosomal recessive)"", ""EGF-like-domain, multiple 10"", ""chromosome 6 open reading frame 178"", ""chromosome 6 open reading frame 179"""	C6orf180, EGFL11, RP25, EGFL10, C6orf178, C6orf179		18836446, 18976725	Standard	NM_001142800		Approved	dJ1018A4.2, bA166P24.2, SPAM, bA307F22.3, dJ303F19.1, bA74E24.1	uc011dxu.1	Q5T1H1	OTTHUMG00000014971	ENST00000370621.3:c.1502delT	chr6.hg19:g.66054028delA	ENSP00000359655:p.Phe502fs	217.0	0.0		170.0	11.0	NM_001142801	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Frame_Shift_Del	DEL	ENST00000370621.3	hg19																																																																																				.	.		0.358	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050	
CEP135	9662	hgsc.bcm.edu	37	4	56841104	56841104	+	Frame_Shift_Del	DEL	A	A	-	rs34965077		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:56841104delA	ENST00000257287.4	+	11	1566	c.1442delA	c.(1441-1443)gaafs	p.E481fs		NM_025009.4	NP_079285.2	Q66GS9	CP135_HUMAN	centrosomal protein 135kDa	481					centriole replication (GO:0007099)|centriole-centriole cohesion (GO:0010457)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)	protein C-terminus binding (GO:0008022)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(9)|lung(26)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	50	Glioma(25;0.08)|all_neural(26;0.101)					AGCGCACGTGAAAAAAGTTCA	0.313																																					p.E481fs		Atlas-INDEL	.											CEP135,NS,carcinoma,0,1	CEP135	115	.	0			c.1441delG						.						62.0	63.0	62.0					4																	56841104		2203	4300	6503	SO:0001589	frameshift_variant	9662	exon11			.	AB014535	CCDS33986.1	4q12	2014-02-20	2005-12-02	2005-12-02	ENSG00000174799	ENSG00000174799			29086	protein-coding gene	gene with protein product		611423	"""KIAA0635"", ""centrosomal protein 4"""	KIAA0635, CEP4		9734811, 14654843	Standard	NM_025009		Approved	FLJ13621	uc003hbi.4	Q66GS9	OTTHUMG00000160748	ENST00000257287.4:c.1442delA	chr4.hg19:g.56841104delA	ENSP00000257287:p.Glu481fs	173.0	0.0		141.0	10.0	NM_025009	B2RMY0|O75130|Q58F25|Q9H8H7	Frame_Shift_Del	DEL	ENST00000257287.4	hg19	CCDS33986.1																																																																																			.	.		0.313	CEP135-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362092.2	NM_025009	
ZNF217	7764	hgsc.bcm.edu	37	20	52193620	52193620	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr20:52193620delA	ENST00000371471.2	-	4	2108	c.1683delT	c.(1681-1683)tttfs	p.F561fs	ZNF217_ENST00000302342.3_Frame_Shift_Del_p.F561fs|RP4-724E16.2_ENST00000424252.1_RNA			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	178.0	0.0		139.0	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	
KMT2A	4297	hgsc.bcm.edu	37	11	118377153	118377153	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:118377153delG	ENST00000389506.5	+	27	10537	c.10537delG	c.(10537-10539)gggfs	p.G3514fs	KMT2A_ENST00000354520.4_Frame_Shift_Del_p.G3476fs|KMT2A_ENST00000534358.1_Frame_Shift_Del_p.G3517fs			Q03164	KMT2A_HUMAN	lysine (K)-specific methyltransferase 2A	3514					anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|DNA methylation (GO:0006306)|embryonic hemopoiesis (GO:0035162)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|histone H4-K16 acetylation (GO:0043984)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cellular response to drug (GO:2001040)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transporter activity (GO:0032411)|protein complex assembly (GO:0006461)|regulation of histone H3-K4 methylation (GO:0051569)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|histone methyltransferase complex (GO:0035097)|MLL1 complex (GO:0071339)|nucleus (GO:0005634)	AT DNA binding (GO:0003680)|chromatin binding (GO:0003682)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|identical protein binding (GO:0042802)|lysine-acetylated histone binding (GO:0070577)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|unmethylated CpG binding (GO:0045322)|zinc ion binding (GO:0008270)										CACCTCTCCTGGGGGTTCTCC	0.552																																					p.P3515fs		Atlas-INDEL	.											.	MLL	548	.	0			c.10545delT						.						70.0	70.0	70.0					11																	118377153		2200	4295	6495	SO:0001589	frameshift_variant	4297	exon27			.	L04284	CCDS31686.1, CCDS55791.1	11q23	2014-09-17	2013-05-09	2013-05-09	ENSG00000118058	ENSG00000118058		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	7132	protein-coding gene	gene with protein product		159555	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog)"", ""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila)"""	MLL		1720549	Standard	NM_001197104		Approved	TRX1, HRX, ALL-1, HTRX1, CXXC7, MLL1A		Q03164	OTTHUMG00000166337	ENST00000389506.5:c.10537delG	chr11.hg19:g.118377153delG	ENSP00000374157:p.Gly3514fs	131.0	0.0		106.0	10.0	NM_001197104	E9PQG7|Q13743|Q13744|Q14845|Q16364|Q59FF2|Q6UBD1|Q9HBJ3|Q9UD94|Q9UMA3	Frame_Shift_Del	DEL	ENST00000389506.5	hg19	CCDS31686.1																																																																																			.	.		0.552	KMT2A-015	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399085.2	NM_005933	
GCN1L1	10985	hgsc.bcm.edu	37	12	120580649	120580649	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:120580649delA	ENST00000300648.6	-	43	5604	c.5592delT	c.(5590-5592)tttfs	p.F1864fs		NM_006836.1	NP_006827	Q92616	GCN1L_HUMAN	GCN1 general control of amino-acid synthesis 1-like 1 (yeast)	1864					regulation of translation (GO:0006417)|translation (GO:0006412)	cytoplasm (GO:0005737)|membrane (GO:0016020)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)			NS(2)|breast(2)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(13)|liver(1)|lung(36)|ovary(4)|prostate(7)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	94	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					GGGCAGTTCCAAAGTTATCAT	0.537																																					p.G1865fs		Atlas-INDEL	.											.	GCN1L1	207	.	0			c.5593delG						.						155.0	156.0	156.0					12																	120580649		2049	4196	6245	SO:0001589	frameshift_variant	10985	exon43			.	U77700	CCDS41847.1	12q24.2	2008-07-03	2001-11-28						4199	protein-coding gene	gene with protein product		605614	"""GCN1 (general control of amino-acid synthesis 1, yeast)-like 1"""			9234705	Standard	NM_006836		Approved	KIAA0219, GCN1, GCN1L	uc001txo.3	Q92616	OTTHUMG00000169338	ENST00000300648.6:c.5592delT	chr12.hg19:g.120580649delA	ENSP00000300648:p.Phe1864fs	290.0	0.0		195.0	12.0	NM_006836	A8KAY1|O95001|O95651|Q6P2S3|Q86X65|Q8N5I5|Q8WU80|Q99736|Q9UE60	Frame_Shift_Del	DEL	ENST00000300648.6	hg19	CCDS41847.1																																																																																			.	.		0.537	GCN1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403592.1		
KIF26B	55083	hgsc.bcm.edu	37	1	245848940	245848940	+	Frame_Shift_Del	DEL	C	C	-	rs190318015	byFrequency	TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:245848940delC	ENST00000407071.2	+	12	3095	c.2655delC	c.(2653-2655)ggcfs	p.G885fs	KIF26B_ENST00000366518.4_Frame_Shift_Del_p.G504fs	NM_018012.3	NP_060482.2	Q2KJY2	KI26B_HUMAN	kinesin family member 26B	885					establishment of cell polarity (GO:0030010)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|ureteric bud invasion (GO:0072092)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(21)|ovary(4)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	51	all_cancers(71;3.86e-05)|all_epithelial(71;0.000121)|Ovarian(71;0.0412)|all_lung(81;0.0498)|Lung NSC(105;0.0708)|Breast(184;0.127)		OV - Ovarian serous cystadenocarcinoma(106;0.022)			ACAACGAGGGCCCCCCAGACT	0.662																																					p.G885fs		Atlas-INDEL	.											.	KIF26B	343	.	0			c.2654delG						.						32.0	36.0	34.0					1																	245848940		2010	4149	6159	SO:0001589	frameshift_variant	55083	exon12			.	AK001019	CCDS44342.1	1q44	2008-02-05			ENSG00000162849	ENSG00000162849		"""Kinesins"""	25484	protein-coding gene	gene with protein product		614026					Standard	NM_018012		Approved	FLJ10157	uc001ibf.1	Q2KJY2	OTTHUMG00000040079	ENST00000407071.2:c.2655delC	chr1.hg19:g.245848940delC	ENSP00000385545:p.Gly885fs	238.0	0.0		341.0	21.0	NM_018012	Q6ZQR9|Q6ZUZ0|Q8IUN3|Q8IVR1|Q9NWB4	Frame_Shift_Del	DEL	ENST00000407071.2	hg19	CCDS44342.1																																																																																			.	.		0.662	KIF26B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381037.1	XM_371354	
SULF1	23213	hgsc.bcm.edu	37	8	70488249	70488249	+	Frame_Shift_Del	DEL	G	G	-	rs201774043		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:70488249delG	ENST00000260128.4	+	6	934	c.217delG	c.(217-219)gggfs	p.G74fs	SULF1_ENST00000402687.4_Frame_Shift_Del_p.G74fs|SULF1_ENST00000458141.2_Frame_Shift_Del_p.G74fs|SULF1_ENST00000419716.3_Frame_Shift_Del_p.G74fs	NM_015170.2	NP_055985.2	Q8IWU6	SULF1_HUMAN	sulfatase 1	74					apoptotic process (GO:0006915)|bone development (GO:0060348)|cartilage development (GO:0051216)|chondrocyte development (GO:0002063)|embryonic skeletal system development (GO:0048706)|esophagus smooth muscle contraction (GO:0014846)|glial cell-derived neurotrophic factor receptor signaling pathway (GO:0035860)|glomerular basement membrane development (GO:0032836)|glomerular filtration (GO:0003094)|heparan sulfate proteoglycan metabolic process (GO:0030201)|innervation (GO:0060384)|kidney development (GO:0001822)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell migration (GO:0030336)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of prostatic bud formation (GO:0060686)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	arylsulfatase activity (GO:0004065)|calcium ion binding (GO:0005509)|N-acetylglucosamine-6-sulfatase activity (GO:0008449)			breast(2)|central_nervous_system(3)|endometrium(5)|kidney(3)|large_intestine(10)|lung(15)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	Breast(64;0.0654)		Epithelial(68;0.0124)|OV - Ovarian serous cystadenocarcinoma(28;0.0265)|all cancers(69;0.0534)			TATGGAACATGGGGGGGCCAC	0.493																																					p.H72fs		Atlas-INDEL	.											.,1	SULF1	153	.	0			c.216delT						.						109.0	89.0	96.0					8																	70488249		2203	4300	6503	SO:0001589	frameshift_variant	23213	exon6			.	AB029000	CCDS6204.1	8q13.2	2014-09-11			ENSG00000137573	ENSG00000137573			20391	protein-coding gene	gene with protein product		610012				12368295	Standard	NM_015170		Approved	KIAA1077, SULF-1	uc003xyd.2	Q8IWU6	OTTHUMG00000164466	ENST00000260128.4:c.217delG	chr8.hg19:g.70488249delG	ENSP00000260128:p.Gly74fs	164.0	0.0		199.0	13.0	NM_001128205	Q86YV8|Q8NCA2|Q9UPS5	Frame_Shift_Del	DEL	ENST00000260128.4	hg19	CCDS6204.1																																																																																			.	.		0.493	SULF1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378885.2	NM_015170	
FEM1B	10116	hgsc.bcm.edu	37	15	68582064	68582064	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:68582064delC	ENST00000306917.4	+	2	983	c.368delC	c.(367-369)accfs	p.T123fs		NM_015322.4	NP_056137.1	Q9UK73	FEM1B_HUMAN	fem-1 homolog b (C. elegans)	123					apoptotic process (GO:0006915)|branching involved in prostate gland morphogenesis (GO:0060442)|epithelial cell maturation involved in prostate gland development (GO:0060743)|regulation of DNA damage checkpoint (GO:2000001)|regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902041)|regulation of ubiquitin-protein transferase activity (GO:0051438)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	death receptor binding (GO:0005123)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|urinary_tract(1)	9						ACTAATTCAACCCCCCTGCGG	0.453																																					p.T123fs		Atlas-INDEL	.											.	FEM1B	38	.	0			c.367delA						.						91.0	77.0	82.0					15																	68582064		2200	4298	6498	SO:0001589	frameshift_variant	10116	exon2			.		CCDS10228.1	15q22	2013-02-19	2001-11-28		ENSG00000169018	ENSG00000169018		"""Ankyrin repeat domain containing"""	3649	protein-coding gene	gene with protein product		613539	"""FEM-1 (C. elegans) homolog b"""			10623617	Standard	NM_015322		Approved		uc002arg.3	Q9UK73	OTTHUMG00000133285	ENST00000306917.4:c.368delC	chr15.hg19:g.68582064delC	ENSP00000307298:p.Thr123fs	260.0	0.0		161.0	11.0	NM_015322	O43146	Frame_Shift_Del	DEL	ENST00000306917.4	hg19	CCDS10228.1																																																																																			.	.		0.453	FEM1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257065.1		
AHI1	54806	hgsc.bcm.edu	37	6	135811800	135811800	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:135811800delT	ENST00000367800.4	-	3	312	c.96delA	c.(94-96)aaafs	p.K32fs	AHI1_ENST00000531527.1_5'Flank|AHI1_ENST00000327035.6_Frame_Shift_Del_p.K32fs|AHI1_ENST00000534469.1_Frame_Shift_Del_p.K32fs|AHI1_ENST00000367798.2_Frame_Shift_Del_p.K32fs|AHI1_ENST00000528103.1_Frame_Shift_Del_p.K32fs|AHI1_ENST00000488690.2_Frame_Shift_Del_p.K32fs|AHI1_ENST00000457866.2_Frame_Shift_Del_p.K32fs	NM_001134830.1	NP_001128302.1	Q8N157	AHI1_HUMAN	Abelson helper integration site 1	32					cellular protein localization (GO:0034613)|central nervous system development (GO:0007417)|cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|cloaca development (GO:0035844)|heart looping (GO:0001947)|hindbrain development (GO:0030902)|Kupffer's vesicle development (GO:0070121)|left/right axis specification (GO:0070986)|morphogenesis of a polarized epithelium (GO:0001738)|negative regulation of apoptotic process (GO:0043066)|otic vesicle development (GO:0071599)|photoreceptor cell outer segment organization (GO:0035845)|positive regulation of polarized epithelial cell differentiation (GO:0030862)|positive regulation of receptor internalization (GO:0002092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|pronephric duct morphogenesis (GO:0039023)|pronephric nephron tubule morphogenesis (GO:0039008)|protein localization to organelle (GO:0033365)|regulation of behavior (GO:0050795)|retina layer formation (GO:0010842)|specification of axis polarity (GO:0065001)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vesicle targeting (GO:0006903)|vesicle-mediated transport (GO:0016192)	adherens junction (GO:0005912)|cell-cell junction (GO:0005911)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|nonmotile primary cilium (GO:0031513)|photoreceptor outer segment (GO:0001750)|primary cilium (GO:0072372)|TCTN-B9D complex (GO:0036038)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(18)|ovary(1)	37	Breast(56;0.239)|Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00904)|OV - Ovarian serous cystadenocarcinoma(155;0.00991)		TTTTCTTCAGTTTTTTCTTTT	0.348																																					p.L33X		Atlas-INDEL	.											.	AHI1	81	.	0			c.97delC						.						205.0	189.0	194.0					6																	135811800		1823	4073	5896	SO:0001589	frameshift_variant	54806	exon4			.	AJ459824	CCDS47483.1, CCDS47484.1	6q23.2	2013-01-10	2005-11-29		ENSG00000135541	ENSG00000135541		"""WD repeat domain containing"""	21575	protein-coding gene	gene with protein product	"""Jouberin"""	608894	"""Abelson helper integration site"""			15060101, 16240161	Standard	NM_017651		Approved	FLJ20069, ORF1, JBTS3	uc003qgj.3	Q8N157	OTTHUMG00000015631	ENST00000367800.4:c.96delA	chr6.hg19:g.135811800delT	ENSP00000356774:p.Lys32fs	277.0	0.0		212.0	13.0	NM_001134832	E1P584|Q4FD35|Q504T3|Q5TCP9|Q6P098|Q6PIT6|Q8NDX0|Q9H0H2	Frame_Shift_Del	DEL	ENST00000367800.4	hg19	CCDS47483.1																																																																																			.	.		0.348	AHI1-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391948.1	NM_017651	
FAM47B	170062	hgsc.bcm.edu	37	X	34961258	34961258	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:34961258delT	ENST00000329357.5	+	1	346	c.310delT	c.(310-312)tttfs	p.F104fs		NM_152631.2	NP_689844.2	Q8NA70	FA47B_HUMAN	family with sequence similarity 47, member B	104										breast(3)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(13)|lung(28)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)	71						AGCGGCCCTATTTTCCGAGCT	0.532																																					p.L103fs		Atlas-INDEL	.											.	FAM47B	209	.	0			c.309delA						.						89.0	82.0	84.0					X																	34961258		2202	4300	6502	SO:0001589	frameshift_variant	170062	exon1			.	BC035026	CCDS14236.1	Xp21.1	2004-08-09			ENSG00000189132	ENSG00000189132			26659	protein-coding gene	gene with protein product						14702039	Standard	NM_152631		Approved	FLJ35782	uc004ddi.2	Q8NA70	OTTHUMG00000021345	ENST00000329357.5:c.310delT	chrX.hg19:g.34961258delT	ENSP00000328307:p.Phe104fs	183.0	0.0		165.0	12.0	NM_152631	Q5JQN5|Q6PIG3	Frame_Shift_Del	DEL	ENST00000329357.5	hg19	CCDS14236.1																																																																																			.	.		0.532	FAM47B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056211.1	NM_152631	
ERCC5	2073	hgsc.bcm.edu	37	13	103508419	103508419	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr13:103508419delA	ENST00000355739.4	+	5	1908	c.485delA	c.(484-486)gaafs	p.E162fs	BIVM-ERCC5_ENST00000602836.1_Frame_Shift_Del_p.*587fs|ERCC5_ENST00000535557.1_Frame_Shift_Del_p.E162fs	NM_000123.3	NP_000114	P28715	ERCC5_HUMAN	excision repair cross-complementation group 5	162					DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|negative regulation of apoptotic process (GO:0043066)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA incision, 3'-to lesion (GO:0006295)|response to UV (GO:0009411)|response to UV-C (GO:0010225)|transcription-coupled nucleotide-excision repair (GO:0006283)|UV protection (GO:0009650)	intermediate filament cytoskeleton (GO:0045111)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	bubble DNA binding (GO:0000405)|double-stranded DNA binding (GO:0003690)|endodeoxyribonuclease activity (GO:0004520)|endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein N-terminus binding (GO:0047485)|single-stranded DNA binding (GO:0003697)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(4)|large_intestine(8)|lung(18)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	51	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.211)					GAGGAAGATGAAAAAGAATGG	0.313			"""Mis, N, F"""			"""skin basal cell, skin squamous cell, melanoma"""		Nucleotide excision repair (NER)	Xeroderma Pigmentosum																												p.E616fs		Atlas-INDEL	.	yes	Rec		Xeroderma pigmentosum (G)	13	13q33	2073	"""excision repair cross-complementing rodent repair deficiency, complementation group 5 (xeroderma pigmentosum, complementation group G (Cockayne syndrome))"""		E	.	.	.	.	0			c.1846delG						.						119.0	120.0	119.0					13																	103508419		2203	4300	6503	SO:0001589	frameshift_variant	0	exon13	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	.	X71342	CCDS32004.1	13q22-q34	2014-09-17	2014-03-07		ENSG00000134899	ENSG00000134899			3437	protein-coding gene	gene with protein product	"""Cockayne syndrome"""	133530	"""xeroderma pigmentosum, complementation group G"", ""excision repair cross-complementing rodent repair deficiency, complementation group 5"""	ERCM2, XPGC		8088806	Standard	NM_000123		Approved			P28715	OTTHUMG00000017310	ENST00000355739.4:c.485delA	chr13.hg19:g.103508419delA	ENSP00000347978:p.Glu162fs	552.0	0.0		333.0	21.0	NM_001204425	A6NGT4|Q5JUS4|Q5JUS5|Q7Z2V3|Q8IZL6|Q8N1B7|Q9HD59|Q9HD60	Frame_Shift_Del	DEL	ENST00000355739.4	hg19	CCDS32004.1																																																																																			.	.		0.313	ERCC5-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045708.1		
GRIN2C	2905	hgsc.bcm.edu	37	17	72838789	72838789	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:72838789delC	ENST00000293190.5	-	13	3633	c.3487delG	c.(3487-3489)gctfs	p.A1163fs		NM_000835.3	NP_000826.2	Q14957	NMDE3_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2C	1163					directional locomotion (GO:0033058)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of protein catabolic process (GO:0042177)|neuromuscular process controlling balance (GO:0050885)|protein localization (GO:0008104)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|response to wounding (GO:0009611)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	cation channel activity (GO:0005261)|extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(15)|ovary(2)|skin(2)|urinary_tract(1)	33	all_lung(278;0.172)|Lung NSC(278;0.207)				Acamprosate(DB00659)|Atomoxetine(DB00289)|Gabapentin(DB00996)|Glycine(DB00145)|Ketobemidone(DB06738)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	GGACAGACAGCCCCCCAGCAA	0.726																																					p.A1163fs		Atlas-INDEL	.											.	GRIN2C	144	.	0			c.3488delC						.						10.0	15.0	13.0					17																	72838789		2152	4233	6385	SO:0001589	frameshift_variant	2905	exon13			.		CCDS32724.1, CCDS62330.1	17q25.1	2012-08-29			ENSG00000161509	ENSG00000161509		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4587	protein-coding gene	gene with protein product		138254		NMDAR2C		9480759	Standard	NM_001278553		Approved	GluN2C	uc002jlt.1	Q14957	OTTHUMG00000044524	ENST00000293190.5:c.3487delG	chr17.hg19:g.72838789delC	ENSP00000293190:p.Ala1163fs	160.0	0.0		165.0	10.0	NM_000835	B2RTT1	Frame_Shift_Del	DEL	ENST00000293190.5	hg19	CCDS32724.1																																																																																			.	.		0.726	GRIN2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103824.1		
USP47	55031	hgsc.bcm.edu	37	11	11970052	11970052	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:11970052delA	ENST00000399455.2	+	23	3475	c.3355delA	c.(3355-3357)aaafs	p.K1120fs	USP47_ENST00000339865.5_Frame_Shift_Del_p.K1032fs|USP47_ENST00000527733.1_Frame_Shift_Del_p.K1100fs|USP47_ENST00000539466.1_5'UTR	NM_001282659.1	NP_001269588.1	Q96K76	UBP47_HUMAN	ubiquitin specific peptidase 47	1120					base-excision repair (GO:0006284)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|monoubiquitinated protein deubiquitination (GO:0035520)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of G2/M transition of mitotic cell cycle (GO:0010972)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell growth (GO:0030307)|response to drug (GO:0042493)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|SCF ubiquitin ligase complex (GO:0019005)	ubiquitin-specific protease activity (GO:0004843)|WD40-repeat domain binding (GO:0071987)			breast(4)|endometrium(7)|kidney(2)|large_intestine(8)|liver(2)|lung(14)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	46				Epithelial(150;0.000339)		GAGAGCACTTAAAAAAGGAGA	0.308																																					p.L1030fs		Atlas-INDEL	.											.	USP47	91	.	0			c.3090delT						.						52.0	53.0	53.0					11																	11970052		1801	4053	5854	SO:0001589	frameshift_variant	55031	exon21			.	AK027362	CCDS41619.1, CCDS60725.1	11p15.2	2008-02-05	2005-08-08		ENSG00000170242	ENSG00000170242		"""Ubiquitin-specific peptidases"""	20076	protein-coding gene	gene with protein product		614460	"""Trf (TATA binding protein-related factor)-proximal homolog (Drosophila)"", ""ubiquitin specific protease 47"""			12838346	Standard	XM_005252997		Approved		uc001mjr.3	Q96K76	OTTHUMG00000165685	ENST00000399455.2:c.3355delA	chr11.hg19:g.11970052delA	ENSP00000382382:p.Lys1120fs	162.0	0.0		159.0	10.0	NM_017944	B3KXF5|E9PM46|Q658U0|Q86Y73|Q8TEP6|Q9BWI0|Q9NWN1	Frame_Shift_Del	DEL	ENST00000399455.2	hg19																																																																																				.	.		0.308	USP47-003	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000385853.2	NM_017944	
RPAP1	26015	hgsc.bcm.edu	37	15	41819194	41819194	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:41819194delC	ENST00000304330.4	-	14	1935	c.1819delG	c.(1819-1821)gcafs	p.A607fs	RPAP1_ENST00000561603.1_Frame_Shift_Del_p.A607fs|RPAP1_ENST00000568413.1_5'Flank	NM_015540.2	NP_056355.2	Q9BWH6	RPAP1_HUMAN	RNA polymerase II associated protein 1	607						nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)			NS(1)|breast(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(6)|lung(16)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	45		all_cancers(109;6.59e-20)|all_epithelial(112;7.67e-17)|Lung NSC(122;5.34e-11)|all_lung(180;4.17e-10)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		OV - Ovarian serous cystadenocarcinoma(18;2.84e-17)|GBM - Glioblastoma multiforme(113;1.68e-06)|Colorectal(105;0.0163)|BRCA - Breast invasive adenocarcinoma(123;0.117)		GTAGGCCCTGCCCCCACAGGA	0.557																																					p.A607fs		Atlas-INDEL	.											.	RPAP1	111	.	0			c.1820delC						.						89.0	90.0	89.0					15																	41819194		2203	4300	6503	SO:0001589	frameshift_variant	26015	exon14			.	BC000246	CCDS10079.1	15q14	2004-03-16			ENSG00000103932	ENSG00000103932			24567	protein-coding gene	gene with protein product		611475				10718198	Standard	XM_005254297		Approved	DKFZP727M111, KIAA1403, MGC858, FLJ12732	uc001zod.3	Q9BWH6	OTTHUMG00000130342	ENST00000304330.4:c.1819delG	chr15.hg19:g.41819194delC	ENSP00000306123:p.Ala607fs	180.0	0.0		151.0	10.0	NM_015540	Q9H9I2|Q9NSQ5|Q9P2E4|Q9UFS7	Frame_Shift_Del	DEL	ENST00000304330.4	hg19	CCDS10079.1																																																																																			.	.		0.557	RPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252694.2	NM_015540	
SLC27A5	10998	hgsc.bcm.edu	37	19	59010549	59010549	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:59010549delC	ENST00000263093.2	-	8	1815	c.1706delG	c.(1705-1707)ggcfs	p.G569fs	SLC27A5_ENST00000594786.1_5'UTR|SLC27A5_ENST00000601355.1_Frame_Shift_Del_p.G485fs|SLC27A5_ENST00000599700.1_5'UTR	NM_012254.2	NP_036386.1	Q9Y2P5	S27A5_HUMAN	solute carrier family 27 (fatty acid transporter), member 5	569					bile acid and bile salt transport (GO:0015721)|bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|ketone body biosynthetic process (GO:0046951)|plasma membrane long-chain fatty acid transport (GO:0015911)|small molecule metabolic process (GO:0044281)|triglyceride mobilization (GO:0006642)|very long-chain fatty acid metabolic process (GO:0000038)	basal plasma membrane (GO:0009925)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|protein complex (GO:0043234)	ATP binding (GO:0005524)|cholate-CoA ligase activity (GO:0047747)|fatty acid transporter activity (GO:0015245)|very long-chain fatty acid-CoA ligase activity (GO:0031957)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(7)|ovary(1)|skin(1)|urinary_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;0.0168)|Lung(386;0.181)		CGACAACACGCCCTCCACCTC	0.607																																					p.G569fs		Atlas-INDEL	.											.	SLC27A5	58	.	0			c.1707delC						.						90.0	81.0	84.0					19																	59010549		2203	4300	6503	SO:0001589	frameshift_variant	10998	exon8			.	AF064255	CCDS12983.1	19q13.43	2013-07-15			ENSG00000083807	ENSG00000083807		"""Acyl-CoA synthetase family"", ""Solute carriers"""	10999	protein-coding gene	gene with protein product	"""fatty-acid-Coenzyme A ligase, very long-chain 3"""	603314				10479480, 10749848	Standard	NM_012254		Approved	FATP5, VLACSR, VLCS-H2, VLCSH2, FACVL3, FLJ22987, ACSVL6, ACSB	uc002qtc.2	Q9Y2P5	OTTHUMG00000183543	ENST00000263093.2:c.1706delG	chr19.hg19:g.59010549delC	ENSP00000263093:p.Gly569fs	249.0	0.0		168.0	11.0	NM_012254	B3KVP6|B4DPQ1	Frame_Shift_Del	DEL	ENST00000263093.2	hg19	CCDS12983.1																																																																																			.	.		0.607	SLC27A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467060.1	NM_012254	
RABEP1	9135	hgsc.bcm.edu	37	17	5268420	5268420	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:5268420delA	ENST00000546142.2	+	11	1859	c.1672delA	c.(1672-1674)aaafs	p.K559fs	RP11-420A6.2_ENST00000572792.1_RNA|RABEP1_ENST00000262477.6_Frame_Shift_Del_p.K559fs|RABEP1_ENST00000408982.2_Frame_Shift_Del_p.K559fs|RABEP1_ENST00000537505.1_Frame_Shift_Del_p.K516fs|RABEP1_ENST00000341923.6_Frame_Shift_Del_p.K559fs|NUP88_ENST00000573169.1_Intron			Q15276	RABE1_HUMAN	rabaptin, RAB GTPase binding effector protein 1	559					apoptotic process (GO:0006915)|endocytosis (GO:0006897)|membrane fusion (GO:0061025)|protein transport (GO:0015031)	early endosome (GO:0005769)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)	GTPase activator activity (GO:0005096)|protein homodimerization activity (GO:0042803)			NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)	8						GATACAGGTGAAAAAACTACA	0.303																																					p.V557fs		Atlas-INDEL	.											.	RABEP1	59	.	0			c.1671delG						.						87.0	78.0	81.0					17																	5268420		1823	4082	5905	SO:0001589	frameshift_variant	9135	exon11			.	AF098638	CCDS42243.1, CCDS45592.1	17p13.2	2008-02-05				ENSG00000029725			17677	protein-coding gene	gene with protein product		603616				8521472	Standard	NM_001291582		Approved	neurocrescin, RAB5EP, RABPT5, rabaptin-5	uc002gbm.4	Q15276		ENST00000546142.2:c.1672delA	chr17.hg19:g.5268420delA	ENSP00000437701:p.Lys559fs	208.0	0.0		191.0	16.0	NM_004703	B2RAG7|O95369|Q8IVX3	Frame_Shift_Del	DEL	ENST00000546142.2	hg19	CCDS45592.1																																																																																			.	.		0.303	RABEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439349.1	NM_004703	
HOOK1	51361	hgsc.bcm.edu	37	1	60325886	60325886	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:60325886delA	ENST00000371208.3	+	15	1675	c.1418delA	c.(1417-1419)gaafs	p.E473fs	HOOK1_ENST00000395561.2_Frame_Shift_Del_p.E431fs|HOOK1_ENST00000465876.1_3'UTR	NM_015888.4	NP_056972.1	Q9UJC3	HOOK1_HUMAN	hook microtubule-tethering protein 1	473	Sufficient for interaction with microtubules.				early endosome to late endosome transport (GO:0045022)|endosome organization (GO:0007032)|endosome to lysosome transport (GO:0008333)|lysosome organization (GO:0007040)|multicellular organismal development (GO:0007275)|protein transport (GO:0015031)|spermatid development (GO:0007286)	FHF complex (GO:0070695)|microtubule (GO:0005874)	identical protein binding (GO:0042802)			biliary_tract(1)|breast(2)|endometrium(3)|kidney(2)|large_intestine(5)|lung(14)|ovary(1)|urinary_tract(1)	29	all_cancers(7;0.000129)					CTGCAACATGAAAATAAGATG	0.333																																					p.E473fs		Atlas-INDEL	.											.	HOOK1	54	.	0			c.1417delG						.						95.0	98.0	97.0					1																	60325886		2203	4300	6503	SO:0001589	frameshift_variant	51361	exon15			.	AF044923	CCDS612.1	1p32.1	2013-08-21	2013-08-21		ENSG00000134709	ENSG00000134709			19884	protein-coding gene	gene with protein product		607820	"""hook homolog 1 (Drosophila)"""			9927460	Standard	XM_005270922		Approved	HK1	uc001czo.3	Q9UJC3	OTTHUMG00000008990	ENST00000371208.3:c.1418delA	chr1.hg19:g.60325886delA	ENSP00000360252:p.Glu473fs	217.0	0.0		178.0	15.0	NM_015888	A8K8E9|A8MU44|B4DX15|O60561|Q5TG44	Frame_Shift_Del	DEL	ENST00000371208.3	hg19	CCDS612.1																																																																																			.	.		0.333	HOOK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024934.1	NM_015888	
CPSF2	53981	hgsc.bcm.edu	37	14	92604666	92604666	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr14:92604666delA	ENST00000298875.4	+	7	921	c.636delA	c.(634-636)agafs	p.R212fs		NM_017437.2	NP_059133.1	Q9P2I0	CPSF2_HUMAN	cleavage and polyadenylation specific factor 2, 100kDa	212					gene expression (GO:0010467)|histone mRNA 3'-end processing (GO:0006398)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA export from nucleus (GO:0006406)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	membrane (GO:0016020)|mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleoplasm (GO:0005654)	RNA binding (GO:0003723)			breast(2)|cervix(1)|endometrium(3)|large_intestine(2)|lung(7)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	24		all_cancers(154;0.0766)		COAD - Colon adenocarcinoma(157;0.222)		AGCCTAGAAGAAAACAGAGAG	0.333																																					p.R212fs	Ovarian(78;28 1788 18702 44111)	Atlas-INDEL	.											.	CPSF2	63	.	0			c.635delG						.						112.0	112.0	112.0					14																	92604666		2203	4300	6503	SO:0001589	frameshift_variant	53981	exon7			.	AB037788	CCDS9902.1	14q31.1	2008-07-28	2002-08-29			ENSG00000165934			2325	protein-coding gene	gene with protein product		606028	"""cleavage and polyadenylation specific factor 2, 100kD subunit"""			7969155, 11124543	Standard	NM_017437		Approved	KIAA1367	uc001yah.2	Q9P2I0		ENST00000298875.4:c.636delA	chr14.hg19:g.92604666delA	ENSP00000298875:p.Arg212fs	437.0	0.0		347.0	23.0	NM_017437	B3KME1|Q6NSJ1|Q9H3W7	Frame_Shift_Del	DEL	ENST00000298875.4	hg19	CCDS9902.1																																																																																			.	.		0.333	CPSF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412123.1		
FAM135B	51059	hgsc.bcm.edu	37	8	139151232	139151232	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:139151232delT	ENST00000395297.1	-	18	4068	c.3898delA	c.(3898-3900)acafs	p.T1300fs		NM_015912.3	NP_056996.2	Q49AJ0	F135B_HUMAN	family with sequence similarity 135, member B	1300										NS(3)|breast(9)|endometrium(21)|kidney(5)|large_intestine(28)|liver(1)|lung(135)|ovary(9)|pancreas(1)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	238	all_epithelial(106;8.29e-14)|Lung NSC(106;6.88e-06)|all_lung(105;1.44e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0805)			CACTGACCTGTTTTTTGGCTT	0.443										HNSCC(54;0.14)																											p.T1300fs		Atlas-INDEL	.											LOC51059,NS,carcinoma,0,2	FAM135B	423	.	0			c.3899delC						.						108.0	106.0	106.0					8																	139151232		1879	4112	5991	SO:0001589	frameshift_variant	51059	exon18			.	AB196635	CCDS6375.2	8q24.23	2008-11-05			ENSG00000147724	ENSG00000147724			28029	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_015912		Approved	C8ORFK32	uc003yuy.3	Q49AJ0	OTTHUMG00000149864	ENST00000395297.1:c.3898delA	chr8.hg19:g.139151232delT	ENSP00000378710:p.Thr1300fs	200.0	0.0		197.0	15.0	NM_015912	B5MDB3|O95879|Q2WGJ7|Q3KP46	Frame_Shift_Del	DEL	ENST00000395297.1	hg19	CCDS6375.2																																																																																			.	.		0.443	FAM135B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313590.3	NM_015912	
LRP1	4035	hgsc.bcm.edu	37	12	57556256	57556256	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:57556256delC	ENST00000243077.3	+	14	2825	c.2359delC	c.(2359-2361)cccfs	p.P788fs		NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	788					aging (GO:0007568)|aorta morphogenesis (GO:0035909)|apoptotic cell clearance (GO:0043277)|beta-amyloid clearance (GO:0097242)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of platelet-derived growth factor receptor-beta signaling pathway (GO:2000587)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of Wnt signaling pathway (GO:0030178)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of lipid transport (GO:0032370)|positive regulation of protein transport (GO:0051222)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|receptor-mediated endocytosis (GO:0006898)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cholesterol transport (GO:0032374)|regulation of phospholipase A2 activity (GO:0032429)|retinoid metabolic process (GO:0001523)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|lipoprotein particle receptor binding (GO:0070325)|lipoprotein transporter activity (GO:0042954)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|receptor activity (GO:0004872)			NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(33)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(26)|lung(58)|ovary(10)|pancreas(2)|prostate(11)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	184				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	CAGTGAGCGGCCCCCCATCTT	0.617																																					p.R786fs		Atlas-INDEL	.											.	LRP1	428	.	0			c.2358delG						.						90.0	80.0	83.0					12																	57556256		2203	4300	6503	SO:0001589	frameshift_variant	4035	exon14			.	X13916	CCDS8932.1	12q13.3	2013-05-28	2010-01-26		ENSG00000123384	ENSG00000123384		"""CD molecules"", ""Low density lipoprotein receptors"""	6692	protein-coding gene	gene with protein product		107770	"""alpha-2-macroglobulin receptor"""	APR, A2MR		2548950	Standard	NM_002332		Approved	LRP, CD91, LRP1A, APOER	uc001snd.3	Q07954	OTTHUMG00000044412	ENST00000243077.3:c.2359delC	chr12.hg19:g.57556256delC	ENSP00000243077:p.Pro788fs	185.0	0.0		118.0	10.0	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Frame_Shift_Del	DEL	ENST00000243077.3	hg19	CCDS8932.1																																																																																			.	.		0.617	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332	
KMT2D	8085	hgsc.bcm.edu	37	12	49444268	49444268	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:49444268delG	ENST00000301067.7	-	11	3102	c.3103delC	c.(3103-3105)caafs	p.Q1035fs		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	1035	Pro-rich.				chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)										GGGGAGTTTTGGGGAACCAGG	0.622																																					p.Q1035fs		Atlas-INDEL	.											.	MLL2	1173	.	0			c.3104delA						.						68.0	77.0	74.0					12																	49444268		2085	4223	6308	SO:0001589	frameshift_variant	8085	exon11			.	AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	7133	protein-coding gene	gene with protein product		602113	"""trinucleotide repeat containing 21"", ""myeloid/lymphoid or mixed-lineage leukemia 2"""	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.3103delC	chr12.hg19:g.49444268delG	ENSP00000301067:p.Gln1035fs	310.0	0.0		223.0	15.0	NM_003482	O14687	Frame_Shift_Del	DEL	ENST00000301067.7	hg19	CCDS44873.1																																																																																			.	.		0.622	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2		
THUMPD1	55623	hgsc.bcm.edu	37	16	20749224	20749224	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:20749224delT	ENST00000381337.2	-	3	805	c.461delA	c.(460-462)aagfs	p.K155fs	THUMPD1_ENST00000396083.2_Frame_Shift_Del_p.K155fs|THUMPD1_ENST00000431224.2_Frame_Shift_Del_p.K241fs	NM_017736.3	NP_060206.2	Q9NXG2	THUM1_HUMAN	THUMP domain containing 1	155	THUMP. {ECO:0000255|PROSITE- ProRule:PRU00529}.						poly(A) RNA binding (GO:0044822)			NS(2)|large_intestine(2)|lung(6)|pancreas(1)|urinary_tract(1)	12						TCGAGTCTTCTTTTTCTTGGT	0.338																																					p.K154fs		Atlas-INDEL	.											.	THUMPD1	33	.	0			c.462delG						.						109.0	120.0	116.0					16																	20749224		2201	4300	6501	SO:0001589	frameshift_variant	55623	exon3			.	BC000448	CCDS10588.1	16p13.11	2010-06-17			ENSG00000066654	ENSG00000066654			23807	protein-coding gene	gene with protein product							Standard	XM_005255422		Approved	FLJ20274	uc002dho.3	Q9NXG2	OTTHUMG00000131558	ENST00000381337.2:c.461delA	chr16.hg19:g.20749224delT	ENSP00000370741:p.Lys155fs	240.0	0.0		193.0	14.0	NM_017736	Q9BWC3	Frame_Shift_Del	DEL	ENST00000381337.2	hg19	CCDS10588.1																																																																																			.	.		0.338	THUMPD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254420.1	NM_017736	
C9orf131	138724	hgsc.bcm.edu	37	9	35042287	35042287	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:35042287delG	ENST00000312292.5	+	1	83	c.36delG	c.(34-36)aagfs	p.K12fs	C9orf131_ENST00000354479.5_Intron|C9orf131_ENST00000421362.2_Intron	NM_001040410.1|NM_203299.2	NP_001035500.1|NP_976044.2	Q5VYM1	CI131_HUMAN	chromosome 9 open reading frame 131	12										cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(23)|prostate(2)|skin(2)|stomach(1)	39	all_epithelial(49;0.22)		LUSC - Lung squamous cell carcinoma(32;0.00117)|Lung(28;0.00309)			TTGGGGCTAAGGGGGATATGG	0.547																																					p.K12fs		Atlas-INDEL	.											.	C9orf131	71	.	0			c.35delA						.						45.0	43.0	44.0					9																	35042287		2203	4300	6503	SO:0001589	frameshift_variant	138724	exon1			.	BC045643	CCDS6572.2, CCDS47961.1, CCDS47962.1	9p13.3	2008-02-05			ENSG00000174038	ENSG00000174038			31418	protein-coding gene	gene with protein product							Standard	NM_001287391		Approved	MGC41945	uc003zvw.3	Q5VYM1	OTTHUMG00000019853	ENST00000312292.5:c.36delG	chr9.hg19:g.35042287delG	ENSP00000308279:p.Lys12fs	170.0	0.0		148.0	11.0	NM_001040410	A6NLE6|E9PB26|Q86XC6|Q9UF74	Frame_Shift_Del	DEL	ENST00000312292.5	hg19	CCDS6572.2																																																																																			.	.		0.547	C9orf131-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052283.5	NM_203299	
DNHD1	144132	hgsc.bcm.edu	37	11	6568378	6568378	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:6568378delA	ENST00000527990.2	+	19	6209	c.6209delA	c.(6208-6210)caafs	p.Q2070fs	DNHD1_ENST00000254579.6_Frame_Shift_Del_p.Q2070fs			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	2070					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)		AACATGGGCCAAAAGAGGCAG	0.547																																					p.Q2070fs		Atlas-INDEL	.											.	DNHD1	198	.	0			c.6208delC						.						124.0	141.0	136.0					11																	6568378		692	1591	2283	SO:0001589	frameshift_variant	144132	exon21			.	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.6209delA	chr11.hg19:g.6568378delA	ENSP00000436180:p.Gln2070fs	225.0	0.0		163.0	12.0	NM_144666	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Frame_Shift_Del	DEL	ENST00000527990.2	hg19	CCDS44532.1																																																																																			.	.		0.547	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666	
ETV4	2118	hgsc.bcm.edu	37	17	41605953	41605953	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:41605953delG	ENST00000319349.5	-	13	1687	c.1389delC	c.(1387-1389)cccfs	p.P463fs	ETV4_ENST00000545089.1_Frame_Shift_Del_p.P409fs|ETV4_ENST00000393664.2_Frame_Shift_Del_p.P463fs|ETV4_ENST00000545954.1_Frame_Shift_Del_p.P424fs|ETV4_ENST00000586826.1_Frame_Shift_Del_p.P186fs|ETV4_ENST00000591713.1_Frame_Shift_Del_p.P463fs|ETV4_ENST00000538265.1_Frame_Shift_Del_p.P424fs	NM_001079675.2	NP_001073143.1	P43268	ETV4_HUMAN	ets variant 4	463					branching involved in mammary gland duct morphogenesis (GO:0060444)|cell differentiation (GO:0030154)|motor neuron axon guidance (GO:0008045)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of branching involved in mammary gland duct morphogenesis (GO:0060762)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell differentiation (GO:0048863)|transcription from RNA polymerase II promoter (GO:0006366)	nucleolus (GO:0005730)	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)		EWSR1/ETV4(6)|CANT1/ETV4(3)|TMPRSS2/ETV4(13)|DDX5_ENST00000540698/ETV4(2)|KLK2/ETV4(2)	ovary(2)|upper_aerodigestive_tract(1)	3		Breast(137;0.00908)		BRCA - Breast invasive adenocarcinoma(366;0.0798)		GGAGGTAGGCGGGGCTCTCAT	0.642			T	"""EWSR1, TMPRSS2, DDX5, KLK2, CANT1"""	"""Ewing sarcoma, Prostate carcinoma"""																																p.A464fs	Esophageal Squamous(116;1540 1611 12927 31103 34118)	Atlas-INDEL	.		Dom	yes		17	17q21	2118	"""ets variant gene 4 (E1A enhancer binding protein, E1AF)"""		"""M, E"""	.	ETV4	36	.	0			c.1390delG						.						39.0	37.0	38.0					17																	41605953		2203	4300	6503	SO:0001589	frameshift_variant	2118	exon13			.	U18018	CCDS11465.1, CCDS58553.1, CCDS59292.1	17q21	2014-04-30	2008-09-12			ENSG00000175832			3493	protein-coding gene	gene with protein product	"""E1A enhancer binding protein"""	600711	"""ets variant gene 4 (E1A enhancer-binding protein, E1AF)"""			8530053, 1547944	Standard	NM_001986		Approved	E1A-F, E1AF, PEA3	uc002idw.3	P43268		ENST00000319349.5:c.1389delC	chr17.hg19:g.41605953delG	ENSP00000321835:p.Pro463fs	221.0	0.0		176.0	11.0	NM_001986	A8K314|B7Z5J3|B7Z9J6|Q96AW9	Frame_Shift_Del	DEL	ENST00000319349.5	hg19	CCDS11465.1																																																																																			.	.		0.642	ETV4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453489.1	NM_001986	
SEZ6L2	26470	hgsc.bcm.edu	37	16	29899871	29899871	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:29899871delG	ENST00000308713.5	-	6	1556	c.1029delC	c.(1027-1029)cccfs	p.P343fs	SEZ6L2_ENST00000350527.3_Frame_Shift_Del_p.P273fs|SEZ6L2_ENST00000562159.1_5'UTR|SEZ6L2_ENST00000537485.1_Frame_Shift_Del_p.P299fs|SEZ6L2_ENST00000346932.5_Frame_Shift_Del_p.P229fs	NM_001114099.2|NM_201575.3	NP_001107571.1|NP_963869.2	Q6UXD5	SE6L2_HUMAN	seizure related 6 homolog (mouse)-like 2	343	Sushi 1. {ECO:0000255|PROSITE- ProRule:PRU00302}.				adult locomotory behavior (GO:0008344)|cerebellar Purkinje cell layer development (GO:0021680)|regulation of protein kinase C signaling (GO:0090036)|synapse maturation (GO:0060074)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(16)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						CCATGCAGCTGGGGGTTTCAC	0.612																																					p.S344fs		Atlas-INDEL	.											.	SEZ6L2	137	.	0			c.1030delA						.						75.0	63.0	67.0					16																	29899871		2197	4300	6497	SO:0001589	frameshift_variant	26470	exon6			.	AY358404	CCDS10658.1, CCDS10659.1, CCDS45458.1, CCDS58447.1, CCDS73865.1	16p12.1	2008-02-05			ENSG00000174938	ENSG00000174938			30844	protein-coding gene	gene with protein product	"""type I transmembrane receptor (seizure related protein)"""					12975309	Standard	NM_012410		Approved	PSK-1, FLJ90517	uc010vec.2	Q6UXD5	OTTHUMG00000132112	ENST00000308713.5:c.1029delC	chr16.hg19:g.29899871delG	ENSP00000312550:p.Pro343fs	133.0	0.0		147.0	10.0	NM_001243332	B7Z1N0|F5H293|H7BXQ6|Q9BW82|Q9UJ45|Q9UJ46|Q9UJ47	Frame_Shift_Del	DEL	ENST00000308713.5	hg19	CCDS10659.1																																																																																			.	.		0.612	SEZ6L2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255154.2	NM_012410	
PLEKHO1	51177	hgsc.bcm.edu	37	1	150129661	150129661	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:150129661delG	ENST00000369124.4	+	5	784	c.506delG	c.(505-507)aggfs	p.R169fs	PLEKHO1_ENST00000369126.1_Intron|PLEKHO1_ENST00000479194.1_3'UTR|PLEKHO1_ENST00000025469.6_Intron	NM_016274.4	NP_057358.2	Q53GL0	PKHO1_HUMAN	pleckstrin homology domain containing, family O member 1	169	Interaction with ATM, CKIP, IFP35 and NMI.|Interaction with capping proteins (CPs).					cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|skin(2)	22	Lung NSC(24;7.78e-28)|Breast(34;0.00211)|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)			CCCCCAACAAGGGGACACCTA	0.522																																					p.R169fs		Atlas-INDEL	.											.	PLEKHO1	37	.	0			c.505delA						.						82.0	69.0	74.0					1																	150129661		2203	4300	6503	SO:0001589	frameshift_variant	51177	exon5			.	AF073836	CCDS945.1	1q21.2	2013-01-10			ENSG00000023902	ENSG00000023902		"""Pleckstrin homology (PH) domain containing"""	24310	protein-coding gene	gene with protein product		608335				10799509	Standard	NM_016274		Approved	CKIP-1, OC120	uc001ett.3	Q53GL0	OTTHUMG00000012510	ENST00000369124.4:c.506delG	chr1.hg19:g.150129661delG	ENSP00000358120:p.Arg169fs	130.0	0.0		141.0	10.0	NM_016274	Q336K5|Q8IZ51|Q9NRV3|Q9UL48	Frame_Shift_Del	DEL	ENST00000369124.4	hg19	CCDS945.1																																																																																			.	.		0.522	PLEKHO1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034962.1	NM_016274	
MTIF2	4528	hgsc.bcm.edu	37	2	55473549	55473549	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:55473549delT	ENST00000263629.4	-	10	1345	c.1030delA	c.(1030-1032)atgfs	p.M344fs	MTIF2_ENST00000394600.3_Frame_Shift_Del_p.M344fs|MTIF2_ENST00000403721.1_Frame_Shift_Del_p.M344fs	NM_002453.2	NP_002444.2	P46199	IF2M_HUMAN	mitochondrial translational initiation factor 2	344	tr-type G.				formation of translation initiation complex (GO:0001732)|regulation of translational initiation (GO:0006446)|ribosome disassembly (GO:0032790)	mitochondrion (GO:0005739)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|ribosomal small subunit binding (GO:0043024)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	24						AATTCTAACATTTCTGCAAGA	0.373																																					p.M344fs		Atlas-INDEL	.											.	MTIF2	64	.	0			c.1031delT						.						167.0	152.0	157.0					2																	55473549		2203	4300	6503	SO:0001589	frameshift_variant	4528	exon10			.	L34600	CCDS1853.1	2p16.1	2008-02-05			ENSG00000085760	ENSG00000085760			7441	protein-coding gene	gene with protein product		603766				9925935, 7829522	Standard	XM_005264335		Approved	IF-2mt	uc002ryo.3	P46199	OTTHUMG00000129338	ENST00000263629.4:c.1030delA	chr2.hg19:g.55473549delT	ENSP00000263629:p.Met344fs	252.0	0.0		143.0	11.0	NM_002453	D6W5D0	Frame_Shift_Del	DEL	ENST00000263629.4	hg19	CCDS1853.1																																																																																			.	.		0.373	MTIF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251486.4	NM_002453	
TSPYL2	64061	hgsc.bcm.edu	37	X	53113779	53113779	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:53113779delT	ENST00000375442.4	+	2	992	c.860delT	c.(859-861)attfs	p.I287fs		NM_022117.3	NP_071400.1	Q9H2G4	TSYL2_HUMAN	TSPY-like 2	287					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cell cycle (GO:0007049)|cellular protein metabolic process (GO:0044267)|chromatin modification (GO:0016568)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell growth (GO:0030308)|negative regulation of DNA replication (GO:0008156)|nucleosome assembly (GO:0006334)|regulation of protein kinase activity (GO:0045859)|regulation of signal transduction (GO:0009966)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	rDNA binding (GO:0000182)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(2)|lung(8)|upper_aerodigestive_tract(1)	19						GATGAAGACATTTTCCGCTAC	0.483																																					p.I287fs		Atlas-INDEL	.											.	TSPYL2	53	.	0			c.859delA						.						145.0	125.0	131.0					X																	53113779		2203	4300	6503	SO:0001589	frameshift_variant	64061	exon2			.	AF273046	CCDS14350.1	Xp11	2014-06-09			ENSG00000184205	ENSG00000184205			24358	protein-coding gene	gene with protein product		300564				11318608, 11395479	Standard	NM_022117		Approved	SE20-4, HRIHFB2216, CTCL, DENTT, CDA1, CINAP, TSPX	uc004drw.3	Q9H2G4	OTTHUMG00000021597	ENST00000375442.4:c.860delT	chrX.hg19:g.53113779delT	ENSP00000364591:p.Ile287fs	201.0	0.0		118.0	10.0	NM_022117	O94799|Q96DG7|Q9BZW6	Frame_Shift_Del	DEL	ENST00000375442.4	hg19	CCDS14350.1																																																																																			.	.		0.483	TSPYL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056718.1	NM_022117	
GP1BA	2811	hgsc.bcm.edu	37	17	4837331	4837331	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:4837331delT	ENST00000329125.5	+	2	1507	c.1432delT	c.(1432-1434)tttfs	p.F478fs		NM_000173.5	NP_000164.5	P07359	GP1BA_HUMAN	glycoprotein Ib (platelet), alpha polypeptide	478	Pro/Thr-rich.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|cell morphogenesis (GO:0000902)|cell surface receptor signaling pathway (GO:0007166)|fibrinolysis (GO:0042730)|platelet activation (GO:0030168)|regulation of blood coagulation (GO:0030193)|thrombin receptor signaling pathway (GO:0070493)	anchored component of external side of plasma membrane (GO:0031362)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	thrombin receptor activity (GO:0015057)			central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(3)|lung(5)|stomach(1)|urinary_tract(1)	20						AAAAAGCACATTTTTAACTAC	0.552																																					p.T477fs		Atlas-INDEL	.											.	GP1BA	53	.	0			c.1431delA						.						43.0	47.0	46.0					17																	4837331		1916	4116	6032	SO:0001589	frameshift_variant	2811	exon2			.		CCDS54068.1	17p13.2	2014-09-17			ENSG00000185245	ENSG00000185245		"""CD molecules"""	4439	protein-coding gene	gene with protein product		606672		GP1B		3353370	Standard	NM_000173		Approved	CD42b	uc021tnz.1	P07359	OTTHUMG00000177946	ENST00000329125.5:c.1432delT	chr17.hg19:g.4837331delT	ENSP00000329380:p.Phe478fs	217.0	0.0		155.0	10.0	NM_000173	E7ES66|Q14441|Q16469|Q8N1F3|Q8NG39|Q9HDC7|Q9UEK1|Q9UQS4	Frame_Shift_Del	DEL	ENST00000329125.5	hg19	CCDS54068.1																																																																																			.	.		0.552	GP1BA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439889.1		
PKHD1	5314	hgsc.bcm.edu	37	6	51503672	51503672	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:51503672delA	ENST00000371117.3	-	64	11756	c.11481delT	c.(11479-11481)tttfs	p.F3827fs		NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	3827					cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					CAGTAAAAATAAAGTGCCAGT	0.353																																					p.I3828fs		Atlas-INDEL	.											.	PKHD1	927	.	0			c.11482delA						.						149.0	153.0	152.0					6																	51503672		2203	4300	6503	SO:0001589	frameshift_variant	5314	exon64			.	AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"""tigmin"", ""polyductin"", ""fibrocystin"""	606702	"""TIG multiple domains 1"""	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.11481delT	chr6.hg19:g.51503672delA	ENSP00000360158:p.Phe3827fs	210.0	0.0		165.0	10.0	NM_138694	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Frame_Shift_Del	DEL	ENST00000371117.3	hg19	CCDS4935.1																																																																																			.	.		0.353	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694	
DNAJC13	23317	hgsc.bcm.edu	37	3	132175174	132175174	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:132175174delG	ENST00000260818.6	+	10	1276	c.1028delG	c.(1027-1029)tggfs	p.W343fs	DNAJC13_ENST00000486798.1_3'UTR	NM_015268.3	NP_056083.3	O75165	DJC13_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 13	343					osteoblast differentiation (GO:0001649)	extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)				breast(4)|endometrium(2)|kidney(2)|large_intestine(5)|lung(15)|ovary(1)|pancreas(2)|prostate(2)|urinary_tract(1)	34						GGTCAGCGATGGGGGTTACTC	0.413																																					p.W343fs		Atlas-INDEL	.											.	DNAJC13	253	.	0			c.1027delT						.						87.0	83.0	85.0					3																	132175174		2203	4300	6503	SO:0001589	frameshift_variant	23317	exon10			.	AB014578	CCDS33857.1	3q22.1	2011-09-02			ENSG00000138246	ENSG00000138246		"""Heat shock proteins / DNAJ (HSP40)"""	30343	protein-coding gene	gene with protein product		614334				12438707	Standard	NM_015268		Approved	RME8, KIAA0678	uc003eor.3	O75165	OTTHUMG00000159674	ENST00000260818.6:c.1028delG	chr3.hg19:g.132175174delG	ENSP00000260818:p.Trp343fs	243.0	0.0		162.0	10.0	NM_015268	Q3L0T1|Q6PI82|Q6UJ77|Q6ZSW1|Q6ZUT5|Q86XG3|Q96DC1|Q9BWK9	Frame_Shift_Del	DEL	ENST00000260818.6	hg19	CCDS33857.1																																																																																			.	.		0.413	DNAJC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356807.2	NM_015268	
WDR19	57728	hgsc.bcm.edu	37	4	39280220	39280220	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:39280220delA	ENST00000399820.3	+	36	4133	c.3979delA	c.(3979-3981)aaafs	p.K1328fs	WDR19_ENST00000288634.7_Frame_Shift_Del_p.K1168fs	NM_025132.3	NP_079408.3	Q8NEZ3	WDR19_HUMAN	WD repeat domain 19	1328					ciliary receptor clustering involved in smoothened signaling pathway (GO:0060830)|cilium assembly (GO:0042384)|digestive system development (GO:0055123)|ear morphogenesis (GO:0042471)|embryonic camera-type eye development (GO:0031076)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic limb morphogenesis (GO:0030326)|in utero embryonic development (GO:0001701)|intraciliary retrograde transport (GO:0035721)|myotome development (GO:0061055)|neurological system process (GO:0050877)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|intraciliary transport particle A (GO:0030991)|motile cilium (GO:0031514)|nonmotile primary cilium (GO:0031513)|photoreceptor connecting cilium (GO:0032391)				large_intestine(1)	1						TGCTCAGCTGAAAAAGATTTC	0.483																																					p.L1326fs		Atlas-INDEL	.											.	WDR19	96	.	0			c.3978delG						.						84.0	82.0	82.0					4																	39280220		2022	4178	6200	SO:0001589	frameshift_variant	57728	exon36			.	AB046858, AY029257	CCDS47042.1	4p14	2014-02-21			ENSG00000157796	ENSG00000157796		"""WD repeat domain containing"", ""Intraflagellar transport homologs"""	18340	protein-coding gene	gene with protein product	"""intraflagellar transport 144 homolog (Chlamydomonas)"""	608151				12906858, 22019273	Standard	XM_005262658		Approved	Pwdmp, KIAA1638, FLJ23127, ORF26, DYF-2, Oseg6, IFT144, NPHP13	uc003gtv.3	Q8NEZ3	OTTHUMG00000160466	ENST00000399820.3:c.3979delA	chr4.hg19:g.39280220delA	ENSP00000382717:p.Lys1328fs	235.0	0.0		183.0	11.0	NM_025132	B5MEF2|Q8N5B4|Q9H5S0|Q9HCD4	Frame_Shift_Del	DEL	ENST00000399820.3	hg19	CCDS47042.1																																																																																			.	.		0.483	WDR19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360689.1		
SPHK1	8877	hgsc.bcm.edu	37	17	74381231	74381231	+	Intron	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:74381231delC	ENST00000545180.1	+	4	615				SPHK1_ENST00000592299.1_Intron|SPHK1_ENST00000323374.4_Frame_Shift_Del_p.L15fs|SPHK1_ENST00000590959.1_Intron|SPHK1_ENST00000392496.3_5'Flank			Q9NYA1	SPHK1_HUMAN	sphingosine kinase 1						'de novo' posttranslational protein folding (GO:0051084)|blood vessel development (GO:0001568)|brain development (GO:0007420)|calcium-mediated signaling (GO:0019722)|cellular protein metabolic process (GO:0044267)|cellular response to growth factor stimulus (GO:0071363)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to starvation (GO:0009267)|cyclooxygenase pathway (GO:0019371)|female pregnancy (GO:0007565)|inflammatory response (GO:0006954)|intracellular signal transduction (GO:0035556)|lipid phosphorylation (GO:0046834)|negative regulation of apoptotic process (GO:0043066)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of neuron projection development (GO:0010976)|positive regulation of neurotransmitter secretion (GO:0001956)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of smooth muscle contraction (GO:0045987)|protein folding (GO:0006457)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of interleukin-1 beta production (GO:0032651)|regulation of tumor necrosis factor-mediated signaling pathway (GO:0010803)|response to amine (GO:0014075)|response to ATP (GO:0033198)|response to interleukin-1 (GO:0070555)|response to magnesium ion (GO:0032026)|response to progesterone (GO:0032570)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingoid catabolic process (GO:0046521)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingosine metabolic process (GO:0006670)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|D-erythro-sphingosine kinase activity (GO:0017050)|diacylglycerol kinase activity (GO:0004143)|DNA binding (GO:0003677)|magnesium ion binding (GO:0000287)|NAD+ kinase activity (GO:0003951)|protein phosphatase 2A binding (GO:0051721)|sphinganine kinase activity (GO:0008481)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)	11					Fingolimod(DB08868)	GGACTCCCCTCCCCCTGGCAG	0.657																																					p.L15fs	GBM(90;966 1307 27369 33775 44498)	Atlas-INDEL	.											.	SPHK1	24	.	0			c.44delT						.						34.0	27.0	29.0					17																	74381231		2193	4292	6485	SO:0001627	intron_variant	8877	exon1			.	BC030553	CCDS11744.1, CCDS45785.1, CCDS59297.1	17q25.2	2004-02-18				ENSG00000176170			11240	protein-coding gene	gene with protein product		603730				9726979	Standard	NM_182965		Approved	SPHK	uc002jrj.2	Q9NYA1		ENST00000545180.1:c.-194-301C>-	chr17.hg19:g.74381231delC		212.0	0.0		222.0	14.0	NM_182965	Q8N632|Q96GK1|Q9HD92|Q9NY70|Q9NYL3	Frame_Shift_Del	DEL	ENST00000545180.1	hg19	CCDS45785.1																																																																																			.	.		0.657	SPHK1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450113.1	NM_182965, NM_021972	
GDF5	8200	hgsc.bcm.edu	37	20	34025211	34025211	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr20:34025211delG	ENST00000374372.1	-	3	1001	c.498delC	c.(496-498)cccfs	p.P166fs	GDF5_ENST00000374369.3_Frame_Shift_Del_p.P166fs			P43026	GDF5_HUMAN	growth differentiation factor 5	166					cell-cell signaling (GO:0007267)|chondrocyte differentiation (GO:0002062)|embryonic limb morphogenesis (GO:0030326)|extracellular matrix organization (GO:0030198)|forelimb morphogenesis (GO:0035136)|growth (GO:0040007)|hindlimb morphogenesis (GO:0035137)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mesenchymal cell apoptotic process (GO:2001054)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of neuron differentiation (GO:0045666)|regulation of multicellular organism growth (GO:0040014)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	growth factor activity (GO:0008083)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(3)|lung(9)|skin(3)	26	Lung NSC(9;0.00642)|all_lung(11;0.0094)		BRCA - Breast invasive adenocarcinoma(18;0.00663)			GGGGTGTGATGGGGGGTGGGC	0.637																																					p.I167fs		Atlas-INDEL	.											.	GDF5	66	.	0			c.499delA						.						64.0	63.0	63.0					20																	34025211		2203	4300	6503	SO:0001589	frameshift_variant	8200	exon1			.	X80915	CCDS13254.1	20q11.2	2008-05-22	2007-04-12		ENSG00000125965	ENSG00000125965			4220	protein-coding gene	gene with protein product	"""cartilage-derived morphogenetic protein-1"""	601146				9288091, 9288098	Standard	NM_000557		Approved	CDMP1, BMP14	uc002xck.1	P43026	OTTHUMG00000032341	ENST00000374372.1:c.498delC	chr20.hg19:g.34025211delG	ENSP00000363492:p.Pro166fs	154.0	0.0		146.0	11.0	NM_000557	E1P5Q2|Q96SB1	Frame_Shift_Del	DEL	ENST00000374372.1	hg19	CCDS13254.1																																																																																			.	.		0.637	GDF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078875.2		
BACH2	60468	hgsc.bcm.edu	37	6	90660586	90660586	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:90660586delC	ENST00000257749.4	-	7	1946	c.1239delG	c.(1237-1239)gggfs	p.G413fs	BACH2_ENST00000343122.3_Frame_Shift_Del_p.G413fs|RP3-512E2.2_ENST00000445838.1_RNA|BACH2_ENST00000537989.1_Frame_Shift_Del_p.G413fs|RP3-512E2.2_ENST00000413986.1_RNA	NM_021813.2	NP_068585.1	Q9BYV9	BACH2_HUMAN	BTB and CNC homology 1, basic leucine zipper transcription factor 2	413						cytoplasm (GO:0005737)|nucleus (GO:0005634)	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 negative regulation of transcription (GO:0001206)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(18)|ovary(5)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	45		all_cancers(76;7.37e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.0063)		BRCA - Breast invasive adenocarcinoma(108;0.0799)		CCAACCCAGGCCCCCTGAGGG	0.582																																					p.P414fs		Atlas-INDEL	.											.	BACH2	224	.	0			c.1240delC						.						26.0	28.0	27.0					6																	90660586		2138	4210	6348	SO:0001589	frameshift_variant	60468	exon7			.	AL121787	CCDS5026.1	6q15	2013-01-10			ENSG00000112182	ENSG00000112182		"""BTB/POZ domain containing"", ""basic leucine zipper proteins"""	14078	protein-coding gene	gene with protein product		605394				10949928, 12829606	Standard	NM_001170794		Approved	BTBD25	uc003pnw.3	Q9BYV9	OTTHUMG00000015216	ENST00000257749.4:c.1239delG	chr6.hg19:g.90660586delC	ENSP00000257749:p.Gly413fs	187.0	0.0		149.0	10.0	NM_021813	E1P518|Q59H70|Q5T793|Q9NTS5	Frame_Shift_Del	DEL	ENST00000257749.4	hg19	CCDS5026.1																																																																																			.	.		0.582	BACH2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041522.2	NM_021813	
SETD4	54093	hgsc.bcm.edu	37	21	37418076	37418076	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr21:37418076delA	ENST00000399215.1	-	5	1902	c.530delT	c.(529-531)ttcfs	p.F177fs	SETD4_ENST00000399207.1_Frame_Shift_Del_p.F177fs|SETD4_ENST00000399205.1_Frame_Shift_Del_p.F153fs|SETD4_ENST00000332131.4_Frame_Shift_Del_p.F177fs|SETD4_ENST00000399212.1_Frame_Shift_Del_p.F153fs|SETD4_ENST00000399201.1_Frame_Shift_Del_p.F153fs|SETD4_ENST00000399208.2_Frame_Shift_Del_p.F177fs|SETD4_ENST00000481477.1_5'UTR			Q9NVD3	SETD4_HUMAN	SET domain containing 4	177	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.						methyltransferase activity (GO:0008168)			autonomic_ganglia(1)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)	15						CAGAGAAGAGAAAAAGTCTCT	0.532																																					p.F177fs		Atlas-INDEL	.											.	SETD4	37	.	0			c.531delC						.						79.0	89.0	86.0					21																	37418076		2203	4300	6503	SO:0001589	frameshift_variant	54093	exon6			.	AK001660	CCDS13640.1, CCDS42923.1, CCDS74791.1, CCDS74792.1	21q22.13	2006-02-15	2006-02-15	2006-02-15	ENSG00000185917	ENSG00000185917			1258	protein-coding gene	gene with protein product			"""chromosome 21 open reading frame 27"", ""chromosome 21 open reading frame 18"""	C21orf27, C21orf18			Standard	XM_005261000		Approved		uc021wiy.1	Q9NVD3	OTTHUMG00000086483	ENST00000399215.1:c.530delT	chr21.hg19:g.37418076delA	ENSP00000382163:p.Phe177fs	215.0	0.0		160.0	10.0	NM_001007259	B4DT14|D3DSG2|D3DSG4|Q8NE19|Q9BU46	Frame_Shift_Del	DEL	ENST00000399215.1	hg19	CCDS13640.1																																																																																			.	.		0.532	SETD4-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194456.1	NM_017438	
PFKP	5214	hgsc.bcm.edu	37	10	3155593	3155593	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:3155593delG	ENST00000381125.4	+	13	1330	c.1254delG	c.(1252-1254)gtgfs	p.V418fs	PFKP_ENST00000381075.2_Frame_Shift_Del_p.V410fs	NM_002627.4	NP_002618.1	Q01813	PFKAP_HUMAN	phosphofructokinase, platelet	418	C-terminal regulatory PFK domain 2.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|fructose 6-phosphate metabolic process (GO:0006002)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	6-phosphofructokinase activity (GO:0003872)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein complex binding (GO:0032403)			breast(2)|central_nervous_system(4)|endometrium(3)|large_intestine(3)|lung(10)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	31				GBM - Glioblastoma multiforme(1;0.000975)|all cancers(11;0.00351)|Epithelial(11;0.142)		TCATCAACGTGGGGGCACCCG	0.597																																					p.V418fs		Atlas-INDEL	.											.	PFKP	182	.	0			c.1253delT						.						43.0	38.0	40.0					10																	3155593		2203	4300	6503	SO:0001589	frameshift_variant	5214	exon13			.	AK092597	CCDS7059.1, CCDS55698.1	10p15.3-p15.2	2006-08-25			ENSG00000067057	ENSG00000067057	2.7.1.11		8878	protein-coding gene	gene with protein product	"""Phosphofructokinase, platelet type"""	171840					Standard	NM_002627		Approved	PFK-C, PFKF	uc001igp.3	Q01813	OTTHUMG00000017556	ENST00000381125.4:c.1254delG	chr10.hg19:g.3155593delG	ENSP00000370517:p.Val418fs	163.0	0.0		146.0	12.0	NM_002627	B3KS15|Q5VSR7|Q5VSR8	Frame_Shift_Del	DEL	ENST00000381125.4	hg19	CCDS7059.1																																																																																			.	.		0.597	PFKP-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046454.1	NM_002627	
C2CD5	9847	hgsc.bcm.edu	37	12	22671015	22671015	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:22671015delG	ENST00000333957.4	-	8	1112	c.857delC	c.(856-858)cctfs	p.P286fs	C2CD5_ENST00000396028.2_Intron|C2CD5_ENST00000545552.1_Intron|C2CD5_ENST00000536386.1_Intron|C2CD5_ENST00000542676.1_Frame_Shift_Del_p.P286fs|C2CD5_ENST00000446597.1_Frame_Shift_Del_p.P286fs|C2CD5_ENST00000540703.1_5'Flank|C2CD5_ENST00000544930.1_Intron	NM_014802.1	NP_055617.1	Q86YS7	C2CD5_HUMAN	C2 calcium-dependent domain containing 5	286					cellular response to insulin stimulus (GO:0032869)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|intracellular protein transmembrane transport (GO:0065002)|positive regulation of glucose transport (GO:0010828)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of vesicle fusion (GO:0031340)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)										GTTTTTCAGAGGGGTTGAGGG	0.428																																					p.P286fs		Atlas-INDEL	.											.	.	.	.	0			c.858delT						.						240.0	229.0	233.0					12																	22671015		2203	4300	6503	SO:0001589	frameshift_variant	9847	exon8			.	AB011100	CCDS31758.1, CCDS66337.1, CCDS66338.1, CCDS66339.1, CCDS66340.1	12p12.1	2012-12-13	2012-12-13	2012-12-13	ENSG00000111731	ENSG00000111731			29062	protein-coding gene	gene with protein product	"""138 kDa C2 domain-containing phosphoprotein"""		"""KIAA0528"""	KIAA0528		21907143	Standard	XM_005253538		Approved	CDP138	uc001rfq.3	Q86YS7	OTTHUMG00000169100	ENST00000333957.4:c.857delC	chr12.hg19:g.22671015delG	ENSP00000334229:p.Pro286fs	220.0	0.0		162.0	10.0	NM_014802	B4DJ03|B4DRN7|B7ZLL0|F5H2A1|F5H5R1|O60280|Q17RY7|Q7Z619|Q86SU3	Frame_Shift_Del	DEL	ENST00000333957.4	hg19	CCDS31758.1																																																																																			.	.		0.428	C2CD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402257.1	NM_014802	
ADK	132	hgsc.bcm.edu	37	10	76153962	76153962	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:76153962delG	ENST00000286621.2	+	5	387	c.337delG	c.(337-339)gggfs	p.G113fs	ADK_ENST00000372734.3_Frame_Shift_Del_p.G96fs|ADK_ENST00000541550.1_Frame_Shift_Del_p.G78fs|ADK_ENST00000539909.1_Frame_Shift_Del_p.G113fs	NM_006721.3	NP_006712.2	P55263	ADK_HUMAN	adenosine kinase	113					adenosine metabolic process (GO:0046085)|AMP salvage (GO:0044209)|circadian regulation of gene expression (GO:0032922)|dATP biosynthetic process (GO:0006175)|nucleobase-containing small molecule metabolic process (GO:0055086)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of T cell proliferation (GO:0042102)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|ribonucleoside monophosphate biosynthetic process (GO:0009156)|small molecule metabolic process (GO:0044281)|type B pancreatic cell proliferation (GO:0044342)	cytosol (GO:0005829)|nucleus (GO:0005634)	adenosine kinase activity (GO:0004001)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|phosphotransferase activity, alcohol group as acceptor (GO:0016773)|poly(A) RNA binding (GO:0044822)			breast(1)|large_intestine(2)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	8	Prostate(51;0.0112)|Ovarian(15;0.148)				Abacavir(DB01048)|Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)|Adenosine(DB00640)|Ribavirin(DB00811)	AGATAAATTTGGGGAGATCCT	0.428																																					p.F112fs		Atlas-INDEL	.											.	ADK	28	.	0			c.336delT						.						120.0	124.0	123.0					10																	76153962		2203	4300	6503	SO:0001589	frameshift_variant	132	exon5			.	U50196	CCDS7343.1, CCDS7344.1, CCDS55716.1, CCDS55717.1	10q22.2	2006-02-21			ENSG00000156110	ENSG00000156110	2.7.1.20		257	protein-coding gene	gene with protein product	"""adenosine 5'-phosphotransferase"""	102750				8577746	Standard	NM_001123		Approved	AK	uc001jwi.3	P55263	OTTHUMG00000018506	ENST00000286621.2:c.337delG	chr10.hg19:g.76153962delG	ENSP00000286621:p.Gly113fs	239.0	0.0		137.0	10.0	NM_001202450	B7Z783|B7Z800|O00741|O00742|Q16710|Q5JQ10|Q5JQ11|Q9BTN2	Frame_Shift_Del	DEL	ENST00000286621.2	hg19	CCDS7343.1																																																																																			.	.		0.428	ADK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048763.1	NM_001123, NM_006721	
DCT	1638	hgsc.bcm.edu	37	13	95118899	95118899	+	Frame_Shift_Del	DEL	G	G	-	rs12876972		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr13:95118899delG	ENST00000377028.5	-	3	1022	c.609delC	c.(607-609)cccfs	p.P203fs	DCT_ENST00000446125.1_Frame_Shift_Del_p.P203fs|DCT_ENST00000490854.1_5'UTR|AL139318.1_ENST00000390768.1_RNA	NM_001922.3	NP_001913.2	P40126	TYRP2_HUMAN	dopachrome tautomerase	203					cell development (GO:0048468)|developmental pigmentation (GO:0048066)|epidermis development (GO:0008544)|melanin biosynthetic process from tyrosine (GO:0006583)|positive regulation of neuroblast proliferation (GO:0002052)|ventricular zone neuroblast division (GO:0021847)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|melanosome (GO:0042470)	copper ion binding (GO:0005507)|dopachrome isomerase activity (GO:0004167)|oxidoreductase activity (GO:0016491)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(14)|liver(1)|lung(16)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	50	all_neural(89;0.0684)|Medulloblastoma(90;0.163)	all_cancers(2;3.71e-42)|all_epithelial(2;3.76e-31)|all_lung(2;5.16e-14)|Lung NSC(4;1.33e-13)|Breast(118;0.0013)|Hepatocellular(115;0.00886)|Renal(2;0.00988)		COAD - Colon adenocarcinoma(199;7.07e-05)|GBM - Glioblastoma multiforme(99;0.000472)		TGGCCCTGTAGGGGCGTCCTG	0.418																																					p.Y204fs		Atlas-INDEL	.											.	DCT	186	.	0			c.610delT						.						56.0	58.0	57.0					13																	95118899		2203	4300	6503	SO:0001589	frameshift_variant	1638	exon3			.	D17547	CCDS9470.1, CCDS45060.1	13q32	2012-09-28	2012-09-28		ENSG00000080166	ENSG00000080166	5.3.3.12		2709	protein-coding gene	gene with protein product	"""dopachrome delta-isomerase"""	191275	"""tyrosine-related protein 2"""	TYRP2		8306979	Standard	NM_001922		Approved		uc010afh.3	P40126	OTTHUMG00000017206	ENST00000377028.5:c.609delC	chr13.hg19:g.95118899delG	ENSP00000366227:p.Pro203fs	293.0	0.0		199.0	12.0	NM_001129889	Q09GT4	Frame_Shift_Del	DEL	ENST00000377028.5	hg19	CCDS9470.1																																																																																			.	.		0.418	DCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045461.3		
ARGLU1	55082	hgsc.bcm.edu	37	13	107219922	107219922	+	Splice_Site	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr13:107219922delT	ENST00000400198.3	-	1	590	c.346delA	c.(346-348)att>tt	p.I116fs		NM_018011.3	NP_060481.3	Q9NWB6	ARGL1_HUMAN	arginine and glutamate rich 1	116	Glu-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	mitochondrion (GO:0005739)|nucleus (GO:0005634)				large_intestine(1)|lung(5)|pancreas(1)	7	Lung NSC(43;0.015)|all_neural(89;0.0741)|Lung SC(71;0.14)|Medulloblastoma(90;0.169)					GGCACTCACATTTTTCGCTGC	0.711																																					p.I116fs		Atlas-INDEL	.											.	ARGLU1	17	.	0			c.347delT						.						40.0	41.0	41.0					13																	107219922		1985	4159	6144	SO:0001630	splice_region_variant	55082	exon1			.	BC071587	CCDS41906.1	13q33.3	2011-10-03	2007-11-28		ENSG00000134884	ENSG00000134884			25482	protein-coding gene	gene with protein product		614046				21454576	Standard	NM_018011		Approved	FLJ10154	uc001vqk.4	Q9NWB6	OTTHUMG00000017321	ENST00000400198.3:c.347+1A>-	chr13.hg19:g.107219922delT		201.0	0.0		140.0	10.0	NM_018011	B4E0Y3|Q5T257|Q6IQ34	Frame_Shift_Del	DEL	ENST00000400198.3	hg19	CCDS41906.1																																																																																			.	.		0.711	ARGLU1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045727.1	NM_018011	Frame_Shift_Del
LCK	3932	hgsc.bcm.edu	37	1	32742265	32742265	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:32742265delC	ENST00000336890.5	+	9	980	c.842delC	c.(841-843)tccfs	p.S281fs	LCK_ENST00000373564.3_Frame_Shift_Del_p.S288fs|LCK_ENST00000333070.4_Frame_Shift_Del_p.S281fs	NM_005356.3	NP_005347.3	P06239	LCK_HUMAN	LCK proto-oncogene, Src family tyrosine kinase	281	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|aging (GO:0007568)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|cellular zinc ion homeostasis (GO:0006882)|dephosphorylation (GO:0016311)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hemopoiesis (GO:0030097)|innate immune response (GO:0045087)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|positive regulation of gamma-delta T cell differentiation (GO:0045588)|positive regulation of gene expression (GO:0010628)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell receptor signaling pathway (GO:0050862)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|positive regulation of uterine smooth muscle contraction (GO:0070474)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of defense response to virus by virus (GO:0050690)|regulation of lymphocyte activation (GO:0051249)|release of sequestered calcium ion into cytosol (GO:0051209)|response to drug (GO:0042493)|response to hydrogen peroxide (GO:0042542)|response to mechanical stimulus (GO:0009612)|response to zinc ion (GO:0010043)|T cell costimulation (GO:0031295)|T cell differentiation (GO:0030217)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|membrane raft (GO:0045121)|pericentriolar material (GO:0000242)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|ATP binding (GO:0005524)|ATPase binding (GO:0051117)|CD4 receptor binding (GO:0042609)|CD8 receptor binding (GO:0042610)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine kinase activity (GO:0004713)|SH2 domain binding (GO:0042169)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(1)|large_intestine(5)|lung(15)|ovary(2)|skin(2)|urinary_tract(1)	37		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.101)|Breast(348;0.212)			Dasatinib(DB01254)|Ponatinib(DB08901)	GGCAGCATGTCCCCGGACGCC	0.632			T	TRB@	T-ALL																																p.S281fs		Atlas-INDEL	.		Dom	yes		1	1p35-p34.3	3932	lymphocyte-specific protein tyrosine kinase		L	.	LCK	124	.	0			c.841delT						.						86.0	73.0	78.0					1																	32742265		2203	4300	6503	SO:0001589	frameshift_variant	3932	exon9			.	M36881	CCDS359.1	1p34.3	2014-09-17	2014-06-25		ENSG00000182866	ENSG00000182866	2.7.10.1	"""SH2 domain containing"""	6524	protein-coding gene	gene with protein product		153390	"""lymphocyte-specific protein tyrosine kinase"""			2787474	Standard	XM_005270862		Approved		uc001buy.3	P06239	OTTHUMG00000007463	ENST00000336890.5:c.842delC	chr1.hg19:g.32742265delC	ENSP00000337825:p.Ser281fs	229.0	0.0		161.0	10.0	NM_005356	D3DPP8|P07100|Q12850|Q13152|Q5TDH8|Q5TDH9|Q7RTZ3|Q96DW4|Q9NYT8	Frame_Shift_Del	DEL	ENST00000336890.5	hg19	CCDS359.1																																																																																			.	.		0.632	LCK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019616.4	NM_005356	
LSP1	4046	hgsc.bcm.edu	37	11	1902755	1902755	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:1902755delG	ENST00000311604.3	+	3	460	c.285delG	c.(283-285)gagfs	p.E95fs	LSP1_ENST00000405957.2_Frame_Shift_Del_p.E33fs|LSP1_ENST00000406638.2_Frame_Shift_Del_p.E33fs|LSP1_ENST00000485341.1_3'UTR|LSP1_ENST00000381775.1_Frame_Shift_Del_p.E223fs	NM_002339.2	NP_002330.1	P33241	LSP1_HUMAN	lymphocyte-specific protein 1	95					cellular component movement (GO:0006928)|cellular defense response (GO:0006968)|chemotaxis (GO:0006935)	actin cytoskeleton (GO:0015629)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|signal transducer activity (GO:0004871)			haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(9)|prostate(1)|skin(1)	16		all_epithelial(84;0.000138)|Breast(177;0.000962)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00147)|Lung(200;0.0729)|LUSC - Lung squamous cell carcinoma(625;0.0856)		AGCAGCACGAGGGGGCGCAGG	0.701																																					p.E223fs		Atlas-INDEL	.											.	LSP1	59	.	0			c.668delA						.						16.0	18.0	17.0					11																	1902755		2173	4239	6412	SO:0001589	frameshift_variant	4046	exon4			.	M33552	CCDS31334.1, CCDS31335.1, CCDS58110.1	11p15.5	2008-02-05			ENSG00000130592	ENSG00000130592			6707	protein-coding gene	gene with protein product		153432				2174784	Standard	NM_001242932		Approved	WP34	uc001luj.3	P33241	OTTHUMG00000012252	ENST00000311604.3:c.285delG	chr11.hg19:g.1902755delG	ENSP00000308383:p.Glu95fs	253.0	0.0		197.0	14.0	NM_001242932	B3KPP1|B3KRR6|E9PBV6|E9PFP3|Q16096|Q53H48|Q6FHM3|Q9BUY8	Frame_Shift_Del	DEL	ENST00000311604.3	hg19	CCDS31334.1																																																																																			.	.		0.701	LSP1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000034045.3	NM_002339	
TULP4	56995	hgsc.bcm.edu	37	6	158915819	158915819	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:158915819delG	ENST00000367097.3	+	11	3168	c.1811delG	c.(1810-1812)tggfs	p.W604fs	TULP4_ENST00000367094.2_Frame_Shift_Del_p.W604fs	NM_020245.4	NP_064630.2	Q9NRJ4	TULP4_HUMAN	tubby like protein 4	604					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)|regulation of transcription, DNA-templated (GO:0006355)|response to nutrient (GO:0007584)	cytoplasm (GO:0005737)	sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(7)|kidney(2)|large_intestine(15)|lung(17)|ovary(1)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	49		Breast(66;0.000781)|Ovarian(120;0.0308)|Lung SC(201;0.164)|Prostate(117;0.171)		OV - Ovarian serous cystadenocarcinoma(65;1.64e-18)|BRCA - Breast invasive adenocarcinoma(81;2.67e-05)		TCTAATATCTGGGGAACCAAA	0.433																																					p.W604fs		Atlas-INDEL	.											.	TULP4	137	.	0			c.1810delT						.						138.0	123.0	128.0					6																	158915819		2203	4300	6503	SO:0001589	frameshift_variant	56995	exon11			.		CCDS34561.1, CCDS34562.1	6q25-q26	2013-01-10			ENSG00000130338	ENSG00000130338		"""WD repeat domain containing"""	15530	protein-coding gene	gene with protein product						11595174	Standard	NM_020245		Approved	TUSP, KIAA1397	uc003qrf.3	Q9NRJ4	OTTHUMG00000015910	ENST00000367097.3:c.1811delG	chr6.hg19:g.158915819delG	ENSP00000356064:p.Trp604fs	291.0	0.0		169.0	11.0	NM_001007466	Q5T3M2|Q5T3M3|Q9HD22|Q9P2F0	Frame_Shift_Del	DEL	ENST00000367097.3	hg19	CCDS34561.1																																																																																			.	.		0.433	TULP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042869.1	NM_020245	
RTP5	285093	hgsc.bcm.edu	37	2	242814476	242814476	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:242814476delG	ENST00000343216.3	+	2	797	c.769delG	c.(769-771)gggfs	p.G258fs		NM_173821.2	NP_776182.2																					GGCCATGCCTGGGGGCAAAGG	0.667																																					p.P256fs		Atlas-INDEL	.											.	.	.	.	0			c.768delT						.						29.0	33.0	32.0					2																	242814476		1905	4115	6020	SO:0001589	frameshift_variant	285093	exon2			.																												ENST00000343216.3:c.769delG	chr2.hg19:g.242814476delG	ENSP00000345374:p.Gly258fs	224.0	0.0		156.0	10.0	NM_173821		Frame_Shift_Del	DEL	ENST00000343216.3	hg19	CCDS42843.1																																																																																			.	.		0.667	CXXC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322310.1		
SMC6	79677	hgsc.bcm.edu	37	2	17888597	17888597	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:17888597delT	ENST00000448223.2	-	18	2164	c.1895delA	c.(1894-1896)aatfs	p.N632fs	SMC6_ENST00000381272.4_Frame_Shift_Del_p.N658fs|SMC6_ENST00000402989.1_Frame_Shift_Del_p.N632fs|SMC6_ENST00000351948.4_Frame_Shift_Del_p.N632fs	NM_001142286.1	NP_001135758.1	Q96SB8	SMC6_HUMAN	structural maintenance of chromosomes 6	632	Flexible hinge.				cellular senescence (GO:0090398)|double-strand break repair via homologous recombination (GO:0000724)|telomere maintenance via recombination (GO:0000722)	chromosome, telomeric region (GO:0000781)|intracellular (GO:0005622)|nucleolus (GO:0005730)|nucleus (GO:0005634)|PML body (GO:0016605)|Smc5-Smc6 complex (GO:0030915)	ATP binding (GO:0005524)			NS(1)|biliary_tract(1)|breast(6)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(3)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	43	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					TTCTCTACAATTTTTGGGTGG	0.338																																					p.N632fs		Atlas-INDEL	.											.	SMC6	102	.	0			c.1896delT						.						101.0	99.0	100.0					2																	17888597		2203	4300	6503	SO:0001589	frameshift_variant	79677	exon18			.	AJ310551	CCDS1690.1	2p24.3	2008-02-05	2006-07-06	2006-07-06	ENSG00000163029	ENSG00000163029		"""Structural maintenance of chromosomes proteins"""	20466	protein-coding gene	gene with protein product		609387	"""SMC6 structural maintenance of chromosomes 6-like 1 (yeast)"""	SMC6L1		11230166	Standard	NM_024624		Approved	FLJ22116	uc002rcn.3	Q96SB8	OTTHUMG00000090675	ENST00000448223.2:c.1895delA	chr2.hg19:g.17888597delT	ENSP00000404092:p.Asn632fs	234.0	0.0		179.0	16.0	NM_001142286	A8K8Q6|D6W518|Q05BV4|Q9H0X3|Q9H6M0	Frame_Shift_Del	DEL	ENST00000448223.2	hg19	CCDS1690.1																																																																																			.	.		0.338	SMC6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207359.1	NM_024624	
VPS13D	55187	hgsc.bcm.edu	37	1	12336449	12336449	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:12336449delC	ENST00000358136.3	+	19	2934	c.2804delC	c.(2803-2805)accfs	p.T935fs	VPS13D_ENST00000356315.4_Frame_Shift_Del_p.T935fs	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)		ATGAATTTAACCCAGAGCATT	0.478											OREG0013110	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.T935fs		Atlas-INDEL	.											.	VPS13D	316	.	0			c.2803delA						.						49.0	51.0	50.0					1																	12336449		2203	4300	6503	SO:0001589	frameshift_variant	55187	exon19			.	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.2804delC	chr1.hg19:g.12336449delC	ENSP00000350854:p.Thr935fs	174.0	0.0	679	125.0	11.0	NM_015378		Frame_Shift_Del	DEL	ENST00000358136.3	hg19	CCDS30588.1																																																																																			.	.		0.478	VPS13D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000036897.2	NM_015378	
TESPA1	9840	hgsc.bcm.edu	37	12	55356761	55356761	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:55356761delG	ENST00000449076.1	-	9	1053	c.921delC	c.(919-921)cccfs	p.P307fs	TESPA1_ENST00000531122.1_Frame_Shift_Del_p.P169fs|TESPA1_ENST00000532804.1_Frame_Shift_Del_p.P169fs|TESPA1_ENST00000524959.1_5'Flank|TESPA1_ENST00000524622.1_Frame_Shift_Del_p.P169fs|TESPA1_ENST00000316577.8_Frame_Shift_Del_p.P307fs	NM_001136030.2	NP_001129502.1	A2RU30	TESP1_HUMAN	thymocyte expressed, positive selection associated 1	307					COP9 signalosome assembly (GO:0010387)|positive regulation of T cell differentiation in thymus (GO:0033089)|positive regulation of T cell receptor signaling pathway (GO:0050862)	COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)											TGTTCCTTTTGGGGGTGTTGT	0.532																																					p.K308fs		Atlas-INDEL	.											.	.	.	.	0			c.922delA						.						62.0	63.0	63.0					12																	55356761		1914	4111	6025	SO:0001589	frameshift_variant	9840	exon9			.	AB018291	CCDS44913.1, CCDS58240.1	12q13.2	2012-03-21	2012-03-21	2012-03-21	ENSG00000135426	ENSG00000135426			29109	protein-coding gene	gene with protein product		615664	"""KIAA0748"""	KIAA0748		9872452	Standard	NM_001136030		Approved		uc001sgn.4	A2RU30	OTTHUMG00000165407	ENST00000449076.1:c.921delC	chr12.hg19:g.55356761delG	ENSP00000400892:p.Pro307fs	169.0	0.0		153.0	12.0	NM_001098815	B4DPM3|B4E048|B7Z9K7|O94849|Q4G0P2|Q9P0C4	Frame_Shift_Del	DEL	ENST00000449076.1	hg19	CCDS44913.1																																																																																			.	.		0.532	TESPA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000383822.1	NM_001098815	
USP24	23358	hgsc.bcm.edu	37	1	55608747	55608747	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:55608747delT	ENST00000294383.6	-	22	2484	c.2485delA	c.(2485-2487)atafs	p.I829fs	USP24_ENST00000407756.1_Frame_Shift_Del_p.I669fs	NM_015306.2	NP_056121.2	Q9UPU5	UBP24_HUMAN	ubiquitin specific peptidase 24	829					ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(4)|cervix(1)|endometrium(8)|kidney(13)|large_intestine(7)|lung(16)|ovary(6)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	60						TCCATGGCTATTTTCCAAATG	0.289																																					p.I829fs		Atlas-INDEL	.											.	USP24	323	.	0			c.2486delT						.						51.0	45.0	47.0					1																	55608747		1776	4000	5776	SO:0001589	frameshift_variant	23358	exon22			.	AB028980	CCDS44154.1, CCDS44154.2	1p32.3	2008-04-11	2005-08-08		ENSG00000162402	ENSG00000162402		"""Ubiquitin-specific peptidases"""	12623	protein-coding gene	gene with protein product		610569	"""ubiquitin specific protease 24"""			12838346	Standard	NM_015306		Approved	KIAA1057	uc021onw.1	Q9UPU5	OTTHUMG00000008135	ENST00000294383.6:c.2485delA	chr1.hg19:g.55608747delT	ENSP00000294383:p.Ile829fs	284.0	0.0		193.0	12.0	NM_015306	Q6ZSY2|Q8N2Y4|Q9NXD1	Frame_Shift_Del	DEL	ENST00000294383.6	hg19	CCDS44154.2																																																																																			.	.		0.289	USP24-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022275.2		
PGAM4	441531	hgsc.bcm.edu	37	X	77224433	77224433	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:77224433delC	ENST00000458128.1	-	1	702	c.703delG	c.(703-705)gatfs	p.D235fs	ATP7A_ENST00000341514.6_Intron|ATP7A_ENST00000350425.4_Intron|ATP7A_ENST00000343533.5_Intron	NM_001029891.2	NP_001025062.1	Q8N0Y7	PGAM4_HUMAN	phosphoglycerate mutase family member 4	235					glycolytic process (GO:0006096)|positive regulation of sperm motility (GO:1902093)	extracellular vesicular exosome (GO:0070062)|sperm principal piece (GO:0097228)	bisphosphoglycerate 2-phosphatase activity (GO:0004083)|bisphosphoglycerate mutase activity (GO:0004082)|phosphoglycerate mutase activity (GO:0004619)			endometrium(2)|lung(4)	6						GTCTCTTCATCCCCCAGAAAC	0.547																																					p.D235fs		Atlas-INDEL	.											.	PGAM4	28	.	0			c.704delA						.						69.0	66.0	67.0					X																	77224433		2203	4296	6499	SO:0001589	frameshift_variant	441531	exon1			.	AF465731	CCDS35338.1	Xq21.1	2011-02-09	2006-02-09		ENSG00000226784	ENSG00000226784			21731	protein-coding gene	gene with protein product		300567	"""phosphoglycerate mutase family 4"""			11961099, 9370262	Standard	NM_001029891		Approved	dJ1000K24.1, PGAM3, PGAM-B, PGAM1	uc004ecy.1	Q8N0Y7	OTTHUMG00000057865	ENST00000458128.1:c.703delG	chrX.hg19:g.77224433delC	ENSP00000412189:p.Asp235fs	226.0	0.0		151.0	11.0	NM_001029891	Q5JPN2|Q8NI24|Q8NI25|Q8NI26	Frame_Shift_Del	DEL	ENST00000458128.1	hg19	CCDS35338.1																																																																																			.	.		0.547	PGAM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128371.2	NM_001029891	
KIAA1045	23349	hgsc.bcm.edu	37	9	34976586	34976586	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:34976586delG	ENST00000242315.3	+	5	780	c.698delG	c.(697-699)cggfs	p.R233fs	KIAA1045_ENST00000544237.1_Frame_Shift_Del_p.R233fs|KIAA1045_ENST00000476115.2_3'UTR	NM_015297.1	NP_056112.1	Q9UPV7	K1045_HUMAN	KIAA1045	233							metal ion binding (GO:0046872)	p.R233Q(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	19			LUSC - Lung squamous cell carcinoma(32;0.00575)			GCAGCCAAGCGGGGGGACCGT	0.632																																					p.R233fs		Atlas-INDEL	.											.	KIAA1045	60	.	1	Substitution - Missense(1)	upper_aerodigestive_tract(1)	c.697delC						.						41.0	49.0	46.0					9																	34976586		2073	4191	6264	SO:0001589	frameshift_variant	23349	exon5			.	AB028968	CCDS43796.1	9p13.2	2008-02-05			ENSG00000122733	ENSG00000122733			29180	protein-coding gene	gene with protein product						10470851	Standard	NM_015297		Approved		uc003zvr.3	Q9UPV7	OTTHUMG00000019844	ENST00000242315.3:c.698delG	chr9.hg19:g.34976586delG	ENSP00000242315:p.Arg233fs	170.0	0.0		110.0	11.0	NM_015297	B7Z253|Q58FE9|Q5T662	Frame_Shift_Del	DEL	ENST00000242315.3	hg19	CCDS43796.1																																																																																			.	.		0.632	KIAA1045-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052256.2	XM_048592	
LAMB1	3912	hgsc.bcm.edu	37	7	107564717	107564717	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:107564717delT	ENST00000222399.6	-	33	5412	c.5182delA	c.(5182-5184)actfs	p.T1728fs	LAMB1_ENST00000393561.1_Frame_Shift_Del_p.T1752fs	NM_002291.2	NP_002282.2	P07942	LAMB1_HUMAN	laminin, beta 1	1728	Domain I.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|embryo implantation (GO:0007566)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell adhesion (GO:0007162)|neuron projection development (GO:0031175)|neuronal-glial interaction involved in cerebral cortex radial glia guided migration (GO:0021812)|odontogenesis (GO:0042476)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell proliferation (GO:0050679)|substrate adhesion-dependent cell spreading (GO:0034446)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-2 complex (GO:0005607)|laminin-8 complex (GO:0043257)|perinuclear region of cytoplasm (GO:0048471)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)|structural molecule activity (GO:0005198)			NS(3)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(11)|lung(37)|ovary(6)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)	82						GCTAAAAGAGTTTTTGCTTCA	0.338																																					p.T1728fs		Atlas-INDEL	.											.	LAMB1	185	.	0			c.5183delC						.						91.0	91.0	91.0					7																	107564717		2203	4300	6503	SO:0001589	frameshift_variant	3912	exon33			.	M61916	CCDS5750.1	7q22	2013-03-01			ENSG00000091136	ENSG00000091136		"""Laminins"""	6486	protein-coding gene	gene with protein product		150240	"""cutis laxa with marfanoid phenotype"""	CLM		2563160, 2704655, 1864606	Standard	NM_002291		Approved		uc003vew.2	P07942	OTTHUMG00000149966	ENST00000222399.6:c.5182delA	chr7.hg19:g.107564717delT	ENSP00000222399:p.Thr1728fs	223.0	0.0		246.0	16.0	NM_002291	Q14D91	Frame_Shift_Del	DEL	ENST00000222399.6	hg19	CCDS5750.1																																																																																			.	.		0.338	LAMB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314584.1	NM_002291	
PLA2G4C	8605	hgsc.bcm.edu	37	19	48558214	48558214	+	Frame_Shift_Del	DEL	G	G	-	rs557617265	byFrequency	TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:48558214delG	ENST00000599921.1	-	15	1707	c.1350delC	c.(1348-1350)cccfs	p.P450fs	PLA2G4C_ENST00000596510.1_5'UTR|PLA2G4C_ENST00000354276.3_Frame_Shift_Del_p.P450fs|PLA2G4C_ENST00000599111.1_Frame_Shift_Del_p.P460fs|PLA2G4C_ENST00000413144.2_Frame_Shift_Del_p.P450fs			Q9UP65	PA24C_HUMAN	phospholipase A2, group IVC (cytosolic, calcium-independent)	450	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.				arachidonic acid metabolic process (GO:0019369)|glycerophospholipid biosynthetic process (GO:0046474)|glycerophospholipid catabolic process (GO:0046475)|inflammatory response (GO:0006954)|intracellular signal transduction (GO:0035556)|parturition (GO:0007567)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cell cortex (GO:0005938)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)	calcium-independent phospholipase A2 activity (GO:0047499)|phospholipid binding (GO:0005543)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(12)|lung(13)|ovary(2)|prostate(1)|skin(3)	38		all_cancers(25;2.84e-05)|all_lung(116;4.62e-05)|Lung NSC(112;7.61e-05)|all_epithelial(76;0.000192)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;8.09e-05)|all cancers(93;0.000517)|Epithelial(262;0.0135)|GBM - Glioblastoma multiforme(486;0.0717)		AGCAGCTGGCGGGGGCCTTGG	0.567																																					p.A461fs		Atlas-INDEL	.											PLA2G4C,NS,carcinoma,0,2	PLA2G4C	76	.	0			c.1381delG						.						99.0	98.0	98.0					19																	48558214		2203	4300	6503	SO:0001589	frameshift_variant	8605	exon15			.	AF065214	CCDS12710.1, CCDS54286.1, CCDS59403.1	19q13.3	2008-09-19					3.1.1.4		9037	protein-coding gene	gene with protein product		603602				9705332	Standard	NM_003706		Approved	cPLA2-gamma	uc002phx.3	Q9UP65		ENST00000599921.1:c.1350delC	chr19.hg19:g.48558214delG	ENSP00000469473:p.Pro450fs	180.0	0.0		171.0	11.0	NM_001159322	B2RB71|B4DI40|O75457|Q6IBI8|Q9UG68	Frame_Shift_Del	DEL	ENST00000599921.1	hg19	CCDS12710.1																																																																																			.	.		0.567	PLA2G4C-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465551.1		
KCNK10	54207	hgsc.bcm.edu	37	14	88693828	88693828	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr14:88693828delA	ENST00000340700.5	-	4	1008	c.557delT	c.(556-558)ttafs	p.L186fs	KCNK10_ENST00000312350.5_Frame_Shift_Del_p.L191fs|KCNK10_ENST00000319231.5_Frame_Shift_Del_p.L191fs	NM_021161.4	NP_066984.1	P57789	KCNKA_HUMAN	potassium channel, subfamily K, member 10	186					signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transport (GO:0006810)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(25)|ovary(3)|pancreas(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	47						GATGGCATATAAAATACAAAA	0.413																																					p.L191fs		Atlas-Indel,Pindel	.											.	KCNK10	273	.	0			c.573delA						.						117.0	122.0	120.0					14																	88693828		2203	4300	6503	SO:0001589	frameshift_variant	54207	exon4			.	AF279890	CCDS9880.1, CCDS9881.1, CCDS9882.1	14q31	2014-06-12						"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Two-P"""	6273	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 97"""	605873				10880510, 16382106	Standard	NM_021161		Approved	K2p10.1, TREK-2, TREK2, PPP1R97	uc001xwn.3	P57789		ENST00000340700.5:c.557delT	chr14.hg19:g.88693828delA	ENSP00000343104:p.Leu186fs	80.0	0.0		96.0	37.0	NM_138318	B2R8T4|B2RCT3|B5TJL4|Q6B014|Q8TDK7|Q8TDK8|Q9HB59	Frame_Shift_Del	DEL	ENST00000340700.5	hg19	CCDS9880.1																																																																																			.	.		0.413	KCNK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410167.1	NM_021161	
SECISBP2L	9728	hgsc.bcm.edu	37	15	49319614	49319614	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:49319614delT	ENST00000559471.1	-	7	1246	c.983delA	c.(982-984)aatfs	p.N328fs	SECISBP2L_ENST00000261847.3_Frame_Shift_Del_p.N328fs	NM_001193489.1	NP_001180418.1	Q93073	SBP2L_HUMAN	SECIS binding protein 2-like	328							poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(5)|kidney(8)|large_intestine(12)|lung(11)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|urinary_tract(1)	46						AAATGTCTGATTTTTTTCCAT	0.318																																					p.N328fs		Atlas-INDEL	.											.	SECISBP2L	118	.	0			c.984delT						.						113.0	113.0	113.0					15																	49319614		2197	4295	6492	SO:0001589	frameshift_variant	9728	exon7			.	BC033001	CCDS32234.1, CCDS53942.1	15q21.1	2014-02-12				ENSG00000138593			28997	protein-coding gene	gene with protein product		615756					Standard	NM_001193489		Approved	KIAA0256	uc001zxe.2	Q93073		ENST00000559471.1:c.983delA	chr15.hg19:g.49319614delT	ENSP00000453854:p.Asn328fs	229.0	0.0		184.0	12.0	NM_001193489	Q8N767	Frame_Shift_Del	DEL	ENST00000559471.1	hg19	CCDS53942.1																																																																																			.	.		0.318	SECISBP2L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417277.1	NM_014701	
DAB2	1601	hgsc.bcm.edu	37	5	39377168	39377168	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:39377168delC	ENST00000320816.6	-	12	2188	c.1721delG	c.(1720-1722)ggcfs	p.G574fs	DAB2_ENST00000509337.1_Frame_Shift_Del_p.G553fs|DAB2_ENST00000339788.6_Frame_Shift_Del_p.G356fs|DAB2_ENST00000545653.1_Frame_Shift_Del_p.G553fs	NM_001343.3	NP_001334.2	P98082	DAB2_HUMAN	Dab, mitogen-responsive phosphoprotein, homolog 2 (Drosophila)	574					activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|cell morphogenesis involved in differentiation (GO:0000904)|cell proliferation (GO:0008283)|cellular response to transforming growth factor beta stimulus (GO:0071560)|clathrin coat assembly (GO:0048268)|endoderm development (GO:0007492)|excretion (GO:0007588)|in utero embryonic development (GO:0001701)|leading edge cell differentiation (GO:0035026)|membrane organization (GO:0061024)|myeloid cell differentiation (GO:0030099)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of protein binding (GO:0032091)|negative regulation of protein localization to plasma membrane (GO:1903077)|negative regulation of transcription, DNA-templated (GO:0045892)|pinocytosis (GO:0006907)|positive regulation of cell migration (GO:0030335)|positive regulation of clathrin-mediated endocytosis (GO:2000370)|positive regulation of early endosome to late endosome transport (GO:2000643)|positive regulation of endocytosis (GO:0045807)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of integrin-mediated signaling pathway (GO:2001046)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of receptor recycling (GO:0001921)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)|protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)|Wnt signaling pathway (GO:0016055)	apical plasma membrane (GO:0016324)|clathrin coat of coated pit (GO:0030132)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	cargo receptor activity (GO:0038024)|clathrin adaptor activity (GO:0035615)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein C-terminus binding (GO:0008022)|SMAD binding (GO:0046332)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(1)|kidney(5)|large_intestine(9)|lung(19)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	47	all_lung(31;0.000197)		Epithelial(62;0.137)			TGCAGAAGGGCCCCAGACAAC	0.527											OREG0016586	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G574fs		Atlas-INDEL	.											.	DAB2	124	.	0			c.1722delC						.						70.0	75.0	73.0					5																	39377168		2203	4300	6503	SO:0001589	frameshift_variant	1601	exon12			.	U53446	CCDS34149.1, CCDS58946.1	5p13.1	2013-10-03	2013-03-08		ENSG00000153071	ENSG00000153071			2662	protein-coding gene	gene with protein product		601236	"""disabled (Drosophila) homolog 2 (mitogen-responsive phosphoprotein)"", ""disabled homolog 2, mitogen-responsive phosphoprotein (Drosophila)"""			8660969, 9620555	Standard	NM_001343		Approved	DOC-2	uc003jlx.3	P98082	OTTHUMG00000162043	ENST00000320816.6:c.1721delG	chr5.hg19:g.39377168delC	ENSP00000313391:p.Gly574fs	251.0	0.0	885	192.0	12.0	NM_001343	A6NES5|Q13598|Q9BTY0|Q9UK04	Frame_Shift_Del	DEL	ENST00000320816.6	hg19	CCDS34149.1																																																																																			.	.		0.527	DAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367014.1	NM_001343	
IL27RA	9466	hgsc.bcm.edu	37	19	14150617	14150617	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:14150617delC	ENST00000263379.2	+	4	554	c.429delC	c.(427-429)gacfs	p.D143fs		NM_004843.3	NP_004834.1	Q6UWB1	I27RA_HUMAN	interleukin 27 receptor, alpha	143	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell surface receptor signaling pathway (GO:0007166)|defense response to Gram-positive bacterium (GO:0050830)|immune response (GO:0006955)|negative regulation of type 2 immune response (GO:0002829)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T-helper 1 type immune response (GO:0002827)|regulation of isotype switching to IgG isotypes (GO:0048302)	integral component of plasma membrane (GO:0005887)	interleukin-27 receptor activity (GO:0045509)|transmembrane signaling receptor activity (GO:0004888)			breast(3)|endometrium(3)|kidney(2)|large_intestine(8)|lung(7)|ovary(1)|skin(1)|urinary_tract(1)	26						CCGAGGATGACCCCCTGGAGG	0.602																																					p.D143fs	Colon(164;1849 1896 4443 37792 47834)	Atlas-INDEL	.											.	IL27RA	56	.	0			c.428delA						.						66.0	68.0	67.0					19																	14150617		2203	4300	6503	SO:0001589	frameshift_variant	9466	exon4			.	AF053004	CCDS12303.1	19p13.11	2013-02-11				ENSG00000104998		"""Interleukins and interleukin receptors"", ""Fibronectin type III domain containing"""	17290	protein-coding gene	gene with protein product	"""T-cell cytokine receptor type 1"""	605350				9600072, 11057672	Standard	NM_004843		Approved	WSX-1, TCCR, CRL1, WSX1, zcytor1, IL-27R	uc002mxx.4	Q6UWB1		ENST00000263379.2:c.429delC	chr19.hg19:g.14150617delC	ENSP00000263379:p.Asp143fs	221.0	0.0		152.0	10.0	NM_004843	A0N0L1|O60624	Frame_Shift_Del	DEL	ENST00000263379.2	hg19	CCDS12303.1																																																																																			.	.		0.602	IL27RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458539.1	NM_004843	
HERC2	8924	hgsc.bcm.edu	37	15	28421641	28421641	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:28421641delC	ENST00000261609.7	-	63	9727	c.9619delG	c.(9619-9621)gtgfs	p.V3207fs		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)		ATCTGGCACACCCCCTGTCCA	0.537																																					p.V3207fs		Atlas-INDEL	.											.	HERC2	501	.	0			c.9620delT						.						82.0	82.0	82.0					15																	28421641		2203	4300	6503	SO:0001589	frameshift_variant	8924	exon63			.	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.9619delG	chr15.hg19:g.28421641delC	ENSP00000261609:p.Val3207fs	283.0	0.0		231.0	15.0	NM_004667		Frame_Shift_Del	DEL	ENST00000261609.7	hg19	CCDS10021.1																																																																																			.	.		0.537	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667	
SMTNL1	219537	hgsc.bcm.edu	37	11	57313466	57313466	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:57313466delC	ENST00000399154.2	+	5	919	c.919delC	c.(919-921)cccfs	p.P307fs	SMTNL1_ENST00000457912.1_Frame_Shift_Del_p.P362fs|SMTNL1_ENST00000527972.1_Frame_Shift_Del_p.P344fs			A8MU46	SMTL1_HUMAN	smoothelin-like 1	307					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						GCCCCGGGGGCCCCGGGCACA	0.667																																					p.G343fs		Atlas-INDEL	.											.	SMTNL1	68	.	0			c.1029delG						.						24.0	29.0	27.0					11																	57313466		1852	4093	5945	SO:0001589	frameshift_variant	219537	exon4			.	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.919delC	chr11.hg19:g.57313466delC	ENSP00000382108:p.Pro307fs	232.0	0.0		165.0	10.0	NM_001105565		Frame_Shift_Del	DEL	ENST00000399154.2	hg19																																																																																				.	.		0.667	SMTNL1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_166203	
ADCY9	115	hgsc.bcm.edu	37	16	4027526	4027526	+	Frame_Shift_Del	DEL	C	C	-	rs144319192		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:4027526delC	ENST00000294016.3	-	9	3323	c.2785delG	c.(2785-2787)gccfs	p.A929fs		NM_001116.3	NP_001107.2	O60503	ADCY9_HUMAN	adenylate cyclase 9	929					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	axon (GO:0030424)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)			breast(4)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(11)|lung(9)|ovary(5)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	47						AGCGGCCCGGCCCCCACGACG	0.667																																					p.A929fs		Atlas-INDEL	.											.	ADCY9	151	.	0			c.2786delC						.						33.0	26.0	28.0					16																	4027526		2182	4295	6477	SO:0001589	frameshift_variant	115	exon9			.	AF036927	CCDS32382.1	16p13.3	2013-02-04				ENSG00000162104	4.6.1.1	"""Adenylate cyclases"""	240	protein-coding gene	gene with protein product		603302				9628827	Standard	NM_001116		Approved	AC9	uc002cvx.3	O60503		ENST00000294016.3:c.2785delG	chr16.hg19:g.4027526delC	ENSP00000294016:p.Ala929fs	306.0	0.0		203.0	13.0	NM_001116	A7E2V5|A7E2X2|D3DUD1|O60273|Q4ZHT9|Q4ZIR5|Q9BWT4|Q9UGP2	Frame_Shift_Del	DEL	ENST00000294016.3	hg19	CCDS32382.1																																																																																			.	.		0.667	ADCY9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438076.1		
TSPYL1	7259	hgsc.bcm.edu	37	6	116600132	116600132	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:116600132delG	ENST00000368608.3	-	1	934	c.862delC	c.(862-864)cagfs	p.Q288fs	RP1-93H18.1_ENST00000449314.1_lincRNA|DSE_ENST00000540275.1_Intron|DSE_ENST00000452085.3_5'Flank	NM_003309.3	NP_003300.1	Q9H0U9	TSYL1_HUMAN	TSPY-like 1	288					nucleosome assembly (GO:0006334)	nucleus (GO:0005634)	enzyme binding (GO:0019899)			breast(1)|endometrium(2)|large_intestine(2)|lung(2)|ovary(3)|urinary_tract(1)	11		all_cancers(87;0.0144)|all_epithelial(87;0.021)|Colorectal(196;0.234)		all cancers(137;0.0235)|OV - Ovarian serous cystadenocarcinoma(136;0.0469)|GBM - Glioblastoma multiforme(226;0.0503)|Epithelial(106;0.094)		GCGGACAACTGGGGGTGGTTT	0.502																																					p.Q288fs		Atlas-INDEL	.											.	TSPYL1	28	.	0			c.863delA						.						126.0	130.0	129.0					6																	116600132		2203	4300	6503	SO:0001589	frameshift_variant	7259	exon1			.	AF042181	CCDS34518.1	6q22.1	2014-09-17	2004-04-05	2004-04-07	ENSG00000189241	ENSG00000189241			12382	protein-coding gene	gene with protein product		604714	"""TSPY-like"""	TSPYL		9730615	Standard	NM_003309		Approved		uc003pwp.4	Q9H0U9	OTTHUMG00000015427	ENST00000368608.3:c.862delC	chr6.hg19:g.116600132delG	ENSP00000357597:p.Gln288fs	203.0	0.0		165.0	11.0	NM_003309	O75885|Q5TFE6	Frame_Shift_Del	DEL	ENST00000368608.3	hg19	CCDS34518.1																																																																																			.	.		0.502	TSPYL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041929.1		
SLC46A3	283537	hgsc.bcm.edu	37	13	29286951	29286951	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr13:29286951delA	ENST00000266943.6	-	3	1295	c.926delT	c.(925-927)ttgfs	p.L309fs	SLC46A3_ENST00000380814.4_Frame_Shift_Del_p.L309fs	NM_001135919.1|NM_181785.3	NP_001129391.1|NP_861450.1	Q7Z3Q1	S46A3_HUMAN	solute carrier family 46, member 3	309					transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(2)|prostate(1)|skin(1)	15		Lung SC(185;0.0367)		all cancers(112;0.159)		GAAACTAGTCAAAAAAGAGGC	0.383																																					p.L309fs		Atlas-INDEL	.											.	SLC46A3	86	.	0			c.927delG						.						94.0	93.0	94.0					13																	29286951		2203	4300	6503	SO:0001589	frameshift_variant	283537	exon3			.		CCDS9332.1, CCDS45021.1	13q12.3	2013-05-22	2007-03-29		ENSG00000139508	ENSG00000139508		"""Solute carriers"""	27501	protein-coding gene	gene with protein product							Standard	NM_001135919		Approved	DKFZp686A1775, FLJ42613	uc001usj.3	Q7Z3Q1	OTTHUMG00000016650	ENST00000266943.6:c.926delT	chr13.hg19:g.29286951delA	ENSP00000266943:p.Leu309fs	204.0	0.0		147.0	10.0	NM_181785	Q3ZCV8|Q6NUK5|Q6P9B3|Q6ZVG5|Q96QA1	Frame_Shift_Del	DEL	ENST00000266943.6	hg19	CCDS9332.1																																																																																			.	.		0.383	SLC46A3-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276111.1	NM_181785	
SOHLH2	54937	hgsc.bcm.edu	37	13	36764122	36764122	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr13:36764122delT	ENST00000379881.3	-	6	690	c.602delA	c.(601-603)aagfs	p.K201fs	SOHLH2_ENST00000554962.1_Frame_Shift_Del_p.K278fs|SOHLH2_ENST00000317764.6_Frame_Shift_Del_p.K201fs|CCDC169-SOHLH2_ENST00000511166.1_Frame_Shift_Del_p.K278fs	NM_017826.2	NP_060296.2	Q9NX45	SOLH2_HUMAN	spermatogenesis and oogenesis specific basic helix-loop-helix 2	201	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				multicellular organismal development (GO:0007275)|oogenesis (GO:0048477)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(13)|lung(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Breast(139;0.0615)|Lung SC(185;0.0743)|Prostate(109;0.184)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;4.63e-08)|Epithelial(112;2.67e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00272)|BRCA - Breast invasive adenocarcinoma(63;0.00685)|GBM - Glioblastoma multiforme(144;0.0273)		AAGAGAGATCTTTTTGTTTTT	0.318																																					p.K278fs		Atlas-INDEL	.											.	.	.	.	0			c.834delG						.						107.0	107.0	107.0					13																	36764122		2203	4300	6503	SO:0001589	frameshift_variant	100526761	exon11			.	AK000456	CCDS9355.1, CCDS61309.1	13q13.3	2013-05-21			ENSG00000120669	ENSG00000120669		"""Basic helix-loop-helix proteins"""	26026	protein-coding gene	gene with protein product	"""spermatogenesis associated 28"""					12477932	Standard	NM_017826		Approved	FLJ20449, TEB1, bHLHe81, SPATA28		Q9NX45	OTTHUMG00000016728	ENST00000379881.3:c.602delA	chr13.hg19:g.36764122delT	ENSP00000369210:p.Lys201fs	216.0	0.0		171.0	11.0	NM_001198910	B4DX90|Q5EGC3|Q8TC74|Q96QX4	Frame_Shift_Del	DEL	ENST00000379881.3	hg19	CCDS9355.1																																																																																			.	.		0.318	SOHLH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044477.2	NM_017826	
AMOTL2	51421	hgsc.bcm.edu	37	3	134084701	134084701	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:134084701delG	ENST00000422605.2	-	5	1403	c.1237delC	c.(1237-1239)cagfs	p.Q413fs	AMOTL2_ENST00000513145.1_Frame_Shift_Del_p.Q413fs|AMOTL2_ENST00000514516.1_Frame_Shift_Del_p.Q471fs|AMOTL2_ENST00000511759.1_5'Flank|AMOTL2_ENST00000249883.5_Frame_Shift_Del_p.Q413fs			Q9Y2J4	AMOL2_HUMAN	angiomotin like 2	413					hippo signaling (GO:0035329)|Wnt signaling pathway (GO:0016055)	apical plasma membrane (GO:0016324)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endosome (GO:0005768)|tight junction (GO:0005923)				endometrium(8)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	19						CTGCCGGCCTGGGCCTCCTGT	0.567																																					p.Q413fs		Atlas-INDEL	.											.	AMOTL2	52	.	0			c.1238delA						.						94.0	91.0	92.0					3																	134084701		2203	4300	6503	SO:0001589	frameshift_variant	51421	exon5			.	AF175966	CCDS33860.1, CCDS63783.1, CCDS63784.1	3q21-q22	2008-07-18			ENSG00000114019	ENSG00000114019			17812	protein-coding gene	gene with protein product	"""Leman coiled-coil protein"", ""angiomotin-like protein 2"""	614658					Standard	NM_016201		Approved	LCCP	uc003eqg.1	Q9Y2J4	OTTHUMG00000159777	ENST00000422605.2:c.1237delC	chr3.hg19:g.134084701delG	ENSP00000409999:p.Gln413fs	218.0	0.0		154.0	11.0	NM_016201	A8K6F1|B7Z5Q1|E9PHW3|Q53EP1|Q96F99|Q9UKB4	Frame_Shift_Del	DEL	ENST00000422605.2	hg19																																																																																				.	.		0.567	AMOTL2-014	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000358149.1	NM_016201	
ZSCAN31	64288	hgsc.bcm.edu	37	6	28295184	28295184	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:28295184delA	ENST00000414429.1	-	7	1411	c.508delT	c.(508-510)tgcfs	p.C170fs	ZSCAN31_ENST00000344279.6_Frame_Shift_Del_p.C170fs|ZSCAN31_ENST00000481934.1_5'Flank|ZSCAN31_ENST00000396838.2_Frame_Shift_Del_p.C170fs|ZSCAN31_ENST00000439158.1_Frame_Shift_Del_p.C170fs|ZSCAN31_ENST00000446474.1_Frame_Shift_Del_p.C11fs			Q96LW9	ZSC31_HUMAN	zinc finger and SCAN domain containing 31	170					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)										TGGTGGAGGCAAAAAGATTCA	0.458																																					p.C170fs		Atlas-INDEL	.											.	.	.	.	0			c.509delG						.		,,,	2,4262		1,0,2131	201.0	176.0	185.0		,,,	-3.2	0.0	6		183	23,8231		11,1,4115	no	frameshift,frameshift,frameshift,frameshift	ZNF323	NM_145909.2,NM_030899.4,NM_001135216.1,NM_001135215.1	,,,	12,1,6246	A1A1,A1R,RR		0.2787,0.0469,0.1997	,,,	,,,	28295184	25,12493	2203	4300	6503	SO:0001589	frameshift_variant	64288	exon3			.		CCDS4649.1, CCDS59001.1	6p	2013-01-09	2013-01-08	2013-01-08	ENSG00000235109	ENSG00000235109		"""-"", ""Zinc fingers, C2H2-type"""	14097	protein-coding gene	gene with protein product		610794	"""zinc finger protein 310 pseudogene"", ""zinc finger protein 323"""	ZNF310P, ZNF323			Standard	NM_001135216		Approved		uc003nla.3	Q96LW9	OTTHUMG00000014518	ENST00000414429.1:c.508delT	chr6.hg19:g.28295184delA	ENSP00000390076:p.Cys170fs	195.0	0.0		143.0	12.0	NM_030899	Q6P178|Q8WWS5	Frame_Shift_Del	DEL	ENST00000414429.1	hg19	CCDS4649.1																																																																																			.	.		0.458	ZSCAN31-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346804.1	NM_030899	
EPX	8288	hgsc.bcm.edu	37	17	56274371	56274371	+	Frame_Shift_Del	DEL	C	C	-	rs186927462		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:56274371delC	ENST00000225371.5	+	7	983	c.873delC	c.(871-873)tgcfs	p.C291fs		NM_000502.4	NP_000493.1	P11678	PERE_HUMAN	eosinophil peroxidase	291					defense response to nematode (GO:0002215)|eosinophil migration (GO:0072677)|hydrogen peroxide catabolic process (GO:0042744)|negative regulation of interleukin-10 production (GO:0032693)|negative regulation of interleukin-5 production (GO:0032714)|positive regulation of interleukin-4 production (GO:0032753)	extracellular vesicular exosome (GO:0070062)	heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			breast(2)|endometrium(9)|kidney(1)|large_intestine(9)|liver(2)|lung(20)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	48					Melatonin(DB01065)	CACCCTCATGCCCCCAAAACA	0.582																																					p.C291fs		Atlas-INDEL	.											.	EPX	95	.	0			c.872delG						.						177.0	160.0	166.0					17																	56274371		2203	4300	6503	SO:0001589	frameshift_variant	8288	exon7			.	M26515	CCDS11602.1	17q23.1	2006-09-25				ENSG00000121053	1.11.1.7		3423	protein-coding gene	gene with protein product		131399				2550461, 2541222	Standard	NM_000502		Approved	EPO, EPP, EPX-PEN	uc002ivq.3	P11678		ENST00000225371.5:c.873delC	chr17.hg19:g.56274371delC	ENSP00000225371:p.Cys291fs	177.0	0.0		189.0	12.0	NM_000502	Q4TVP3	Frame_Shift_Del	DEL	ENST00000225371.5	hg19	CCDS11602.1																																																																																			.	.		0.582	EPX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443367.1	NM_000502	
CNTN3	5067	hgsc.bcm.edu	37	3	74385778	74385778	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:74385778delT	ENST00000263665.6	-	11	1423	c.1396delA	c.(1396-1398)atafs	p.I466fs		NM_020872.1	NP_065923.1	Q9P232	CNTN3_HUMAN	contactin 3 (plasmacytoma associated)	466	Ig-like C2-type 5.				cell adhesion (GO:0007155)|nervous system development (GO:0007399)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(39)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	83		Lung NSC(201;0.138)|Lung SC(41;0.21)		Epithelial(33;0.00212)|BRCA - Breast invasive adenocarcinoma(55;0.00258)|LUSC - Lung squamous cell carcinoma(21;0.00461)|Lung(16;0.01)		ACATTGGCTATTTTGAGTCCT	0.338																																					p.I466fs		Atlas-INDEL	.											.	CNTN3	174	.	0			c.1397delT						.						109.0	93.0	99.0					3																	74385778		2203	4299	6502	SO:0001589	frameshift_variant	5067	exon11			.	AB040929	CCDS33790.1	3p12.3	2013-02-11			ENSG00000113805	ENSG00000113805		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	2173	protein-coding gene	gene with protein product		601325		PANG		8661054, 8586965	Standard	XM_005264757		Approved	BIG-1	uc003dpm.1	Q9P232	OTTHUMG00000158813	ENST00000263665.6:c.1396delA	chr3.hg19:g.74385778delT	ENSP00000263665:p.Ile466fs	228.0	0.0		219.0	14.0	NM_020872	B9EK50|Q9H039	Frame_Shift_Del	DEL	ENST00000263665.6	hg19	CCDS33790.1																																																																																			.	.		0.338	CNTN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352306.1	NM_020872	
DMD	1756	hgsc.bcm.edu	37	X	31198546	31198546	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:31198546delA	ENST00000357033.4	-	69	10233	c.10027delT	c.(10027-10029)tctfs	p.S3343fs	DMD_ENST00000474231.1_Frame_Shift_Del_p.S883fs|DMD_ENST00000378677.2_Frame_Shift_Del_p.S3339fs|DMD_ENST00000541735.1_Frame_Shift_Del_p.S883fs|DMD_ENST00000343523.2_Frame_Shift_Del_p.S883fs|DMD_ENST00000359836.1_Frame_Shift_Del_p.S883fs|DMD_ENST00000378680.2_Frame_Shift_Del_p.S275fs|DMD_ENST00000378707.3_Frame_Shift_Del_p.S883fs|DMD_ENST00000361471.4_Frame_Shift_Del_p.S275fs|DMD_ENST00000378702.4_Frame_Shift_Del_p.S275fs|DMD_ENST00000378723.3_Frame_Shift_Del_p.S275fs	NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2	NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1	P11532	DMD_HUMAN	dystrophin	3343	Interaction with SYNM. {ECO:0000250}.				cardiac muscle cell action potential (GO:0086001)|cardiac muscle contraction (GO:0060048)|cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|extracellular matrix organization (GO:0030198)|motile cilium assembly (GO:0044458)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|peptide biosynthetic process (GO:0043043)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of heart rate (GO:0002027)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of skeletal muscle contraction (GO:0014819)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|regulation of voltage-gated calcium channel activity (GO:1901385)	cell junction (GO:0030054)|cell surface (GO:0009986)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dystrophin-associated glycoprotein complex (GO:0016010)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|dystroglycan binding (GO:0002162)|myosin binding (GO:0017022)|nitric-oxide synthase binding (GO:0050998)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2)	77		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)				ACTCGACCAGAAAAAAAGCAG	0.408																																					p.S3343fs		Atlas-INDEL	.											.	DMD	2127	.	0			c.10028delC						.						121.0	104.0	110.0					X																	31198546		2202	4300	6502	SO:0001589	frameshift_variant	1756	exon69			.	AF047505	CCDS14231.1, CCDS14232.1, CCDS14233.1, CCDS14234.1, CCDS48091.1, CCDS55394.1, CCDS55395.1, CCDS75965.1	Xp21.2	2014-09-17	2008-08-01		ENSG00000198947	ENSG00000198947			2928	protein-coding gene	gene with protein product	"""muscular dystrophy, Duchenne and Becker types"""	300377	"""dystrophin (muscular dystrophy, Duchenne and Becker types), includes DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272"", ""mental retardation, X-linked 85"""	MRX85		3282674, 3607877, 23900271	Standard	NM_004019		Approved	BMD, DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272	uc004dda.1	P11532	OTTHUMG00000021336	ENST00000357033.4:c.10027delT	chrX.hg19:g.31198546delA	ENSP00000354923:p.Ser3343fs	261.0	0.0		221.0	14.0	NM_004006	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Frame_Shift_Del	DEL	ENST00000357033.4	hg19	CCDS14233.1																																																																																			.	.		0.408	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006	
NRIP1	8204	hgsc.bcm.edu	37	21	16339766	16339766	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr21:16339766delT	ENST00000400202.1	-	3	1460	c.748delA	c.(748-750)aggfs	p.R250fs	NRIP1_ENST00000318948.4_Frame_Shift_Del_p.R250fs|NRIP1_ENST00000400199.1_Frame_Shift_Del_p.R250fs			P48552	NRIP1_HUMAN	nuclear receptor interacting protein 1	250	Interaction with ZNF366.|Repression domain 1.				androgen receptor signaling pathway (GO:0030521)|lipid storage (GO:0019915)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|ovarian follicle rupture (GO:0001543)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|histone deacetylase complex (GO:0000118)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|estrogen receptor binding (GO:0030331)|glucocorticoid receptor binding (GO:0035259)|nuclear hormone receptor binding (GO:0035257)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			cervix(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(6)|lung(13)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	39				Epithelial(23;1.19e-05)|all cancers(11;4.64e-05)|COAD - Colon adenocarcinoma(22;0.000232)|Colorectal(24;0.0006)|OV - Ovarian serous cystadenocarcinoma(11;0.00418)|Lung(58;0.199)|LUSC - Lung squamous cell carcinoma(23;0.24)		GGACTAGCCCTTTTTTCCACC	0.468																																					p.R250fs		Atlas-INDEL	.											.	NRIP1	103	.	0			c.749delG						.						187.0	164.0	172.0					21																	16339766		2203	4300	6503	SO:0001589	frameshift_variant	8204	exon4			.	X84373	CCDS13568.1	21q11.2	2008-07-31			ENSG00000180530	ENSG00000180530			8001	protein-coding gene	gene with protein product	"""receptor interacting protein 140"", ""nuclear factor RIP140"""	602490				7641693, 9521594	Standard	NM_003489		Approved	RIP140	uc002yjx.2	P48552	OTTHUMG00000074323	ENST00000400202.1:c.748delA	chr21.hg19:g.16339766delT	ENSP00000383063:p.Arg250fs	177.0	0.0		144.0	12.0	NM_003489	Q8IWE8	Frame_Shift_Del	DEL	ENST00000400202.1	hg19	CCDS13568.1																																																																																			.	.		0.468	NRIP1-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157926.1	NM_003489	
RHOBTB3	22836	hgsc.bcm.edu	37	5	95099309	95099309	+	Frame_Shift_Del	DEL	A	A	-	rs539979625		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:95099309delA	ENST00000379982.3	+	7	1654	c.1146delA	c.(1144-1146)ttafs	p.L382fs	GLRX_ENST00000508780.1_Intron	NM_014899.3	NP_055714.3	O94955	RHBT3_HUMAN	Rho-related BTB domain containing 3	382					ATP catabolic process (GO:0006200)|retrograde transport, endosome to Golgi (GO:0042147)|small GTPase mediated signal transduction (GO:0007264)	Golgi apparatus (GO:0005794)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|GTP binding (GO:0005525)|Rab GTPase binding (GO:0017137)			breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(5)|skin(1)	16		all_cancers(142;2.58e-06)|all_epithelial(76;4.19e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.0164)|Colorectal(57;0.0846)|Breast(839;0.198)		all cancers(79;8.79e-16)		AATGCATTTTAAAAACACCAG	0.328																																					p.L382X		Atlas-INDEL	.											.	RHOBTB3	43	.	0			c.1145delT						.						85.0	88.0	87.0					5																	95099309		2203	4299	6502	SO:0001589	frameshift_variant	22836	exon7			.	AB020685	CCDS4077.1	5q15	2014-05-09			ENSG00000164292	ENSG00000164292		"""BTB/POZ domain containing"""	18757	protein-coding gene	gene with protein product		607353				11222756, 17035353	Standard	NM_014899		Approved	KIAA0878	uc003klm.3	O94955	OTTHUMG00000121171	ENST00000379982.3:c.1146delA	chr5.hg19:g.95099309delA	ENSP00000369318:p.Leu382fs	219.0	0.0		172.0	11.0	NM_014899	A0PJA4|A8K1W9|Q8IW06	Frame_Shift_Del	DEL	ENST00000379982.3	hg19	CCDS4077.1																																																																																			.	.		0.328	RHOBTB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241658.1	NM_014899	
ZNF157	7712	hgsc.bcm.edu	37	X	47271956	47271956	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:47271956delT	ENST00000377073.3	+	4	570	c.484delT	c.(484-486)tttfs	p.F162fs		NM_003446.3	NP_003437.2	P51786	ZN157_HUMAN	zinc finger protein 157	162					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(5)|upper_aerodigestive_tract(1)	11						AGATAAAAACTTTGAATGTCA	0.393																																					p.N161fs		Atlas-INDEL	.											.	ZNF157	46	.	0			c.483delC						.						71.0	60.0	64.0					X																	47271956		2203	4300	6503	SO:0001589	frameshift_variant	7712	exon4			.	U28687	CCDS14278.1	Xp11.2	2013-01-08	2006-08-22		ENSG00000147117	ENSG00000147117		"""Zinc fingers, C2H2-type"", ""-"""	12942	protein-coding gene	gene with protein product		300024	"""zinc finger protein 157 (HZF22)"""			8586441	Standard	NM_003446		Approved	HZF22	uc004dhr.1	P51786	OTTHUMG00000021443	ENST00000377073.3:c.484delT	chrX.hg19:g.47271956delT	ENSP00000366273:p.Phe162fs	182.0	0.0		162.0	10.0	NM_003446	Q96LE9	Frame_Shift_Del	DEL	ENST00000377073.3	hg19	CCDS14278.1																																																																																			.	.		0.393	ZNF157-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056415.1	NM_003446	
FARP1	10160	hgsc.bcm.edu	37	13	99092237	99092237	+	Frame_Shift_Del	DEL	G	G	-	rs201529177		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr13:99092237delG	ENST00000319562.6	+	22	2721	c.2456delG	c.(2455-2457)tggfs	p.W819fs	FARP1_ENST00000595437.1_Frame_Shift_Del_p.W850fs|FARP1_ENST00000376586.2_Frame_Shift_Del_p.W850fs	NM_005766.2	NP_005757.1	Q9Y4F1	FARP1_HUMAN	FERM, RhoGEF (ARHGEF) and pleckstrin domain protein 1 (chondrocyte-derived)	819	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.				dendrite morphogenesis (GO:0048813)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|synapse assembly (GO:0007416)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|synapse (GO:0045202)	Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|endometrium(6)|kidney(6)|large_intestine(13)|lung(16)|ovary(1)|skin(3)|urinary_tract(1)	49	all_neural(89;0.0982)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.233)			GAAGACGAGTGGGGGGTGCCC	0.617																																					p.W819fs		Atlas-INDEL	.											.	FARP1	207	.	0			c.2455delT						.						142.0	158.0	153.0					13																	99092237		2203	4300	6503	SO:0001589	frameshift_variant	10160	exon22			.	AB008430	CCDS9487.1, CCDS32000.1, CCDS66572.1	13q32.2	2013-01-10			ENSG00000152767	ENSG00000152767		"""Rho guanine nucleotide exchange factors"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Pleckstrin homology (PH) domain containing"""	3591	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 75"""	602654				9425278	Standard	NM_005766		Approved	CDEP, PLEKHC2, MGC87400, PPP1R75	uc001vnj.3	Q9Y4F1	OTTHUMG00000017248	ENST00000319562.6:c.2456delG	chr13.hg19:g.99092237delG	ENSP00000322926:p.Trp819fs	143.0	0.0		122.0	10.0	NM_005766	Q5JVI9|Q6IQ29	Frame_Shift_Del	DEL	ENST00000319562.6	hg19	CCDS9487.1																																																																																			.	.		0.617	FARP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045541.3	NM_005766	
CHD1	1105	hgsc.bcm.edu	37	5	98232103	98232103	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:98232103delT	ENST00000284049.3	-	11	1686	c.1537delA	c.(1537-1539)acafs	p.T513fs		NM_001270.2	NP_001261.2	O14646	CHD1_HUMAN	chromodomain helicase DNA binding protein 1	513	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|methylated histone binding (GO:0035064)			NS(1)|breast(4)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(12)|ovary(2)|pancreas(1)|prostate(7)|skin(3)|urinary_tract(2)	49		all_cancers(142;5.36e-08)|all_epithelial(76;6.97e-11)|Lung NSC(167;0.000693)|Prostate(80;0.000986)|all_lung(232;0.00119)|Ovarian(225;0.024)|Colorectal(57;0.117)		COAD - Colon adenocarcinoma(37;0.0717)	Epirubicin(DB00445)	GTCTGTATTGTTTTTCCAAGG	0.338																																					p.T513fs		Atlas-INDEL	.											.	CHD1	137	.	0			c.1538delC						.						81.0	86.0	84.0					5																	98232103		2203	4300	6503	SO:0001589	frameshift_variant	1105	exon11			.	AF006513	CCDS34204.1	5q15-q21	2008-07-18			ENSG00000153922	ENSG00000153922			1915	protein-coding gene	gene with protein product		602118				8460153, 9326634	Standard	XM_005271866		Approved		uc003knf.3	O14646	OTTHUMG00000162744	ENST00000284049.3:c.1537delA	chr5.hg19:g.98232103delT	ENSP00000284049:p.Thr513fs	206.0	0.0		167.0	11.0	NM_001270	Q17RZ3	Frame_Shift_Del	DEL	ENST00000284049.3	hg19	CCDS34204.1																																																																																			.	.		0.338	CHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370295.1	NM_001270	
CYP2S1	29785	hgsc.bcm.edu	37	19	41700601	41700601	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:41700601delT	ENST00000310054.4	+	2	546	c.330delT	c.(328-330)actfs	p.T110fs	CYP2S1_ENST00000542619.1_5'UTR	NM_030622.6	NP_085125.1	Q96SQ9	CP2S1_HUMAN	cytochrome P450, family 2, subfamily S, polypeptide 1	110					small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			breast(1)|endometrium(3)|large_intestine(3)|lung(5)|skin(2)	14						TGGAAGGGACTTTTGATGGCC	0.612																																					p.T110fs		Atlas-INDEL	.											.	CYP2S1	47	.	0			c.329delC						.						135.0	103.0	114.0					19																	41700601		2203	4300	6503	SO:0001589	frameshift_variant	29785	exon2			.	AA301039	CCDS12573.1	19q13.2	2013-11-11	2003-01-14		ENSG00000167600	ENSG00000167600		"""Cytochrome P450s"""	15654	protein-coding gene	gene with protein product		611529	"""cytochrome P450, subfamily IIS, polypeptide 1"""			11181079	Standard	NM_030622		Approved		uc002opw.3	Q96SQ9	OTTHUMG00000182721	ENST00000310054.4:c.330delT	chr19.hg19:g.41700601delT	ENSP00000308032:p.Thr110fs	328.0	0.0		229.0	14.0	NM_030622	Q9BZ66	Frame_Shift_Del	DEL	ENST00000310054.4	hg19	CCDS12573.1																																																																																			.	.		0.612	CYP2S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463287.1		
ATAD3B	83858	hgsc.bcm.edu	37	1	1431107	1431107	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:1431107delG	ENST00000308647.7	+	16	1973	c.1857delG	c.(1855-1857)atgfs	p.M619fs		NM_031921.4	NP_114127.3	Q5T9A4	ATD3B_HUMAN	ATPase family, AAA domain containing 3B	619						mitochondrial inner membrane (GO:0005743)	ATP binding (GO:0005524)			endometrium(2)|large_intestine(1)|lung(3)|ovary(1)|skin(2)|urinary_tract(1)	10	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;1.79e-36)|OV - Ovarian serous cystadenocarcinoma(86;3.94e-22)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.00461)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.145)		GCTCCTGGATGGGGACTGGGC	0.667																																					p.M619fs		Atlas-INDEL	.											.	ATAD3B	68	.	0			c.1856delT						.						40.0	41.0	41.0					1																	1431107		2201	4300	6501	SO:0001589	frameshift_variant	83858	exon16			.	AL834179	CCDS30.1	1p36.33	2010-04-21		2007-02-08	ENSG00000160072	ENSG00000160072		"""ATPases / AAA-type"""	24007	protein-coding gene	gene with protein product		612317				10574462	Standard	XM_005244806		Approved	TOB3, KIAA1273	uc001afv.3	Q5T9A4	OTTHUMG00000000577	ENST00000308647.7:c.1857delG	chr1.hg19:g.1431107delG	ENSP00000311766:p.Met619fs	324.0	0.0		225.0	14.0	NM_031921	A8K3H1|Q6ZRB5|Q9BUK4|Q9ULE7	Frame_Shift_Del	DEL	ENST00000308647.7	hg19	CCDS30.1																																																																																			.	.		0.667	ATAD3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001369.2	NM_031921	
ATAD2B	54454	hgsc.bcm.edu	37	2	24042637	24042637	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:24042637delT	ENST00000238789.5	-	17	2590	c.2247delA	c.(2245-2247)aaafs	p.K749fs	ATAD2B_ENST00000474583.1_5'UTR	NM_001242338.1|NM_017552.2	NP_001229267.1|NP_060022.1	Q9ULI0	ATD2B_HUMAN	ATPase family, AAA domain containing 2B	749						nucleus (GO:0005634)	ATP binding (GO:0005524)|lysine-acetylated histone binding (GO:0070577)			central_nervous_system(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GAAGGTAGGGTTTATGTATAG	0.294																																					p.P750fs		Atlas-Indel,Pindel	.											.	ATAD2B	110	.	0			c.2248delC						.						124.0	114.0	117.0					2																	24042637		1852	4095	5947	SO:0001589	frameshift_variant	54454	exon17			.	AB033066	CCDS46227.1	2p24.1-p23.3	2010-04-21		2007-02-08	ENSG00000119778	ENSG00000119778		"""ATPases / AAA-type"""	29230	protein-coding gene	gene with protein product		615347					Standard	XM_005264372		Approved	KIAA1240	uc002rek.4	Q9ULI0	OTTHUMG00000151902	ENST00000238789.5:c.2247delA	chr2.hg19:g.24042637delT	ENSP00000238789:p.Lys749fs	121.0	0.0		86.0	23.0	NM_017552	B9ZVQ5|Q6ZNA6|Q8N9E7	Frame_Shift_Del	DEL	ENST00000238789.5	hg19	CCDS46227.1																																																																																			.	.		0.294	ATAD2B-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324333.1	NM_017552	
RDX	5962	hgsc.bcm.edu	37	11	110126047	110126047	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:110126047delT	ENST00000343115.4	-	8	1081	c.762delA	c.(760-762)aaafs	p.K254fs	RDX_ENST00000544551.1_Frame_Shift_Del_p.K118fs|RDX_ENST00000405097.1_Frame_Shift_Del_p.K254fs|RDX_ENST00000528900.1_Intron|RDX_ENST00000530301.1_Intron|RDX_ENST00000528498.1_Frame_Shift_Del_p.K254fs	NM_001260494.1|NM_002906.3	NP_001247423.1|NP_002897.1	P35241	RADI_HUMAN	radixin	254	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				actin filament capping (GO:0051693)|apical protein localization (GO:0045176)|establishment of endothelial barrier (GO:0061028)|microvillus assembly (GO:0030033)|positive regulation of gene expression (GO:0010628)	apical part of cell (GO:0045177)|cell tip (GO:0051286)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|stereocilium (GO:0032420)|T-tubule (GO:0030315)	poly(A) RNA binding (GO:0044822)			endometrium(3)|kidney(2)|large_intestine(3)|lung(8)|skin(1)|urinary_tract(1)	18		all_cancers(61;7.18e-13)|all_epithelial(67;2.61e-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;1.13e-06)|BRCA - Breast invasive adenocarcinoma(274;9.75e-06)|all cancers(92;5.9e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0248)		TTATAACAAATTTTTTGTCAT	0.294																																					p.F255fs	Esophageal Squamous(55;25 1062 11040 28755 44273)	Atlas-INDEL	.											.	RDX	59	.	0			c.763delT						.						40.0	41.0	40.0					11																	110126047		2196	4284	6480	SO:0001589	frameshift_variant	5962	exon8			.	BC020751	CCDS8343.1, CCDS58171.1, CCDS58172.1, CCDS58173.1, CCDS58174.1	11q23	2008-03-17				ENSG00000137710			9944	protein-coding gene	gene with protein product		179410	"""deafness, autosomal recessive 24"""	DFNB24		8486357, 17226784	Standard	NM_001260492		Approved		uc031qdy.1	P35241		ENST00000343115.4:c.762delA	chr11.hg19:g.110126047delT	ENSP00000342830:p.Lys254fs	264.0	0.0		233.0	16.0	NM_001260493	A7YIJ8|A7YIK0|A7YIK3|B7Z9U6|F5H1A7|Q86Y61	Frame_Shift_Del	DEL	ENST00000343115.4	hg19	CCDS8343.1																																																																																			.	.		0.294	RDX-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000390535.2	NM_002906	
LNPEP	4012	hgsc.bcm.edu	37	5	96341897	96341897	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:96341897delT	ENST00000231368.5	+	10	2598	c.1906delT	c.(1906-1908)tttfs	p.F636fs	LNPEP_ENST00000395770.3_Frame_Shift_Del_p.F622fs	NM_005575.2	NP_005566.2	Q9UIQ6	LCAP_HUMAN	leucyl/cystinyl aminopeptidase	636					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cell-cell signaling (GO:0007267)|female pregnancy (GO:0007565)|membrane organization (GO:0061024)|protein catabolic process (GO:0030163)|protein polyubiquitination (GO:0000209)|proteolysis (GO:0006508)	cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|early endosome lumen (GO:0031905)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(10)|ovary(3)|skin(1)|urinary_tract(1)	34		all_cancers(142;7e-07)|all_epithelial(76;9.52e-10)|all_lung(232;0.00101)|Lung NSC(167;0.00137)|Ovarian(225;0.024)|Colorectal(57;0.0269)|Breast(839;0.244)		COAD - Colon adenocarcinoma(37;0.072)		AGAGAGATTCTTTTTAAATAT	0.358																																					p.F635fs		Atlas-INDEL	.											LNPEP,caecum,carcinoma,0,1	LNPEP	80	.	0			c.1905delC						.						73.0	80.0	78.0					5																	96341897		2202	4296	6498	SO:0001589	frameshift_variant	4012	exon10			.	D50810	CCDS4087.1, CCDS43346.1	5q15	2011-07-25			ENSG00000113441	ENSG00000113441	3.4.11.3		6656	protein-coding gene	gene with protein product	"""cystinyl aminopeptidase"", ""placental leucine aminopeptidase"""	151300				8550619	Standard	NM_175920		Approved	CAP, PLAP, P-LAP	uc003kmw.1	Q9UIQ6	OTTHUMG00000128719	ENST00000231368.5:c.1906delT	chr5.hg19:g.96341897delT	ENSP00000231368:p.Phe636fs	188.0	0.0		165.0	10.0	NM_005575	O00769|Q15145|Q59H76|Q9TNQ2|Q9TNQ3|Q9UIQ7	Frame_Shift_Del	DEL	ENST00000231368.5	hg19	CCDS4087.1																																																																																			.	.		0.358	LNPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250624.1	NM_005575	
FGFR3	2261	hgsc.bcm.edu	37	4	1803669	1803669	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:1803669delC	ENST00000260795.2	+	6	949	c.847delC	c.(847-849)cccfs	p.P283fs	FGFR3_ENST00000340107.4_Frame_Shift_Del_p.P283fs|FGFR3_ENST00000481110.2_Frame_Shift_Del_p.P283fs|FGFR3_ENST00000474521.1_3'UTR|FGFR3_ENST00000352904.1_Frame_Shift_Del_p.P283fs|FGFR3_ENST00000412135.2_Frame_Shift_Del_p.P283fs|FGFR3_ENST00000440486.2_Frame_Shift_Del_p.P283fs			P22607	FGFR3_HUMAN	fibroblast growth factor receptor 3	283	Ig-like C2-type 3.				alveolar secondary septum development (GO:0061144)|axonogenesis involved in innervation (GO:0060385)|bone maturation (GO:0070977)|bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|cell-cell signaling (GO:0007267)|central nervous system myelination (GO:0022010)|chondrocyte differentiation (GO:0002062)|chondrocyte proliferation (GO:0035988)|cochlea development (GO:0090102)|digestive tract morphogenesis (GO:0048546)|endochondral bone growth (GO:0003416)|endochondral ossification (GO:0001958)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell fate commitment (GO:0072148)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor apoptotic signaling pathway (GO:1902178)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inner ear receptor cell differentiation (GO:0060113)|insulin receptor signaling pathway (GO:0008286)|JAK-STAT cascade (GO:0007259)|lens fiber cell development (GO:0070307)|lens morphogenesis in camera-type eye (GO:0002089)|MAPK cascade (GO:0000165)|morphogenesis of an epithelium (GO:0002009)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of developmental growth (GO:0048640)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitosis (GO:0045839)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|protein autophosphorylation (GO:0046777)|response to axon injury (GO:0048678)|skeletal system development (GO:0001501)|somatic stem cell maintenance (GO:0035019)|substantia nigra development (GO:0021762)	cell surface (GO:0009986)|cytoplasmic side of plasma membrane (GO:0009898)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|protein tyrosine kinase activity (GO:0004713)	p.P283S(1)		NS(1)|central_nervous_system(5)|cervix(6)|endometrium(2)|haematopoietic_and_lymphoid_tissue(40)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|pancreas(2)|prostate(9)|skin(339)|soft_tissue(4)|testis(2)|upper_aerodigestive_tract(58)|urinary_tract(2607)	3091		Breast(71;0.212)|all_epithelial(65;0.241)	all cancers(2;0.000145)|OV - Ovarian serous cystadenocarcinoma(23;0.0019)|Epithelial(3;0.00221)|GBM - Glioblastoma multiforme(2;0.234)		Palifermin(DB00039)|Pazopanib(DB06589)|Ponatinib(DB08901)	TGACGCACAGCCCCACATCCA	0.672		1	"""Mis, T"""	"""IGH@, ETV6"""	"""bladder, MM, T-cell lymphoma"""		"""Hypochondroplasia, Thanatophoric dysplasia"""		Saethre-Chotzen syndrome;Muenke syndrome																												p.Q282fs		Atlas-INDEL	.		Dom	yes		4	4p16.3	2261	fibroblast growth factor receptor 3	yes	"""L, E"""	.	FGFR3	3320	.	1	Substitution - Missense(1)	urinary_tract(1)	c.846delG						.						50.0	44.0	46.0					4																	1803669		2203	4299	6502	SO:0001589	frameshift_variant	2261	exon7	Familial Cancer Database	Acrocephalosyndactyly type III;Muenke Nonsyndromic Coronal Craniosynostosis, FGFR3-related Craniosynostosis	.	M64347	CCDS3353.1, CCDS3354.1, CCDS54706.1	4p16.3	2013-01-11	2008-08-01		ENSG00000068078	ENSG00000068078		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"""	3690	protein-coding gene	gene with protein product		134934	"""achondroplasia, thanatophoric dwarfism"""	ACH		1847508	Standard	NM_000142		Approved	CEK2, JTK4, CD333	uc003gdu.2	P22607	OTTHUMG00000121148	ENST00000260795.2:c.847delC	chr4.hg19:g.1803669delC	ENSP00000260795:p.Pro283fs	234.0	0.0		148.0	11.0	NM_001163213	D3DVP9|D3DVQ0|Q14308|Q16294|Q16608|Q59FL9	Frame_Shift_Del	DEL	ENST00000260795.2	hg19	CCDS3353.1																																																																																			.	.		0.672	FGFR3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000241632.2	NM_000142	
CNOT4	4850	hgsc.bcm.edu	37	7	135106990	135106990	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:135106990delT	ENST00000315544.5	-	3	566	c.287delA	c.(286-288)aatfs	p.N96fs	CNOT4_ENST00000428680.2_Frame_Shift_Del_p.N96fs|CNOT4_ENST00000361528.4_Frame_Shift_Del_p.N96fs|CNOT4_ENST00000541284.1_Frame_Shift_Del_p.N96fs|CNOT4_ENST00000356162.4_Frame_Shift_Del_p.N96fs|CNOT4_ENST00000451834.1_Frame_Shift_Del_p.N96fs|CNOT4_ENST00000414802.1_Frame_Shift_Del_p.N96fs|CNOT4_ENST00000423368.2_Frame_Shift_Del_p.N96fs	NM_001190848.1	NP_001177777.1	O95628	CNOT4_HUMAN	CCR4-NOT transcription complex, subunit 4	96					gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|protein autoubiquitination (GO:0051865)|RNA metabolic process (GO:0016070)	cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(10)|prostate(1)|skin(1)	22						ATGTTTGCGATTTTCTGATAT	0.403																																					p.N96fs	Ovarian(51;766 1130 5502 35047 50875)	Atlas-INDEL	.											.	CNOT4	146	.	0			c.288delT						.						182.0	167.0	172.0					7																	135106990		1845	4085	5930	SO:0001589	frameshift_variant	4850	exon3			.	AF180475	CCDS43650.1, CCDS47719.1, CCDS55164.1, CCDS55165.1, CCDS55166.1, CCDS55167.1	7q33	2013-09-19			ENSG00000080802	ENSG00000080802		"""RNA binding motif (RRM) containing"""	7880	protein-coding gene	gene with protein product		604911		NOT4		10637334	Standard	NM_013316		Approved	CLONE243, NOT4H	uc011kpy.2	O95628	OTTHUMG00000155568	ENST00000315544.5:c.287delA	chr7.hg19:g.135106990delT	ENSP00000326731:p.Asn96fs	246.0	0.0		239.0	16.0	NM_001190850	B7Z6I4|E7ET38|F8VQP3|O95339|O95627|Q8IYM7|Q8NCL0|Q9NPQ1|Q9NZN6	Frame_Shift_Del	DEL	ENST00000315544.5	hg19	CCDS55166.1																																																																																			.	.		0.403	CNOT4-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_013316	
RPE65	6121	hgsc.bcm.edu	37	1	68905279	68905279	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:68905279delG	ENST00000262340.5	-	7	743	c.690delC	c.(688-690)cccfs	p.P230fs		NM_000329.2	NP_000320.1	Q16518	RPE65_HUMAN	retinal pigment epithelium-specific protein 65kDa	230					cellular response to electrical stimulus (GO:0071257)|detection of light stimulus involved in visual perception (GO:0050908)|insulin receptor signaling pathway (GO:0008286)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin gene expression (GO:0007468)|retina homeostasis (GO:0001895)|retina morphogenesis in camera-type eye (GO:0060042)|retinal metabolic process (GO:0042574)|retinoid metabolic process (GO:0001523)|visual perception (GO:0007601)|vitamin A metabolic process (GO:0006776)	endoplasmic reticulum (GO:0005783)|plasma membrane (GO:0005886)	all-trans-retinyl-ester hydrolase, 11-cis retinol forming activity (GO:0052885)|all-trans-retinyl-palmitate hydrolase, 11-cis retinol forming activity (GO:0052884)|metal ion binding (GO:0046872)|retinal isomerase activity (GO:0004744)			central_nervous_system(1)|kidney(3)|large_intestine(12)|lung(15)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	35						GGTCACTGCAGGGGAATTGTA	0.378																																					p.C231fs		Atlas-INDEL	.											.	RPE65	87	.	0			c.691delT						.						188.0	180.0	183.0					1																	68905279		2203	4300	6503	SO:0001589	frameshift_variant	6121	exon7			.	U18991	CCDS643.1	1p31	2014-05-13	2002-08-29		ENSG00000116745	ENSG00000116745	3.1.1.64		10294	protein-coding gene	gene with protein product	"""retinol isomerase"", ""all-trans-retinyl-palmitate hydrolase"", ""retinoid isomerohydrolase"", ""BCO family, member 3"""	180069	"""retinal pigment epithelium-specific protein (65kD)"""	RP20		8340400	Standard	XM_006710811		Approved	LCA2, rd12, BCO3	uc001dei.1	Q16518	OTTHUMG00000009208	ENST00000262340.5:c.690delC	chr1.hg19:g.68905279delG	ENSP00000262340:p.Pro230fs	231.0	0.0		145.0	10.0	NM_000329	A8K1L0|Q5T9U3	Frame_Shift_Del	DEL	ENST00000262340.5	hg19	CCDS643.1																																																																																			.	.		0.378	RPE65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025509.1	NM_000329	
CNP	1267	hgsc.bcm.edu	37	17	40123969	40123969	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:40123969delC	ENST00000393892.3	+	3	880	c.736delC	c.(736-738)cccfs	p.P247fs	CNP_ENST00000591072.1_Frame_Shift_Del_p.P12fs|CNP_ENST00000393888.1_Frame_Shift_Del_p.P227fs|CNP_ENST00000472031.1_Frame_Shift_Del_p.D21fs	NM_033133.4	NP_149124.3	P09543	CN37_HUMAN	2',3'-cyclic nucleotide 3' phosphodiesterase	247					adult locomotory behavior (GO:0008344)|aging (GO:0007568)|axonogenesis (GO:0007409)|cyclic nucleotide catabolic process (GO:0009214)|microtubule cytoskeleton organization (GO:0000226)|oligodendrocyte differentiation (GO:0048709)|regulation of mitochondrial membrane permeability (GO:0046902)|response to lipopolysaccharide (GO:0032496)|response to toxic substance (GO:0009636)|substantia nigra development (GO:0021762)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|microtubule (GO:0005874)|microvillus (GO:0005902)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|myelin sheath abaxonal region (GO:0035748)|myelin sheath adaxonal region (GO:0035749)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|pseudopodium (GO:0031143)	2',3'-cyclic-nucleotide 3'-phosphodiesterase activity (GO:0004113)|cyclic nucleotide binding (GO:0030551)|RNA binding (GO:0003723)			breast(1)|kidney(2)|large_intestine(1)|lung(4)|upper_aerodigestive_tract(1)	9		all_cancers(22;2.38e-06)|all_epithelial(22;6.79e-05)|Breast(137;0.000143)		UCEC - Uterine corpus endometrioid carcinoma (308;0.171)		TGGAAAGAGACCCCCAGGCGT	0.592																																					p.R245fs		Atlas-INDEL	.											.	CNP	58	.	0			c.735delA						.						56.0	58.0	57.0					17																	40123969		1986	4151	6137	SO:0001589	frameshift_variant	1267	exon3			.		CCDS11414.2	17q21	2008-02-05			ENSG00000173786	ENSG00000173786	3.1.4.37		2158	protein-coding gene	gene with protein product		123830				1322358	Standard	XM_006721701		Approved		uc002hyl.1	P09543	OTTHUMG00000133502	ENST00000393892.3:c.736delC	chr17.hg19:g.40123969delC	ENSP00000377470:p.Pro247fs	324.0	0.0		193.0	12.0	NM_033133		Frame_Shift_Del	DEL	ENST00000393892.3	hg19	CCDS11414.2																																																																																			.	.		0.592	CNP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257443.2		
LILRA1	11024	hgsc.bcm.edu	37	19	55105714	55105714	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:55105714delC	ENST00000251372.3	+	2	187	c.5delC	c.(4-6)accfs	p.T2fs	LILRB1_ENST00000418536.2_Intron|LILRA1_ENST00000473156.1_Intron|LILRA1_ENST00000453777.1_Frame_Shift_Del_p.T2fs|LILRB1_ENST00000448689.1_Intron|LILRB1_ENST00000396321.2_Intron	NM_006863.2	NP_006854.1	O75019	LIRA1_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 1	2					cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)|regulation of immune response (GO:0050776)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(5)|liver(1)|lung(23)|ovary(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)	47				GBM - Glioblastoma multiforme(193;0.0348)		GACGCTATGACCCCCATCGTC	0.587																																					p.T2fs		Atlas-INDEL	.											.	LILRA1	105	.	0			c.4delA						.						93.0	108.0	103.0					19																	55105714		2203	4300	6503	SO:0001589	frameshift_variant	11024	exon2			.	AF025530	CCDS12901.1, CCDS62802.1	19q13.4	2013-01-11			ENSG00000104974	ENSG00000104974		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6602	protein-coding gene	gene with protein product		604810				9548455	Standard	NM_006863		Approved	LIR-6, CD85i, LIR6	uc002qgh.2	O75019	OTTHUMG00000065701	ENST00000251372.3:c.5delC	chr19.hg19:g.55105714delC	ENSP00000251372:p.Thr2fs	254.0	0.0		216.0	15.0	NM_006863	O75018|Q3MJA6	Frame_Shift_Del	DEL	ENST00000251372.3	hg19	CCDS12901.1																																																																																			.	.		0.587	LILRA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140807.2	NM_006863	
IFNA17	3451	hgsc.bcm.edu	37	9	21227622	21227622	+	Frame_Shift_Del	DEL	A	A	-	rs9298814	byFrequency	TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:21227622delA	ENST00000413767.2	-	1	599	c.551delT	c.(550-552)atafs	p.I184fs		NM_021268.2	NP_067091.1	P01571	IFN17_HUMAN	interferon, alpha 17	184			I -> R (in dbSNP:rs9298814). {ECO:0000269|PubMed:3767336, ECO:0000269|PubMed:4008999, ECO:0000269|PubMed:9712362}.		adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|natural killer cell activation involved in immune response (GO:0002323)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|T cell activation involved in immune response (GO:0002286)|type I interferon signaling pathway (GO:0060337)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|type I interferon receptor binding (GO:0005132)			breast(1)|endometrium(2)|lung(4)|ovary(1)|skin(1)	9				Lung(24;2.13e-22)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.116)		CCTCCTTAATATTTTTTGCAA	0.378																																					p.I184fs		Atlas-INDEL	.											.	IFNA17	17	.	0			c.552delA	GRCh37	CM041015	IFNA17	M	rs9298814	.						112.0	143.0	133.0					9																	21227622		2197	4296	6493	SO:0001589	frameshift_variant	3451	exon1			.		CCDS6500.1	9p22	2010-12-10			ENSG00000234829	ENSG00000234829		"""Interferons"""	5422	protein-coding gene	gene with protein product		147583				1385305	Standard	NM_021268		Approved	LEIF2C1, IFN-alphaI	uc003zos.1	P01571	OTTHUMG00000019667	ENST00000413767.2:c.551delT	chr9.hg19:g.21227622delA	ENSP00000411940:p.Ile184fs	426.0	0.0		344.0	24.0	NM_021268	Q14639|Q4KMT4|Q5VZ53|Q7M4Q4	Frame_Shift_Del	DEL	ENST00000413767.2	hg19	CCDS6500.1																																																																																			.	.		0.378	IFNA17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051896.1	NM_021268	
GOLGA4	2803	hgsc.bcm.edu	37	3	37366955	37366955	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:37366955delA	ENST00000361924.2	+	14	3952	c.3578delA	c.(3577-3579)gaafs	p.E1193fs	GOLGA4_ENST00000356847.4_Frame_Shift_Del_p.E1215fs|GOLGA4_ENST00000444882.1_Intron	NM_002078.4	NP_002069.2	Q13439	GOGA4_HUMAN	golgin A4	1193	Glu-rich.				Golgi to plasma membrane protein transport (GO:0043001)|protein targeting to Golgi (GO:0000042)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	GTPase binding (GO:0051020)			NS(2)|breast(3)|central_nervous_system(3)|endometrium(6)|kidney(2)|large_intestine(17)|liver(2)|lung(16)|ovary(4)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	65						TCTTCACATGAAAAAAGTAAC	0.393																																					p.E1215fs		Atlas-INDEL	.											.	GOLGA4	173	.	0			c.3643delG						.						36.0	39.0	38.0					3																	37366955		2201	4296	6497	SO:0001589	frameshift_variant	2803	exon15			.	U31906	CCDS2666.1, CCDS54564.1	3p22-p21.3	2010-02-12	2010-02-12		ENSG00000144674	ENSG00000144674			4427	protein-coding gene	gene with protein product	"""golgin 245"""	602509	"""golgi autoantigen, golgin subfamily a, 4"""			8626529	Standard	NM_002078		Approved	GOLG, GCP2, p230, golgin-240	uc003cgw.3	Q13439	OTTHUMG00000130799	ENST00000361924.2:c.3578delA	chr3.hg19:g.37366955delA	ENSP00000354486:p.Glu1193fs	288.0	0.0		233.0	15.0	NM_001172713	F8W8Q7|Q13270|Q13654|Q14436|Q59EW8	Frame_Shift_Del	DEL	ENST00000361924.2	hg19	CCDS2666.1																																																																																			.	.		0.393	GOLGA4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253339.2	NM_002078	
SLC39A7	7922	hgsc.bcm.edu	37	6	33169107	33169107	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:33169107delG	ENST00000374677.3	+	1	458	c.85delG	c.(85-87)gggfs	p.G30fs	RXRB_ENST00000413614.2_5'Flank|RNY4P10_ENST00000365571.1_RNA|RXRB_ENST00000374685.4_5'Flank|RXRB_ENST00000374680.3_5'Flank|SLC39A7_ENST00000374675.3_Frame_Shift_Del_p.G30fs|RXRB_ENST00000544186.1_5'Flank	NM_006979.2	NP_008910.2	Q92504	S39A7_HUMAN	solute carrier family 39 (zinc transporter), member 7	30	His-rich.				transmembrane transport (GO:0055085)|zinc ion transport (GO:0006829)	endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	metal ion transmembrane transporter activity (GO:0046873)			NS(1)|breast(3)|endometrium(2)|large_intestine(5)|lung(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	18						GGCTGGACTCGGGGGTCATGA	0.647																																					p.L28fs		Atlas-INDEL	.											.	SLC39A7	32	.	0			c.84delC						.						57.0	66.0	63.0					6																	33169107		2069	4211	6280	SO:0001589	frameshift_variant	7922	exon2			.	AF117221	CCDS43453.1	6p21.3	2014-01-28		2003-10-27	ENSG00000112473	ENSG00000112473		"""Solute carriers"""	4927	protein-coding gene	gene with protein product		601416	"""HLA class II region expressed gene KE4"""	HKE4		8812499, 1855816, 19246244, 15705588	Standard	NM_006979		Approved	H2-KE4, D6S2244E, KE4, RING5, ZIP7	uc003odf.3	Q92504	OTTHUMG00000031238	ENST00000374677.3:c.85delG	chr6.hg19:g.33169107delG	ENSP00000363809:p.Gly30fs	204.0	0.0		157.0	11.0	NM_001077516	B0UXF6|Q5STP8|Q9UIQ0	Frame_Shift_Del	DEL	ENST00000374677.3	hg19	CCDS43453.1																																																																																			.	.		0.647	SLC39A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076499.2	NM_006979	
CYP4V2	285440	hgsc.bcm.edu	37	4	187130116	187130116	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:187130116delT	ENST00000378802.4	+	9	1492	c.1188delT	c.(1186-1188)cctfs	p.P396fs	CYP4V2_ENST00000502665.1_3'UTR	NM_207352.3	NP_997235.3	Q6ZWL3	CP4V2_HUMAN	cytochrome P450, family 4, subfamily V, polypeptide 2	396					fatty acid omega-oxidation (GO:0010430)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen (GO:0016705)			breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(9)|skin(1)|stomach(2)	20		all_cancers(14;4.27e-52)|all_epithelial(14;7.69e-39)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.0066)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.243)		OV - Ovarian serous cystadenocarcinoma(60;1.33e-10)|BRCA - Breast invasive adenocarcinoma(30;3.84e-05)|GBM - Glioblastoma multiforme(59;0.000132)|STAD - Stomach adenocarcinoma(60;0.000293)|LUSC - Lung squamous cell carcinoma(40;0.00242)|READ - Rectum adenocarcinoma(43;0.17)		CTTCTGTTCCTTTATTTGCCC	0.448																																					p.P396fs		Atlas-INDEL	.											.	CYP4V2	49	.	0			c.1187delC						.						179.0	169.0	172.0					4																	187130116		2203	4300	6503	SO:0001589	frameshift_variant	285440	exon9			.	AK022114	CCDS34119.1	4q35.2	2004-07-05			ENSG00000145476	ENSG00000145476		"""Cytochrome P450s"""	23198	protein-coding gene	gene with protein product		608614				15042513	Standard	NM_207352		Approved	CYP4AH1	uc003iyw.4	Q6ZWL3	OTTHUMG00000160379	ENST00000378802.4:c.1188delT	chr4.hg19:g.187130116delT	ENSP00000368079:p.Pro396fs	236.0	0.0		161.0	10.0	NM_207352	B7U6W2|Q6ZTM4	Frame_Shift_Del	DEL	ENST00000378802.4	hg19	CCDS34119.1																																																																																			.	.		0.448	CYP4V2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360398.1	XM_209612	
USP15	9958	hgsc.bcm.edu	37	12	62785098	62785098	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:62785098delA	ENST00000280377.5	+	16	2180	c.2122delA	c.(2122-2124)aaafs	p.K709fs	USP15_ENST00000393654.3_Frame_Shift_Del_p.K684fs|USP15_ENST00000353364.3_Frame_Shift_Del_p.K680fs	NM_001252078.1	NP_001239007.1	Q9Y4E8	UBP15_HUMAN	ubiquitin specific peptidase 15	709	USP.				BMP signaling pathway (GO:0030509)|monoubiquitinated protein deubiquitination (GO:0035520)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|protein deubiquitination (GO:0016579)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|identical protein binding (GO:0042802)|SMAD binding (GO:0046332)|transforming growth factor beta receptor binding (GO:0005160)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(8)|lung(15)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	37			GBM - Glioblastoma multiforme(1;0.000276)	GBM - Glioblastoma multiforme(28;0.0622)		CACGGGACACAAAAAACGATT	0.368																																					p.H707fs	Melanoma(181;615 2041 39364 49691 50001)	Atlas-INDEL	.											.	USP15	105	.	0			c.2121delC						.						116.0	114.0	115.0					12																	62785098		2203	4300	6503	SO:0001589	frameshift_variant	9958	exon16			.	AB011101	CCDS8963.1, CCDS58250.1, CCDS58251.1	12q14	2006-07-18	2005-08-08					"""Ubiquitin-specific peptidases"""	12613	protein-coding gene	gene with protein product		604731	"""ubiquitin specific protease 15"""			12838346	Standard	NM_001252078		Approved	KIAA0529, UNPH4	uc001src.2	Q9Y4E8	OTTHUMG00000170186	ENST00000280377.5:c.2122delA	chr12.hg19:g.62785098delA	ENSP00000280377:p.Lys709fs	213.0	0.0		164.0	11.0	NM_001252078	Q08AL5|Q9H8G9|Q9HCA6|Q9UNP0|Q9Y5B5	Frame_Shift_Del	DEL	ENST00000280377.5	hg19	CCDS58251.1																																																																																			.	.		0.368	USP15-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000407831.2	NM_006313	
MFSD1	64747	hgsc.bcm.edu	37	3	158524843	158524843	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:158524843delT	ENST00000264266.8	+	4	406	c.344delT	c.(343-345)attfs	p.I115fs	MFSD1_ENST00000415822.2_Frame_Shift_Del_p.I164fs|MFSD1_ENST00000392813.4_Frame_Shift_Del_p.I125fs			Q9H3U5	MFSD1_HUMAN	major facilitator superfamily domain containing 1	115					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(3)|lung(15)|skin(1)	26			Lung(72;0.00372)|LUSC - Lung squamous cell carcinoma(72;0.00523)			GGCACAATCATTTTTAGCTGC	0.308																																					p.I164fs	Pancreas(62;1186 1654 36636 37908)	Atlas-INDEL	.											.	MFSD1	88	.	0			c.490delA						.						112.0	104.0	107.0					3																	158524843		2203	4299	6502	SO:0001589	frameshift_variant	64747	exon4			.	BC017661	CCDS3185.1, CCDS3185.2, CCDS54666.1	3q25.32	2005-11-17			ENSG00000118855	ENSG00000118855			25874	protein-coding gene	gene with protein product							Standard	NM_022736		Approved	FLJ14153, UG0581B09	uc003fcl.2	Q9H3U5	OTTHUMG00000158835	ENST00000264266.8:c.344delT	chr3.hg19:g.158524843delT	ENSP00000264266:p.Ile115fs	378.0	0.0		269.0	17.0	NM_022736	B4DGJ8|B4DMR8|B4DU49|B4DWU1|C9JS94|J3KQL7|Q05C07|Q5XKJ1|Q8IVS1|Q8IXG4|Q9H7X1	Frame_Shift_Del	DEL	ENST00000264266.8	hg19																																																																																				.	.		0.308	MFSD1-018	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000470730.1	NM_022736	
HIPK1	204851	hgsc.bcm.edu	37	1	114515848	114515848	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:114515848delC	ENST00000369558.1	+	16	3579	c.3347delC	c.(3346-3348)gccfs	p.A1116fs	HIPK1_ENST00000369555.2_Frame_Shift_Del_p.A1071fs|HIPK1_ENST00000369554.2_Frame_Shift_Del_p.A1071fs|HIPK1_ENST00000369561.4_Frame_Shift_Del_p.A1082fs|HIPK1_ENST00000340480.4_Frame_Shift_Del_p.A742fs|HIPK1_ENST00000369553.1_Frame_Shift_Del_p.A722fs|HIPK1_ENST00000426820.2_Frame_Shift_Del_p.A1116fs|HIPK1_ENST00000406344.1_Frame_Shift_Del_p.A722fs			Q86Z02	HIPK1_HUMAN	homeodomain interacting protein kinase 1	1116					anterior/posterior pattern specification (GO:0009952)|definitive hemopoiesis (GO:0060216)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|endothelial cell apoptotic process (GO:0072577)|extrinsic apoptotic signaling pathway (GO:0097191)|eye development (GO:0001654)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|iris morphogenesis (GO:0061072)|lens induction in camera-type eye (GO:0060235)|neuron differentiation (GO:0030182)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|regulation of transcription, DNA-templated (GO:0006355)|regulation of tumor necrosis factor-mediated signaling pathway (GO:0010803)|retina layer formation (GO:0010842)|smoothened signaling pathway (GO:0007224)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|PML body (GO:0016605)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(15)|ovary(4)|prostate(2)	39	Lung SC(450;0.184)	all_cancers(81;4.5e-08)|all_epithelial(167;1.09e-07)|all_lung(203;1.53e-05)|Lung NSC(69;2.76e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		ACGTATGCTGCCCCGACTTCT	0.602																																					p.A1116fs		Atlas-INDEL	.											.	HIPK1	195	.	0			c.3346delG						.						175.0	156.0	163.0					1																	114515848		2203	4300	6503	SO:0001589	frameshift_variant	204851	exon16			.	AB089957	CCDS867.1, CCDS868.1, CCDS869.1, CCDS41370.1	1p13.1	2008-02-05			ENSG00000163349	ENSG00000163349			19006	protein-coding gene	gene with protein product		608003					Standard	NM_198268		Approved	KIAA0630, Myak, MGC26642, Nbak2, MGC33446, MGC33548	uc001eem.3	Q86Z02	OTTHUMG00000011983	ENST00000369558.1:c.3347delC	chr1.hg19:g.114515848delC	ENSP00000358571:p.Ala1116fs	203.0	0.0		162.0	11.0	NM_198268	A6NJ34|O75125|Q5SQL2|Q5SQL4|Q5SQL5|Q8IYD7|Q8NDN5|Q8NEB6|Q8TBZ1	Frame_Shift_Del	DEL	ENST00000369558.1	hg19	CCDS867.1																																																																																			.	.		0.602	HIPK1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000033127.1	NM_198268	
XIRP1	165904	hgsc.bcm.edu	37	3	39227535	39227535	+	Frame_Shift_Del	DEL	C	C	-	rs575108313		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:39227535delC	ENST00000340369.3	-	2	3630	c.3402delG	c.(3400-3402)gggfs	p.G1134fs	XIRP1_ENST00000421646.1_Intron|XIRP1_ENST00000396251.1_Intron	NM_194293.2	NP_919269.2	Q702N8	XIRP1_HUMAN	xin actin-binding repeat containing 1	1134					cardiac muscle cell development (GO:0055013)|negative regulation of cell proliferation (GO:0008285)|regulation of membrane potential (GO:0042391)|sarcomere organization (GO:0045214)	fascia adherens (GO:0005916)	poly(A) RNA binding (GO:0044822)			breast(4)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(14)|lung(22)|ovary(4)|pancreas(1)|prostate(2)|skin(6)	71				KIRC - Kidney renal clear cell carcinoma(284;0.0517)|Kidney(284;0.065)		TTGTCACCCACCCCCCAGGCA	0.607																																					p.W1135fs		Atlas-INDEL	.											.	XIRP1	173	.	0			c.3403delT						.						67.0	70.0	69.0					3																	39227535		2203	4300	6503	SO:0001589	frameshift_variant	165904	exon2			.	AW755250	CCDS2683.1, CCDS56245.1	3p21.33	2008-02-05	2007-06-27	2007-06-27	ENSG00000168334	ENSG00000168334			14301	protein-coding gene	gene with protein product		609777	"""cardiomyopathy associated 1"""	CMYA1		12203715, 15454575	Standard	NM_001198621		Approved	DKFZp451D042, Xin	uc003cjk.2	Q702N8	OTTHUMG00000131297	ENST00000340369.3:c.3402delG	chr3.hg19:g.39227535delC	ENSP00000343140:p.Gly1134fs	222.0	0.0		164.0	11.0	NM_194293	A0JP25|A4QPE2|Q68DF2|Q6ZTR3|Q702N9|Q8IVN7|Q8N1N3|Q8N904|Q8TCG7	Frame_Shift_Del	DEL	ENST00000340369.3	hg19	CCDS2683.1																																																																																			.	.		0.607	XIRP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254065.1	XM_093522	
XIRP2	129446	hgsc.bcm.edu	37	2	168108333	168108333	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:168108333delA	ENST00000409195.1	+	9	10520	c.10431delA	c.(10429-10431)agafs	p.R3477fs	XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409273.1_Frame_Shift_Del_p.R3255fs|XIRP2_ENST00000295237.9_Frame_Shift_Del_p.R3477fs|XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000409043.1_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	3302					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						AAGAAGTAAGAAAAAATTTTC	0.433																																					p.R3477fs		Atlas-INDEL	.											.,1	XIRP2	914	.	0			c.10430delG						.						58.0	59.0	58.0					2																	168108333		1856	4087	5943	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.10431delA	chr2.hg19:g.168108333delA	ENSP00000386840:p.Arg3477fs	208.0	0.0		175.0	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																																																																																			.	.		0.433	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381	
FMNL3	91010	hgsc.bcm.edu	37	12	50100871	50100871	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:50100871delG	ENST00000293590.5	-	1	326	c.93delC	c.(91-93)cccfs	p.P31fs	FMNL3_ENST00000335154.5_Frame_Shift_Del_p.P31fs|FMNL3_ENST00000352151.5_Frame_Shift_Del_p.P31fs|FMNL3_ENST00000550488.1_Frame_Shift_Del_p.P31fs			Q8IVF7	FMNL3_HUMAN	formin-like 3	31	GBD/FH3. {ECO:0000255|PROSITE- ProRule:PRU00579}.				actin cytoskeleton organization (GO:0030036)|cell migration (GO:0016477)|cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)	GTPase activating protein binding (GO:0032794)			breast(4)|endometrium(7)|kidney(2)|large_intestine(6)|lung(11)|ovary(2)|pancreas(2)|prostate(2)|skin(2)|stomach(1)	39						CCAGCTCACAGGGCTCAGGCA	0.716																																					p.C32fs		Atlas-INDEL	.											.	FMNL3	137	.	0			c.94delT						.						14.0	22.0	19.0					12																	50100871		2011	4175	6186	SO:0001589	frameshift_variant	91010	exon1			.	AK128195	CCDS41780.1, CCDS44874.1	12q13.12	2006-04-10							23698	protein-coding gene	gene with protein product						12684686	Standard	NM_198900		Approved	DKFZp762B245, MGC45819, WBP3	uc001ruv.1	Q8IVF7	OTTHUMG00000169651	ENST00000293590.5:c.93delC	chr12.hg19:g.50100871delG	ENSP00000293590:p.Pro31fs	321.0	0.0		228.0	14.0	NM_175736	B0JZA7|Q6ZRJ1	Frame_Shift_Del	DEL	ENST00000293590.5	hg19																																																																																				.	.		0.716	FMNL3-201	KNOWN	basic	protein_coding	protein_coding		NM_175736	
ATP13A2	23400	hgsc.bcm.edu	37	1	17312586	17312586	+	3'UTR	DEL	G	G	-	rs189334432	byFrequency	TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:17312586delG	ENST00000326735.8	-	0	3706				ATP13A2_ENST00000341676.5_Frame_Shift_Del_p.P1124fs|RP1-37C10.3_ENST00000446261.1_RNA|ATP13A2_ENST00000452699.1_3'UTR			Q9NQ11	AT132_HUMAN	ATPase type 13A2						cell death (GO:0008219)|cellular response to manganese ion (GO:0071287)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(11)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		Colorectal(325;0.000147)|Breast(348;0.00104)|Renal(390;0.00145)|Lung NSC(340;0.00566)|all_lung(284;0.00797)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|COAD - Colon adenocarcinoma(227;1.11e-05)|BRCA - Breast invasive adenocarcinoma(304;1.99e-05)|Kidney(64;0.000171)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00645)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.182)		GGGTGGTCTCGGGGGAGGAGT	0.647																																					p.P1124fs		Atlas-INDEL	.											.	ATP13A2	85	.	0			c.3372delG						.						50.0	54.0	53.0					1																	17312586		692	1591	2283	SO:0001624	3_prime_UTR_variant	23400	exon27			.	AL354615	CCDS175.1, CCDS44072.1, CCDS44073.1	1p36	2014-09-17			ENSG00000159363	ENSG00000159363		"""ATPases / P-type"", ""Parkinson disease"""	30213	protein-coding gene	gene with protein product		610513	"""Parkinson disease (autosomal recessive) 9 (Kufor-Rakeb syndrome)"""	PARK9		15381061, 16964263	Standard	XM_005245809		Approved	HSA9947, CLN12	uc001baa.2	Q9NQ11	OTTHUMG00000002293	ENST00000326735.8:c.*130C>-	chr1.hg19:g.17312586delG		247.0	0.0		160.0	10.0	NM_001141974	O75700|Q5JXY1|Q5JXY2|Q6S9Z9	Frame_Shift_Del	DEL	ENST00000326735.8	hg19	CCDS175.1																																																																																			.	.		0.647	ATP13A2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000006617.1	NM_022089	
ZNF585B	92285	hgsc.bcm.edu	37	19	37678072	37678072	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:37678072delT	ENST00000532828.2	-	5	618	c.367delA	c.(367-369)attfs	p.I123fs	ZNF585B_ENST00000531805.1_Frame_Shift_Del_p.I68fs|ZNF585B_ENST00000527838.1_Frame_Shift_Del_p.I123fs|ZNF585B_ENST00000312908.5_5'Flank|CTC-454I21.3_ENST00000585860.2_Intron	NM_152279.3	NP_689492.3	Q52M93	Z585B_HUMAN	zinc finger protein 585B	123					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(3)|endometrium(1)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)	29			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			CCAGAATAAATTTTTTGATCT	0.373																																					p.I123fs	Melanoma(93;882 1454 18863 28917 48427)	Atlas-INDEL	.											.	ZNF585B	91	.	0			c.368delT						.						59.0	64.0	62.0					19																	37678072		2202	4299	6501	SO:0001589	frameshift_variant	92285	exon5			.	AK027834	CCDS12500.1	19q13.13	2013-01-08				ENSG00000245680		"""Zinc fingers, C2H2-type"", ""-"""	30948	protein-coding gene	gene with protein product						12477932	Standard	NM_152279		Approved	FLJ14928, SZFP41	uc002ofq.3	Q52M93		ENST00000532828.2:c.367delA	chr19.hg19:g.37678072delT	ENSP00000433773:p.Ile123fs	206.0	0.0		191.0	16.0	NM_152279	Q8IZD3|Q96JW6	Frame_Shift_Del	DEL	ENST00000532828.2	hg19	CCDS12500.1																																																																																			.	.		0.373	ZNF585B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388272.2	NM_152279	
MARCH8	220972	hgsc.bcm.edu	37	10	45954578	45954578	+	Frame_Shift_Del	DEL	C	C	-	rs201346647		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:45954578delC	ENST00000319836.3	-	6	1310	c.561delG	c.(559-561)gggfs	p.G187fs	MARCH8_ENST00000395769.2_Frame_Shift_Del_p.G187fs|MARCH8_ENST00000395771.3_Frame_Shift_Del_p.G187fs|MARCH8_ENST00000453424.2_Frame_Shift_Del_p.G469fs|MARCH8_ENST00000476962.1_5'UTR	NM_145021.4	NP_659458.2	Q5T0T0	MARH8_HUMAN	membrane-associated ring finger (C3HC4) 8, E3 ubiquitin protein ligase	187					immune system process (GO:0002376)|protein polyubiquitination (GO:0000209)	cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(5)|lung(4)	12						CTGTTGCCTGCCCCTGCTTGA	0.532																																					p.Q188fs	NSCLC(102;658 1594 2173 16344 34808)	Atlas-INDEL	.											.	MARCH8	29	.	0			c.562delC						.						143.0	114.0	124.0					10																	45954578		2203	4300	6503	SO:0001589	frameshift_variant	220972	exon6			.	AL833316	CCDS7213.1, CCDS60519.1	10q11.22	2013-01-09	2012-02-23	2005-01-27	ENSG00000165406	ENSG00000165406		"""MARCH membrane-associated ring fingers"", ""RING-type (C3HC4) zinc fingers"""	23356	protein-coding gene	gene with protein product		613335	"""c-mir, cellular modulator of immune recognition"", ""membrane-associated ring finger (C3HC4) 8"""	MIR		12582153, 14722266	Standard	XM_005271804		Approved	c-MIR, MARCH-VIII, RNF178	uc001jch.2	Q5T0T0	OTTHUMG00000019345	ENST00000319836.3:c.561delG	chr10.hg19:g.45954578delC	ENSP00000317087:p.Gly187fs	196.0	0.0		126.0	10.0	NM_001002266	B2R8E7|H0Y7C6|Q5T0S8|Q8TC72	Frame_Shift_Del	DEL	ENST00000319836.3	hg19	CCDS7213.1																																																																																			.	.		0.532	MARCH8-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051217.1	NM_145021	
C2CD5	9847	hgsc.bcm.edu	37	12	22666279	22666279	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:22666279delC	ENST00000333957.4	-	9	1242	c.987delG	c.(985-987)gggfs	p.G329fs	C2CD5_ENST00000396028.2_Frame_Shift_Del_p.G320fs|C2CD5_ENST00000545552.1_Frame_Shift_Del_p.G320fs|C2CD5_ENST00000536386.1_Frame_Shift_Del_p.G320fs|C2CD5_ENST00000542676.1_Frame_Shift_Del_p.G329fs|C2CD5_ENST00000446597.1_Frame_Shift_Del_p.G329fs|C2CD5_ENST00000544930.1_Frame_Shift_Del_p.G122fs	NM_014802.1	NP_055617.1	Q86YS7	C2CD5_HUMAN	C2 calcium-dependent domain containing 5	329					cellular response to insulin stimulus (GO:0032869)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|intracellular protein transmembrane transport (GO:0065002)|positive regulation of glucose transport (GO:0010828)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of vesicle fusion (GO:0031340)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)										CTTTAAAGGGCCCCCCTTCTT	0.363																																					p.P330fs		Atlas-INDEL	.											.	.	.	.	0			c.988delC						.						144.0	133.0	137.0					12																	22666279		2203	4300	6503	SO:0001589	frameshift_variant	9847	exon9			.	AB011100	CCDS31758.1, CCDS66337.1, CCDS66338.1, CCDS66339.1, CCDS66340.1	12p12.1	2012-12-13	2012-12-13	2012-12-13	ENSG00000111731	ENSG00000111731			29062	protein-coding gene	gene with protein product	"""138 kDa C2 domain-containing phosphoprotein"""		"""KIAA0528"""	KIAA0528		21907143	Standard	XM_005253538		Approved	CDP138	uc001rfq.3	Q86YS7	OTTHUMG00000169100	ENST00000333957.4:c.987delG	chr12.hg19:g.22666279delC	ENSP00000334229:p.Gly329fs	180.0	0.0		163.0	11.0	NM_014802	B4DJ03|B4DRN7|B7ZLL0|F5H2A1|F5H5R1|O60280|Q17RY7|Q7Z619|Q86SU3	Frame_Shift_Del	DEL	ENST00000333957.4	hg19	CCDS31758.1																																																																																			.	.		0.363	C2CD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402257.1	NM_014802	
ZNF480	147657	hgsc.bcm.edu	37	19	52824876	52824876	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:52824876delA	ENST00000595962.1	+	5	439	c.373delA	c.(373-375)aaafs	p.K126fs	ZNF480_ENST00000335090.6_Frame_Shift_Del_p.K49fs|ZNF480_ENST00000334564.7_Frame_Shift_Del_p.K83fs|CTD-2525I3.6_ENST00000594379.1_RNA|ZNF480_ENST00000490272.1_Frame_Shift_Del_p.L39fs	NM_144684.2	NP_653285.2	Q8WV37	ZN480_HUMAN	zinc finger protein 480	126					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			endometrium(2)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	12				GBM - Glioblastoma multiforme(134;0.00212)|OV - Ovarian serous cystadenocarcinoma(262;0.00369)		CAAACCAATTAAAAAACAACT	0.363																																					p.I124fs		Atlas-INDEL	.											.	ZNF480	123	.	0			c.372delT						.						73.0	69.0	70.0					19																	52824876		2203	4300	6503	SO:0001589	frameshift_variant	147657	exon5			.	AY512662	CCDS12850.2, CCDS74437.1	19q13.41	2013-01-08			ENSG00000198464	ENSG00000198464		"""Zinc fingers, C2H2-type"", ""-"""	23305	protein-coding gene	gene with protein product		613910				15219843	Standard	XM_005258525		Approved	MGC32104	uc010ydl.2	Q8WV37	OTTHUMG00000157507	ENST00000595962.1:c.373delA	chr19.hg19:g.52824876delA	ENSP00000471754:p.Lys126fs	127.0	0.0		104.0	12.0	NM_144684	Q5JPG9|Q6P0Q4|Q8N1M5	Frame_Shift_Del	DEL	ENST00000595962.1	hg19	CCDS12850.2																																																																																			.	.		0.363	ZNF480-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349001.3	NM_144684	
SPAG1	6674	hgsc.bcm.edu	37	8	101237506	101237506	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:101237506delA	ENST00000388798.2	+	14	1985	c.1794delA	c.(1792-1794)gcafs	p.A598fs	SPAG1_ENST00000523302.1_3'UTR|SPAG1_ENST00000251809.3_Frame_Shift_Del_p.A598fs	NM_003114.4	NP_003105.2	Q07617	SPAG1_HUMAN	sperm associated antigen 1	598					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)		GGCATCCGGCAAAAGAGATGA	0.522																																					p.A598fs		Atlas-INDEL	.											.	SPAG1	80	.	0			c.1793delC						.						56.0	52.0	54.0					8																	101237506		2203	4300	6503	SO:0001589	frameshift_variant	6674	exon14			.	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.1794delA	chr8.hg19:g.101237506delA	ENSP00000373450:p.Ala598fs	156.0	0.0		166.0	11.0	NM_172218	A6NP70|B3KQ58|G3XAM3|Q7Z5G1	Frame_Shift_Del	DEL	ENST00000388798.2	hg19	CCDS34930.1																																																																																			.	.		0.522	SPAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379853.2	NM_172218	
CEP128	145508	hgsc.bcm.edu	37	14	81227952	81227952	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr14:81227952delT	ENST00000555265.1	-	17	2757	c.2382delA	c.(2380-2382)aaafs	p.K794fs	CEP128_ENST00000281129.3_Frame_Shift_Del_p.K794fs			Q6ZU80	CE128_HUMAN	centrosomal protein 128kDa	794						centriole (GO:0005814)|cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|spindle pole (GO:0000922)				NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(22)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	51						TGCTTATATGTTTTTCCTAAG	0.383																																					p.H795fs		Atlas-INDEL	.											.	CEP128	146	.	0			c.2383delC						.						94.0	82.0	86.0					14																	81227952		2203	4300	6503	SO:0001589	frameshift_variant	145508	exon16			.	AK056756	CCDS32130.1	14q31.1	2014-02-20	2011-05-06	2011-05-06	ENSG00000100629	ENSG00000100629			20359	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 61"", ""chromosome 14 open reading frame 145"""	C14orf61, C14orf145		21399614	Standard	NM_152446		Approved		uc001xux.2	Q6ZU80		ENST00000555265.1:c.2382delA	chr14.hg19:g.81227952delT	ENSP00000451162:p.Lys794fs	234.0	0.0		173.0	12.0	NM_152446	B9EK52|Q86X97|Q96ML4	Frame_Shift_Del	DEL	ENST00000555265.1	hg19	CCDS32130.1																																																																																			.	.		0.383	CEP128-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413415.1	NM_152446	
NCOA3	8202	hgsc.bcm.edu	37	20	46252672	46252672	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr20:46252672delA	ENST00000371998.3	+	4	292	c.101delA	c.(100-102)gaafs	p.E34fs	NCOA3_ENST00000371997.3_Frame_Shift_Del_p.E34fs|NCOA3_ENST00000341724.6_Frame_Shift_Del_p.E34fs|NCOA3_ENST00000372004.3_Frame_Shift_Del_p.E34fs			Q9Y6Q9	NCOA3_HUMAN	nuclear receptor coactivator 3	34	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				androgen receptor signaling pathway (GO:0030521)|developmental growth (GO:0048589)|histone acetylation (GO:0016573)|labyrinthine layer morphogenesis (GO:0060713)|mammary gland branching involved in thelarche (GO:0060744)|multicellular organism growth (GO:0035264)|positive regulation of gene expression (GO:0010628)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|receptor transactivation (GO:0035624)|regulation of RNA biosynthetic process (GO:2001141)|transcription, DNA-templated (GO:0006351)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|protein N-terminus binding (GO:0047485)|signal transducer activity (GO:0004871)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)			breast(3)|endometrium(3)|kidney(4)|large_intestine(12)|lung(19)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	52						TGCAGTGGTGAAAAACGGAGA	0.398																																					p.E34fs		Atlas-INDEL	.											.	NCOA3	156	.	0			c.100delG						.						64.0	68.0	67.0					20																	46252672		2203	4300	6503	SO:0001589	frameshift_variant	8202	exon4			.	AF012108	CCDS13406.1, CCDS13407.1, CCDS54472.1	20q12	2011-07-01			ENSG00000124151	ENSG00000124151		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Basic helix-loop-helix proteins"""	7670	protein-coding gene	gene with protein product	"""receptor-associated coactivator 3"", ""thyroid hormone receptor activator molecule 1"""	601937				9252329, 9346901	Standard	NM_181659		Approved	RAC3, AIB1, ACTR, p/CIP, TRAM-1, CAGH16, TNRC16, KAT13B, bHLHe42, SRC-3, SRC3	uc002xtk.3	Q9Y6Q9	OTTHUMG00000033061	ENST00000371998.3:c.101delA	chr20.hg19:g.46252672delA	ENSP00000361066:p.Glu34fs	225.0	0.0		180.0	11.0	NM_181659	A4LAZ5|Q0VF45|Q5JYD9|Q5JYE0|Q9BR49|Q9UPC9|Q9UPG4|Q9UPG7	Frame_Shift_Del	DEL	ENST00000371998.3	hg19	CCDS13407.1																																																																																			.	.		0.398	NCOA3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080405.1	NM_006534	
BACH1	571	hgsc.bcm.edu	37	21	30701858	30701858	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr21:30701858delT	ENST00000399921.1	+	4	1863	c.1620delT	c.(1618-1620)gatfs	p.D540fs	BACH1_ENST00000286800.3_Frame_Shift_Del_p.D540fs	NM_206866.1	NP_996749.1	Q9BX63	FANCJ_HUMAN	BTB and CNC homology 1, basic leucine zipper transcription factor 1	0			Q -> L (in dbSNP:rs4988349). {ECO:0000269|PubMed:12872252}.		DNA damage checkpoint (GO:0000077)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(5)|kidney(2)|large_intestine(8)|liver(1)|lung(7)|ovary(1)|urinary_tract(2)	27						CTCGAAATGATTTTCAGTCCT	0.328																																					p.D540fs		Atlas-INDEL	.											.	BACH1	66	.	0			c.1619delA						.						74.0	71.0	72.0					21																	30701858		2203	4300	6503	SO:0001589	frameshift_variant	571	exon4			.	AF026200	CCDS13585.1	21q22.1	2013-01-10			ENSG00000156273	ENSG00000156273		"""BTB/POZ domain containing"", ""basic leucine zipper proteins"""	935	protein-coding gene	gene with protein product		602751				9544839, 9479503	Standard	NR_027655		Approved	BACH-1, BTBD24	uc002ynj.3	O14867	OTTHUMG00000078878	ENST00000399921.1:c.1620delT	chr21.hg19:g.30701858delT	ENSP00000382805:p.Asp540fs	301.0	0.0		181.0	12.0	NM_206866	Q3MJE2|Q8NCI5	Frame_Shift_Del	DEL	ENST00000399921.1	hg19	CCDS13585.1																																																																																			.	.		0.328	BACH1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171974.1	NM_206866	
LMBRD1	55788	hgsc.bcm.edu	37	6	70411386	70411386	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:70411386delA	ENST00000370577.3	-	11	1261	c.1032delT	c.(1030-1032)tttfs	p.F344fs	LMBRD1_ENST00000370570.1_Frame_Shift_Del_p.F271fs	NM_018368.3	NP_060838.3	Q9NUN5	LMBD1_HUMAN	LMBR1 domain containing 1	344					cobalamin metabolic process (GO:0009235)|insulin receptor internalization (GO:0038016)|negative regulation of glucose import (GO:0046325)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of protein kinase B signaling (GO:0051898)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	clathrin-coated endocytic vesicle (GO:0045334)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cobalamin binding (GO:0031419)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(7)|lung(11)|ovary(2)|upper_aerodigestive_tract(1)	31						GGTTAGCTCCAAAAATTATGA	0.274																																					p.G345fs		Atlas-INDEL	.											LMBRD1,NS,carcinoma,0,1	LMBRD1	61	.	0			c.1033delG						.						57.0	58.0	57.0					6																	70411386		2199	4290	6489	SO:0001589	frameshift_variant	55788	exon11			.	AF113224	CCDS4969.1	6q13	2011-05-12	2005-07-25	2005-07-25	ENSG00000168216	ENSG00000168216			23038	protein-coding gene	gene with protein product		612625	"""chromosome 6 open reading frame 209"""	C6orf209		19136951	Standard	NM_018368		Approved	FLJ11240, bA810I22.1, cblF	uc003pfa.3	Q9NUN5	OTTHUMG00000014985	ENST00000370577.3:c.1032delT	chr6.hg19:g.70411386delA	ENSP00000359609:p.Phe344fs	209.0	0.0		148.0	10.0	NM_018368	A8K204|E1P531|Q5VUN6|Q86Y70|Q96FW4|Q9BY56|Q9NZD6	Frame_Shift_Del	DEL	ENST00000370577.3	hg19	CCDS4969.1																																																																																			.	.		0.274	LMBRD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041124.1	NM_018368	
SEZ6	124925	hgsc.bcm.edu	37	17	27284100	27284100	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:27284100delG	ENST00000317338.12	-	13	3083	c.2655delC	c.(2653-2655)cccfs	p.P885fs	SEZ6_ENST00000442608.3_Frame_Shift_Del_p.P885fs|SEZ6_ENST00000360295.9_Frame_Shift_Del_p.P885fs|PIPOX_ENST00000583215.1_Intron|SEZ6_ENST00000335960.6_Intron			Q53EL9	SEZ6_HUMAN	seizure related 6 homolog (mouse)	885	Sushi 5. {ECO:0000255|PROSITE- ProRule:PRU00302}.				adult locomotory behavior (GO:0008344)|cerebellar Purkinje cell layer development (GO:0021680)|negative regulation of dendrite development (GO:2000171)|positive regulation of dendrite development (GO:1900006)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of protein kinase C signaling (GO:0090036)|synapse maturation (GO:0060074)	apical dendrite (GO:0097440)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(4)|lung(11)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	29	Lung NSC(42;0.0137)		Epithelial(11;4.73e-06)|all cancers(11;2.91e-05)|BRCA - Breast invasive adenocarcinoma(11;8.06e-05)|OV - Ovarian serous cystadenocarcinoma(11;0.111)			TCCAATGCGAGGGGTGCCCAG	0.617																																					p.S886fs		Atlas-INDEL	.											.	SEZ6	61	.	0			c.2656delT						.						22.0	24.0	23.0					17																	27284100		2050	4181	6231	SO:0001589	frameshift_variant	124925	exon13			.	AY038048	CCDS45638.1, CCDS45639.1	17q11.2	2008-03-06	2001-11-28		ENSG00000063015	ENSG00000063015			15955	protein-coding gene	gene with protein product			"""seizure related gene 6 (mouse) homolog"""			17086543	Standard	NM_178860		Approved		uc002hdp.2	Q53EL9	OTTHUMG00000168010	ENST00000317338.12:c.2655delC	chr17.hg19:g.27284100delG	ENSP00000312942:p.Pro885fs	196.0	0.0		156.0	10.0	NM_001098635	B6ZDN1|Q8N701|Q8NB57|Q8ND50|Q8TD25|Q96NI5|Q96NQ3	Frame_Shift_Del	DEL	ENST00000317338.12	hg19	CCDS45639.1																																																																																			.	.		0.617	SEZ6-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397475.3		
IFT52	51098	hgsc.bcm.edu	37	20	42249541	42249541	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	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	259.0	0.0		208.0	13.0	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	
NKAIN1	79570	hgsc.bcm.edu	37	1	31656681	31656681	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:31656681delG	ENST00000373736.2	-	4	460	c.454delC	c.(454-456)ctgfs	p.L152fs	NKAIN1_ENST00000263693.1_Frame_Shift_Del_p.L108fs|NKAIN1_ENST00000528449.1_5'Flank|NKAIN1_ENST00000398657.2_Frame_Shift_Del_p.L81fs	NM_024522.2	NP_078798.2	Q4KMZ8	NKAI1_HUMAN	Na+/K+ transporting ATPase interacting 1	152						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|cervix(1)|endometrium(1)|kidney(2)|ovary(1)|prostate(1)	7		Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.127)|Breast(348;0.141)|all_neural(195;0.146)|Medulloblastoma(700;0.151)		STAD - Stomach adenocarcinoma(196;0.0184)|READ - Rectum adenocarcinoma(331;0.148)		AAGATCTGCAGGGCGCTGCTG	0.577																																					p.L152fs		Atlas-INDEL	.											.	NKAIN1	21	.	0			c.455delT						.						136.0	130.0	132.0					1																	31656681		2203	4300	6503	SO:0001589	frameshift_variant	79570	exon4			.	AK022712	CCDS339.1, CCDS339.2	1p35.2	2010-06-25	2007-10-04	2007-10-04	ENSG00000084628	ENSG00000084628		"""Na+/K+ transporting ATPase interacting"""	25743	protein-coding gene	gene with protein product		612871	"""family with sequence similarity 77, member C"""	FAM77C		17606467	Standard	NM_024522		Approved	FLJ12650	uc010ogd.2	Q4KMZ8	OTTHUMG00000003788	ENST00000373736.2:c.454delC	chr1.hg19:g.31656681delG	ENSP00000362841:p.Leu152fs	217.0	0.0		171.0	12.0	NM_024522	A2VDJ3|B7Z5F5|B7Z5W9|Q9H9M7	Frame_Shift_Del	DEL	ENST00000373736.2	hg19	CCDS339.2																																																																																			.	.		0.577	NKAIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010655.2	NM_024522	
SRSF12	135295	hgsc.bcm.edu	37	6	89827583	89827583	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:89827583delG	ENST00000452027.2	-	1	217	c.24delC	c.(22-24)cccfs	p.P8fs		NM_080743.4	NP_542781.3	Q8WXF0	SRS12_HUMAN	serine/arginine-rich splicing factor 12	8					cytoplasmic transport (GO:0016482)|mRNA 5'-splice site recognition (GO:0000395)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|spliceosomal tri-snRNP complex assembly (GO:0000244)	nucleoplasm (GO:0005654)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|RS domain binding (GO:0050733)|unfolded protein binding (GO:0051082)			autonomic_ganglia(1)|breast(1)|endometrium(2)|large_intestine(4)	8						GGGAGGTGTTGGGGGGCCTCG	0.711																																					p.N9fs		Atlas-INDEL	.											.	SRSF12	17	.	0			c.25delA						.						19.0	27.0	24.0					6																	89827583		2035	4179	6214	SO:0001589	frameshift_variant	135295	exon1			.	AF449428	CCDS47459.1	6q16.1	2013-02-12	2010-06-22	2010-06-22	ENSG00000154548	ENSG00000154548		"""Serine/arginine-rich splicing factors"", ""RNA binding motif (RRM) containing"""	21220	protein-coding gene	gene with protein product	"""splicing factor, arginine/serine-rich 19"", ""SR splicing factor 12"""		"""splicing factor, arginine/serine-rich 13B"""	SFRS13B		11684676, 20516191	Standard	NM_080743		Approved	SRrp35, SFRS19	uc021zcq.1	Q8WXF0	OTTHUMG00000015192	ENST00000452027.2:c.24delC	chr6.hg19:g.89827583delG	ENSP00000414302:p.Pro8fs	250.0	0.0		140.0	11.0	NM_080743	B2RA22|Q5T7K0|Q8WW25	Frame_Shift_Del	DEL	ENST00000452027.2	hg19	CCDS47459.1																																																																																			.	.		0.711	SRSF12-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041474.2	NM_080743	
C17orf75	64149	hgsc.bcm.edu	37	17	30660500	30660500	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:30660500delA	ENST00000577809.1	-	9	960	c.911delT	c.(910-912)ttafs	p.L304fs	C17orf75_ENST00000225805.4_Frame_Shift_Del_p.L304fs|RP11-227G15.3_ENST00000581915.1_RNA	NM_022344.3	NP_071739.2	Q9HAS0	NJMU_HUMAN	chromosome 17 open reading frame 75	304										ovary(1)	1		Breast(31;0.116)|Ovarian(249;0.182)	BRCA - Breast invasive adenocarcinoma(9;0.239)			GGCACCATTTAAAAAAGCTTG	0.338																																					p.L304fs		Atlas-INDEL	.											.	C17orf75	23	.	0			c.912delA						.						141.0	139.0	140.0					17																	30660500		1816	4073	5889	SO:0001589	frameshift_variant	64149	exon9			.	AB062437	CCDS58537.1	17q11.2	2013-01-21			ENSG00000108666	ENSG00000108666			30173	protein-coding gene	gene with protein product							Standard	NM_022344		Approved	NJMU-R1	uc002hhg.3	Q9HAS0		ENST00000577809.1:c.911delT	chr17.hg19:g.30660500delA	ENSP00000464275:p.Leu304fs	234.0	0.0		224.0	16.0	NM_022344	Q7Z2H4	Frame_Shift_Del	DEL	ENST00000577809.1	hg19	CCDS58537.1																																																																																			.	.		0.338	C17orf75-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447204.1	NM_022344	
TLR10	81793	hgsc.bcm.edu	37	4	38776490	38776490	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:38776490delT	ENST00000308973.4	-	4	1327	c.722delA	c.(721-723)aatfs	p.N241fs	TLR10_ENST00000506111.1_Frame_Shift_Del_p.N241fs|TLR10_ENST00000508334.1_Frame_Shift_Del_p.N241fs|TLR10_ENST00000361424.2_Frame_Shift_Del_p.N241fs|TLR10_ENST00000507953.1_5'Flank	NM_001017388.2|NM_001195107.1|NM_030956.3	NP_001017388.1|NP_001182036.1|NP_112218.2	Q9BXR5	TLR10_HUMAN	toll-like receptor 10	241			N -> H (in dbSNP:rs11096957). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of inflammatory response (GO:0050729)|regulation of cytokine secretion (GO:0050707)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor signaling pathway (GO:0002224)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(11)|prostate(1)|urinary_tract(2)	25						TGTCTTAGCATTTTCTAAACT	0.323																																					p.N241fs		Atlas-INDEL	.											.	TLR10	87	.	0			c.723delT						.						61.0	60.0	60.0					4																	38776490		2203	4300	6503	SO:0001589	frameshift_variant	81793	exon4			.	AF296673	CCDS3445.1	4p14	2009-11-23			ENSG00000174123	ENSG00000174123		"""CD molecules"""	15634	protein-coding gene	gene with protein product		606270				11267672	Standard	NM_030956		Approved	CD290	uc003gtk.3	Q9BXR5	OTTHUMG00000128578	ENST00000308973.4:c.722delA	chr4.hg19:g.38776490delT	ENSP00000308925:p.Asn241fs	129.0	0.0		120.0	10.0	NM_030956	A8K7L1|B3Y668|D1CS21|D1CS22|Q32MI7|Q32MI8|Q5FWG4|Q6UXL3	Frame_Shift_Del	DEL	ENST00000308973.4	hg19	CCDS3445.1																																																																																			.	.		0.323	TLR10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250430.1		
PLEKHG4B	153478	hgsc.bcm.edu	37	5	163580	163580	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:163580delC	ENST00000283426.6	+	11	2375	c.2325delC	c.(2323-2325)agcfs	p.S775fs		NM_052909.3	NP_443141.3	Q96PX9	PKH4B_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 4B	775							Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(1)|large_intestine(2)|lung(2)|prostate(3)|skin(3)	11			all cancers(22;0.0253)|Lung(60;0.113)	Kidney(1;0.119)		ATGCCAGGAGCCCCCCGGTCA	0.652																																					p.S775fs		Atlas-INDEL	.											.	PLEKHG4B	167	.	0			c.2324delG						.						25.0	28.0	27.0					5																	163580		2200	4300	6500	SO:0001589	frameshift_variant	153478	exon11			.	BC008352	CCDS34124.1	5p15.33	2013-01-11			ENSG00000153404	ENSG00000153404		"""Pleckstrin homology (PH) domain containing"""	29399	protein-coding gene	gene with protein product						11572484	Standard	NM_052909		Approved	KIAA1909	uc003jak.2	Q96PX9	OTTHUMG00000161570	ENST00000283426.6:c.2325delC	chr5.hg19:g.163580delC	ENSP00000283426:p.Ser775fs	167.0	0.0		193.0	12.0	NM_052909		Frame_Shift_Del	DEL	ENST00000283426.6	hg19	CCDS34124.1																																																																																			.	.		0.652	PLEKHG4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365359.1	NM_052909	
FBXO36	130888	hgsc.bcm.edu	37	2	230841022	230841022	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:230841022delA	ENST00000283946.3	+	2	180	c.162delA	c.(160-162)gcafs	p.A54fs	FBXO36_ENST00000373652.3_Frame_Shift_Del_p.A23fs|RNU6-1027P_ENST00000383998.1_RNA|FBXO36_ENST00000409992.1_Frame_Shift_Del_p.A54fs	NM_174899.4	NP_777559.3	Q8NEA4	FBX36_HUMAN	F-box protein 36	54										endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|ovary(1)	7		Renal(207;0.0112)|all_lung(227;0.0179)|Lung NSC(271;0.0804)|all_hematologic(139;0.103)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;7.56e-14)|all cancers(144;7.74e-11)|Lung(119;0.00488)|LUSC - Lung squamous cell carcinoma(224;0.008)		CTGGAGAAGCAAAAGAAACCC	0.338																																					p.A54fs		Atlas-INDEL	.											.	FBXO36	22	.	0			c.161delC						.						67.0	69.0	68.0					2																	230841022		2203	4300	6503	SO:0001589	frameshift_variant	130888	exon2			.	BC033935	CCDS2472.1	2q37.1	2008-02-05	2004-06-15		ENSG00000153832	ENSG00000153832		"""F-boxes /  ""other"""""	27020	protein-coding gene	gene with protein product		609105	"""F-box only protein 36"""			12477932	Standard	NM_174899		Approved	Fbx36, FLJ37592	uc002vqa.3	Q8NEA4	OTTHUMG00000133206	ENST00000283946.3:c.162delA	chr2.hg19:g.230841022delA	ENSP00000283946:p.Ala54fs	218.0	0.0		150.0	10.0	NM_174899	B3KVQ6|Q53TE6|Q8WWD4	Frame_Shift_Del	DEL	ENST00000283946.3	hg19	CCDS2472.1																																																																																			.	.		0.338	FBXO36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256919.2	NM_174899	
TMEM200B	399474	hgsc.bcm.edu	37	1	29447550	29447550	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:29447550delC	ENST00000420504.2	-	2	948	c.791delG	c.(790-792)ggcfs	p.G264fs	TMEM200B_ENST00000521452.1_Frame_Shift_Del_p.G264fs	NM_001171868.1	NP_001165339.1	Q69YZ2	T200B_HUMAN	transmembrane protein 200B	264						integral component of membrane (GO:0016021)				ovary(1)	1		Colorectal(325;3.46e-05)|Breast(348;0.00765)|Lung NSC(340;0.0153)|all_lung(284;0.0173)|all_neural(195;0.0199)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)|Medulloblastoma(700;0.123)		Colorectal(126;7.32e-08)|COAD - Colon adenocarcinoma(152;4.92e-06)|STAD - Stomach adenocarcinoma(196;0.00618)|BRCA - Breast invasive adenocarcinoma(304;0.0501)|READ - Rectum adenocarcinoma(331;0.0649)|KIRC - Kidney renal clear cell carcinoma(1967;0.126)		CTCCCCAAGGCCCAGATCCAG	0.637																																					p.G264fs		Atlas-INDEL	.											.	TMEM200B	9	.	0			c.792delC						.						26.0	28.0	28.0					1																	29447550		2203	4300	6503	SO:0001589	frameshift_variant	399474	exon2			.		CCDS30658.1	1p35	2007-12-18			ENSG00000253304	ENSG00000253304			33785	protein-coding gene	gene with protein product						15722956	Standard	NM_001003682		Approved	TTMB	uc001brn.2	Q69YZ2	OTTHUMG00000003658	ENST00000420504.2:c.791delG	chr1.hg19:g.29447550delC	ENSP00000428544:p.Gly264fs	236.0	0.0		192.0	12.0	NM_001171868	Q6P2G8|Q6P2Q5	Frame_Shift_Del	DEL	ENST00000420504.2	hg19	CCDS30658.1																																																																																			.	.		0.637	TMEM200B-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010377.2	NM_001003682	
PGC	5225	hgsc.bcm.edu	37	6	41708310	41708310	+	Frame_Shift_Del	DEL	C	C	-	rs572661097		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:41708310delC	ENST00000373025.3	-	6	748	c.686delG	c.(685-687)ggtfs	p.G229fs		NM_002630.3	NP_002621.1	P20142	PEPC_HUMAN	progastricsin (pepsinogen C)	229					digestion (GO:0007586)|proteolysis (GO:0006508)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	aspartic-type endopeptidase activity (GO:0004190)			endometrium(3)|kidney(1)|large_intestine(5)|lung(6)|skin(1)	16	Ovarian(28;0.0355)|Colorectal(47;0.121)		Epithelial(12;0.000132)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00507)			GCTATCCACACCCCCAAAGAC	0.602																																					p.G229fs		Atlas-INDEL	.											.	PGC	56	.	0			c.687delT						.						103.0	103.0	103.0					6																	41708310		2203	4300	6503	SO:0001589	frameshift_variant	5225	exon6			.		CCDS4859.1, CCDS55000.1	6p21.1	2012-10-02			ENSG00000096088	ENSG00000096088	3.4.23.3		8890	protein-coding gene	gene with protein product		169740					Standard	NM_002630		Approved		uc003ora.2	P20142	OTTHUMG00000014683	ENST00000373025.3:c.686delG	chr6.hg19:g.41708310delC	ENSP00000362116:p.Gly229fs	153.0	0.0		147.0	13.0	NM_002630	B4DVZ3|Q5T3D7|Q5T3D8	Frame_Shift_Del	DEL	ENST00000373025.3	hg19	CCDS4859.1																																																																																			.	.		0.602	PGC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040521.2		
ZNF280B	140883	hgsc.bcm.edu	37	22	22842771	22842771	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr22:22842771delT	ENST00000406426.1	-	4	1695	c.953delA	c.(952-954)aatfs	p.N318fs	ZNF280B_ENST00000360412.2_Frame_Shift_Del_p.N318fs			Q86YH2	Z280B_HUMAN	zinc finger protein 280B	318					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			autonomic_ganglia(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(9)|ovary(2)	22	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.74e-30)|Acute lymphoblastic leukemia(6;7.75e-22)		READ - Rectum adenocarcinoma(21;0.145)		AAACTTAACATTTTTTAGAAC	0.463																																					p.N318fs		Atlas-INDEL	.											.	ZNF280B	67	.	0			c.954delT						.						139.0	130.0	133.0					22																	22842771		2203	4300	6503	SO:0001589	frameshift_variant	140883	exon4			.	AK097608	CCDS13799.1	22q11.2	2007-09-20	2007-09-20	2007-09-20	ENSG00000198477	ENSG00000275004			23022	protein-coding gene	gene with protein product			"""zinc finger protein 279"", ""suppressor of hairy wing homolog 2 (Drosophila)"""	ZNF279, SUHW2		9074928	Standard	NM_080764		Approved	5'OY11.1, ZNF632	uc002zwc.1	Q86YH2	OTTHUMG00000151066	ENST00000406426.1:c.953delA	chr22.hg19:g.22842771delT	ENSP00000385998:p.Asn318fs	204.0	0.0		166.0	12.0	NM_080764		Frame_Shift_Del	DEL	ENST00000406426.1	hg19	CCDS13799.1																																																																																			.	.		0.463	ZNF280B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321170.2	NM_080764	
ZNF518B	85460	hgsc.bcm.edu	37	4	10447095	10447095	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:10447095delT	ENST00000326756.3	-	3	1296	c.858delA	c.(856-858)aaafs	p.K286fs		NM_053042.2	NP_444270.2	Q9C0D4	Z518B_HUMAN	zinc finger protein 518B	286					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			breast(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(16)|ovary(3)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	42						AAACTACATCTTTTTGGTATT	0.358																																					p.D287fs		Atlas-INDEL	.											ZNF518B,mouth,carcinoma,0,1	ZNF518B	116	.	0			c.859delG						.						183.0	180.0	181.0					4																	10447095		2203	4300	6503	SO:0001589	frameshift_variant	85460	exon3			.	AB051516	CCDS33960.1	4p16.1	2007-12-07				ENSG00000178163		"""Zinc fingers, C2H2-type"""	29365	protein-coding gene	gene with protein product						11214970	Standard	XM_005248193		Approved	KIAA1729	uc003gmn.3	Q9C0D4		ENST00000326756.3:c.858delA	chr4.hg19:g.10447095delT	ENSP00000317614:p.Lys286fs	167.0	0.0		164.0	13.0	NM_053042	Q96LN8	Frame_Shift_Del	DEL	ENST00000326756.3	hg19	CCDS33960.1																																																																																			.	.		0.358	ZNF518B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359040.1	NM_053042	
JAK2	3717	hgsc.bcm.edu	37	9	5077574	5077574	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:5077574delT	ENST00000381652.3	+	15	2480	c.1986delT	c.(1984-1986)catfs	p.H662fs	JAK2_ENST00000539801.1_Frame_Shift_Del_p.H662fs|AL161450.1_ENST00000601793.1_Intron|JAK2_ENST00000544510.1_Frame_Shift_Del_p.H513fs	NM_004972.3	NP_004963.1	O60674	JAK2_HUMAN	Janus kinase 2	662	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin filament polymerization (GO:0030041)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097296)|activation of JAK2 kinase activity (GO:0042977)|activation of MAPKK activity (GO:0000186)|apoptotic process (GO:0006915)|axon regeneration (GO:0031103)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cellular component movement (GO:0006928)|cytokine-mediated signaling pathway (GO:0019221)|enzyme linked receptor protein signaling pathway (GO:0007167)|erythrocyte differentiation (GO:0030218)|extrinsic apoptotic signaling pathway (GO:0097191)|G-protein coupled receptor signaling pathway (GO:0007186)|growth hormone receptor signaling pathway (GO:0060396)|histone H3-Y41 phosphorylation (GO:0035409)|hormone-mediated signaling pathway (GO:0009755)|host programmed cell death induced by symbiont (GO:0034050)|interferon-gamma-mediated signaling pathway (GO:0060333)|interleukin-12-mediated signaling pathway (GO:0035722)|intracellular signal transduction (GO:0035556)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|mammary gland epithelium development (GO:0061180)|mesoderm development (GO:0007498)|mineralocorticoid receptor signaling pathway (GO:0031959)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of DNA binding (GO:0043392)|negative regulation of heart contraction (GO:0045822)|negative regulation of neuron apoptotic process (GO:0043524)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell activation (GO:0050867)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of DNA binding (GO:0043388)|positive regulation of growth hormone receptor signaling pathway (GO:0060399)|positive regulation of inflammatory response (GO:0050729)|positive regulation of insulin secretion (GO:0032024)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of inflammatory response (GO:0050727)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|response to antibiotic (GO:0046677)|response to hydroperoxide (GO:0033194)|response to interleukin-12 (GO:0070671)|response to lipopolysaccharide (GO:0032496)|response to tumor necrosis factor (GO:0034612)|signal transduction (GO:0007165)|STAT protein import into nucleus (GO:0007262)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|tyrosine phosphorylation of STAT protein (GO:0007260)|tyrosine phosphorylation of Stat1 protein (GO:0042508)|tyrosine phosphorylation of Stat3 protein (GO:0042503)|tyrosine phosphorylation of Stat5 protein (GO:0042506)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|endosome lumen (GO:0031904)|membrane raft (GO:0045121)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|heme binding (GO:0020037)|histone binding (GO:0042393)|histone kinase activity (H3-Y41 specific) (GO:0035401)|interleukin-12 receptor binding (GO:0005143)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein tyrosine kinase activity (GO:0004713)|receptor binding (GO:0005102)|SH2 domain binding (GO:0042169)		BCR/JAK2(6)|SSBP2/JAK2(4)|SEC31A/JAK2(4)|ETV6/JAK2(11)|PCM1/JAK2(30)|PAX5/JAK2(18)	breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(32944)|kidney(4)|large_intestine(10)|liver(1)|lung(20)|ovary(3)|prostate(4)|skin(2)|urinary_tract(1)	32998	all_hematologic(13;0.137)	Acute lymphoblastic leukemia(23;0.0198)|Breast(48;0.147)		GBM - Glioblastoma multiforme(50;0.0237)|Lung(218;0.133)	Ruxolitinib(DB08877)|Tofacitinib(DB08895)	GGGCCATGCATTTTCTAGTAA	0.244		1	"""T, Mis, O"""	"""ETV6, PCM1, BCR"""	"""ALL, AML, MPD,  CML"""				Polycythemia Vera, Familial																												p.H662fs		Atlas-INDEL	.		Dom	yes		9	9p24	3717	Janus kinase 2		L	.	JAK2	35466	.	0			c.1985delA						.						19.0	22.0	21.0					9																	5077574		2120	4217	6337	SO:0001589	frameshift_variant	3717	exon15	Familial Cancer Database		.		CCDS6457.1	9p24	2014-09-17	2009-04-23		ENSG00000096968	ENSG00000096968	2.7.10.1	"""SH2 domain containing"""	6192	protein-coding gene	gene with protein product		147796				1848670	Standard	NM_004972		Approved	JTK10	uc003ziw.3	O60674	OTTHUMG00000019490	ENST00000381652.3:c.1986delT	chr9.hg19:g.5077574delT	ENSP00000371067:p.His662fs	122.0	0.0		164.0	10.0	NM_004972	O14636|O75297	Frame_Shift_Del	DEL	ENST00000381652.3	hg19	CCDS6457.1																																																																																			.	.		0.244	JAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051609.1		
SMARCAD1	56916	hgsc.bcm.edu	37	4	95162076	95162076	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:95162076delA	ENST00000354268.4	+	6	697	c.624delA	c.(622-624)agafs	p.R208fs	SMARCAD1_ENST00000457823.2_Frame_Shift_Del_p.R208fs			Q9H4L7	SMRCD_HUMAN	SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1	208					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)		CCAGGAAAAGAAAATTATCTT	0.323																																					p.R208fs		Atlas-INDEL	.											.	SMARCAD1	97	.	0			c.623delG						.						64.0	66.0	65.0					4																	95162076		2203	4299	6502	SO:0001589	frameshift_variant	56916	exon6			.	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.624delA	chr4.hg19:g.95162076delA	ENSP00000346217:p.Arg208fs	278.0	0.0		189.0	12.0	NM_001128429	B7Z799|Q05D56|Q96SX1|Q9H017|Q9H860|Q9NPU9|Q9ULU7	Frame_Shift_Del	DEL	ENST00000354268.4	hg19	CCDS3639.1																																																																																			.	.		0.323	SMARCAD1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253583.1	NM_020159	
ZFYVE9	9372	hgsc.bcm.edu	37	1	52705235	52705235	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:52705235delA	ENST00000371591.1	+	3	2277	c.2146delA	c.(2146-2148)aaafs	p.K716fs	ZFYVE9_ENST00000287727.3_Frame_Shift_Del_p.K716fs|ZFYVE9_ENST00000357206.2_Frame_Shift_Del_p.K716fs	NM_004799.2|NM_007324.2	NP_004790.2|NP_015563.2	O95405	ZFYV9_HUMAN	zinc finger, FYVE domain containing 9	716					endocytosis (GO:0006897)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|proteolysis (GO:0006508)|SMAD protein complex assembly (GO:0007183)|SMAD protein import into nucleus (GO:0007184)|transforming growth factor beta receptor signaling pathway (GO:0007179)	early endosome (GO:0005769)|early endosome membrane (GO:0031901)	1-phosphatidylinositol binding (GO:0005545)|metal ion binding (GO:0046872)|serine-type peptidase activity (GO:0008236)			breast(1)|central_nervous_system(4)|endometrium(3)|kidney(1)|large_intestine(12)|lung(17)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	53						TACATTCACCAAAAGGAGGCA	0.443																																					p.T715fs		Atlas-INDEL	.											.	ZFYVE9	131	.	0			c.2145delC						.						53.0	53.0	53.0					1																	52705235		2203	4299	6502	SO:0001589	frameshift_variant	9372	exon4			.	AF104304	CCDS563.1, CCDS564.1	1p32.3	2014-06-13	2004-05-21	2004-05-26	ENSG00000157077	ENSG00000157077		"""Zinc fingers, FYVE domain containing"""	6775	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 173"""	603755	"""MAD, mothers against decapentaplegic homolog (Drosophila) interacting protein, receptor activation anchor"""	MADHIP		9865696	Standard	NM_007324		Approved	SMADIP, SARA, PPP1R173	uc001cto.4	O95405	OTTHUMG00000008061	ENST00000371591.1:c.2146delA	chr1.hg19:g.52705235delA	ENSP00000360647:p.Lys716fs	223.0	0.0		155.0	11.0	NM_007324	Q5T0F6|Q5T0F7|Q9UNE1|Q9Y5R7	Frame_Shift_Del	DEL	ENST00000371591.1	hg19	CCDS563.1																																																																																			.	.		0.443	ZFYVE9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022083.1	NM_007324	
OGFRL1	79627	hgsc.bcm.edu	37	6	72011155	72011155	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:72011155delT	ENST00000370435.4	+	7	893	c.759delT	c.(757-759)agtfs	p.S253fs	RP11-154D6.1_ENST00000586030.1_RNA|RP11-154D6.1_ENST00000412751.1_RNA|RP11-154D6.1_ENST00000423255.1_RNA|RP11-154D6.1_ENST00000587253.1_RNA|RP11-154D6.1_ENST00000588612.1_RNA|RP11-154D6.1_ENST00000587397.1_RNA|RP3-331H24.5_ENST00000602823.1_lincRNA|RP11-154D6.1_ENST00000432050.1_RNA|RP11-154D6.1_ENST00000450998.1_RNA|RP11-154D6.1_ENST00000585882.1_RNA|RP11-154D6.1_ENST00000587036.1_RNA|RP11-154D6.1_ENST00000586232.1_RNA|RP11-154D6.1_ENST00000591156.1_RNA	NM_024576.3	NP_078852.3	Q5TC84	OGRL1_HUMAN	opioid growth factor receptor-like 1	253						membrane (GO:0016020)	receptor activity (GO:0004872)			NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|upper_aerodigestive_tract(1)	13						GATATGAAAGTTTTAAATCTC	0.353																																					p.S253fs		Atlas-INDEL	.											.	OGFRL1	44	.	0			c.758delG						.						142.0	164.0	156.0					6																	72011155		2203	4300	6503	SO:0001589	frameshift_variant	79627	exon7			.		CCDS34482.1	6q13	2008-02-05			ENSG00000119900	ENSG00000119900			21378	protein-coding gene	gene with protein product							Standard	NM_024576		Approved	dJ331H24.1	uc003pfx.1	Q5TC84	OTTHUMG00000015000	ENST00000370435.4:c.759delT	chr6.hg19:g.72011155delT	ENSP00000359464:p.Ser253fs	176.0	0.0		156.0	12.0	NM_024576	Q2TAC1|Q8NEQ4|Q9H7B5	Frame_Shift_Del	DEL	ENST00000370435.4	hg19	CCDS34482.1																																																																																			.	.		0.353	OGFRL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041153.2	NM_024576	
USP53	54532	hgsc.bcm.edu	37	4	120192499	120192499	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:120192499delC	ENST00000274030.6	+	16	2663	c.1484delC	c.(1483-1485)gccfs	p.A495fs	USP53_ENST00000450251.1_Frame_Shift_Del_p.A495fs	NM_019050.2	NP_061923.2			ubiquitin specific peptidase 53											breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(5)|ovary(1)|pancreas(1)|skin(2)|stomach(1)	27						TCACCTCCTGCCCCAAATGGT	0.378																																					p.A495fs		Atlas-INDEL	.											.	USP53	69	.	0			c.1483delG						.						68.0	64.0	65.0					4																	120192499		1846	4098	5944	SO:0001589	frameshift_variant	54532	exon15			.	BC017382	CCDS43265.1	4q26	2010-05-12	2005-08-08		ENSG00000145390	ENSG00000145390		"""Ubiquitin-specific peptidases"""	29255	protein-coding gene	gene with protein product			"""ubiquitin specific protease 53"""			10718198, 14715245	Standard	NM_019050		Approved	KIAA1350	uc003ics.4	Q70EK8	OTTHUMG00000161331	ENST00000274030.6:c.1484delC	chr4.hg19:g.120192499delC	ENSP00000274030:p.Ala495fs	166.0	0.0		142.0	11.0	NM_019050		Frame_Shift_Del	DEL	ENST00000274030.6	hg19	CCDS43265.1																																																																																			.	.		0.378	USP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364564.2	XM_052597	
CNOT1	23019	hgsc.bcm.edu	37	16	58621151	58621151	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:58621151delA	ENST00000317147.5	-	6	719	c.387delT	c.(385-387)tttfs	p.F129fs	CNOT1_ENST00000441024.2_Frame_Shift_Del_p.F129fs|CNOT1_ENST00000569240.1_Frame_Shift_Del_p.F129fs	NM_001265612.1|NM_016284.4	NP_001252541.1|NP_057368.3	A5YKK6	CNOT1_HUMAN	CCR4-NOT transcription complex, subunit 1	129					gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of cytoplasmic mRNA processing body assembly (GO:0010606)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of stem cell maintenance (GO:2000036)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|transcription, DNA-templated (GO:0006351)|trophectodermal cell differentiation (GO:0001829)	CCR4-NOT complex (GO:0030014)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|extracellular space (GO:0005615)|membrane (GO:0016020)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)	estrogen receptor binding (GO:0030331)|poly(A) RNA binding (GO:0044822)|retinoic acid receptor binding (GO:0042974)			breast(1)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(24)|lung(25)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(2)	87				Kidney(780;0.0722)|OV - Ovarian serous cystadenocarcinoma(108;0.173)|Epithelial(162;0.239)		GGGCAAGGCCAAAAATTACCT	0.358																																					p.G130fs		Atlas-INDEL	.											.	CNOT1	359	.	0			c.388delG						.						104.0	107.0	106.0					16																	58621151		2198	4300	6498	SO:0001589	frameshift_variant	23019	exon6			.	AL833549	CCDS10799.1, CCDS45501.1, CCDS58468.1	16q21	2008-02-05			ENSG00000125107	ENSG00000125107			7877	protein-coding gene	gene with protein product		604917		NOT1		14702039	Standard	NM_016284		Approved	CDC39, NOT1H, KIAA1007, AD-005	uc002env.4	A5YKK6	OTTHUMG00000133487	ENST00000317147.5:c.387delT	chr16.hg19:g.58621151delA	ENSP00000320949:p.Phe129fs	125.0	0.0		122.0	12.0	NM_206999	Q68DX7|Q7Z3K2|Q8IWB8|Q8TB53|Q9BVZ6|Q9UFR8|Q9UI27|Q9Y2L0	Frame_Shift_Del	DEL	ENST00000317147.5	hg19	CCDS10799.1																																																																																			.	.		0.358	CNOT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257385.3	NM_016284	
FIP1L1	81608	hgsc.bcm.edu	37	4	54294251	54294251	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:54294251delT	ENST00000337488.6	+	13	1269	c.1075delT	c.(1075-1077)tttfs	p.F360fs	FIP1L1_ENST00000507166.1_Intron|FIP1L1_ENST00000507922.1_Frame_Shift_Del_p.F345fs|FIP1L1_ENST00000306932.6_Frame_Shift_Del_p.F286fs|FIP1L1_ENST00000358575.5_Frame_Shift_Del_p.F345fs	NM_030917.3	NP_112179.2	Q6UN15	FIP1_HUMAN	factor interacting with PAPOLA and CPSF1	360	Pro-rich.				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)			ACCACCTCCGTTTTTCCCTCC	0.463			T	PDGFRA	idiopathic hypereosinophilic syndrome																																p.P358fs		Atlas-INDEL	.		Dom	yes		4	4q12	81608	FIP1 like 1 (S. cerevisiae)		L	.	FIP1L1	60	.	0			c.1074delG						.						106.0	103.0	104.0					4																	54294251		2203	4300	6503	SO:0001589	frameshift_variant	81608	exon13			.	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.1075delT	chr4.hg19:g.54294251delT	ENSP00000336752:p.Phe360fs	278.0	0.0		192.0	15.0	NM_030917	B4DIR3|G3XAD6|Q0VGE0|Q499Y4|Q49AU3|Q7Z608|Q8WVN3|Q96F80|Q9H077	Frame_Shift_Del	DEL	ENST00000337488.6	hg19	CCDS3491.1																																																																																			.	.		0.463	FIP1L1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250602.1	NM_030917	
PLEKHH3	79990	hgsc.bcm.edu	37	17	40823047	40823047	+	Frame_Shift_Del	DEL	C	C	-	rs538834328		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:40823047delC	ENST00000591022.1	-	9	1773	c.1386delG	c.(1384-1386)gggfs	p.G462fs	PLEKHH3_ENST00000412503.1_Frame_Shift_Del_p.G462fs|PLEKHH3_ENST00000293349.6_Frame_Shift_Del_p.G462fs|PLEKHH3_ENST00000456950.2_5'UTR	NM_024927.4	NP_079203	Q7Z736	PKHH3_HUMAN	pleckstrin homology domain containing, family H (with MyTH4 domain) member 3	462	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				signal transduction (GO:0007165)	cytoskeleton (GO:0005856)|extracellular space (GO:0005615)				endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|prostate(2)|skin(2)	13		Breast(137;0.00116)		BRCA - Breast invasive adenocarcinoma(366;0.14)		CCACGAGGGTCCCCCCAGCCA	0.652																																					p.T463fs		Atlas-INDEL	.											.	PLEKHH3	49	.	0			c.1387delA						.						40.0	48.0	45.0					17																	40823047		2141	4246	6387	SO:0001589	frameshift_variant	79990	exon9			.	BC052978	CCDS11434.1	17q21.2	2013-01-11				ENSG00000068137		"""Pleckstrin homology (PH) domain containing"""	26105	protein-coding gene	gene with protein product						12477932	Standard	NM_024927		Approved	FLJ21019	uc002iau.3	Q7Z736		ENST00000591022.1:c.1386delG	chr17.hg19:g.40823047delC	ENSP00000468678:p.Gly462fs	132.0	0.0		116.0	10.0	NM_024927	C9JQ76|Q59H20|Q96B28|Q9H7D6|Q9NT18	Frame_Shift_Del	DEL	ENST00000591022.1	hg19	CCDS11434.1																																																																																			.	.		0.652	PLEKHH3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452332.1	NM_024927	
CD97	976	hgsc.bcm.edu	37	19	14508727	14508727	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:14508727delC	ENST00000242786.5	+	8	879	c.799delC	c.(799-801)cccfs	p.P268fs	CD97_ENST00000358600.3_Frame_Shift_Del_p.P175fs|CD97_ENST00000357355.3_Frame_Shift_Del_p.P219fs	NM_078481.3	NP_510966.1	P48960	CD97_HUMAN	CD97 molecule	268					cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular component movement (GO:0006928)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|neuropeptide signaling pathway (GO:0007218)	extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|endometrium(3)|kidney(1)|large_intestine(6)|liver(1)|lung(9)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	30						CTGGACCCCGCCCCCTGGAGT	0.607																																					p.P266fs		Atlas-INDEL	.											.	CD97	86	.	0			c.798delG						.						6.0	9.0	8.0					19																	14508727		1874	3927	5801	SO:0001589	frameshift_variant	976	exon8			.		CCDS32929.1, CCDS32930.1, CCDS32931.1	19p13	2014-08-08	2006-03-28			ENSG00000123146		"""CD molecules"", ""-"", ""GPCR / Class B : Orphans"""	1711	protein-coding gene	gene with protein product	"""leukocyte antigen CD97"", ""seven-span transmembrane protein"", ""seven-transmembrane, heterodimeric receptor associated with inflammation"", ""seven transmembrane helix receptor"""	601211	"""CD97 antigen"""			7636245, 8786105	Standard	NM_078481		Approved	TM7LN1	uc002myl.3	P48960		ENST00000242786.5:c.799delC	chr19.hg19:g.14508727delC	ENSP00000242786:p.Pro268fs	183.0	0.0		170.0	12.0	NM_078481	A8K7Z4|B2RBJ9|O00718|O76101|Q8NG72|Q8TBQ7	Frame_Shift_Del	DEL	ENST00000242786.5	hg19	CCDS32929.1																																																																																			.	.		0.607	CD97-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459821.2	NM_078481	
PLEKHG2	64857	hgsc.bcm.edu	37	19	39906055	39906055	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:39906055delT	ENST00000409794.3	+	4	1305	c.455delT	c.(454-456)attfs	p.I152fs	PLEKHG2_ENST00000409797.2_Frame_Shift_Del_p.I152fs|PLEKHG2_ENST00000378550.1_Frame_Shift_Del_p.I152fs|PLEKHG2_ENST00000425673.1_Frame_Shift_Del_p.I152fs|PLEKHG2_ENST00000458508.2_Frame_Shift_Del_p.I93fs	NM_022835.2	NP_073746.2	Q9H7P9	PKHG2_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 2	152	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(2)|liver(1)|lung(13)|pancreas(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	40	all_cancers(60;3.08e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;6.57e-07)|Ovarian(47;0.0569)		Epithelial(26;2.92e-26)|all cancers(26;2.01e-23)|Lung(45;0.000499)|LUSC - Lung squamous cell carcinoma(53;0.000657)			TTTGCCAACATTGAGGACATC	0.602																																					p.I152fs		Atlas-INDEL	.											.	PLEKHG2	329	.	0			c.454delA						.						41.0	39.0	40.0					19																	39906055		2203	4300	6503	SO:0001589	frameshift_variant	64857	exon4			.	AK024429	CCDS33022.2	19q13.2	2013-01-11			ENSG00000090924	ENSG00000090924		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	29515	protein-coding gene	gene with protein product		611893				11839748, 18045877	Standard	NM_022835		Approved	CLG, FLJ00018, ARHGEF42	uc010xuz.2	Q9H7P9	OTTHUMG00000152570	ENST00000409794.3:c.455delT	chr19.hg19:g.39906055delT	ENSP00000386733:p.Ile152fs	218.0	0.0		205.0	13.0	NM_022835	B8ZZK6|C9J0Y4|Q6DHV6|Q96BU2|Q96D18|Q9H699	Frame_Shift_Del	DEL	ENST00000409794.3	hg19	CCDS33022.2																																																																																			.	.		0.602	PLEKHG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326802.1	NM_022835	
POLE2	5427	hgsc.bcm.edu	37	14	50141076	50141076	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr14:50141076delT	ENST00000216367.5	-	4	414	c.315delA	c.(313-315)aaafs	p.K105fs	POLE2_ENST00000554396.1_Frame_Shift_Del_p.K105fs|POLE2_ENST00000556584.1_Intron|POLE2_ENST00000539565.2_Intron	NM_002692.3	NP_002683.2	P56282	DPOE2_HUMAN	polymerase (DNA directed), epsilon 2, accessory subunit	105					DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|G1/S transition of mitotic cell cycle (GO:0000082)|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)	epsilon DNA polymerase complex (GO:0008622)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)			kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	10	all_epithelial(31;0.0021)|Breast(41;0.0124)				Cladribine(DB00242)	ACGGAAGAAATTTTTTTCTTT	0.328																																					p.F106fs		Atlas-INDEL	.											.	POLE2	36	.	0			c.316delT						.						73.0	75.0	74.0					14																	50141076		2203	4300	6503	SO:0001589	frameshift_variant	5427	exon4			.	AF025840	CCDS32073.1, CCDS55914.1, CCDS55915.1	14q21-q22	2012-05-18	2012-05-18		ENSG00000100479	ENSG00000100479		"""DNA polymerases"""	9178	protein-coding gene	gene with protein product	"""DNA polymerase epsilon subunit B"""	602670	"""polymerase (DNA directed), epsilon 2 (p59 subunit)"""			9405441, 9443964	Standard	NM_002692		Approved	DPE2	uc001wwu.3	P56282	OTTHUMG00000170813	ENST00000216367.5:c.315delA	chr14.hg19:g.50141076delT	ENSP00000216367:p.Lys105fs	236.0	0.0		163.0	10.0	NM_001197331	A0AV55|A4FU92|A4LBB7|A6NH58|B4DDE6|O43560	Frame_Shift_Del	DEL	ENST00000216367.5	hg19	CCDS32073.1																																																																																			.	.		0.328	POLE2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410512.1	NM_002692	
SPAG9	9043	hgsc.bcm.edu	37	17	49071274	49071274	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:49071274delT	ENST00000262013.7	-	19	2457	c.2249delA	c.(2248-2250)aatfs	p.N750fs	SPAG9_ENST00000510283.1_Frame_Shift_Del_p.N593fs|SPAG9_ENST00000505279.1_Frame_Shift_Del_p.N740fs|SPAG9_ENST00000357122.4_Frame_Shift_Del_p.N736fs	NM_001130528.2	NP_001124000.1	O60271	JIP4_HUMAN	sperm associated antigen 9	750					activation of JUN kinase activity (GO:0007257)|muscle cell differentiation (GO:0042692)|negative regulation of protein homodimerization activity (GO:0090074)|positive regulation of cell migration (GO:0030335)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuron differentiation (GO:0045666)|protein homooligomerization (GO:0051260)|retrograde transport, endosome to Golgi (GO:0042147)|spermatogenesis (GO:0007283)|striated muscle cell differentiation (GO:0051146)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)				NS(1)|breast(3)|endometrium(3)|kidney(4)|large_intestine(8)|lung(14)|ovary(1)|prostate(1)|skin(1)|stomach(1)	37			BRCA - Breast invasive adenocarcinoma(22;4.24e-07)			TTCTTCTTGATTTTTTAACTC	0.358																																					p.N750fs		Atlas-Indel,Pindel	.											.	SPAG9	151	.	0			c.2250delT						.						100.0	91.0	94.0					17																	49071274		2203	4300	6503	SO:0001589	frameshift_variant	9043	exon19			.	AB011088	CCDS11577.1, CCDS45740.1, CCDS58577.1, CCDS58578.1	17q21.33	2013-09-23			ENSG00000008294	ENSG00000008294			14524	protein-coding gene	gene with protein product	"""sperm surface protein"", ""JNK/SAPK-associated protein"", ""JNK interacting protein"", ""sperm specific protein"", ""c-Jun NH2-terminal kinase-associated leucine zipper protein"", ""Max-binding protein"", ""JNK-associated leucine-zipper protein"", ""HLC-4 protein"", ""lung cancer oncogene 4"", ""proliferation-inducing gene 6"", ""cancer/testis antigen 89"""	605430				9480848, 11106729	Standard	NM_003971		Approved	HSS, SYD1, KIAA0516, MGC14967, MGC74461, MGC117291, JLP, PHET, HLC4, PIG6, FLJ13450, FLJ14006, FLJ26141, FLJ34602, CT89	uc002itc.3	O60271	OTTHUMG00000162316	ENST00000262013.7:c.2249delA	chr17.hg19:g.49071274delT	ENSP00000262013:p.Asn750fs	313.0	0.0		192.0	15.0	NM_001130528	A6H8U5|A8MSX0|B4DHH2|O60905|Q3KQU8|Q3MKM7|Q86WC7|Q86WC8|Q8IZX7|Q96II0|Q9H811	Frame_Shift_Del	DEL	ENST00000262013.7	hg19	CCDS45740.1																																																																																			.	.		0.358	SPAG9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000368543.2	NM_003971	
CFH	3075	hgsc.bcm.edu	37	1	196697534	196697534	+	Frame_Shift_Del	DEL	A	A	-	rs551215138		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:196697534delA	ENST00000367429.4	+	15	2535	c.2295delA	c.(2293-2295)ttafs	p.L765fs		NM_000186.3	NP_000177.2	P08603	CFAH_HUMAN	complement factor H	765	Sushi 13. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	heparan sulfate proteoglycan binding (GO:0043395)|heparin binding (GO:0008201)			NS(3)|breast(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(24)|lung(33)|ovary(1)|prostate(5)|skin(9)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	101						AGGAACATTTAAAAAACAAGA	0.279																																					p.L765X		Atlas-INDEL	.											.	CFH	251	.	0			c.2294delT						.						48.0	47.0	47.0					1																	196697534		2203	4298	6501	SO:0001589	frameshift_variant	3075	exon15			.	Y00716	CCDS1385.1	1q32	2014-09-17	2004-08-09	2004-08-12	ENSG00000000971	ENSG00000000971		"""Complement system"""	4883	protein-coding gene	gene with protein product	"""beta-1H"", ""H factor 2 (complement)"", ""age-related maculopathy susceptibility 1"""	134370	"""H factor 1 (complement)"""	HF, HF1, HF2		2889480, 2963625	Standard	NM_000186		Approved	HUS, FHL1, ARMS1, ARMD4	uc001gtj.4	P08603	OTTHUMG00000035607	ENST00000367429.4:c.2295delA	chr1.hg19:g.196697534delA	ENSP00000356399:p.Leu765fs	137.0	0.0		191.0	12.0	NM_000186	A5PL14|P78435|Q14570|Q2TAZ5|Q38G77|Q5TFM3|Q8N708|Q9NU86	Frame_Shift_Del	DEL	ENST00000367429.4	hg19	CCDS1385.1																																																																																			.	.		0.279	CFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086412.2	NM_000186	
ZFYVE16	9765	hgsc.bcm.edu	37	5	79769620	79769620	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:79769620delA	ENST00000338008.5	+	16	4415	c.4235delA	c.(4234-4236)gaafs	p.E1412fs	ZFYVE16_ENST00000510158.1_Frame_Shift_Del_p.E1412fs|ZFYVE16_ENST00000505560.1_Frame_Shift_Del_p.E1412fs	NM_001284236.1|NM_014733.3	NP_001271165.1|NP_055548	Q7Z3T8	ZFY16_HUMAN	zinc finger, FYVE domain containing 16	1412					BMP signaling pathway (GO:0030509)|endosomal transport (GO:0016197)|protein targeting to lysosome (GO:0006622)|regulation of endocytosis (GO:0030100)|signal transduction (GO:0007165)|vesicle organization (GO:0016050)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|early endosome membrane (GO:0031901)|intracellular membrane-bounded organelle (GO:0043231)	1-phosphatidylinositol binding (GO:0005545)|metal ion binding (GO:0046872)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|protein transporter activity (GO:0008565)			breast(4)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(14)|liver(1)|lung(6)|ovary(2)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	51		Lung NSC(167;0.00428)|all_lung(232;0.00455)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;1.6e-46)|Epithelial(54;2.02e-41)|all cancers(79;5.05e-36)		TTTCCAAGTGAAAAAATAAAA	0.313																																					p.E1412fs	Melanoma(150;1452 1854 16018 17851 37292)	Atlas-INDEL	.											.	ZFYVE16	100	.	0			c.4234delG						.						60.0	67.0	65.0					5																	79769620		2203	4300	6503	SO:0001589	frameshift_variant	9765	exon17			.	AB002303	CCDS4050.1	5q14.1	2012-09-20			ENSG00000039319	ENSG00000039319		"""Zinc fingers, FYVE domain containing"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	20756	protein-coding gene	gene with protein product	"""endofin"", ""protein phosphatase 1, regulatory subunit 69"""	608880				11546807	Standard	NM_014733		Approved	KIAA0305, PPP1R69	uc003kgq.4	Q7Z3T8	OTTHUMG00000108178	ENST00000338008.5:c.4235delA	chr5.hg19:g.79769620delA	ENSP00000337159:p.Glu1412fs	206.0	0.0		167.0	12.0	NM_001105251	O15023|Q5H9U2|Q7LAU7|Q86T69|Q8N5L3|Q8NEK3	Frame_Shift_Del	DEL	ENST00000338008.5	hg19	CCDS4050.1																																																																																			.	.		0.313	ZFYVE16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226982.2	NM_014733	
C10orf120	399814	hgsc.bcm.edu	37	10	124457833	124457833	+	Frame_Shift_Del	DEL	T	T	-	rs569498958		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:124457833delT	ENST00000329446.4	-	3	455	c.424delA	c.(424-426)atafs	p.I142fs		NM_001010912.1	NP_001010912.1	Q5SQS8	CJ120_HUMAN	chromosome 10 open reading frame 120	142										endometrium(1)|kidney(1)|large_intestine(6)|lung(9)|skin(2)|stomach(1)|urinary_tract(1)	21		all_neural(114;0.169)|Glioma(114;0.222)				GCTGTCCATATTTTTTCTAGG	0.458																																					p.I142fs		Atlas-INDEL	.											C10orf120,NS,carcinoma,0,1	C10orf120	55	.	0			c.425delT						.						117.0	122.0	121.0					10																	124457833		2203	4300	6503	SO:0001589	frameshift_variant	399814	exon3			.		CCDS31302.1	10q26.13	2012-06-12			ENSG00000183559	ENSG00000183559			25707	protein-coding gene	gene with protein product							Standard	NM_001010912		Approved	bA318C4.1	uc001lgn.3	Q5SQS8	OTTHUMG00000019187	ENST00000329446.4:c.424delA	chr10.hg19:g.124457833delT	ENSP00000331012:p.Ile142fs	133.0	0.0		135.0	10.0	NM_001010912	B2RU17	Frame_Shift_Del	DEL	ENST00000329446.4	hg19	CCDS31302.1																																																																																			.	.		0.458	C10orf120-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050803.1	NM_001010912	
MICAL3	57553	hgsc.bcm.edu	37	22	18364031	18364031	+	Intron	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr22:18364031delT	ENST00000441493.2	-	16	2594				MICAL3_ENST00000207726.7_Intron|MICAL3_ENST00000383094.3_Intron|MICAL3_ENST00000414725.2_Intron|MICAL3_ENST00000585038.1_Frame_Shift_Del_p.K760fs|MICAL3_ENST00000400561.2_Intron|MICAL3_ENST00000444520.1_Intron|MICAL3_ENST00000429452.1_Frame_Shift_Del_p.K760fs	NM_015241.2	NP_056056.2	Q7RTP6	MICA3_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 3						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)		GGGTGATCACTTTTTTGGGGC	0.537																																					p.V761X		Atlas-INDEL	.											.	MICAL3	53	.	0			c.2281delG						.						158.0	155.0	156.0					22																	18364031		1568	3582	5150	SO:0001627	intron_variant	57553	exon17			.	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.2241+4612A>-	chr22.hg19:g.18364031delT		258.0	0.0		222.0	14.0	NM_001136004	B2RXJ5|E9PEF0|O94909|Q5U4P4|Q6ICK4|Q96DF2|Q9P2I3	Frame_Shift_Del	DEL	ENST00000441493.2	hg19	CCDS46659.1																																																																																			.	.		0.537	MICAL3-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447351.1		
TMPRSS6	164656	hgsc.bcm.edu	37	22	37480793	37480793	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr22:37480793delG	ENST00000346753.3	-	9	1203	c.1087delC	c.(1087-1089)caafs	p.Q363fs	TMPRSS6_ENST00000406725.1_Frame_Shift_Del_p.Q354fs|RP5-1170K4.7_ENST00000414203.2_RNA|TMPRSS6_ENST00000381792.2_Frame_Shift_Del_p.Q354fs|TMPRSS6_ENST00000442782.2_Frame_Shift_Del_p.Q363fs|TMPRSS6_ENST00000406856.1_Frame_Shift_Del_p.Q354fs	NM_153609.2	NP_705837.1	Q8IU80	TMPS6_HUMAN	transmembrane protease, serine 6	363	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.				angiogenesis (GO:0001525)|extracellular matrix organization (GO:0030198)|fibrinolysis (GO:0042730)|intracellular signal transduction (GO:0035556)|iron ion homeostasis (GO:0055072)|proteolysis (GO:0006508)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)			breast(5)|central_nervous_system(4)|endometrium(4)|kidney(4)|large_intestine(3)|lung(13)|ovary(1)|prostate(1)|skin(2)|stomach(3)	40						CAGTGGGTTTGGGGCGAGTAG	0.647																																					p.Q363fs		Atlas-INDEL	.											.	TMPRSS6	99	.	0			c.1088delA						.						83.0	70.0	75.0					22																	37480793		2199	4292	6491	SO:0001589	frameshift_variant	164656	exon9			.	AY055383	CCDS13941.1, CCDS74856.1, CCDS74857.1	22q13.1	2010-04-13			ENSG00000187045	ENSG00000187045		"""Serine peptidases / Transmembrane"""	16517	protein-coding gene	gene with protein product		609862					Standard	NM_001289000		Approved	FLJ30744	uc003aqs.1	Q8IU80	OTTHUMG00000150541	ENST00000346753.3:c.1087delC	chr22.hg19:g.37480793delG	ENSP00000334962:p.Gln363fs	144.0	0.0		147.0	10.0	NM_153609	B0QYB4|B0QYB7|B0QYB8|Q5TI06|Q6ICC2|Q6UXD8|Q8IUE2|Q8IXV8	Frame_Shift_Del	DEL	ENST00000346753.3	hg19	CCDS13941.1																																																																																			.	.		0.647	TMPRSS6-003	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000318822.1	NM_153609	
SI	6476	hgsc.bcm.edu	37	3	164710135	164710135	+	Frame_Shift_Del	DEL	C	C	-	rs371948467		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:164710135delC	ENST00000264382.3	-	42	4954	c.4892delG	c.(4891-4893)ggtfs	p.G1631fs		NM_001041.3	NP_001032.2	P14410	SUIS_HUMAN	sucrase-isomaltase (alpha-glucosidase)	1631	Sucrase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	brush border (GO:0005903)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|carbohydrate binding (GO:0030246)|oligo-1,6-glucosidase activity (GO:0004574)|sucrose alpha-glucosidase activity (GO:0004575)			NS(4)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(6)|kidney(10)|large_intestine(18)|lung(124)|ovary(9)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(16)|urinary_tract(1)	218		Prostate(884;0.00314)|Melanoma(1037;0.0153)|all_neural(597;0.0199)			Acarbose(DB00284)|Scopolamine(DB00747)	AAATGCTGGACCCCATAAGAA	0.318										HNSCC(35;0.089)																											p.G1631fs		Atlas-INDEL	.											.	SI	500	.	0			c.4893delT						.						57.0	60.0	59.0					3																	164710135		2202	4300	6502	SO:0001589	frameshift_variant	6476	exon42			.	X63597	CCDS3196.1	3q25.2-q26.2	2004-04-06	2004-04-06		ENSG00000090402	ENSG00000090402	3.2.1.10		10856	protein-coding gene	gene with protein product	"""Oligosaccharide alpha-1,6-glucosidase"""	609845	"""sucrase-isomaltase"""			2962903, 1353958	Standard	NM_001041		Approved		uc003fei.3	P14410	OTTHUMG00000158065	ENST00000264382.3:c.4892delG	chr3.hg19:g.164710135delC	ENSP00000264382:p.Gly1631fs	189.0	0.0		170.0	12.0	NM_001041	A2RUC3|Q1JQ80|Q1RMC2	Frame_Shift_Del	DEL	ENST00000264382.3	hg19	CCDS3196.1																																																																																			.	.		0.318	SI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350116.1	NM_001041	
PCP4	5121	hgsc.bcm.edu	37	21	41300935	41300935	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr21:41300935delT	ENST00000328619.5	+	3	273	c.88delT	c.(88-90)tttfs	p.F30fs	PCP4_ENST00000468717.1_3'UTR	NM_006198.2	NP_006189.2	P48539	PCP4_HUMAN	Purkinje cell protein 4	30					central nervous system development (GO:0007417)	cytosol (GO:0005829)|nucleus (GO:0005634)				large_intestine(2)|lung(1)|skin(1)	4		Prostate(19;2.65e-06)|all_epithelial(19;0.138)				TCAAGAAGAATTTGACATTGA	0.448																																					p.E29fs		Atlas-INDEL	.											.	PCP4	11	.	0			c.87delA						.						117.0	107.0	110.0					21																	41300935		2203	4300	6503	SO:0001589	frameshift_variant	5121	exon3			.	X93349, U53709	CCDS33563.1	21q22.2	2006-12-01			ENSG00000183036	ENSG00000183036			8742	protein-coding gene	gene with protein product		601629				8931698, 8914602	Standard	NM_006198		Approved	PEP-19	uc002yyp.3	P48539	OTTHUMG00000086731	ENST00000328619.5:c.88delT	chr21.hg19:g.41300935delT	ENSP00000329403:p.Phe30fs	239.0	0.0		188.0	12.0	NM_006198	A6NDJ9|Q6ICS4|Q93059	Frame_Shift_Del	DEL	ENST00000328619.5	hg19	CCDS33563.1																																																																																			.	.		0.448	PCP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195025.1	NM_006198	
KLF15	28999	hgsc.bcm.edu	37	3	126071137	126071137	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:126071137delC	ENST00000296233.3	-	2	859	c.629delG	c.(628-630)ggcfs	p.G210fs	KLF15_ENST00000509675.1_5'Flank	NM_014079.3	NP_054798.1	Q9UIH9	KLF15_HUMAN	Kruppel-like factor 15	210					cardiac muscle hypertrophy in response to stress (GO:0014898)|cellular response to peptide (GO:1901653)|glial cell differentiation (GO:0010001)|glomerular visceral epithelial cell differentiation (GO:0072112)|glucose transport (GO:0015758)|negative regulation of peptidyl-lysine acetylation (GO:2000757)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|transcription regulatory region DNA binding (GO:0044212)			endometrium(1)|lung(7)|ovary(2)|skin(2)	12				GBM - Glioblastoma multiforme(114;0.147)		AGGCGTGGGGCCCCCACCTGG	0.687																																					p.G210fs		Atlas-INDEL	.											.	KLF15	40	.	0			c.630delC						.						21.0	22.0	21.0					3																	126071137		2198	4299	6497	SO:0001589	frameshift_variant	28999	exon2			.	AB029254	CCDS3036.1	3q21.3	2013-01-08			ENSG00000163884	ENSG00000163884		"""Kruppel-like transcription factors"", ""Zinc fingers, C2H2-type"""	14536	protein-coding gene	gene with protein product	"""kidney-enriched Kruppel-like factor"""	606465				10982849	Standard	NM_014079		Approved	KKLF	uc011bkk.1	Q9UIH9	OTTHUMG00000162689	ENST00000296233.3:c.629delG	chr3.hg19:g.126071137delC	ENSP00000296233:p.Gly210fs	182.0	0.0		144.0	10.0	NM_014079		Frame_Shift_Del	DEL	ENST00000296233.3	hg19	CCDS3036.1																																																																																			.	.		0.687	KLF15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370096.1	NM_014079	
CHRNA1	1134	hgsc.bcm.edu	37	2	175622346	175622346	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:175622346delT	ENST00000261007.5	-	5	433	c.367delA	c.(367-369)attfs	p.I123fs	CHRNA1_ENST00000348749.5_Frame_Shift_Del_p.I98fs|CHRNA1_ENST00000409219.1_Frame_Shift_Del_p.I98fs|CHRNA1_ENST00000409542.1_Intron|CHRNA1_ENST00000409323.1_Frame_Shift_Del_p.I98fs|AC018890.6_ENST00000442996.1_RNA	NM_001039523.2	NP_001034612.1	P02708	ACHA_HUMAN	cholinergic receptor, nicotinic, alpha 1 (muscle)	123					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|muscle cell cellular homeostasis (GO:0046716)|musculoskeletal movement (GO:0050881)|neuromuscular junction development (GO:0007528)|neuromuscular process (GO:0050905)|neuromuscular synaptic transmission (GO:0007274)|neuron cellular homeostasis (GO:0070050)|neuronal action potential (GO:0019228)|regulation of membrane potential (GO:0042391)|signal transduction (GO:0007165)|skeletal muscle contraction (GO:0003009)|skeletal muscle tissue growth (GO:0048630)|synaptic transmission (GO:0007268)|transport (GO:0006810)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|cell surface (GO:0009986)|neuromuscular junction (GO:0031594)|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)|ion channel activity (GO:0005216)			breast(3)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(15)|ovary(3)|prostate(3)|skin(4)	37					Galantamine(DB00674)	GGAATGTGAATTTTTTTCACA	0.443																																					p.I123fs		Atlas-INDEL	.											.	CHRNA1	92	.	0			c.368delT						.						83.0	81.0	82.0					2																	175622346		2203	4300	6503	SO:0001589	frameshift_variant	1134	exon5			.	Y00762	CCDS2261.1, CCDS33331.1	2q31.1	2012-02-11	2006-02-01		ENSG00000138435	ENSG00000138435		"""Cholinergic receptors"", ""Ligand-gated ion channels / Acetylcholine receptors, nicotinic"""	1955	protein-coding gene	gene with protein product	"""acetylcholine receptor, nicotinic, alpha 1 (muscle)"""	100690	"""cholinergic receptor, nicotinic, alpha polypeptide 1 (muscle)"""	CHRNA			Standard	NM_001039523		Approved		uc002uje.2	P02708	OTTHUMG00000132357	ENST00000261007.5:c.367delA	chr2.hg19:g.175622346delT	ENSP00000261007:p.Ile123fs	253.0	0.0		179.0	11.0	NM_001039523	B4DRV6|D3DPE8	Frame_Shift_Del	DEL	ENST00000261007.5	hg19	CCDS33331.1																																																																																			.	.		0.443	CHRNA1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000334116.1		
ZCCHC11	23318	hgsc.bcm.edu	37	1	52891114	52891114	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:52891114delG	ENST00000371544.3	-	29	5036	c.4774delC	c.(4774-4776)cttfs	p.L1592fs	ZCCHC11_ENST00000257177.4_Frame_Shift_Del_p.L1593fs	NM_001009881.2|NM_015269.2	NP_001009881.1|NP_056084.1	Q5TAX3	TUT4_HUMAN	zinc finger, CCHC domain containing 11	1592	Pro-rich.				cytokine production (GO:0001816)|miRNA catabolic process (GO:0010587)|miRNA metabolic process (GO:0010586)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|pre-miRNA processing (GO:0031054)|regulation of lipopolysaccharide-mediated signaling pathway (GO:0031664)|RNA 3'-end processing (GO:0031123)|stem cell maintenance (GO:0019827)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|RNA uridylyltransferase activity (GO:0050265)|zinc ion binding (GO:0008270)			NS(2)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(17)|ovary(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	58						GCTGGGACAAGGGGGAAATGG	0.483																																					p.L1593fs		Atlas-INDEL	.											.	ZCCHC11	151	.	0			c.4778delT						.						84.0	84.0	84.0					1																	52891114		2203	4300	6503	SO:0001589	frameshift_variant	23318	exon29			.	D83776	CCDS30715.1, CCDS30716.1	1p32.3	2014-03-05			ENSG00000134744	ENSG00000134744		"""Zinc fingers, CCHC domain containing"""	28981	protein-coding gene	gene with protein product	"""TUTase4"""	613692				8724849, 12239557	Standard	NM_015269		Approved	KIAA0191, PAPD3, TUT4	uc001cty.2	Q5TAX3	OTTHUMG00000008200	ENST00000371544.3:c.4774delC	chr1.hg19:g.52891114delG	ENSP00000360599:p.Leu1592fs	224.0	0.0		145.0	11.0	NM_001009881	A2RRP0|B7Z8J5|D3DQ35|Q12764|Q5TAX2|Q5TAX4|Q86XZ3	Frame_Shift_Del	DEL	ENST00000371544.3	hg19	CCDS30716.1																																																																																			.	.		0.483	ZCCHC11-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000022462.1	XM_038288	
CCDC144A	9720	hgsc.bcm.edu	37	17	16638176	16638176	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:16638176delA	ENST00000360524.8	+	12	2667	c.2591delA	c.(2590-2592)caafs	p.Q864fs	CCDC144A_ENST00000399273.1_Frame_Shift_Del_p.Q864fs|RP11-219A15.1_ENST00000448331.3_Frame_Shift_Del_p.Q864fs|CCDC144A_ENST00000443444.2_Frame_Shift_Del_p.Q864fs|CCDC144A_ENST00000456009.1_Frame_Shift_Del_p.Q584fs	NM_014695.1	NP_055510.1	A2RUR9	C144A_HUMAN	coiled-coil domain containing 144A	864																	GATAACCTTCAAAAAATTATA	0.318																																					p.Q864fs		Atlas-INDEL	.											.	CCDC144A	53	.	0			c.2590delC						.						4.0	4.0	4.0					17																	16638176		1599	3602	5201	SO:0001589	frameshift_variant	9720	exon12			.	BC133019	CCDS45621.1	17p11.2	2008-10-23			ENSG00000170160	ENSG00000170160			29072	protein-coding gene	gene with protein product						9628581, 11997339	Standard	NM_014695		Approved	KIAA0565, FLJ43983	uc002gqk.1	A2RUR9	OTTHUMG00000059178	ENST00000360524.8:c.2591delA	chr17.hg19:g.16638176delA	ENSP00000353717:p.Gln864fs	183.0	0.0		169.0	12.0	NM_014695	O60311|Q6ZU57	Frame_Shift_Del	DEL	ENST00000360524.8	hg19	CCDS45621.1																																																																																			.	.		0.318	CCDC144A-013	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000444093.1		
WDR37	22884	hgsc.bcm.edu	37	10	1170240	1170240	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:1170240delA	ENST00000358220.1	+	12	1330	c.1186delA	c.(1186-1188)aaafs	p.K396fs	WDR37_ENST00000263150.4_Frame_Shift_Del_p.K396fs|WDR37_ENST00000482165.1_3'UTR			Q9Y2I8	WDR37_HUMAN	WD repeat domain 37	396										breast(2)|endometrium(2)|kidney(1)|lung(9)|prostate(2)|skin(1)	17		all_epithelial(10;0.0449)|Colorectal(49;0.142)		Epithelial(11;0.134)		CTGGGACTTGAAAAATATGAG	0.473																																					p.L395fs		Atlas-INDEL	.											.	WDR37	52	.	0			c.1185delG						.						136.0	122.0	127.0					10																	1170240		2203	4300	6503	SO:0001589	frameshift_variant	22884	exon12			.	AB023199	CCDS7057.1	10p15.3	2013-01-09			ENSG00000047056	ENSG00000047056		"""WD repeat domain containing"""	31406	protein-coding gene	gene with protein product						10231032, 11230166	Standard	NM_014023		Approved	KIAA0982	uc001igf.1	Q9Y2I8	OTTHUMG00000017540	ENST00000358220.1:c.1186delA	chr10.hg19:g.1170240delA	ENSP00000350954:p.Lys396fs	140.0	0.0		117.0	11.0	NM_014023	A8K976|D3DRQ7|Q5SW03|Q8WVG2|Q9NTJ6	Frame_Shift_Del	DEL	ENST00000358220.1	hg19	CCDS7057.1																																																																																			.	.		0.473	WDR37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046418.1	NM_014023	
ARFGEF1	10565	hgsc.bcm.edu	37	8	68130371	68130371	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:68130371delT	ENST00000262215.3	-	31	4730	c.4341delA	c.(4339-4341)aaafs	p.K1447fs	ARFGEF1_ENST00000520381.1_Frame_Shift_Del_p.K901fs|ARFGEF1_ENST00000518230.1_Frame_Shift_Del_p.K285fs	NM_006421.4	NP_006412.2	Q9Y6D6	BIG1_HUMAN	ADP-ribosylation factor guanine nucleotide-exchange factor 1 (brefeldin A-inhibited)	1447					endomembrane system organization (GO:0010256)|exocytosis (GO:0006887)|Golgi organization (GO:0007030)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of Rho GTPase activity (GO:0034259)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein glycosylation in Golgi (GO:0090284)|positive regulation of wound healing (GO:0090303)|protein transport (GO:0015031)|regulation of ARF protein signal transduction (GO:0032012)|regulation of establishment of cell polarity (GO:2000114)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|small nuclear ribonucleoprotein complex (GO:0030532)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|guanyl-nucleotide exchange factor activity (GO:0005085)|myosin binding (GO:0017022)|protein kinase A regulatory subunit binding (GO:0034237)			breast(1)|endometrium(14)|kidney(4)|large_intestine(17)|lung(20)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	65	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.0043)|OV - Ovarian serous cystadenocarcinoma(28;0.00578)|all cancers(69;0.0173)|BRCA - Breast invasive adenocarcinoma(89;0.206)			TCCATTCAGCTTTCTGGGGAA	0.274																																					p.A1448fs		Atlas-INDEL	.											.	ARFGEF1	196	.	0			c.4342delG						.						85.0	74.0	78.0					8																	68130371		2203	4300	6503	SO:0001589	frameshift_variant	10565	exon31			.	AF084520	CCDS6199.1	8q13	2011-08-18	2011-08-18		ENSG00000066777	ENSG00000066777			15772	protein-coding gene	gene with protein product		604141				10212200, 8917509	Standard	NM_006421		Approved	DKFZP434L057, BIG1, ARFGEP1, p200	uc003xxo.2	Q9Y6D6	OTTHUMG00000164626	ENST00000262215.3:c.4341delA	chr8.hg19:g.68130371delT	ENSP00000262215:p.Lys1447fs	194.0	0.0		179.0	13.0	NM_006421	Q9NV46|Q9UFV2|Q9UNL0	Frame_Shift_Del	DEL	ENST00000262215.3	hg19	CCDS6199.1																																																																																			.	.		0.274	ARFGEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379441.4	NM_006421	
RILPL2	196383	hgsc.bcm.edu	37	12	123907659	123907659	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:123907659delT	ENST00000280571.8	-	3	833	c.537delA	c.(535-537)aaafs	p.K179fs		NM_145058.1	NP_659495.1	Q969X0	RIPL2_HUMAN	Rab interacting lysosomal protein-like 2	179					epithelial cell morphogenesis (GO:0003382)|intracellular protein transport (GO:0006886)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|primary cilium (GO:0072372)	identical protein binding (GO:0042802)			endometrium(1)|large_intestine(2)|lung(2)|skin(1)	6	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000546)|Epithelial(86;0.00179)|all cancers(50;0.0168)		CCACAGCATCTTTTTCTCTTC	0.443																																					p.D180fs		Atlas-INDEL	.											.	RILPL2	10	.	0			c.538delG						.						172.0	159.0	163.0					12																	123907659		2203	4300	6503	SO:0001589	frameshift_variant	196383	exon3			.	AB085763	CCDS9248.1	12q24.31	2007-11-27				ENSG00000150977			28787	protein-coding gene	gene with protein product		614093				14668488	Standard	NM_145058		Approved	MGC7036, FLJ30380, FLJ32372	uc001uey.1	Q969X0		ENST00000280571.8:c.537delA	chr12.hg19:g.123907659delT	ENSP00000280571:p.Lys179fs	321.0	0.0		255.0	16.0	NM_145058		Frame_Shift_Del	DEL	ENST00000280571.8	hg19	CCDS9248.1																																																																																			.	.		0.443	RILPL2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_145058	
ADH7	131	hgsc.bcm.edu	37	4	100348965	100348965	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:100348965delA	ENST00000209665.4	-	5	805	c.565delT	c.(565-567)tccfs	p.S189fs	ADH7_ENST00000437033.2_Frame_Shift_Del_p.S177fs|ADH7_ENST00000482593.1_Frame_Shift_Del_p.S120fs|ADH7_ENST00000476959.1_Frame_Shift_Del_p.S197fs	NM_000673.4	NP_000664.2	P40394	ADH7_HUMAN	alcohol dehydrogenase 7 (class IV), mu or sigma polypeptide	189					ethanol catabolic process (GO:0006068)|ethanol oxidation (GO:0006069)|extracellular negative regulation of signal transduction (GO:1900116)|fatty acid omega-oxidation (GO:0010430)|oxidation-reduction process (GO:0055114)|response to bacterium (GO:0009617)|response to ethanol (GO:0045471)|retinoic acid metabolic process (GO:0042573)|retinoid metabolic process (GO:0001523)|retinol metabolic process (GO:0042572)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular region (GO:0005576)	alcohol dehydrogenase (NAD) activity (GO:0004022)|alcohol dehydrogenase activity, zinc-dependent (GO:0004024)|aldehyde oxidase activity (GO:0004031)|ethanol binding (GO:0035276)|receptor antagonist activity (GO:0048019)|retinol binding (GO:0019841)|retinol dehydrogenase activity (GO:0004745)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|large_intestine(4)|lung(11)|skin(1)	19				OV - Ovarian serous cystadenocarcinoma(123;1.75e-08)		TATCCAGTGGAAAACCCACAG	0.408																																					p.S197fs		Atlas-INDEL	.											.	ADH7	76	.	0			c.590delC						.						104.0	94.0	98.0					4																	100348965		2203	4300	6503	SO:0001589	frameshift_variant	131	exon5			.	X76342	CCDS34034.1, CCDS54781.1	4q23-q24	2008-02-05			ENSG00000196344	ENSG00000196344	1.1.1.1	"""Alcohol dehydrogenases"""	256	protein-coding gene	gene with protein product		600086				8195208	Standard	NM_000673		Approved	ADH-4	uc021xqj.1	P40394	OTTHUMG00000159318	ENST00000209665.4:c.565delT	chr4.hg19:g.100348965delA	ENSP00000209665:p.Ser189fs	223.0	0.0		144.0	10.0	NM_001166504	A2RRB6|A8MVN9|B2R760|B4DWV6|Q13713	Frame_Shift_Del	DEL	ENST00000209665.4	hg19	CCDS34034.1																																																																																			.	.		0.408	ADH7-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_000673	
KLHDC1	122773	hgsc.bcm.edu	37	14	50190646	50190646	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr14:50190646delT	ENST00000359332.2	+	5	549	c.459delT	c.(457-459)tgtfs	p.C153fs		NM_172193.2	NP_751943.1	Q8N7A1	KLDC1_HUMAN	kelch domain containing 1	153						cytoplasm (GO:0005737)				kidney(1)|large_intestine(1)|liver(2)|lung(5)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	12	all_epithelial(31;0.00244)|Breast(41;0.00964)					TCCAAGACTGTTTTGATGTTC	0.353																																					p.C153fs		Atlas-INDEL	.											.	KLHDC1	24	.	0			c.458delG						.						206.0	182.0	190.0					14																	50190646		2203	4300	6503	SO:0001589	frameshift_variant	122773	exon5			.	AF111806	CCDS9692.1	14q21.3	2007-08-01			ENSG00000197776	ENSG00000197776			19836	protein-coding gene	gene with protein product		611281					Standard	NM_172193		Approved	MST025	uc001www.3	Q8N7A1	OTTHUMG00000140295	ENST00000359332.2:c.459delT	chr14.hg19:g.50190646delT	ENSP00000352282:p.Cys153fs	178.0	0.0		143.0	10.0	NM_172193	B3KXD9|Q8WYI1	Frame_Shift_Del	DEL	ENST00000359332.2	hg19	CCDS9692.1																																																																																			.	.		0.353	KLHDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276882.2	NM_172193	
TLR3	7098	hgsc.bcm.edu	37	4	186998188	186998188	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:186998188delA	ENST00000296795.3	+	2	519	c.415delA	c.(415-417)aaafs	p.K139fs		NM_003265.2	NP_003256.1	O15455	TLR3_HUMAN	toll-like receptor 3	139					activation of NF-kappaB-inducing kinase activity (GO:0007250)|cellular response to drug (GO:0035690)|cellular response to exogenous dsRNA (GO:0071360)|cellular response to interferon-beta (GO:0035458)|cellular response to interferon-gamma (GO:0071346)|cellular response to mechanical stimulus (GO:0071260)|defense response to bacterium (GO:0042742)|defense response to virus (GO:0051607)|detection of virus (GO:0009597)|extrinsic apoptotic signaling pathway (GO:0097191)|hyperosmotic response (GO:0006972)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|male gonad development (GO:0008584)|microglial cell activation involved in immune response (GO:0002282)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|necroptotic signaling pathway (GO:0097527)|negative regulation of osteoclast differentiation (GO:0045671)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of apoptotic process (GO:0043065)|positive regulation of chemokine biosynthetic process (GO:0045080)|positive regulation of chemokine production (GO:0032722)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of JNK cascade (GO:0046330)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of toll-like receptor signaling pathway (GO:0034123)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of type III interferon production (GO:0034346)|response to exogenous dsRNA (GO:0043330)|signal transduction (GO:0007165)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|endolysosome membrane (GO:0036020)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	double-stranded RNA binding (GO:0003725)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(5)|large_intestine(8)|lung(8)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	29		all_cancers(14;4.27e-52)|all_epithelial(14;7.69e-39)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.0066)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.243)		OV - Ovarian serous cystadenocarcinoma(60;1.47e-11)|BRCA - Breast invasive adenocarcinoma(30;1.14e-05)|GBM - Glioblastoma multiforme(59;0.000107)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.16)		CCAGAAAATTAAAAATAATCC	0.353																																					p.I138fs		Atlas-INDEL	.											.	TLR3	83	.	0			c.414delT						.						36.0	38.0	37.0					4																	186998188		2203	4300	6503	SO:0001589	frameshift_variant	7098	exon2			.	U88879	CCDS3846.1	4q35	2014-09-17				ENSG00000164342		"""CD molecules"""	11849	protein-coding gene	gene with protein product		603029				9435236	Standard	NM_003265		Approved	CD283	uc003iyq.3	O15455		ENST00000296795.3:c.415delA	chr4.hg19:g.186998188delA	ENSP00000296795:p.Lys139fs	150.0	0.0		119.0	10.0	NM_003265	B2RAI7|B7Z7K0|E6Y0F0|E6Y0F1|E9PGH4|Q4VAL2|Q504W0	Frame_Shift_Del	DEL	ENST00000296795.3	hg19	CCDS3846.1																																																																																			.	.		0.353	TLR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360313.4		
ITIH5	80760	hgsc.bcm.edu	37	10	7618714	7618714	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:7618714delG	ENST00000256861.6	-	10	1758	c.1680delC	c.(1678-1680)cccfs	p.P560fs	ITIH5_ENST00000298441.6_Frame_Shift_Del_p.P346fs|ITIH5_ENST00000397145.2_Frame_Shift_Del_p.P560fs|ITIH5_ENST00000446830.2_Frame_Shift_Del_p.P342fs|ITIH5_ENST00000397146.2_Frame_Shift_Del_p.P560fs|ITIH5_ENST00000434980.1_5'UTR	NM_030569.6	NP_085046.5	Q86UX2	ITIH5_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 5	560					hyaluronan metabolic process (GO:0030212)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(5)|kidney(6)|large_intestine(21)|lung(25)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|urinary_tract(3)	75						CTCCAGGCCTGGGGCTTCCTG	0.577																																					p.R561fs		Atlas-INDEL	.											.	ITIH5	343	.	0			c.1681delA						.						59.0	58.0	58.0					10																	7618714		2203	4300	6503	SO:0001589	frameshift_variant	80760	exon10			.			10p14	2011-10-26	2011-10-26		ENSG00000123243	ENSG00000123243			21449	protein-coding gene	gene with protein product		609783	"""inter-alpha (globulin) inhibitor H5"""			14744536	Standard	NM_001001851		Approved	MGC10848	uc021pmv.1	Q86UX2	OTTHUMG00000017635	ENST00000256861.6:c.1680delC	chr10.hg19:g.7618714delG	ENSP00000256861:p.Pro560fs	219.0	0.0		144.0	11.0	NM_001001851	Q5T664|Q5T665|Q5T666|Q6AI60|Q6UXB7|Q8TF48|Q8WYV2|Q96K70	Frame_Shift_Del	DEL	ENST00000256861.6	hg19																																																																																				.	.		0.577	ITIH5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000046688.1	NM_030569	
DOCK6	57572	hgsc.bcm.edu	37	19	11363499	11363499	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:11363499delG	ENST00000294618.7	-	3	279	c.268delC	c.(268-270)cggfs	p.R90fs		NM_020812.3	NP_065863.2	Q96HP0	DOCK6_HUMAN	dedicator of cytokinesis 6	90					blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|central_nervous_system(1)|endometrium(11)|large_intestine(8)|liver(2)|lung(9)|ovary(4)|prostate(1)|skin(1)|urinary_tract(1)	39						CGGCATTCCCGGGGCTGCAGC	0.632																																					p.R90fs		Atlas-INDEL	.											.	DOCK6	104	.	0			c.269delG						.						24.0	27.0	26.0					19																	11363499		1891	4110	6001	SO:0001589	frameshift_variant	57572	exon3			.		CCDS45975.1	19p13.2	2011-08-04			ENSG00000130158	ENSG00000130158			19189	protein-coding gene	gene with protein product		614194				12432077	Standard	NM_020812		Approved	KIAA1395, ZIR1	uc002mqs.5	Q96HP0		ENST00000294618.7:c.268delC	chr19.hg19:g.11363499delG	ENSP00000294618:p.Arg90fs	231.0	0.0		165.0	11.0	NM_020812	A6H8X5|Q7Z7P4|Q9P2F2	Frame_Shift_Del	DEL	ENST00000294618.7	hg19	CCDS45975.1																																																																																			.	.		0.632	DOCK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453155.1	NM_020812	
PPIC	5480	hgsc.bcm.edu	37	5	122364469	122364469	+	Splice_Site	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:122364469delC	ENST00000306442.4	-	3	441		c.e3+1			NM_000943.4	NP_000934.1	P45877	PPIC_HUMAN	peptidylprolyl isomerase C (cyclophilin C)						protein folding (GO:0006457)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	cyclosporin A binding (GO:0016018)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)|urinary_tract(1)	6		all_cancers(142;0.0168)|Prostate(80;0.0322)|Lung NSC(810;0.102)|all_lung(232;0.163)	KIRC - Kidney renal clear cell carcinoma(527;0.0897)|Kidney(363;0.137)	OV - Ovarian serous cystadenocarcinoma(64;0.000331)|Epithelial(69;0.000553)|all cancers(49;0.00505)	L-Proline(DB00172)	AAAGACGTTACCCCCAGTGCC	0.413																																					.	Ovarian(99;690 1502 20765 45543 49568)	Atlas-INDEL	.											.	PPIC	18	.	0			c.325+2G>-						.						135.0	107.0	116.0					5																	122364469		2203	4300	6503	SO:0001630	splice_region_variant	5480	exon4			.	S71018	CCDS4133.1	5q23.2	2008-02-05			ENSG00000168938	ENSG00000168938	5.2.1.8		9256	protein-coding gene	gene with protein product		123842				1383094, 8031755	Standard	NM_000943		Approved	CYPC	uc003kth.3	P45877	OTTHUMG00000128921	ENST00000306442.4:c.325+1G>-	chr5.hg19:g.122364469delC		211.0	0.0		164.0	10.0	NM_000943	A4LBB5	Splice_Site	DEL	ENST00000306442.4	hg19	CCDS4133.1																																																																																			.	.		0.413	PPIC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250898.2	NM_000943	Intron
KALRN	8997	hgsc.bcm.edu	37	3	124174076	124174076	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:124174076delA	ENST00000240874.3	+	22	3756	c.3599delA	c.(3598-3600)gaafs	p.E1200fs	KALRN_ENST00000360013.3_Frame_Shift_Del_p.E1200fs|KALRN_ENST00000460856.1_Frame_Shift_Del_p.E1191fs	NM_003947.4	NP_003938.1	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase	1200					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						AGCTTTGTGGAAAAAGGCCAC	0.468																																					p.E1200fs		Atlas-INDEL	.											.	KALRN	556	.	0			c.3598delG						.						129.0	119.0	122.0					3																	124174076		2203	4300	6503	SO:0001589	frameshift_variant	8997	exon22			.	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.3599delA	chr3.hg19:g.124174076delA	ENSP00000240874:p.Glu1200fs	173.0	0.0		140.0	10.0	NM_003947	A8MSI4|C9JQ37|Q6ZN45|Q8TBQ5|Q9NSZ4|Q9Y2A5	Frame_Shift_Del	DEL	ENST00000240874.3	hg19	CCDS3027.1																																																																																			.	.		0.468	KALRN-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000258843.4	NM_003947	
SPAST	6683	hgsc.bcm.edu	37	2	32340780	32340780	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:32340780delA	ENST00000315285.3	+	6	1005	c.880delA	c.(880-882)aaafs	p.K294fs	SPAST_ENST00000345662.1_Frame_Shift_Del_p.K262fs	NM_014946.3	NP_055761.2			spastin											breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(8)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)					GGGTACTCCGAAAACAAATAG	0.323																																					p.P293fs		Atlas-INDEL	.											.	SPAST	61	.	0			c.879delG						.						62.0	68.0	66.0					2																	32340780		2202	4299	6501	SO:0001589	frameshift_variant	6683	exon6			.	AJ246001	CCDS1778.1, CCDS1779.1	2p24-p21	2014-09-17	2005-03-15	2005-03-17	ENSG00000021574	ENSG00000021574		"""ATPases / AAA-type"""	11233	protein-coding gene	gene with protein product		604277	"""spastic paraplegia 4 (autosomal dominant; spastin)"""	SPG4		10493830, 10610178	Standard	NM_014946		Approved	FSP2, ADPSP, KIAA1083	uc002roc.3	Q9UBP0	OTTHUMG00000128455	ENST00000315285.3:c.880delA	chr2.hg19:g.32340780delA	ENSP00000320885:p.Lys294fs	171.0	0.0		150.0	10.0	NM_014946		Frame_Shift_Del	DEL	ENST00000315285.3	hg19	CCDS1778.1																																																																																			.	.		0.323	SPAST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250253.1	NM_199436	
ABHD3	171586	hgsc.bcm.edu	37	18	19231648	19231648	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr18:19231648delA	ENST00000289119.2	-	9	1273	c.1134delT	c.(1132-1134)tttfs	p.F378fs	ABHD3_ENST00000580981.1_Frame_Shift_Del_p.F325fs|ABHD3_ENST00000578270.1_Frame_Shift_Del_p.F183fs	NM_138340.4	NP_612213.2	Q8WU67	ABHD3_HUMAN	abhydrolase domain containing 3	378						integral component of membrane (GO:0016021)	carboxylic ester hydrolase activity (GO:0052689)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(2)|prostate(2)	10						TTCCCTCCAGAAAACCAATAT	0.418																																					p.L379fs		Atlas-INDEL	.											.	ABHD3	32	.	0			c.1135delC						.						117.0	102.0	107.0					18																	19231648		2203	4300	6503	SO:0001589	frameshift_variant	171586	exon9			.	AK024880	CCDS32802.1	18q11.1	2011-02-16			ENSG00000158201	ENSG00000158201		"""Abhydrolase domain containing"""	18718	protein-coding gene	gene with protein product		612197					Standard	NM_138340		Approved	LABH3	uc002ktl.2	Q8WU67		ENST00000289119.2:c.1134delT	chr18.hg19:g.19231648delA	ENSP00000289119:p.Phe378fs	228.0	0.0		139.0	12.0	NM_138340	B0YIV0|B7Z5C2|O43411	Frame_Shift_Del	DEL	ENST00000289119.2	hg19	CCDS32802.1																																																																																			.	.		0.418	ABHD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444757.1		
CYP26B1	56603	hgsc.bcm.edu	37	2	72359653	72359653	+	Frame_Shift_Del	DEL	G	G	-	rs150438812		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:72359653delG	ENST00000001146.2	-	6	1445	c.1242delC	c.(1240-1242)cccfs	p.P414fs	CYP26B1_ENST00000412253.1_Frame_Shift_Del_p.P223fs|CYP26B1_ENST00000546307.1_Frame_Shift_Del_p.P339fs	NM_001277742.1|NM_019885.2	NP_001264671.1|NP_063938.1	Q9NR63	CP26B_HUMAN	cytochrome P450, family 26, subfamily B, polypeptide 1	414					bone morphogenesis (GO:0060349)|cell fate determination (GO:0001709)|cellular response to retinoic acid (GO:0071300)|cornification (GO:0070268)|embryonic limb morphogenesis (GO:0030326)|establishment of skin barrier (GO:0061436)|male meiosis (GO:0007140)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|oxidation-reduction process (GO:0055114)|positive regulation of gene expression (GO:0010628)|positive regulation of tongue muscle cell differentiation (GO:2001037)|proximal/distal pattern formation (GO:0009954)|retinoic acid catabolic process (GO:0034653)|retinoic acid receptor signaling pathway (GO:0048384)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|tongue morphogenesis (GO:0043587)|vitamin metabolic process (GO:0006766)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|retinoic acid 4-hydroxylase activity (GO:0008401)|retinoic acid binding (GO:0001972)			breast(1)|kidney(3)|large_intestine(2)|lung(16)|ovary(2)|prostate(2)|skin(2)	28						TGAAGCGATCGGGGTCGAACA	0.617																																					p.D415fs		Atlas-INDEL	.											CYP26B1,NS,carcinoma,0,1	CYP26B1	73	.	0			c.1243delG						.						56.0	49.0	51.0					2																	72359653		2203	4300	6503	SO:0001589	frameshift_variant	56603	exon6			.		CCDS1919.1, CCDS62934.1	2p12	2006-11-24			ENSG00000003137	ENSG00000003137		"""Cytochrome P450s"""	20581	protein-coding gene	gene with protein product		605207				10545224	Standard	NM_019885		Approved	P450RAI-2	uc002sih.2	Q9NR63	OTTHUMG00000129756	ENST00000001146.2:c.1242delC	chr2.hg19:g.72359653delG	ENSP00000001146:p.Pro414fs	290.0	0.0		202.0	14.0	NM_019885	B2R8M7|B7Z2K6|B7Z2P4|B7Z3B8|E4W5W7|Q32MC0|Q53TW1|Q9NP41	Frame_Shift_Del	DEL	ENST00000001146.2	hg19	CCDS1919.1																																																																																			.	.		0.617	CYP26B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251969.1	NM_019885	
MPDZ	8777	hgsc.bcm.edu	37	9	13123168	13123168	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:13123168delC	ENST00000319217.7	-	36	5184	c.4937delG	c.(4936-4938)ggtfs	p.G1646fs	MPDZ_ENST00000541093.1_5'UTR|MPDZ_ENST00000546205.1_Frame_Shift_Del_p.G1660fs|MPDZ_ENST00000538841.1_Frame_Shift_Del_p.G505fs|MPDZ_ENST00000536827.1_Frame_Shift_Del_p.G1613fs|MPDZ_ENST00000541718.1_Frame_Shift_Del_p.G1646fs|MPDZ_ENST00000381015.4_Frame_Shift_Del_p.G1646fs|MPDZ_ENST00000447879.1_Frame_Shift_Del_p.G1613fs|MPDZ_ENST00000381022.2_Frame_Shift_Del_p.G1646fs	NM_001261406.1	NP_001248335.1	O75970	MPDZ_HUMAN	multiple PDZ domain protein	1646	PDZ 10. {ECO:0000255|PROSITE- ProRule:PRU00143}.				cell adhesion (GO:0007155)|myelination (GO:0042552)|viral process (GO:0016032)	apical plasma membrane (GO:0016324)|apicolateral plasma membrane (GO:0016327)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|neuron projection (GO:0043005)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)|tight junction (GO:0005923)	protein C-terminus binding (GO:0008022)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(14)|lung(15)|ovary(5)|prostate(7)|stomach(1)|urinary_tract(2)	61				GBM - Glioblastoma multiforme(50;2.03e-06)		CGTGTCTGAACCCCCAACGAT	0.557																																					p.G1646fs		Atlas-INDEL	.											.	MPDZ	324	.	0			c.4938delT						.						50.0	52.0	52.0					9																	13123168		1939	4140	6079	SO:0001589	frameshift_variant	8777	exon36			.	AF093419	CCDS47951.1, CCDS59119.1, CCDS59120.1	9p23	2008-05-15			ENSG00000107186	ENSG00000107186			7208	protein-coding gene	gene with protein product		603785					Standard	NM_003829		Approved	MUPP1	uc003zlb.4	O75970	OTTHUMG00000021031	ENST00000319217.7:c.4937delG	chr9.hg19:g.13123168delC	ENSP00000320006:p.Gly1646fs	202.0	0.0		145.0	10.0	NM_003829	A6NLC2|B2RTS3|B7ZMI4|O43798|Q4LE30|Q5CZ80|Q5JTX3|Q5JTX6|Q5JTX7|Q5JUC3|Q5JUC4|Q5VZ62|Q8N790	Frame_Shift_Del	DEL	ENST00000319217.7	hg19																																																																																				.	.		0.557	MPDZ-001	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000055485.2	NM_003829	
TTLL2	83887	hgsc.bcm.edu	37	6	167755064	167755064	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:167755064delT	ENST00000239587.5	+	3	1764	c.1676delT	c.(1675-1677)gttfs	p.V559fs		NM_031949.4	NP_114155.4	Q9BWV7	TTLL2_HUMAN	tubulin tyrosine ligase-like family, member 2	559			V -> I (in dbSNP:rs34931196).		cellular protein modification process (GO:0006464)		ligase activity (GO:0016874)			central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(17)|ovary(1)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	39		Breast(66;7.8e-06)|Ovarian(120;0.024)		OV - Ovarian serous cystadenocarcinoma(33;2.22e-20)|BRCA - Breast invasive adenocarcinoma(81;6.17e-07)|GBM - Glioblastoma multiforme(31;0.00492)		TTTGTTCTTGTTTTTCCTTTC	0.468																																					p.V559fs		Atlas-INDEL	.											.	TTLL2	82	.	0			c.1675delG						.						92.0	89.0	90.0					6																	167755064		2203	4300	6503	SO:0001589	frameshift_variant	83887	exon3			.	AK093039	CCDS5301.1	6q27	2013-02-14		2004-01-14	ENSG00000120440	ENSG00000120440		"""Tubulin tyrosine ligase-like family"""	21211	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 104"""	C6orf104		11054573	Standard	XM_006715572		Approved	NYD-TSPG, dJ366N23.3	uc003qvs.1	Q9BWV7	OTTHUMG00000016023	ENST00000239587.5:c.1676delT	chr6.hg19:g.167755064delT	ENSP00000239587:p.Val559fs	233.0	0.0		186.0	12.0	NM_031949	B2RB11|B3KS77|Q7Z6R8|Q86X22	Frame_Shift_Del	DEL	ENST00000239587.5	hg19	CCDS5301.1																																																																																			.	.		0.468	TTLL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043127.3	NM_031949	
GK5	256356	hgsc.bcm.edu	37	3	141896386	141896386	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:141896386delT	ENST00000392993.2	-	12	1232	c.1081delA	c.(1081-1083)atgfs	p.M361fs		NM_001039547.2	NP_001034636.1	Q6ZS86	GLPK5_HUMAN	glycerol kinase 5 (putative)	361					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						CTTTTGGCCATTTTTTCAGTC	0.338																																					p.M361fs		Atlas-INDEL	.											.,1	GK5	45	.	0			c.1082delT						.						115.0	123.0	121.0					3																	141896386		2203	4300	6503	SO:0001589	frameshift_variant	256356	exon12			.	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.1081delA	chr3.hg19:g.141896386delT	ENSP00000418001:p.Met361fs	269.0	0.0		191.0	12.0	NM_001039547	B2R9I2|D3DNG2|Q8N2A7|Q8N5E6	Frame_Shift_Del	DEL	ENST00000392993.2	hg19	CCDS33871.1																																																																																			.	.		0.338	GK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353999.1	NM_001039547	
BNIP2	663	hgsc.bcm.edu	37	15	59970126	59970126	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:59970126delT	ENST00000607373.1	-	5	658	c.456delA	c.(454-456)aaafs	p.K152fs	BNIP2_ENST00000415213.2_Frame_Shift_Del_p.K214fs|BNIP2_ENST00000267859.3_Frame_Shift_Del_p.K273fs	NM_004330.2	NP_004321.2	Q12982	BNIP2_HUMAN	BCL2/adenovirus E1B 19kDa interacting protein 2	152	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.				apoptotic process (GO:0006915)|muscle cell differentiation (GO:0042692)|negative regulation of apoptotic process (GO:0043066)|positive regulation of GTPase activity (GO:0043547)|positive regulation of muscle cell differentiation (GO:0051149)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nuclear envelope (GO:0005635)	calcium ion binding (GO:0005509)|GTPase activator activity (GO:0005096)|identical protein binding (GO:0042802)			NS(1)|large_intestine(2)|lung(5)|ovary(1)	9						GGCTGATAACTTTTTTATAGG	0.388																																					p.V274fs	Ovarian(174;1936 1978 6671 8240 38212)	Atlas-INDEL	.											.	BNIP2	27	.	0			c.820delG						.						130.0	130.0	130.0					15																	59970126		2190	4290	6480	SO:0001589	frameshift_variant	663	exon5			.	U15173	CCDS10174.2	15q21.3	2008-07-18	2002-08-29		ENSG00000140299	ENSG00000140299			1083	protein-coding gene	gene with protein product		603292	"""BCL2/adenovirus E1B 19kD-interacting protein 2"""			7954800	Standard	NM_004330		Approved	Nip2, BNIP-2	uc010uhc.2	Q12982	OTTHUMG00000132727	ENST00000607373.1:c.456delA	chr15.hg19:g.59970126delT	ENSP00000475320:p.Lys152fs	259.0	0.0		204.0	13.0	NM_004330	B4DS94	Frame_Shift_Del	DEL	ENST00000607373.1	hg19																																																																																				.	.		0.388	BNIP2-012	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000470740.1	NM_004330	
HNRNPU	3192	hgsc.bcm.edu	37	1	245027581	245027581	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:245027581delT	ENST00000283179.9	-	1	192	c.29delA	c.(28-30)aagfs	p.K10fs	HNRNPU_ENST00000444376.2_Frame_Shift_Del_p.K10fs|RP11-11N7.4_ENST00000610145.1_lincRNA			Q00839	HNRPU_HUMAN	heterogeneous nuclear ribonucleoprotein U (scaffold attachment factor A)	10	Asp/Glu-rich (acidic).|SAP. {ECO:0000255|PROSITE- ProRule:PRU00186}.				CRD-mediated mRNA stabilization (GO:0070934)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|osteoblast differentiation (GO:0001649)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|CRD-mediated mRNA stability complex (GO:0070937)|cytoplasmic ribonucleoprotein granule (GO:0036464)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|endometrium(2)|large_intestine(1)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20	all_cancers(71;6.97e-06)|all_epithelial(71;0.000104)|all_neural(11;0.0269)|Breast(184;0.0545)|Glioma(6;0.0724)|Ovarian(71;0.0761)|all_lung(81;0.0989)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.00868)			CACCTTCAGCTTTTTTACATT	0.597																																					p.K10fs	NSCLC(33;911 1010 3329 23631 49995)	Atlas-INDEL	.											.	HNRNPU	64	.	0			c.30delG						.						25.0	29.0	27.0					1																	245027581		2201	4295	6496	SO:0001589	frameshift_variant	3192	exon1			.	X65488	CCDS31081.1, CCDS41479.1	1q44	2011-10-24		2007-08-16	ENSG00000153187	ENSG00000153187			5048	protein-coding gene	gene with protein product		602869		HNRPU		7509195, 8068679	Standard	NM_031844		Approved	SAF-A, hnRNPU	uc001iaz.1	Q00839	OTTHUMG00000040396	ENST00000283179.9:c.29delA	chr1.hg19:g.245027581delT	ENSP00000283179:p.Lys10fs	267.0	0.0		316.0	19.0	NM_004501	O75507|Q8N174|Q96HY9|Q9BQ09	Frame_Shift_Del	DEL	ENST00000283179.9	hg19	CCDS41479.1																																																																																			.	.		0.597	HNRNPU-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000097163.3	NM_031844	
PGBD2	267002	hgsc.bcm.edu	37	1	249211954	249211954	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:249211954delA	ENST00000329291.5	+	3	1318	c.1171delA	c.(1171-1173)aaafs	p.K392fs	PGBD2_ENST00000355360.4_Frame_Shift_Del_p.K141fs|PGBD2_ENST00000539153.1_Frame_Shift_Del_p.K389fs	NM_170725.2	NP_733843.1	Q6P3X8	PGBD2_HUMAN	piggyBac transposable element derived 2	392										NS(1)|endometrium(3)|lung(6)|ovary(1)|skin(3)	14	all_cancers(71;3.33e-06)|all_epithelial(71;2.41e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.0458)|Lung NSC(105;0.0494)|Melanoma(84;0.199)	all_cancers(173;0.012)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)			CAAAGAACTGAAAAAAATGAA	0.463																																					p.L390fs		Atlas-INDEL	.											.	PGBD2	103	.	0			c.1170delG						.						59.0	64.0	62.0					1																	249211954		2203	4300	6503	SO:0001589	frameshift_variant	267002	exon3			.	AF229602	CCDS31128.1, CCDS31129.1	1q	2008-02-05			ENSG00000185220	ENSG00000185220			19399	protein-coding gene	gene with protein product							Standard	XM_005270333		Approved		uc001ifh.3	Q6P3X8	OTTHUMG00000040424	ENST00000329291.5:c.1171delA	chr1.hg19:g.249211954delA	ENSP00000331643:p.Lys392fs	158.0	0.0		229.0	14.0	NM_170725	B3KVR8|Q6MZF8	Frame_Shift_Del	DEL	ENST00000329291.5	hg19	CCDS31128.1																																																																																			.	.		0.463	PGBD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000097318.1		
B3GNT4	79369	hgsc.bcm.edu	37	12	122691000	122691000	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:122691000delC	ENST00000324189.4	+	3	558	c.202delC	c.(202-204)cccfs	p.P69fs	B3GNT4_ENST00000545141.1_Intron|B3GNT4_ENST00000546192.1_Frame_Shift_Del_p.P44fs|B3GNT4_ENST00000535274.1_Frame_Shift_Del_p.P44fs	NM_030765.2	NP_110392.1	Q9C0J1	B3GN4_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 4	69					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	galactosyltransferase activity (GO:0008378)			NS(2)|breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	13	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000297)|Epithelial(86;0.000497)|BRCA - Breast invasive adenocarcinoma(302;0.222)		TTTCTGGGCTCCCCCAACACC	0.637																																					p.A67fs		Atlas-INDEL	.											.	B3GNT4	35	.	0			c.201delT						.						130.0	136.0	134.0					12																	122691000		2203	4300	6503	SO:0001589	frameshift_variant	79369	exon3			.	AB049586	CCDS9227.1	12q24	2013-02-19						"""Beta 3-glycosyltransferases"""	15683	protein-coding gene	gene with protein product		605864				11042166	Standard	NM_030765		Approved	B3GN-T4, beta3Gn-T4	uc001ubx.3	Q9C0J1		ENST00000324189.4:c.202delC	chr12.hg19:g.122691000delC	ENSP00000319636:p.Pro69fs	227.0	0.0		138.0	10.0	NM_030765	Q8N5W4|Q8N934|Q8ND21|Q8WWR5|Q8WY02|Q96QH5	Frame_Shift_Del	DEL	ENST00000324189.4	hg19	CCDS9227.1																																																																																			.	.		0.637	B3GNT4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000401595.1	NM_030765	
TNXB	7148	hgsc.bcm.edu	37	6	32036432	32036432	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:32036432delG	ENST00000375244.3	-	17	6156	c.5955delC	c.(5953-5955)cccfs	p.P1985fs	TNXB_ENST00000375247.2_Frame_Shift_Del_p.P1985fs			P22105	TENX_HUMAN	tenascin XB	2067	Fibronectin type-III 12. {ECO:0000255|PROSITE-ProRule:PRU00316}.				actin cytoskeleton organization (GO:0030036)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|fatty acid metabolic process (GO:0006631)|regulation of JUN kinase activity (GO:0043506)|single organismal cell-cell adhesion (GO:0016337)|triglyceride metabolic process (GO:0006641)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						GAGGCTTGATGGGGGGCTCGG	0.632																																					p.I1986fs		Atlas-INDEL	.											.	TNXB	553	.	0			c.5956delA						.						44.0	50.0	48.0					6																	32036432		1943	4133	6076	SO:0001589	frameshift_variant	7148	exon17			.	X71923	CCDS4736.1	6p21.3	2013-02-11			ENSG00000168477	ENSG00000168477		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	11976	protein-coding gene	gene with protein product		600985		TNXB1, TNXB2		8530023	Standard	NM_019105		Approved	TNXBS, XBS, XB	uc021yvf.2	P22105	OTTHUMG00000031088	ENST00000375244.3:c.5955delC	chr6.hg19:g.32036432delG	ENSP00000364393:p.Pro1985fs	215.0	0.0		190.0	12.0	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Frame_Shift_Del	DEL	ENST00000375244.3	hg19																																																																																				.	.		0.632	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105	
ITGA4	3676	hgsc.bcm.edu	37	2	182339748	182339748	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:182339748delG	ENST00000397033.2	+	3	811	c.381delG	c.(379-381)ttgfs	p.L127fs	ITGA4_ENST00000339307.4_Frame_Shift_Del_p.L127fs|ITGA4_ENST00000478440.1_3'UTR	NM_000885.4	NP_000876.3	P13612	ITA4_HUMAN	integrin, alpha 4 (antigen CD49D, alpha 4 subunit of VLA-4 receptor)	127					B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|blood vessel remodeling (GO:0001974)|cell-matrix adhesion (GO:0007160)|cell-matrix adhesion involved in ameboidal cell migration (GO:0003366)|chorio-allantoic fusion (GO:0060710)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|face development (GO:0060324)|heart development (GO:0007507)|heterophilic cell-cell adhesion (GO:0007157)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)|negative regulation of protein homodimerization activity (GO:0090074)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|substrate adhesion-dependent cell spreading (GO:0034446)|T cell migration (GO:0072678)	cell surface (GO:0009986)|cell-cell junction (GO:0005911)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integrin alpha4-beta7 complex (GO:0034669)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(27)|ovary(3)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	58			OV - Ovarian serous cystadenocarcinoma(117;0.0593)		Natalizumab(DB00108)|Tinzaparin(DB06822)	ATCAGTGGTTGGGGGTCACAC	0.438																																					p.L127fs		Atlas-INDEL	.											.	ITGA4	142	.	0			c.380delT						.						92.0	92.0	92.0					2																	182339748		1899	4127	6026	SO:0001589	frameshift_variant	3676	exon3			.		CCDS42788.1	2q31-q32	2010-03-23			ENSG00000115232	ENSG00000115232		"""CD molecules"", ""Integrins"""	6140	protein-coding gene	gene with protein product		192975		CD49D		1537388	Standard	NM_000885		Approved	CD49d	uc002unu.3	P13612	OTTHUMG00000154212	ENST00000397033.2:c.381delG	chr2.hg19:g.182339748delG	ENSP00000380227:p.Leu127fs	322.0	0.0		250.0	15.0	NM_000885	D3DPG4|Q7Z4L6	Frame_Shift_Del	DEL	ENST00000397033.2	hg19	CCDS42788.1																																																																																			.	.		0.438	ITGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334427.1		
KIAA1467	57613	hgsc.bcm.edu	37	12	13237891	13237891	+	IGR	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:13237891delC	ENST00000197268.8	+	0	4808				GSG1_ENST00000537302.1_Frame_Shift_Del_p.A281fs|GSG1_ENST00000432710.2_Frame_Shift_Del_p.A322fs|GSG1_ENST00000396310.2_Frame_Shift_Del_p.A278fs|GSG1_ENST00000351606.6_3'UTR|GSG1_ENST00000396302.3_3'UTR|GSG1_ENST00000324458.8_Frame_Shift_Del_p.A345fs|GSG1_ENST00000337630.6_Frame_Shift_Del_p.A309fs|GSG1_ENST00000457134.2_Frame_Shift_Del_p.A258fs	NM_020853.1	NP_065904.1	A2RU67	K1467_HUMAN	KIAA1467							integral component of membrane (GO:0016021)				NS(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(13)|ovary(1)|prostate(1)|skin(4)	36		Prostate(47;0.184)		BRCA - Breast invasive adenocarcinoma(232;0.157)		TCCTGGCTGGCCCCTCTTTGA	0.517																																					p.A345fs		Atlas-INDEL	.											.	GSG1	62	.	0			c.1034delC						.						95.0	104.0	101.0					12																	13237891		1280	2295	3575	SO:0001628	intergenic_variant	83445	exon7			.	AB040900	CCDS31750.1	12p13.1	2006-01-23				ENSG00000084444			29288	protein-coding gene	gene with protein product						10819331	Standard	XM_005253450		Approved		uc001rbi.3	A2RU67			chr12.hg19:g.13237891delC		342.0	0.0		209.0	13.0	NM_001080555	Q49AF2|Q5CZ81|Q6ZUV7|Q9P261	Frame_Shift_Del	DEL	ENST00000197268.8	hg19	CCDS31750.1																																																																																			.	.		0.517	KIAA1467-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401007.1	NM_020853	
EPHA8	2046	hgsc.bcm.edu	37	1	22927800	22927800	+	Frame_Shift_Del	DEL	C	C	-	rs571732433		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:22927800delC	ENST00000166244.3	+	16	2809	c.2737delC	c.(2737-2739)cccfs	p.P914fs		NM_020526.3	NP_065387.1	P29322	EPHA8_HUMAN	EPH receptor A8	914					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|ephrin receptor signaling pathway (GO:0048013)|neuron projection development (GO:0031175)|neuron remodeling (GO:0016322)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|protein autophosphorylation (GO:0046777)|regulation of cell adhesion (GO:0030155)|regulation of cell adhesion mediated by integrin (GO:0033628)|substrate-dependent cell migration (GO:0006929)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)			breast(3)|central_nervous_system(5)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(9)|large_intestine(6)|lung(22)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	61		Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;7.29e-27)|Colorectal(126;1.61e-07)|COAD - Colon adenocarcinoma(152;1.14e-05)|GBM - Glioblastoma multiforme(114;1.74e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000554)|KIRC - Kidney renal clear cell carcinoma(1967;0.00272)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		CAGGTGCCCACCCCCTGCCTT	0.697																																					p.P912fs		Atlas-INDEL	.											.	EPHA8	221	.	0			c.2736delA						.						36.0	41.0	40.0					1																	22927800		2176	4230	6406	SO:0001589	frameshift_variant	2046	exon16			.	BC038796	CCDS225.1, CCDS30626.1	1p36.12	2013-02-11	2004-10-28		ENSG00000070886	ENSG00000070886	2.7.10.1	"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3391	protein-coding gene	gene with protein product		176945	"""EphA8"""	EEK		1648701	Standard	NM_001006943		Approved	Hek3	uc001bfx.1	P29322	OTTHUMG00000002892	ENST00000166244.3:c.2737delC	chr1.hg19:g.22927800delC	ENSP00000166244:p.Pro914fs	271.0	0.0		222.0	14.0	NM_020526	Q6IN80|Q8IUX6|Q9NUA9|Q9P269	Frame_Shift_Del	DEL	ENST00000166244.3	hg19	CCDS225.1																																																																																			.	.		0.697	EPHA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008085.1	NM_020526	
SWT1	54823	hgsc.bcm.edu	37	1	185143640	185143640	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:185143640delA	ENST00000367500.4	+	5	526	c.361delA	c.(361-363)aaafs	p.K122fs	SWT1_ENST00000367501.3_Frame_Shift_Del_p.K122fs	NM_017673.6	NP_060143.4	Q5T5J6	SWT1_HUMAN	SWT1 RNA endoribonuclease homolog (S. cerevisiae)	122										breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(11)|liver(1)|lung(16)|ovary(1)|prostate(1)|urinary_tract(1)	41						AAATGGAACTAAAAAAGACAT	0.323																																					p.T120fs		Atlas-INDEL	.											.	SWT1	88	.	0			c.360delT						.						40.0	41.0	40.0					1																	185143640		2203	4300	6503	SO:0001589	frameshift_variant	54823	exon5			.	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.361delA	chr1.hg19:g.185143640delA	ENSP00000356470:p.Lys122fs	207.0	0.0		238.0	15.0	NM_017673	Q8NEK9|Q9BZQ7|Q9NXQ0	Frame_Shift_Del	DEL	ENST00000367500.4	hg19	CCDS1367.1																																																																																			.	.		0.323	SWT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085790.1	NM_017673	
ZNF71	58491	hgsc.bcm.edu	37	19	57133366	57133366	+	Frame_Shift_Del	DEL	G	G	-	rs373155014		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:57133366delG	ENST00000328070.6	+	3	945	c.711delG	c.(709-711)acgfs	p.T237fs		NM_021216.4	NP_067039.1	Q9NQZ8	ZNF71_HUMAN	zinc finger protein 71	237					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|large_intestine(5)|lung(13)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	26				GBM - Glioblastoma multiforme(193;0.062)|Lung(386;0.0681)|LUSC - Lung squamous cell carcinoma(496;0.18)		GGATCCACACGGGGGAGAAGC	0.652																																					p.T237fs		Atlas-INDEL	.											.	ZNF71	69	.	0			c.710delC						.						50.0	47.0	48.0					19																	57133366		2203	4300	6503	SO:0001589	frameshift_variant	58491	exon3			.	X60074	CCDS12947.1	19q13.4	2013-01-08	2006-05-12			ENSG00000197951		"""Zinc fingers, C2H2-type"""	13141	protein-coding gene	gene with protein product		194545	"""zinc finger protein 71 (Cos26)"""			1639391	Standard	NM_021216		Approved	Cos26, EZFIT	uc002qnm.4	Q9NQZ8		ENST00000328070.6:c.711delG	chr19.hg19:g.57133366delG	ENSP00000328245:p.Thr237fs	239.0	0.0		163.0	10.0	NM_021216	Q15919|Q9UC09|Q9UQD3	Frame_Shift_Del	DEL	ENST00000328070.6	hg19	CCDS12947.1																																																																																			.	.		0.652	ZNF71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459798.2	NM_021216	
INTS1	26173	hgsc.bcm.edu	37	7	1517412	1517412	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:1517412delC	ENST00000404767.3	-	34	4876	c.4791delG	c.(4789-4791)gggfs	p.G1597fs	INTS1_ENST00000389470.4_Frame_Shift_Del_p.G1796fs	NM_001080453.2	NP_001073922.2	Q8N201	INT1_HUMAN	integrator complex subunit 1	1597					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)				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)		CACCCGGCTTCCCCCCAGCCA	0.697																																					p.K1598fs		Atlas-INDEL	.											.	INTS1	145	.	0			c.4792delA						.						22.0	28.0	26.0					7																	1517412		2046	4170	6216	SO:0001589	frameshift_variant	26173	exon34			.	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.4791delG	chr7.hg19:g.1517412delC	ENSP00000385722:p.Gly1597fs	177.0	0.0		195.0	13.0	NM_001080453	A6NJ44|Q6NT70|Q6UX74|Q8WV40|Q96D36|Q9NTD1|Q9P2A8|Q9Y3W8	Frame_Shift_Del	DEL	ENST00000404767.3	hg19	CCDS47526.1																																																																																			.	.		0.697	INTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323683.1		
MIR205HG	642587	hgsc.bcm.edu	37	1	209602687	209602687	+	lincRNA	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:209602687delC	ENST00000384891.1	+	0	0					NR_029622.1				MIR205 host gene (non-protein coding)																		TCAGGACCGGCCCCCACCTTT	0.502																																					p.G15fs		Atlas-INDEL	.											.	.	.	.	0			c.44delG						.						60.0	62.0	62.0					1																	209602687		1874	4086	5960			642587	exon2			.			1q32.2	2014-02-12	2011-11-07		ENSG00000230937	ENSG00000230937		"""Long non-coding RNAs"""	43562	non-coding RNA	RNA, long non-coding	"""long intergenic non-protein coding RNA 510"""						Standard	NM_001104548		Approved	LINC00510	uc009xcn.3		OTTHUMG00000036267		chr1.hg19:g.209602687delC		164.0	0.0		195.0	14.0	NM_001104548		Frame_Shift_Del	DEL	ENST00000384891.1	hg19																																																																																				.	.		0.502	MIR205HG-202	KNOWN	basic	miRNA	lincRNA			
C3orf38	285237	hgsc.bcm.edu	37	3	88205437	88205437	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:88205437delC	ENST00000318887.3	+	3	952	c.642delC	c.(640-642)agcfs	p.S214fs	C3orf38_ENST00000486971.1_3'UTR	NM_173824.3	NP_776185.2	Q5JPI3	CC038_HUMAN	chromosome 3 open reading frame 38	214					apoptotic process (GO:0006915)					breast(1)|large_intestine(2)|lung(6)|prostate(1)|skin(1)|urinary_tract(1)	12		Lung NSC(201;0.17)		UCEC - Uterine corpus endometrioid carcinoma (27;0.194)|LUSC - Lung squamous cell carcinoma(29;0.00353)|Lung(72;0.00661)		TTTTTCTCAGCCCCAACCTAG	0.433																																					p.S214fs		Atlas-INDEL	.											.	C3orf38	29	.	0			c.641delG						.						133.0	128.0	130.0					3																	88205437		2203	4300	6503	SO:0001589	frameshift_variant	285237	exon3			.	AL832398	CCDS2921.1, CCDS2921.2	3p11.1	2011-01-25			ENSG00000179021	ENSG00000179021			28384	protein-coding gene	gene with protein product						12477932	Standard	NM_173824		Approved	MGC26717	uc003dqw.3	Q5JPI3	OTTHUMG00000155752	ENST00000318887.3:c.642delC	chr3.hg19:g.88205437delC	ENSP00000322469:p.Ser214fs	189.0	0.0		143.0	10.0	NM_173824	B2R8X6|Q8TC85	Frame_Shift_Del	DEL	ENST00000318887.3	hg19	CCDS2921.2																																																																																			.	.		0.433	C3orf38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341513.1	NM_173824	
TNFSF11	8600	hgsc.bcm.edu	37	13	43180938	43180938	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr13:43180938delT	ENST00000239849.6	+	5	989	c.838delT	c.(838-840)tttfs	p.F281fs	TNFSF11_ENST00000405262.2_Frame_Shift_Del_p.F208fs|TNFSF11_ENST00000398795.2_Frame_Shift_Del_p.F208fs|TNFSF11_ENST00000544862.1_Frame_Shift_Del_p.F208fs|TNFSF11_ENST00000358545.2_Frame_Shift_Del_p.F208fs			O14788	TNF11_HUMAN	tumor necrosis factor (ligand) superfamily, member 11	281					activation of JUN kinase activity (GO:0007257)|bone resorption (GO:0045453)|calcium ion homeostasis (GO:0055074)|cytokine-mediated signaling pathway (GO:0019221)|ERK1 and ERK2 cascade (GO:0070371)|immune response (GO:0006955)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell proliferation (GO:0033598)|monocyte chemotaxis (GO:0002548)|organ morphogenesis (GO:0009887)|ossification (GO:0001503)|osteoclast differentiation (GO:0030316)|osteoclast proliferation (GO:0002158)|positive regulation of bone resorption (GO:0045780)|positive regulation of corticotropin-releasing hormone secretion (GO:0051466)|positive regulation of ERK1 and ERK2 cascade via TNFSF11-mediated signaling (GO:0071848)|positive regulation of fever generation by positive regulation of prostaglandin secretion (GO:0071812)|positive regulation of homotypic cell-cell adhesion (GO:0034112)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of JNK cascade (GO:0046330)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of osteoclast development (GO:2001206)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of T cell activation (GO:0050870)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein homooligomerization (GO:0051260)|TNFSF11-mediated signaling pathway (GO:0071847)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)	cytokine activity (GO:0005125)|tumor necrosis factor receptor binding (GO:0005164)|tumor necrosis factor receptor superfamily binding (GO:0032813)			kidney(1)|large_intestine(4)|lung(3)|prostate(1)|urinary_tract(1)	10		Lung NSC(96;1.11e-05)|Breast(139;0.00868)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;0.000249)|GBM - Glioblastoma multiforme(144;0.00119)|BRCA - Breast invasive adenocarcinoma(63;0.073)	Denosumab(DB06643)|Lenalidomide(DB00480)	CGTTGGTGGATTTTTTAAGTT	0.428																																					p.G279fs		Atlas-INDEL	.											.	TNFSF11	43	.	0			c.837delA						.						91.0	91.0	91.0					13																	43180938		2203	4300	6503	SO:0001589	frameshift_variant	8600	exon5			.	AF013171	CCDS9384.1, CCDS9385.1	13q14	2008-02-05			ENSG00000120659	ENSG00000120659		"""Tumor necrosis factor (ligand) superfamily"", ""CD molecules"""	11926	protein-coding gene	gene with protein product		602642				9312132, 9367155	Standard	NM_003701		Approved	TRANCE, RANKL, OPGL, ODF, CD254	uc001uyu.2	O14788	OTTHUMG00000016807	ENST00000239849.6:c.838delT	chr13.hg19:g.43180938delT	ENSP00000239849:p.Phe281fs	303.0	0.0		194.0	13.0	NM_003701	O14723|Q96Q17|Q9P2Q3	Frame_Shift_Del	DEL	ENST00000239849.6	hg19	CCDS9384.1																																																																																			.	.		0.428	TNFSF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044702.2		
C16orf71	146562	hgsc.bcm.edu	37	16	4797357	4797357	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:4797357delA	ENST00000299320.5	+	9	1772	c.1294delA	c.(1294-1296)aaafs	p.K432fs	C16orf71_ENST00000590191.1_Frame_Shift_Del_p.K449fs|RP11-127I20.7_ENST00000588099.1_RNA	NM_139170.2	NP_631909.2	Q8IYS4	CP071_HUMAN	chromosome 16 open reading frame 71	432										breast(1)|central_nervous_system(1)|large_intestine(4)|lung(4)|ovary(1)	11						CTGTACCGGGAAAAGCCAGCT	0.632																																					p.G431fs		Atlas-INDEL	.											.	C16orf71	46	.	0			c.1293delG						.						55.0	64.0	61.0					16																	4797357		2187	4280	6467	SO:0001589	frameshift_variant	146562	exon9			.	AF447587	CCDS10521.1	16p13.3	2008-02-05			ENSG00000166246	ENSG00000166246			25081	protein-coding gene	gene with protein product						12477932	Standard	XM_005255144		Approved	FLJ43261, DKFZp686H2240	uc002cxn.3	Q8IYS4	OTTHUMG00000129480	ENST00000299320.5:c.1294delA	chr16.hg19:g.4797357delA	ENSP00000299320:p.Lys432fs	296.0	0.0		191.0	12.0	NM_139170	Q8NCV0	Frame_Shift_Del	DEL	ENST00000299320.5	hg19	CCDS10521.1																																																																																			.	.		0.632	C16orf71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251644.1	NM_139170	
DPP6	1804	hgsc.bcm.edu	37	7	154263979	154263979	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:154263979delT	ENST00000377770.3	+	5	746	c.605delT	c.(604-606)cttfs	p.L202fs	DPP6_ENST00000404039.1_Frame_Shift_Del_p.L138fs|DPP6_ENST00000496611.1_3'UTR|DPP6_ENST00000427557.1_Frame_Shift_Del_p.L140fs|DPP6_ENST00000332007.3_Frame_Shift_Del_p.L140fs|DPP6_ENST00000406326.1_Frame_Shift_Del_p.L202fs			P42658	DPP6_HUMAN	dipeptidyl-peptidase 6	202					cell death (GO:0008219)|neuronal action potential (GO:0019228)|positive regulation of potassium ion transmembrane transport (GO:1901381)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	dipeptidyl-peptidase activity (GO:0008239)|serine-type peptidase activity (GO:0008236)			NS(3)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|lung(35)|pancreas(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	71	all_neural(206;0.181)	all_hematologic(28;0.0044)|all_lung(21;0.0176)|Lung NSC(21;0.0204)	OV - Ovarian serous cystadenocarcinoma(82;0.0562)			GAGTATGCACTTTTTTCATAC	0.294																																					p.L202fs	NSCLC(125;1384 1783 2490 7422 34254)	Atlas-INDEL	.											.	DPP6	383	.	0			c.604delC						.						86.0	86.0	86.0					7																	154263979		1802	4062	5864	SO:0001589	frameshift_variant	1804	exon5			.	M96859	CCDS75682.1, CCDS75683.1, CCDS75684.1	7q36.2	2006-08-07	2006-01-12		ENSG00000130226	ENSG00000130226			3010	protein-coding gene	gene with protein product		126141	"""dipeptidylpeptidase VI"", ""dipeptidylpeptidase 6"""			1729689	Standard	XM_006715871		Approved	DPPX	uc003wlk.3	P42658	OTTHUMG00000151511	ENST00000377770.3:c.605delT	chr7.hg19:g.154263979delT	ENSP00000367001:p.Leu202fs	115.0	0.0		139.0	10.0	NM_130797		Frame_Shift_Del	DEL	ENST00000377770.3	hg19																																																																																				.	.		0.294	DPP6-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000322932.1	NM_130797	
PCGF2	7703	hgsc.bcm.edu	37	17	36891838	36891838	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:36891838delG	ENST00000580830.1	-	12	1374	c.673delC	c.(673-675)ctcfs	p.L225fs	PCGF2_ENST00000581345.1_Frame_Shift_Del_p.L225fs|PCGF2_ENST00000360797.2_Frame_Shift_Del_p.L225fs|PCGF2_ENST00000585100.1_Frame_Shift_Del_p.P226fs|PCGF2_ENST00000578109.1_Frame_Shift_Del_p.P172fs|PCGF2_ENST00000579882.1_Frame_Shift_Del_p.P226fs			P35227	PCGF2_HUMAN	polycomb group ring finger 2	225					anterior/posterior pattern specification (GO:0009952)|cellular response to hydrogen peroxide (GO:0070301)|embryonic skeletal system morphogenesis (GO:0048704)|histone acetylation (GO:0016573)|in utero embryonic development (GO:0001701)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nuclear body (GO:0016604)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|skin(1)	10	Breast(7;9.07e-22)					CGGTACTTGAGGGGGAGAGGC	0.652											OREG0024367	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L225fs		Atlas-INDEL	.											.	PCGF2	24	.	0			c.674delT						.						6.0	7.0	7.0					17																	36891838		2160	4243	6403	SO:0001589	frameshift_variant	7703	exon11			.	D13969	CCDS32638.1	17q12	2013-01-09	2005-01-17	2005-01-19		ENSG00000277258		"""RING-type (C3HC4) zinc fingers"", ""Polycomb group ring fingers"""	12929	protein-coding gene	gene with protein product		600346	"""ring finger protein 110"""	ZNF144, RNF110		8325509	Standard	NM_007144		Approved	MEL-18	uc002hqp.1	P35227		ENST00000580830.1:c.673delC	chr17.hg19:g.36891838delG	ENSP00000461961:p.Leu225fs	124.0	0.0	866	133.0	10.0	NM_007144	A6NGD8	Frame_Shift_Del	DEL	ENST00000580830.1	hg19	CCDS32638.1																																																																																			.	.		0.652	PCGF2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442246.2	NM_007144	
FIBCD1	84929	hgsc.bcm.edu	37	9	133799700	133799700	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:133799700delC	ENST00000372338.4	-	3	878	c.636delG	c.(634-636)gggfs	p.G212fs	FIBCD1_ENST00000372337.2_Frame_Shift_Del_p.G54fs|FIBCD1_ENST00000253018.4_Frame_Shift_Del_p.G54fs|FIBCD1_ENST00000448616.1_Frame_Shift_Del_p.G212fs	NM_032843.4	NP_116232.3	Q8N539	FBCD1_HUMAN	fibrinogen C domain containing 1	212						integral component of membrane (GO:0016021)|membrane (GO:0016020)	chitin binding (GO:0008061)|metal ion binding (GO:0046872)			kidney(1)|large_intestine(3)|lung(2)|prostate(5)|urinary_tract(1)	12	all_hematologic(7;0.0028)			OV - Ovarian serous cystadenocarcinoma(145;3.52e-05)|Epithelial(140;0.00019)		GCCGGCCCAGCCCCCGGTCCC	0.706																																					p.L213fs		Atlas-INDEL	.											.	FIBCD1	34	.	0			c.637delC						.						10.0	14.0	12.0					9																	133799700		2191	4286	6477	SO:0001589	frameshift_variant	84929	exon3			.	AK027716	CCDS6937.1	9q34.2	2013-02-06			ENSG00000130720	ENSG00000130720		"""Fibrinogen C domain containing"""	25922	protein-coding gene	gene with protein product		613357				12975309	Standard	NM_001145106		Approved	FLJ14810	uc004bzz.3	Q8N539	OTTHUMG00000020814	ENST00000372338.4:c.636delG	chr9.hg19:g.133799700delC	ENSP00000361413:p.Gly212fs	185.0	0.0		131.0	12.0	NM_032843	A3KFK0|Q6UXK6|Q96SJ7	Frame_Shift_Del	DEL	ENST00000372338.4	hg19	CCDS6937.1																																																																																			.	.		0.706	FIBCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054687.2	NM_032843	
SENP7	57337	hgsc.bcm.edu	37	3	101051684	101051684	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:101051684delT	ENST00000394095.2	-	18	2556	c.2503delA	c.(2503-2505)agafs	p.R835fs	SENP7_ENST00000394094.2_Frame_Shift_Del_p.R770fs|SENP7_ENST00000394091.1_Frame_Shift_Del_p.R671fs|SENP7_ENST00000358203.3_Frame_Shift_Del_p.R671fs|SENP7_ENST00000394085.3_Frame_Shift_Del_p.R23fs|SENP7_ENST00000348610.3_Frame_Shift_Del_p.R802fs|SENP7_ENST00000314261.7_Frame_Shift_Del_p.R769fs	NM_001282802.1|NM_020654.3	NP_001269731.1|NP_065705.3	Q9BQF6	SENP7_HUMAN	SUMO1/sentrin specific peptidase 7	835	Protease.					intracellular (GO:0005622)|nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)			breast(2)|endometrium(1)|kidney(1)|large_intestine(16)|lung(15)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						GTTCTTACTCTTTTATGTCTT	0.279																																					p.R835fs		Atlas-INDEL	.											.	SENP7	170	.	0			c.2504delG						.						101.0	100.0	100.0					3																	101051684		2203	4275	6478	SO:0001589	frameshift_variant	57337	exon18			.		CCDS2941.2, CCDS43121.1, CCDS63704.1, CCDS63705.1, CCDS63706.1	3q12	2008-02-05	2005-08-17		ENSG00000138468	ENSG00000138468			30402	protein-coding gene	gene with protein product		612846	"""SUMO1/sentrin specific protease 7"""			11214970, 11230166	Standard	NM_001282802		Approved		uc003dut.3	Q9BQF6	OTTHUMG00000149927	ENST00000394095.2:c.2503delA	chr3.hg19:g.101051684delT	ENSP00000377655:p.Arg835fs	264.0	0.0		223.0	15.0	NM_020654	A1L3A5|A8MW39|B7WNW8|Q7Z3F4|Q96PS5|Q9C0F6|Q9HBT5	Frame_Shift_Del	DEL	ENST00000394095.2	hg19	CCDS2941.2																																																																																			.	.		0.279	SENP7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313957.2	NM_020654	
PDPK1	5170	hgsc.bcm.edu	37	16	2607955	2607955	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:2607955delT	ENST00000342085.4	+	2	425	c.276delT	c.(274-276)tctfs	p.S92fs	PDPK1_ENST00000354836.5_Frame_Shift_Del_p.S92fs|PDPK1_ENST00000441549.3_Frame_Shift_Del_p.S92fs|PDPK1_ENST00000389224.3_Frame_Shift_Del_p.S65fs|PDPK1_ENST00000268673.7_Frame_Shift_Del_p.S92fs|RP11-20I23.13_ENST00000563449.2_RNA|RP11-20I23.11_ENST00000569220.1_RNA	NM_002613.4	NP_002604.1	O15530	PDPK1_HUMAN	3-phosphoinositide dependent protein kinase 1	92	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton organization (GO:0030036)|activation of protein kinase B activity (GO:0032148)|blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|cell migration (GO:0016477)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to insulin stimulus (GO:0032869)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway (GO:0097191)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|focal adhesion assembly (GO:0048041)|hyperosmotic response (GO:0006972)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|intracellular signal transduction (GO:0035556)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-threonine phosphorylation (GO:0018107)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of endothelial cell migration (GO:0010594)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of mast cell degranulation (GO:0043304)|regulation of transcription, DNA-templated (GO:0006355)|synaptic transmission (GO:0007268)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|transcription, DNA-templated (GO:0006351)|type B pancreatic cell development (GO:0003323)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	3-phosphoinositide-dependent protein kinase activity (GO:0004676)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phospholipase activator activity (GO:0016004)|phospholipase binding (GO:0043274)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(2)|endometrium(1)|large_intestine(1)|lung(2)|ovary(1)	7		Ovarian(90;0.17)			Celecoxib(DB00482)	GGGAAGGCTCTTTTTCCACGG	0.607																																					p.S92fs		Atlas-INDEL	.											.	PDPK1	37	.	0			c.275delC						.						49.0	56.0	54.0					16																	2607955		2103	4138	6241	SO:0001589	frameshift_variant	5170	exon2			.	AF017995	CCDS10472.1, CCDS10473.1, CCDS58411.1	16p13.3	2014-03-20	2014-03-20		ENSG00000140992	ENSG00000140992			8816	protein-coding gene	gene with protein product	"""PkB kinase"""	605213				9094314, 9445477	Standard	NM_002613		Approved	PDK1	uc002cqs.4	O15530	OTTHUMG00000128874	ENST00000342085.4:c.276delT	chr16.hg19:g.2607955delT	ENSP00000344220:p.Ser92fs	339.0	0.0		208.0	16.0	NM_001261816	H0Y4Z0|Q59EH6|Q6FI20|Q8IV52|Q9BRD5	Frame_Shift_Del	DEL	ENST00000342085.4	hg19	CCDS10472.1																																																																																			.	.		0.607	PDPK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250831.3		
SYNGAP1	8831	hgsc.bcm.edu	37	6	33388070	33388070	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:33388070delG	ENST00000418600.2	+	1	130	c.29delG	c.(28-30)cggfs	p.R10fs	CUTA_ENST00000607266.1_5'Flank|CUTA_ENST00000492510.1_5'Flank|CUTA_ENST00000374496.3_5'Flank|SYNGAP1_ENST00000293748.5_Frame_Shift_Del_p.R10fs|CUTA_ENST00000374500.5_5'Flank|CUTA_ENST00000488034.1_5'Flank|CUTA_ENST00000494751.1_5'Flank|CUTA_ENST00000488478.1_5'Flank|CUTA_ENST00000440279.3_5'Flank	NM_006772.2	NP_006763.2	Q96PV0	SYGP1_HUMAN	synaptic Ras GTPase activating protein 1	10					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						TCCATCCATCGGGGGAGCATC	0.682																																					p.R10fs		Atlas-INDEL	.											.	SYNGAP1	202	.	0			c.28delC						.						4.0	3.0	3.0					6																	33388070		1493	2602	4095	SO:0001589	frameshift_variant	8831	exon1			.	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.29delG	chr6.hg19:g.33388070delG	ENSP00000403636:p.Arg10fs	264.0	0.0		193.0	13.0	NM_006772	A2AB17|A2BEL6|A2BEL7|A8MQC4|Q8TCS2|Q9UGE2	Frame_Shift_Del	DEL	ENST00000418600.2	hg19	CCDS34434.2																																																																																			.	.		0.682	SYNGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076151.4	XM_166407	
GREM1	26585	hgsc.bcm.edu	37	15	33022990	33022990	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:33022990delC	ENST00000300177.4	+	2	288	c.99delC	c.(97-99)atcfs	p.I33fs	GREM1_ENST00000560677.1_Frame_Shift_Del_p.I33fs|GREM1_ENST00000560830.1_Frame_Shift_Del_p.I33fs|GREM1_ENST00000322805.4_Frame_Shift_Del_p.I33fs	NM_001191322.1|NM_001191323.1|NM_013372.6	NP_001178251.1|NP_001178252.1|NP_037504.1	O60565	GREM1_HUMAN	gremlin 1, DAN family BMP antagonist	33					activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|cell migration involved in sprouting angiogenesis (GO:0002042)|cell morphogenesis (GO:0000902)|collagen fibril organization (GO:0030199)|determination of dorsal identity (GO:0048263)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of bone mineralization (GO:0030502)|negative regulation of bone mineralization involved in bone maturation (GO:1900158)|negative regulation of bone remodeling (GO:0046851)|negative regulation of bone trabecula formation (GO:1900155)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of monocyte chemotaxis (GO:0090027)|negative regulation of osteoblast proliferation (GO:0033689)|negative regulation of osteoclast proliferation (GO:0090291)|negative regulation of pathway-restricted SMAD protein phosphorylation (GO:0060394)|positive regulation of cardiac muscle cell differentiation (GO:2000727)|positive regulation of cell proliferation (GO:0008284)|positive regulation of peptidyl-tyrosine autophosphorylation (GO:1900086)|positive regulation of receptor activity (GO:2000273)|positive regulation of receptor internalization (GO:0002092)|positive regulation of telomerase activity (GO:0051973)|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)|regulation of epithelial to mesenchymal transition (GO:0010717)|signal transduction (GO:0007165)	extracellular space (GO:0005615)	BMP binding (GO:0036122)|morphogen activity (GO:0016015)|receptor agonist activity (GO:0048018)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)|vascular endothelial growth factor receptor 2 binding (GO:0043184)			breast(1)|endometrium(1)|large_intestine(1)|lung(6)|prostate(1)	10		all_lung(180;1.49e-09)		all cancers(64;2.97e-18)|Epithelial(43;3.15e-12)|GBM - Glioblastoma multiforme(186;2.32e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0107)		AAGGTGCCATCCCCCCGCCAG	0.662																																					p.I33fs		Atlas-INDEL	.											.	GREM1	18	.	0			c.98delT						.						27.0	31.0	30.0					15																	33022990		2199	4296	6495	SO:0001589	frameshift_variant	26585	exon2			.		CCDS10029.1, CCDS53927.1	15q13.3	2014-02-07	2013-02-26	2004-05-07	ENSG00000166923	ENSG00000166923			2001	protein-coding gene	gene with protein product		603054	"""cysteine knot superfamily 1, BMP antagonist 1"", ""gremlin 1, cysteine knot superfamily, homolog (Xenopus laevis)"", ""gremlin 1"", ""colorectal adenoma and carcinoma 1"""	CKTSF1B1, CRAC1		9660951, 10026205, 22561515	Standard	NM_013372		Approved	DRM, gremlin, DAND2, HMPS	uc001zhe.2	O60565	OTTHUMG00000129319	ENST00000300177.4:c.99delC	chr15.hg19:g.33022990delC	ENSP00000300177:p.Ile33fs	143.0	0.0		114.0	11.0	NM_013372	Q52LV3|Q8N914|Q8N936	Frame_Shift_Del	DEL	ENST00000300177.4	hg19	CCDS10029.1																																																																																			.	.		0.662	GREM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251455.2	NM_013372	
SPIN2B	474343	hgsc.bcm.edu	37	X	57146927	57146927	+	Frame_Shift_Del	DEL	G	G	-	rs201872206		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:57146927delG	ENST00000333933.3	-	2	446	c.136delC	c.(136-138)cgcfs	p.R47fs	SPIN2B_ENST00000460948.1_5'UTR|RP3-323P24.3_ENST00000439622.1_RNA|SPIN2B_ENST00000374912.5_Frame_Shift_Del_p.R47fs|SPIN2B_ENST00000374910.3_Frame_Shift_Del_p.R47fs|SPIN2B_ENST00000275988.5_Frame_Shift_Del_p.R47fs	NM_001006681.1	NP_001006682.1	Q9BPZ2	SPI2B_HUMAN	spindlin family, member 2B	47					apoptotic process (GO:0006915)|cell cycle (GO:0007049)|gamete generation (GO:0007276)|regulation of cell cycle (GO:0051726)	nucleus (GO:0005634)				endometrium(3)|large_intestine(1)|skin(1)	5						ATGTTCCTGCGGGGCTGGGAT	0.532																																					p.R46fs		Atlas-INDEL	.											.	SPIN2B	11	.	0			c.137delG						.																																			SO:0001589	frameshift_variant	474343	exon2			.	AF356353	CCDS35311.1, CCDS65274.1	Xp11.1	2014-02-12	2006-12-05		ENSG00000186787	ENSG00000186787			33147	protein-coding gene	gene with protein product		300517				12145692	Standard	XM_005262010		Approved	SPIN-2	uc004dva.3	Q9BPZ2	OTTHUMG00000021680	ENST00000333933.3:c.136delC	chrX.hg19:g.57146927delG	ENSP00000335008:p.Arg47fs	279.0	0.0		157.0	10.0	NM_001006683	Q7Z2M0	Frame_Shift_Del	DEL	ENST00000333933.3	hg19	CCDS35311.1																																																																																			.	.		0.532	SPIN2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056912.1	NM_001006681	
COL16A1	1307	hgsc.bcm.edu	37	1	32136240	32136240	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:32136240delG	ENST00000373672.3	-	49	3674	c.3158delC	c.(3157-3159)ccafs	p.P1053fs	COL16A1_ENST00000271069.6_Frame_Shift_Del_p.P1053fs	NM_001856.3	NP_001847.3	Q07092	COGA1_HUMAN	collagen, type XVI, alpha 1	1053	Collagen-like 6.|Triple-helical region 2 (COL2) with 2 imperfections.				cell adhesion (GO:0007155)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|female pregnancy (GO:0007565)|integrin-mediated signaling pathway (GO:0007229)	collagen type XVI trimer (GO:0005597)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	integrin binding (GO:0005178)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(7)|lung(15)|ovary(8)|prostate(4)	48		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0423)|all_neural(195;0.0837)|Breast(348;0.116)		STAD - Stomach adenocarcinoma(196;0.059)		AGGAAAACCTGGGGGGCCCTG	0.637																																					p.P1053fs	Colon(143;498 1786 21362 25193 36625)	Atlas-INDEL	.											.	COL16A1	137	.	0			c.3159delA						.						8.0	12.0	11.0					1																	32136240		1542	3202	4744	SO:0001589	frameshift_variant	1307	exon49			.	M92642	CCDS41297.1	1p35-p34	2013-01-16			ENSG00000084636	ENSG00000084636		"""Collagens"""	2193	protein-coding gene	gene with protein product		120326				1631157	Standard	NM_001856		Approved		uc001btk.1	Q07092	OTTHUMG00000003883	ENST00000373672.3:c.3158delC	chr1.hg19:g.32136240delG	ENSP00000362776:p.Pro1053fs	187.0	0.0		193.0	12.0	NM_001856	Q16593|Q59F89|Q71RG9	Frame_Shift_Del	DEL	ENST00000373672.3	hg19	CCDS41297.1																																																																																			.	.		0.637	COL16A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011057.2	NM_001856	
METTL4	64863	hgsc.bcm.edu	37	18	2544668	2544668	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr18:2544668delT	ENST00000574538.1	-	7	1940	c.1165delA	c.(1165-1167)actfs	p.T389fs	METTL4_ENST00000319888.6_Frame_Shift_Del_p.T389fs	NM_022840.3	NP_073751.3	Q8N3J2	METL4_HUMAN	methyltransferase like 4	389					nucleobase-containing compound metabolic process (GO:0006139)		methyltransferase activity (GO:0008168)|nucleic acid binding (GO:0003676)			breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(7)|prostate(1)|skin(2)|urinary_tract(1)	17						GGTAGAGCAGTTTTTTCTTGA	0.328																																					p.T389fs		Atlas-INDEL	.											.	METTL4	40	.	0			c.1166delC						.						104.0	100.0	102.0					18																	2544668		2203	4300	6503	SO:0001589	frameshift_variant	64863	exon7			.		CCDS11826.1	18p11.31	2008-02-05			ENSG00000101574	ENSG00000101574			24726	protein-coding gene	gene with protein product						12477932	Standard	NM_022840		Approved	FLJ23017, HsT661	uc002klh.4	Q8N3J2	OTTHUMG00000131482	ENST00000574538.1:c.1165delA	chr18.hg19:g.2544668delT	ENSP00000458290:p.Thr389fs	257.0	0.0		165.0	12.0	NM_022840	B2RNA1|Q2TAA7|Q9H5U9	Frame_Shift_Del	DEL	ENST00000574538.1	hg19	CCDS11826.1																																																																																			.	.		0.328	METTL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254326.3	NM_022840	
TMEM126B	55863	hgsc.bcm.edu	37	11	85346800	85346800	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:85346800delA	ENST00000358867.6	+	4	510	c.487delA	c.(487-489)aaafs	p.K163fs	TMEM126B_ENST00000534341.1_Frame_Shift_Del_p.K163fs|TMEM126B_ENST00000393375.1_Frame_Shift_Del_p.K133fs	NM_018480.4	NP_060950.3	Q8IUX1	T126B_HUMAN	transmembrane protein 126B	163						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				kidney(1)|large_intestine(2)|lung(3)|prostate(1)	7		Acute lymphoblastic leukemia(157;4.88e-06)|all_hematologic(158;0.00572)				GGCTTTTACTAAAAATGGACG	0.318																																					p.T162fs		Atlas-INDEL	.											.	TMEM126B	13	.	0			c.486delT						.						117.0	117.0	117.0					11																	85346800		2203	4299	6502	SO:0001589	frameshift_variant	55863	exon4			.		CCDS8267.1, CCDS8267.2, CCDS53686.1	11q14.1	2013-05-24				ENSG00000171204		"""Mitochondrial respiratory chain complex assembly factors"""	30883	protein-coding gene	gene with protein product		615533				22982022	Standard	NM_018480		Approved	HT007	uc001pap.4	Q8IUX1		ENST00000358867.6:c.487delA	chr11.hg19:g.85346800delA	ENSP00000351737:p.Lys163fs	180.0	0.0		161.0	10.0	NM_018480	A8K535|A8MSS0|Q32Q09|Q8WVU3|Q96EP3|Q9NZ29	Frame_Shift_Del	DEL	ENST00000358867.6	hg19	CCDS8267.2																																																																																			.	.		0.318	TMEM126B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000392164.1	NM_018480	
UGT1A3	54659	hgsc.bcm.edu	37	2	234638491	234638492	+	Frame_Shift_Del	DEL	AG	AG	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:234638491_234638492delAG	ENST00000482026.1	+	1	738_739	c.719_720delAG	c.(718-720)cagfs	p.Q240fs	UGT1A9_ENST00000354728.4_Intron|UGT1A7_ENST00000373426.3_Intron|UGT1A1_ENST00000609637.1_Intron|UGT1A6_ENST00000373424.1_Intron|UGT1A6_ENST00000406651.1_Intron|UGT1A1_ENST00000609767.1_Frame_Shift_Del_p.Q240fs|UGT1A4_ENST00000373409.3_Intron|UGT1A10_ENST00000373445.1_Intron|UGT1A6_ENST00000305139.6_Intron|UGT1A1_ENST00000373450.4_Intron|UGT1A10_ENST00000344644.5_Intron|UGT1A6_ENST00000480628.1_Intron|UGT1A5_ENST00000373414.3_Intron|UGT1A1_ENST00000608381.1_Intron			P35503	UD13_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A3	240					cellular glucuronidation (GO:0052695)|flavonoid glucuronidation (GO:0052696)|metabolic process (GO:0008152)|retinoic acid metabolic process (GO:0042573)|xenobiotic glucuronidation (GO:0052697)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	enzyme binding (GO:0019899)|glucuronosyltransferase activity (GO:0015020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|retinoic acid binding (GO:0001972)|UDP-glycosyltransferase activity (GO:0008194)			breast(2)|endometrium(7)|kidney(18)|large_intestine(6)|lung(10)|ovary(1)|skin(1)|urinary_tract(1)	46		Breast(86;0.000765)|all_lung(227;0.00266)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0327)|Lung NSC(271;0.0456)|Lung SC(224;0.128)		Epithelial(121;2.4e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000476)|Lung(119;0.00243)|LUSC - Lung squamous cell carcinoma(224;0.00599)	Atorvastatin(DB01076)|Candesartan(DB00796)|Cyproheptadine(DB00434)|Eltrombopag(DB06210)|Etodolac(DB00749)|Ezetimibe(DB00973)|Ezogabine(DB04953)|Flunitrazepam(DB01544)|Flurbiprofen(DB00712)|Fluvastatin(DB01095)|Ibuprofen(DB01050)|Irbesartan(DB01029)|Lamotrigine(DB00555)|Losartan(DB00678)|Lovastatin(DB00227)|Mitiglinide(DB01252)|Morphine(DB00295)|Pitavastatin(DB08860)|Simvastatin(DB00641)|Valproic Acid(DB00313)	GAGCTTTTTCAGAGAGAGGTGT	0.505																																					p.240_240del		Atlas-Indel,Pindel	.											.	UGT1A3	91	.	0			c.718_719del						.																																			SO:0001589	frameshift_variant	54659	exon1			.	M84127	CCDS2509.1	2q37	2010-03-05	2005-07-20		ENSG00000243135	ENSG00000243135		"""UDP glucuronosyltransferases"""	12535	other	complex locus constituent		606428	"""UDP glycosyltransferase 1 family, polypeptide A3"""			9295054, 1339448, 11434514	Standard	NM_019093		Approved	UGT1C		P35503	OTTHUMG00000059118	ENST00000482026.1:c.719_720delAG	chr2.hg19:g.234638497_234638498delAG	ENSP00000418532:p.Gln240fs	473.0	0.0		327.0	72.0	NM_019093	B8K287	Frame_Shift_Del	DEL	ENST00000482026.1	hg19	CCDS2509.1																																																																																			.	.		0.505	UGT1A3-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000130983.1	NM_019093	
GALNT12	79695	hgsc.bcm.edu	37	9	101606479	101606479	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:101606479delG	ENST00000375011.3	+	8	1446	c.1446delG	c.(1444-1446)atgfs	p.M482fs		NM_024642.4	NP_078918.3	Q8IXK2	GLT12_HUMAN	polypeptide N-acetylgalactosaminyltransferase 12	482	Ricin B-type lectin. {ECO:0000255|PROSITE-ProRule:PRU00174}.				cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			breast(1)|endometrium(2)|large_intestine(3)|lung(8)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	17		Acute lymphoblastic leukemia(62;0.0559)				GTCATGGGATGGGCCAGAATC	0.383																																					p.M482fs		Atlas-INDEL	.											.	GALNT12	37	.	0			c.1445delT						.						91.0	83.0	86.0					9																	101606479		2203	4300	6503	SO:0001589	frameshift_variant	79695	exon8			.	AB078146	CCDS6737.1	9q22.33	2014-03-13	2014-03-13		ENSG00000119514	ENSG00000119514	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	19877	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 12"""	610290	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 12 (GalNAc-T12)"""			12135769	Standard	NM_024642		Approved	GalNAc-T12	uc004ayz.3	Q8IXK2	OTTHUMG00000020348	ENST00000375011.3:c.1446delG	chr9.hg19:g.101606479delG	ENSP00000364150:p.Met482fs	249.0	0.0		149.0	10.0	NM_024642	Q5TCF7|Q8NG54|Q96CT9|Q9H771	Frame_Shift_Del	DEL	ENST00000375011.3	hg19	CCDS6737.1																																																																																			.	.		0.383	GALNT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053382.1	NM_024642	
LRFN4	78999	hgsc.bcm.edu	37	11	66627620	66627620	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:66627620delG	ENST00000309602.4	+	2	2105	c.1862delG	c.(1861-1863)cggfs	p.R621fs	LRFN4_ENST00000393952.3_Intron|PC_ENST00000393960.1_Intron|PC_ENST00000393958.2_Intron|PC_ENST00000393955.2_Intron	NM_024036.4	NP_076941.2	Q6PJG9	LRFN4_HUMAN	leucine rich repeat and fibronectin type III domain containing 4	621						integral component of membrane (GO:0016021)				breast(1)|lung(1)|prostate(1)	3						GCAGGGTGCCGGGGGGTAGGA	0.692																																					p.R621fs		Atlas-INDEL	.											.	LRFN4	25	.	0			c.1861delC						.						8.0	12.0	11.0					11																	66627620		1948	3901	5849	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.1862delG	chr11.hg19:g.66627620delG	ENSP00000312535:p.Arg621fs	98.0	0.0		147.0	10.0	NM_024036	Q4VBZ3|Q59GV4|Q8N644|Q9BWJ0	Frame_Shift_Del	DEL	ENST00000309602.4	hg19	CCDS8153.1																																																																																			.	.		0.692	LRFN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393127.1	NM_024036	
PARP8	79668	hgsc.bcm.edu	37	5	50129819	50129819	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:50129819delA	ENST00000281631.5	+	24	2472	c.2314delA	c.(2314-2316)aaafs	p.K773fs	PARP8_ENST00000505697.2_Frame_Shift_Del_p.K773fs|PARP8_ENST00000503750.2_Frame_Shift_Del_p.K731fs|PARP8_ENST00000505554.1_Frame_Shift_Del_p.K752fs|PARP8_ENST00000514342.2_Splice_Site_p.K484fs|PARP8_ENST00000514067.2_Frame_Shift_Del_p.K731fs|PARP8_ENST00000511363.2_3'UTR	NM_001178056.1|NM_024615.3	NP_001171527.1|NP_078891.2	Q8N3A8	PARP8_HUMAN	poly (ADP-ribose) polymerase family, member 8	773	PARP catalytic. {ECO:0000255|PROSITE- ProRule:PRU00397}.					intracellular (GO:0005622)	NAD+ ADP-ribosyltransferase activity (GO:0003950)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(10)|lung(23)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	49		Lung NSC(810;0.0305)|Breast(144;0.222)				TTAGTCACAGAAAAAAGGACA	0.328																																					p.Q771fs		Atlas-INDEL	.											.	PARP8	93	.	0			c.2313delG						.						76.0	78.0	77.0					5																	50129819		2203	4300	6503	SO:0001589	frameshift_variant	79668	exon25			.	AL834477	CCDS3954.1, CCDS54849.1	5q11.2	2010-02-16			ENSG00000151883	ENSG00000151883		"""Poly (ADP-ribose) polymerases"""	26124	protein-coding gene	gene with protein product						15273990	Standard	NM_001178055		Approved	FLJ21308, pART16	uc003joo.3	Q8N3A8	OTTHUMG00000096969	ENST00000281631.5:c.2314delA	chr5.hg19:g.50129819delA	ENSP00000281631:p.Lys773fs	242.0	0.0		157.0	11.0	NM_001178055	Q3KRB7|Q6DHZ1|Q9H754	Frame_Shift_Del	DEL	ENST00000281631.5	hg19	CCDS3954.1																																																																																			.	.		0.328	PARP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214035.3	NM_024615	
PAPOLA	10914	hgsc.bcm.edu	37	14	97022557	97022557	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr14:97022557delT	ENST00000216277.8	+	19	2031	c.1811delT	c.(1810-1812)attfs	p.I604fs	PAPOLA_ENST00000392990.2_Frame_Shift_Del_p.I604fs	NM_032632.4	NP_116021.2	P51003	PAPOA_HUMAN	poly(A) polymerase alpha	604	Ser/Thr-rich.				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)		CAACCAGCCATTTCTCCACCA	0.413																																					p.I604fs	NSCLC(19;254 734 11908 35501 39234)	Atlas-INDEL	.											.	PAPOLA	58	.	0			c.1810delA						.						160.0	145.0	150.0					14																	97022557		2203	4300	6503	SO:0001589	frameshift_variant	10914	exon19			.	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.1811delT	chr14.hg19:g.97022557delT	ENSP00000216277:p.Ile604fs	209.0	0.0		169.0	13.0	NM_032632	Q86SX4|Q86TV0|Q8IYF5|Q9BVU2	Frame_Shift_Del	DEL	ENST00000216277.8	hg19	CCDS9946.1																																																																																			.	.		0.413	PAPOLA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413411.2		
KAT6A	7994	hgsc.bcm.edu	37	8	41792228	41792228	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:41792228delT	ENST00000396930.3	-	18	4053	c.3510delA	c.(3508-3510)aaafs	p.K1170fs	KAT6A_ENST00000265713.2_Frame_Shift_Del_p.K1170fs|KAT6A_ENST00000406337.1_Frame_Shift_Del_p.K1170fs	NM_001099412.1	NP_001092882.1	Q92794	KAT6A_HUMAN	K(lysine) acetyltransferase 6A	1170					aorta morphogenesis (GO:0035909)|cellular senescence (GO:0090398)|chromatin organization (GO:0006325)|DNA packaging (GO:0006323)|embryonic hemopoiesis (GO:0035162)|face morphogenesis (GO:0060325)|heart morphogenesis (GO:0003007)|histone acetylation (GO:0016573)|histone H3 acetylation (GO:0043966)|myeloid cell differentiation (GO:0030099)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of transcription, DNA-templated (GO:0045893)|protein acetylation (GO:0006473)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	Golgi apparatus (GO:0005794)|MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|PML body (GO:0016605)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)										TAAATCCTGGTTTTCGACCAG	0.463																																					p.P1171fs		Atlas-INDEL	.											.	.	.	.	0			c.3511delC						.						149.0	152.0	151.0					8																	41792228		2203	4300	6503	SO:0001589	frameshift_variant	7994	exon17			.	U47742	CCDS6124.1	8p11	2013-01-28	2011-07-21	2011-07-21	ENSG00000083168	ENSG00000083168		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Zinc fingers, C2HC-type containing"", ""Zinc fingers, PHD-type"""	13013	protein-coding gene	gene with protein product	"""Monocytic leukemia zinc finger protein"""	601408	"""runt-related transcription factor binding protein 2"", ""MYST histone acetyltransferase (monocytic leukemia) 3"""	ZNF220, RUNXBP2, MYST3		8849440, 8782817	Standard	NM_001099412		Approved	MOZ, ZC2HC6A	uc003xon.4	Q92794	OTTHUMG00000150453	ENST00000396930.3:c.3510delA	chr8.hg19:g.41792228delT	ENSP00000380136:p.Lys1170fs	252.0	0.0		194.0	14.0	NM_006766	Q76L81	Frame_Shift_Del	DEL	ENST00000396930.3	hg19	CCDS6124.1																																																																																			.	.		0.463	KAT6A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318163.1	NM_006766	
CNTNAP5	129684	hgsc.bcm.edu	37	2	125261880	125261880	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:125261880delT	ENST00000431078.1	+	8	1435	c.1071delT	c.(1069-1071)actfs	p.T357fs		NM_130773.2	NP_570129.1	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5	357	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)				NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(24)|lung(100)|ovary(10)|prostate(12)|skin(4)|upper_aerodigestive_tract(3)	176				BRCA - Breast invasive adenocarcinoma(221;0.248)		GCAATGTCACTTTTTCCTGCT	0.463																																					p.T357fs		Atlas-INDEL	.											.	CNTNAP5	405	.	0			c.1070delC						.						119.0	106.0	110.0					2																	125261880		1866	4114	5980	SO:0001589	frameshift_variant	129684	exon8			.	AB077881	CCDS46401.1	2q14.1	2008-02-05			ENSG00000155052	ENSG00000155052			18748	protein-coding gene	gene with protein product		610519					Standard	NM_130773		Approved	caspr5, FLJ31966	uc002tno.3	Q8WYK1	OTTHUMG00000153356	ENST00000431078.1:c.1071delT	chr2.hg19:g.125261880delT	ENSP00000399013:p.Thr357fs	223.0	0.0		173.0	12.0	NM_130773	Q4ZFW2|Q4ZG21|Q53R09|Q53RX1|Q53SG3|Q584P3|Q96MS7	Frame_Shift_Del	DEL	ENST00000431078.1	hg19	CCDS46401.1																																																																																			.	.		0.463	CNTNAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330864.3		
OLFML3	56944	hgsc.bcm.edu	37	1	114524304	114524304	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:114524304delC	ENST00000320334.4	+	3	1208	c.1134delC	c.(1132-1134)aacfs	p.N378fs	OLFML3_ENST00000393300.2_Frame_Shift_Del_p.N358fs|OLFML3_ENST00000491700.1_3'UTR|OLFML3_ENST00000369551.1_Frame_Shift_Del_p.N358fs	NM_020190.2	NP_064575.1	Q9NRN5	OLFL3_HUMAN	olfactomedin-like 3	378	Olfactomedin-like. {ECO:0000255|PROSITE- ProRule:PRU00446}.				multicellular organismal development (GO:0007275)	extracellular region (GO:0005576)|vesicle (GO:0031982)				breast(1)|endometrium(2)|large_intestine(3)|lung(3)|prostate(2)|skin(2)|urinary_tract(1)	14	Lung SC(450;0.184)	all_cancers(81;4.5e-08)|all_epithelial(167;1.09e-07)|all_lung(203;1.53e-05)|Lung NSC(69;2.76e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		TCCGCTATAACCCCCGAGAAC	0.562																																					p.N378fs		Atlas-INDEL	.											.	OLFML3	42	.	0			c.1133delA						.						50.0	50.0	50.0					1																	114524304		2203	4300	6503	SO:0001589	frameshift_variant	56944	exon3			.	AF201945	CCDS870.1, CCDS65618.1, CCDS72839.1	1p13.1	2008-02-05			ENSG00000116774	ENSG00000116774			24956	protein-coding gene	gene with protein product		610088					Standard	NM_001286353		Approved	HNOEL-iso, OLF44	uc001eer.1	Q9NRN5	OTTHUMG00000011980	ENST00000320334.4:c.1134delC	chr1.hg19:g.114524304delC	ENSP00000322273:p.Asn378fs	214.0	0.0		181.0	11.0	NM_020190	Q53FR1|Q53HV9|Q5SQL6|Q69AX9|Q8NBJ2	Frame_Shift_Del	DEL	ENST00000320334.4	hg19	CCDS870.1																																																																																			.	.		0.562	OLFML3-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033119.1	NM_020190	
FGF9	2254	hgsc.bcm.edu	37	13	22246178	22246178	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr13:22246178delG	ENST00000382353.5	+	1	657	c.127delG	c.(127-129)gggfs	p.G44fs		NM_002010.2	NP_002001.1	P31371	FGF9_HUMAN	fibroblast growth factor 9	44					angiogenesis (GO:0001525)|cell-cell signaling (GO:0007267)|chondrocyte differentiation (GO:0002062)|embryonic digestive tract development (GO:0048566)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal system development (GO:0048706)|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)|inner ear morphogenesis (GO:0042472)|insulin receptor signaling pathway (GO:0008286)|lung-associated mesenchyme development (GO:0060484)|male gonad development (GO:0008584)|male sex determination (GO:0030238)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of Wnt signaling pathway (GO:0030178)|neurotrophin TRK receptor signaling pathway (GO:0048011)|osteoblast differentiation (GO:0001649)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of gene expression (GO:0010628)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein import into nucleus (GO:0006606)|regulation of timing of cell differentiation (GO:0048505)|signal transduction (GO:0007165)|substantia nigra development (GO:0021762)	basement membrane (GO:0005604)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	growth factor activity (GO:0008083)|heparin binding (GO:0008201)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|skin(2)	9		all_cancers(29;1.23e-20)|all_epithelial(30;9.83e-19)|all_lung(29;9.64e-17)|Lung SC(185;0.0262)|Breast(139;0.106)		all cancers(112;3.92e-05)|Epithelial(112;0.000166)|OV - Ovarian serous cystadenocarcinoma(117;0.00314)|Lung(94;0.163)		GTCCGAAGCAGGGGGGCTCCC	0.562																																					p.A42fs	Melanoma(195;1939 2127 12623 13963 52730)	Atlas-INDEL	.											.	FGF9	25	.	0			c.126delA						.						68.0	74.0	72.0					13																	22246178		2203	4300	6503	SO:0001589	frameshift_variant	2254	exon1			.	D14838	CCDS9298.1	13q11-q12	2014-01-30	2013-06-18		ENSG00000102678	ENSG00000102678		"""Endogenous ligands"""	3687	protein-coding gene	gene with protein product	"""glia-activating factor"""	600921	"""fibroblast growth factor 9 (glia-activating factor)"""			8321227	Standard	NM_002010		Approved		uc001uog.2	P31371	OTTHUMG00000017412	ENST00000382353.5:c.127delG	chr13.hg19:g.22246178delG	ENSP00000371790:p.Gly44fs	227.0	0.0		175.0	12.0	NM_002010	A8K427|Q3SY32	Frame_Shift_Del	DEL	ENST00000382353.5	hg19	CCDS9298.1																																																																																			.	.		0.562	FGF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046002.2		
IQGAP3	128239	hgsc.bcm.edu	37	1	156503821	156503821	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:156503821delC	ENST00000361170.2	-	30	3863	c.3853delG	c.(3853-3855)gagfs	p.E1285fs		NM_178229.4	NP_839943.2	Q86VI3	IQGA3_HUMAN	IQ motif containing GTPase activating protein 3	1285					activation of MAPK activity (GO:0000187)|cellular response to organic substance (GO:0071310)|ERK1 and ERK2 cascade (GO:0070371)|G1/S transition of mitotic cell cycle (GO:0000082)|negative regulation of gene expression (GO:0010629)|positive regulation of gene expression (GO:0010628)|positive regulation of mammary gland epithelial cell proliferation (GO:0033601)|Ras protein signal transduction (GO:0007265)|regulation of cell size (GO:0008361)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|lateral plasma membrane (GO:0016328)	Ras GTPase activator activity (GO:0005099)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(14)|lung(29)|ovary(5)|prostate(5)|skin(5)|urinary_tract(3)	75	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					TTGACCAGCTCCCCCACGGTG	0.612																																					p.E1285fs		Atlas-INDEL	.											.	IQGAP3	146	.	0			c.3854delA						.						134.0	112.0	119.0					1																	156503821		2203	4300	6503	SO:0001589	frameshift_variant	128239	exon30			.	AY253300	CCDS1144.1	1q21.3	2008-02-05			ENSG00000183856	ENSG00000183856			20669	protein-coding gene	gene with protein product							Standard	NM_178229		Approved		uc001fpf.3	Q86VI3	OTTHUMG00000033114	ENST00000361170.2:c.3853delG	chr1.hg19:g.156503821delC	ENSP00000354451:p.Glu1285fs	127.0	0.0		168.0	11.0	NM_178229	Q5T3H8	Frame_Shift_Del	DEL	ENST00000361170.2	hg19	CCDS1144.1																																																																																			.	.		0.612	IQGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080657.1	NM_178229	
EFTUD1	79631	hgsc.bcm.edu	37	15	82512000	82512000	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:82512000delA	ENST00000268206.7	-	14	1772	c.1604delT	c.(1603-1605)ttafs	p.L535fs	EFTUD1_ENST00000359445.3_Frame_Shift_Del_p.L484fs	NM_024580.5	NP_078856.4	Q7Z2Z2	ETUD1_HUMAN	elongation factor Tu GTP binding domain containing 1	535					GTP catabolic process (GO:0006184)|mature ribosome assembly (GO:0042256)		GTP binding (GO:0005525)|GTPase activity (GO:0003924)|ribosome binding (GO:0043022)|translation elongation factor activity (GO:0003746)			cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(14)|ovary(1)|pancreas(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	32						TACCCTTCGTAAAAACTCAAG	0.378																																					p.L535fs		Atlas-INDEL	.											.	EFTUD1	74	.	0			c.1605delA						.						20.0	20.0	20.0					15																	82512000		1777	4045	5822	SO:0001589	frameshift_variant	79631	exon14			.	AK056656	CCDS42070.1, CCDS42071.1	15q25.2	2012-07-04			ENSG00000140598	ENSG00000140598			25789	protein-coding gene	gene with protein product	"""ribosome assembly 1 homolog (yeast)"""					14702039	Standard	NM_024580		Approved	FLJ13119, FAM42A, HsT19294, RIA1	uc002bgt.1	Q7Z2Z2	OTTHUMG00000172573	ENST00000268206.7:c.1604delT	chr15.hg19:g.82512000delA	ENSP00000268206:p.Leu535fs	253.0	0.0		244.0	19.0	NM_024580	A6NKY5|B7Z6I0|Q9H8Z6	Frame_Shift_Del	DEL	ENST00000268206.7	hg19	CCDS42071.1																																																																																			.	.		0.378	EFTUD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419252.1	NM_024580	
ATG13	9776	hgsc.bcm.edu	37	11	46670721	46670721	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:46670721delA	ENST00000434074.1	+	5	994	c.305delA	c.(304-306)gaafs	p.E102fs	ATG13_ENST00000451945.1_Frame_Shift_Del_p.E102fs|ATG13_ENST00000312040.4_Frame_Shift_Del_p.E102fs|ATG13_ENST00000530500.1_Frame_Shift_Del_p.E23fs|ATG13_ENST00000529655.1_Frame_Shift_Del_p.E102fs|ATG13_ENST00000526508.1_Frame_Shift_Del_p.E102fs|ATG13_ENST00000528494.1_Frame_Shift_Del_p.E102fs|ATG13_ENST00000359513.4_Frame_Shift_Del_p.E102fs|ATG13_ENST00000524625.1_Frame_Shift_Del_p.E102fs	NM_001205120.1	NP_001192049.1	O75143	ATG13_HUMAN	autophagy related 13	102					autophagic vacuole assembly (GO:0000045)	ATG1/UKL1 signaling complex (GO:0034273)|cytosol (GO:0005829)|pre-autophagosomal structure (GO:0000407)|ULK1-ATG13-FIP200 complex (GO:0070969)	protein kinase binding (GO:0019901)	p.M103fs*1(1)		NS(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(5)|prostate(1)|skin(1)	15						TGGTGTCTTGAAATGAATGAA	0.358																																					p.E102fs		Atlas-INDEL	.											ATG13_ENST00000528494,NS,carcinoma,0,2	ATG13	60	.	1	Deletion - Frameshift(1)	central_nervous_system(1)	c.304delG						.						265.0	237.0	246.0					11																	46670721		2201	4299	6500	SO:0001589	frameshift_variant	9776	exon6			.	AB014552	CCDS7921.1, CCDS44582.1, CCDS55760.1, CCDS55761.1	11p11.2	2014-02-12	2012-06-06	2010-06-29	ENSG00000175224	ENSG00000175224			29091	protein-coding gene	gene with protein product		615088	"""KIAA0652"", ""ATG13 autophagy related 13 homolog (S. cerevisiae)"""	KIAA0652		15169610, 18339812, 17204848	Standard	NM_001205120		Approved		uc001nda.3	O75143	OTTHUMG00000166538	ENST00000434074.1:c.305delA	chr11.hg19:g.46670721delA	ENSP00000400642:p.Glu102fs	265.0	0.0		192.0	12.0	NM_001142673	B4DFI4|D3DQQ1|D3DQQ2|E9PQZ8|Q53EN6|Q9BRL3|Q9H8B0	Frame_Shift_Del	DEL	ENST00000434074.1	hg19	CCDS44582.1																																																																																			.	.		0.358	ATG13-202	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000390300.2	NM_014741	
HSPB3	8988	hgsc.bcm.edu	37	5	53751734	53751734	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:53751734delG	ENST00000302005.1	+	1	290	c.115delG	c.(115-117)gggfs	p.G39fs		NM_006308.2	NP_006299.1	Q12988	HSPB3_HUMAN	heat shock 27kDa protein 3	39					cell death (GO:0008219)|response to unfolded protein (GO:0006986)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|large_intestine(4)|prostate(3)	8		Lung NSC(810;0.00104)				TGCACTGCCTGGGCCAACCAT	0.547																																					p.P38fs		Atlas-INDEL	.											.	HSPB3	17	.	0			c.114delT						.						74.0	71.0	72.0					5																	53751734		2203	4300	6503	SO:0001589	frameshift_variant	8988	exon1			.	Y17782	CCDS3961.1	5q11.2	2011-09-02	2002-08-29		ENSG00000169271	ENSG00000169271		"""Heat shock proteins / HSPB"""	5248	protein-coding gene	gene with protein product		604624	"""heat shock 27kD protein 3"""			8972725, 9858786	Standard	NM_006308		Approved	HSPL27	uc003jph.2	Q12988	OTTHUMG00000096995	ENST00000302005.1:c.115delG	chr5.hg19:g.53751734delG	ENSP00000303394:p.Gly39fs	201.0	0.0		147.0	11.0	NM_006308		Frame_Shift_Del	DEL	ENST00000302005.1	hg19	CCDS3961.1																																																																																			.	.		0.547	HSPB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214074.2		
SWT1	54823	hgsc.bcm.edu	37	1	185175808	185175808	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:185175808delA	ENST00000367500.4	+	13	2050	c.1885delA	c.(1885-1887)aaafs	p.K630fs	SWT1_ENST00000367501.3_Frame_Shift_Del_p.K630fs	NM_017673.6	NP_060143.4	Q5T5J6	SWT1_HUMAN	SWT1 RNA endoribonuclease homolog (S. cerevisiae)	630										breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(11)|liver(1)|lung(16)|ovary(1)|prostate(1)|urinary_tract(1)	41						ACAGTGCTTTAAAAAACATTG	0.313																																					p.F628fs		Atlas-INDEL	.											.	SWT1	88	.	0			c.1884delT						.						67.0	70.0	69.0					1																	185175808		2202	4295	6497	SO:0001589	frameshift_variant	54823	exon13			.	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.1885delA	chr1.hg19:g.185175808delA	ENSP00000356470:p.Lys630fs	158.0	0.0		181.0	11.0	NM_017673	Q8NEK9|Q9BZQ7|Q9NXQ0	Frame_Shift_Del	DEL	ENST00000367500.4	hg19	CCDS1367.1																																																																																			.	.		0.313	SWT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085790.1	NM_017673	
TMEM168	64418	hgsc.bcm.edu	37	7	112424114	112424114	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:112424114delA	ENST00000312814.6	-	2	1327	c.767delT	c.(766-768)ttgfs	p.L256fs	TMEM168_ENST00000454074.1_Frame_Shift_Del_p.L256fs	NM_022484.4	NP_071929.3	Q9H0V1	TM168_HUMAN	transmembrane protein 168	256						integral component of membrane (GO:0016021)|transport vesicle (GO:0030133)				breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(10)|lung(12)|ovary(1)|prostate(2)|stomach(1)	32						TCCACGGTACAAAAAGGGTTT	0.363																																					p.L256fs		Atlas-INDEL	.											.	TMEM168	84	.	0			c.768delG						.						123.0	137.0	132.0					7																	112424114		2202	4299	6501	SO:0001589	frameshift_variant	64418	exon2			.		CCDS5757.1	7q31.32	2006-08-08			ENSG00000146802	ENSG00000146802			25826	protein-coding gene	gene with protein product						12477932	Standard	XM_005250527		Approved	DKFZp564C012,FLJ13576	uc003vgn.3	Q9H0V1	OTTHUMG00000155188	ENST00000312814.6:c.767delT	chr7.hg19:g.112424114delA	ENSP00000323068:p.Leu256fs	113.0	0.0		154.0	11.0	NM_022484	A4D0T9|B4DDS0|Q8NEK4|Q9H8J2	Frame_Shift_Del	DEL	ENST00000312814.6	hg19	CCDS5757.1																																																																																			.	.		0.363	TMEM168-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338696.4	NM_022484	
THOC2	57187	hgsc.bcm.edu	37	X	122802060	122802060	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chrX:122802060delT	ENST00000245838.8	-	10	998	c.967delA	c.(967-969)atgfs	p.M323fs	THOC2_ENST00000491737.1_Frame_Shift_Del_p.M208fs|THOC2_ENST00000355725.4_Frame_Shift_Del_p.M323fs	NM_001081550.1	NP_001075019.1	Q8NI27	THOC2_HUMAN	THO complex 2	323					mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|poly(A)+ mRNA export from nucleus (GO:0016973)|RNA splicing (GO:0008380)|viral mRNA export from host cell nucleus (GO:0046784)	THO complex (GO:0000347)|THO complex part of transcription export complex (GO:0000445)|transcription export complex (GO:0000346)	RNA binding (GO:0003723)			breast(2)|endometrium(13)|kidney(4)|large_intestine(11)|lung(26)|ovary(3)|skin(1)|upper_aerodigestive_tract(3)	63						cgctcatccattttttcAGAA	0.343																																					p.M323fs		Atlas-INDEL	.											.	THOC2	310	.	0			c.968delT						.						186.0	166.0	172.0					X																	122802060		1819	4070	5889	SO:0001589	frameshift_variant	57187	exon10			.	AF441770	CCDS43988.1	Xq25-q26.3	2013-02-11	2004-08-09		ENSG00000125676	ENSG00000125676		"""THO complex subunits"""	19073	protein-coding gene	gene with protein product		300395	"""chromosome X open reading frame 3"""	CXorf3		11979277	Standard	NM_001081550		Approved	THO2, dJ506G2.1	uc004etu.3	Q8NI27	OTTHUMG00000022334	ENST00000245838.8:c.967delA	chrX.hg19:g.122802060delT	ENSP00000245838:p.Met323fs	220.0	0.0		163.0	10.0	NM_001081550	A6NM50|Q5JZ12|Q6IN92|Q9H8I6	Frame_Shift_Del	DEL	ENST00000245838.8	hg19	CCDS43988.1																																																																																			.	.		0.343	THOC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058153.3		
AHNAK	79026	hgsc.bcm.edu	37	11	62288928	62288928	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:62288928delT	ENST00000378024.4	-	5	13235	c.12961delA	c.(12961-12963)atgfs	p.M4321fs	AHNAK_ENST00000257247.7_Intron|AHNAK_ENST00000530124.1_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	4321					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)				AATTTGGGCATTTTCACCTTG	0.522																																					p.M4321fs		Atlas-INDEL	.											.	AHNAK	532	.	0			c.12962delT						.						174.0	174.0	174.0					11																	62288928		2202	4299	6501	SO:0001589	frameshift_variant	79026	exon5			.	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.12961delA	chr11.hg19:g.62288928delT	ENSP00000367263:p.Met4321fs	255.0	0.0		163.0	10.0	NM_001620	A1A586	Frame_Shift_Del	DEL	ENST00000378024.4	hg19	CCDS31584.1																																																																																			.	.		0.522	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060	
AP4B1	10717	hgsc.bcm.edu	37	1	114442999	114442999	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:114442999delC	ENST00000369569.1	-	5	921	c.641delG	c.(640-642)ggcfs	p.G214fs	AP4B1-AS1_ENST00000419536.1_RNA|AP4B1_ENST00000369567.1_Frame_Shift_Del_p.G46fs|AP4B1_ENST00000369566.3_Frame_Shift_Del_p.G121fs|AP4B1_ENST00000256658.4_Frame_Shift_Del_p.G214fs|AP4B1_ENST00000462591.1_5'Flank	NM_001253852.1	NP_001240781.1	Q9Y6B7	AP4B1_HUMAN	adaptor-related protein complex 4, beta 1 subunit	214					intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	clathrin adaptor complex (GO:0030131)|coated pit (GO:0005905)|trans-Golgi network (GO:0005802)	protein transporter activity (GO:0008565)|transporter activity (GO:0005215)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(9)|ovary(3)|prostate(3)	25	Lung SC(450;0.184)	all_cancers(81;4.5e-08)|all_epithelial(167;1.1e-07)|all_lung(203;1.53e-05)|Lung NSC(69;2.76e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		TTCAGCCTGGCCCCATTGGTC	0.418																																					p.G214fs		Atlas-INDEL	.											.	AP4B1	72	.	0			c.642delC						.						62.0	57.0	59.0					1																	114442999		2203	4300	6503	SO:0001589	frameshift_variant	10717	exon6			.	AF092094	CCDS865.1	1p13.2	2012-03-30			ENSG00000134262	ENSG00000134262			572	protein-coding gene	gene with protein product	"""beta 4 subunit of AP-4"""	607245	"""spastic paraplegia 47"""	SPG47		10066790	Standard	NM_006594		Approved	BETA-4	uc001eeb.3	Q9Y6B7	OTTHUMG00000011943	ENST00000369569.1:c.641delG	chr1.hg19:g.114442999delC	ENSP00000358582:p.Gly214fs	238.0	0.0		188.0	13.0	NM_006594	B7Z4X3|Q59EJ4|Q96CL6	Frame_Shift_Del	DEL	ENST00000369569.1	hg19	CCDS865.1																																																																																			.	.		0.418	AP4B1-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033037.1	NM_006594	
CENPC	1060	hgsc.bcm.edu	37	4	68374713	68374713	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr4:68374713delT	ENST00000273853.6	-	10	1973	c.1723delA	c.(1723-1725)actfs	p.T575fs		NM_001812.2	NP_001803.2	Q03188	CENPC_HUMAN	centromere protein C	575					chromosome segregation (GO:0007059)|kinetochore assembly (GO:0051382)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	condensed nuclear chromosome, centromeric region (GO:0000780)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)	centromeric DNA binding (GO:0019237)|DNA binding (GO:0003677)										AGTGGAATAGTTTTTTTCCTA	0.343																																					p.T575fs		Atlas-INDEL	.											.	CENPC1	66	.	0			c.1724delC						.						145.0	132.0	136.0					4																	68374713		1822	4072	5894	SO:0001589	frameshift_variant	1060	exon10			.	M95724	CCDS47063.1	4q13.2	2013-11-05	2013-07-03	2013-07-03	ENSG00000145241	ENSG00000145241			1854	protein-coding gene	gene with protein product		117141	"""centromere protein C 1"""	CENPC1		7959789	Standard	XR_245245		Approved	CENP-C, hcp-4, MIF2	uc003hdd.1	Q03188	OTTHUMG00000160735	ENST00000273853.6:c.1723delA	chr4.hg19:g.68374713delT	ENSP00000273853:p.Thr575fs	208.0	0.0		205.0	13.0	NM_001812	Q8IW27|Q9P0M5	Frame_Shift_Del	DEL	ENST00000273853.6	hg19	CCDS47063.1																																																																																			.	.		0.343	CENPC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362001.2		
ANKRD26	22852	hgsc.bcm.edu	37	10	27337888	27337888	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:27337888delT	ENST00000376087.4	-	17	1821	c.1656delA	c.(1654-1656)aaafs	p.K552fs	ANKRD26_ENST00000376070.3_Frame_Shift_Del_p.K109fs|ANKRD26_ENST00000436985.2_Frame_Shift_Del_p.K568fs	NM_001256053.1|NM_014915.2	NP_001242982.1|NP_055730.2	Q9UPS8	ANR26_HUMAN	ankyrin repeat domain 26	552					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						TATTTCTGTGTTTTTTCCTTT	0.279																																					p.H553fs		Atlas-INDEL	.											.	ANKRD26	179	.	0			c.1657delC						.						145.0	133.0	137.0					10																	27337888		1896	4120	6016	SO:0001589	frameshift_variant	22852	exon17			.	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.1656delA	chr10.hg19:g.27337888delT	ENSP00000365255:p.Lys552fs	270.0	0.0		198.0	15.0	NM_014915	A6NH29|Q2TAZ3|Q6ZR14|Q9H1Q1|Q9NSK9|Q9NTD5|Q9NW69	Frame_Shift_Del	DEL	ENST00000376087.4	hg19	CCDS41499.1																																																																																			.	.		0.279	ANKRD26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047296.1		
UPF2	26019	hgsc.bcm.edu	37	10	11997384	11997384	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:11997384delA	ENST00000356352.2	-	13	3170	c.2697delT	c.(2695-2697)tttfs	p.F899fs	UPF2_ENST00000357604.5_Frame_Shift_Del_p.F899fs|UPF2_ENST00000397053.2_Frame_Shift_Del_p.F899fs			Q9HAU5	RENT2_HUMAN	UPF2 regulator of nonsense transcripts homolog (yeast)	899	MIF4G 3.|Sufficient for interaction with EIF4A1 and EIF1.|Sufficient for interaction with UPF3A and UPF3B.				gene expression (GO:0010467)|liver development (GO:0001889)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|organ regeneration (GO:0031100)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|exon-exon junction complex (GO:0035145)|nucleus (GO:0005634)	RNA binding (GO:0003723)			breast(3)|central_nervous_system(3)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(14)|lung(17)|ovary(2)|skin(3)|urinary_tract(2)	56		Renal(717;0.228)				GATTAACACCAAATGAGGTAA	0.438																																					p.G900fs		Atlas-INDEL	.											.	UPF2	111	.	0			c.2698delG						.						79.0	72.0	75.0					10																	11997384		2203	4300	6503	SO:0001589	frameshift_variant	26019	exon14			.	AB037829	CCDS7086.1	10p14-p13	2011-06-21			ENSG00000151461	ENSG00000151461			17854	protein-coding gene	gene with protein product	"""smg-3 homolog, nonsense mediated mRNA decay factor (C. elegans)"""	605529				11073994, 11113196	Standard	NM_080599		Approved	RENT2, DKFZP434D222, KIAA1408, smg-3	uc001ilb.3	Q9HAU5	OTTHUMG00000017678	ENST00000356352.2:c.2697delT	chr10.hg19:g.11997384delA	ENSP00000348708:p.Phe899fs	202.0	0.0		127.0	10.0	NM_080599	A6NLJ5|D3DRS0|Q14BM1|Q5W0J4|Q8N8U1|Q9H1J2|Q9NWL1|Q9P2D9|Q9Y4M9	Frame_Shift_Del	DEL	ENST00000356352.2	hg19	CCDS7086.1																																																																																			.	.		0.438	UPF2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046783.1		
PREX2	80243	hgsc.bcm.edu	37	8	68995503	68995503	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr8:68995503delT	ENST00000288368.4	+	18	2184	c.1907delT	c.(1906-1908)attfs	p.I636fs	PREX2_ENST00000529398.1_3'UTR|RP11-403D15.2_ENST00000526901.1_RNA	NM_024870.2|NM_025170.4	NP_079146.2|NP_079446.3	Q70Z35	PREX2_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2	636	PDZ 1. {ECO:0000255|PROSITE- ProRule:PRU00143}.				adult locomotory behavior (GO:0008344)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of Rac GTPase activity (GO:0032855)		Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			NS(6)|biliary_tract(1)|breast(4)|endometrium(11)|kidney(16)|large_intestine(25)|liver(4)|lung(57)|ovary(2)|pancreas(4)|prostate(3)|skin(42)|upper_aerodigestive_tract(1)|urinary_tract(2)	178						GGGAAAAAGATTTTTGCTATT	0.318																																					p.I636fs		Atlas-INDEL	.											.	PREX2	614	.	0			c.1906delA						.						93.0	94.0	93.0					8																	68995503		2203	4300	6503	SO:0001589	frameshift_variant	80243	exon18			.	AK024079	CCDS6201.1	8q13.1	2014-06-13	2008-09-15	2008-09-15	ENSG00000046889	ENSG00000046889		"""Rho guanine nucleotide exchange factors"""	22950	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 129"""	612139	"""DEP domain containing 2"""	DEPDC2		15304342, 15304343	Standard	NM_024870		Approved	DEP.2, FLJ12987, P-REX2, PPP1R129	uc003xxv.1	Q70Z35	OTTHUMG00000164402	ENST00000288368.4:c.1907delT	chr8.hg19:g.68995503delT	ENSP00000288368:p.Ile636fs	157.0	0.0		159.0	10.0	NM_025170	B4DFX0|Q32KL0|Q32KL1|Q6R7Q3|Q6R7Q4|Q9H805|Q9H961	Frame_Shift_Del	DEL	ENST00000288368.4	hg19	CCDS6201.1																																																																																			.	.		0.318	PREX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378620.1	NM_025170	
SH3GL1	6455	hgsc.bcm.edu	37	19	4364123	4364123	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr19:4364123delG	ENST00000269886.3	-	5	605	c.427delC	c.(427-429)ctcfs	p.L143fs	AC007292.6_ENST00000594444.1_RNA|SH3GL1_ENST00000417295.2_Frame_Shift_Del_p.L95fs|SH3GL1_ENST00000598564.1_Intron	NM_003025.3	NP_003016.1	Q99961	SH3G1_HUMAN	SH3-domain GRB2-like 1	143	BAR. {ECO:0000255|PROSITE- ProRule:PRU00361}.				central nervous system development (GO:0007417)|endocytosis (GO:0006897)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|endosome (GO:0005768)|membrane (GO:0016020)	identical protein binding (GO:0042802)|lipid binding (GO:0008289)			NS(1)|endometrium(2)|kidney(16)|large_intestine(3)|lung(2)|ovary(2)	26				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0152)|STAD - Stomach adenocarcinoma(1328;0.182)		AGGTTCTGGAGGGGGTCAATG	0.622			T	MLL	AL																																p.L143fs	NSCLC(94;1152 2133 30346 33362)	Atlas-INDEL	.		Dom	yes		19	19p13.3	6455	SH3-domain GRB2-like 1 (EEN)		L	.	SH3GL1	52	.	0			c.428delT						.						45.0	40.0	42.0					19																	4364123		2203	4300	6503	SO:0001589	frameshift_variant	6455	exon5			.		CCDS32874.1, CCDS56076.1, CCDS59335.1	19p13.3	2008-07-22							10830	protein-coding gene	gene with protein product	"""extra 11-19 leukemia fusion"", ""fusion partner of MLL"", ""SH3-containing Grb-2-like 1 protein"", ""SH3-containing protein EEN"", ""SH3 domain GRB2-like 1"""	601768				9169142	Standard	NM_003025		Approved	SH3P8, SH3D2B, CNSA1, EEN, MGC111371	uc002maj.3	Q99961		ENST00000269886.3:c.427delC	chr19.hg19:g.4364123delG	ENSP00000269886:p.Leu143fs	299.0	0.0		206.0	14.0	NM_003025	B4DRA1|E7EVZ4|M0QZV5|Q99668	Frame_Shift_Del	DEL	ENST00000269886.3	hg19	CCDS32874.1																																																																																			.	.		0.622	SH3GL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458302.1	NM_003025	
PKHD1	5314	hgsc.bcm.edu	37	6	51927342	51927342	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:51927342delA	ENST00000371117.3	-	14	1368	c.1093delT	c.(1093-1095)tggfs	p.W365fs	PKHD1_ENST00000340994.4_Frame_Shift_Del_p.W365fs|AL590391.1_ENST00000408630.2_RNA	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	365					cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					TCCTGTGACCAAAACCCAAAT	0.488																																					p.W365fs		Atlas-INDEL	.											.	PKHD1	927	.	0			c.1094delG						.						151.0	140.0	143.0					6																	51927342		2203	4300	6503	SO:0001589	frameshift_variant	5314	exon14			.	AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"""tigmin"", ""polyductin"", ""fibrocystin"""	606702	"""TIG multiple domains 1"""	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.1093delT	chr6.hg19:g.51927342delA	ENSP00000360158:p.Trp365fs	216.0	0.0		162.0	10.0	NM_170724	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Frame_Shift_Del	DEL	ENST00000371117.3	hg19	CCDS4935.1																																																																																			.	.		0.488	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694	
LYST	1130	hgsc.bcm.edu	37	1	235964220	235964220	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:235964220delA	ENST00000389794.3	-	9	4064	c.3890delT	c.(3889-3891)ttgfs	p.L1297fs	LYST_ENST00000536965.1_Frame_Shift_Del_p.L1297fs|LYST_ENST00000389793.2_Frame_Shift_Del_p.L1297fs			Q99698	LYST_HUMAN	lysosomal trafficking regulator	1297					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)			AATAATTTTCAAAAAACTCTC	0.318																																					p.L1297fs		Atlas-INDEL	.											.	LYST	370	.	0			c.3891delG						.						54.0	54.0	54.0					1																	235964220		2203	4300	6503	SO:0001589	frameshift_variant	1130	exon9			.	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.3890delT	chr1.hg19:g.235964220delA	ENSP00000374444:p.Leu1297fs	136.0	0.0		151.0	12.0	NM_000081	O43274|Q5T2U9|Q96TD7|Q96TD8|Q99709|Q9H133	Frame_Shift_Del	DEL	ENST00000389794.3	hg19	CCDS31062.1																																																																																			.	.		0.318	LYST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097533.5		
MAP3K4	4216	hgsc.bcm.edu	37	6	161455391	161455391	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:161455391delC	ENST00000392142.4	+	2	401	c.253delC	c.(253-255)cccfs	p.P86fs	MAP3K4_ENST00000366919.2_Frame_Shift_Del_p.P86fs|MAP3K4_ENST00000348824.7_Frame_Shift_Del_p.P86fs|MAP3K4_ENST00000366920.2_Frame_Shift_Del_p.P86fs|MAP3K4_ENST00000446500.1_3'UTR	NM_005922.2	NP_005913	Q9Y6R4	M3K4_HUMAN	mitogen-activated protein kinase kinase kinase 4	86					activation of MAPKK activity (GO:0000186)|chorionic trophoblast cell differentiation (GO:0060718)|intracellular signal transduction (GO:0035556)|male germ-line sex determination (GO:0019100)|MAPK cascade (GO:0000165)|placenta development (GO:0001890)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of p38MAPK cascade (GO:1900745)|regulation of gene expression (GO:0010468)|response to UV-C (GO:0010225)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|metal ion binding (GO:0046872)			breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|lung(28)|ovary(3)|skin(2)|stomach(1)	77		Breast(66;0.000776)|Ovarian(120;0.0367)|Prostate(117;0.0771)		OV - Ovarian serous cystadenocarcinoma(65;1.85e-18)|BRCA - Breast invasive adenocarcinoma(81;3.04e-05)		TGGTACCTCTCCCCCCAGCAC	0.473																																					p.S84fs		Atlas-INDEL	.											.	MAP3K4	364	.	0			c.252delT						.						90.0	87.0	88.0					6																	161455391		2203	4300	6503	SO:0001589	frameshift_variant	4216	exon2			.	AF002715	CCDS34565.1, CCDS34566.1, CCDS75544.1	6q26	2012-10-02			ENSG00000085511	ENSG00000085511		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6856	protein-coding gene	gene with protein product		602425		MEKK4		9305639	Standard	XM_005266988		Approved	MTK1, MAPKKK4, KIAA0213	uc003qtn.3	Q9Y6R4	OTTHUMG00000015968	ENST00000392142.4:c.253delC	chr6.hg19:g.161455391delC	ENSP00000375986:p.Pro86fs	195.0	0.0		157.0	10.0	NM_006724	A6H8W0|B7ZLD3|B9EG75|Q5VTT8|Q5VTT9|Q92612|Q9H408	Frame_Shift_Del	DEL	ENST00000392142.4	hg19	CCDS34565.1																																																																																			.	.		0.473	MAP3K4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042988.3		
ABCB4	5244	hgsc.bcm.edu	37	7	87079305	87079305	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr7:87079305delC	ENST00000265723.4	-	8	923	c.812delG	c.(811-813)ggcfs	p.G271fs	ABCB4_ENST00000359206.3_Frame_Shift_Del_p.G271fs|ABCB4_ENST00000545634.1_Frame_Shift_Del_p.G271fs|ABCB4_ENST00000358400.3_Frame_Shift_Del_p.G271fs|ABCB4_ENST00000453593.1_Frame_Shift_Del_p.G271fs	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	271	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)	TTTGTTCTGGCCCCCGAAAGC	0.468																																					p.G271fs		Atlas-INDEL	.											.	ABCB4	177	.	0			c.813delC						.						117.0	97.0	104.0					7																	87079305		2203	4300	6503	SO:0001589	frameshift_variant	5244	exon8			.	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.812delG	chr7.hg19:g.87079305delC	ENSP00000265723:p.Gly271fs	305.0	0.0		297.0	18.0	NM_018849	A0A2V7|A4D1D3|A4D1D4|A4D1D5|D6W5P3|D6W5P4|Q14813	Frame_Shift_Del	DEL	ENST00000265723.4	hg19	CCDS5606.1																																																																																			.	.		0.468	ABCB4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000336083.1	NM_000443	
PARN	5073	hgsc.bcm.edu	37	16	14576541	14576541	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:14576541delG	ENST00000437198.2	-	22	1765	c.1624delC	c.(1624-1626)cagfs	p.Q542fs	PARN_ENST00000420015.2_Frame_Shift_Del_p.Q496fs|PARN_ENST00000341484.7_Frame_Shift_Del_p.Q481fs|PARN_ENST00000539279.1_Frame_Shift_Del_p.Q367fs	NM_001134477.2|NM_002582.3	NP_001127949.1|NP_002573.1	O95453	PARN_HUMAN	poly(A)-specific ribonuclease	542					female gamete generation (GO:0007292)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|RNA metabolic process (GO:0016070)|RNA modification (GO:0009451)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|mRNA 3'-UTR binding (GO:0003730)|nuclease activity (GO:0004518)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|poly(A)-specific ribonuclease activity (GO:0004535)|protein kinase binding (GO:0019901)			cervix(2)|endometrium(2)|kidney(3)|large_intestine(2)|lung(9)|ovary(2)|urinary_tract(1)	21						GGTATGCACTGGGGGTTTAAC	0.443																																					p.Q542fs		Atlas-INDEL	.											.	PARN	72	.	0			c.1625delA						.						213.0	194.0	200.0					16																	14576541		1889	4130	6019	SO:0001589	frameshift_variant	5073	exon22			.	AJ005698	CCDS45419.1, CCDS45420.1, CCDS58425.1	16p13	2014-08-08	2011-07-07		ENSG00000140694	ENSG00000140694	3.1.13.4		8609	protein-coding gene	gene with protein product	"""deadenylation nuclease"""	604212	"""poly(A)-specific ribonuclease (deadenylation nuclease)"""			10640832	Standard	NM_002582		Approved	DAN	uc010uzd.2	O95453	OTTHUMG00000173199	ENST00000437198.2:c.1624delC	chr16.hg19:g.14576541delG	ENSP00000387911:p.Gln542fs	317.0	0.0		200.0	15.0	NM_002582	B2RCB3|B4DDG8|B4DWR4|B4E1H6	Frame_Shift_Del	DEL	ENST00000437198.2	hg19	CCDS45419.1																																																																																			.	.		0.443	PARN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422383.1	NM_002582	
LRP1	4035	hgsc.bcm.edu	37	12	57550002	57550002	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr12:57550002delG	ENST00000243077.3	+	9	1819	c.1353delG	c.(1351-1353)cagfs	p.Q451fs		NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	451					aging (GO:0007568)|aorta morphogenesis (GO:0035909)|apoptotic cell clearance (GO:0043277)|beta-amyloid clearance (GO:0097242)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of platelet-derived growth factor receptor-beta signaling pathway (GO:2000587)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of Wnt signaling pathway (GO:0030178)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of lipid transport (GO:0032370)|positive regulation of protein transport (GO:0051222)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|receptor-mediated endocytosis (GO:0006898)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cholesterol transport (GO:0032374)|regulation of phospholipase A2 activity (GO:0032429)|retinoid metabolic process (GO:0001523)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|lipoprotein particle receptor binding (GO:0070325)|lipoprotein transporter activity (GO:0042954)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|receptor activity (GO:0004872)			NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(33)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(26)|lung(58)|ovary(10)|pancreas(2)|prostate(11)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	184				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	CCGAGTACCAGGTTGTCACCC	0.572																																					p.Q451fs		Atlas-INDEL	.											.	LRP1	428	.	0			c.1352delA						.						146.0	113.0	124.0					12																	57550002		2203	4300	6503	SO:0001589	frameshift_variant	4035	exon9			.	X13916	CCDS8932.1	12q13.3	2013-05-28	2010-01-26		ENSG00000123384	ENSG00000123384		"""CD molecules"", ""Low density lipoprotein receptors"""	6692	protein-coding gene	gene with protein product		107770	"""alpha-2-macroglobulin receptor"""	APR, A2MR		2548950	Standard	NM_002332		Approved	LRP, CD91, LRP1A, APOER	uc001snd.3	Q07954	OTTHUMG00000044412	ENST00000243077.3:c.1353delG	chr12.hg19:g.57550002delG	ENSP00000243077:p.Gln451fs	225.0	0.0		177.0	11.0	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Frame_Shift_Del	DEL	ENST00000243077.3	hg19	CCDS8932.1																																																																																			.	.		0.572	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332	
AGBL2	79841	hgsc.bcm.edu	37	11	47721054	47721054	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr11:47721054delT	ENST00000525123.1	-	8	923	c.638delA	c.(637-639)aagfs	p.K213fs	AGBL2_ENST00000528244.1_Frame_Shift_Del_p.K175fs|AGBL2_ENST00000298861.4_Frame_Shift_Del_p.K213fs|AGBL2_ENST00000357610.3_Frame_Shift_Del_p.K213fs|AGBL2_ENST00000529712.1_5'UTR	NM_024783.3	NP_079059.2	Q5U5Z8	CBPC2_HUMAN	ATP/GTP binding protein-like 2	213						cytosol (GO:0005829)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			NS(1)|endometrium(5)|kidney(1)|large_intestine(8)|liver(1)|lung(14)|ovary(2)|prostate(1)|skin(1)	34						CTCTGGTACCTTTTCATTTCC	0.338																																					p.K213fs		Atlas-INDEL	.											.	AGBL2	73	.	0			c.639delG						.						170.0	164.0	166.0					11																	47721054		2201	4298	6499	SO:0001589	frameshift_variant	79841	exon8			.		CCDS7944.1	11p11.2	2014-06-23			ENSG00000165923	ENSG00000165923			26296	protein-coding gene	gene with protein product	"""cytoplasmic carboxypeptidase 2"""					12738998, 21303978	Standard	NM_024783		Approved	FLJ23598, CCP2	uc001ngg.3	Q5U5Z8	OTTHUMG00000165368	ENST00000525123.1:c.638delA	chr11.hg19:g.47721054delT	ENSP00000435582:p.Lys213fs	198.0	0.0		149.0	10.0	NM_024783	A8MPX2|Q53FV5|Q8IV57|Q9H5C0	Frame_Shift_Del	DEL	ENST00000525123.1	hg19	CCDS7944.1																																																																																			.	.		0.338	AGBL2-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000383726.2	NM_024783	
USP31	57478	hgsc.bcm.edu	37	16	23093870	23093870	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:23093870delG	ENST00000219689.7	-	12	1838	c.1839delC	c.(1837-1839)cccfs	p.P613fs		NM_020718.3	NP_065769.3	Q86UV5	UBP48_HUMAN	ubiquitin specific peptidase 31	264	DUSP 2. {ECO:0000255|PROSITE- ProRule:PRU00613}.				ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ubiquitin-specific protease activity (GO:0004843)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(17)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	57				GBM - Glioblastoma multiforme(48;0.0187)		AGGCATCATCGGGGGCAAGCT	0.498																																					p.D614fs		Atlas-INDEL	.											USP31,right_lower_lobe,carcinoma,0,1	USP31	122	.	0			c.1840delG						.						76.0	65.0	68.0					16																	23093870		2197	4300	6497	SO:0001589	frameshift_variant	57478	exon12			.	AB033029	CCDS10607.1	16p12.3	2008-02-05	2005-08-08		ENSG00000103404	ENSG00000103404		"""Ubiquitin-specific peptidases"""	20060	protein-coding gene	gene with protein product			"""ubiquitin specific protease 31"""			12838346	Standard	NM_020718		Approved	KIAA1203	uc002dll.3	Q70CQ4	OTTHUMG00000094793	ENST00000219689.7:c.1839delC	chr16.hg19:g.23093870delG	ENSP00000219689:p.Pro613fs	253.0	0.0		147.0	10.0	NM_020718	B7ZKS7|Q2M3I4|Q5SZI4|Q5T3T5|Q6NX53|Q8N3F6|Q96F64|Q96IQ3|Q9H5N3|Q9H5T7|Q9NUJ6|Q9NXR0	Frame_Shift_Del	DEL	ENST00000219689.7	hg19	CCDS10607.1																																																																																			.	.		0.498	USP31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211607.1	NM_020718	
FBXO5	26271	hgsc.bcm.edu	37	6	153296240	153296240	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:153296240delT	ENST00000229758.3	-	2	678	c.620delA	c.(619-621)aagfs	p.K207fs	FBXO5_ENST00000477822.1_5'Flank|FBXO5_ENST00000367241.3_Frame_Shift_Del_p.K161fs	NM_012177.3	NP_036309.1	Q9UKT4	FBX5_HUMAN	F-box protein 5	207	Interaction with EVI5.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|G1/S transition of mitotic cell cycle (GO:0000082)|inhibition of mitotic anaphase-promoting complex activity (GO:0060565)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|microtubule polymerization (GO:0046785)|mitotic cell cycle (GO:0000278)|negative regulation of meiosis (GO:0045835)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|oocyte maturation (GO:0001556)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|regulation of mitotic cell cycle (GO:0007346)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|spindle assembly involved in female meiosis I (GO:0007057)|vesicle organization (GO:0016050)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(3)|prostate(2)|upper_aerodigestive_tract(1)	15		Ovarian(120;0.125)		OV - Ovarian serous cystadenocarcinoma(155;4.38e-10)|BRCA - Breast invasive adenocarcinoma(81;0.0893)		TTTTGCATTCTTTTTTAATGT	0.373																																					p.K207fs	NSCLC(121;372 1757 17721 17977 29669)	Atlas-INDEL	.											.	FBXO5	40	.	0			c.621delG						.						90.0	94.0	93.0					6																	153296240		2203	4300	6503	SO:0001589	frameshift_variant	26271	exon2			.	AF129535	CCDS5242.1, CCDS47501.1	6q25-q26	2008-02-05	2004-06-15		ENSG00000112029	ENSG00000112029		"""F-boxes /  ""other"""""	13584	protein-coding gene	gene with protein product		606013	"""F-box only protein 5"""			10531035, 10531037	Standard	NM_012177		Approved	FBX5, Fbxo31, EMI1	uc003qpg.3	Q9UKT4	OTTHUMG00000015854	ENST00000229758.3:c.620delA	chr6.hg19:g.153296240delT	ENSP00000229758:p.Lys207fs	243.0	0.0		148.0	11.0	NM_012177	B3KNX5|Q5TF47|Q8WV29|Q9UGC8	Frame_Shift_Del	DEL	ENST00000229758.3	hg19	CCDS5242.1																																																																																			.	.		0.373	FBXO5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042757.1		
RUSC2	9853	hgsc.bcm.edu	37	9	35557957	35557957	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr9:35557957delT	ENST00000455600.1	+	6	3599	c.3030delT	c.(3028-3030)catfs	p.H1010fs		NM_001135999.1	NP_001129471	Q8N2Y8	RUSC2_HUMAN	RUN and SH3 domain containing 2	1010						cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)	Rab GTPase binding (GO:0017137)			NS(1)|breast(3)|endometrium(4)|kidney(1)|large_intestine(9)|lung(4)|ovary(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32			Lung(28;0.000837)|LUSC - Lung squamous cell carcinoma(32;0.00109)|STAD - Stomach adenocarcinoma(86;0.194)			TTGTGGCTCATTTTGGCACAA	0.557																																					p.H1010fs		Atlas-INDEL	.											.	RUSC2	88	.	0			c.3029delA						.						156.0	134.0	141.0					9																	35557957		2203	4300	6503	SO:0001589	frameshift_variant	9853	exon6			.	AB002373	CCDS35008.1	9p13.2	2003-12-02			ENSG00000198853	ENSG00000198853			23625	protein-coding gene	gene with protein product		611053				9205841	Standard	NM_001135999		Approved	KIAA0375	uc003zww.3	Q8N2Y8	OTTHUMG00000019861	ENST00000455600.1:c.3030delT	chr9.hg19:g.35557957delT	ENSP00000393922:p.His1010fs	204.0	0.0		148.0	10.0	NM_014806	A2RU62|A7E2A9|O15080|Q5W134|Q641Q6|Q6P1W7	Frame_Shift_Del	DEL	ENST00000455600.1	hg19	CCDS35008.1																																																																																			.	.		0.557	RUSC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052309.1	XM_048462	
ZNF646	9726	hgsc.bcm.edu	37	16	31092588	31092588	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr16:31092588delC	ENST00000394979.2	+	1	5366	c.4943delC	c.(4942-4944)accfs	p.T1648fs	ZNF646_ENST00000300850.5_Frame_Shift_Del_p.T1648fs			O15015	ZN646_HUMAN	zinc finger protein 646	1648					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(4)|cervix(2)|endometrium(8)|kidney(4)|large_intestine(1)|lung(21)|ovary(1)|prostate(4)|skin(3)	49						CCATCAGAAACCCCCAGAGGC	0.657																																					p.T1648fs		Atlas-INDEL	.											.	ZNF646	133	.	0			c.4942delA						.						43.0	53.0	50.0					16																	31092588		2196	4299	6495	SO:0001589	frameshift_variant	9726	exon2			.	AB002294	CCDS10702.1	16p11.2	2013-01-08			ENSG00000167395	ENSG00000167395		"""Zinc fingers, C2H2-type"""	29004	protein-coding gene	gene with protein product							Standard	NM_014699		Approved	KIAA0296	uc002eap.3	O15015	OTTHUMG00000047355	ENST00000394979.2:c.4943delC	chr16.hg19:g.31092588delC	ENSP00000378429:p.Thr1648fs	230.0	0.0		165.0	10.0	NM_014699	Q8IVD8	Frame_Shift_Del	DEL	ENST00000394979.2	hg19																																																																																				.	.		0.657	ZNF646-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000108510.2	NM_014699	
AMER3	205147	hgsc.bcm.edu	37	2	131520663	131520663	+	Frame_Shift_Del	DEL	T	T	-	rs1905235	byFrequency	TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:131520663delT	ENST00000423981.1	+	2	1128	c.1018delT	c.(1018-1020)tccfs	p.S340fs	AMER3_ENST00000321420.4_Frame_Shift_Del_p.S340fs	NM_001105193.1|NM_001105194.1|NM_001105195.1|NM_152698.2	NP_001098663.1|NP_001098664.1|NP_001098665.1|NP_689911.2	Q8N944	AMER3_HUMAN	APC membrane recruitment protein 3	340			S -> P (in dbSNP:rs1905235). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:15815621}.		Wnt signaling pathway (GO:0016055)	plasma membrane (GO:0005886)	lipid binding (GO:0008289)										CAGGGACCAATCCCGGCTGGA	0.667																																					p.Q339fs		Atlas-INDEL	.											.	.	.	.	0			c.1017delA						.						32.0	37.0	36.0					2																	131520663		2203	4300	6503	SO:0001589	frameshift_variant	205147	exon2			.	AK095696	CCDS2164.1	2q21.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000178171	ENSG00000178171		"""-"""	26771	protein-coding gene	gene with protein product			"""family with sequence similarity 123C"""	FAM123C		20843316	Standard	NM_001105195		Approved	FLJ38377	uc002trw.2	Q8N944	OTTHUMG00000131637	ENST00000423981.1:c.1018delT	chr2.hg19:g.131520663delT	ENSP00000392700:p.Ser340fs	221.0	0.0		157.0	10.0	NM_001105195	B7ZLH6	Frame_Shift_Del	DEL	ENST00000423981.1	hg19	CCDS2164.1																																																																																			.	.		0.667	AMER3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254531.3	NM_152698	
MAPKBP1	23005	hgsc.bcm.edu	37	15	42092080	42092080	+	Frame_Shift_Del	DEL	C	C	-	rs367612663		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:42092080delC	ENST00000456763.2	+	3	370	c.174delC	c.(172-174)gacfs	p.D58fs	MAPKBP1_ENST00000507762.1_3'UTR|MAPKBP1_ENST00000457542.2_Frame_Shift_Del_p.D58fs|MAPKBP1_ENST00000221214.6_Frame_Shift_Del_p.D58fs|MAPKBP1_ENST00000514566.1_Frame_Shift_Del_p.D58fs|MAPKBP1_ENST00000260357.7_Intron	NM_001128608.1	NP_001122080.1	O60336	MABP1_HUMAN	mitogen-activated protein kinase binding protein 1	58										breast(6)|central_nervous_system(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	56		all_cancers(109;7.71e-14)|all_epithelial(112;5.15e-12)|Lung NSC(122;3.74e-08)|all_lung(180;1.81e-07)|Melanoma(134;0.0262)		OV - Ovarian serous cystadenocarcinoma(18;3.95e-17)|GBM - Glioblastoma multiforme(94;5.71e-07)|Lung(196;0.0436)|BRCA - Breast invasive adenocarcinoma(123;0.203)|LUSC - Lung squamous cell carcinoma(244;0.225)		TTGCCTGTGACCCCCGATCAG	0.502																																					p.D58fs		Atlas-INDEL	.											.	MAPKBP1	120	.	0			c.173delA						.						169.0	146.0	154.0					15																	42092080		2203	4300	6503	SO:0001589	frameshift_variant	23005	exon3			.	AB011168	CCDS32201.1, CCDS45239.1, CCDS58359.1	15q15.1	2013-01-10	2008-01-30		ENSG00000137802	ENSG00000137802		"""WD repeat domain containing"""	29536	protein-coding gene	gene with protein product			"""mitogen activated protein kinase binding protein 1"""			9628581, 10471813	Standard	NM_014994		Approved	KIAA0596	uc001zok.4	O60336	OTTHUMG00000160227	ENST00000456763.2:c.174delC	chr15.hg19:g.42092080delC	ENSP00000393099:p.Asp58fs	254.0	0.0		158.0	14.0	NM_001128608	A6NM93|A8K8P9|Q14CB5|Q14CD8|Q49AJ8|Q5W9G9	Frame_Shift_Del	DEL	ENST00000456763.2	hg19	CCDS45239.1																																																																																			.	.		0.502	MAPKBP1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000359745.1	NM_014994	
SLC9A2	6549	hgsc.bcm.edu	37	2	103300596	103300596	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:103300596delT	ENST00000233969.2	+	5	1368	c.1226delT	c.(1225-1227)gttfs	p.V409fs		NM_003048.3	NP_003039.2	Q9UBY0	SL9A2_HUMAN	solute carrier family 9, subfamily A (NHE2, cation proton antiporter 2), member 2	409					ion transport (GO:0006811)|protein localization (GO:0008104)|regulation of pH (GO:0006885)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium:proton antiporter activity (GO:0015385)			breast(5)|central_nervous_system(3)|endometrium(3)|kidney(1)|large_intestine(3)|lung(17)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	42						TTTGCAGGTGTTTTTGTCCTG	0.453																																					p.V409fs		Atlas-INDEL	.											.	SLC9A2	112	.	0			c.1225delG						.						96.0	86.0	89.0					2																	103300596		2203	4300	6503	SO:0001589	frameshift_variant	6549	exon5			.		CCDS2062.1	2q11.2	2013-05-22	2012-03-22		ENSG00000115616	ENSG00000115616		"""Solute carriers"""	11072	protein-coding gene	gene with protein product		600530	"""solute carrier family 9 (sodium/hydrogen exchanger), isoform 2"", ""solute carrier family 9 (sodium/hydrogen exchanger), member 2"""	NHE2			Standard	NM_003048		Approved		uc002tca.3	Q9UBY0	OTTHUMG00000130778	ENST00000233969.2:c.1226delT	chr2.hg19:g.103300596delT	ENSP00000233969:p.Val409fs	268.0	0.0		177.0	11.0	NM_003048	B2RMS2	Frame_Shift_Del	DEL	ENST00000233969.2	hg19	CCDS2062.1																																																																																			.	.		0.453	SLC9A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253292.2		
SEMA6D	80031	hgsc.bcm.edu	37	15	48056088	48056088	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr15:48056088delG	ENST00000316364.5	+	10	1228	c.789delG	c.(787-789)atgfs	p.M263fs	SEMA6D_ENST00000389428.3_Frame_Shift_Del_p.M263fs|SEMA6D_ENST00000558014.1_Frame_Shift_Del_p.M263fs|SEMA6D_ENST00000558816.1_Frame_Shift_Del_p.M263fs|SEMA6D_ENST00000358066.4_Frame_Shift_Del_p.M263fs|SEMA6D_ENST00000389425.3_Frame_Shift_Del_p.M263fs|SEMA6D_ENST00000355997.3_Frame_Shift_Del_p.M263fs|SEMA6D_ENST00000389433.2_Frame_Shift_Del_p.M263fs|SEMA6D_ENST00000389432.2_Frame_Shift_Del_p.M263fs|SEMA6D_ENST00000537942.1_Frame_Shift_Del_p.M263fs|SEMA6D_ENST00000536845.2_Frame_Shift_Del_p.M263fs|SEMA6D_ENST00000354744.4_Frame_Shift_Del_p.M263fs	NM_153618.1	NP_705871.1	Q8NFY4	SEM6D_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D	263	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|negative regulation of smooth muscle cell migration (GO:0014912)|positive regulation of smooth muscle cell migration (GO:0014911)|ventricular system development (GO:0021591)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			biliary_tract(1)|breast(4)|endometrium(4)|kidney(5)|large_intestine(10)|lung(42)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	77		all_lung(180;0.000635)|Myeloproliferative disorder(241;0.116)|Melanoma(134;0.18)		all cancers(107;1.2e-11)|GBM - Glioblastoma multiforme(94;1.2e-06)		AAAACGACATGGGTGGTTCCC	0.488																																					p.M263fs		Atlas-INDEL	.											.	SEMA6D	322	.	0			c.788delT						.						152.0	145.0	148.0					15																	48056088		2198	4297	6495	SO:0001589	frameshift_variant	80031	exon10			.	AF389430	CCDS32224.1, CCDS32225.1, CCDS32226.1, CCDS32227.1, CCDS32228.1, CCDS32229.1	15q21.1	2006-09-18				ENSG00000137872		"""Semaphorins"""	16770	protein-coding gene	gene with protein product		609295				12110693, 14977921	Standard	NM_020858		Approved	KIAA1479, FLJ11598	uc001zvy.3	Q8NFY4		ENST00000316364.5:c.789delG	chr15.hg19:g.48056088delG	ENSP00000324857:p.Met263fs	301.0	0.0		193.0	12.0	NM_153617	A6NF10|A6NM95|A6NNK1|A7E2A0|Q8NFY3|Q8NFY5|Q8NFY6|Q8NFY7|Q9P249	Frame_Shift_Del	DEL	ENST00000316364.5	hg19	CCDS32225.1																																																																																			.	.		0.488	SEMA6D-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416868.1	NM_024966	
MAP2	4133	hgsc.bcm.edu	37	2	210558065	210558065	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:210558065delC	ENST00000360351.4	+	7	1677	c.1171delC	c.(1171-1173)cccfs	p.P391fs	MAP2_ENST00000392194.1_Intron|MAP2_ENST00000361559.4_Intron|MAP2_ENST00000447185.1_Frame_Shift_Del_p.P387fs|MAP2_ENST00000199940.6_Intron	NM_002374.3	NP_002365.3	P11137	MTAP2_HUMAN	microtubule-associated protein 2	391					axonogenesis (GO:0007409)|cellular response to organic substance (GO:0071310)|central nervous system neuron development (GO:0021954)|dendrite morphogenesis (GO:0048813)|microtubule bundle formation (GO:0001578)|neuron projection development (GO:0031175)	cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|neuronal cell body (GO:0043025)|nuclear periphery (GO:0034399)	dystroglycan binding (GO:0002162)|structural molecule activity (GO:0005198)			breast(7)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(36)|liver(2)|lung(42)|ovary(11)|pancreas(2)|prostate(2)|skin(2)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	124		Hepatocellular(293;0.137)|Lung NSC(271;0.163)|Renal(323;0.202)		UCEC - Uterine corpus endometrioid carcinoma (47;6.64e-05)|Epithelial(149;3.12e-100)|all cancers(144;6.88e-91)|Lung(261;0.0624)|LUSC - Lung squamous cell carcinoma(261;0.0662)|STAD - Stomach adenocarcinoma(1183;0.18)	Docetaxel(DB01248)|Estramustine(DB01196)|Paclitaxel(DB01229)	AATGACCTTACCCAAAGATGC	0.448																																					p.L390fs	Pancreas(27;423 979 28787 29963)	Atlas-INDEL	.											.	MAP2	372	.	0			c.1170delA						.						64.0	65.0	65.0					2																	210558065		2203	4300	6503	SO:0001589	frameshift_variant	4133	exon7			.		CCDS2384.1, CCDS2385.1, CCDS33369.1	2q34-q35	2008-05-27			ENSG00000078018	ENSG00000078018		"""A-kinase anchor proteins"""	6839	protein-coding gene	gene with protein product		157130				3103857, 7479905	Standard	XM_005246554		Approved	MAP2A, MAP2B, MAP2C	uc002vde.1	P11137	OTTHUMG00000132962	ENST00000360351.4:c.1171delC	chr2.hg19:g.210558065delC	ENSP00000353508:p.Pro391fs	260.0	0.0		182.0	11.0	NM_002374	Q17S04|Q8IUX2|Q99975|Q99976	Frame_Shift_Del	DEL	ENST00000360351.4	hg19	CCDS2384.1																																																																																			.	.		0.448	MAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256521.2	NM_001039538	
ATF4	468	hgsc.bcm.edu	37	22	39917489	39917489	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr22:39917489delG	ENST00000337304.2	+	1	921	c.39delG	c.(37-39)gtgfs	p.V13fs	ATF4_ENST00000396680.1_Frame_Shift_Del_p.V13fs|ATF4_ENST00000404241.2_Frame_Shift_Del_p.V13fs	NM_001675.2	NP_001666.2	P18848	ATF4_HUMAN	activating transcription factor 4	13					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular amino acid metabolic process (GO:0006520)|cellular protein metabolic process (GO:0044267)|circadian regulation of gene expression (GO:0032922)|endoplasmic reticulum unfolded protein response (GO:0030968)|gamma-aminobutyric acid signaling pathway (GO:0007214)|gluconeogenesis (GO:0006094)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of oxidative stress-induced neuron death (GO:1903204)|negative regulation of potassium ion transport (GO:0043267)|positive regulation of apoptotic process (GO:0043065)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to endoplasmic reticulum stress (GO:1990440)|positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0036091)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|response to endoplasmic reticulum stress (GO:0034976)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dendrite membrane (GO:0032590)|Lewy body core (GO:1990037)|neuron projection (GO:0043005)|nuclear periphery (GO:0034399)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|endometrium(2)|large_intestine(2)|lung(5)|skin(1)	11	Melanoma(58;0.04)				Pseudoephedrine(DB00852)	AGGTGTTGGTGGGGGACTTGA	0.522																																					p.V13fs		Atlas-INDEL	.											.	ATF4	27	.	0			c.38delT						.						70.0	69.0	69.0					22																	39917489		2203	4300	6503	SO:0001589	frameshift_variant	468	exon1			.	D90209	CCDS13996.1	22q13.1	2013-05-23	2013-05-23		ENSG00000128272	ENSG00000128272		"""basic leucine zipper proteins"""	786	protein-coding gene	gene with protein product	"""tax-responsive enhancer element B67"""	604064	"""activating transcription factor 4 (tax-responsive enhancer element B67)"""	TXREB		1847461, 1534408	Standard	NM_182810		Approved	TAXREB67, CREB-2	uc003axz.3	P18848	OTTHUMG00000151099	ENST00000337304.2:c.39delG	chr22.hg19:g.39917489delG	ENSP00000336790:p.Val13fs	215.0	0.0		181.0	11.0	NM_001675	Q9UH31	Frame_Shift_Del	DEL	ENST00000337304.2	hg19	CCDS13996.1																																																																																			.	.		0.522	ATF4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321305.1	NM_001675	
POC5	134359	hgsc.bcm.edu	37	5	74998581	74998581	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:74998581delA	ENST00000428202.2	-	5	551	c.362delT	c.(361-363)ttcfs	p.F121fs	POC5_ENST00000504862.1_5'UTR|POC5_ENST00000380475.2_Frame_Shift_Del_p.F4fs|POC5_ENST00000510798.1_Frame_Shift_Del_p.F4fs|POC5_ENST00000514838.2_Frame_Shift_Del_p.F93fs|POC5_ENST00000446329.2_Frame_Shift_Del_p.F96fs	NM_001099271.1	NP_001092741.1	Q8NA72	POC5_HUMAN	POC5 centriolar protein	121					cell cycle (GO:0007049)	centrosome (GO:0005813)|cytoplasm (GO:0005737)				breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(4)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	15						ATGTGAACTGAAAAAATCCAT	0.388																																					p.F121fs		Atlas-INDEL	.											.	POC5	82	.	0			c.363delC						.						93.0	96.0	95.0					5																	74998581		1994	4182	6176	SO:0001589	frameshift_variant	134359	exon5			.	AK093098	CCDS47236.1, CCDS47237.1	5q13.3	2013-08-05	2013-08-05	2010-03-26	ENSG00000152359	ENSG00000152359			26658	protein-coding gene	gene with protein product			"""chromosome 5 open reading frame 37"", ""POC5 centriolar protein homolog (Chlamydomonas)"""	C5orf37		19349582	Standard	NM_152408		Approved	FLJ35779, MGC120442, MGC120443, MGC120444, hPOC5	uc003keh.4	Q8NA72	OTTHUMG00000162487	ENST00000428202.2:c.362delT	chr5.hg19:g.74998581delA	ENSP00000410216:p.Phe121fs	258.0	0.0		173.0	15.0	NM_001099271	B4DJG7|Q494X7|Q494X9|Q6P085	Frame_Shift_Del	DEL	ENST00000428202.2	hg19	CCDS47236.1																																																																																			.	.		0.388	POC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369124.1	NM_152408	
DNAJB12	54788	hgsc.bcm.edu	37	10	74104834	74104834	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr10:74104834delG	ENST00000444643.2	-	2	517	c.185delC	c.(184-186)ccafs	p.P63fs	DNAJB12_ENST00000338820.3_Frame_Shift_Del_p.P97fs|DNAJB12_ENST00000394903.2_Frame_Shift_Del_p.P97fs|DNAJB12_ENST00000461919.1_Intron			Q9NXW2	DJB12_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 12	63						integral component of membrane (GO:0016021)|membrane (GO:0016020)				endometrium(1)|large_intestine(2)|skin(1)	4						GTCTGTGGGTGGGGGTTGGTC	0.597																																					p.P96fs		Atlas-INDEL	.											.	DNAJB12	22	.	0			c.288delA						.						135.0	145.0	142.0					10																	74104834		2203	4300	6503	SO:0001589	frameshift_variant	54788	exon2			.	AK000034	CCDS7316.2	10q22	2011-09-02			ENSG00000148719	ENSG00000148719		"""Heat shock proteins / DNAJ (HSP40)"""	14891	protein-coding gene	gene with protein product		608376				11147971	Standard	NM_001002762		Approved	DJ10, FLJ20027	uc001jta.2	Q9NXW2	OTTHUMG00000018436	ENST00000444643.2:c.185delC	chr10.hg19:g.74104834delG	ENSP00000403313:p.Pro63fs	167.0	0.0		155.0	10.0	NM_017626	B7Z7I3|Q9H6H0	Frame_Shift_Del	DEL	ENST00000444643.2	hg19																																																																																				.	.		0.597	DNAJB12-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000048581.2		
ERBB2IP	55914	hgsc.bcm.edu	37	5	65374265	65374265	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:65374265delT	ENST00000284037.5	+	26	4535	c.4146delT	c.(4144-4146)agtfs	p.S1382fs	ERBB2IP_ENST00000506030.1_Frame_Shift_Del_p.S1389fs|ERBB2IP_ENST00000380935.1_Frame_Shift_Del_p.S1272fs|ERBB2IP_ENST00000511297.1_Frame_Shift_Del_p.S1337fs|ERBB2IP_ENST00000416865.2_Frame_Shift_Del_p.S580fs|ERBB2IP_ENST00000380939.2_Frame_Shift_Del_p.S1330fs|ERBB2IP_ENST00000380943.2_Frame_Shift_Del_p.S1341fs|ERBB2IP_ENST00000380936.1_Frame_Shift_Del_p.S1310fs|ERBB2IP_ENST00000380938.2_Frame_Shift_Del_p.S1316fs|ERBB2IP_ENST00000503913.1_3'UTR|ERBB2IP_ENST00000508515.1_Frame_Shift_Del_p.S1272fs	NM_001253697.1	NP_001240626.1	Q96RT1	LAP2_HUMAN	erbb2 interacting protein	1382	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				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)		ATGGCTACAGTTTTATAAATA	0.333																																					p.S1389fs		Atlas-INDEL	.											.	ERBB2IP	120	.	0			c.4166delG						.						54.0	56.0	55.0					5																	65374265		2203	4300	6503	SO:0001589	frameshift_variant	55914	exon26			.		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.4146delT	chr5.hg19:g.65374265delT	ENSP00000284037:p.Ser1382fs	309.0	0.0		216.0	13.0	NM_001253699	A0AVR1|B4E3F1|B7ZLV9|E7EQW9|E9PCR8|Q1RMD0|Q86W38|Q9NR18|Q9NW48|Q9ULJ5	Frame_Shift_Del	DEL	ENST00000284037.5	hg19	CCDS58953.1																																																																																			.	.		0.333	ERBB2IP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000215070.1	NM_018695	
CFAP61	26074	hgsc.bcm.edu	37	20	20226815	20226815	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr20:20226815delA	ENST00000245957.5	+	19	2191	c.2115delA	c.(2113-2115)ggafs	p.G705fs	C20orf26_ENST00000389656.3_Frame_Shift_Del_p.G61fs|C20orf26_ENST00000377309.2_Frame_Shift_Del_p.G61fs|C20orf26_ENST00000377293.1_Frame_Shift_Del_p.G61fs	NM_015585.3	NP_056400.3	Q8NHU2	CT026_HUMAN		705										NS(2)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(42)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	77				READ - Rectum adenocarcinoma(2;0.171)		GACTCCCAGGAAAAAAACTTC	0.353																																					p.G705fs		Pindel	.											.	C20orf26	188	.	0			c.2114delG						.						77.0	86.0	83.0					20																	20226815		2203	4300	6503	SO:0001589	frameshift_variant	26074	exon19			.																												ENST00000245957.5:c.2115delA	chr20.hg19:g.20226815delA	ENSP00000245957:p.Gly705fs	237.0	0.0		217.0	10.0	NM_015585	A6NHA1|Q5JXV4|Q5TE18|Q8N5R9|Q96M59|Q9BQL2|Q9H127|Q9H128|Q9NQH4|Q9UFV8|Q9Y4V7	Frame_Shift_Del	DEL	ENST00000245957.5	hg19	CCDS33447.1																																																																																			.	.		0.353	C20orf26-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078228.3		
SUCLG2	8801	hgsc.bcm.edu	37	3	67570955	67570955	+	Frame_Shift_Del	DEL	C	C	-	rs527536615		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr3:67570955delC	ENST00000307227.5	-	5	548	c.521delG	c.(520-522)ggcfs	p.G174fs	SUCLG2_ENST00000492795.1_Frame_Shift_Del_p.G174fs|SUCLG2_ENST00000493112.1_Frame_Shift_Del_p.G174fs	NM_003848.3	NP_003839.2	Q96I99	SUCB2_HUMAN	succinate-CoA ligase, GDP-forming, beta subunit	174	ATP-grasp.			GV -> RS (in Ref. 4; AAC64397). {ECO:0000305}.	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)	AATGTCGACGCCCCCCTGGGG	0.502																																					p.G174fs		Pindel	.											.	SUCLG2	95	.	0			c.522delC						.						67.0	70.0	69.0					3																	67570955		1823	4072	5895	SO:0001589	frameshift_variant	8801	exon5			.	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.521delG	chr3.hg19:g.67570955delC	ENSP00000307432:p.Gly174fs	342.0	0.0		242.0	11.0	NM_001177599	C9JVT2|O95195|Q6NUH7|Q86VX8|Q8WUQ1	Frame_Shift_Del	DEL	ENST00000307227.5	hg19	CCDS43104.1																																																																																			.	.		0.502	SUCLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351993.1	NM_003848	
ZNF362	149076	hgsc.bcm.edu	37	1	33745933	33745933	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr1:33745933delC	ENST00000539719.1	+	5	728	c.558delC	c.(556-558)ggcfs	p.G186fs	ZNF362_ENST00000373428.5_Frame_Shift_Del_p.G186fs	NM_152493.2	NP_689706.2	Q5T0B9	ZN362_HUMAN	zinc finger protein 362	186					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)|kidney(1)|large_intestine(4)|lung(2)	10		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)				GCCTGCTTGGCCCCCCCAAGT	0.657																																					p.G186fs	Pancreas(162;1431 2676 35353 38425)	Pindel	.											.	ZNF362	31	.	0			c.557delG						.						42.0	41.0	41.0					1																	33745933		2203	4300	6503	SO:0001589	frameshift_variant	149076	exon5			.		CCDS377.1	1p35.1	2013-01-08			ENSG00000160094	ENSG00000160094		"""Zinc fingers, C2H2-type"""	18079	protein-coding gene	gene with protein product	"""rotund homolog (Drosophila)"""						Standard	NM_152493		Approved	FLJ25476, lin-29, RN	uc001bxc.1	Q5T0B9	OTTHUMG00000004124	ENST00000539719.1:c.558delC	chr1.hg19:g.33745933delC	ENSP00000446335:p.Gly186fs	264.0	0.0		231.0	10.0	NM_152493	Q8WYU4	Frame_Shift_Del	DEL	ENST00000539719.1	hg19	CCDS377.1																																																																																			.	.		0.657	ZNF362-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011857.2	NM_152493	
POLR1A	25885	hgsc.bcm.edu	37	2	86259442	86259442	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr2:86259442delC	ENST00000263857.6	-	29	4603	c.4225delG	c.(4225-4227)gacfs	p.D1409fs	POLR1A_ENST00000409681.1_Frame_Shift_Del_p.D1409fs			O95602	RPA1_HUMAN	polymerase (RNA) I polypeptide A, 194kDa	1409					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						GCATCGGCGTCCCCCTCCTCA	0.582																																					p.D1409fs		Pindel	.											.	POLR1A	137	.	0			c.4226delA						.						166.0	180.0	175.0					2																	86259442		2123	4233	6356	SO:0001589	frameshift_variant	25885	exon29			.	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.4225delG	chr2.hg19:g.86259442delC	ENSP00000263857:p.Asp1409fs	283.0	0.0		243.0	10.0	NM_015425	B7Z7T0|D6W5M0|Q0VG05|Q9UEH0|Q9UFT9	Frame_Shift_Del	DEL	ENST00000263857.6	hg19	CCDS42706.1																																																																																			.	.		0.582	POLR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329830.2	NM_015425	
GAPT	202309	hgsc.bcm.edu	37	5	57790552	57790552	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr5:57790552delC	ENST00000396776.2	+	3	651	c.189delC	c.(187-189)ggcfs	p.G63fs	GAPT_ENST00000318469.2_Frame_Shift_Del_p.G63fs	NM_152687.2	NP_689900.1	Q8N292	GAPT_HUMAN	GRB2-binding adaptor protein, transmembrane	63					B cell activation (GO:0042113)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|endometrium(2)|large_intestine(1)|lung(2)|skin(1)	7						CATTCTTGGGCCCCCGCATCA	0.448																																					p.G63fs		Pindel	.											.	GAPT	21	.	0			c.188delG						.						60.0	61.0	61.0					5																	57790552		2203	4300	6503	SO:0001589	frameshift_variant	202309	exon3			.	AK090960	CCDS3975.1	5q11.2	2011-11-01	2008-10-07	2008-10-07	ENSG00000175857	ENSG00000175857			26588	protein-coding gene	gene with protein product	"""GRB2-binding transmembrane adaptor"""		"""chromosome 5 open reading frame 29"""	C5orf29			Standard	NM_152687		Approved	FLJ33641	uc003jro.1	Q8N292	OTTHUMG00000131219	ENST00000396776.2:c.189delC	chr5.hg19:g.57790552delC	ENSP00000379997:p.Gly63fs	230.0	0.0		186.0	10.0	NM_152687		Frame_Shift_Del	DEL	ENST00000396776.2	hg19	CCDS3975.1																																																																																			.	.		0.448	GAPT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253963.1	NM_152687	
MPRIP	23164	hgsc.bcm.edu	37	17	17061760	17061760	+	Frame_Shift_Del	DEL	A	A	-	rs551557602		TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr17:17061760delA	ENST00000341712.4	+	14	1490	c.1490delA	c.(1489-1491)gaafs	p.E497fs	MPRIP_ENST00000395804.3_Frame_Shift_Del_p.E497fs|MPRIP_ENST00000395811.5_Frame_Shift_Del_p.E497fs|MPRIP_ENST00000444976.1_Frame_Shift_Del_p.E459fs			Q6WCQ1	MPRIP_HUMAN	myosin phosphatase Rho interacting protein	497						actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)				biliary_tract(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(9)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	31						TTGCCAGAGGAAAAAAACAAG	0.612																																					p.E497fs		Pindel	.											.	MPRIP	87	.	0			c.1489delG						.						18.0	22.0	21.0					17																	17061760		2201	4289	6490	SO:0001589	frameshift_variant	23164	exon14			.	BC014102	CCDS32578.1, CCDS42268.1	17p11.2	2013-01-10			ENSG00000133030	ENSG00000133030		"""Pleckstrin homology (PH) domain containing"""	30321	protein-coding gene	gene with protein product	"""Rho interacting protein 3"""	612935				10048485	Standard	NM_201274		Approved	RHOIP3, M-RIP, p116Rip	uc002gqy.2	Q6WCQ1	OTTHUMG00000059276	ENST00000341712.4:c.1490delA	chr17.hg19:g.17061760delA	ENSP00000342379:p.Glu497fs	432.0	0.0		273.0	12.0	NM_015134	Q3KQZ5|Q5FB94|Q6DHW2|Q7Z5Y2|Q8N390|Q96G40	Frame_Shift_Del	DEL	ENST00000341712.4	hg19	CCDS32578.1																																																																																			.	.		0.612	MPRIP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000131587.1	NM_015134	
SLC29A1	2030	hgsc.bcm.edu	37	6	44197187	44197187	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A3CJ-01A-11D-A20W-10	TCGA-G3-A3CJ-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b064bc29-9a26-41f6-b49a-ae77a15d4967	fe4fd074-ca2d-42c3-9851-1c874d1f51fd	g.chr6:44197187delT	ENST00000393841.1	+	4	581	c.90delT	c.(88-90)aatfs	p.N30fs	SLC29A1_ENST00000371713.1_Frame_Shift_Del_p.N30fs|SLC29A1_ENST00000371724.1_Frame_Shift_Del_p.N30fs|SLC29A1_ENST00000313248.7_Frame_Shift_Del_p.N109fs|SLC29A1_ENST00000371740.5_Frame_Shift_Del_p.N30fs|SLC29A1_ENST00000371731.1_Frame_Shift_Del_p.N30fs|SLC29A1_ENST00000393844.1_Frame_Shift_Del_p.N30fs|SLC29A1_ENST00000371755.3_Frame_Shift_Del_p.N30fs|SLC29A1_ENST00000427851.2_Frame_Shift_Del_p.N30fs|SLC29A1_ENST00000371708.1_Frame_Shift_Del_p.N30fs	NM_001078177.1	NP_001071645.1	Q99808	S29A1_HUMAN	solute carrier family 29 (equilibrative nucleoside transporter), member 1	30					cellular response to glucose stimulus (GO:0071333)|cellular response to hypoxia (GO:0071456)|lactation (GO:0007595)|nucleobase-containing compound metabolic process (GO:0006139)|nucleoside transmembrane transport (GO:1901642)|nucleoside transport (GO:0015858)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|sleep (GO:0030431)|transmembrane transport (GO:0055085)|uridine transport (GO:0015862)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	nucleoside transmembrane transporter activity (GO:0005337)			endometrium(3)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|skin(2)	17	all_cancers(18;3.19e-06)|Lung NSC(15;0.00108)|all_lung(25;0.00278)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)		Cytarabine(DB00987)|Didanosine(DB00900)|Fludarabine(DB01073)|Fluorouracil(DB00544)|Gemcitabine(DB00441)|Mercaptopurine(DB01033)|Pemetrexed(DB00642)|Ribavirin(DB00811)|Zalcitabine(DB00943)	TCCCGTGGAATTTTTTCATGA	0.557																																					p.N30fs		Pindel	.											.	SLC29A1	45	.	0			c.89delA						.						161.0	153.0	156.0					6																	44197187		2203	4300	6503	SO:0001589	frameshift_variant	2030	exon3			.	U81375	CCDS4908.1	6p21.1	2013-07-17	2013-07-17		ENSG00000112759	ENSG00000112759		"""Solute carriers"""	11003	protein-coding gene	gene with protein product		602193	"""solute carrier family 29 (nucleoside transporters), member 1"""	ENT1		8986748, 9344680	Standard	NM_004955		Approved		uc003owy.2	Q99808	OTTHUMG00000014759	ENST00000393841.1:c.90delT	chr6.hg19:g.44197187delT	ENSP00000377424:p.Asn30fs	371.0	0.0		282.0	12.0	NM_004955	B3KQV7|B3KQY5|Q5T9W9|Q9UJY2	Frame_Shift_Del	DEL	ENST00000393841.1	hg19	CCDS4908.1																																																																																			.	.		0.557	SLC29A1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040721.1		
